DNA recognition by intercalator-minor-groove binder hybrid molecules

Bioconjugate

Chemistry NOVEMBER/DECEMBER 1991 Volume 2, Number 6 0 Copyright 1991 by the American Chemical Society

REVIEW DNA Recognition by Intercalator-Minor-Groove Binder Hybrid Molecules Christian Bailly and Jean-Pierre Hhichart’ INSERM Unit6 16, Place de Verdun, 59045 Lille, France. Received January 29, 1991 Recently many research efforts have been aimed at targeting specific sequences in DNA with synthetic ligands with the idea of designing both drugs and molecular probes for DNA polymorphism. The selective inhibition of transcription from particular sequences by the specific targeting of a ligand, in other words the control of gene expression, has become a very attractive and productive research area ( I ) . Many groups have spelled out a strategy to reach this objective with the common and ultimate goal to design agents which can effectively read DNA in a manner analogous to regulatory proteins. Among the various proposed approaches, oligonucleotides able to recognize DNA via the formation of triple helices (2-9) appear to be by far the most sequence-specificagents able to read DNA with an extreme fidelity. However, if their utility as tools for molecular biology is indisputable, they are not yet pharmacologicallyuseful. Binding mostly to homopurinehomopyrimidine sequences of duplex, low ability to penetrate the cells, or sensitivity to cellular nucleases are examples of problems encountered with these ligands. Changes in the anomeric configuration of nucleotides (10, 1 1 ) and/or combination of the oligonucleotide witha DNA carrier or chelating agent (10-23) represent elegant extensions of this approach which might lead to the development of more efficient compounds. These oligonucleotides bind to the major groove of DNA (24)because of the greater width of the major over the minor groove in B-DNA (25). Also, they are directly able to compete with DNA-binding proteins. Most protein-DNA (26-31) complexes characterized to date involve major-groove contacts. However, minor-groove protein-DNA contacts conferring sequence specific binding are also reported (3236). In parallel to this oligonucleotide-based approach, low molecular weight agents which would be able to fit isohelically in the minor groove of DNA have been designed 1043-1802/91/2902-0379~02.50/0

and are now known to be endowed with sequence specific recognition properties (37). Isohelical sequence-reading drug polymers,initially called “isolexins”(38),are currently the subject of a great deal of work to evaluate their real potential in terms of compounds of biological interest. They show promise even if their usefulness as efficient anticancer or antiviral drugs is not yet definitively proved. Difficulties in these studies arise from the need to correlate changes in sequence specificity to the nature and location of particular substituents introduced into a drug molecule. Put another way, the problem lies in the interpretation of the relationships between structure and DNA binding. In their extensive studies of the sequencespecific DNA binding properties of minor-groove binders, Lown (39), Dervan (401, and their collaborators, by reference to the pioneer computer analysis study of Goodsell and Dickerson (38), have in part achieved this distinction by comparing the binding specificity of homologous compounds in which the overall balance between AT/GC selectivity could be controlled (more or less) by judicious substitutions with H bond donor or acceptor heteroatoms. The expected GC recognition should involve a specific hydrogen bond between a heteroatom of the ligand and the 2-aminogroups of guanine bases protruding into the minor groove. In this way, they have succeeded in identifying sites of the well-known naturally occurring oligopeptides netropsin and distamycin (Figure l),where substitution may alter their high A T specificity and enhance their GC acceptance without change to their mode of binding. These efforts, which led to the synthesis of “lexitropsins”, or sequence-reading oligopeptides structurally related to netropsin (41,42),are still going on with the aim to design pure GC-specific minor-groove binders and drugs able to recognize a portion of DNA of definite sequence. The rational structural modification of natural DNA-sequenceselective agents has evidenced the importance of several 0 1991 American Chemical Society

380

Bailly and H6nichart

Bioconjugate Chem., Vol. 2, No. 6, 1991 uu

A 1

NH"a-NHh I \ I

O

I

WC-NH.

2

3

mH3EH3

CHI

II

NH

'CH-C-NH

0

7

Sar L-Pro'

MeV#

D-Vd

>,,,-" 'NU

4

I

I

I

-CH-C-N-CH-C

II

I

I l l

-N-CH

,CHI

\CH

I

-C

//" I I

S.r

L.Pro'

\L.N.

I

I CH1 I

HIC

I

\L.N.

I

MeVal

DVd >T-ThrRO /

NH

I HIM

CH,

CH3 NHCHl

Figure 1. Structure of netropsin (l),distamycin (2), amsacrine (3),actinomycin D (4), daunomycin (5), nogalamycin (6), echinomycin (7), and neocarzinostatin chromophore (8).

of the structural, stereochemical, conformational, and electrostatic factors necessary for a better understanding and control of drug-DNA molecular-recognitionprocesses. However, we must admit that to date the success of converting from an A T word to a word that will also tolerate GC with less binding affinity for AT is obvious but still limited. The significance of hydrogen bonds between the ligands and DNA for determination of sequence specificity could be overestimated. Geometrical and electrostatic factors must be considered more carefully. The distribution of the electrostatic potential in B-DNA favors the minor groove of A T sequences over the minor groove of GC sequences (43,44). The narrownessof the minor groove in AT-rich regions, compared with the markedly wider minor groove in GC-rich regions, suggests an explanation for the marked A T selectivity almost invariably observed with netropsin analogues (45). Minor-groovebinders seem to recognize potential binding sites more by the shapes of the DNA than by the specific sequence that is contained in the site. The DNA flexibility will also be an important feature to consider. Because of the inherently lower

flexibility of GC-rich regions (46), the design of GC recognition elements will require extremely accurate matching of groove and ligands surfaces, whereas a much cruder match may suffice for A T recognition (47). Considering the notions of geometrical fitting, hydrogenbonding capabilities, and the overall electronic properties of the interacting species, a new generation of isolexins was recently proposed. A significant increase both in GC specificity and in DNA binding energy is expected by replacing the amide linkage between the N-methylpyrrole units of netropsin by C = C double bonds (yielding the so called "vinylexins") (48). The success of such an endeavour may ultimately open the road to the creation of drugs able to read DNA fragments of any proposed base sequences. An alternative and complementary approach to the oligonucleotide and lexitropsin efforts is the design of ligands of mixed modes of binding. Indeed, many minor-groove binders such as netropsin, distamycin, DAPI [which can also intercalate (49,50)],berenil, and Hoechst 33258 bind DNA with a powerful AT specificity (51-60). A marked

Review

lack of binding to AT-rich sequences is observed with many intercalators [such as ethidium (61) and different anthraquinones (62) or benzophenanthridines (63)], some of which exhibiting a more pronounced GC selectivity [ellipticine (64,65) and acridine derivatives (66)l. It should, however, be pointed out here that GC-specific minorgroove binders [such as chromomycin A3 (52,67-70) and mithramycin (67, 71-77)] as well as AT-selective intercalators (78) exist. With this in mind, an apparently simple way to associate A T and GC specificities lies in the design of hybrid molecules combining a potentially intercalating heteropolyaromatic moiety with a peptidic or pseudopeptidic groove-binding entity. The aims of such a strategy include increasing intrinsic drug potency as well as controlling the pattern of DNA-sequence-specific recognition. T h e intricate shape of such hybrid molecules-which we name “combilexins” by analogy with the “1exitropsins”-would provide opportunities for binding in several distinct orientations and modes along the helix. This interesting and original approach, first introduced by Krivtsora et al. (79) and Dervan (80)is simple only in appearance because, apart from the complex chemical aspect, the approach is further complicated by druginduced DNA conformational changes. Indeed, theoretical and experimental studies have both clearly shown that binding to DNA, whatever the nature of the implied process, results in an adaptation of the DNA conformation to that of the ligand and vice versa. In attempting the design of hybrid ligands, it must be kept in mind that intercalators and minor-groove binders affect the DNA backbone conformation in very different ways (25) and that the susceptibility of DNA to such changes may vary with the nature of the targeted sequence. Minor-groove binding results in the removal of the ordered water molecules located in AT-rich regions (81-83) [a network termed the spine of hydration (84, 8 5 ) ] . Only slight changes in the gross DNA structure was observed, typified by a maximal 2-8,widening of the minor groove, a bending of the helix by 8 O per drug molecule, and an unwinding and stiffening of the DNA helix in some extent (81, 82, 86-89). In contrast, in order to produce the binding site, intercalators involve a large-scale local structural change such as large unwinding, stiffening, and lengthening of the DNA sugar-phosphate backbone by 3.4 8, per drug molecule. Long-range DNA structural distortions remote from the site of intercalation are also frequently observed, extending over at least four to five base pairs (90). Footprinting studies confirm that intercalation jointly results in sequence-dependent structural changes [probably an increased width of the minor groove (91)]in regions surrounding the binding sites and that these can be cooperatively propagated over several turns of the DNA helix (deduced from DNAase I hypersensitivity a t these sites). Detailed studies, using echinomycin (92-96) and actinomycin D (51,97-loo), clearly show that such effects propagate most efficiently through sequences that are relatively unstable to helix melting, such as d(AT),, i.e. at favored binding sites for minor-groove binders. Therefore, to design a minor-groove binder-intercalator hybrid is thus a challenge, but it is known that DNA can accept two types of binding in a very close proximity (51, 101103). The scope of this review is not to cover all studies which have been devoted to the development of ligands of mixed modes of binding, but to focus mainly on the design of minor-groove binder-intercalator hybrid molecules and on the binding of these synthetic drugs to nucleic acids. Moreover, it would appear simplistic to design drugs with

Bioconjugate Chem., Vol. 2, No. 6, 1991 381

the expectation that chemotherapeutic selectivity will be improved by virtue of only an increase in sequence selectivity. A direct correlation between DNA-sequence selectivity and antitumor activity has not yet been evidenced. It is at best a hypothesis yet to be tested. Associated factors, such as modulation of topoisomerase activity and cellular uptake, should also be taken into account for the rational design of hybrid ligands. Before discussingthe DNA binding properties of recently designed netropsin-intercalator combilexins, it is worth remembering that this new topic has its origin in natural drugs. NATURALLY OCCURRING HYBRID MOLECULES Nature provides examples of drugs whose binding to DNA simultaneously implicates various processes. Such is the case for actinomycin D (Figure l),a natural antitumor agent which consists of a phenoxazone disubstituted by cyclic pentapeptides. Intercalation of actinomycin (90,104,105)occurs preferentially a t some, but not a t all, GpC sequences (51-53,97-99) with the cyclic peptides fitting above and below the intercalating ring in the minor groove, each covering three base pairs [strong binding was also shown to occur at non-GpC sites (106)l. The symmetrically disposed peptides actively participate in the GC-specific recognition process through hydrogenbonding interactions between the N-3 atoms and 2-amino groups of the guanines and the amide groups of the threonine residues (107, 108). Because of these sequencespecific peptide-DNA interactions, intercalation of the phenoxazone between GC base pairs is strongly preferred only if the 5’-flanking base is a pyrimidine and the 3’flanking base is not a cytosine (109). This mode of binding was used for the rational design of the first intercalatorminor-groove binder hybrid molecule (vide infra). Such a bimodal binding process has been found in the interaction with DNA of different natural antitumor anthracyclines, typified by daunomycin and doxorubicin (Figure 1). The elucidation of the detailed interaction between these two related drugs and a short DNA duplex by X-ray diffraction analysis (110-1 13) has definitely demonstrated that while the chromophore intercalates CpG steps, the glycan moiety lies in the minor groove. The sugar forms several bonds with DNA and so greatly contributes to the stability of the complex. But its binding is also important in terms of sequence specificity. Solution (114, 115), crystallographic (110-113), and theoretical studies (116, 117) have converged to show that daunomycin preferentially recognizes triplet sequences, 5’-ACG and 5’-TCG being the most preferred. The chromophore intercalates between the CG base pair and the sugar moiety interacts with A or T through several key hydrogen bonds (for comprehensive reviews see refs 118 and 119). A considerable number of DNA-binding natural products contain carbohydrate residues that are likely to serve as DNA recognition elements. The molecular architecture is even more complicated with another natural anthracycline, nogalamycin (Figure l),which differs from doxorubicin and daunomycin in that it contains two sugar moieties attached to the chromophore. The binding of nogalamycin to DNA consists of the combination of intercalation of the anthracycline ring and groove binding of the sugar moieties (120-124). The nogalose is lying in the minor groove, and the positively charged aminoglucose is lying in the major groove, with the two sugars pointing on the same side of the aglycon ring. Studies on the sequence-specific binding of this compound have not revealed any strongly preferred triplet sequences for nogalamycin binding, as determined for doxorubicin. Foot-

Ballly and Hhichart

382 Bioconlugete Chem., Vol. 2, No. 6, 1991

printing experiments (125) have demonstrated that its binding sites are located in regions of alternating purinepyrimidine sequences, most commonly associated to the dinucleotide steps TpG (CpA) and GpT (ApC). Assuming that the drug preferentially intercalates between GpC steps and taking into account the footprinting data, triplet sequences in which a GC dinucleotide is juxtaposed to an A or T residue may certainly provide strong binding sites for nogalamycin. A similar bimodal binding process has been recently evidenced with the anthracycline antibiotic arugomycin (126). Another example of natural drugs presenting these binding characteristics concerns the quinoxaline antibiotics. Quinoxaline antibiotics are a family of antitumor drugs, of which echinomycin (Figure 1)is the best-known member, and in which two quinoxaline-2-carboxylicacid chromophores are attached to a cross-bridged cyclic octapeptide dilactone containing both L- and D-amino acids. This group of compounds include triostin (127-129) and synthetic analogues (130-133), which have the common properties with echinomycin to bisintercalate with DNA placing the peptide ring into the minor groove. [It should be noted that bisintercalation can also occur through the major groove, as it was demonstrated with the synthetic molecule ditercalinium (134-136).] Here again specific hydrogen bonds between the peptide ring and DNA bases are determinant for sequence specific recognition by the drug (for recent and comprehensive reviews, see refs 58, 133, 137, and 138). The models of echinomycin and triostin A bound to DNA provide instructive examples of drug-induced DNA polymorphism. On the basis of crystallographic data, Wang, Rich, and co-workers (127-129) have shown that when the two quinoxalines of triostin A intercalate between the two distal GC base pairs of the DNA hexamer d(CGTACG)z, the central AT bases are paired through Hoogsteen hydrogen bonds (a pairing arrangement where the purines adopt a syn conformation). In solution, the existence of Hoogsteen base pairs in DNA upon binding of echinomycin or triostin A remains controversial. Thus unusual base pairing, first observed in the crystalline state, has been also detected by NMR studies of echinomycin complexed to small oligonucleotides and appears to be highly dependent on the temperature and the DNA sequence. For example, Hoogsteen base pairs have been found in d(GCGC)z (68),d(ACGT)z (139), and d(ACGTACGT)2 (140,141)complexes but not with d(TCGA)zand d(TCGATCGA)2-echinomycincomplexes. With the octamer of d(ACGTACGT)Z,Hoogsteen pairs are formed in the presence of echinomycin with the two terminal and the central A T base pairs at low temperature. But at physiological temperature, only the terminal A T pairs remains Hoogsteen paired while the central ones are converted to either an open or a Watson-Crick base-paired state (140). Therefore, if the echinomycin-induced Hoogsteen base pairs seem to appear as an artefact of crystallization, the question is yet not definitively resolved. However, NMR (68, 13s141) and footprinting (93-96) studies concur in finding that the binding of echinomycin does not necessarily implicate Hoogsteen pairs. Whatever the exact conformation of the central AT base pairs between the two CpG intercalation sites, clearly the drug induces large changes in DNA conformation which allows close packing of the peptide portion of the molecule in the minor groove against the newly shaped DNA helix, thereby stabilizing the complex via close van der Waals contacts. This example illustrates the fact that the high degree of

DNA distortions induced by intercalating agents can be useful and can serve for adjacent minor-groove binding. Thus actinomycin,doxorubicin,daunomycin, nogalamycin, and the quinoxaline antibiotics are many examples of drugs whose binding to short DNA sequences implicates two processes, intercalation and groove binding simultaneously and in close proximity. Both processes contribute to the affinity and sequence-specific recognition. As a last example (and the list is not exhaustive) supporting this conclusion, we can mention two natural alkylating agents of the enediyne family, dynemicin A (142)and neocarzinostatin (Figure 1) (143, 144). They bind DNA by intercalation of their chromophore (naphtoate for neocarzinostatin and anthraquinone for dynemicin), placing their reactive enediyne containing bicyclic core moiety in the minor groove in a suitable position for selective DNA cleavage (these two compounds are primarily DNA-strand cleavers by free-radical mechanism). All these natural compounds could provide models for the rational design of ligands exhibiting mixed modes of binding. ACRIDINE-LINKED OLIGOPYRROLECARBOXAMIDES

The DNA Target. The two naturally occurring oligopeptides, netropsin and distamycin, are the most frequently used compounds for the synthesis of hybrid molecules. The molecular basis governingtheir selectivity has been well-elucidated (81, 82, 86, 145-151). Their binding, almost exclusively at AT-rich sites, is stabilized by a combination of hydrogen-bonding, van der Waals, and electrostatic interactions. On the other hand, acridines can be considered as the archetype of the intercalators. This heterocycle is not only the first model compound used for the discovery of the intercalation process (152, 153), but because of its synthetic accessibility, it is also certainly the most extensively used intercalator for the design of anticancer drugs (154-156). Studies on acridine derivatives have culminated with the synthesis of amsacrine (Figure l),an anilinoaminoacridine derivative particularly active in the treatment of acute leukemia (157160). Acridines, and amsacrine in particular, are still subject to considerable attention and more efficient analogues are in clinical trials (161, 162). The first example of acridine-linked netropsin bifunctional mixed ligands was reported by Eliadis et al. (163). In the described molecules, the nature of the aliphatic spacer was found to be crucial for the affinities of the hybrid compoundsto DNA. The optimum fit was obtained with a butyroyl chain between the 9-amino group of acridine and the 3-amino group of the N-terminal methylpyrrole of distamycin. Although the intercalation of the acridine chromophore and the minor-groove binding of the oligopyrrolecarboxamidepart have been demonstrated, footprinting experiments only reveal identical binding site sizes and locations for netropsin and netropsin-acridine hybrids. Only the preference of the pyrrolamide residues for AT-rich regions was shown (163). The influence of the intercalative moiety was clearly shown with other acridine-linked oligopeptide carboxamides. These molecules were built using a combination of the natural antitumor agents distamycin or netropsin and the anilinoacridine chromophore related to the synthetic antileukemic drug amsacrine (164). Apart from its evident pharmacological interest, the model of amsacrine was also attractive in our case since it had been postulated (165, 166) that intercalation of the acridine ring was accompanied by minor-groove binding of the adjacent anilino ring [this model has been recently

Review

Bloconjugate Chem., Vol. 2, No. 6, 1991 383

I

O

CHi

C "

Figure 2. Structure of the netropsin-acridine hybrid compound NetGA. Computer-generateddepiction of the binding of NetGA to DNA. The left view shows the minor-groove binding of the bis-pyrrole moiety and the aniline. On the right view, the drug-DNA complex has been rotated in space to focus on the intercalation of the acridine.

questioned and major-groove binding of the aniline is proposed (167,168)]. Based on thisassumption, it seemed very interesting to covalently tether netropsin to acridine through attachment on the anilino ring. However CPK models showed that direct linkage of netropsin to the aniline was disfavorable for DNA binding and that alinker was required. The choice of a linker connecting the recognition elements may be a critical design feature with regard to simultaneous binding of all moieties (80), so we elaborated a first series of netropsin-acridine hybrid molecules in which the two parts were linked by a glycine connector (164).This short tether should provide a frame for anchoring the minor groove moiety in the proper orientation. Their DNA-binding properties were determined using a wide range of biochemical and physicochemical techniques (164,169).Binding data were found to be consistent with a model in which the acridine nucleus occupies an intercalation site and the netropsin or distamycin residue lies in the DNA minor groove. One of these pseudopeptides, named NetGA (Figure 2), was studied in detail for its DNA-sequence specificity, Complementary strand MPE-Fe(I1) footprinting showed that NetGA binds to 5'-AAAT. It is interesting to note that both types of netropsin-acridine ligands [i.e. using aminoacridine (163)and anilinoacridine (l69)]concur in finding that protected sites are of the strict AT type. Regions of enhanced cleavage by MPE, particularly at GC-rich sequences, were observed adjacent to and even remote from the binding site. It is interesting to note that NetGA exhibits a strict preference for AAAT dominated by the oligopeptide moiety at high concentration of ligand and reveals evidencefor intercalation of the acridine moiety at lower concentration. Intercalation of the acridine part of NetGA is influenced by the netropsin part. Linear dichroism measurements revealed an insertion of the acridine into the DNA helix with a tilt of about 20° relative

to the plane of the DNA base pairs, higher than that measured for the acridine alone and reflecting the influence of the netropsin moiety. Nevertheless, the short spacer glycinyl, in spite of its relative rigidity, was apparently not an obstacle for the binding of the two parts of the molecules. This was further supported by a molecular modeling study which shows not only that minor-groove binding of the netropsin part and intercalation of the acridine can effectively occur simultaneously but also that this bimodal binding process induces a local distortion of the DNA helix near the intercalation site. An energyminimized model of the NetGA-DNA complex is presented in Figure 2. Thus the hybrid molecule NetGA interacts with DNA in a well-defined geometry at specific sequences. On the unique basis of DNA specificity, the intercalating moiety of the drug could appear to be useless since the hybrid drug is essentially AT selective as the netropsin half of the hybrid. However, the intercalating chromophore provides a better anchorage of the drug to the DNA helix. At low drug to DNA ratio, the affinity of NetGA for DNA ( K , = 9.1 X 105 M-l) is approximately 3-fold larger than that of netropsin ( K , = 2.9 X lo5 M-l) (169). This also suggests that the two parts of the molecule are bound to DNA. Thus, the intercalating part of NetGA efficiently compensates the absence of the amidine and guanidine side chains of netropsin. Increase in DNA-sequence specificity would possibly not directly result in an improved antitumor activity. This is borne out by the observation that drugs such as daunomycin, nogalamycin, or echinomycin (Figure 1) exhibit noticeable sequence selectivity but they have therapeutic selectivity beyond what would be expected, based upon mere consideration of DNA-binding specificity. Thus other receptors are determinant (170).Future design of DNA-binding ligands will demand a more careful con-

384

Bioconjugate Chem., Vol. 2, No. 6, 1991

sideration of other cellular targets. In particular there are now clear indications that topoisomerases, among other DNA-binding proteins, represent preferred targets for a large number of anticancer drug acting a t the DNA level. The Topoisomerase Target. Briefly it is worth remembering that topoisomerases are enzymes that alter DNA topology. The two major distinctions between type I and type I1 topoisomerases are single- versus doublestranded-DNA cleavage and the energy requirement of type I1 enzymes (for a more precise definition see refs 171-176). Topoisomerases are extremely relevant in the area of human cancers and viral diseases, as these enzymes are privileged targets for a variety of antineoplastic and antiviral agents (177-186). These enzymes now appear as one of the most promising target for the design of more active antitumor drugs. Topoisomerase I1 introduces a transient double-strand break in the DNA and forms a protein-DNA complex referred to as the cleavable complex. Certain intercalating agents, m-AMSA and some related acridines in particular (187-1961, trap the enzyme at this stage, stabilizing the cleavable complex and thus preventing the restoration of intact DNA structure. The molecular basis for the design of topoisomerase poisons are yet to be elucidated. However, the most satisfying model to account for the effects of intercalating agents would be able to distinguish between the two functional domains in the drug (197). With amsacrine, it is highly suspected that the acridine ring would represent the DNA binding domain and that the aniline would allow the interaction with the topoisomerase I1 (198). Modifications of the protein-binding domain have already been correlated with altered biological properties of the tested ligands. Also it may be interesting to introduce on the aniline ring another substituent known for its capability to interact with the topoisomerases. In this perspective, the choice of a minor-groove-binding ligand is perfectly justified. Indeed certain minor-groove binders are also to impede the catalytic activity of topoisomerases I (199, 200) and I1 (201-203). Beside the alteration in topoisomerase activity, the effects of minorgroove binders on other DNA-reactive enzymes have been reported (204-206). With this in mind, the combination of minor-groove binders and intercalators could be potentially useful as topoisomerase-mediated antitumor agents. Such hybrid drugs would thus be able to target both a DNA sequence (sequence s p e c i f i c i t y ) and a DNA conformation which is a consequence of protein-DNA interaction. At present it is not definitively proved that the topoisomerase poisons directly interact with the enzyme. The modulation of the catalytic activity of the enzyme may simply result from ligand-induced DNA structural changes without physical interaction with the proteins. Combilexins, because of their bifunctional mode of binding to DNA, would probably induce particular constraints of the helix structure and thus they could provide interesting tools for the modulation of the topoisomerase activities. For example, the curvature of the DNA upon hybrid-ligand binding may contribute to targeting the topoisomerase I to particular sites (207). Thus, in this area too, the design of hybrid ligands offers stimulating opportunites. Before reaching the DNA target, the drug has to enter the cell easily, to join the nucleus and to bind DNA associated with histones in a nucleosomal structure. The highly ordered structures of DNA in vivo may alter the drug accessibility to DNA, although the drug-targeted DNA is generally believed to be in its nucleosome-free

Bailly and Hhichart

transcriptionally active form. Needless to say, many problems have to be solved to direct the drug selectively toward cancer cells. The intricacy of the mechanism of tumor proliferation significantly increases the complexity of the drug-design problem. It is thus obvious that any chemical strategy, as efficient as it can be, cannot address all the problems simultaneously. However, efforts must be made to consider different putative targets whenever possible. Cellular Uptake. With hybrid compounds and in particular with longer ligands, the problem of cellular transport will emerge. Poor ability to penetrate the cells is one of the major problems encountered with oligonucleotide-based DNA probes. Therefore, a cellular transport program has to be considered in addition to the DNAbinding unit strategy currently in use. This problem can be addressed through the design of hybrid ligands. Netropsin exhibits rather slow kinetics of cell penetration and only a moderate amount of drug can be recovered in the nucleus (208). On the other hand, acridine derivatives rapidly enter the cells and efficiently accumulate in the nucleus rather than in the cytoplasm (209). For this supplementary reason, the coupling of a minorgroove entity to an intercalating chromophore appears extremely interesting. It was effectively shown that the hybrid NetGA penetrates very rapidly into the cell and preferentially concentrates into the nucleus rather than in the cytoplasm. The vector for the nucleus was found to be the acridine chromophore (210). DNA-sequence-specific targeting, modulation of topoisomerase activity, and rapid cellular uptake are complementary effects observed with the netropsin-acridine hybrid molecules. Each half of the molecule has a defined function (sequence specificity by the groove-binding moiety and nuclear targeting by the intercalating moiety). Therefore, with judicious combination, synergistic effects could be expected. Of course the model compound NetGA needs various improvements, essentially to increase its affinity and specificity for definite duplex sequences and to elevate its antitumor activity to a clinically useful level. An approach to reach these two objectives might be to combine netropsin or distamycin entities with very active amsacrine analogues. We are currently examining this possibility. Another way might consist of combining other intercalators with different groove-binding drugs which would lead to efficient synergistic effects. The last section of this article briefly summarizes the recent advances into this subject which undoubtedly shows promise and merits further development. OTHER GROOVE BINDER-INTERCALATOR HYBRID LIGANDS Netropsin and distamycin have been subjected to extensive studies aimed a t modulating their DNA sequence recognition properties. These modifications include deletion, substitution (211-213, or increase in the number of N-methylpyrrole units by polymerization of units (218221) or coupling of fragments (222-229). In addition, the pyrrole ring has been replaced by other heterocycles such as imidazole (230-239), thiazole (240-245), furan (246), thiophene (247), pyridine (248), and other heterocycles (249-256). Groove-binding entities have also been attached to alkylating agents (257-264) or nonintercalating compounds such as metal chelates (265-267) and amino acids (268). Similarly, intercalators have been condensed with a variety of agents such as alkylating (269-282) or metalcomplexing agents (283-292), amino acids and peptides

Bioconjugate Chem., Vol. 2, No. 6, 1991 385

Review DHC-HN

h

NH

Figure 3. Structure of the distamycin-ellipticine hybrid compound.

(293-297), and photoreactive groups (298 and references cited therein). But to date, very few studies have been devoted to the design of netropsin-intercalator conjugates and, to our knowledge, none to the synthesis of intercalator-minor-groove binder conjugates containing a minorgroove binder other than netropsin. As already mentioned above, the first hybrid molecule of this class (79, 80) consisted of an actinomycin-like molecule in which two distamycin moieties sandwiched a phenoxazone ring. This hybrid molecule, named "distactin", was shown to span over 10 base pairs. The existence of such a large binding site supported the conclusion that the drug was able to bind DNA by intercalation of its chromophore between a GC step, ideally placing the two distamycin moieties above and below the site of intercalation, presumably in the minor groove, exactly as actinomycin does. Shorter binding sites, consistent with a binding of only one distamycin part to AT-rich sequences,were also located. Even if its biological properties were never reported, this pioneer hybrid model was extremely interesting with respect to its DNA-binding properties and has provided guidelines for the design of other ligands of this class. Very recently we examined the DNA-binding ability of a distamycin-ellipticine hybrid compound (Figure 3). This agent was built by linking the AT-specific agent distamycin to an ellipticine derivative endowed with marked GCselectiverecognition properties (65). By means of several complementary spectroscopic techniques, it was clearly demonstrated that the drug intercalates and wedges in the minor groove simultaneously (Figure 4). Its propensity to read DNA sequences was analyzed by DNAase I footprinting experiments. These analyses gave conflicting results compared to those obtained with the acridine-linked netropsin molecules (163,169)described above. Indeed, with the acridine-netropsin combilexins, the binding sites were confined to AT-rich sequences while, with the distamycin-ellipticine ligand, binding sites mainly consisting of GC-rich sequences were protected from cleavage by DNAase I. This distamycin-ellipticine hybrid compound retains the specificity of the ellipticine moiety alone (65). Thus in this case, as in triostin and other related structures, intercalation appears to be the crucial element. This demonstrates that depending on the nature of the coupled drugs and of the DNA sequences, one or the other of the two binding modes can predominate. An identical situation was recently exposed with an oxazolopyridocarbazole (0PC)-netropsin hybrid (OPC derivatives can be considered as ellipticine analogues) where intercalation and groove binding would be both implicated at AT-rich sequences and where intercalative binding only would be involved at GC-rich sequences (299). Here again, while spectroscopic analysis supported the involvement of the two DNA binding modes, footprinting experiments failed to exhibit the complementary effects expected from the

L

pv c

I

c

, \

Figure 4. Molecular graphics models showing (from top to bottom) the minor-groove binding of distamycin, the intercalation of ellipticine, and the simultaneous minor-groove binding and intercalation of the distamycin-ellipticine hybrid ligand. Models were constructed using the Jumna package software (by Dr. J. S. Sun). coupling of a GC-selective intercalator to a powerful AT-

specific groove binder.

388 Bioconlugete Chem., Vol. 2, No. 6, 1991

CONCLUSION To date our knowledge of the sequence-dependent variation in DNA structure (300) and the structural perturbation produced by simultaneous intercalation and groove binding is incomplete and does not allow a full understanding of the subject. It is too early to propose any guidelines for the design of hybrid molecules. With the present state of knowledge, the actual determinant (groove binding or intercalation) for retention of the sequence specificity is not very clear and more extensive analysis for dissociating the two effects is required. The manner in which the two halves of the molecule need to be linked awaits molecular modeling studies and more accurate physical measurements. Whatever the chemical strategies adopted to decipher and ultimately to control sequence-specific DNA recognition (Le. triple helix, lexitropsin, and combilexin) it will be necessary to combine our knowledge of the sequence dependence of DNA flexibility and of the ligand-induced DNA structural deformation. Unfortunately, it must also be admitted that the design of ligands capable of attaining sufficient sequence specificity to bind a DNA sites critical for a cell is still a purely conjectural idea and only a small part of the overall problem. Many equally important questions remain to be answered. Inhibition of the DNA repair system, development of a cell-specific delivery system, cellular drug resistance, drug distribution, toxicity, etc., are other topics capable of adding further complexity to this picture. Interdisciplinary approaches are essential. Many studies, many compounds, and hence much time will be necessary before we may perfectly control the targeting to definite DNA sequences with agents combining different DNA-binding processes. This new topic is a real challenge far from being solved, and during this time, cancer and viral diseases are still booming. But this approach has the merit of being highly rational and as such should deservedly be retained, developed, and improved and hopefully might lead to the discovery of tumor-active compounds. ACKNOWLEDGMENT

This work has received the financial support from the INSERM and the Association pour la Recherche contre le Cancer. The authors express their gratitude to Dr. J. S. Sun for his invaluable molecular modeling analysis and to E. Sayers for advice. LITERATURE CITED (1) Nielsen, P. E. (1991) Sequence-selective DNA recognition by synthetic ligands. Bioconjugate Chem. 2, 1-12. (2) Lyamichev, V. I., Mirkin, S. M., Frank-Kamenetskii, M. D., and Cantor, C. R. (1988) A stable complex between homopyrimidine oligomers and the homologous regions of duplex DNAs. Nucleic Acids Res. 16, 2165-2178. (3) Francois, J. C., Saison-Behmoaras, T., and HBlBne, C. (1988) Sequence-specific recognition of the major groove of DNA by oligodeoxynucleotides via triple helix formation. Footprinting studies. Nucleic Acids Res. 16, 11431-11440. (4) Povsic, T. J., and Dervan, P. B. (1989)Triple helix formation by oligonucleotides on DNA extended to the physiological pH range. J. Am. Chem. Soc. 111, 3059-3061. (5) Griffin, L. C., and Dervan, P. B. (1989) Recognition of thymine-adenine base pairs by guanine in a pyrimidine triple helix motif. Science 245, 967-971. (6) Umemoto, K., Sarma, M. H., Gupta, G., Luo, J., and Sarma, R. H. (1990) Structure and stability of a DNA triple helix in solution: NMR studies on d(T)rd(A)gd(T)Band its complex with a minor groove binder drug. J. Am. Chem. Soc. 112, 4539-4545.

b i l l y and HBnichart

(7) Strobel, S. A., and Dervan, P. B. (1991) Single-site enzymatic cleavage of yeast genomic DNA mediated by triple helix formation. Nature 350, 172-174. (8) Beal, P. A., and Dervan, P. B. (1991) Second structural motif for recognition of DNA by oligonucleotide-directed triple-helix formation. Science 251, 1360-1363. (9) Pilch, D. S.,Levenson, C.,andShafer,R. H. (1991)Structure, stability, and thermodynamics of a short intermolecular purine-purine-pyrimidine triple helix. Biochemistry 30,60816087. (10) Le Doan, T., Perrouault, L., Praseuth, D., Habhoub, N., Decout, J. L., Thuong, N. T., Lhomme, J., and HBlBne, C. (1987) Sequence-specific recognition, photocrosslinking and cleavage of the DNA double helix by an [a]-thymidylate covalently linked to an azidoproflavine derivative. Nucleic Acids Res. 15, 7749-7760. (11) Praseuth, D., Perrouault, L., Le Doan, T., Chassignol, M., Thuong, N., and HBlBne, C. (1988) Sequence-specific binding and photocrosslinking of a and p oligodeoxy nucleotides to the major groove of DNA via triple helix formation. Proc. Natl. Acad. Sei. U.S.A. 85, 1349-1353. (12) Moser, H. E., and Dervan, P. B. (1987) Sequence-specific cleavage of double helical DNA by triple helix formation. Science 238, 645-650. (13) Boidot-Forget, M., Chassignol, M., Takasugi, M., Thuong, N. T., and HBlBne, C. (1988) Site-specific cleavage of singlestranded and double-stranded DNA sequences by oligodeoxynucleotides covalently linked to an intercalating agent and an EDTA-Fe chelate. Gene 72, 361-371. (14) Franqois, J. C., Saison-Behmoaras, T., Chassignol, M., Thuong, N. T., and HBlBne, C. (1988) Sequence-targeted cleavage of single- and double-stranded DNA by oligothymidyl a b s covalently linked to 1,lO-phenanthroline. J.Biol. Chem. 264, 5891-5898. (15) Perrouault, L., Asseline, U., Rivalle, C., Thuong, N. T., Bisagni, E., Giovannangeli, C., Le Doan, T., and HBlBne, C. (1988) Sequence-specificartificial photo-induced endonucleasesbased on triple helix-forming oligonucleotides. Nature 344, 358360. (16) Strobe1,S. A.,Moser,H. E.,andDervan,P. B. (1988) Doublestrand cleavage of genomic DNA at a single site by triple-helix formation. J. Am. Chem. Soc. 110, 7927-7929. (17) Vlassov, V. V., Gaidamakov, S. A., Zarytova, V. F., Knorre, D. G., Levina, A. S., Nikonova, A. A., Podust, L. M., and Fedorova, 0. S. (1988) Sequence-specific chemical modification of double-stranded DNA with alkylating oligodeoxyribonucleotide derivatives. Gene 72, 313-322. (18) Sun, J. S., Franqois, J. C., Montenay-Garestier, T., SaisonBehmoaras, T.,Roig, V., Thuong, N. T., and HBlBne, C. (1989) Sequence-specific intercalating agents: Intercalation a t specific sequences on duplex DNA via major groove recognition by oligonucleotide-intercalatorconjugates. Proc. Natl. Acad. Sei. U.S.A. 86, 9198-9202. (19) Franqois, J. C., Saison-Behmoaras, T., Barbier, C., Chassignol, M., Thuong, N. T., HBlBne, C. (1989) Sequence-specific recognition and cleavage of duplex DNA via triple-helix formation by oligonucleotides covalently linked to a phenanthroline-copper chelate. Proc. Natl. Acad. Sei. U.S.A. 86, 9702-9706. (20) Corey, D. R., Pei, D., and Schultz, P. G. (1989) Sequencespecific hydrolysis of duplex DNA by an oligonucleotidedirected nuclease. J. Am. Chem. SOC.111, 8523-8525. (21) Povsic, T. J., and Dervan, P. B. (1990) Sequence-specific alkylation of double-helical DNA by oligonucleotide-directed triple-helix formation. J. Am. Chem. SOC.112, 9428-9430. (22) Pei, D., Corey, D. R., and Schultz, P. G. (1990)Site-specific cleavage of duplex DNA by a semisynthetic nuclease via triplehelix formation. Proc. Natl. Acad. Sei. U.S.A.87,9858-9862. (23) Collier, D. A., Thuong, N. T., and HBlBne, C. (1991) Sequence-specific bifunctional DNA ligands based on triplehelix-forming oligonucleotides inhibit restriction enzyme cleavage under physiological conditions. J. Am. Chem. Soc. 113, 1457-1458. (24) Wells, R. D., Collier, D. A., Hanvey, J. C., Shimizu, M., and Wohlrab, F. (1988)The chemistry and biology of unusual DNA structures adopted by oligopurine-oligopyrimidinesequences. FASEB J . 2. 2939-2949.

Review

(25) Neidle, S., Pearl, L. H., and Skelly, J. V. (1987) DNA structure and perturbation by drug binding. Biochem. J.243, 1-13. (26) Ohlendorf, D. H., Anderson, W. F., Fisher, R. G., Takeda, Y., and Matthews, B. W. (1982) The molecular basis of DNAprotein recognition inferred from the structure of cro repressor. Nature 298, 718-723. (27) Pabo, C. O., and Saver, R. T. (1984) Protein-DNA recognition. Ann. Reu. Biochem. 53, 293-321. (28) Ollis, D. L., and White, S. W. (1987) Structural basis of protein-nucleic acid interactions. Chem. Rev. 87, 981-995. (29) Schleif, R. (1987) DNA binding by proteins. Science 241, 1182-1 187. (30) Travers, A. A. (1989) DNA conformation and protein binding. Annu. Rev. Biochem. 58, 427-452. (31) Brennan, R. G., and Matthews, B. W. (1989) Structural basis of DNA-protein recognition. Trends Biol. Sei. 14,286290. (32) Sluka, J. P., Horwath, S. J., Glasgow, A. C., Simon, M. I., and Dervan, P. B. (1990) Importance of minor groove contacts for recognition of DNA by the binding domain of Hin recombinase. Biochemistry 29, 6551-6561. (33) Segers, A,, Wyns, L., and Lasters, I. (1991) A model for histone H5-DNA interaction: simultaneous minor and major groove binding. Biochem. Biophys. Res. Commun. 174,898902. (34) Churchill, M. E. A., and Travers, A. A. (1991) Protein motifs that recognize structural features of DNA. Trends Biol. Sei. 16, 92-97. (35) Friedman, D. I. (1988) Integration host factor: A protein for all reasons. Cell 55, 545-554. (36) Bonnefoy, E., and Rouviere-Yaniv, J. (1991) HU and IHF, two homologous histone-like proteins of Escherichia coli, form different protein-DNA complexes with short DNA fragments. EMBO J. 10, 687-696. (37) Zimmer, C., and Wahnert, U. (1986)Non-intercalatingDNAbinding ligands: Specificity of the interaction and there use as tools in biophysical,biochemical and biological investigations of the genetic material. Prog. Biophys. Mol. Biol. 47,31-112. (38) Goodsell, D., and Dickerson, R. E. (1986) Isohelical analysis of DNA groove-binding drugs. J. Mol. Biol. 29, 727-733. (39) Zimmer, C., Luck, G., Burckhardt, G., Krowicki, K., and Lown, J. W. (1986) The molecular mechanism of interaction of non-intercalative groove binding antitumor drugs with DNA. Molecular Mechanisms of Carcinogenic and Antitumor Activity (C. Chagas, and B. Pullman, Eds.) pp 339-363, Adenine Press, New York. (40) Dervan, P. B. (1986) Design of synthetic sequence specific DNA binding molecules. Molecular Mechanisms of Carcinogenic and Antitumor Activity (C, Chagas, and B. Pullman, Eds.) pp 365-384, Adenine Press, New York. (41) Lown, J. W. (1988) Lexitropsins: rational design of DNA sequence reading agents as novel anti-cancer agents and potential cellular probes. Anti-Cancer Drug Des. 3, 25-40. (42) Lown, J. W. (1989) Synthetic chemistry of naturally occuring oligopeptide antibiotics and related lexitropsins. Org. Prep. Proc. Znt. 21, 1-46. (43) Zakrzewska, K., Lavery, R., and Pullman, B. (1983) Theoretical studies of the selective binding to DNA of two nonintercalatingligands: netropsin and SN 18071. Nucleic Acids Res. 11,8825-8839. (44) Zakrzewska, K., and Pullman, B. (1983) A theoretical evaluation of the effect of netropsin binding on the reactivity of DNA towards alkylating agents. Nucleic Acids Res. 11, 8841-8845. (45) Gago, F., Reynolds, C. A., and Richards, W. G. (1989) The binding of non intercalative drugs to alternating DNA sequences. Mol. Pharmacol. 35, 232-241. (46) Drew, H. R., and Travers, A. A. (1984) DNA structural variations in the E. coli tyr T promoter. Cell 37, 491-502. (47) Laughton, C. A., Jenkins, T. C., Fox, K. R., and Neidle, S. (1990) Interaction of berenil with the tyrT DNA sequence studied by footprinting and molecular modelling. Implications for the design of sequence-specific DNA recognition agents. Nucleic Acids Res. 18, 4479-4488.

Bioconjupte Chem., Vol. 2, No. 6, 1991 387

(48) Zakrzewska, K., Randrianarivelina, M., and Pullman, B. (1988) Drug recognition of DNA. Proposal for GC minor groove specific ligands: Vinylexins. J.Biomol. Struct. Dyn. 6,331344. (49) Wilson, W. D., Tanious, F. A., Barton, H. J., Strekowski, L., and Boykin, D. W. (1989) Binding of 4’-6-diamidino-2-phenylindole (DAPI) to GC and mixed sequences in DNA: Intercalation of a classical groove-binding molecules. J. Am. 111, 5008-5010. Chem. SOC. (50) Wilson, W. D., Tanious, F. A., Barton, H. J., Jones, R. L., Fox, K. R., Wydra, R. L., and Strekowski, L. (1990) DNA sequence dependent binding modes of 4’,6-diamidino-2-phenylindole (DAPI). Biochemistry 29, 8452-8461. (51) Lane, M. J., Dabrowiak, J. C., and Vournakis, J. N. (1983) Sequence specificity of actinomycin D and netropsin binding to pBR322 DNA analyzed by protection from DNase I. Proc. Natl. Acad. Sei. U.S.A. 80, 3260-3264. (52) Van Dyke, M. W., and Dervan, P. B. (1983) Methidiumpropyl-EDTA-Fe(I1) and DNAase I footprinting report different small molecule binding site sizes on DNA. Nucleic Acids Res. 11, 5555-5567. (53) VanDyke, M. W., Hertzberg, R. P.,andDervan,P. B. (1983) Map of distamycin, netropsin, and actinomycin binding sites on heterogeneous DNA: DNA cleavage-inhibition patterns Proc. Natl. Acad. Sci. with methidiumpropyl-EDTA-Fe(I1). U.S.A. 79, 5470-5474. (54) Harshman, K. D., and Dervan, P. B. (1985) Molecular recognition of B-DNA by Hoescht 33258. Nucleic Acids Res. 13,4825-4835. (55) Portugal, J.,and Waring, M. J. (1987)Comparisonofbinding sites in DNA for berenil, netropsin and distamycin. A footprinting study. Eur. J. Biochem. 167, 281-289. (56) Portugal, J., and Waring, M. J. (1987) Hydroxyl radical footprinting of the sequence-selective binding of netropsin and distamycin to DNA. FEBS Lett. 225, 195-200. (57) Fox, K. R., and Waring, M. J. (1987)The use of micrococcal nuclease as a probe for drug-binding sites on DNA. Biochim. Biophys. Acta 909, 145-155. (58) Ward, B., Rehfuss, R., and Dabrowiak, J. C. (1987) Quantitative footprinting analysis of the netropsin-DNA interaction. J. Biomol. Struct. Dyn. 4, 685-695. (59) Portugal, J., and Waring, M. J. (1988) Assignment of DNA and bisbenzbinding sites for 4’,6-diamidine-e-phenylindole imide (Hoechst 33258). A comparative footprinting study. Biochim. Biophys. Acta 949, 158-168. (60) Churchill, M. E. A., Hayes, J. J., and Tullius, T. D. (1990) Detection of drug binding to DNA by hydroxyl radical footprinting. Relationship of distamycin binding sites to DNA structure and positioned nucleosomes on 5s RNA genes of Xenopus. Biochemistry 29, 6043-6050. (61) Fox, K. R., and Waring, M. J. (1987) Footprinting a t low temperature: Evidence that ethidium and other simple intercalators can discriminate between different nucleotide sequences. Nucleic Acids Res. 15, 491-507. (62) Fox, K. R., Waring, M. J., Brown, J. R., and Neidle, S. (1986) DNA sequence preferences for anti-cancer drug mitoxanthrone and related anthraquinones revealed by DNase1 footprinting. FEBS Lett. 202, 289-294. (63) Bajaj, N. P. S., McLean, M. J., Waring, M. J., and Smekal, E. (1990) Sequence-selective pH-dependent binding to DNA of benzophenanthridine alkaloids. J.Mol. Recognit. 3,48-54. (64) Schwaller, M. A., Aubard, J., Auclair, C., Paoletti, C., and Dodin, G. (1989) The GC base-pair preference of 2-N-methyl 9-hydroxyellipticinium. Eur. J. Biochem. 181, 129-134. (65) Bailly, C., OhUigin, C., Rivalle, C., Bisagni, E., Hhichart, J. P., and Waring, M. J. (1990) Sequence-selective binding of an ellipticine derivative to DNA. Nucleic Acids Res. 18,62836291. (66) Bailly, C., Denny, W. A., Mellor, L. E., Wakelin, L. P. G., and Waring, M. J. Sequence-specificity of the binding of antitumor amsacrine-4-carboxamidesto DNA studied by DNAase I footprinting. Biochemistry, submitted. (67) VanDyke,M. W., Dervan, P. B. (1983) Chromomycin, mithramycin, and olivomycin binding sites on heterogeneous deoxiribonucleic acid. Footprinting with (methidiumpropylEDTA)iron(II). Biochemistry 22, 2373-2377.

300

Bioconjugate Chem.. Vol. 2, No. 6, 1991

(68) Gao, X., and Patel, D. J. (1989) Antitumor drug-DNA interactions: NMR studies of echinomycin and chromomycin complexes. Q.Rev. Biophys. 22, 93-138. (69) Gao, X., and Patel, D. J. (1989) Chromomycin dimer-DNA oligomere complexes. Sequence selectivity and divalent cation specificity. Biochemistry 29, 10940-10956. (70) Sakaguchi,R.,Katahira,M.,Kyogoku,Y.,andFujii,S. (1991) An NMR study on the conformation of a deoxyribonucleotide duplex, d(GGGGCCCC)z, and its complex with chromomycin. J . Biochem. 209, 317-327. (71) Banville, D. L., Keniry, M. A., and Shafer, R. H. (1990) NMR investigation of mithramycin A binding to d(ATGCAT)*: A comparative study with chromomycin A3. Biochemistry 29, 9294-9304. (72) Fox, K. R., and Howarth, N. R. (1985) Investigations into the sequence-selective binding of mithramycin and related ligands to DNA. Nucleic Acids Res. 13, 8695-8714. (73) Sarker, M., and Chen, F. M. (1989) Binding of mithramycin to DNA in the presence of second drugs. Biochemistry 28, 6651-6657. (74) Cons, B. M. G., and Fox, K. R. (1989) Interaction of mithramycin with metal ions and DNA. Biochem. Biophys. Res. Commun. 160, 517-524. (75) Cons, B. M. G., and Fox, K. R. (1989) High resolution hydroxyl radical footprinting of the binding of mithramycin and related antibiotics to DNA. Nucleic Acids Res. 17,5447-5459. (76) Cons, B. M. G., and Fox, K. R. (1990) Footprinting studies of sequence recognition by mithramycin. Anti-Cancer Drug Des. 5, 93-97. (77) Cons, B. M. G., and Fox, K. R. (1991) Effects of the antitumor antibiotic mithramycin on the structure of repetitive DNA regions adjacent to its GC-rich binding site. Biochemistry 30, 6314-6321. (78) Wilson, W. D., Wang, Y. H., Kusuma, S., Chandrasekaran, S., Yang, N. C., and Boykin, D. W. (1985) Binding strength and specificity in DNA interactions: the design of A T specific intercalators. J . Am. Chem. SOC. 107, 4989-4995. (79) Krivtsora, M. A,, Moroshkina, E. B., and Glibin, E. (1984) DNA interaction with low molecular weight ligands with different structures. 111. Complexes of DNA with distactins. Mol. Biol. 18, 950-956. (80) Dervan, P. B. (1986) Design of sequence-specific DNAbinding molecules. Science 232, 464-471. (81) Kopka, M. L., Yoon, C., Goodsell, D., Pjura, P., and Dickerson, R. E. (1985) The molecular origin of DNA-drug specificit in netropsin and distamycin. Proc. Natl. Acad. Sci. U.S.A. 82, 1376-1380. (82) Kopka, M. L., Yoon, C., Goodsell, D., Pjura, P., and Dickerson, R. E. (1985) Binding of an antitumor drug to DNA: Netropsin and CGCGAATTBrCGCG. J . Mol. Biol. 183,553563. (83) Patel, D. J., and Shapiro, L. (1986) Sequence-dependent recognition of DNA duplexes. J . Biol. Chem. 261,1230-1240. (84) Dickerson, R. E., and Drew, H. R. (1981) Structure of a B-DNA dodecamer. 11. Influence of base sequence on helix structure. J . Mol. Biol. 149, 761-786. (85) Drew, H. R., and Dickerson, R. E. (1981) Structure of a B-DNA dodecamer. 111. Geometryof hydration. J . Mol. Biol. 151, 535-556. (86) Klevit, R. E., Wemmer, D. E., and Reid, B. R. (1986) 'H NMR studies on the interaction between distamycin A and a symmetrical DNA dodecamer. Biochemistry 25,3296-3303. (87) Carrondo, M. A. A., de C. T., Coll, M., Aymami, J., Wang, A. H. J., Van der Marel, G. A., Van Boom, J. H., and Rich, A. (1989) Binding of a Hoechst dye to d(CGCGATATCGCG) and its influence on the conformation of the DNA fragment. Biochemistry 28, 7849-7859. (88) Pjura, P. E., Grzeskoniak, K., and Dickerson, R. E. (1987) Binding of Hoechst 33258 to the minor groove of B-DNA. J. Mol. Biol. 197, 257-271. (89) Larsen, T. A., Goodsell, D. S., Cascio, D., Grezeskowiak, K., and Dickerson, R. E. (1989) The structure of DAPI bound to DNA. J . Biomol. Struct. Dyn. 7, 477-491. (90) Neidle, S.,and Abraham, Z. (1984) Structural and sequencedependent aspects of drug intercalation into nucleic acids. CRC Crit. Rev. Biochem. 17, 73-121.

Bailly and HBnichart

(91) Fox, K. R., and Waring, M. J. (1984) DNA structural variations produced by actinomycin and distamycin as revealed by DNAase I footprinting. Nucleic Acids Res. 12,9271-9285. (92) Low, C. M. L., Drew, H. R., and Waring, M. J. (1984) Sequence-specific binding of echinomycin to DNA evidence for conformational changes affecting flanking sequences. Nucleic Acids Res. 12, 4865-4879. (93) Portugal, J., Fox, K. R., McLean, M. J., Richenberg, J. L., and Waring, M. J. (1988) Diethyl pyrocarbonate can detect a modified DNA structure induced by the binding of quinoxaline antibiotics. Nucleic Acids Res. 16, 3655-43670. (94) McLean, M. J., and Waring, M. J. (1988) Chemical probes reveal no evidence of Hoogsteen base pairing in complexes formed between echinomycin and DNA in solution. J. Mol. Recog. 1, 138-151. (95) McLean, M. J., Seela, F., and Waring, M. J. (1989) Echinomycin-induced hypersensitivity to osmium tetroxide of DNA fragments incapable of forming Hoogsteen base pairs. Proc. Natl. Acad. Sci. U.S.A. 86, 9687-9691. (96) Fox, K. R., and Kentebe, E. (1990) Echinomycin binding to the sequence CG(AT)nCG alters the structure of the central A T region. Nucleic Acids Res. 18, 1957-1963. (97) Lane, M. J., LaPlante, S. R., Rehfuss, R. P., Borer, P. N., and Cantor, C. R. (1987) Actinomycin D facilitates transition of AT domains in molecules of sequence (AT),AGCT(AT). to a DNAse I detectable alternating structure. Nucleic Acids Res. 15, 839-852. (98) Huang,Y. Q.,Rehfuss,R. P.,LaPlante, S. R.,Boudreau, E., Borer, P. N., and Lane, M. J. (1988) Actinomycin D induced DNase I cleavage enhancement caused by sequence specific propagation of an altered DNA structure. Nucleic Acids Res. 16, 11125-11137. (99) Bishop, K. D., Borer, P. N., Huang, Y. Q., and Lane, M. J. (1991) Actinomycin D induced DNase I hypersensitivity and asymmetric structure transmission in a DNA hexadecamer. Nucleic Acids Res. 19, 871-875. (100) Waterloh, K., and Fox, K. R. (1991) The effects of actinomycin on the structure of dA,,.dT, and (dA-dT), regions surrounding its GC binding site. J . Biol. Chem. 266, 63816388. (101) Wartell, R. M., Larson, J. E., and Wells, R. D. (1975) The compatibility of netropsin and actinomycin binding to natural deoxyribonucleic acid. J. Biol. Chem. 250, 2698-2702. (102) Patel, D. J., Pardi, A., and Itakura, K. (1982) DNA conformation, dynamics, and interactions in solution. Science 216, 581-590. (103) Patel, D. J., Kozlowski, S. A., Rice, J. A., Broka, C., and Itakura, K. (1981) Mutual interaction between adjacent dG-dC actinomycin binding sites and dA.dT netropsin binding sites on the self-complementary d(CGCGAATTCGCG) duplex in solution. Proc. Natl. Acad. Sci. U.S.A. 78, 7281-7284. (104) Takusagawa, F., Dabrow, M., Neidle, S., and Berman, H. M. (1982) The structure of a pseudo intercalated complex between actinomycin and the DNA binding sequence d(GpC). Nature 296, 466-469. (105) Brown, S. C., Mullis, K., Levenson, C., and Shafer, R. H. (1984) Aqueous solution structure of an intercalated actinomycin D-dATGCAT complex by two-dimensional and onedimensional proton NMR. Biochemistry 23, 403-408. (106) Snyder, J. G., Hartman, N. G., Langlois D'Estantoit, B., Kennard, O., Remeta, D. P., and Breslauer, K. J. (1989) Binding of actinomycin D to DNA: Evidence for a nonclassical highaffinity binding mode that does not require GpC sites. Proc. Natl. Acad. Sci. U.S.A. 86, 3968-3972. (107) Scott, E. V., Zon, G., Marzilli, L. G., and Wilson, W. D. (1988) 2D NMR investigation of the binding of the anticancer drug actinomycin D to duplexed dATCGCGAT: Conformational features of the unique 2:l adduct. Biochemistry 27, 7940-7951. (108) Scott, E. V., Jones, R. L., Banville, D. L., Zon, G., Marzilli, L. G., and Wilson, W. D. (1988) 'Hand 31P NMR investigations of actinomycin D binding selectivity with oligodeoxyribonucleotides containing multiple adjacent d(GC) sites. Biochemistry 27, 915-923. (109) Rill, R. L., Marsch, G. A., and Graves, D. E. (1989) 7-Azidoactinomycin D: a photoaffinity probe of the sequence spec-

Review

ificity of DNA binding by actinomycin D. J . Biomol. Struct.

Dyn. 7, 591-605. (110) Quigley, G. J., Wang, A. H. J., Ughetto, G., Van der Marel, G. A.; Van Boom, J. H., and Rich, A. (1980) Molecular structure of an anticancer drug-DNA complex: Daunomycin plus d(CpGpTpApCpG). Proc. Natl. Acad. Sci. U.S.A. 77,72047208. 11) Wang, A. H. J., Ughetto, G., Quigley, G. J., and Rich, A. (1987) Interactions between an anthracycline antibiotic and DNA: Molecular structure of daunomycin complexed to d(CpGpTpApCpG) at 1 . 2 4 resolution. Biochemistry 26, 1152-1163. 12) Holbrook, S. R., Wang, A. H. J., Rich, A., and Kim, S. H. (1988) Local mobility of nucleic acids as determined from crystallographic data. 111. A daunomycin-DNA complex. J. Mol. Biol. 199, 349-357. 13) Frederick, C. A., Williams, L. D., Ughetto, G., van der Marel, G. A., van Boom, J. H., Rich, A,, and Wang, A. H. J. (1990) Structural comparison of anticancer drug-DNA complexes: Adriamycin and daunomycin. Biochemistry 29, 2538-2549. 14) Chaires, J. B., Fox, K. R., Herrera, J. E., Britt, M., and Waring, M. J. (1987) Site and sequence specificity of the daunomycin-DNA interaction. Biochemistry 26, 8227-8236. 15) Chaires, J. B., Herrera, J. E., and Waring, M. J. (1990) Preferential binding of daunomycin to 5’A/TCG and 5’A/ TGC sequences revealed by footprinting titration experiments. Biochemistry 29, 6145-6153. 16) Gresh, N., Pullman, B., and Arcamone, F. (1985) A theoretical investigation on the sequence selective binding of daunomycin to double-stranded polynucleotides. J. Biomol. Struct. Dvn. 3. 445-466. (117) Gresh N., Pullman, B., Arcamone, F., Menozzi, M., and Tonani, R. (1989) Joint experimental and theoretical investigation of the comparative DNA binding affinities of intercalating anthracycline derivatives. Mol. Pharmacol. 35,251256. (118) Chaires, J. B. (1990) Biophysical chemistry of the daunomycin-DNA interaction. Biophys. Chem. 35, 191-202. (119) Chaires, J. B. (1990) Daunomycin binding to DNA: from the macroscopic to the microscopic. Molecular Basis of Specificity in Nucleic Acid-Drug Interactions (B. Pullman, and J. Jortner, Eds.) pp 225-245, Kluwer Academic Publishers, Dordrecht, Netherlands. (120) Searle, M. S., Hall, J. G., Denny, W. A., and Wakelin, L. P. G. (1988) NMR studies of the interactions of the antibiotic nogalamycin with the hexadeoxyribonucleotide duplex d(5’GCATGC)z. Biochemistry 27, 4340-4349. (121) Liaw, Y. C., Gao, Y. G., Robinson, H., Van der Marel, G. A,, van Boom, J. H., and Wang, A. H. J. (1989) Antitumor drug nogalamycin binds DNA in both grooves simultaneously: Molecular structure of nogalamycin-DNA complex. Biochemistry 28, 9913-9918. (122) Gao, Y. G., Liaw, Y. C., Robinson, H., and Wang, A. H. J. (1990) Binding of the antitumor drug nogalamycin and its derivatives to DNA: structural comparison. Biochemistry 29, 10307-10316. (123) Williams, L. D., Egli, M., Gao,Q., Bash, P., Vander Marel, G. A., Van Boom, J. H., Rich, A., and Frederick, C. A. (1990) Structure of nogalamycin bound to a DNA hexamer. Proc. Natl. Acad. Sci. U.S.A. 87, 2225-2229. (124) Egli, M., Williams, L. D., Frederick, C. A,, and Rich, A. (1991) DNA-nogalamycin interactions. Biochemistry 30, 1364-1372. (125) Fox, K. R., and Waring, M. J. (1986) Nucleotide sequence binding preferences of nogalamycin investigated by DNAase I footprinting. Biochemistry 25, 4349-4356. (126) Searle, M., Bicknell, W., Wakelin, L. P. G., andDenny, W. A. (1991) Anthracycline antibiotic arugomycin binds in both grooves of the DNA helix simultaneously: An NMR and molecular modelling study. Nucleic Acids Res. 19, 2897-2906. (127) Wang, A. H. J., Ughetto, G., Quigley, G. J., Hakoshima, T., Van der Marel, G. A., Van Boom, J. H., and Rich, A. (1984) The molecular structure of a DNA-Triostin A complex. Science 225, 1115-1121. (128) Ughetto, G., Wang, A. H. J., Quigley, G. J., Van der Marel, G. A,, Van Boom, J. H., and Rich, A. (1985) A comparison of

Bioconjugate Chem., Vol. 2, No. 6, 1991 389 the structure of echinomycin and triostin A complexed to a DNA fragment. Nucleic Acids Res. 13, 2305-2323. (129) Quigley, G. J., Ughetto, G., Van der Marel, G. A., Van Boom, J. H., Wang, A. H. J., and Rich, A. (1986) Non-WatsonCrick G-C and A.T base pairs in a DNA-antibiotic complex. Science 232, 1255-1258. (130) Bernier, J. L., HBnichart, J. P., and Catteau, J. P. (1981) Design, synthesis and DNA-binding capacity of a new peptidic bifunctional intercalating agent. Biochem. J . 199,479484. (131) Helbecque, N., Bernier, J. L., and HBnichart, J. P. (1985) Design of a new DNA-polyintercalating drug, a bisacridinyl peptidic analogue of Triostin A. Biochem. J . 225, 829-832. (132) Viswamitra, M. A., Kennard, O., Cruse, W. B. T., Egert, E., Sheldrick, G. M., Jones, P. G., Waring, M. J., Wakelin, L. P. G., and Olsen, R. K. (1981) Structure of TANDEM and its implication for bifunctional intercalation into DNA. Nature 289, 817-819. (133) Wakelin, L. P. G. (1986) Polyfunctional DNA intercalating agents. Med. Res. Reo. 6, 275-340. (134) Delbarre, A., Delepierre, M., D’Estaintot, B. L., Igolen, J., and Roques, B. P. (1987) Bisintercalation of ditercalinium into a d(CGCG) minihelix: Structure and dynamic aspects-A 400 MHz NMR study. Biopolymers 26, 1001-1033. (135) Delbarre, A., Delepierre, M., Garbay, C., Igolen, J., Le Pecq, J. B., and Roques, B. P. (1987) Geometry of the antitumor drug ditercalinium bis intercalated into d(CpGpCpG)z by ‘H NMR. Proc. Natl. Acad. Sci. U.S.A. 84, 2155-2159. (136) Maroun, R. C., and Roques, J. B. (1991) Induction of DNA bending by bifunctional intercalating agents of the 7H-pyridocarbazole family. Biophys. Chem. 39, 45-56. (137) Waring, M. J. (1986) Recognition of DNA by quinoxaline antibiotics. Molecular Mechanisms of Carcinogenic and Antitumor Activity (C. Chagas, B. Pullman, Eds.) pp 317-337, Adenine Press, New York. (138) Waring, M. J. (1990) The molecular basis of specific recognition between echinomycin and DNA. Molecular Basis of Specificity in Nucleic Acid-Drug Interactions (B. Pullman, and J. Jortner, Eds.) pp 225-245, Kluwer Academic Publishers, Dordrecht, Netherlands. (139) Gao, X., and Patel, D. J. (1988) NMR studies of echinomycin bisintercalation complexes with d(Al-C2-G3-T4) and d(Tl-C2-G3-A4)duplexes in aqueous solution: Sequence-dependent formation of Hoogsteen AleT4 and Watson-Crick TleA4 base pairs flanking the bisintercalation site. Biochemistry 27, 1744-1751. (140) Gilbert, D. A., van der Marel, G. A., van Boom, J. H., and Feigon, J. (1989) Unstable Hoogsteen base pairs adjacent to echinomycin binding sites within a DNA duplex. Proc. Natl. Acad. Sci. U.S.A. 86, 3006-3010. (141) Gilbert, D. E., and Feigon, J. (1991) The DNA sequence a t echinomycin binding sites determines the structural changes induced by drug binding: NMR studies of echinomycin binding to [d(ACGTACGT)I2and [d(TCGATCGA)]z. Biochemistry 30, 2483-2494. (142) Sugiura, Y., Shiraki, T., Konishi, M., and Oki, T. (1990) DNA intercalation and cleavage of an antitumor antibiotic dynemicin that contains anthracycline and enediyne cores. Proc. Natl. Acad. Sci. U.S.A. 87, 3831-3835. (143) Dasgupta, D., and Goldberg, I. H. (1986) Mode of reversible binding of neocarzinostatin chromophore to DNA: Base sequence dependency of binding. Nucleic Acid Res. 14,10891105. (144) Lee, S. H., and Goldberg, I. H. (1989) Sequence-specific, strand-selective, and directional binding of neocarzinostatin chromophore to oligodeoxyribonucleotides. Biochemistry 28, 1019-1026. (145) Patel, D. J. (1982) Antibiotic-DNA interactions: intermolecular nuclear Overhauser effects in the netropsin-d(CGCGAATTCGCG) complex in solution. Proc. Natl. Acad. Sci. U.S.A. 79, 6424-6428. (146) Marky, L. A., and Breslauer, K. J. (1987) Origins of netropsin binding affinity and specificity: Correlation of thermodynamic and structural data. Proc. Natl. Acad. Sci. U.S.A. 84, 4359-4363. (147) Coll, M., Aymami, J., Van der Marel, G. A., Van Boom, J. H., Rich, A., and Wang, A. H. J. (1989) Molecular structure

390

Bloconjugate Chem., Vol. 2, No. 6, 1991

of the netropsin-d(CGCGATATCGCG)complex: DNA conformation in an alternating AT segment. Biochemistry 28, 310-320. (148) Pelton, J. G., and Wemmer, D. E. (1990) Binding modes of distamycin A with d(CGCAAATTTGCG)Z determined by two-dimensional NMR. J. Am. Chem. SOC.112, 1393-1399. (149) Caldwell, J., and Kollman, P. A. (1986) A molecular mechanical study of netropsin-DNA interactions. Biopolymers 25, 249-266. (150) Coll, M., Frederick, C. A., Wang, A. H. J., and Rich, A. (1987) A bifurcated hydrogen bonded conformation in the d(A.T) base pairsof the DNA dodecamer of d(CGCAATTGCG) and its complex withdistamycin. Proc. Natl. Acad. Sci. U.S.A. 84,8385-8389. (151) Boehncke, K., Nonella, M., Schulten, K., and Wang, A. H. J. (1991) Molecular dynamics investigation of the interaction between DNA and distamycin. Biochemistry 30,5465-5475. (152) Lerman, L. S. (1961) Structural considerations in the interaction of DNA and acridines. J. Mol. Biol. 3, 18-30. (153) Lerman, L. S. (1963) The structure of the DNA-acridine complex. Proc. Natl. Acad. Sci. U.S.A. 49, 94-105. (154) Denny, W. A., Baguley, B. C., Cain, B. F., and Waring, M. J. (1983) Antitumour acridines. Molecular Aspects of Anticancer Drug Action (S. Neidle, and M. J. Waring, Eds.) pp 1-34, Verlag Chemie, Sutton, England. (155) Denny, W. A. (1990) DNA-intercalating ligands as anticancer drugs: Prospects for future design. Anti-Cancer Drug. Des. 4, 241-263. (156) Baguley, B. C. (1991) DNA intercalating anti-tumour agents. Anti-Cancer Drug. Des. 6, 1-35. (157) Arlin, Z. (1983) Current status of amsacrine combination chemotherapy programs in acute leukemia. Cancer Treat. Rep. 67,969-970. (158) Louie, A. C., and Issell, B. F. (1985) Amsacrine (AMSA)-A clinical review. J. Clin. Oncol. 3, 562-592. (159) Zittoun, R. (1985) m-AMSA: A review of clinical data. Eur. J. Cancer Clin. Oncol. 21, 649-653. (160) Cassileth, P. A., and Gale, R. P. (1986)Amsacrine: A review. Leukemia Res. 10, 1257-1265. (161) Leopold, W. R., 111, Corbett, T. H., Griswold, D. P., Plowman, J., and Baguley, B. C. (1987) Experimental antitumor activity of the amsacrine analogue CI-921. J. Natl. Cancer Inst. 79, 343-349. (162) Hardy, J. R., Harvey, V. J., Paxton, J. W., Evans, P., Smith, S., Grove, W., Grillo-Lopex, A. J., and Baguley, B. C. (1988) A phase I trial of the amsacrine analog 9-[ [2-methoxy-4-[(methylsulfonyl)amino]phenyl]amino]-N,5-dimethyl-4-acridinecarboxamide ((3-921). Cancer Res. 48, 6593-6596. (163) Eliadis, A,, Phillips, D. R., Reiss, J. A., and Skorobogaty, A. (1988) The synthesis and DNA footprinting of acridinelinked netropsin and distamycin bifunctional mixed ligands. J. Chem. SOC.,Chem. Commun. 1049-1052. (164) Bailly, C., Pommery, N., Houssin, R., and Hhichart, J. P. (1989) Design, synthesis, DNA binding and biological activity of a series of DNA minor-groove-binding intercalating drugs. J. Pharm. Sei. 78, 910-917. (165) Denny, W. A., Atwell, G. J., and Baguley, B. C. (1983) Potential antitumor agents. 39. Anilino ring geometry of amsacrine and derivatives: Relationship to DNA binding and antitumor activity. J. Med. Chem. 26, 1625-1630. (166) Chen, K. X., Gresh, N., and Pullman, B. (1988) Energetics and stereochemistry of DNA complexation with the antitumor AT specific intercalators tilorane and m-AMSA. Nucleic Acids Res. 16, 3061-3073. (167) Denny, W. A., and Wakelin, L. P. G. (1986) Kinetic and equilibrium studies of the interaction of amsacrine and anilino ring-substituted analogues with DNA. Cancer Res. 46,17171721. 68) Wakelin, L. P. G., Chetcuti, P., and Denny, W. A. (1990) Kinetic and equilibrium binding studies of amsacrine-4-carboxamides: a class of asymmetrical DNA-intercalating agents which bind by threading through the DNA helix. J . Med. Chem. 33, 2039-2044. 69) Bailly, C., Helbecque, N., HBnichart, J. P., Colson, P., Houssier, C., Rao, K. E., Shea, R. G., and Lown, J. W. (1990) Molecular recognition between oligopeptides and nucleic acids.

Bailly and tihichart

DNA sequence specificity and binding properties of an acridine-linked netropsin hybrid ligand. J . Mol. Recognit. 3,2635. (170) Hurley, L. H. (1989) DNA and associated targets for drug design. J . Med. Chem. 32, 2027-2033. (171) Gellert, M. (1981) DNA topoisomerases. Annu. Reu. Biochem. 50,879-910. (172) Liu, L. F. (1983) DNA topoisomerases-enzymes that catalyse the breaking and rejoining of DNA. Crit. Rev. Biochem. 15, 1-24. (173) Wang, J. C. (1985) DNA topoisomerases. Annu. Rev. Biochem. 54,665-697. (174) Maxwell, A., and Gellert, M. (1986) Mechanistic aspects of DNA topoisomerases. Adu. Protein Chem. 38, 69-107. (175) Wang, J. C. (1987) Recent studies of DNA topoisomerases. Biochim. Biophys. Acta 909, 1-9. (176) Sutcliffe, J. A., Gootz, T. D., and Barrett, J. F. (1989) Biochemical characteristics and physiological significance of major DNA topoisomerases. Antimicrob. Agents Chemother. 33, 2027-2033. (177) Ross, W. E. (1985) DNA topoisomerases as targets for cancer therapy. Biochem. Pharmacol. 34,4191-4195. (178) Lock, R. B., and Ross, W. E. (1987) DNA topoisomerases in cancer therapy. Anti-Cancer Drug Des. 2, 151-164. (179) Kohn, K. W., Pommier, Y., Kerrigan, D., Markovits, J., and Covey, J. M. (1987) Topoisomerase I1 as a target of anticancer drug action in mammalian cells. Natl. Cancer Inst. Monogr. 4, 61-71. (180) Glisson, B. S., and Ross, W. E. (1987) DNA topoisomerase 11: a primer on the enzyme and its unique role as a multidrug in cancer chemotherapy. Pharmacol. Ther. 32, 89-106. (181) Drlica, K., and Franco, R. J. (1988) Inhibitors of DNA topoisomerases. Biochemistry 27, 2253-2259. (182) D’Arpa, P., and Liu, L. F. (1989) Topoisomerase-targeting antitumor drugs. Biochim. Biophys. Acta 989, 163-177. (183) Liu, L. F. (1989) DNA topoisomerase poisons as antitumor drugs. Annu. Rev. Biochem. 58, 351-375. (184) Zwelling, L. A. (1989) Topoisomerase I1 as a target of antileukemia drugs: A review of controversial areas. Hum. Pathol. 3,101-112. (185) Kreuzer, K. N. (1989) DNA topoisomerases as potential targets of antiviral action. Pharm. Ther. 43, 377-395. (186) Zunino, F., and Capranico, G. (1990) DNA topoisomerase I1 as the primary target of anti-tumor anthracyclines. AntiCancer Drug Des. 5, 307-317. (187) Pommier, Y., Mattern, M. R., Scharwtz, R. E., Zwelling, L. A., and Kohn, K. N. (1984) Changes in deoxyribonucleic acid linking number due to treatment of mammalian cells with the intercalating agents 4’-(9-acridinylamino)methanesulfonm-anisidide. Biochemistry 23, 2927-2932. (188) Nelson, E. M., Tewey, K. M., and Liu, L. F. (1984) Mechanism of antitumor drug action. Poisoning of mammalian DNA topoisomerase I1 on DNA by 4’-(9-acridinylamino)methanesulfon-m-anisidide. Proc. Natl. Acad. Sei. U.S.A. 81, 13611365. (189) Marshall, B., and Ralph, R. K. (1985) The mechanism of action of mAMSA. Adu. Cancer Res. 44, 267-293. (190) Pommier, Y., Schwartz, R. E., Zwelling, L. A., and Kohn, K. W. (1985) Effects of DNA intercalating agents on topoisomerase I1 induced DNA strand cleavage in isolated mammalian cell nuclei. Biochemistry 24, 6406-6410. (191) Pommier, Y., Minford, J. K., Schwartz, R. E., Zwelling, L. A., and Kohn, K. W. (1985) Effects of the DNA intercalators 4’-(9-acridinylamino)methanesulfon-m-anisidide and 2-methyl-9-hydroxyellipticiniumon topoisomerase I1 mediated DNA strand cleavage and strand passage. Biochemistry 24,64106416. (192) Rowe, T. C., Chen, G. L., Hsiang, Y. H., and Liu, L. F. (1986) DNA damage by antitumor acridines mediated by mammalian DNA topoisomerase 11. Cancer Res. 46, 20212026. (193) Pommier, Y., Covey, J., Kerrigan, D., Mattes, W., Markovits, J., and Kohn, K. W. (1987) Role of DNA intercalation in the inhibition of purified mouse leukemia-(11210) DNA topoisomerase I1 by amino-9-acridines. Biochem. PharmaC O ~ .36, 3477-3486.

Review

(194) Covey, J. M., Kohn, K. W., Kerrigan, D., Tilchen, E. J., and Pommier, Y. (1988) Topoisomerase 11-mediated DNA damage produced by 4f-(9-acridinylamino)methanesulfon-manisidide and related acridines in L1210 cells and isolated nuclei: Relation to cytotoxicity. Cancer Res. 48, 860-865. (195) Fox, M. E., and Smith, P. J. (1990) Long term inhibition of DNA synthesis and the persistence of trapped topoisomerase I1 complexes in determining the toxicity of the antitumor DNA intercalators m-AMSA and mitoxantrone. Cancer Res. 50, 5813-5818. 96) Finlay, G. J., Wilson, W. R., and Baguley, B. C. (1989) Chemoprotection by 9-aminoacridine derivatives against the cytotoxicity of topoisomerase 11-directeddrugs. Eur. J.Cancer Clin. Oncol. 25, 1695-1701. 97) Chow, K. C., MacDonald, T.L., and Ross, W. E. (1989) DNA binding by epipodophyllotoxins and N-acyl anthracyclines: Implications for mechanism of topoisomerase I1 inhibition. Mol. Pharmacol. 34, 467-473. (198) Baguley, B. C., Holdaway, K. M., and Fray, L. M. (1990) Design of DNA intercalators to overcome topoisomerase IImediated multidrug resistance. J.Natl. Cancer Inst. 82,399402. (199) McHugh, M., Woynarowski, J. M., Sigmund, R. D., and Beerman, T.A. (1989) Effect of minor groove binding drugs on mammalian topoisomerase I activity. Biochem. PharmaC O ~ .38, 2323-2328. (200) McHugh, M., Sigmund, R. D., and Beerman, T.A. (1990) Effect of minor groove binding drugs on camptothecin-induced DNA lesions in L1210 nuclei. Biochem. Pharmacol. 39,707714. (201) Fesen, M., and Pommier, Y. (1989) Mammalian topoisomerase I1 activity is modulated by the DNA minor groove binder distamycin in simian virus 40 DNA. J. Biol. Chem. 264, 11354-11359. (202) Woynarowski, J. M., McHugh, M., Sigmund, R. D., and Beerman, T. A. (1989)Modulation of topoisomerase IIcatalytic activity by DNA minor groove binding agents distamycin, Hoechst 33258, and 4’,6-diamidine-2-phenylindole. Mol. Pharmacol. 35, 177-182. (203) Woynarowski, J. M., Sigmund, R. D., and Beerman, T. A. (1989)DNA minor groove binding agents interfere with topoisomerase I1 mediated lesions induced by epipodophyllotoxin derivative VM-26 and acridine derivative m-AMSA in nuclei from L1210 cells. Biochemistry 28, 3850-3855. (204) Shishedo, K., Sakaguchi, R., and Nosoh, Y. (1984) Enhancement of S1 nuclease-susceptibility of negatively superhelical DNA by netropsin. Biochem. Biophys. Res. Commun. 124, 388-392. (205) Bruzik, J. P., Auble, D. T., and DeHaseth, P . L. (1987) Specific activation of transcription initiation by the sequence specific DNA-binding agents distamycin A and netropsin. Biochemistry 26, 950-956. (206) Straney, D. C., and Crothers, D. M. (1987) Effect of drugDNA interactions upon transcription initiation at the lac promoter. Biochemistry 26, 1987-1995. (207) Krogh, S., Mortensen, U. H., Westergaard, O., and Bonven, B. (1991)Eukaryotic topoisomerase I-DNA interaction is stabilized by helix curvature. Nucleic Acids Res. 19, 12351241. (208) Bailly, C., Catteau, J. P., Hbnichart, J. P., Reszka,K., Shea, R. G., Krowicki, K., and Lown, J. W. (1989) Subcellular distribution of a nitroxide spin-labeled netropsin in living KB cells. Biochem. Pharmacol. 38, 1625-1630. (209) Lemay, P., Bernier, J. L., HBnichart, J. P., and Catteau, J. P. (1983)Subcellular distribution of nitroxide spin-labelled 9-aminoacridine in living KB cells. Biochem. Biophys. Res. Commun. 111, 1074-1081. (210) Bailly, C., and Hhichart, J. P. (1990) Subcellular distribution of a nitroxide spin-labeled netropsine-acridine hybrid in living KB cells. Electron spin resonance study. Biochem. Biophys. Res. Commun. 167,798-806. (211) Bialer,M.,Yagen,B.,Mechoulam,R.,andBecker,Y. (1980) Structure-activity relationships of pyrrole amidine antiviral antibiotics 111. Preparation of distamycin and congocidine derivatives based on 2,5-disubstituted pyrroles. J. Pharm. Sei. 69, 1334-1338.

Bioconjugate Chem., Vol. 2, No. 6, 1991 381

(212) Bialer,M.,Yagen,B.,andMechoulam,R. (1980)Structureactivity relationships of pyrrole amidine antiviral antibiotics 11. Preparation of mono- and tripyrrole derivatives of congocidine. J. Med. Chem. 23, 1144-1148. (213) Gendler, P. L., and Rapoport, H. (1981)Permethyl analogue of the pyrrolic antibiotic distamycin A. J. Med. Chem. 24, 33-38. (214) Grehn, L., Ragnarsson, U., and Datema, R. (1983)Synthesis and antiviral activity of distamycin A analogues: Substitutions on the different pyrrole nitrogens and in the amidine function. J. Med. Chem. 26, 1042-1049. (215) Grehn, L., Ragnarsson, U., and Datema, R. (1986) Structure-activity relationships in distamycin A analogues: effect of alkyl groups on the pyrrole nitrogen at the non-amidine end of the molecule combined with methyl elimination in the following ring. Acta Chem. Scand. 40, 145-151. (216) Lee, M., Krowicki, K., Hartley, J. A,, Pon, R. T., andLown, J. W. (1988) Molecular recognition between oligopeptides and nucleic acids: Influence of van der Waals contacts in determining the 3’4erminus of DNA sequences read by monocationic lexitropsins. J. Am. Chem. SOC.110, 3641-3649. (217) Wang, A. H. J., Cottens, S., Dervan, P. B., and Yesinowski, J. P., van der Marel, G. A., and van Boom, J. H. (1989) Interactions between a symmetrical minor groove binding compound and DNA oligonucleotides;lH and 19FNMR studies. J. Biomol. Struct. Dyn. 7, 101-117. (218) Grokhovsky, S. L., Zhuze, A. L., and Gottikh, B. P. (1975) DNA base pair specific ligands. I. Synthesis of distamycin A and its analogs with different number of N-methyl and N-propylpyrrole residues. Bioorgan. Khim. 1 , 1616-1623. (219) Schultz, P. G., and Dervan, P. B. (1983) Distamycin and penta-N-methylpyrrole-carboxamidebinding sites on native DNA, a comparison of methidiumpropyl-EDTA-iron(I1) footprinting and DNA affinity cleaving. J. Biomol. Struct. Dyn. 1,1133-1140. (220) Schultz, P. G., and Dervan, P. B. (1983) Sequence-specific double-strand cleavage of DNA by penta-N-methylpyrrolecarboxamide-EDTA-Fe(I1). Proc. Natl. Acad. Sci. U.S.A.80, 6834-6837. (221) Youngquist, R. S., and Dervan, P. B. (1985) Sequence specific recognition of B-DNA by oligo(N-methylpyrrole carboxamides). Proc. Natl. Acad. Sei. U.S.A. 82, 2565-2569. (222) Khorlin, A. A., Krylov, A. S., Grokhovsky, S. L., Zhuze, A. L., Zasedatelev, A. S., Gursky, G. V., and Gottikh, B. P. (1980) A new type of AT-specific ligand constructed of two netropsinlike molecules. FEBS Lett. 118, 311-314. (223) Schultz, P. G., and Dervan, P. B. (1983) Sequence-specific double-strand cleavage of DNA by bis(EDTA-distamycin-Fen) and EDTA-bis(distamycin)Fe”.J.Am. Chem. SOC.105,77487750. (224) Youngquist, R. S., and Dervan, P. B. (1985) Sequencespecific recognition of B-DNA by bis(EDTA-distamycin)fumaramide. J. Am. Chem. SOC.107,5528-5529. (225) Youngquist, R. S., and Dervan, P. B. (1987) A synthetic peptide binds 16 base pairs of A,T double helical DNA. J. Am. Chem. SOC.109, 7564-7566. (226) Lown, J. W., Krowicki, K., Balzarini, J., Newman, R. A., and De Clercq, E. (1989) Novel linked antiviral and antitumor agents related to netropsin and distamycin: Synthesis and biological evaluation. J. Med. Chem. 32, 2368-2375. (227) Kissinger, K. L., Dabrowiak, J. C., and Lown, J. W. (1990) Molecular recognition between oligopeptides and nucleic acids: DNA binding specificity of a series of bis-netropsin analogues deduced from footprinting analysis. Chem. Res. Toxicol. 3, 162-168. (228) Rao, K. E., Zimmermann, J., and Lown, J. W. (1991) Sequence-selective DNA binding by linked bis-N-methylpyrrole dipeptides: An analysis by MPE footprinting and force field calculations. J. Org. Chem. 56, 786-797. (229) Lown, J. W. (1990) Molecular mechanisms of DNA sequence recognition by groove binding ligands: Biochemical and biological consequences. Molecular Basis of Specificity in Nucleic Acid-Drug Interactions (B. Pullman, and J. Jortner, Eds.) pp 103-122, Kluwer Academic Publishers, Dordrecht, Netherlands. (230) Lown, J. W., Krowicki, K., Balzarini, J., and De Clercq, E. (1986) Structure-activity relationship of novel oligopeptide

382

Bioconjugate Chem., Vol. 2, No. 6, 1991

antiviral and antitumor agents related to netropsin and distamycin. J. Med. Chem. 29, 1210-1214. (231) Lown, J. W., Krowicki, K., Bhat, U. G., Skorobogaty, A., Ward, B.,and Dabrowiak, J. C. (1986) Molecular recognition between oligopeptides and nucleic acids: Novel imidazolecontaining oligopeptides related to netropsin that exhibit altered DNA sequence specificity. Biochemistry 25, 74087416. (232) Krowicki, K., and Lown, J. W. (1987) Synthesis of novel imidazole-containing DNA minor groove binding oligopeptides related to the antiviral antibiotic netropsin. J.Org. Chem. 52,3493-3501. (233) Kissinger, K. L., Krowicki, K., Dabrowiak, J. C., and Lown, J. W. (1987) Molecular recognition between oligopeptides and nucleic acids: Monocationic imidazole lexitropsins that display enhanced GC sequence dependent DNA binding. Biochemistry 26,5590-5595. (234) Lee, M., Hartley, J. A., Pon, R. T., Krowicki, K., andLown, J. W. (1988) Sequence specific molecular recognition by a monocationic lexitropsin of the decadeoxyribonucleotide d(CATGGCCATG),: Structural and dynamic aspects deduced from high field 1H-NMR studies. Nucleic Acids Res. 16,665-684. (235) Lee, M., Chang, D. K., Hartley, J. A,, Pon, R. T., Krowicki, K., and Lown, J. W. (1988) Structural and dynamic aspects of binding of a prototype lexitropsin to the decadeoxyribonucleotide d(CGCAATTGCG)z deduced from high resolution lH NMR studies. Biochemistry, 27, 445-455. (236) Lee, M., Coulter, D. M., Pon, R. T., Krowicki, K., and Lown, J. W. (1988) Sequence specific molecular recognition and binding of a monocationic bis-imidazole lexitropsin to the decadeoxyribonucleotide d[ (GATCCGTATG):(CATACGGATC)]: Structural and dynamic aspects of intermolecular exchange studied by 1H-NMR. J . Biomol. Struct. Dyn. 5, 1059-1087. (237) Lee, M., Pon, R. T., Krowicki, K., and Lown, J. W. (1988) Structuraland dynamic aspects of the sequence specific binding of netropsin and its bis-imidazole analogue on the decadeoxyribonucleotide d(CGCAATTGCG)2. J. Biomol. Struct. Dyn. 5,939-949. (238) Burckhardt, G., Luck, G., Zimmer, C., Storl, J., Krowicki, K., and Lown, J. W. (1989) Variation of DNA sequence specificity of DNA-oligopeptide binding ligands related to netropsin: imidazole-containing lexitropsins. Biochim. Biophys. Acta 1009, 11-18. (239) Randrianarivelo, M., Zakrzewska, K., and Pullman, B. (1989) Theoretical modeling of DNA-monocationic lexitropsin complexation: Influence of ligand binding on DNA curvature. J. Biomol. Struct. Dyn. 6, 769-779. (240) Bailly, C., Houssin, R., Bernier, J. L., and HBnichart, J. P. (1988) Depsipeptide analogs of the antitumor drug distamycin containing thiazole amino acids residues. Tetrahedron 44, 5833-5843. (241) Plouvier, B., Houssin, R., Bailly, C., and HBnichart, J. P. (1989) Synthesis and DNA-binding study of a thiazolecontaining analog of netropsin. J . Heterocycl. Chem. 26,16431647. (242) Kumar, So,Jaseja, M., Zimmermann, J., Yadagiri,B., Pon, R. T., Sapse, A. M., and Lown, J. W. (1990) Molecular recognition and binding of a GC site-avoiding thiazole-lexitropsin to the decadeoxyribonucleotide d-(CGCAATTGCG)Z: 'H-NMR evidence for thiazole intercalation. J . Biomol. Struct . Dyn. 8, 99-121. (243) Rao, K. E., Shea, R. G., Yadagiri, B., and Lown, J. W. (1990) Molecular recognition between oligopeptides and nucleic acids: DNA sequence specificity and binding properties of thiazole-lexitropsins incorporating the concepts of base site acceptance and avoidance. Anti-Cancer Drug Des. 5, 3-20. (244) Rao, K. E., Bathini, Y., and Lown, J. W. (1990) Synthesis of novel thiazole containing DNA minor groove binding oligopeptides related to the antibiotic distamycin. J . Org. Chem. 55, 728-737. (245) Plouvier, B., Bailly, C., Houssin, R., and HBnichart, J. P. (1991) Synthesis of two new thiazole-containing oligopeptides as potential DNA minor groove binding analogs of netropsin. Heterocycles 32, 693-701. (246) Lee, M., Krowicki, K., Shea, R. G., Lown, J. W., and Pon, R. T. (1991) Molecular recognition between oligopeptides and

Bailly and Hbnlchart

nucleic acids: Specificity of binding of a monocationic bisfuran lexitropsin to DNA deduced from footprinting and 1HNMR studies. J. Mol. Recogit. 2, 84-93. (247) Jones, D. H., and Wooldridge, R. H. (1968) Amidines and guanidines related to congocidine. Part IV. Thiophene, pyridine, and benzene analogues. J . Chem. SOC.550-554. (248) Wade, W. S., and Dervan, P. B. (1987) Alteration of the sequence specificity of distamycin on DNA by replacement of an N-methylpyrrole carboxamide with pyridine-2-carboxamide. J. Am. Chem. SOC. 109, 1574-1675. (249) Braithwaite, A. W., and Baguley, B. C. (1980) Existence of an extended series of antitumor compounds which bind to deoxyribonucleic acid by nonintercalative means. Biochemistry 19, 1101-1106. (250) Baguley, B. C. (1982) Non intercalative DNA-binding antitumour compounds. Mol. Cell. Biochem. 43, 167-181. (251) Rajagopalan, M., Ayyer, J., and Sasisekharan, V. (1985) Interaction of non-intercalative drugs with DNA: Distamycin analogues. J. Biosci. 7, 27-32. (252) Dasgupta, D., Rajagopalan, M., and Sasisekharan, V. (1986) DNA-binding characteristics of a synthetic analogue of distamycin. Biochem. Biophys. Res. Commun. 140, 626-631. (253) Dasgupta, D., Parrack, P., and Sasisekharan, V. (1987) Interaction of synthetic analogues of distamycin with poly(dA-dT): Role of the conjugated N-methylpyrrole system. Biochemistry 26, 6381-6386. (254) Parrack, P., Dasgupta, D., Ayyer, J., and Sasisekharan, V. (1987)Interactionof synthetic analogs of distamycin with DNA. Role of the conjugated N-methylpyrrole system in specificity of binding. FEBS Lett. 212, 297-301. (255) Rao, K. E., Dasgupta, D., and Sasisekharan, V. (1988) Interaction of a synthetic analogues of distamycin and netropsin with nucleic acids. Does curvature of ligand play a role in distamycin-DNA interactions? Biochemistry27,301& 3024. (256) Arcamone, F. A., Lazzari, E., Menozzi, M., Soranzo, C., and Verini, M. A. (1989) Synthesis, DNA binding and antiviral activity of distamycin analogues containing different heterocyclic moities. Anti-Cancer Drug Des. 1, 235-244. (257) Arcamone, F. A., Animati, F., Barbieri, B., Configliacchi, E., D'Alesio, R., Geroni, C., Giulani, F. C., Lazzari, E., Menozzi, M., Mongelli, N., Penco, S.,and Verini, M. A. (1989) Synthesis, DNA-binding properties, and antitumor activity of novel distamycin derivatives. J. Med. Chem. 32, 774-778. (258) Baker, B. F., and Dervan, P. B. (1985) Sequence-specific cleavage of double-helical DNA. N-bromoacetyldistamycin. J . Am. Chem. SOC.107, 8266-8268. (259) Baker, B. F., and Dervan, P. B. (1989) Sequence-specific cleavage of DNA by N-bromoacetyldistamycin. Product and kinetic analyses. J. Am. Chem. SOC.111, 2700-2712. (260) Krowicki, K., Balzarini, J., De Clercq, E., Newman, R. A., and Lown, J. W. (1988) Novel DNA groove binding alkylators: design, synthesis, and biological evaluation. J. Med. Chem. 31, 341-345. (261) Church, K. M., Wurdeman, R. L., Zhang, Y., and Gold, B. (1990)N-(2-chloroethyl)-N-nitrosoureasbound to nonionic and monocationic lexitropsin dipeptides. Synthesis, DNA affinity binding characteristics, and reactions with 32P-end-labeled DNA. Biochemistry 29, 6827-6838. (262) Broggini, M., Erba, E., Ponti, M., Ballinari, D., Geroni, C., Spreafico, F., and D'Incalci, M. (1991) Selective DNA interaction of the novel distamycin derivative FCE 24517. Cancer Res. 51, 199-204. (263) Grokhovsky, S. L., and Zubarev, V. E. (1991) Sequencespecific cleavage of double-stranded DNA caused by X-ray ionization of the platinum atom in the Pt-bis-netropsin-DNA complex. Nucleic Acids Res. 19, 257-264. (264) Gravatt, G. L., Baguley, B. C., Wilson, W. R., and Denny, W. A. (1991) DNA-directed alkylating agents. 4. 4-anilinoquinoline-based minor groove directed aniline mustards. J. Med. Chem. 34, 1552-1560. (265) Schultz, P. G., Taylor, J. S.,and Dervan, P. B. (1982) Design and synthesis of a sequence-specific DNA cleaving molecule. (distamycin-EDTA)iron(II). J . Am. Chem. SOC.104, 68616863. (266) Taylor, J. S., Schultz, P. G., and Dervan, P. B. (1984) DNA affinity cleaving. Sequence specific cleavage of DNA by dis-

Review

tamycin-EDTA.Fe(I1) and EDTA-distamycin.Fe(I1). Tet rahydron 40, 457-465. (267) Otsuka, M.,Masuda,T., Haupt,A.,Ohno,M., Shiraki, T., Sugiura, Y., and Maeda, K. (1990) Man-designed bleomycin with altered sequence specificity in DNA cleavage. J. Am. Chem. Soc. 112, 838-845. (268) Debart, F., Perigaud, C., Gosselin, G., Mrani, D., Rayner, B., Le Ber, P., Auclair, C., Balzarini, J.,De Clercq, E., Paoletti, C., and Imbach, J. L. (1989) Synthesis, DNA binding, and biological evaluation of synthetic precursors and novel analogues of netropsin. J. Med. Chem. 32, 1074-1083. 269) Bowler, B. E., Hollis, L. S., and Lippard, S. J. (1984) Synthesis and DNA binding and photonicking properties of acridine orange linked by a polymethylene tether to (1,2-diaminoethane)dichloroplatinium(II). J. Am. Chem. SOC.106, 6102-6104. 270) Bowler, B. E., Ahmed, K. J., Sundquist, W. I., Hollis, L. S., Whang, E. E., and Lippard, S. J. (1989) Synthesis and DNAbinding properties of (18-diaminoethane) platinum(I1) complexes linked to the DNA intercalator acridine orange by trimethylene and hexamethylene chains. J. Am. Chem. SOC. I 1 I , 1299-1306. (271) Koyama, M., Kelly, T. R., and Watanabe, K. A. (1988) Novel type of potential anticancer agents derived from chrysophanol and emodin. Some structureactivity relationship studies. J. Med. Chem. 31, 383-384. (272) Koyama, M., Takahashi, K., Chou, T. C., Darzynkiewicz, Z., Kapucinski, J., Kelly, T. R., and Watanabe, K. A. (1989) Intercalating agents with covalent bond forming capability. A novel type of potential anticancer agents. 2. Derivatives of chrysophanol and emodin. J. Med. Chem. 32,1594-1599. (273) Ferguson, L. R., Gourdie, T. A,, Valu, and Denny, W. A. (1989) Bacterial mutagenicity studies of DNA-intercalating aniline mustard: An insight into the mode of action of a novel class of antitumour drugs. Anti-Cancer Drug Des. 4, 209219. (274) Gourdie, T. A,, Valu, K. K., Gravatt, G. L., Boritzki, T. J., Baguley, B. C., Wakelin, L. P. G., Wilson, W. R., Woodgate, P. D., and Denny, W. A. (1990) DNA-directed alkylating agents. 1. Structure-activity relationships for acridine-linked aniline mustards: consequences of varying the reactivity of the mustard. J. Med. Chem. 33, 1177-1186. (275) Palmer, B. D., Lee, H. H., Johnson, P., Baguley, B. C., Wicklam, G., Wakelin, L. P. G., McFadyen, W. D., and Denny, W. A. (1990) DNA-directed alkylating agents. 2. Synthesis and biological activity of platinum complexes linked to 9-anilinoacridine. J. Med. Chem. 33, 3008-3014. (276) Valu, K. K., Gourdie, T. A., Boritzki, T. J., Gravatt, G. L., Baguley, B. C., Wilson, W. R., Wakelin, L. P. G., Woodgate, P. D., and Denny, W. A. (1990) DNA-directed alkylatingagents. 3. Structure-activity relationships for acridine-linked aniline mustards: Consequences of varying the length of the linker chain. J . Med. Chem. 33, 3014-3019. (277) Prakash, A. S., Denny, W. A., Gourdie, T. A., Valu, K. K., Woodgate, P. D., and Wakelin, L. P. G. (1990) DNA-directed alkylating ligands as potential antitumor agents: Sequence specificity of alkylation by intercalating aniline mustards. Biochemistry 29, 9799-9807. (278) Prakash, A. S., Denny, W. A,, and Wakelin, L. P. G. (1990) Differences in sequence selectivity of DNA alkylation by isomeric intercalating aniline mustards. Chem.-Biol. Interact. 76, 241-248. (279) Gourdie, T. A., Prakash, A. S., Wakelin, L. P. G., Woodgate, P. D., and Denny, W. A. (1991) Synthesis and evaluation of DNA-targeted spatially separated bis(ani1ine mustards) as potential alkylating agents with enhanced DNA cross-linking capability. J. Med. Chem. 34, 240-248. (280) Wickham, G., Prakash, A. S., Wakelin, L. P. G., and McFadyen, W. D. (1991) DNA-binding properties and antitumour activity of monofunctional alkylating groups attached to the DNA-intercalating chromophore phenanthridine: n-Bromoalkylphenanthridinium bromides. Biochim. Biophys. Acta 1073, 528-537. (281) Farquhar, D., Newman, R. A., Zuckerman, J. E., and Anderson, B. S. (1991) Doxorubicin analogues incorporating chemically reactive substituents. J . Med. Chem. 34,561-564.

Bioconjugate Chem., Vol. 2, No. 8, 1991 383

(282) Gibson, D., Gean, K. F., Ben-Shoshan, R., Ramu, A., Ringel, I., and Katzhendler, J. (1991)Preparation, characterization, and anticancer activity of a series of cis-PtCl:, complexes linked to anthraquinone intercalators. J. Med. Chem. 34,414-420. (283) Hertzberg, R. P., and Dervan, P. B. (1982) Cleavage of double helical DNA by (methidium propyl-EDTA)iron(II). J. Am. Chem. SOC.104, 313-315. (284) Hertzberg, R. P., and Dervan, P. B. (1984) Cleavage of DNA with methidiumpropyl-EDTA-iron(I1): Reaction conditions and product analyses. Biochemistry 23, 3934-3945. (285) Lown, J. W., and Joshua, A. V. (1982) Bleomycin models. Haemin-acridines which bind to DNA and cause oxygen-dependent scission. J.Chem. SOC.,Chem. Commun. 1298-1300. (286) Hashimoto, Y., Iijima, H., Nozaki, Y., and Shudo, K. (1986) Functional analogues of bleomycin: DNA cleavage by bleomycin and hemin-intercalators. Biochemistry 25,5103-5110. (287) Lown, J. W., Sondhi, S. M., Ong, C. W., Skorobogaty, A., Kishikawa, H., and Dabrowiak, J. C. (1986) Deoxyribonucleic acid cleavage specificity of a series of acridine- and acodazoleiron porphyrins as functional bleomycin models. Biochemistry 25, 5111-5117. (288) Bailly, C., Bernier, J. L., Houssin, R., Helbecque, N., and HBnichart, J. P. (1987) Design of two metal-chelating, DNAbinding models. Molecular combinations of bleomycin and amsacrine anti-tumour drugs. Anti-Cancer Drug Des. I,303, 312. (289) Bailly, C., Kenani, A,, Helbecque, N., Bernier, J. L., Houssin, R., and HBnichart, J. P. (1988) DNA-binding and DNA cleaving properties of a synthetic model AGAGLU related to the antitumour drugs AMSA and bleomycin. Biochem. Biophys. Res. Commun. 152, 695-702. (290) Hosseini, M. W., Blacker, A. J., and Lehn, J. M. (1990) Multiple molecular recognition and catalysis. A multifunctional anion receptor bearing an anion binding site, an intercalating group, and a catalytic site for nucleotide binding and hydrolysis. J. Am. Chem. Soc. 112, 3896-3904. (291) Ding, L., Etemad-Moghadam, G., and Meunier, B. (1990) Oxidative cleavage of DNA mediated by hybrid metalloporphyrin-ellipticine molecules and functionalized metalloporphyrin precursors. Biochemistry 29, 7868-7875. (292) Ding, L., Etemad-Moghadam, G., Cros, S.,Auclair, C., and Meunier, B. (1991) Syntheses and in vitro evaluation of water soluble “cationic metalloporphyrin-ellipticine” molecules having a high affinity for DNA. J. Med. Chem. 34, 900-906. (293) HBnichart, J. P., Bernier, J. L., and Catteau, J. P. (1982) Interaction of 4-(9-acridinylamino)aniline and derivatives with DNA. Hoppe-Seyler’s 2.Physiol. Chem. 363,835-841. (294) Karup, G., Meldal, M., Nielsen, P. E., and Buchardt, 0. (1988) 9-Acridinylpeptides and 9-acridinyl-4-nitrophenylsulfonylpeptides. Synthesis, binding to DNA, and photoinduced DNA cleavage. Znt. J. Pept. Protein Res. 32, 331-343. (295) Larsen, A. K., Paoletti, J., Belehradek, J., Jr., and Paoletti, C. (1986) Uptake, cytofluorescence, and cytotoxicity of oxazolopyrido carbazoles (amino acid-ellipticine conjugates) in murine sarcoma cells. Cancer Res. 46, 5236-5240. (296) Morier-Teissier, E., Bailly, C., Bernier, J. L., Houssin, R., Helbecque, N., Catteau, J. P., Colson, P., Houssier, C., and HBnichart, J. P. (1989) Synthesis, biological activity and DNA interaction of anilinoacridine and bithiazole peptide derivatives related to the antitumor drugs m-amsa and bleomycin. AntiCancer Drug Des. 4, 37-52. (297) Morier-Teissier, E., Bernier, J. L., Lohez, M., Catteau, J. P., HBnichart, J. P. (1990) Free radical production and DNA cleavage by copper chelating peptide-anthraquinones. AntiCancer Drug Des. 5 , 291-305. (298) Nielsen, P. E. (1990) Chemical and photochemical probing of DNA complexes. J. Mol. Recognit. 3, 1-25. (299) Subra, F., Carteau, S., Pager, J., Paoletti, J., Paoletti, C., Auclair, C., Mrani, D., Gosselin, G., and Imbach, J. L. (1991) Bis(pyrro1ecarboxamide)linked to intercalating chromophore oxazolopyridocarbazole (OPC): Selective binding to DNA and polynucleotides. Biochemistry 30, 1642-1650. (300) Shakked, Z., and Rabinovich, D. (1986) The effect of the base sequence on the fine structure of the DNA double helix. Prog. Biophys. Mol. Biol. 47, 159-195.