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Stacking with No Planarity? Hakan Gunaydin*,† and Michael D. Bartberger‡ †
Department of Structural Chemistry, Merck & Co., Inc., 33 Avenue Louis Pasteur, Boston, Massachusetts 02115, United States Department of Molecular Engineering, Therapeutic Discovery, One Amgen Center Drive, Thousand Oaks, California 91320, United States
‡
S Supporting Information *
ABSTRACT: This viewpoint describes the results obtained from matched molecular pair analyses and quantum mechanics calculations that show unsaturated rings found in drug-like molecules may be replaced with their saturated counterparts without losing potency even if they are engaged in stacking interactions with the side chains of aromatic residues.
KEYWORDS: Stacking, matched molecular pair, drug design
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In an attempt to test our hypothesis, we queried Merck, Amgen, and BindingDB10 databases for matched molecular pairs (MMP) that correspond to the replacement of a singly substituted phenyl group with a cyclohexyl group. The summaries of the results obtained from these analyses are shown in Figure 1. The decision to investigate this transformation at the periphery of the molecules was driven by the expectation that the effect of such transformation on the overall 3D conformation of the molecule would be minimal. Analysis of Merck, Amgen, and BindingDB data revealed 11021, 1341, and 2468 such molecular pairs, respectively. Of these pairs, 36− 45% showed that replacement of the phenyl group with a cyclohexyl group resulted in affinities that are within 2-fold. Twenty-five to 30% of the pairs showed that the cyclohexyl analogue is ≥2-fold more potent, and 25−39% of the pairs showed that phenyl analogue is ≥2-fold more potent against their targets. The origin of the data used in these analyses did not seem to change the conclusions. The corresponding drug targets in these analyses consist of a wide range of target classes such as kinases, membrane proteins, nuclear receptors, hydrolases, and peptidases and show that it is possible to replace a phenyl group with a cyclohexyl group and maintain or improve the potency 60−75% of the time. However, statistical analysis of the data set in this form is not specific enough to discern the preference of phenyl or cyclohexyl groups toward stacking type interactions. Thus, one cannot conclude that the histograms shown in Figure 1 represent the cases in which the terminal phenyl or cyclohexyl group is engaged in stacking interactions. Publicly available PDB structures were queried for the pairs identified in BindingDB in order to identify structures in which
election of a compound that is more likely to progress through clinical trials is a key factor that contributes to the developability of drug candidates.1−4 Topological descriptors such as increased fraction of sp3 atoms (fsp3) and reduced number of aromatic rings have been shown to be associated with clinical success.3,4 Hence, it may be beneficial to replace aromatic rings with their saturated counterparts in drug-like molecules. The nature of the interaction between aromatic rings and amino acid side chains is well documented in the literature.5 The magnitude of the substituted benzene−benzene stacking interaction has been shown to be determined mainly by the local interaction of the substituent and the stacking partner.6 The relative energies obtained from substituted benzene− benzene stacking interaction calculations are sometimes used as a means to rationally optimize potency when structural information is not available.7 Therefore, there exists a perception that stacking interaction among unsaturated rings is special in nature. However, the validity of the term stacking interaction has been challenged in the literature, and it was suggested that stacking interactions may not be as specific as once perceived.8 It has also been reported that cyclohexylphenyl stacking interactions can stabilize oligonucleotides more than phenyl−phenyl stacking interactions. 9 Hence, we hypothesized that aromatic rings may be replaced with their saturated counterparts even when they are engaged in stacking interactions with the side chains of the aromatic residues. The ability to replace aromatic rings with their saturated counterparts has the potential to create more diverse molecules with increased fsp3 character. These types of rational modifications may improve the properties and increase the success rate in the clinical trials. © XXXX American Chemical Society
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DOI: 10.1021/acsmedchemlett.6b00099 ACS Med. Chem. Lett. XXXX, XXX, XXX−XXX
ACS Medicinal Chemistry Letters
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Figure 1. Histograms demonstrating affinity differences for the phenyl-cyclohexyl MMP. Green bars, cyclohexyl analogue is more potent than the phenyl analogue; blue bars, the affinity is within 2-fold; red bars, phenyl analogue is more potent.
Figure 2. MMPs and corresponding crystal structures that show the cases in which both phenyl and cyclohexyl analogues engage in stacking interactions with equal magnitude (top panel), with >10-fold preference for the cyclohexyl analogue (middle panel), or >10-fold preference for the phenyl analogues (bottom panel).
upon replacing a benzene ring with a cyclohexane ring even in cases in which the phenyl ring is engaged in stacking interactions with the side chains of aromatic residues. It is also interesting to analyze the structures of cyclohexyl/ phenyl matched pairs in which there is a >10-fold difference in affinities. Three examples in which the phenyl analogue is >10fold less potent are shown in the middle panel of Figure 2. In the first example, there are TRP, PHE, and HIS residues surrounding the cyclohexane binding pocket (even though the crystal structure was obtained for the methyl analogue (5AKZ), two alternate positions of the ligand were refined and both sides of the pocket include these aromatic residues).15 A significant preference for the cyclohexyl analogue (C8) against epoxide hydratase suggests that aromatic−aromatic interactions are not always more beneficial. Another example is a MMP of inhibitors of aminopeptidase B. In this example, there is, again, >10-fold preference for the cyclohexyl analogue (C10) despite the fact that a crystal structure of C9 obtained in bacterial aminopeptidase (1XRY) reveals that the terminal phenyl group is surrounded by two PHE and one TYR residues. In the third example, a pair of BACE-1 inhibitors (C11/C12) is shown. In this example, the crystal structure obtained for C12 in BACE-1 (3MSL) illustrates that the terminal cyclohexyl group is stacked against the Cl-benzimidazole ring and is also in the vicinity of an aromatic PHE residue.16 The cyclohexyl analogue was significantly more potent against BACE-1 than the correspond-
the peripheral phenyl or cyclohexyl group is engaged in stacking interactions. This analysis, unfortunately, did not produce a large enough number of structures where a meaningful statistical analysis of aromatic residue orientations that are beneficial for the phenyl or cyclohexyl groups could be obtained. However, we were able to identify structures that unambiguously show the presence of stacking interactions with the peripheral phenyl or cyclohexyl groups with the side chains of the aromatic residues. Thus, these structures can be used to interrogate the specificity of the stacking interactions. Examples that show that a cyclohexyl and phenyl groups can interact equally well with the side chains of aromatic residues are shown in the top panel of Figure 2. Reported Ki values for C1 and C2 are 0.090 and 0.084 μM against influenza endonuclease, respectively.11 The published PDB structure (4AVG) reveals that the cyclohexyl group of C2 is interacting with the side chain of TYR24 in a face-to-face fashion.12 The overlay of the cocrystal structures obtained for compounds C3 and C4 in thrombin highlight the fact that the magnitude of the phenyl−TRP edge-to-face stacking interaction can be maintained with a cyclohexyl group (2ZC9/3DUX).13 Lastly, the crystal structure of C5 obtained in acetylcholinesterase (1EVE) shows that a face-to-face TRP−phenyl stacking interaction can be replaced with TRP−cyclohexyl interaction without any loss in affinity.10,14 These examples illustrate that it is indeed possible to maintain the magnitude of the binding interaction B
DOI: 10.1021/acsmedchemlett.6b00099 ACS Med. Chem. Lett. XXXX, XXX, XXX−XXX
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performed on various different data sets corroborate this hypothesis.
ing phenyl analogue. The fact that cyclohexyl analogue C12 can adopt the desired self-stacking geometry makes this a compelling example. The bottom panel of Figure 2 highlights examples in which phenyl analogues are preferred over cyclohexyl analogues. In the first example, the phenyl analogue C13 is >10-fold more potent than cyclohexyl analogue C14 against AKT1. A crystal structure of C14 in AKT1 (2UZT) demonstrates the engagement of the terminal phenyl group with the side chain of a PHE residue in an edge-to-edge fashion.17 The second example shows a pair of glycylpeptide N-tetradecanoyltransferase inhibitors. In this example, measured IC50 values illustrate that the phenyl analogue (C15) is significantly more potent than the cyclohexyl analogue (C16).18 A crystal structure of a meta-methoxy analogue of C15 (4B14) reveals that the terminal phenyl group is engaged in a face-to-face stacking interaction with the side chain of a nearby PHE residue.18 In the last example, a pair of cytoplasmic epoxide hydrolase 2 inhibitors demonstrates that the phenyl analogue (C17) is more potent than the cyclohexyl analogue (C18).19 A crystal structure of a related compound (4HAI) in human epoxide hydrolase shows that the terminal phenyl group is likely to engage in an edge-toface stacking interaction with a nearby TRP residue.19 Data for all pairs identified through the analysis of BindingDB and the corresponding PDB codes (where available) are given in the Supporting Information. Analysis of several crystal structures of the pairs shown here reveals that phenyl and cyclohexyl groups can engage in similar types of stacking interactions across a range of targets. This suggests that there may not be a preference for the side chains of aromatic residues to engage in stacking interactions primarily with unsaturated rings found in inhibitors. In order to assess the thermodynamics of binding in the case of saturated and unsaturated rings, dimerization energies for benzene and cyclohexane homo- and heterodimers were calculated at the CCSD(T)/cc-pVTZ level (see Supporting Information). Interaction energies computed for the heterodimers were found to be energetically more favorable than those of homodimers (see Supporting Information). Results obtained from these calculations, again, call into question the commonly held misperception that unsaturated ring−unsaturated ring stacking interactions are special in nature and suggest that binding interactions of the same magnitude or better can be achieved by bringing aromatic and aliphatic groups together. The importance of the control of physicochemical properties in compound design has been emphasized in the literature.3 The results shown here highlight the favorable association of cyclohexane- and benzene-containing molecules with the side chains of the aromatic residues. Crystal structures obtained in various targets and affinity data given for the MMPs suggest that stacking interactions between two unsaturated rings may not be as optimal as initially perceived, and the replacement of phenyl groups with cyclohexyl groups in drug-like molecules may afford compounds with similar or improved affinities. Increased fsp3 character in molecules may lead to compounds with improved physical properties and thus a potentially higher success rate in clinical trials. However, compounds with cyclohexyl groups will always have higher liphophilicities than the corresponding phenyl analogues, which may require attenuation through other changes to the molecule. However, the ability to rationally explore more complex (higher fsp3) chemical space is an important tool in medicinal chemistry. Results obtained from ab initio calculations and MMP analyses
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ASSOCIATED CONTENT
S Supporting Information *
The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acsmedchemlett.6b00099. Geometries and energies obtained from ab initio calculations and BindingDB pairs with the BindingDB ids, affinity data, smiles strings, and target information (PDF)
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AUTHOR INFORMATION
Corresponding Author
*E-mail:
[email protected]. Notes
Views expressed in this editorial are those of the authors and not necessarily the views of the ACS. The authors declare no competing financial interest.
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