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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: 12] [Impact Index Per Article: 4.0] [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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Sajadi MS, Darehkordi A, Hosseini SMS. Synthesis of N-aryl-3H-indazol-3-imine and N-aryl-1H-indazol-3-amine via Na2WO4/H2O2 mediated by intramolecular N–N coupling. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Turpin JA. The next generation of HIV/AIDS drugs: novel and developmental antiHIV drugs and targets. Expert Rev Anti Infect Ther 2014; 1:97-128. [PMID: 15482105 DOI: 10.1586/14787210.1.1.97] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
There are presently 42 million people worldwide living with HIV/AIDS, the majority of which have limited access to antiretrovirals. Even if worldwide penetration was possible, our current chemotherapeutic strategies still suffer from issues of cost, patient compliance, deleterious acute and chronic side effects, emerging single and multidrug resistance, and generalized treatment and economic issues. Even our best antiretroviral therapeutic strategy, highly active antiretroviral therapy (HAART), falls short of completely suppressing HIV replication. Therefore, expansion of current therapeutic options by discovering new antiretrovirals and targets will be critical in the coming years. This review addresses the current status of reverse transcriptase and protease inhibitor development, and summarizes the progress in emerging classes of HIV inhibitors, including entry (T-20, T-1249), coreceptor (SCH-C, SCH-D), integrase (beta-Diketos) and p7 nucleocapsid Zn finger inhibitors (thioesters and PATEs). In addition, the processes of virus entry, PIC transport to the nucleus, HIV interaction with nuclear pores, Tat function, Rev function and virus budding (Tsg101 and ubiquitination) are examined, and proof of concept inhibitors and potential antiviral targets discussed.
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Affiliation(s)
- Jim A Turpin
- HowPin Consulting International, PO Box B Frederick, MD 21705, USA.
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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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Lefebvre V, Cailly T, Fabis F, Rault S. Two-Step Synthesis of Substituted 3-Aminoindazoles from 2-Bromobenzonitriles. J Org Chem 2010; 75:2730-2. [DOI: 10.1021/jo100243c] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Valerie Lefebvre
- Centre d’Etudes et de Recherche sur le Médicament de Normandie, UPRES EA 4258, INC3M FR-CNRS 3038, UFR des Sciences Pharmaceutiques, Université de Caen Basse-Normandie, boulevard Becquerel 14032 Caen Cedex, France
| | - Thomas Cailly
- Centre d’Etudes et de Recherche sur le Médicament de Normandie, UPRES EA 4258, INC3M FR-CNRS 3038, UFR des Sciences Pharmaceutiques, Université de Caen Basse-Normandie, boulevard Becquerel 14032 Caen Cedex, France
| | - Frederic Fabis
- Centre d’Etudes et de Recherche sur le Médicament de Normandie, UPRES EA 4258, INC3M FR-CNRS 3038, UFR des Sciences Pharmaceutiques, Université de Caen Basse-Normandie, boulevard Becquerel 14032 Caen Cedex, France
| | - Sylvain Rault
- Centre d’Etudes et de Recherche sur le Médicament de Normandie, UPRES EA 4258, INC3M FR-CNRS 3038, UFR des Sciences Pharmaceutiques, Université de Caen Basse-Normandie, boulevard Becquerel 14032 Caen Cedex, France
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Harper S, Ferrara M, Crescenzi B, Pompei M, Palumbi MC, DiMuzio JM, Donghi M, Fiore F, Koch U, Liverton NJ, Pesci S, Petrocchi A, Rowley M, Summa V, Gardelli C. Inhibitors of the Hepatitis C Virus NS3 Protease with Basic Amine Functionality at the P3-Amino Acid N-Terminus: Discovery and Optimization of a New Series of P2−P4 Macrocycles. J Med Chem 2009; 52:4820-37. [DOI: 10.1021/jm900372w] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Steven Harper
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy
| | - Marco Ferrara
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy
| | - Benedetta Crescenzi
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy
| | - Marco Pompei
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy
| | - Maria Cecilia Palumbi
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy
| | - Jillian M. DiMuzio
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy
| | - Monica Donghi
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy
| | - Fabrizio Fiore
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy
| | - Uwe Koch
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy
| | - Nigel J. Liverton
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy
| | - Silvia Pesci
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy
| | - Alessia Petrocchi
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy
| | - Michael Rowley
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy
| | - Vincenzo Summa
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy
| | - Cristina Gardelli
- IRBM (Merck Research Laboratories Rome), Via Pontina km 30,600, 00040 Pomezia, Rome, Italy
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Takkis K, Sild S. QSAR Modeling of HIV-1 Protease Inhibition on Six- and Seven-membered Cyclic Ureas. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200860006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Fernández M, Caballero J. Modeling of activity of cyclic urea HIV-1 protease inhibitors using regularized-artificial neural networks. Bioorg Med Chem 2006; 14:280-94. [PMID: 16202604 DOI: 10.1016/j.bmc.2005.08.022] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2005] [Revised: 08/04/2005] [Accepted: 08/05/2005] [Indexed: 11/26/2022]
Abstract
Artificial neural networks (ANNs) were used to model both inhibition of HIV-1 protease (K(i)) and inhibition of HIV replication (IC90) for 55 cyclic urea derivatives using constitutional and 2D descriptors. As a preliminary step, linear dependences were established by multiple linear regression (MLR) approaches, selecting the relevant descriptors by genetic algorithm (GA) feature selection. For ANN models non-linear GA feature selection was also applied. Non-linear modeling of K(i) overcame the results of the linear one using four properties, keeping in mind standard Pearson R correlation coefficients (0.931 vs. 0.862) and leave one out (LOO) cross-validation analysis (Q(LOO)2 = 0.703 vs. 0.510). On the other hand, IC90 modeling was insoluble by a linear approach: no predictive model was achieved; however, a non-linear relation was encountered according to statistic results (R = 0.891; Q(LOO)2 = 0.568). The best non-linear models suggested the influence of the presence of nitrogen atoms and the molecular volume distribution in the inhibitor structures on the HIV-1 protease inhibition as well as that the inhibition of HIV replication was dependent on the occurrence of five-member rings. Finally, inhibitors were well distributed regarding its activity levels in a Kohonen self-organizing map built using the input variables of the best non-linear models.
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Affiliation(s)
- Michael Fernández
- Molecular Modeling Group, Center for Biotechnological Studies, University of Matanzas, Matanzas, Cuba
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Frecer V, Burello E, Miertus S. Combinatorial design of nonsymmetrical cyclic urea inhibitors of aspartic protease of HIV-1. Bioorg Med Chem 2005; 13:5492-501. [PMID: 16054372 DOI: 10.1016/j.bmc.2005.06.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The aspartic protease (PR) of the human immunodeficiency virus type 1 (HIV-1) is an important target for the design of specific antiviral agents dedicated to treatment of HIV-1 infection. We have employed computer-assisted combinatorial chemistry methods to design a small focused virtual library of nonsymmetrically substituted cyclic urea inhibitors of the PR. Nonsymmetrical compounds with decreased peptidic character were namely found to inhibit the PR with comparable inhibition potencies as their C2-pseudosymmetric counterparts and to possess superior pharmacokinetic properties. To generate the virtual library of fully nonsymmetrical cyclic urea analogs, diverse reagents were selected from databases of available chemicals with characteristics similar to those of the building blocks of known potent PR inhibitors. The X-ray structure of the protease-inhibitor complex PR-XV-638 was used as the receptor model in the structure-based focusing and in silico screening of the virtual library. A target-specific LUDI-type scoring function, parameterized for a QSAR training set of known cyclic urea inhibitors and validated on a set of compounds not included into the training set, was used to predict the inhibition constants (Ki) of the generated analogs toward the HIV-1 PR. The fragments most frequently occurring in the analogs with the highest predicted inhibition potencies (Ki*<10 pM) were then selected to constitute a highly focused library subset containing novel nonsymmetrical cyclic ureas with predicted Ki*s 1 order of magnitude lower than the most potent known cyclic urea inhibitors. ADME properties calculated for the most promising analogs suggested that the cyclic ureas are endowed with a wide range of favorable pharmacokinetic properties, which may favor the discovery of a potent orally administrable antiviral drug.
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Affiliation(s)
- Vladimír Frecer
- International Centre for Science and High Technology, UNIDO, AREA Science Park, Padriciano 99, I-34012 Trieste, Italy
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12
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Harper S, Avolio S, Pacini B, Di Filippo M, Altamura S, Tomei L, Paonessa G, Di Marco S, Carfi A, Giuliano C, Padron J, Bonelli F, Migliaccio G, De Francesco R, Laufer R, Rowley M, Narjes F. Potent Inhibitors of Subgenomic Hepatitis C Virus RNA Replication through Optimization of Indole-N-Acetamide Allosteric Inhibitors of the Viral NS5B Polymerase. J Med Chem 2005; 48:4547-57. [PMID: 15999993 DOI: 10.1021/jm050056+] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Infections caused by hepatitis C virus (HCV) are a significant world health problem for which novel therapies are in urgent demand. Compounds that block replication of subgenomic HCV RNA in liver cells are of interest because of their demonstrated antiviral effect in the clinic. In followup to our recent report that indole-N-acetamides (e.g., 1) are potent allosteric inhibitors of the HCV NS5B polymerase enzyme, we describe here their optimization as cell-based inhibitors. The crystal structure of 1 bound to NS5B was a guide in the design of a two-dimensional compound array that highlighted that formally zwitterionic inhibitors have strong intracellular potency and that pregnane X receptor (PXR) activation (an undesired off-target activity) is linked to a structural feature of the inhibitor. Optimized analogues devoid of PXR activation (e.g., 55, EC(50) = 127 nM) retain strong cell-based efficacy under high serum conditions and show acceptable pharmacokinetics parameters in rat and dog.
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Affiliation(s)
- Steven Harper
- IRBM (Merck Research Laboratories, Rome), Pomezia, Italy.
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Affiliation(s)
- Wendy A Loughlin
- School of Science, Nathan Campus, Griffith University, Brisbane, QLD 4111, Australia.
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Parish CA, Yarger M, Sinclair K, Dure M, Goldberg A. Comparing the conformational behavior of a series of diastereomeric cyclic urea HIV-1 inhibitors using the low mode:monte carlo conformational search method. J Med Chem 2004; 47:4838-50. [PMID: 15369387 DOI: 10.1021/jm049716l] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The conformational flexibility of a series of diastereomeric cyclic urea HIV-1 protease inhibitors has been examined using the Low Mode:Monte Carlo conformational search method. Force fields were validated by a comparison of the energetic ordering of the minimum energy structures on the AMBER/GBSA(water), OPLSAA/GBSA(water) and HF/6-311G/SCRF(water) surfaces. The energetic ordering of the minima on the OPLSAA /GBSA(water) surface was in better agreement with the quantum calculations than the ordering on the AMBER/GBSA(water) surface. An ensemble of low energy structures was generated using OPLSAA/GBSA(water) and used to compare the molecular shape and flexibility of each diastereomer to the experimentally determined binding affinities and crystal structures of closely related systems. The results indicate that diastereomeric solution-phase energetic stability, conformational rigidity and ability to adopt a chair conformation correlate strongly with experimental binding affinities. Rigid body docking suggests that all of the diastereomers adopt solution-phase conformations suitable for alignment with the HIV-1 protease; however, these results indicate that the binding affinities are dependent upon subtle differences in the P1/P1' and P2/P2' substituent orientations.
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Affiliation(s)
- Carol A Parish
- Department of Chemistry, Hobart and William Smith Colleges, Geneva, New York 14456, USA.
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Kaltenbach RF, Patel M, Waltermire RE, Harris GD, Stone BRP, Klabe RM, Garber S, Bacheler LT, Cordova BC, Logue K, Wright MR, Erickson-Viitanen S, Trainor GL. Synthesis, antiviral activity and pharmacokinetics of P1/P1' substituted 3-aminoindazole cyclic urea HIV protease inhibitors. Bioorg Med Chem Lett 2003; 13:605-8. [PMID: 12639540 DOI: 10.1016/s0960-894x(02)01064-8] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A series of P1/P1' substituted cyclic urea analogues were prepared in an attempt to increase the intra-cellular antiviral potency of the nonsymmetrical 3-aminoindazoles DMP 850 and DMP 851. The effect of alkyl substitution of the P1/P1' residues on cellular antiviral potency, protein binding, resistance profile and pharmacokinetics are described.
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Affiliation(s)
- Robert F Kaltenbach
- Bristol-Myers Squibb Company, Experimental Station, Wilmington, DE 19880, USA.
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Ahlsén G, Hultén J, Shuman CF, Poliakov A, Lindgren MT, Alterman M, Samuelsson B, Hallberg A, Danielson UH. Resistance profiles of cyclic and linear inhibitors of HIV-1 protease. Antivir Chem Chemother 2002; 13:27-37. [PMID: 12180647 DOI: 10.1177/095632020201300103] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Resistance to anti-HIV protease drugs is a major problem in the design of AIDS drugs with long-term efficacy. To identify structural features associated with a certain resistance profile, the inhibitory properties of a series of symmetric and asymmetric cyclic sulfamide, cyclic urea and linear transition-state analogue inhibitors of HIV-1 protease were investigated using wild-type and mutant enzyme. To allow a detailed structure-inhibition analysis, enzyme with single, double, triple and quadruple combinations of G48V, V82A, 184V and L90M substitutions was used. Kinetic analysis of the mutants revealed that catalytic efficiency was 1-30% of that for the wild-type enzyme, a consequence of reduced kcat in all cases and an increased KM for all mutants except for the G48V enzyme. The overall structure-inhibitory profiles of the cyclic compounds were similar, and the inhibition of the V82A, 184V and G48V/L90M mutants were less efficient than of the wild-type enzyme. The greatest increase in Ki was generally observed for the 184V mutant and least for the G48V/L90M mutant, and additional combinations of mutations did not result in improved inhibition profiles for the cyclic compounds. An extended analysis of additional mutants, and including a set of linear compounds, showed that the profile was unique for each compound, and did not reveal any general structural features associated with a certain inhibition profile. The effects of structural modifications in the inhibitors, or of mutations, were not additive and they differed depending on their context. The results demonstrate the difficulties in predicting resistance, even for closely related compounds, and designing compounds with improved resistance profiles.
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Affiliation(s)
- G Ahlsén
- Department of Biochemistry, Uppsala University, Sweden
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Huff JR, Kahn J. Discovery and clinical development of HIV-1 protease inhibitors. ADVANCES IN PROTEIN CHEMISTRY 2001; 56:213-51. [PMID: 11329855 DOI: 10.1016/s0065-3233(01)56007-6] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
- J R Huff
- Department of Medicinal Chemistry, Merck Research Laboratories, West Point, Pennsylvania 19486, USA
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Abstract
The design of new HIV protease inhibitors requires an improved understanding of the physical basis of inhibitor/protein binding. Here, the binding affinities of seven aliphatic cyclic ureas to HIV-1 protease are calculated using a predominant states method and an implicit solvent model based upon finite difference solutions of the Poisson-Boltzmann equation. The calculations are able to reproduce the observed U-shaped trend of binding free energy as a function of aliphatic chain length. Interestingly, the decrease in affinity for the longest chains is attributable primarily to the energy cost of partly desolvating charged aspartic and arginine groups at the mouths of the active site. Even aliphatic chains too short to contact these charged groups directly are subject to considerable desolvation penalties. We are not aware of other systems where binding affinity trends have been attributed to long-ranged electrostatic desolvation of ionized groups. A generalized Born/surface area solvation model yields a much smaller change in desolvation energy with chain length and, therefore, does not reproduce the experimental binding affinity trends. This result suggests that the generalized Born model should be used with caution for complex, partly desolvated systems like protein binding sites. We also find that changing the assumed protonation state of the active site aspartyl dyad significantly affects the computed binding affinity trends. The protonation state of the aspartyl dyad in the presence of cyclic ureas is discussed in light of the observation that the monoprotonated state reproduces the experimental results best.
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Affiliation(s)
- K L Mardis
- Center for Advanced Research in Biotechnology, 9600 Gudelsky Drive, Rockville, MD 20850, USA
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Dorsey BD, McDonough C, McDaniel SL, Levin RB, Newton CL, Hoffman JM, Darke PL, Zugay-Murphy JA, Emini EA, Schleif WA, Olsen DB, Stahlhut MW, Rutkowski CA, Kuo LC, Lin JH, Chen IW, Michelson SR, Holloway MK, Huff JR, Vacca JP. Identification of MK-944a: a second clinical candidate from the hydroxylaminepentanamide isostere series of HIV protease inhibitors. J Med Chem 2000; 43:3386-99. [PMID: 10978186 DOI: 10.1021/jm9903848] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Recent results from human clinical trials have established the critical role of HIV protease inhibitors in the treatment of acquired immune-deficiency syndrome (AIDS). However, the emergence of viral resistance, demanding treatment protocols, and adverse side effects have exposed the urgent need for a second generation of HIV protease inhibitors. The continued exploration of our hydroxylaminepentanamide (HAPA) transition-state isostere series of HIV protease inhibitors, which initially resulted in the identification of Crixivan (indinavir sulfate, MK-639, L-735,524), has now yielded MK-944a (L-756,423). This compound is potent, is selective, and competitively inhibits HIV-1 PR with a K(i) value of 0.049 nM. It stops the spread of the HIV(IIIb)-infected MT4 lymphoid cells at 25.0-50.0 nM, even in the presence of alpha(1) acid glycoprotein, human serum albumin, normal human serum, or fetal bovine serum. MK-944a has a longer half-life in several animal models (rats, dogs, and monkeys) than indinavir sulfate and is currently in advanced human clinical trials.
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Affiliation(s)
- B D Dorsey
- Departments of Medicinal Chemistry, Antiviral Research, Drug Metabolism, and Molecular Systems, Merck Research Laboratories, West Point, Pennsylvania 19486, USA.
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Cain GA. AN IMPROVED SYNTHESIS OF 3-CYANO-4-FLUOROBENZYL BROMIDE. ORG PREP PROCED INT 2000. [DOI: 10.1080/00304940009356752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Gary A. Cain
- a Chemical & Physical Sciences Department , DuPont Pharmaceuticals Company , E336/109 Experimental Station P.O. Box 80336, Wilmington , DE , 19880-0336 , USA
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Chapter 16. Recent developments in antiretroviral therapies. ANNUAL REPORTS IN MEDICINAL CHEMISTRY 2000. [DOI: 10.1016/s0065-7743(00)35017-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
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Patel M, Rodgers JD, McHugh RJ, Johnson BL, Cordova BC, Klabe RM, Bacheler LT, Erickson-Viitanen S, Ko SS. Unsymmetrical cyclic ureas as HIV-1 protease inhibitors: novel biaryl indazoles as P2/P2' substituents. Bioorg Med Chem Lett 1999; 9:3217-20. [PMID: 10576691 DOI: 10.1016/s0960-894x(99)00564-8] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The preparation of unsymmetrical cyclic ureas bearing novel biaryl indazoles as P2/P2' substituents was undertaken, utilizing a Suzuki coupling reaction as the key step. Compound 6i was equipotent to the lead compound of the series SE063.
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Affiliation(s)
- M Patel
- DuPont Pharmaceuticals Company, Experimental Station, Wilmington, DE 19880-0500, USA
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Takashiro E, Nakamura Y, Miyamoto S, Ozawa Y, Sugiyama A, Fujimoto K. Design and synthesis of a novel series of HIV-1 protease inhibitors. Bioorg Med Chem 1999; 7:2105-14. [PMID: 10530961 DOI: 10.1016/s0968-0896(99)00163-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The synthesis and the SAR study of novel pseudo symmetric inhibitors of HIV-1 protease are described. Michael addition of amino acid derivatives to vinyl ketones was utilized to derive a potent (nM) series of HIV-1 protease inhibitors.
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Affiliation(s)
- E Takashiro
- Exploratory Chemistry Research Laboratories, Sankyo Co. Ltd., Tokyo, Japan
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24
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Takashiro E, Hayakawa I, Nitta T, Kasuya A, Miyamoto S, Ozawa Y, Yagi R, Yamamoto I, Shibayama T, Nakagawa A, Yabe Y. Structure-activity relationship of HIV-1 protease inhibitors containing alpha-hydroxy-beta-amino acids. Detailed study of P1 site. Bioorg Med Chem 1999; 7:2063-72. [PMID: 10530956 DOI: 10.1016/s0968-0896(99)00127-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The structure-activity relationship of HIV-1 protease (HIV-1 PR) inhibitors containing alpha-hydroxy-beta-amino acids is discussed. We demonstrated that substituent groups on the P1 aromatic rings of the inhibitors exert significant influence on their biological activity. Inhibitors bearing an alkyl or a fluorine atom at the meta and para position on their P1 benzene ring were found to be good inhibitors. We also discovered that the substitution positions of the P2 benzamides were crucial for good antiviral potency. In this study, inhibitor 48 was the most potent [IC90 (CEM/HIV-1 IIIB) 27 nM] and showed good pharmacokinetics in rats.
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Affiliation(s)
- E Takashiro
- Exploratory Chemistry Research Laboratory, Sankyo Co. Ltd., Tokyo, Japan
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25
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Kaltenbach RF, Klabe RM, Cordova BC, Seitz SP. Increased antiviral activity of cyclic urea HIV protease inhibitors by modifying the P1/P1' substituents. Bioorg Med Chem Lett 1999; 9:2259-62. [PMID: 10465557 DOI: 10.1016/s0960-894x(99)00367-4] [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: 10/27/2022]
Abstract
A series of alkyl substituted P1/P1' analogs was prepared in an attempt to increase translation of the 3-aminoindazole class of HIV protease inhibitors. Increasing the lipophilicity of the P1/P1' residues dramatically improved translation of enzyme activity to antiviral activity in the whole cell assay.
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Affiliation(s)
- R F Kaltenbach
- DuPont Pharmaceuticals Company, Experimental Station, Wilmington, DE 19880-0500, USA
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26
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Abstract
[formula: see text] A series of simple heterocyclic HIV-1 protease inhibitors were developed on the basis of size, shape, and electronic complementarity to the active site of the enzyme. The C2-symmetric heterocycles do not contain a transition-state isostere nor are they active site directed irreversible inhibitors; thus, they represent the success of a new design strategy. The first generation heterocycles inhibit the protease in the micromolar range, whereas control compounds show no bioactivity at the same concentrations.
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Affiliation(s)
- P W Baures
- Department of Chemistry, Kansas State University, Manhattan 66506, USA.
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