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Qin J, Cheng W, Duan YT, Yang H, Yao Y. Indazole as a Privileged Scaffold: The Derivatives and their Therapeutic Applications. Anticancer Agents Med Chem 2021; 21:839-860. [PMID: 32819234 DOI: 10.2174/1871520620999200818160350] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 06/09/2020] [Accepted: 06/25/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Heterocyclic compounds, also called heterocycles, are a major class of organic chemical compound that plays a vital role in the metabolism of all living cells. The heterocyclic compound, indazole, has attracted more attention in recent years and is widely present in numerous commercially available drugs. Indazole-containing derivatives, representing one of the most important heterocycles in drug molecules, are endowed with a broad range of biological properties. METHODS A literature search was conducted in PubMed, Google Scholar and Web of Science regarding articles related to indazole and its therapeutic application. RESULTS The mechanism and structure-activity relationship of indazole and its derivatives were described. Based on their versatile biological activities, the compounds were divided into six groups: anti-inflammatory, antibacterial, anti-HIV, antiarrhythmic, antifungal and antitumour. At least 43 indazole-based therapeutic agents were found to be used in clinical application or clinical trials. CONCLUSION This review is a guide for pharmacologists who are in search of valid preclinical/clinical drug compounds where the progress of approved marketed drugs containing indazole scaffold is examined from 1966 to the present day. Future direction involves more diverse bioactive moieties with indazole scaffold and greater insights into its mechanism.
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Affiliation(s)
- Jinling Qin
- School of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Weyland Cheng
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affilited to Zhengzhou University, Zhengzhou University, Henan 450018, China
| | - Yong-Tao Duan
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affilited to Zhengzhou University, Zhengzhou University, Henan 450018, China
| | - Hua Yang
- School of Pharmaceutical Science, Zhengzhou University, Zhengzhou, Henan 450001, China
| | - Yongfang Yao
- Henan Provincial Key Laboratory of Children's Genetics and Metabolic Diseases, Children's Hospital Affilited to Zhengzhou University, Zhengzhou University, Henan 450018, China
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2
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Jeszenői N, Schilli G, Bálint M, Horváth I, Hetényi C. Analysis of the influence of simulation parameters on biomolecule-linked water networks. J Mol Graph Model 2018; 82:117-128. [DOI: 10.1016/j.jmgm.2018.04.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 03/27/2018] [Accepted: 04/21/2018] [Indexed: 12/11/2022]
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3
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Meanwell NA. Drug-target interactions that involve the replacement or displacement of magnesium ions. Bioorg Med Chem Lett 2017; 27:5355-5372. [DOI: 10.1016/j.bmcl.2017.11.002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 10/30/2017] [Accepted: 11/02/2017] [Indexed: 01/11/2023]
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4
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Abstract
The need for antiviral drugs is growing rapidly as more viral diseases are recognized. The methods used to discover these drugs have evolved considerably over the past 40 years and the overall process of discovery can be broken down into sub-processes which include lead generation, lead optimization and lead development. Various methods are now employed to ensure these processes are carried out efficiently. For lead generation, screening methodologies have developed to the extent where hundreds of thousands of compounds can be screened against a particular target. An alternative approach is to use the structures of enzyme substrates as a starting point for drug discovery. Much use is now made of X-ray crystallographic data of target–inhibitor complexes for the optimization of lead structures, and methods for preparing libraries of compounds to assist both generation and optimization of leads are welldeveloped. The methods used to predict and improve the pharmacokinetic properties of compounds are also changing rapidly. Finally, novel approaches to antiviral therapy using oligonucleotide-based compounds or modulating the host immune response are also being explored. This review discusses these approaches, provides examples of where their application has been successful and sets them against a historical background.
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Affiliation(s)
- PS Jones
- Roche Discovery Welwyn, 40 Broadwater Road, Welwyn Garden City, AL7 3AY, UK
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5
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Activity of phosphino palladium(II) and platinum(II) complexes against HIV-1 and Mycobacterium tuberculosis. Biometals 2016; 29:637-50. [DOI: 10.1007/s10534-016-9940-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Accepted: 05/24/2016] [Indexed: 10/21/2022]
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Sabbadin D, Ciancetta A, Moro S. Perturbation of fluid dynamics properties of water molecules during G protein-coupled receptor-ligand recognition: the human A2A adenosine receptor as a key study. J Chem Inf Model 2014; 54:2846-55. [PMID: 25245783 DOI: 10.1021/ci500397y] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Recent advances in structural biology revealed that water molecules play a crucial structural role in the protein architecture and ligand binding of G protein-coupled receptors. In this work, we present an alternative approach to monitor the time-dependent organization of water molecules during the final stage of the ligand-receptor recognition process by means of membrane molecular dynamics simulations. We inspect the variation of fluid dynamics properties of water molecules upon ligand binding with the aim to correlate the results with the binding affinities. The outcomes of this analysis are transferred into a bidimensional graph called water fluid dynamics maps, that allow a fast graphical identification of protein "hot-spots" characterized by peculiar shape and electrostatic properties that can play a critical role in ligand binding. We hopefully believe that the proposed approach might represent a valuable tool for structure-based drug discovery that can be extended to cases where crystal structures are not yet available, or have not been solved at high resolution.
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Affiliation(s)
- Davide Sabbadin
- Molecular Modeling Section (MMS), Dipartimento di Scienze del Farmaco, Università di Padova , via Marzolo 5, 35131 Padova, Italy
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Bodnarchuk MS, Viner R, Michel J, Essex JW. Strategies to calculate water binding free energies in protein-ligand complexes. J Chem Inf Model 2014; 54:1623-33. [PMID: 24684745 DOI: 10.1021/ci400674k] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Water molecules are commonplace in protein binding pockets, where they can typically form a complex between the protein and a ligand or become displaced upon ligand binding. As a result, it is often of great interest to establish both the binding free energy and location of such molecules. Several approaches to predicting the location and affinity of water molecules to proteins have been proposed and utilized in the literature, although it is often unclear which method should be used under what circumstances. We report here a comparison between three such methodologies, Just Add Water Molecules (JAWS), Grand Canonical Monte Carlo (GCMC), and double-decoupling, in the hope of understanding the advantages and limitations of each method when applied to enclosed binding sites. As a result, we have adapted the JAWS scoring procedure, allowing the binding free energies of strongly bound water molecules to be calculated to a high degree of accuracy, requiring significantly less computational effort than more rigorous approaches. The combination of JAWS and GCMC offers a route to a rapid scheme capable of both locating and scoring water molecules for rational drug design.
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Affiliation(s)
- Michael S Bodnarchuk
- School of Chemistry, University of Southampton , Highfield, Southampton, SO17 1BJ, U.K
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8
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Meanwell NA. The Influence of Bioisosteres in Drug Design: Tactical Applications to Address Developability Problems. TACTICS IN CONTEMPORARY DRUG DESIGN 2014; 9. [PMCID: PMC7416817 DOI: 10.1007/7355_2013_29] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The application of bioisosteres in drug discovery is a well-established design concept that has demonstrated utility as an approach to solving a range of problems that affect candidate optimization, progression, and durability. In this chapter, the application of isosteric substitution is explored in a fashion that focuses on the development of practical solutions to problems that are encountered in typical optimization campaigns. The role of bioisosteres to affect intrinsic potency and selectivity, influence conformation, solve problems associated with drug developability, including P-glycoprotein recognition, modulating basicity, solubility, and lipophilicity, and to address issues associated with metabolism and toxicity is used as the underlying theme to capture a spectrum of creative applications of structural emulation in the design of drug candidates.
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Gros G, Martinez L, Gimenez AS, Adler P, Maurin P, Wolkowicz R, Falson P, Hasserodt J. Modular construction of quaternary hemiaminal-based inhibitor candidates and their in cellulo assessment with HIV-1 protease. Bioorg Med Chem 2013; 21:5407-13. [PMID: 23911197 DOI: 10.1016/j.bmc.2013.06.018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2013] [Revised: 05/30/2013] [Accepted: 06/06/2013] [Indexed: 01/25/2023]
Abstract
Non-peptidomimetic drug-like protease inhibitors have potential for circumventing drug resistance. We developed a much-improved synthetic route to our previously reported inhibitor candidate displaying an unusual quaternized hemi-aminal. This functional group forms from a linear precursor upon passage into physiological media. Seven variants were prepared and tested in cellulo with our HIV-1 fusion-protein technology that result in an eGFP-based fluorescent readout. Three candidates showed inhibition potency above 20μM and toxicity at higher concentrations, making them attractive targets for further refinement. Importantly, our class of original inhibitor candidates is not recognized by two major multidrug resistance pumps, quite in contrast to most clinically applied HIV-1 protease inhibitors.
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Affiliation(s)
- Guillaume Gros
- Laboratoire de Chimie, Université de Lyon - ENS, 46 allée d'Italie, 69364 Lyon, France
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Bhattacharya AK, Rana KC, Pannecouque C, De Clercq E. An Efficient Synthesis of a Hydroxyethylamine (HEA) Isostere and Its α-Aminophosphonate and Phosphoramidate Derivatives as Potential Anti-HIV Agents. ChemMedChem 2012; 7:1601-11. [DOI: 10.1002/cmdc.201200271] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2012] [Revised: 06/12/2012] [Indexed: 11/09/2022]
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11
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Nimmanpipug P, Khampa C, Lee VS, Nangola S, Tayapiwatana C. Identification of amino acid residues of a designed ankyrin repeat protein potentially involved in intermolecular interactions with CD4: Analysis by molecular dynamics simulations. J Mol Graph Model 2011; 31:65-75. [DOI: 10.1016/j.jmgm.2011.09.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2011] [Revised: 08/30/2011] [Accepted: 09/01/2011] [Indexed: 11/16/2022]
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12
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13
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Meanwell NA. Synopsis of Some Recent Tactical Application of Bioisosteres in Drug Design. J Med Chem 2011; 54:2529-91. [DOI: 10.1021/jm1013693] [Citation(s) in RCA: 1876] [Impact Index Per Article: 144.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Nicholas A. Meanwell
- Department of Medicinal Chemistry, Bristol-Myers Squibb Pharmaceutical Research and Development, 5 Research Parkway, Wallingford, Connecticut 06492, United States
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14
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15
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16
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Kaye PT, Musa MA, Nchinda AT, Nocanda XW. Novel Heterocyclic Analogues of the HIV‐1 Protease Inhibitor, Ritonavir. SYNTHETIC COMMUN 2011. [DOI: 10.1081/scc-200025617] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Perry T. Kaye
- a Department of Chemistry , Rhodes University , Grahamstown, 6140, South Africa
| | - Musiliyu A. Musa
- a Department of Chemistry , Rhodes University , Grahamstown, 6140, South Africa
| | - Aloysius T. Nchinda
- a Department of Chemistry , Rhodes University , Grahamstown, 6140, South Africa
| | - Xolani W. Nocanda
- a Department of Chemistry , Rhodes University , Grahamstown, 6140, South Africa
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17
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Waibel M, Pitrat D, Hasserodt J. On the inhibition of HIV-1 protease by hydrazino-ureas displaying the N→CO interaction. Bioorg Med Chem 2009; 17:3671-9. [DOI: 10.1016/j.bmc.2009.03.059] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2008] [Revised: 03/23/2009] [Accepted: 03/29/2009] [Indexed: 01/23/2023]
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18
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Waibel M, Hasserodt J. Diversity-Oriented Synthesis of a Drug-Like System Displaying the Distinctive N→C═O Interaction. J Org Chem 2008; 73:6119-26. [DOI: 10.1021/jo800719j] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Michael Waibel
- Laboratoire de Chimie, UMR CNRS 5182, Université de Lyon-ENS, 46 allée d’Italie, 69364 Lyon cedex 07, France
| | - Jens Hasserodt
- Laboratoire de Chimie, UMR CNRS 5182, Université de Lyon-ENS, 46 allée d’Italie, 69364 Lyon cedex 07, France
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19
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Leroux V, Gresh N, Liu WQ, Garbay C, Maigret B. Role of water molecules for binding inhibitors in the SH2 domain of Grb2: A molecular dynamics study. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2006.11.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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20
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McGlacken GP, Fairlamb IJS. 2-Pyrone natural products and mimetics: isolation, characterisation and biological activity. Nat Prod Rep 2005; 22:369-85. [PMID: 16010346 DOI: 10.1039/b416651p] [Citation(s) in RCA: 268] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The review summarises natural products containing the 2-pyrone moiety. An emphasis has been placed upon the biological activity associated with 2-pyrones, particularly with respect to potential therapeutic or anti-microbial agents. Where appropriate, non-natural 2-pyrone analogues are discussed, particularly those derived from natural product lead compounds.
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Affiliation(s)
- Gerard P McGlacken
- Department of Chemistry, University of York, Heslington, York, UK YO10 5DD
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21
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Lather V, Madan AK. Topological models for the prediction of HIV-protease inhibitory activity of tetrahydropyrimidin-2-ones. J Mol Graph Model 2005; 23:339-45. [PMID: 15670954 DOI: 10.1016/j.jmgm.2004.11.005] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2004] [Revised: 10/21/2004] [Accepted: 11/02/2004] [Indexed: 11/28/2022]
Abstract
Relationship between the topological indices and HIV-protease inhibitory activity of tetrahydropyrimidine-2-ones has been investigated. Three topological indices, Wiener's index--a distance based topological descriptor, Zagreb group parameter--an adjacency based topological descriptor and eccentric connectivity index--an adjacency-cum-distance based topological descriptor were used for the present investigations. A dataset comprising of 80 substituted tetrahydropyrimidine-2-one analogues was selected for the present studies. The values of the Wiener's index, Zagreb group parameter and eccentric connectivity index for each of the 80 compounds comprising the dataset were computed using an in-house computer program. The dataset was divided randomly into training and test sets. Resultant data was analyzed and suitable models were developed after identifying the active ranges in the training set. Subsequently, a biological activity was assigned to each of the compound involved in the test set using these models, which was then compared with the reported HIV-protease inhibitory activity. Accuracy of prediction using these models was found to vary from a minimum of approximately 86% to a maximum of approximately 88%.
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Affiliation(s)
- Viney Lather
- Faculty of Pharmaceutical Sciences, M. D. University, Rohtak-124001, India
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22
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Enders D, Wortmann L, Raabe G, Dücker B. A Highly Flexible Route to 1,2,3,4,5,6- Hexahydro-5-hydroxypyrimidin-2-ones as Potential HIV Protease Inhibitors. HETEROCYCLES 2004. [DOI: 10.3987/com-03-s(p)51] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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23
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Lloyd DG, Buenemann CL, Todorov NP, Manallack DT, Dean PM. Scaffold Hopping in De Novo Design. Ligand Generation in the Absence of Receptor Information. J Med Chem 2004; 47:493-6. [PMID: 14736231 DOI: 10.1021/jm034222u] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report here the de novo generation of chemotypes and scaffolds for the estrogen receptor, without use of the receptor structure in the assembly phase. Through use of ligand superpositions or a single bound conformation of a known active, a pseudoreceptor can be generated as a design envelope, within which novel structures are readily assembled. Many of these structures have high similarity to known chemotypes. Scaffold hopping is readily achieved within this pseudoreceptor, indicating the advantages of such an approach in discovery research.
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Affiliation(s)
- David G Lloyd
- De Novo Pharmaceuticals, Compass House, Vision Park Histon, Cambridge, CB4 9ZR, UK.
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24
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Salim SS, Bellingham RK, Satcharoen V, Brown RCD. Synthesis of heterocyclic and carbocyclic fluoro-olefins by ring-closing metathesis. Org Lett 2003; 5:3403-6. [PMID: 12967285 DOI: 10.1021/ol035065w] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
[reaction: see text] Ring-closing metathesis (RCM) of vinyl fluoride-containing dienes in the presence of ruthenium alkylidene carbene complex 11 proceeded efficiently to give six- and seven-membered cyclic vinyl fluorides. The RCM reaction was used to prepare amine- and sulfamide-linked cyclo-olefins, as well as carbocyclic systems, from a simple commercial fluoro-olefin.
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Affiliation(s)
- Sofia S Salim
- Department of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, U.K
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25
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Mak CC, Brik A, Lerner DL, Elder JH, Morris GM, Olson AJ, Wong CH. Design and synthesis of broad-based mono- and bi- cyclic inhibitors of FIV and HIV proteases. Bioorg Med Chem 2003; 11:2025-40. [PMID: 12670654 DOI: 10.1016/s0968-0896(03)00054-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Based on the substrate transition state and our strategy to tackle the problem of drug resistance, a series of HIV/FIV protease (HIV /FIV PR) monocyclic inhibitors incorporating a 15- or 17-membered macrocycle with an equivalent P3 or P3' group and a unique unnatural amino acid, (2R, 3S)-3-amino-2-hydroxy-4-phenylbutyric acid, have been designed and synthesized. In addition, based on the structure of TL3 with small P3/P3' group, we have synthesized two conformationally restricted bicyclic inhibitors containing the macrocycle, which mimic the P1/P1'-P3/P3' tripeptide [Phe-Val-Ala] of TL3. We have found that the contribution of the macrocycle in our monocyclic inhibitors is important to the overall activity, but the ring size does not affect the activity to a significant extent. Several inhibitors that were developed in this work, exhibit low nanomolar inhibitory activity against the wild-type HIV/FIV PR and found to be highly effective against some drug-resistant as well as TL3-resistant mutants of HIV PRs. Compound 15, in particular, is the most effective cyclic inhibitor in hand to inhibit FIV replication in tissue culture at a concentration of 1.0 micro g/mL (1.2 microM).
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Affiliation(s)
- Chi Ching Mak
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550North Torrey Pines Road, La Jolla, CA 92037, USA.
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26
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Hillisch A, Hilgenfeld R. The role of protein 3D-structures in the drug discovery process. EXS 2003:157-81. [PMID: 12613176 DOI: 10.1007/978-3-0348-7997-2_8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
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27
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Enders D, Wortmann L. Asymmetric Synthesis of 4,6-Disubstituted 1,2,3,4,5,6-Hexahydro-5-hydroxypyrimidin-2-ones as Potential HIV-Protease-Inhibitors. HETEROCYCLES 2002. [DOI: 10.3987/com-02-s(m)20] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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28
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Tomasselli AG, Heinrikson RL. Targeting the HIV-protease in AIDS therapy: a current clinical perspective. BIOCHIMICA ET BIOPHYSICA ACTA 2000; 1477:189-214. [PMID: 10708858 DOI: 10.1016/s0167-4838(99)00273-3] [Citation(s) in RCA: 84] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This review deals with clinical applications of compounds that inhibit the action of the protease encoded within the genome of human immunodeficiency virus (HIV). The HIV-protease is essential for viral maturation and represents an important therapeutic target in the fight against AIDS. Following a brief overview of the enzyme structure and function, the article focuses on a number of peptide and non-peptide based HIV-protease inhibitors that are in current clinical use. These drugs are discussed both with respect to their efficacy in treatment of AIDS, and to problems related to insurgence of viral resistance and side effects seen to date in patient populations.
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Affiliation(s)
- A G Tomasselli
- Department of Protein Science, Pharmacia and Upjohn, Kalamazoo, MI 49001, USA
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Alterman M, Andersson HO, Garg N, Ahlsén G, Lövgren S, Classon B, Danielson UH, Kvarnström I, Vrang L, Unge T, Samuelsson B, Hallberg A. Design and fast synthesis of C-terminal duplicated potent C(2)-symmetric P1/P1'-modified HIV-1 protease inhibitors. J Med Chem 1999; 42:3835-44. [PMID: 10508432 DOI: 10.1021/jm9910371] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An analysis of the X-ray structure of a complex of HIV-1 protease with a linear C(2)-symmetric C-terminal duplicated inhibitor guided the selection of a series of diverse target compounds. These were synthesized with the objective to identify suitable P1/P1' substituents to provide inhibitors with improved antiviral activity. Groups with various physical properties were attached to the para-positions of the P1/P1' benzyloxy groups in the parent inhibitor. A p-bromobenzyloxy compound, prepared in only three steps from commercially available starting materials, was utilized as a common precursor in all reactions. The subsequent coupling reactions were completed within a few minutes and relied on palladium catalysis and flash heating with microwave irradiation. All of the compounds synthesized exhibited good inhibitory potency in the protease assay, with K(i) values ranging from 0.09 to 3.8 nM. A 30-fold improvement of the antiviral effect in cell culture, compared to the parent compound, was achieved with four of the inhibitors. The differences in K(i) values were not correlated to the differences in antiviral effect, efficiency against mutant virus, or reduced potency in the presence of human serum. The poorest enzyme inhibitors in fact belong to the group with the best antiviral effect. The binding features of two structurally related inhibitors, cocrystallized with HIV-1 protease, are discussed with special emphasis on the interaction at the enzyme/water phase.
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Affiliation(s)
- M Alterman
- Department of Organic Pharmaceutical Chemistry, Uppsala University, BMC, Box 574, SE-751 23 Uppsala, Sweden
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30
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Local Electron Densities and Functional Groups in Quantum Chemistry. Top Curr Chem (Cham) 1999. [DOI: 10.1007/3-540-48972-x_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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31
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A convergent, stereocontrolled synthesis of C2-symmetrical and pseudosymmetrical sulfur-tethered bis(amino alcohols). Tetrahedron Lett 1999. [DOI: 10.1016/s0040-4039(99)00568-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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32
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Lee T, Le VD, Lim D, Lin YC, Morris GM, Wong AL, Olson AJ, Elder JH, Wong CH. Development of a New Type of Protease Inhibitors, Efficacious against FIV and HIV Variants. J Am Chem Soc 1999. [DOI: 10.1021/ja982893p] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Taekyu Lee
- Contribution from the Department of Chemistry and the Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Van-Duc Le
- Contribution from the Department of Chemistry and the Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Dongyeol Lim
- Contribution from the Department of Chemistry and the Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Ying-Chuan Lin
- Contribution from the Department of Chemistry and the Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Garrett M. Morris
- Contribution from the Department of Chemistry and the Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Andrew L. Wong
- Contribution from the Department of Chemistry and the Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Arthur J. Olson
- Contribution from the Department of Chemistry and the Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - John H. Elder
- Contribution from the Department of Chemistry and the Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
| | - Chi-Huey Wong
- Contribution from the Department of Chemistry and the Skaggs Institute for Chemical Biology and the Department of Molecular Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037
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33
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Topology and the quantum chemical shape concept. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1873-9776(98)80010-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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34
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Ala PJ, Huston EE, Klabe RM, Jadhav PK, Lam PY, Chang CH. Counteracting HIV-1 protease drug resistance: structural analysis of mutant proteases complexed with XV638 and SD146, cyclic urea amides with broad specificities. Biochemistry 1998; 37:15042-9. [PMID: 9790666 DOI: 10.1021/bi980386e] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The long-term therapeutic benefit of HIV antiretroviral therapy is still threatened by drug-resistant variants. Mutations in the S1 subsite of the protease are the primary cause for the loss of sensitivity toward many HIV protease inhibitors, including our first-generation cyclic urea-based inhibitors DMP323 and DMP450. We now report the structures of the three active-site mutant proteases V82F, I84V, and V82F/I84V in complex with XV638 and SD146, two P2 analogues of DMP323 that are 8-fold more potent against the wild type and are able to inhibit a broad panel of drug-resistant variants [Jadhav, P. K., et al. (1997) J. Med. Chem. 40, 181-191]. The increased efficacy of XV638 and SD146 is due primarily to an increase in P2-S2 interactions: 30-40% more van der Waals contacts and two to four additional hydrogen bonds. Furthermore, because these new interactions do not perturb other subsites in the protease, it appears that the large complementary surface areas of their P2 substituents compensate for the loss of P1-S1 interactions and reduce the probability of selecting for drug-resistant variants.
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Affiliation(s)
- P J Ala
- Experimental Station, DuPont Pharmaceuticals, Wilmington, Delaware 19880, USA
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35
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De Lucca GV, Jadhav PK, Waltermire RE, Aungst BJ, Erickson-Viitanen S, Lam PY. De novo design and discovery of cyclic HIV protease inhibitors capable of displacing the active-site structural water molecule. PHARMACEUTICAL BIOTECHNOLOGY 1998; 11:257-84. [PMID: 9760684 DOI: 10.1007/0-306-47384-4_12] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Affiliation(s)
- G V De Lucca
- DuPont Merck Pharmaceutical Company, Wilmington, Delaware 19880-0500, USA
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36
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Rodgers JD, Lam PY, Johnson BL, Wang H, Li R, Ru Y, Ko SS, Seitz SP, Trainor GL, Anderson PS, Klabe RM, Bacheler LT, Cordova B, Garber S, Reid C, Wright MR, Chang CH, Erickson-Viitanen S. Design and selection of DMP 850 and DMP 851: the next generation of cyclic urea HIV protease inhibitors. CHEMISTRY & BIOLOGY 1998; 5:597-608. [PMID: 9818151 DOI: 10.1016/s1074-5521(98)90117-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
BACKGROUND Recent clinical trials have demonstrated that HIV protease inhibitors are useful in the treatment of AIDS. It is necessary, however, to use HIV protease inhibitors in combination with other antiviral agents to inhibit the development of resistance. The daunting ability of the virus to rapidly generate resistant mutants suggests that there is an ongoing need for new HIV protease inhibitors with superior pharmacokinetic and efficacy profiles. In our attempts to design and select improved cyclic urea HIV protease inhibitors, we have simultaneously optimized potency, resistance profile, protein binding and oral bioavailability. RESULTS We have discovered that nonsymmetrical cyclic ureas containing a 3-aminoindazole P2 group are potent inhibitors of HIV protease with excellent oral bioavailability. Furthermore, the 3-aminoindazole group forms four hydrogen bonds with the enzyme and imparts a good resistance profile. The nonsymmetrical 3-aminoindazoles DMP 850 and DMP 851 were selected as our next generation of cyclic urea HIV protease inhibitors because they achieve 8 h trough blood levels in dog, with a 10 mg/kg dose, at or above the protein-binding-adjusted IC90 value for the worst single mutant--that containing the Ile84-->Val mutation. CONCLUSIONS In selecting our next generation of cyclic urea HIV protease inhibitors, we established a rigorous set of criteria designed to maximize chances for a sustained antiviral effect in HIV-infected individuals. As DMP 850 and DMP 851 provide plasma levels of free drug that are sufficient to inhibit wild-type HIV and several mutant forms of HIV, they could show improved ability to decrease viral load for clinically significant time periods. The ultimate success of DMP 850 and DMP 851 in clinical trials might depend on achieving or exceeding the oral bioavailability seen in dog.
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Affiliation(s)
- J D Rodgers
- DuPont Merck Pharmaceutical Company, Wilmington, DE 19880-0500, USA.
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37
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Abstract
Major discoveries have been made of new type-I and type-III peptidomimetic inhibitors of peptide-derived systems. Innovative reversible inhibitors of cysteine proteases and renin, and additional examples of peptidomimetic inhibitors of interleukin-1 beta-converting enzyme, neutral endopeptidase, herpes simplex virus protease, thrombin, HIV protease, Ras farnesyltransferase, the RGD motif, Factor Xa and various aspartic proteases have been discovered.
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Affiliation(s)
- A S Ripka
- Department of Chemistry and School of Pharmacy, University of Wisconsin-Madison 53706, USA
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38
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Han Q, Chang CH, Li R, Ru Y, Jadhav PK, Lam PY. Cyclic HIV protease inhibitors: design and synthesis of orally bioavailable, pyrazole P2/P2' cyclic ureas with improved potency. J Med Chem 1998; 41:2019-28. [PMID: 9622543 DOI: 10.1021/jm9704199] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Highly potent HIV-1 protease (HIVPR) inhibitors have been designed and synthesized by introducing bidentate hydrogen-bonding oxime and pyrazole groups at the meta-position of the phenyl ring on the P2/P2' substituents of cyclic ureas. Nonsymmetrical cyclic ureas incorporating 3(1H)-pyrazolylbenzyl as P2 and hydrophilic functionalities as P2' show potent protease inhibition and antiviral activities against HIV and have good oral bioavailabilities. The X-ray structure of HIVPR.10A complex confirms that the two pyrazole rings of 10A form bidentate hydrogen bonds with the side-chain oxygen (C=O) and backbone nitrogen (N-H) of Asp30/30' of HIVPR.
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Affiliation(s)
- Q Han
- Chemical and Physical Sciences, The DuPont Merck Pharmaceutical Company, Experimental Station, P.O. Box 80500, Wilmington, Delaware 19880-0500, USA
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39
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Ala PJ, DeLoskey RJ, Huston EE, Jadhav PK, Lam PY, Eyermann CJ, Hodge CN, Schadt MC, Lewandowski FA, Weber PC, McCabe DD, Duke JL, Chang CH. Molecular recognition of cyclic urea HIV-1 protease inhibitors. J Biol Chem 1998; 273:12325-31. [PMID: 9575185 DOI: 10.1074/jbc.273.20.12325] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
As long as the threat of human immunodeficiency virus (HIV) protease drug resistance still exists, there will be a need for more potent antiretroviral agents. We have therefore determined the crystal structures of HIV-1 protease in complex with six cyclic urea inhibitors: XK216, XK263, DMP323, DMP450, XV638, and SD146, in an attempt to identify 1) the key interactions responsible for their high potency and 2) new interactions that might improve their therapeutic benefit. The structures reveal that the preorganized, C2 symmetric scaffolds of the inhibitors are anchored in the active site of the protease by six hydrogen bonds and that their P1 and P2 substituents participate in extensive van der Waals interactions and hydrogen bonds. Because all of our inhibitors possess benzyl groups at P1 and P1', their relative binding affinities are modulated by the extent of their P2 interactions, e.g. XK216, the least potent inhibitor (Ki (inhibition constant) = 4.70 nM), possesses the smallest P2 and the lowest number of P2-S2 interactions; whereas SD146, the most potent inhibitor (Ki = 0.02 nM), contains a benzimidazolylbenzamide at P2 and participates in fourteen hydrogen bonds and approximately 200 van der Waals interactions. This analysis identifies the strongest interactions between the protease and the inhibitors, suggests ways to improve potency by building into the S2 subsite, and reveals how conformational changes and unique features of the viral protease increase the binding affinity of HIV protease inhibitors.
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Affiliation(s)
- P J Ala
- DuPont Merck Pharmaceutical Company, Experimental Station, Wilmington, Delaware 19880, USA
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40
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Rodgers JD, Johnson BL, Wang H, Erickson-Viitanen S, Klabe RM, Bacheler L, Cordova BC, Chang CH. Potent cyclic urea HIV protease inhibitors with 3-aminoindazole P2/P2' groups. Bioorg Med Chem Lett 1998; 8:715-20. [PMID: 9871528 DOI: 10.1016/s0960-894x(98)00118-8] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Cyclic ureas containing 3-aminoindazole P2/P2' groups are extremely potent inhibitors of HIV protease. The parent 3-aminoindazole 6 showed a Ki < 0.01 nM but poor translation of enzyme activity to antiviral activity was observed. A series of 3-alkylaminoindazoles revealed that translation improved with increasing lipophilicity. An X-ray crystal structure of 6 bound to HIV protease was obtained.
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Affiliation(s)
- J D Rodgers
- DuPont Merck Pharmaceutical Company, Wilmington, Delaware 19880-0500, USA
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41
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Lee T, Laco GS, Torbett BE, Fox HS, Lerner DL, Elder JH, Wong CH. Analysis of the S3 and S3' subsite specificities of feline immunodeficiency virus (FIV) protease: development of a broad-based protease inhibitor efficacious against FIV, SIV, and HIV in vitro and ex vivo. Proc Natl Acad Sci U S A 1998; 95:939-44. [PMID: 9448264 PMCID: PMC18632 DOI: 10.1073/pnas.95.3.939] [Citation(s) in RCA: 69] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The S3 and S3' subsite binding specificities of HIV and feline immunodeficiency virus proteases (FIV) proteases (PRs) have been explored by using C2-symmetric competitive inhibitors. The inhibitors evaluated contained (1S, 2R, 3R, 4S)-1,4-diamino-1, 4-dibenzyl-2,3-diol as P1 and P1' units, Val as P2 and P2' residues, and a variety of amino acids at the P3 and P3' positions. All inhibitors showed very high potency against HIV PR in vitro, and their Ki values ranged between 1.1 and 2.6 nM. In contrast to the low restriction of P3 and P3' residues observed in HIV PR, FIV PR exhibited strong preference for small hydrophobic groups at the S3 and S3' subsites. Within this series, the most effective inhibitor against FIV PR contained Ala at P3 and P3'. Its Ki of 41 nM was 415- and 170-fold lower than those of the inhibitors without the P3 and P3' moieties or with the Phe at these positions, respectively. In addition, these compounds were tested against mutant FIV PRs, which contain amino acid substitutions corresponding to those in native HIV PR at homologous sites, and their efficacy of inhibition progressively increased up to 5-fold. The most potent FIV PR inhibitor was selected for examination of its effectiveness in tissue culture, and it was able to block nearly 100% of virus production in an acute infection at 1 microg/ml (1.1 microM) against HIV, FIV, and simian immunodeficiency virus. Furthermore, it was not toxic to cells, and even after 2 months of culture there was no sign of resistance development by virus. The findings suggest that inhibitors with small P3 residue may be efficacious against a broad range of HIV variants as well as interspecies PRs.
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Affiliation(s)
- T Lee
- Department of Chemistry and the Skaggs Institute for Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
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42
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Mezey PG. A crystallographic structure refinement approach using ab initio quality additive, fuzzy density fragments. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s1087-3295(98)80006-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
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