551
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A Convergent Synthesis of Bis-2-oxo Amide Triacylglycerol Analogues as Potent Lipase Inhibitors Using Acyl Cyanophosphorane Methodology. B KOREAN CHEM SOC 2002. [DOI: 10.5012/bkcs.2002.23.2.351] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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552
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Sawa M, Kiyoi T, Kurokawa K, Kumihara H, Yamamoto M, Miyasaka T, Ito Y, Hirayama R, Inoue T, Kirii Y, Nishiwaki E, Ohmoto H, Maeda Y, Ishibushi E, Inoue Y, Yoshino K, Kondo H. New type of metalloproteinase inhibitor: design and synthesis of new phosphonamide-based hydroxamic acids. J Med Chem 2002; 45:919-29. [PMID: 11831904 DOI: 10.1021/jm0103211] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A series of phosphonamide-based hydroxamate derivatives were synthesized, and the inhibitory activities were evaluated against various metalloproteinases in order to clarify its selectivity profile. Among the four diastereomeric isomers resulting from the chirality at the C-3 and P atoms, the compound with a (R,R)-configuration both at the C-3 position and the phosphorus atom was found to be potently active, while the other diastereomeric isomers were almost inactive. A number of (R,R)-compounds synthesized here exhibited broad spectrum activities with nanomolar K(i) values against MMP-1, -3, -9, and TACE and also showed nanomolar IC(50) values against HB-EGF shedding in a cell-based inhibition assay. The modeling study using X-ray structure of MMP-3 suggested the possible binding mode of the phosphonamide-based inhibitors.
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Affiliation(s)
- Masaaki Sawa
- Department of Chemistry, R&D Laboratories, Nippon Organon K.K., 1-5-90, Tomobuchi-cho, Miyakojima-ku, Osaka 534-0016, Japan.
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553
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Nair AC, Jayatilleke P, Wang X, Miertus S, Welsh WJ. Computational studies on tetrahydropyrimidine-2-one HIV-1 protease inhibitors: improving three-dimensional quantitative structure-activity relationship comparative molecular field analysis models by inclusion of calculated inhibitor- and receptor-based properties. J Med Chem 2002; 45:973-83. [PMID: 11831910 DOI: 10.1021/jm010417v] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A computational chemistry study has been performed on a series of tetrahydropyrimidine-2-ones (THPs) as HIV-1 protease (HIV-1 PR) inhibitors. The present investigation focuses on the correlation of inhibitor-enzyme complexation energies (E(compl)), inhibitor solvation energies E(solv)[I], and both polar and nonpolar buried surface areas (BSAs) with the observed values of the binding affinity (pK(I)). Various combinations of these specific inhibitor- and receptor-based properties were also evaluated as additional descriptors to three-dimensional quantitative structure-activity relationship (3D-QSAR) models constructed using comparative molecular field analysis (CoMFA). Linear regression of the observed pK(I) values with E(compl), E(solv)[I], and the BSAs yielded a strong correlation in terms of both self-consistency (r(2) approximately equal to 0.90) and internal predictive ability (r(cv)(2) > 0.50). The 3D-QSAR models obtained from CoMFA using standard partial least-squares (PLS) analysis also yielded a strong correlation between the CoMFA fields and the experimental pK(i) (r(2) = 0.96; r(cv)(2) = 0.58). Various "enhanced" 3D-QSAR models were constructed in which different combinations of the E(compl), E(solv)[I], and BSAs were added as additional descriptors to the default steric-electrostatic CoMFA fields. Inclusion of E(solv)[I] in particular yielded significant improvement in the predictive ability (r(cv)(2) approximately equal to 0.80) of the resultant 3D-QSAR model.
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Affiliation(s)
- Anil C Nair
- Department of Chemistry & Biochemistry and Center for Molecular Electronics, University of Missouri-St. Louis, St. Louis, MO 63121, USA
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554
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Yamamoto M, Ikeda S, Kondo H, Inoue S. Design and synthesis of dual inhibitors for matrix metalloproteinase and cathepsin. Bioorg Med Chem Lett 2002; 12:375-8. [PMID: 11814800 DOI: 10.1016/s0960-894x(01)00755-7] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
The first example of dual inhibitors for matrix metalloproteinase (MMP) and cathepsin is described. An appropriate alignment of peptide-parts and two different specific functional groups in one molecule led to the discovery of a potent dual inhibitor (3a).
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Affiliation(s)
- Minoru Yamamoto
- Chemistry Group R&D Laboratories, Nippon Organon K.K., 1-5-90 Tomobuchi-Cho, Miyakojima-Ku, Osaka, Japan
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555
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Grzybowski BA, Ishchenko AV, Kim CY, Topalov G, Chapman R, Christianson DW, Whitesides GM, Shakhnovich EI. Combinatorial computational method gives new picomolar ligands for a known enzyme. Proc Natl Acad Sci U S A 2002; 99:1270-3. [PMID: 11818565 PMCID: PMC122179 DOI: 10.1073/pnas.032673399] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Combinatorial small molecule growth algorithm was used to design inhibitors for human carbonic anhydrase II. Two enantiomeric candidate molecules were predicted to bind with high potency (with R isomer binding stronger than S), but in two distinct conformations. The experiments verified that computational predictions concerning the binding affinities and the binding modes were correct for both isomers. The designed R isomer is the best-known inhibitor (K(d) approximately 30 pM) of human carbonic anhydrase II.
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Affiliation(s)
- Bartosz A Grzybowski
- Harvard University, Department of Chemistry and Chemical Biology, 12 Oxford Street, Cambridge, MA 02138, USA
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556
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Volonterio A, Bellosta S, Bravo P, Canavesi M, Corradi E, Meille S, Monetti M, Moussier N, Zanda M. Solution/Solid-Phase Synthesis of Partially Modified Retro- and Retro-Inverso-ψ[NHCH(CF3)]-Peptidyl Hydroxamates and Their Evaluation as MMP-9 Inhibitors. European J Org Chem 2002. [DOI: 10.1002/1099-0690(20022)2002:3<428::aid-ejoc428>3.0.co;2-j] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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557
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Bursavich MG, Rich DH. Designing non-peptide peptidomimetics in the 21st century: inhibitors targeting conformational ensembles. J Med Chem 2002; 45:541-58. [PMID: 11806706 DOI: 10.1021/jm010425b] [Citation(s) in RCA: 171] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthew G Bursavich
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, USA
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558
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Glenn MP, Pattenden LK, Reid RC, Tyssen DP, Tyndall JDA, Birch CJ, Fairlie DP. Beta-strand mimicking macrocyclic amino acids: templates for protease inhibitors with antiviral activity. J Med Chem 2002; 45:371-81. [PMID: 11784141 DOI: 10.1021/jm010414i] [Citation(s) in RCA: 59] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
New amino acids are reported in which component macrocycles are constrained to mimic tripeptides locked in a beta-strand conformation. The novel amino acids involve macrocycles functionalized with both an N- and a C-terminus enabling addition of appendages at either end to modify receptor affinity, selectivity, or membrane permeability. We show that the cycles herein are effective templates within inhibitors of HIV-1 protease. Eleven compounds originating from such bifunctionalized cyclic templates are potent inhibitors of HIV-1 protease (Ki 0.3-50 nM; pH 6.5, I = 0.1 M). Unlike normal peptides comprising amino acids, five of these macrocycle-containing compounds are potent antiviral agents with sub-micromolar potencies (IC(50) 170-900 nM) against HIV-1 replication in human MT2 cells. The most active antiviral agents are the most lipophilic, with calculated values of LogD(6.5) > or = 4. All molecules have a conformationally constrained 17-membered macrocyclic ring that has been shown to structurally mimic a tripeptide segment (Xaa)-(Val/Ile)-(Phe/Tyr) of a peptide substrate in the extended conformation. The presence of two trans amide bonds and a para-substituted aromatic ring prevents intramolecular hydrogen bonds and fixes the macrocycle in the extended conformation. Similarly constrained macrocycles may be useful templates for the creation of inhibitors for the many other proteins and proteases that recognize peptide beta-strands.
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Affiliation(s)
- Matthew P Glenn
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane Qld 4072, Australia
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559
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Davidson JP, Lubman O, Rose T, Waksman G, Martin SF. Calorimetric and structural studies of 1,2,3-trisubstituted cyclopropanes as conformationally constrained peptide inhibitors of Src SH2 domain binding. J Am Chem Soc 2002; 124:205-15. [PMID: 11782172 DOI: 10.1021/ja011746f] [Citation(s) in RCA: 73] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Isothermal titration calorimetry and X-ray crystallography have been used to determine the structural and thermodynamic consequences associated with constraining the pTyr residue of the pYEEI ligand for the Src Homology 2 domain of the Src kinase (Src SH2 domain). The conformationally constrained peptide mimics that were used are cyclopropane-derived isosteres whereby a cyclopropane ring substitutes to the N-Calpha-Cbeta atoms of the phosphotyrosine. Comparison of the thermodynamic data for the binding of the conformationally constrained peptide mimics relative to their equivalent flexible analogues as well as a native tetrapeptide revealed an entropic advantage of 5-9 cal mol(-1) K(-1) for the binding of the conformationally constrained ligands. However, an unexpected drop in enthalpy for the binding of the conformationally constrained ligands relative to their flexible analogues was also observed. To evaluate whether these differences reflected conformational variations in peptide binding modes, we have determined the crystal structure of a complex of the Src SH2 domain bound to one of the conformationally constrained peptide mimics. Comparison of this new structure with that of the Src SH2 domain bound to a natural 11-mer peptide (Waksman et al. Cell 1993, 72, 779-790) revealed only very small differences. Hence, cyclopropane-derived peptides are excellent mimics of the bound state of their flexible analogues. However, a rigorous analysis of the structures and of the surface areas at the binding interface, and subsequent computational derivation of the energetic binding parameters, failed to predict the observed differences between the binding thermodynamics of the rigidified and flexible ligands, suggesting that the drop in enthalpy observed with the conformationally constrained peptide mimic arises from sources other than changes in buried surface areas, though the exact origin of the differences remains unclear.
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Affiliation(s)
- James P Davidson
- Department of Chemistry and Biochemistry and The Institute of Cellular and Molecular Biology, The University of Texas, Austin, Texas 78712, USA
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560
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Wong MK, Yu CW, Yuen WH, Yang D. Synthesis of alpha-keto esters and amides via oxidative cleavage of cyanoketophosphoranes by dimethyldioxirane. J Org Chem 2002; 66:3606-9. [PMID: 11348154 DOI: 10.1021/jo0015974] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M K Wong
- Department of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong
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561
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Vystorop IV, Lyssenko KA, Voznesensky VN, Lodygina VP, Kostyanovsky RG. General regioselective synthesis of 2,2-disubstituted 3-hydroxyimidazolidin-4-ones. MENDELEEV COMMUNICATIONS 2002. [DOI: 10.1070/mc2002v012n05abeh001657] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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562
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Fei X, Zheng QH, Hutchins GD, Liu X, Stone KL, Carlson KA, Mock BH, Winkle WL, Glick-Wilson BE, Miller KD, Fife RS, Sledge GW, Sun HB, Carr RE. Synthesis of MMP inhibitor radiotracers [11C]methyl-CGS 27023A and its analogs, new potential PET breast cancer imaging agents. J Labelled Comp Radiopharm 2002. [DOI: 10.1002/jlcr.570] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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563
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Wang R, Lai L, Wang S. Further development and validation of empirical scoring functions for structure-based binding affinity prediction. J Comput Aided Mol Des 2002; 16:11-26. [PMID: 12197663 DOI: 10.1023/a:1016357811882] [Citation(s) in RCA: 849] [Impact Index Per Article: 38.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
New empirical scoring functions have been developed to estimate the binding affinity of a given protein-ligand complex with known three-dimensional structure. These scoring functions include terms accounting for van der Waals interaction, hydrogen bonding, deformation penalty, and hydrophobic effect. A special feature is that three different algorithms have been implemented to calculate the hydrophobic effect term, which results in three parallel scoring functions. All three scoring functions are calibrated through multivariate regression analysis of a set of 200 protein-ligand complexes and they reproduce the binding free energies of the entire training set with standard deviations of 2.2 kcal/mol, 2.1 kcal/mol, and 2.0 kcal/mol, respectively. These three scoring functions are further combined into a consensus scoring function, X-CSCORE. When tested on an independent set of 30 protein-ligand complexes. X-CSCORE is able to predict their binding free energies with a standard deviation of 2.2 kcal/mol. The potential application of X-CSCORE to molecular docking is also investigated. Our results show that this consensus scoring function improves the docking accuracy considerably when compared to the conventional force field computation used for molecular docking.
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Affiliation(s)
- Renxiao Wang
- Medical Chemistry and Comprehensive Cancer Center, University of Michigan, Ann Arbor 48109-0934, USA
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564
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Gobec S, Štrancar K, Urleb U. A general synthesis of ethyl 4-aminophenyl and ethyl 4-[amino(hydroxyimino)methyl]phenyl phosphonates. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(01)02100-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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565
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Yamauchi O, Odani A, Takani M. Metal–amino acid chemistry. Weak interactions and related functions of side chain groups. ACTA ACUST UNITED AC 2002. [DOI: 10.1039/b202385g] [Citation(s) in RCA: 180] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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566
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Guimarães CRW, Bicca de Alencastro R. Thermodynamic Analysis of Thrombin Inhibition by Benzamidine and p-Methylbenzamidine via Free-Energy Perturbations: Inspection of Intraperturbed-Group Contributions Using the Finite Difference Thermodynamic Integration (FDTI) Algorithm. J Phys Chem B 2001. [DOI: 10.1021/jp013563l] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cristiano Ruch Werneck Guimarães
- Physical Organic Chemistry Group, Departamento de Química Orgânica, Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, CT, Bloco A, Sala 609, Rio de Janeiro, RJ 21949-900, Brazil
| | - Ricardo Bicca de Alencastro
- Physical Organic Chemistry Group, Departamento de Química Orgânica, Instituto de Química, Universidade Federal do Rio de Janeiro, Cidade Universitária, CT, Bloco A, Sala 609, Rio de Janeiro, RJ 21949-900, Brazil
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567
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Leung D, Schroder K, White H, Fang NX, Stoermer MJ, Abbenante G, Martin JL, Young PR, Fairlie DP. Activity of recombinant dengue 2 virus NS3 protease in the presence of a truncated NS2B co-factor, small peptide substrates, and inhibitors. J Biol Chem 2001; 276:45762-71. [PMID: 11581268 DOI: 10.1074/jbc.m107360200] [Citation(s) in RCA: 252] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Recombinant forms of the dengue 2 virus NS3 protease linked to a 40-residue co-factor, corresponding to part of NS2B, have been expressed in Escherichia coli and shown to be active against para-nitroanilide substrates comprising the P6-P1 residues of four substrate cleavage sequences. The enzyme is inactive alone or after the addition of a putative 13-residue co-factor peptide but is active when fused to the 40-residue co-factor, by either a cleavable or a noncleavable glycine linker. The NS4B/NS5 cleavage site was processed most readily, with optimal processing conditions being pH 9, I = 10 mm, 1 mm CHAPS, 20% glycerol. A longer 10-residue peptide corresponding to the NS2B/NS3 cleavage site (P6-P4') was a poorer substrate than the hexapeptide (P6-P1) para-nitroanilide substrate under these conditions, suggesting that the prime side substrate residues did not contribute significantly to protease binding. We also report the first inhibitors of a co-factor-complexed, catalytically active flavivirus NS3 protease. Aprotinin was the only standard serine protease inhibitor to be active, whereas a number of peptide substrate analogues were found to be competitive inhibitors at micromolar concentrations.
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Affiliation(s)
- D Leung
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland 4072, Australia
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568
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Bravo P, Bruché L, Pesenti C, Viani F, Volonterio A, Zanda M. Solution and solid-phase synthesis of trifluoromethyl peptides and mimetics. J Fluor Chem 2001. [DOI: 10.1016/s0022-1139(01)00485-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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569
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Winkler FK, Banner DW, Böhm HJ. Structure-based approaches in modern drug discovery research. ERNST SCHERING RESEARCH FOUNDATION WORKSHOP 2001:123-42. [PMID: 11394042 DOI: 10.1007/978-3-662-04645-6_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- F K Winkler
- Swiss Federal Institute of Technology, ETH Center, 8092 Zürich, Switzerland
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570
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Snider MJ, Wolfenden R. Site-bound water and the shortcomings of a less than perfect transition state analogue. Biochemistry 2001; 40:11364-71. [PMID: 11560484 DOI: 10.1021/bi011189+] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Kinetic measurements have shown that substantial enthalpy changes accompany substrate binding by cytidine deaminase, increasing markedly as the reaction proceeds from the ground state (1/K(m), DeltaH = -13 kcal/mol) to the transition state (1/K(tx), DeltaH = -20 kcal/mol) [Snider, M. J., et al. (2000) Biochemistry 39, 9746-9753]. In the present work, we determined the thermodynamic changes associated with the equilibrium binding of inhibitors by cytidine deaminase by isothermal titration calorimetry and van't Hoff analysis of the temperature dependence of their inhibition constants. The results indicate that the binding of the transition state analogue 3,4-dihydrouridine DeltaH = -21 kcal/mol), like that of the transition state itself (DeltaH = -20 kcal/mol), is associated with a large favorable change in enthalpy. The significantly smaller enthalpy change that accompanies the binding of 3,4-dihydrozebularine (DeltaH = -10 kcal/mol), an analogue of 3,4-dihydrouridine in which a hydrogen atom replaces this inhibitor's 4-OH group, is consistent with the view that polar interactions with the substrate at the site of its chemical transformation play a critical role in reducing the enthalpy of activation for substrate hydrolysis. The entropic shortcomings of 3,4-dihydrouridine, in capturing all of the free energy involved in binding the actual transition state, may arise from its inability to displace a water molecule that occupies the binding site normally occupied by product ammonia.
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Affiliation(s)
- M J Snider
- Department of Biochemistry and Biophysics, University of North Carolina, Chapel Hill, North Carolina 27599-7260, USA
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571
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Schmitt S, Hendlich M, Klebe G. Von der Struktur zur Funktion: ein neuer Ansatz zum Erkennen von funktionellen Ähnlichkeiten zwischen Proteinen unabhängig von Sequenz- und Faltungshomologie. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010903)113:17<3237::aid-ange3237>3.0.co;2-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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572
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Schmitt S, Hendlich M, Klebe G. From Structure to Function: A New Approach to Detect Functional Similarity among Proteins Independent from Sequence and Fold Homology. Angew Chem Int Ed Engl 2001; 40:3141-3144. [PMID: 29712060 DOI: 10.1002/1521-3773(20010903)40:17<3141::aid-anie3141>3.0.co;2-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2001] [Indexed: 11/10/2022]
Abstract
Protein function is almost invariably linked with the specific recognition of substrates or endogenous ligands in particular binding pockets; proteins of related function should, therefore, share comparable recognition pockets. On the basis of this idea a new computer method has been developed to detect functional relationships among proteins, independent of a particular sequence or fold homology, in which the functionality of the residues is translated into simple physicochemical descriptors. By this method novel ligands in drug design can be suggested.
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Affiliation(s)
- Stefan Schmitt
- Philipps-Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6, 35032 Marburg (Germany) Fax: (+49) 6421-282-8994
| | - Manfred Hendlich
- Philipps-Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6, 35032 Marburg (Germany) Fax: (+49) 6421-282-8994
| | - Gerhard Klebe
- Philipps-Universität Marburg Institut für Pharmazeutische Chemie Marbacher Weg 6, 35032 Marburg (Germany) Fax: (+49) 6421-282-8994
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573
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Synthesis of phosphinic alanyl-proline surrogates Alaψ(PO2R-CH)Pro as potential inhibitors of the human cyclophilin hCyp-18. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)01255-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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574
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Pikul S, Ohler NE, Ciszewski G, Laufersweiler MC, Almstead NG, De B, Natchus MG, Hsieh LC, Janusz MJ, Peng SX, Branch TM, King SL, Taiwo YO, Mieling GE. Potent and selective carboxylic acid-based inhibitors of matrix metalloproteinases. J Med Chem 2001; 44:2499-502. [PMID: 11472202 DOI: 10.1021/jm015531s] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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575
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Kumita H, Kato T, Jitsukawa K, Einaga H, Masuda H. Characterization of an NH-pi interaction in Co(III) ternary complexes with aromatic amino acids. Inorg Chem 2001; 40:3936-42. [PMID: 11466051 DOI: 10.1021/ic000990p] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The NH-pi interaction has been detected in the crystal structures of Co(III) ternary complexes with N,N-bis(carboxymethyl)-(S)-phenylalanine (BCMPA) and aromatic amino acids including (S)-phenylalanine ((S)-Phe), (R)-phenylalanine ((R)-Phe), and (S)-tryptophan ((S)-Trp)). Additionally, this interaction has been studied in solution for Co(III) ternary complexes with BCMPA or NTA (NTA = nitrilotriacetic acid) and several amino acids (AA) by means of electronic absorption, circular dichroism (CD), and (1)H NMR spectroscopies. The CD intensities of the Co(III) complexes with aromatic amino acids measured in the d-d region ( approximately 20.5 x 10(3) cm(-)(1)) are significantly decreased in ethanol solutions relative to water. Analogous complexes with aliphatic amino acids do not exhibit this solvent effect. The (1)H NMR spectra of the Co(III) complexes with aromatic amino acids measured in DMSO-d(6) exhibit upfield shifts of the NH peaks compared with those with aliphatic amino acids, which suggest a shielding effect due to the aromaticity. The upshift values coincide with those experimentally evaluated from the crystal structures. The magnitude of the upfield shifts agrees well with Hammett's rule, indicating that the increase of pi-electron densities on the aromatic rings leads attractive NH-pi interaction that exerts a larger shielding effect for the NH protons. In ligand-substitution reactions of the carbonatocobalt(III) complexes with amino acids, the yields of those with aromatic amino acids are higher than the yields obtained for complexes with aliphatic amino acids. This observation is discussed in connection with the important contribution of the NH-pi interaction as one of the promotion factors in the reaction.
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Affiliation(s)
- H Kumita
- Department of Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan
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576
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Bursavich MG, West CW, Rich DH. From peptides to non-peptide peptidomimetics: design and synthesis of new piperidine inhibitors of aspartic peptidases. Org Lett 2001; 3:2317-20. [PMID: 11463305 DOI: 10.1021/ol016092u] [Citation(s) in RCA: 50] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] The 3-alkoxy-4-arylpiperidine inhibitors of aspartic peptidases are shown to be a new type of non-peptide peptidomimetic inhibitor. These piperidines can be designed from peptide-derived inhibitors by use of a structure-generating program but only after the enzyme active site conformation has been modified in a mechanistically related fashion. New enantioselective syntheses of 3-alkoxy-4-arylpiperidine analogues are described.
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Affiliation(s)
- M G Bursavich
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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577
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Harrison BA, Verdine GL. The synthesis of an exhaustively stereodiversified library of cis-1,5 enediols by silyl-tethered ring-closing metathesis. Org Lett 2001; 3:2157-9. [PMID: 11440568 DOI: 10.1021/ol0159569] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
[reaction: see text] This report describes the parallel synthesis of all 16 stereoisomers of the cis-1,5 enediol module 1. Compounds 1 derive from 2 by silicon-tethered ring-closing metathesis. Such libraries of stereodiversified ligands provide a unique approach to ligand discovery that employs exhaustive searching of conformational space.
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Affiliation(s)
- B A Harrison
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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578
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Klebe G. [Molecular modeling in the battle against AIDS. Drugs design in the development of substrate-like HIV protease inhibitors]. PHARMAZIE IN UNSERER ZEIT 2001; 30:194-201. [PMID: 11400666 DOI: 10.1002/1615-1003(200105)30:3<194::aid-pauz194>3.0.co;2-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- G Klebe
- Institut für Pharmazeutische Chemie, Philipps-Universität Marburg, Marbacher Weg 6, 35032 Marburg.
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579
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Zhang X, Neamati N, Lee YK, Orr A, Brown RD, Whitaker N, Pommier Y, Burke TR. Arylisothiocyanate-containing esters of caffeic acid designed as affinity ligands for HIV-1 integrase. Bioorg Med Chem 2001; 9:1649-57. [PMID: 11425564 DOI: 10.1016/s0968-0896(01)00075-x] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Integrase is an enzyme found in human immunodeficiency virus, which is required for the viral life cycle, yet has no human cellular homologue. For this reason, HIV integrase (IN) has become an important target for the development of new AIDS therapeutics. Irreversible affinity ligands have proven to be valuable tools for studying a number of enzyme and protein systems, yet to date there have been no reports of such affinity ligands for the study of IN. As an initial approach toward irreversible ligand design directed against IN, we appended isothiocyanate functionality onto caffeic acid phenethyl ester (CAPE), a known HIV integrase inhibitor. The choice of isothiocyanate as the reactive functionality, was based on its demonstrated utility in the preparation of affinity ligands directed against a number of other protein targets. Several isomeric CAPE isothiocyanates were prepared to explore the enzyme topography for reactive nitrogen and sulfur nucleophiles vicinal to the enzyme-bound CAPE. The preparation of these CAPE isothiocyanates, required development of new synthetic methodology which employed phenyl thiocarbamates as latent isothiocyanates which could be unmasked near the end of the synthetic sequence. When it was observed that beta-mercaptoethanol (beta-ME), which is required to maintain the catalytic activity of soluble IN (a F185KC280S mutant), reacted with CAPE isothiocyanate functionality to form the corresponding hydroxyethylthiocarbamate, a variety of mutant IN were examined which did not require the presence of beta-ME for catalytic activity. Although in these latter enzymes, CAPE isothiocyanate functionality was presumed to be present and available for acylation by IN nucleophiles, they were equally effective against Cys to Ser mutants. One conclusion of these studies, is that upon binding of CAPE to the integrase, nitrogen or sulfur nucleophiles may not be properly situated in the vicinity of the phenethyl aryl ring to allow reaction with and covalent modification of reactive functionality, such as isothiocyanate groups. The fact that introduction of the isothiocyanate group onto various positions of the phenethyl ring or replacement of the phenyl ring with naphthyl rings, failed to significantly affect inhibitory potency, indicates a degree of insensitivity of this region of the molecule toward structural modification. These findings may be useful in future studies concerned with the development and use of HIV-1 integrase affinity ligands.
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Affiliation(s)
- X Zhang
- Laboratory of Medicinal Chemistry, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bldg. 376, Boyles Street, NCI-FCRDC, PO Box 13, Frederick, MD 21702-1201, USA
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580
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Pesenti C, Arnone A, Bellosta S, Bravo P, Canavesi M, Corradi E, Frigerio M, Meille SV, Monetti M, Panzeri W, Viani F, Venturini R, Zanda M. Total synthesis of a pepstatin analog incorporating two trifluoromethyl hydroxymethylene isosteres (Tfm-GABOB) and evaluation of Tfm-GABOB containing peptides as inhibitors of HIV-1 protease and MMP-9. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(01)00543-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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581
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Clare BW, Scozzafava A, Supuran CT. Protease inhibitors: synthesis of a series of bacterial collagenase inhibitors of the sulfonyl amino acyl hydroxamate type. J Med Chem 2001; 44:2253-8. [PMID: 11405662 DOI: 10.1021/jm010087e] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of sulfonyl amino acyl hydroxamates incorporating alkyl/arylsulfonyl-N-2-nitrobenzyl-L-alanine was prepared. Related compounds were obtained by reaction of N-2-nitrobenzyl-L-Ala with aryl isocyanates, arylsulfonyl isocyanates, or benzoyl isothiocyanate, followed by the conversion of the COOH into the CONHOH moiety. The new compounds were assayed as inhibitors of the Clostridium histolyticum collagenase (ChC), a bacterial protease involved in the degradation of extracellular matrix. Many of the obtained hydroxamates proved to be effective bacterial collagenase inhibitors, the main contributor to activity being the substitution pattern at the sulfonamido moiety. The best ChC inhibitors were those containing pentafluorophenylsulfonyl and 3- and 4-protected-aminophenylsulfonyl P(1)(') groups among others, with affinities in the low nanomolar range. This study also proves that the 2-nitrobenzyl- moiety, similarly to the 4-nitrobenyl one previously investigated (Scozzafava, A.; Supuran, C. T. J. Med. Chem. 2000, 43, 1858-1865) is an efficient P(2)(') anchoring moiety for obtaining potent bacterial collagenase inhibitors.
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Affiliation(s)
- B W Clare
- Department of Chemistry, The University of Western Australia, 35 Stirling Highway, Crawley, W.A. 6009 Australia.
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582
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Groutas WC, He S, Kuang R, Ruan S, Tu J, Chan HK. Inhibition of serine proteases by functionalized sulfonamides coupled to the 1,2,5-thiadiazolidin-3-one 1,1 dioxide scaffold. Bioorg Med Chem 2001; 9:1543-8. [PMID: 11408173 DOI: 10.1016/s0968-0896(01)00037-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
A challenge associated with drug design is the development of selective inhibitors of proteases (serine or cysteine) that exhibit the same primary substrate specificity, that is, show a preference for the same P(1) residue. While these proteases have similar active sites, nevertheless there are subtle differences in their S and S' subsites which can be exploited. We describe herein for the first time the use of functionalized sulfonamides as a design and diversity element which, when coupled to the 1,2,5-thiadiazolidin-3-one 1,1 dioxide scaffold yields potent, time-dependent inhibitors of the serine proteases human leukocyte elastase (HLE), proteinase 3 (PR 3) and cathepsin G(Cat G). Our preliminary findings suggest that (a) appending to the 1,2,5-thiadiazolidin-3-one 1,1 dioxide scaffold recognition and diversity elements that interact with both the S and S' subsites of a target protease may result in optimal enzyme selectivity and potency and, (b) functionalized sulfonamides constitute a powerful design and diversity element with low intrinsic chemical reactivity and potentially wide applicability.
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Affiliation(s)
- W C Groutas
- Department of Chemistry, Wichita State University, Wichita, KS 67260, USA.
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583
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Enyedy IJ, Lee SL, Kuo AH, Dickson RB, Lin CY, Wang S. Structure-based approach for the discovery of bis-benzamidines as novel inhibitors of matriptase. J Med Chem 2001; 44:1349-55. [PMID: 11311057 DOI: 10.1021/jm000395x] [Citation(s) in RCA: 67] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Matriptase, a trypsin-like serine protease, which may be involved in tissue remodeling, cancer invasion, and metastasis. Potent and selective matriptase inhibitors not only would be useful pharmacological tools for further elucidation of the role of matriptase in these processes but also could have therapeutic potential for the treatment and/or prevention of cancers. We report herein the structure-based approach for the discovery of bis-benzamidines as a novel class of potent matriptase inhibitors. The lead compound, hexamidine (1), inhibits not only the proteolytic activity of matriptase, (K(i) = 924 nM) but also of thrombin K(i) = 224 nM). By testing several available analogues, we identified a new analogue (7) that has a K(i) = 208 nM against matriptase and has only weak inhibitory activity against thrombin (K(i) = 2670 nM), thus displaying a 13-fold selectivity toward matriptase. Our results demonstrated that structure-based database screening is effective in the discovery of matriptase inhibitors and that bis-benzamidines represent a class of promising matriptase inhibitors that can be used for further drug design studies. Finally, our study suggested that there is sufficient structural differences between matriptase and its closely related serine proteases, such as thrombin, for the design of potent and selective matriptase inhibitors.
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Affiliation(s)
- I J Enyedy
- Structural Biology and Cancer Drug Discovery Program, Lombardi Cancer Center, and Department of Oncology, Georgetown University Medical Center, 3900 Reservoir Road, Washington DC 20007, USA
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584
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Pikul S, Dunham KM, Almstead NG, De B, Natchus MG, Taiwo YO, Williams LE, Hynd BA, Hsieh LC, Janusz MJ, Gu F, Mieling GE. Heterocycle-based MMP inhibitors with P2' substituents. Bioorg Med Chem Lett 2001; 11:1009-13. [PMID: 11327577 DOI: 10.1016/s0960-894x(01)00137-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Potent and selective inhibition of matrix metalloproteinases was demonstrated for a series of sulfonamide-based hydroxamic acids. The design of the heterocyclic sulfonamides incorporates a six- or seven-member central ring with a P2' substituent that can be modified. Binding interactions of this substituent at the S2' site are believed to contribute to high inhibitory potency against stromelysin, collagenase-3 and gelatinases A and B, and to provide selectivity against collagenase-1 and matrilysin. An X-ray structure of a stromelysin inhibitor complex was obtained to provide insights into the SAR and selectivity trends observed for the series.
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Affiliation(s)
- S Pikul
- Procter and Gamble Pharmaceuticals, Health Care Research Center, Mason, OH 45040, USA.
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585
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Efficient synthesis of unsymmetrically disubstituted ferrocenes: towards electrochemical dipeptide-Fc-biosensors. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)00251-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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586
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Volonterio A, Bravo P, Zanda M. Solution/solid-phase synthesis of partially modified retro- ψ [NHCH(CF 3 )]-peptidyl hydroxamates. Tetrahedron Lett 2001. [DOI: 10.1016/s0040-4039(01)00375-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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587
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Gall AL, Ruff M, Kannan R, Cuniasse P, Yiotakis A, Dive V, Rio MC, Basset P, Moras D. Crystal structure of the stromelysin-3 (MMP-11) catalytic domain complexed with a phosphinic inhibitor mimicking the transition-state. J Mol Biol 2001; 307:577-86. [PMID: 11254383 DOI: 10.1006/jmbi.2001.4493] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Stromelysin-3 (ST3) is a matrix metalloproteinase (MMP-11) whose proteolytic activity plays an important role in tumorigenicity enhancement. In breast cancer, ST3 is a bad prognosis marker: its expression is associated with a poor clinical outcome. This enzyme therefore represents an attractive therapeutic target. The topology of matrix metalloproteinases (MMPs) is remarkably well conserved, making the design of highly specific inhibitors difficult. The major difference between MMPs lies in the S(1)' subsite, a well-defined hydrophobic pocket of variable depth. The present crystal structure, the first 3D-structure of the ST3 catalytic domain in interaction with a phosphinic inhibitor mimicking a (d, l) peptide, clearly demonstrates that its S(1)' pocket corresponds to a tunnel running through the enzyme. This open channel is filled by the inhibitor P(1)' group which adopts a constrained conformation to fit this pocket, together with two water molecules interacting with the ST3-specific residue Gln215. These observations provide clues for the design of more specific inhibitors and show how ST3 can accommodate a phosphinic inhibitor mimicking a (d, l) peptide. The presence of a water molecule interacting with one oxygen atom of the inhibitor phosphinyl group and the proline residue of the Met-turn suggests how the intermediate formed during proteolysis may be stabilized. Furthermore, the hydrogen bond distance observed between the methyl of the phosphinic group and the carbonyl group of Ala182 mimics the interaction between this carbonyl group and the amide group of the cleaved peptidic bond. Our crystal structure provides a good model to study the MMPs mechanism of proteolysis.
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Affiliation(s)
- A L Gall
- Structural Biology and Genomics Laboratory, I.G.B.M.C., B.P. 163, F67404, Illkirch Cedex, France
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588
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Supuran CT, Briganti F, Scozzafava A, Ilies MA. Protease inhibitors: Part 4. Synthesis of weakly basic thrombin inhibitors incorporating pyridinium-sulfanilylaminoguanidine moieties. JOURNAL OF ENZYME INHIBITION 2001; 15:335-56. [PMID: 10995066 DOI: 10.1080/14756360009040692] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Three series of derivatives have been prepared by reaction of sulfanilylaminoguanidine with pyrylium salts, with the pyridinium derivatives of glycine and with the pyridinium derivatives of beta-alanine, respectively. The new compounds were assayed as inhibitors of two serine proteases, thrombin and trypsin. The study showed that in contrast to the leads, possessing KI's around 100-300 nM against thrombin, and 450-1420 nM against trypsin, respectively, the new derivatives showed inhibition constants in the range of 15-50 nM against thrombin, whereas their affinity for trypsin remained relatively low. Derivatives of beta-alanine were more active than the corresponding glycine derivatives, which in turn were more inhibitory than the pyridinium derivatives of sulfanilylaminoguanidine possessing the same substitution pattern at the pyridinium ring. Thus, the present study proposes two novel approaches for the preparation of high affinity, specific thrombin inhibitors: a novel S1 anchoring moiety in the already large family of arginine/amidine-based inhibitors, i.e., the SO2NHNHC(=NH)NH2 group, and novel non-peptidomimetic scaffolds obtained by incorporating alkyl-/aryl-substituted-pyridinium moieties in the hydrophobic binding site(s). The first one is important for obtaining bioavailable thrombin inhibitors, devoid of the high basicity of the commonly used arginine/amidine-based inhibitors, whereas the second one may lead to improved water solubility of such compounds.
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Affiliation(s)
- C T Supuran
- Università degli Studi, Laboratorio di Chimica Inorganica e Bioinorganica, Florence, Italy.
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589
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Fray MJ, Dickinson RP. Discovery of potent and selective succinyl hydroxamate inhibitors of matrix metalloprotease-3 (stromelysin-1). Bioorg Med Chem Lett 2001; 11:571-4. [PMID: 11229774 DOI: 10.1016/s0960-894x(00)00720-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Structure activity relationships are described for a series of succinyl hydroxamic acids 4a-o as potent and selective inhibitors of matrix metalloprotease-3 (stromelysin-1). Optimisation of P1' and P3' groups gave compound 4j (MMP-3 IC50=5.9nM) which was >140-fold less potent against MMP-1 (IC50=51,000nM), MMP-2 (IC50=1790nM), MMP-9 (IC50=840nM) and MMP-14 (IC50=1900nM).
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Affiliation(s)
- M J Fray
- Department of Discovery Chemistry, Pfizer Global Research and Development, Sandwich, Kent, UK.
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590
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Lamb ML, Burdick KW, Toba S, Young MM, Skillman AG, Zou X, Arnold JR, Kuntz ID. Design, docking, and evaluation of multiple libraries against multiple targets. Proteins 2001; 42:296-318. [PMID: 11151003 DOI: 10.1002/1097-0134(20010215)42:3<296::aid-prot20>3.0.co;2-f] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
We present a general approach to the design, docking, and virtual screening of multiple combinatorial libraries against a family of proteins. The method consists of three main stages: docking the scaffold, selecting the best substituents at each site of diversity, and comparing the resultant molecules within and between the libraries. The core "divide-and-conquer" algorithm for side-chain selection, developed from an earlier version (Sun et al., J Comp Aided Mol Design 1998;12:597-604), provides a way to explore large lists of substituents with linear rather than combinatorial time dependence. We have applied our method to three combinatorial libraries and three serine proteases: trypsin, chymotrypsin, and elastase. We show that the scaffold docking procedure, in conjunction with a novel vector-based orientation filter, reproduces crystallographic binding modes. In addition, the free-energy-based scoring procedure (Zou et al., J Am Chem Soc 1999;121:8033-8043) is able to reproduce experimental binding data for P1 mutants of macromolecular protease inhibitors. Finally, we show that our method discriminates between a peptide library and virtual libraries built on benzodiazepine and tetrahydroisoquinolinone scaffolds. Implications of the docking results for library design are explored.
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Affiliation(s)
- M L Lamb
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco, California, USA
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591
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Espino CG, Du Bois J. A Rh-Catalyzed C−H Insertion Reaction for the Oxidative Conversion of Carbamates to Oxazolidinones. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010202)113:3<618::aid-ange618>3.0.co;2-f] [Citation(s) in RCA: 99] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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592
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Clements JM, Beckett RP, Brown A, Catlin G, Lobell M, Palan S, Thomas W, Whittaker M, Wood S, Salama S, Baker PJ, Rodgers HF, Barynin V, Rice DW, Hunter MG. Antibiotic activity and characterization of BB-3497, a novel peptide deformylase inhibitor. Antimicrob Agents Chemother 2001; 45:563-70. [PMID: 11158755 PMCID: PMC90327 DOI: 10.1128/aac.45.2.563-570.2001] [Citation(s) in RCA: 165] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Peptide deformylase (PDF) is an essential bacterial metalloenzyme which deformylates the N-formylmethionine of newly synthesized polypeptides and as such represents a novel target for antibacterial chemotherapy. To identify novel PDF inhibitors, we screened a metalloenzyme inhibitor library and identified an N-formyl-hydroxylamine derivative, BB-3497, and a related natural hydroxamic acid antibiotic, actinonin, as potent and selective inhibitors of PDF. To elucidate the interactions that contribute to the binding affinity of these inhibitors, we determined the crystal structures of BB-3497 and actinonin bound to Escherichia coli PDF at resolutions of 2.1 and 1.75 A, respectively. In both complexes, the active-site metal atom was pentacoordinated by the side chains of Cys 90, His 132, and His 136 and the two oxygen atoms of N-formyl-hydroxylamine or hydroxamate. BB-3497 had activity against gram-positive bacteria, including methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus faecalis, and activity against some gram-negative bacteria. Time-kill analysis showed that the mode of action of BB-3497 was primarily bacteriostatic. The mechanism of resistance was via mutations within the formyltransferase gene, as previously described for actinonin. While actinonin and its derivatives have not been used clinically because of their poor pharmacokinetic properties, BB-3497 was shown to be orally bioavailable. A single oral dose of BB-3497 given 1 h after intraperitoneal injection of S. aureus Smith or methicillin-resistant S. aureus protected mice from infection with median effective doses of 8 and 14 mg/kg of body weight, respectively. These data validate PDF as a novel target for the design of a new generation of antibacterial agents.
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Affiliation(s)
- J M Clements
- British Biotech Pharmaceuticals Ltd., Oxford OX4 6LY, United Kingdom.
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593
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Espino CG, Du Bois J. A Rh-Catalyzed C−H Insertion Reaction for the Oxidative Conversion of Carbamates to Oxazolidinones. Angew Chem Int Ed Engl 2001; 40:598-600. [DOI: 10.1002/1521-3773(20010202)40:3<598::aid-anie598>3.0.co;2-9] [Citation(s) in RCA: 414] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2000] [Indexed: 11/10/2022]
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594
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Mak CC, Le VD, Lin YC, Elder JH, Wong CH. Design, synthesis, and biological evaluation of HIV/FIV protease inhibitors incorporating a conformationally constrained macrocycle with a small P3' residue. Bioorg Med Chem Lett 2001; 11:219-22. [PMID: 11206463 DOI: 10.1016/s0960-894x(00)00641-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
A series of norstatine-based HIV/FIV protease inhibitors incorporating a 15-membered macrocycle as a mimic of the tripeptide (Ala-Val-Phe), a motif with a small P3' residue elective against the FIV protease and the drug-resistant HIV proteases, has been synthesized. It was found that the macrocycle is important to the overall activity of the inhibitors. Certain inhibitors were developed expressing low nanomolar inhibitory activity against the HIV/FIV proteases and they are also effective against some drug-resistant as well as TL3-resistant HIV proteases.
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Affiliation(s)
- C C Mak
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
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595
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Grüneberg S, Wendt B, Klebe G. Subnanomolar wirksame Inhibitoren aus dem Computerscreening: eine Modellstudie an der humanen Carboanhydrase II. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010119)113:2<404::aid-ange404>3.0.co;2-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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596
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Grüneberg S, Wendt B, Klebe G. Subnanomolar Inhibitors from Computer Screening: A Model Study Using Human Carbonic Anhydrase II. Angew Chem Int Ed Engl 2001; 40:389-393. [PMID: 11180334 DOI: 10.1002/1521-3773(20010119)40:2<389::aid-anie389>3.0.co;2-#] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Sven Grüneberg
- Institut für Pharmazeutische Chemie der Universität Marbacher Weg 6, 35032 Marburg (Germany)
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597
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Belen’kii L, Kruchkovskaya N, Gramenitskaya V. The Literature of Heterocyclic Chemistry, Part VII: 1997–1999. ADVANCES IN HETEROCYCLIC CHEMISTRY 2001. [DOI: 10.1016/s0065-2725(01)79024-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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598
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Yamamura H, Rekharsky M, Akasaki A, Araki S, Kawai M, Inoue Y. Calorimetric and NMR studies on the direct correlation between supramolecular complex structure and the thermodynamics ofN-benzyloxycarbonyl-L-aspartic and -glutamic acid inclusion complexes with mono- and bis(trimethylammonio)-?-cyclodextrins. J PHYS ORG CHEM 2001. [DOI: 10.1002/poc.381] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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599
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Groutas WC, Epp JB, Kuang R, Ruan S, Chong LS, Venkataraman R, Tu J, He S, Yu H, Fu Q, Li YH, Truong TM, Vu NT. 1,2,5-Thiadiazolidin-3-one 1,1 Dioxide: A Powerful Scaffold for Probing the S′ Subsites of (Chymo)trypsin-Like Serine Proteases. Arch Biochem Biophys 2001; 385:162-9. [PMID: 11361013 DOI: 10.1006/abbi.2000.2139] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The 1,2,5-thiadiazolidin-3-one 1,1 dioxide scaffold (I) embodies a motif that allows it to dock to the active site of (chymo)trypsin-like proteases in a predictable and substrate-like fashion. Consequently, inhibitors derived from this heterocyclic scaffold interact with both the S and S' subsites of an enzyme. Exploitation of binding interactions with both the S and S' subsites of a target enzyme may lead to compounds with greatly enhanced enzyme selectivity and inhibitory potency. This preliminary report describes the use of a series of compounds having the heterocyclic scaffold linked to various amino acids to probe the S' subsites of human leukocyte elastase (HLE), proteinase 3 (PR 3), and cathepsin G (Cat G). For comparative purposes, a series of compounds derived from a related scaffold, isothiazolidin-3-one 1,1 dioxide (II), was also generated. Several of the compounds were found to be highly potent and selective time-dependent inhibitors of HLE, PR 3, and Cat G.
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Affiliation(s)
- W C Groutas
- Department of Chemistry, Wichita State University, Kansas 67260, USA.
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600
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