© Copyright 2001 by the American Chemical Society
Volume 40, Number 3
January 23, 2001
Accelerated Publications Synthetic Inhibitors of the Processing of Pretransfer RNA by the Ribonuclease P Ribozyme: Enzyme Inhibitors Which Act by Binding to Substrate† Yoshiaki Hori,‡ Elena V. Bichenkova,§ Amanda N. Wilton,§ Mohamed N. El-Attug,§ Seyed Sadat-Ebrahimi,§ Terumichi Tanaka,‡ Yo Kikuchi,‡ Michihiro Araki,| Yukio Sugiura,| and Kenneth T. Douglas*,§ School of Pharmacy and Pharmaceutical Sciences, UniVersity of Manchester, Manchester M13 9PL, U.K., DiVision of Bioscience and Biotechnology, Department of Ecological Engineering, Toyohashi UniVersity of Technology, Tempaku-cho, Toyohashi 441-8580, Japan, and Institute for Chemical Research, Kyoto UniVersity, Uji, Kyoto 611-0011, Japan ReceiVed October 12, 2000; ReVised Manuscript ReceiVed December 4, 2000
ABSTRACT:
2,2′-p-Phenylene bis[6-(4-methyl-1-piperazinyl)]benzimidazole, 2,2′-bis(3,5-dihydroxyphenyl)6,6′-bis benzimidazole, and 2,2′-bis(4-hydroxyphenyl)-6,6′-bis benzimidazole are shown by UV-visible and fluorescence spectrophotometry to be strong ligands for tRNA, giving simple, hyperbolic binding isotherms with apparent dissociation constants in the micromolar range. Hydroxyl radical footprinting indicates that they may bind in the D and T loops. On the basis of this tRNA recognition as a rationale, they were tested as inhibitors of the processing of precursor tRNAs by the RNA subunit of Escherichia coli RNase P (M1 RNA). Preliminary studies show that inhibition of the processing of Drosophila tRNA precursor molecules by phosphodiester bond cleavage, releasing the extraneous 5′-portion of RNA and the mature tRNA molecule, was dependent on both the structure of the inhibitor and the structure of the particular tRNA precursor substrate for tRNAAla, tRNAVal, and tRNAHis. In more detailed followup using the tRNAHis precursor as the substrate, experiments to determine the concentration dependence of the reaction showed that inhibition took time to reach its maximum extent. I50 values (concentrations for 50% inhibition) were between 5.3 and 20.8 µM, making these compounds among the strongest known inhibitors of this ribozyme, and the first inhibitors of it not based on natural products. These compounds effect their inhibition by binding to the substrate of the enzyme reaction, making them examples of an unusual class of enzyme inhibitors. They provide novel, small-molecule, inhibitor frameworks for this endoribonuclease ribozyme.
In all organisms studied to date, the transfer RNA genes express tRNA as precursors requiring processing to give the functional tRNA molecules. This maturation of the tRNA † We are grateful to the British Council for a Collaborative Research Project Grant (K.T.D.), the Libyan General Secretariat of Education and Vocational Formation (M.N.E.A.), and the “Research for the Future” programme of the Japan Society for the Promotion of Science (Grant JSPS-RFTF97I00301 to Y.K.). * To whom correspondence should be addressed: School of Pharmacy and Pharmaceutical Sciences, University of Manchester, Manchester M13 9Pl, U.K. Telephone: 44 (0)161 275 2371. Fax: 44 (0)161 275 2481. E-mail:
[email protected]. ‡ Toyohashi University of Technology. § University of Manchester. | Kyoto University.
5′-terminus is effected by ribonuclease P (RNase P),1 an endoribonuclease, formed in eubacteria from an RNA subunit of approximately 400 nucleotides and a 14 kDa protein subunit. The catalytic activity is provided by the RNA, which under suitable conditions can even cleave its substrate correctly in the absence of protein. The protein subunit appears to aid product release and reduce the level of rebinding of the matured tRNA to the enzyme (1). Some aminoglycosides inhibit RNase P (2), and given that RNase P is essential and exhibits differences between species (3), 1 Abbreviations: DMSO, dimethyl sulfoxide; MPE-Fe(II), methidiumpropyl-EDTA-Fe(II); RNase P, ribonuclease P.
10.1021/bi002378f CCC: $20.00 © 2001 American Chemical Society Published on Web 12/28/2000
604 Biochemistry, Vol. 40, No. 3, 2001 it has been suggested that these antibiotics might serve as lead structures for drug design (2). The structure of the catalytic RNA of the eubacterial RNase P contains many of the three-dimensional structural motifs of a mature tRNA molecule, at least in an incipient form (4-8). Thus, we decided to use the tRNA tertiary structure as a scaffold from which to initiate lead drug/ inhibitor design against this ribozyme. However, there are rather few reversible and specific ligands known for tRNA (9). Porphyrins bind (10) in the TΨC arm of brewer’s yeast tRNAPhe near residues T54 and Ψ55 (11). X-ray diffraction data for distamycin bound to tRNA show specific hydrogen bonds to G51, U52, and G53 with electrostatic links to phosphates P61-P63 in the same groove region in the T-stem (12). Our NMR data confirm that distamycin selectively line broadens imino proton resonances of G18 and ψ55 in this region (13). Such binding was also detected by theoretical calculations (14). We have discovered recently that certain benzimidazole ligands bind reversibly to Escherichia coli tRNAPhe with micromolar apparent dissociation constants (15), preliminary studies implicating the T-stem groove of E. coli tRNAPhe in this region as a possible ligand-binding site for 2 (13). This T-loop region is also implicated in recognition by RNase P; e.g., disruption of the G53‚C61 base pair significantly decreases the cleavage rate (16). The 2′-OH groups of riboses 54 and 55, important for catalysis, may interact specifically with groups in the RNase P RNA (17). Thus, we tested tRNA ligands (1b-d and 2-4) as inhibitors of the ribozyme of E. coli RNase P (M1 RNA) using a variety of tRNA precursor substrates in a preliminary evaluation. We now report that 2-4 offer lead inhibition of the activity of M1 RNA, although the inhibitions are caused by the unusual mechanism of the binding of 2-4 to the substrates. To our knowledge, these are the first synthetic organic ligands reported to inhibit the M1 RNA reaction, whose structures are not based on natural products.
Accelerated Publications MATERIALS AND METHODS Synthesis of 2 and 3. To a solution of 3,3′-diaminobenzidine (2.164 g, 10 mmol) in glacial acetic acid (40 mL) was added ethyl 4-hydroxybenzimidate hydrochloride (4.201 g, 20 mmol, 96% pure, Aldrich Chemical Co.), and the mixture was stirred over a water bath under reflux and nitrogen for 4 h to give a light-brown mixture. Acetic acid was removed by rotovap, the residue dissolved in hot water (10 mL), a mixture of 2-propanol and ammonia (10:1, 2 mL) added, and the resulting mixture stirred over a water bath for 1 h. The isolated precipitate was recrystallized from methanol to give a cream product (two crops, 3.52 g, 84%): mp >350 °C; 1H NMR (270 MHz, DMSO-d6] δH 6.95 (d, 4H, Ar-H, J ) 8.6 Hz), 7.54 (d, 2H, Ar-H, J ) 8.6 Hz), 7.66 (d, 2H, Ar-H, J ) 8.6 Hz), 7.82 (s, 2H, Ar-H), 8.08 (d, 4H, Ar-H, J ) 8.6 Hz), 10.5 (s, 2H, Ar-OH); electrospray MS (m/z, relative intensity) 420 (M + H + 1, 30%), 419 (M + H, 100%); TLC Rf 0.79 (30% NaOH/70% ethyl acetate), 0.75 (1:3 CH2Cl2/CH3CN), 0.60 (3:1 CH2Cl2/ MeOH). Anal. Calcd for C26H18N4O2‚H2O, CH3OH, 2HCl: C, 59.9; H, 4.6; N, 10.1; Cl, 13.1. Found: C, 59.7; H, 4.7; N, 9.8; Cl, 12.8. Similarly, 3 was prepared from 3,3′-diaminobenzidine (0.65 g, 3 mmol) and ethyl-3,5-dihydroxybenzimidate hydrochloride (1.30 g, 6 mmol) as a brown product (1.45 g, 89.3%): mp g350 °C; 1H NMR (270 MHz, DMSO-d6) δH 6.5 (s, 2H, Ar-H), 7.10 (d, 4H, Ar-H, J ) 7.75 Hz), 7.75 (dd, 4H, Ar-H), 7.9 (s, 2H, Ar-H), 9.9 (s, 4H, Ar-OH); electrospray MS (m/z, relative intensity) 453 (M + H + 2, 5%), 452 (M + H + 1, 35%), 451 (M + H, 100%); TLC Rf 0.65 (3:1 CH2Cl2/MeOH), 0.41 (1:2 CH2Cl2/CH3CN). Anal. Calcd for C26H18N4O4, CH3OH, 2HCl: C, 58.3; H, 4.3; N, 10.1; Cl, 12.8. Found: C, 58.5; H, 4.4; N, 10.4; Cl, 13.0. Synthesis of 4. 1,4-Benzene-bis-ethylimidate hydrochloride (586 mg, 2 mmol) was added to 4-N-piperidino-2-aminoaniline (824 mg, 4 mmol) in glacial acetic acid (5 mL) and refluxed under nitrogen with a CaCl2 drying tube. Acetic acid was removed by rotavap, the residue dissolved in hot water (10 mL), and the solution filtered hot. The filtrate was evaporated by rotavap, the residue dissolved in MeOH (10 mL), triturated with ether, and filtered, and the solid purified as described for 3,4-dihydroxy-Hoechst (18) to give a browngray solid (650 mg, 64% yield): λmax ) 374 nm in MeOH; 1H NMR (270 MHz, DMSO-d ) δ 2.25 (s, 6H, N-CH ), 6 H 3 3.14 (m, 8H, N-CH2), 3.54 (m, 8H, N-CH2), 6.97 (s, 2H, Ar-H), 7.49 (d, 2H, Ar-H, J ) 7.25 Hz), 8.26 (s, 4H, Ar-H), 12.73 (brs 2H, NH); FAB MS (m/z, relative intensity) 509 (M + H + 2, 6.83), 508 (M + H + 1, 33), 507 (M + H, 100); accurate mass calcd for C30H35N8 507.2985, measured 507.2971 (error of 2.7 ppm). 1,4-Benzene-bis-ethylimidate hydrochloride was synthesized (18) from 1,4-dicyanobenzene (2.563 g, 20 mmol) in super-dry ethanol (8 mL) and anhydrous tetrahydrofuran (72 mL) with HCl gas at
