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Schmidt EY, Trofimov BA. Acetylene in Organic Synthesis. From the Chaos of Small Molecules to Highly Organized Structures. A Review. DOKLADY CHEMISTRY 2022. [DOI: 10.1134/s0012500822700069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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2
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Schmidt EY, Semenova NV, Ushakov IA, Vashchenko AV, Trofimov BA. Multimolecular Self-Organization of 1-Acetyl-1,3-bis(haloarylamines) in KOH/DMSO System: From Acetylene Gas and o-Halo Arylamines toward a Higher Molecular Complexity and Diversity. Org Lett 2021; 23:4743-4748. [PMID: 34077231 DOI: 10.1021/acs.orglett.1c01460] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An unprecedented self-organization of three molecules of acetylene, two molecules of o-halo arylamine, and one molecule of water to 1-acetyl-1,3-bis(haloarylamines) in the KOH/DMSO system has been discovered. These high-value 1,3-bis(arylamines) are capable of acting as efficient "platform molecules" to provide one-pot access to hexahydropyrrolo[3,2-b]indoles, 3-haloarylamino-pyrrolidines, benzyliden piperidinols, and other functionalized diamines.
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Affiliation(s)
- Elena Yu Schmidt
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Russian Academy of Sciences, 1 Favorsky Str., 664033 Irkutsk, Russia
| | - Nadezhda V Semenova
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Russian Academy of Sciences, 1 Favorsky Str., 664033 Irkutsk, Russia
| | - Igor A Ushakov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Russian Academy of Sciences, 1 Favorsky Str., 664033 Irkutsk, Russia
| | - Alexander V Vashchenko
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Russian Academy of Sciences, 1 Favorsky Str., 664033 Irkutsk, Russia
| | - Boris A Trofimov
- A. E. Favorsky Irkutsk Institute of Chemistry, Siberian Branch, Russian Academy of Sciences, 1 Favorsky Str., 664033 Irkutsk, Russia
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Vinyukov AV, Borodachev AV, Starikov AS, Afanasyev AV, Dmitriev ME, Lednev BV, Ragulin VV. An efficient one-pot synthesis of bis(α-aminoalkyl)phosphinic acids, phosphorus-isosteric analogues of HIV protease inhibitors. MENDELEEV COMMUNICATIONS 2018. [DOI: 10.1016/j.mencom.2018.05.022] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Piasta K, Dziełak A, Mucha A, Gumienna-Kontecka E. Non-symmetrical bis(aminoalkyl)phosphinates: new ligands with enhanced binding of Cu(ii) ions. NEW J CHEM 2018. [DOI: 10.1039/c8nj01094c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Novel, non-symmetrical bis(aminoalkyl)phosphinic acids exhibit enhanced efficiency in Cu(ii) ion binding.
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Affiliation(s)
- Karolina Piasta
- Faculty of Chemistry
- University of Wrocław
- 50-383 Wrocław
- Poland
| | - Anna Dziełak
- Department of Bioorganic Chemistry
- Faculty of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
| | - Artur Mucha
- Department of Bioorganic Chemistry
- Faculty of Chemistry
- Wrocław University of Science and Technology
- 50-370 Wrocław
- Poland
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Ahmed L, Rasulev B, Kar S, Krupa P, Mozolewska MA, Leszczynski J. Inhibitors or toxins? Large library target-specific screening of fullerene-based nanoparticles for drug design purpose. NANOSCALE 2017; 9:10263-10276. [PMID: 28696446 DOI: 10.1039/c7nr00770a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Fullerene-based nanoparticles have been the subject of vital interest due to their unique properties and potential application in many areas, including medicine. Here we explore their characteristics that could make them prospective leads for known disease-related proteins. High-throughput virtual screening supported by comprehensive multi-software protein-ligand docking simulation and cheminformatics approaches has been applied in investigation of interactions of 1117 proteins with a 169 fullerene nanoparticles decorated with different small molecules. Moreover, obtained docking results were confirmed by the series of unrestricted all-atom molecular dynamics (MD) simulations. Hydrophobicity of fullerene core along with hydrophilic interaction of side chains plays a key role in binding with the studied proteins. We identified a series of nanoparticles that can lead to development of robust drugs for target proteins and another series that can behave as a highly toxic agent. The structure-activity relationship analysis revealed two significant molecular properties responsible for the binding score values. The application of carefully selected computational techniques and described outcome of the study facilitate development of functional fullerene nanoparticles for drug-like and drug delivery applications.
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Affiliation(s)
- Lucky Ahmed
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA.
| | - Bakhtiyor Rasulev
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA. and Center for Computationally Assisted Science and Technology (CCAST), North Dakota State University, 1805 NDSU Research Park Dr, PO Box 6050, Fargo, ND 58108, USA and Department of Coatings and Polymer Materials, North Dakota State University, NDSU Dept. 2760, PO Box 6050, Fargo, ND 58108, USA
| | - Supratik Kar
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA.
| | - Paweł Krupa
- Institute of Physics, Polish Academy of Sciences, Aleja Lotnikow 32/46, PL-02668 Warsaw, Poland
| | - Magdalena A Mozolewska
- Institute of Computer Science, Polish Academy of Sciences, ul. Jana Kazimierza 5, Warszaw, 01-248, Poland
| | - Jerzy Leszczynski
- Interdisciplinary Center for Nanotoxicity, Department of Chemistry and Biochemistry, Jackson State University, 1400 J.R. Lynch Street, P.O. Box 17910, Jackson, MS 39217, USA.
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6
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Cinchona based squaramide catalysed enantioselective Michael addition of α-nitrophosphonates to aryl acrylates: enantioselective synthesis of quaternary α-aminophosphonates. ACTA ACUST UNITED AC 2013. [DOI: 10.1016/j.tetasy.2013.10.008] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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7
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Kang H, Sheng Z, Zhu R, Huang Q, Liu Q, Cao Z. Virtual drug screen schema based on multiview similarity integration and ranking aggregation. J Chem Inf Model 2012; 52:834-43. [PMID: 22332590 DOI: 10.1021/ci200481c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The current drug virtual screen (VS) methods mainly include two categories. i.e., ligand/target structure-based virtual screen and that, utilizing protein-ligand interaction fingerprint information based on the large number of complex structures. Since the former one focuses on the one-side information while the later one focuses on the whole complex structure, they are thus complementary and can be boosted by each other. However, a common problem faced here is how to present a comprehensive understanding and evaluation of the various virtual screen results derived from various VS methods. Furthermore, there is still an urgent need for developing an efficient approach to fully integrate various VS methods from a comprehensive multiview perspective. In this study, our virtual screen schema based on multiview similarity integration and ranking aggregation was tested comprehensively with statistical evaluations, providing several novel and useful clues on how to perform drug VS from multiple heterogeneous data sources. (1) 18 complex structures of HIV-1 protease with ligands from the PDB were curated as a test data set and the VS was performed with five different drug representations. Ritonavir ( 1HXW ) was selected as the query in VS and the weighted ranks of the query results were aggregated from multiple views through four similarity integration approaches. (2) Further, one of the ranking aggregation methods was used to integrate the similarity ranks calculated by gene ontology (GO) fingerprint and structural fingerprint on the data set from connectivity map, and two typical HDAC and HSP90 inhibitors were chosen as the queries. The results show that rank aggregation can enhance the result of similarity searching in VS when two or more descriptions are involved and provide a more reasonable similarity rank result. Our study shows that integrated VS based on multiple data fusion can achieve a remarkable better performance compared to that from individual ones and, thus, serves as a promising way for efficient drug screening, taking advantages of the rapidly accumulated molecule representations and heterogeneous data in the pharmacological area.
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Affiliation(s)
- Hong Kang
- School of Life Sciences and Technology, Tongji University, 200092, China
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8
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Loughlin WA, Tyndall JDA, Glenn MP, Hill TA, Fairlie DP. Update 1 of: Beta-Strand Mimetics. Chem Rev 2011; 110:PR32-69. [DOI: 10.1021/cr900395y] [Citation(s) in RCA: 83] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wendy A. Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Joel D. A. Tyndall
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Matthew P. Glenn
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - Timothy A. Hill
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
| | - David P. Fairlie
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia, and Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD 4072, Australia This is a Chemical Reviews Perennial Review. The root paper of this title was published in Chem. Rev. 2004, 104 (12), 6085−6117, DOI: 10.1021/cr040648k; Published (Web) Nov. 4, 2004. Updates to the text appear in red type
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9
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Pham TS, Czirok JB, Balázs L, Pál K, Kubinyi M, Bitter I, Jászay Z. BINOL-based azacrown ether catalyzed enantioselective Michael addition: asymmetric synthesis of α-aminophosphonates. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.tetasy.2011.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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10
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Pham TS, Balázs L, Petneházy I, Jászay Z. Enantioselective Michael addition of diethyl cyanomethylphosphonate to chalcones using bifunctional cinchona-derived organocatalysts: synthesis of chiral precursors of α-substituted β-aminophosphonates. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.tetasy.2010.01.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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11
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Lu D, Vince R. Discovery of potent HIV-1 protease inhibitors incorporating sulfoximine functionality. Bioorg Med Chem Lett 2007; 17:5614-9. [PMID: 17822899 DOI: 10.1016/j.bmcl.2007.07.095] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Revised: 07/25/2007] [Accepted: 07/26/2007] [Indexed: 10/22/2022]
Abstract
Based on the unique property of sulfoximine and the homodimeric C(2) structural symmetry of HIV-1 protease, a novel class of sulfoximine-based pseudosymmetric HIV-1 protease inhibitors was designed and synthesized. The sulfoximine moiety was demonstrated to be important for HIV-1 protease inhibitor potency. The most active stereoisomer (2S,2'S) displays a potency of 2.5 nM (IC(50)) against HIV-1 protease and an anti-HIV-1 activity of 408 nM (IC(50)). A possible mode of action is proposed.
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Affiliation(s)
- Ding Lu
- Department of Medicinal Chemistry, College of Pharmacy, 308 Harvard Street SE, University of Minnesota, Minneapolis, MN 55455, USA
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12
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Affiliation(s)
- Marcin Drag
- a Department of Chemistry , Wroclaw University of Technology , Wroclaw, Poland
| | - Katarzyna Dlugosz
- a Department of Chemistry , Wroclaw University of Technology , Wroclaw, Poland
| | - Józef Oleksyszyn
- a Department of Chemistry , Wroclaw University of Technology , Wroclaw, Poland
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Thorsteinsdottir HB, Schwede T, Zoete V, Meuwly M. How inaccuracies in protein structure models affect estimates of protein-ligand interactions: computational analysis of HIV-I protease inhibitor binding. Proteins 2006; 65:407-23. [PMID: 16941468 DOI: 10.1002/prot.21096] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The influence of possible inaccuracies that can arise during homology modeling of protein structures used for ligand binding studies were investigated with the molecular mechanics generalized Born surface area (MM-GBSA) method. For this, a family of well-characterized HIV-I protease-inhibitor complexes was used. Validation of MM-GBSA led to a correlation coefficient ranging from 0.72 to 0.93 between calculated and experimental binding free energies DeltaG. All calculated DeltaG values were based on molecular dynamics simulations with explicit solvent. Errors introduced into the protein structure through misplacement of side-chains during rotamer modeling led to a correlation coefficient between DeltaG(calc) and DeltaG(exp) of 0.75 compared with 0.90 for the correctly placed side chains. This is in contrast to homology models for members of the retroviral protease family with template structures ranging in sequence identity between 32% and 51%. For these protein models, the correlation coefficients vary between 0.84 and 0.87, which is considerably closer to the original protein (0.90). It is concluded that HIV-I low sequence identity with the template structure still allows creating sufficiently reliable homology models to be used for ligand-binding studies, although placement of the rotamers is a critical step during the modeling.
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14
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Zheltukhin VF, Dovbysh AI, Sadkova DN, Dobrynin AB, Kataeva ON, Litvinov IA, Alfonsov VA. Synthesis of stereoisomeric P—H-spirophosphoranes based on hydrobenzoin. Russ Chem Bull 2005. [DOI: 10.1007/s11172-006-0060-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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15
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Mucha A, Paweł M, Hurek J, Kafarski P. Synthesis and activity of phosphinic tripeptide inhibitors of cathepsin C. Bioorg Med Chem Lett 2005; 14:3113-6. [PMID: 15149655 DOI: 10.1016/j.bmcl.2004.04.028] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2004] [Revised: 04/06/2004] [Accepted: 04/08/2004] [Indexed: 11/30/2022]
Abstract
Phosphinic tripeptide analogues Gly-Xaapsi[P(O)(OH)CH(2)]-Gly have been developed as inhibitors of cathepsin C (DPP I), a lysosomal, papain-like cysteine protease. The target compounds were synthesised by addition of methyl acrylate to the appropriate phosphinic acids followed by the N-terminus elongation using mixed anhydride procedure. The latter step has been demonstrated to be a suitable method for N-terminal extension of the phosphinic pseudopeptide analogues without requirement of hydroxyphosphinyl protection. The title compounds appeared to be moderate inhibitors of the cathepsin C. However, although designed as transition state analogues, they surprisingly exhibited noncompetitive mode of binding to cathepsin C. Differences in kinetics of C-terminal acids and esters have been additionally observed.
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Affiliation(s)
- Artur Mucha
- Institute of Organic Chemistry, Biochemistry and Biotechnology, Wrocław University of Technology, Wybrzeze Wyspiańskiego 27, 50-370 Wrocław, Poland.
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16
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17
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Smith R, Hubbard RE, Gschwend DA, Leach AR, Good AC. Analysis and optimization of structure-based virtual screening protocols. (3). New methods and old problems in scoring function design. J Mol Graph Model 2003; 22:41-53. [PMID: 12798390 DOI: 10.1016/s1093-3263(03)00125-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Scoring function research remains a primary focus of current structure-based virtual screening (SVS) technology development. Here, we present an alternative method for scoring function design that attempts to combine crystallographic structural information with data derived from directly within SVS calculations. The technique utilizes a genetic algorithm (GA) to optimize functions based on binding property data derived from multiple virtual screening calculations. These calculations are undertaken on protein data bank (PDB) complex active sites using ligands of known binding mode in conjunction with "noise" compounds. The advantages of such an approach are that the function does not rely on assay data and that it can potentially use the "noise" binding data to recognize the sub-optimal docking interactions inherent in SVS calculations. Initial efforts in technique exploration using DOCK are presented, with comparisons made to existing DOCK scoring functions. An analysis of the problems inherent to scoring function development is also made, including issues in dataset creation and limitations in descriptor utility when viewed from the perspective of docking mode resolution. The future directions such studies might take are also discussed in detail.
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Affiliation(s)
- Ryan Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York, YO10 4DD, UK
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18
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Banerji B, Bhattacharya M, Madhu RB, Kumar Das S, Iqbal J. Synthesis of cyclic β-turn mimics from l-Pro-Phe/Phe-l-Pro derived di- and tripeptides via ring closing metathesis: the role of chirality of the Phe residue during cyclization. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)01238-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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19
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Saha B, Das D, Banerji B, Iqbal J. Synthesis of β-methyl-β-alanine-l-proline-XAA tripeptides by Yb(OTf)3 catalysed Michael addition of amines to N-crotonyl-l-proline-XAA: a versatile route to cyclic β-methyl-β-alanine-derived tripeptides via ring closing metathesis. Tetrahedron Lett 2002. [DOI: 10.1016/s0040-4039(02)01237-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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20
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Zoete V, Michielin O, Karplus M. Relation between sequence and structure of HIV-1 protease inhibitor complexes: a model system for the analysis of protein flexibility. J Mol Biol 2002; 315:21-52. [PMID: 11771964 DOI: 10.1006/jmbi.2001.5173] [Citation(s) in RCA: 123] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The flexibility of different regions of HIV-1 protease was examined by using a database consisting of 73 X-ray structures that differ in terms of sequence, ligands or both. The root-mean-square differences of the backbone for the set of structures were shown to have the same variation with residue number as those obtained from molecular dynamics simulations, normal mode analyses and X-ray B-factors. This supports the idea that observed structural changes provide a measure of the inherent flexibility of the protein, although specific interactions between the protease and the ligand play a secondary role. The results suggest that the potential energy surface of the HIV-1 protease is characterized by many local minima with small energetic differences, some of which are sampled by the different X-ray structures of the HIV-1 protease complexes. Interdomain correlated motions were calculated from the structural fluctuations and the results were also in agreement with molecular dynamics simulations and normal mode analyses. Implications of the results for the drug-resistance engendered by mutations are discussed briefly.
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Affiliation(s)
- V Zoete
- Laboratoire de Chimie Biophysique, Institut Le Bel, Université Louis Pasteur, 4 rue Blaise Pascal, Strasbourg, 67000, France
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21
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Georgiadis D, Dive V, Yiotakis A. Synthesis and comparative study on the reactivity of peptidyl-type phosphinic esters: intramolecular effects in the alkaline and acidic cleavage of methyl beta-carboxyphosphinates. J Org Chem 2001; 66:6604-10. [PMID: 11578210 DOI: 10.1021/jo0156363] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using the phosphinic analogue of Cbz-Phe-Gly-OEt 1a as a template for this study, several phosphinic esters (2a-g) were prepared, employing an efficient method for each case. The reactivity of these derivatives under conventional deprotection conditions was studied, and the results are listed comparatively. The effect of steric hindrance as well as the contribution of neighboring groups in the rate of hydrolysis of suitably selected beta-carboxyphosphinates under acidic and alkaline deprotection conditions was examined. The results clearly demonstrate that a significant acceleration of phosphinate cleavage occurs due to the intermediacy of a five-membered, mixed anhydride-type species. This was supported by the observation that similar interactions were not observed in the case of hindered alpha-carboxyphosphinate homologous derivatives.
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Affiliation(s)
- D Georgiadis
- Department of Chemistry, Laboratory of Organic Chemistry, University of Athens, Panepistimiopolis Zografou, 15771, Athens, Greece
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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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Prabu-Jeyabalan M, Nalivaika E, Schiffer CA. How does a symmetric dimer recognize an asymmetric substrate? A substrate complex of HIV-1 protease. J Mol Biol 2000; 301:1207-20. [PMID: 10966816 DOI: 10.1006/jmbi.2000.4018] [Citation(s) in RCA: 146] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The crystal structure of an actual HIV-1 protease-substrate complex is presented at 2.0 A resolution (R-value of 19.7 % (R(free) 23.3 %)) between an inactive variant (D25N) of HIV-1 protease and a long substrate peptide, Lys-Ala-Arg-Val-Leu-Ala-Glu-Ala-Met-Ser, which covers a full binding epitope of capsid(CA)-p2, cleavage site. The substrate peptide is asymmetric in both size and charge distribution. To accommodate this asymmetry the two protease monomers adopt different conformations burying a total of 1038 A(2) of surface area at the protease-substrate interface. The specificity for the CA-p2 substrate peptide is mainly hydrophobic, as most of the hydrogen bonds are made with the backbone of the peptide substrate. Two water molecules bridge the two monomers through the loops Gly49-Gly52 (Gly49'-Gly52') and Pro79'-Val82' (Pro79-Val82). When other complexes are compared, the mobility of these loops is correlated with the content of the P1 and P1' sites. Interdependence of the conformational changes allows the protease to exhibit its wide range of substrate specificity.
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Affiliation(s)
- M Prabu-Jeyabalan
- Department of Pharmacology and Molecular Toxicology, University of Massachusetts Medical School, Worcester, MA, 01655, USA
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24
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Makino S, Ewing TJ, Kuntz ID. DREAM++: flexible docking program for virtual combinatorial libraries. J Comput Aided Mol Des 1999; 13:513-32. [PMID: 10483532 DOI: 10.1023/a:1008066310669] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
We present a set of programs, DREAM+2 (Docking and Reaction programs using Efficient seArch Methods written in C++), for docking computationally generated ligands into macromolecular binding sites. DREAM++ is composed of three programs: ORIENT++, REACT++ and SEARCH++. The program ORIENT++ positions molecules in a binding site with the DOCK algorithm. Its output can be used as input to REACT++ and SEARCH+2. The program REACT++ performs user-specific chemical reactions on a docked molecule, so that reaction products can be evaluated for three dimensional complementarity with the macromolecular site. The program SEARCH++ performs an efficient conformation search on the reaction products using a hybrid backtrack and incremental construction algorithm. We have applied the programs to HIV protease-inhibitor complexes as test systems. We found that we can differentiate high-affinity ligands based on several measures: interaction energies, occupancy of protein subsites and the number of successfully docked conformations for each product. Encouraged by the results in the test case, we applied the programs to propose novel inhibitors of HIV protease. These inhibitors can be generated by organic reactions using commercially available reagents. They are alternatives to the inhibitors synthesized by Glaxo.
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Affiliation(s)
- S Makino
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco 94143-0446, USA
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Marrone TJ, Resat H, Hodge CN, Chang CH, McCammon JA. Solvation studies of DMP323 and A76928 bound to HIV protease: analysis of water sites using grand canonical Monte Carlo simulations. Protein Sci 1998; 7:573-9. [PMID: 9541388 PMCID: PMC2143944 DOI: 10.1002/pro.5560070305] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
We examine the water solvation of the complex of the inhibitors DMP323 and A76928 bound to HIV-1 protease through grand canonical Monte Carlo simulations, and demonstrate the ability of this method to reproduce crystal waters and effectively predict water positions not seen in the DMP323 or A76928 structures. The simulation method is useful for identifying structurally important waters that may not be resolved in the crystal structures. It can also be used to identify water positions around a putative drug candidate docked into a binding pocket. Knowledge of these water positions may be useful in designing drugs to utilize them as bridging groups or displace them in the binding pocket. In addition, the method should be useful in finding water sites in homology models of enzymes for which crystal structures are unavailable.
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Affiliation(s)
- T J Marrone
- Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla 92093-0365, USA
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26
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Towards understanding ligand specificity of retroviral proteases. Implications for the design of human immunodeficiency virus type 1 and 2 protease inhibitors. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0166-1280(97)00121-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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27
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Mu YQ, Gibbs RA. Design and synthesis of chiral and racemic phosphonate-based haptens for the induction of aldolase catalytic antibodies. Bioorg Med Chem 1997; 5:1327-37. [PMID: 9377093 DOI: 10.1016/s0968-0896(97)00088-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A novel strategy for the generation of aldolase catalytic antibodies, based on the use of antibody-catalyzed enol ester hydrolysis as a 'trigger' to generate a reactive enolate intermediate, is described. A model system to test this strategy was developed and substrate 8 was synthesized. However, the targeted bifunctional haptens 11 and 33 were synthetically inaccessible, and therefore the alternative phosphonate hapten 39 was prepared. The key step in the synthesis of 39 was the direct generation of an unprotected phosphonate precursor via coupling of the secondary alcohol 37 with CH3P(O)Cl2. The chiral counterpart of hapten 39 was also synthesized from alcohol 46, prepared by Corey's asymmetric reduction method. One polyclonal antibody preparation generated from 39 appeared to catalyze the hydrolysis of the secondary acetate 49, but not the desired aldol cyclization of 8. Possible rationales for this finding are discussed.
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Affiliation(s)
- Y Q Mu
- Department of Pharmaceutical Sciences, College of Pharmacy and Allied Health Professions, Wayne State University, Detroit, MI 48202, U.S.A
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28
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Abstract
Until recently, applications of molecular docking assumed that the macromolecular receptor exists in a single, rigid conformation. However, structural studies involving different ligands bound to the same target biomolecule frequently reveal modest but significant conformational changes in the target. In this paper, two related methods for molecular docking are described that utilize information on conformational variability from ensembles of experimental receptor structures. One method combines the information into an "energy-weighted average" of the interaction energy between a ligand and each receptor structure. The other method performs the averaging on a structural level, producing a "geometry-weighted average" of the inter-molecular force field score used in DOCK 3.5. Both methods have been applied in docking small molecules to ensembles of crystal and solution structures, and we show that experimentally determined binding orientations and computed energies of known ligands can be reproduced accurately. The use of composite grids, when conformationally different protein structures are available, yields an improvement in computational speed for database searches in proportion to the number of structures.
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Affiliation(s)
- R M Knegtel
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of California, San Francisco 94143-0446, USA
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29
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McPhee F, Good AC, Kuntz ID, Craik CS. Engineering human immunodeficiency virus 1 protease heterodimers as macromolecular inhibitors of viral maturation. Proc Natl Acad Sci U S A 1996; 93:11477-81. [PMID: 8876160 PMCID: PMC56635 DOI: 10.1073/pnas.93.21.11477] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Dimerization of human immunodeficiency virus type 1 protease (HIV-1 PR) monomers is an essential prerequisite for viral proteolytic activity and the subsequent generation of infectious virus particles. Disruption of the dimer interface inhibits this activity as does formation of heterodimers between wild-type and defective monomers. A structure-based approach was used to identify amino acid substitutions at the dimer interface of HIV-1 PR that facilitate preferential association of heterodimers and inhibit self-association of the defective monomers. Expression of the designed PR monomers inhibits activity of wild-type HIV-1 PR and viral infectivity when assayed in an ex vivo model system. These results show that it is possible to design PR monomers as macromolecular inhibitors that may provide an alternative to small molecule inhibitors for the treatment of HIV infection.
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Affiliation(s)
- F McPhee
- Department of Pharmaceutical Chemisty, University of California, San Francisco 94143, USA
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30
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Rutenber EE, McPhee F, Kaplan AP, Gallion SL, Hogan JC, Craik CS, Stroud RM. A new class of HIV-1 protease inhibitor: the crystallographic structure, inhibition and chemical synthesis of an aminimide peptide isostere. Bioorg Med Chem 1996; 4:1545-58. [PMID: 8894111 DOI: 10.1016/0968-0896(96)00147-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The essential role of HIV-1 protease (HIV-1 PR) in the viral life cycle makes it an attractive target for the development of substrate-based inhibitors that may find efficacy as anti-AIDS drugs. However, resistance has arisen to potent peptidomimetic drugs necessitating the further development of novel chemical backbones for diversity based chemistry focused on probing the active site for inhibitor interactions and binding modes that evade protease resistance. AQ148 is a potent inhibitor of HIV-1 PR and represents a new class of transition state analogues incorporating an aminimide peptide isostere. A 3-D crystallographic structure of AQ148, a tetrapeptide isostere, has been determined in complex with its target HIV-1 PR to a resolution of 2.5 A and used to evaluate the specific structural determinants of AQ148 potency and to correlate structure-activity relationships within the class of related compounds. AQ148 is a competitive inhibitor of HIV-1 PR with a Ki value of 137 nM. Twenty-nine derivatives have been synthesized and chemical modifications have been made at the P1, P2, P1', and P2' sites. The atomic resolution structure of AQ148 bound to HIV-1 PR reveals both an inhibitor binding mode that closely resembles that of other peptidomimetic inhibitors and specific protein/inhibitor interactions that correlate with structure-activity relationships. The structure provides the basis for the design, synthesis and evaluation of the next generation of hydroxyethyl aminimide inhibitors. The aminimide peptide isostere is a scaffold with favorable biological properties well suited to both the combinatorial methods of peptidomimesis and the rational design of potent and specific substrate-based analogues.
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Affiliation(s)
- E E Rutenber
- Department of Biochemistry and Biophysics, University of California at San Francisco 94143, USA
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31
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32
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Affiliation(s)
- V M Vogt
- Section of Biochemistry, Molecular and Cell Biology, Cornell University, Ithaca, NY 14853, USA
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33
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34
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Camp NP, Perrey DA, Kinchington D, Hawkins PC, Gani D. Synthesis of peptide analogues containing phosphonamidate methyl ester functionality: HIV-1 proteinase inhibitors possessing unique cell uptake properties. Bioorg Med Chem 1995; 3:297-12. [PMID: 7606391 DOI: 10.1016/0968-0896(95)00022-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Stereochemically defined and epimeric phosphonamidate methyl ester-containing peptide analogues were synthesised and were found to be moderate inhibitors of the HIV-1 proteinase. All of the analogues containing the phosphonamidate ester grouping showed a marked ability to enter cells, as highlighted by the approximate equivalence of the IC50 values for enzyme inhibition in solution and inhibition of HIV-1 replication in virus infected cells.
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Affiliation(s)
- N P Camp
- School of Chemistry, The University, St. Andrews, Fife, U.K
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35
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Abdel-Meguid SS, Metcalf BW, Carr TJ, Demarsh P, DesJarlais RL, Fisher S, Green DW, Ivanoff L, Lambert DM, Murthy KH. An orally bioavailable HIV-1 protease inhibitor containing an imidazole-derived peptide bond replacement: crystallographic and pharmacokinetic analysis. Biochemistry 1994; 33:11671-7. [PMID: 7918383 DOI: 10.1021/bi00205a001] [Citation(s) in RCA: 50] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
(2R,4S,5S,1'S)-2-Phenylmethyl-4-hydroxy-5-(tert-butoxycarbonyl) amino-6-phenylhexanoyl-N-(1'-imidazo-2-yl)-2'-methylpropanamide (compound 2) is a tripeptide analogue inhibitor of HIV-1 protease in which a C-terminal imidazole substituent constitutes an isoelectronic, structural mimic of a carboxamide group. Compound 2 is a potent inhibitor of the protease (K(i) = 18 nM) and inhibits HIV-1 acute infectivity of CD4+ T-lymphocytes (IC50 = 570 nM). Crystallographic analysis of an HIV-1 protease-compound 2 complex demonstrates that the nitrogen atoms of the imidazole ring assume the same hydrogen-bonding interactions with the protease as amide linkages in other peptide analogue inhibitors. The sole substitution of the C-terminal carboxamide of a hydroxyethylene-containing tripeptide analogue with an imidazole group imparts greatly improved pharmacokinetic and oral bioavailability properties on the compound compared to its carboxamide-containing homologue (compound 1). While the oral bioavailability of compound 1 in rats was negligible, compound 2 displayed oral bioavailabilities of 30% and 14%, respectively, in rats and monkeys.
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Affiliation(s)
- S S Abdel-Meguid
- Department of Macromolecular Sciences, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406
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36
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Chau PL, Dean PM. Electrostatic complementarity between proteins and ligands. 2. Ligand moieties. J Comput Aided Mol Des 1994; 8:527-44. [PMID: 7876899 DOI: 10.1007/bf00123664] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Drug design strategies consider factors governing intermolecular interactions to build up putative ligands. In many strategies, the ligand is constructed using fragments which are placed in the site sequentially. The optimization is then performed with each fragment. We would like to examine if this optimization strategy could generate ligands with optimal electrostatic interactions. The electrostatic complementarities between constituent moieties and the receptor site have been calculated. The whole-ligand complementarity does not appear to be the mathematical mean of the individual complementarities, nor have we found a simple relationship between the moiety and whole-ligand complementarities. The results demonstrate clearly that, using a simple model, it is very difficult to predict the electrostatic potential complementarity of the whole ligand from the complementarities of its constituent chemical moieties. This means that ligand design strategies must optimize the electrostatic complementarity globally, and not moiety by moiety.
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Affiliation(s)
- P L Chau
- Department of Pharmacology, University of Cambridge, U.K
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37
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Thompson SK, Eppley AM, Frazee JS, Darcy MG, Lum RT, Tomaszek TA, Ivanoff LA, Morris JF, Sternberg EJ, Lambert DM, Fernandez AV, Petteway SR, Meek TD, Metcalf BW, Gleason JG. Synthesis and antiviral activity of a novel class of HIV-1 protease inhibitors containing a heterocyclic P1′-P2′ amide bond isostere. Bioorg Med Chem Lett 1994. [DOI: 10.1016/s0960-894x(01)80406-6] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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38
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Chau PL, Dean PM. Electrostatic complementarity between proteins and ligands. 1. Charge disposition, dielectric and interface effects. J Comput Aided Mol Des 1994; 8:513-25. [PMID: 7876898 DOI: 10.1007/bf00123663] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Electrostatic interactions have always been considered an important factor governing ligand-receptor interactions. Previous work in this field has established the existence of electrostatic complementarity between the ligand and its receptor site. However, this property has not been treated rigorously, and the description remains largely qualitative. In this work, 34 data sets of high quality were chosen from the Brookhaven Protein Databank. The electrostatic complementary has been calculated between the surface potentials; complementarity is absent between adjacent or neighbouring atoms of the ligand and the receptor. There is little difference between complementarities on the total ligand surface and the interfacial region. Altering the homogeneous dielectric to distance-dependent dielectrics reduces the complementarity slightly, but does not affect the pattern of complementarity.
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Affiliation(s)
- P L Chau
- Department of Pharmacology, University of Cambridge, U.K
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39
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40
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Watson KA, Mitchell EP, Johnson LN, Son JC, Bichard CJ, Orchard MG, Fleet GW, Oikonomakos NG, Leonidas DD, Kontou M. Design of inhibitors of glycogen phosphorylase: a study of alpha- and beta-C-glucosides and 1-thio-beta-D-glucose compounds. Biochemistry 1994; 33:5745-58. [PMID: 8180201 DOI: 10.1021/bi00185a011] [Citation(s) in RCA: 101] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
alpha-D-Glucose is a weak inhibitor of glycogen phosphorylase b (Ki = 1.7 mM) and acts as a physiological regulator of hepatic glycogen metabolism. Glucose binds to phosphorylase at the catalytic site and results in a conformational change that stabilizes the inactive T state of the enzyme, promoting the action of protein phosphatase 1 and stimulating glycogen synthase. It has been suggested that, in the liver, glucose analogues with greater affinity for glycogen phosphorylase may result in a more effective regulatory agent. Several alpha- and beta-anhydroglucoheptonic acid derivatives and 1-deoxy-1-thio-beta-D-glucose analogues have been synthesized and tested in a series of crystallographic and kinetic binding studies with glycogen phosphorylase. The structural results of the bound enzyme-ligand complexes have been analyzed, together with the resulting affinities, in an effort to understand and exploit the molecular interactions that might give rise to a better inhibitor. This work has shown the following: (i) Similar affinities may be obtained through different sets of interactions. Specifically, in the case of the alpha- and beta-glucose-C-amides, similar Ki's (0.37 and 0.44 mM, respectively) are obtained with the alpha-anomer through interactions from the ligand via water molecules to the protein and with the beta-anomer through direct interaction from the ligand to the protein. Thus, hydrogen bonds through water can contribute binding energy similar to that of hydrogen bonds directly to the protein. (ii) Attempts to improve the inhibition by additional groups did not always lead to the expected result. The addition of nonpolar groups to the alpha-carboxamide resulted in a change in conformation of the pyranose ring from a chair to a skew boat and the consequent loss of favorable hydrogen bonds and increase in the Ki. (iii) The addition of polar groups to the alpha-carboxamide led to compounds with the chair conformation, and in the examples studied, it appears that hydration by a water molecule may provide sufficient stabilization to retain the chair conformation. (iv) The best inhibitor was N-methyl-beta-glucose-C-carboxamide (Ki = 0.16 mM), which showed a 46-fold improvement in Ki from the parent beta-D-glucose. The decrease in Ki may be accounted for by a single hydrogen bond from the amide nitrogen to a main-chain carbonyl oxygen, an increase in entropy through displacement of a water molecule, and favorable van der Waals contacts between the methyl substituent and nonpolar protein residues.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- K A Watson
- Oxford Centre for Molecular Sciences, U.K
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41
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Inhibition of human immunodeficiency virus-1 protease by a C2-symmetrical phosphinic acid amide. Bioorg Med Chem Lett 1994. [DOI: 10.1016/s0960-894x(01)80327-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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42
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Mazaleyrat JP, Rage I, Šavrda J, Mouna M, Wakselman M, Boulay R, Lelièvre Y. Synthesis of C2-symmetric inhibitors of the HIV-1 protease, with N,N′-substituted ethylenediamide and ethylenediamine linkers. Bioorg Med Chem Lett 1994. [DOI: 10.1016/s0960-894x(01)80173-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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43
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Chapter 14. HIV Protease Inhibitors. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 1994. [DOI: 10.1016/s0065-7743(08)60727-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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44
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Meek TD, Rodriguez EJ, Angeles TS. Use of steady state kinetic methods to elucidate the kinetic and chemical mechanisms of retroviral proteases. Methods Enzymol 1994; 241:127-56. [PMID: 7854175 DOI: 10.1016/0076-6879(94)41063-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Despite the current plethora of structural data of HIV-1 protease and the availability of potent inhibitors, whose structures are based in part on the presumed mechanism of action of this enzyme, our actual understanding of its chemical mechanism has been until now based largely on the precedents of the mammalian and fungal aspartic proteases and static three-dimensional data. The available steady state kinetic data of the protease, as reviewed here, constitute a first step in a detailed description of the mechanism of the enzyme to complement the structural data.
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Affiliation(s)
- T D Meek
- Department of Cardiovascular Biochemistry, Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, New Jersey 08540
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45
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Affiliation(s)
- D Ringe
- Rosenstiel Basic Medical Sciences Research Center, Brandeis University, Waltham, Massachusetts 02254
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46
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Kempf DJ. Design of symmetry-based, peptidomimetic inhibitors of human immunodeficiency virus protease. Methods Enzymol 1994; 241:334-54. [PMID: 7854187 DOI: 10.1016/0076-6879(94)41072-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- D J Kempf
- Pharmaceutical Products Division, Abott Laboratories, Abott Park, Illinois 60064
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47
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Chenera B, DesJarlais RL, Finkelstein JA, Eggleston DS, Meek TD, Tomaszek TA, Dreyer GB. Nonpeptide HIV protease inhibitors designed to replace a bound water. Bioorg Med Chem Lett 1993. [DOI: 10.1016/s0960-894x(01)80749-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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48
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Rodriguez EJ, Angeles TS, Meek TD. Use of nitrogen-15 kinetic isotope effects to elucidate details of the chemical mechanism of human immunodeficiency virus 1 protease. Biochemistry 1993; 32:12380-5. [PMID: 8241126 DOI: 10.1021/bi00097a015] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
We have used 15N kinetic isotope effects of the HIV-1 protease-catalyzed peptidolysis of Ac-Ser-Gln-Asn-Tyr-Pro-Val-Val-NH2 to characterize the chemical mechanism of this enzyme. In addition, the multiple isotope effects have been determined by measuring the 15N kinetic isotope effects in both H2O and D2O. The isotope effects, measured on values of V/K, were determined by the incorporation of a radiolabel (tritium and 14C in peptides bearing the heavy and light isotopes, respectively) at a position remote from the isotopically labeled scissile peptide bond, such that the isotope effect was determined by measurement of the change in the 14C/3H ratio in recovered substrates at various fractions of reaction. At pH = 6.0 (37 degrees C), the nitrogen isotope effects were slightly, but significantly, inverse in both solvents: 15(V/K)H2O = 0.995 +/- 0.002, and 15(V/K)D2O = 0.992 +/- 0.003. The observation of an inverse nitrogen kinetic isotope effect implies that bonding to the nitrogen atom is becoming stiffened in a reaction transition state, and since this inverse isotope effect is enhanced in D2O, this isotope effect likely arises from protonation of the proline nitrogen atom.(ABSTRACT TRUNCATED AT 250 WORDS)
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Affiliation(s)
- E J Rodriguez
- Department of Pharmaceutical Technologies, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406
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49
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Affiliation(s)
- S S Abdel-Meguid
- Department of Macromolecular Sciences, SmithKline Beecham, King of Prussia, Pennsylvania 19406
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50
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