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Huang M, Saragih M, Tambunan USF. In silico Antivirus Repurposing and its Modification to Organoselenium Compounds as SARS-CoV-2 Spike Inhibitors. Pak J Biol Sci 2023; 26:81-90. [PMID: 37265039 DOI: 10.3923/pjbs.2023.81.90] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
<b>Background and Objective:</b> The COVID-19, which has been circulating since late 2019, is caused by SARS-CoV-2. Because of its high infectivity, this virus has spread widely throughout the world. Spike glycoprotein is one of the proteins found in SARS-CoV-2. Spike glycoproteins directly affect infection by forming ACE-2 receptors on host cells. Inhibiting glycoprotein spikes could be one method of treating COVID-19. In this study, the antivirus marketed as a database will be repurposed into an antiviral SARS-CoV-2 and the selected compounds will be modified to become organoselenium compounds. <b>Materials and Methods:</b> The research was carried out using <i>in silico</i> methods, such as rigid docking and flexible docking. To obtain information about the interaction between spike glycoprotein and ligands, MOE 2014.09 was used to perform the molecular docking simulation. <b>Results:</b> The analysis of binding energy values was used to select the ten best ligands from the first stage of the molecular docking simulation, which was then modified according to the previous QSAR study to produce 96 new molecules. The second stage of molecular docking simulation was performed with modified molecules. The best-modified ligand was chosen by analyzing the ADME-Tox property, RMSD value and binding energy value. <b>Conclusion:</b> The best three unmodified ligands, Ombitasvir, Elbasvir and Ledipasvir, have a binding energy value of -15.8065, -15.3842 and -15.1255 kcal mol<sup>1</sup>, respectively and the best three modified ligands ModL1, ModL2 and ModL3 has a binding value of -15.6716, -13.9489 and -13.2951 kcal mol<sup>1</sup>, respectively with an RMSD value of 1.7109 Å, 2.3179 Å and 1.7836 Å.
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Al-Ansi AY, Lin Z. MDO: A Computational Protocol for Prediction of Flexible Enzyme-Ligand Binding Mode. Curr Comput Aided Drug Des 2022; 18:CAD-EPUB-125919. [PMID: 36043706 DOI: 10.2174/1573409918666220827151546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 06/15/2022] [Accepted: 07/05/2022] [Indexed: 11/22/2022]
Abstract
AIM Developing a method for use in computer aided drug design Background: Predicting the structure of enzyme-ligand binding mode is essential for understanding the properties, functions, and mechanisms of the bio-complex, but is rather difficult due to the enormous sampling space involved. OBJECTIVE Accurate prediction of enzyme-ligand binding mode conformation. METHOD A new computational protocol, MDO, is proposed for finding the structure of ligand binding pose. MDO consists of sampling enzyme sidechain conformations via molecular dynamics simulation of enzyme-ligand system and clustering of the enzyme configurations, sampling ligand binding poses via molecular docking and clustering of the ligand conformations, and the optimal ligand binding pose prediction via geometry optimization and ranking by the ONIOM method. MDO is tested on 15 enzyme-ligand complexes with known accurate structures. RESULTS The success rate of MDO predictions, with RMSD < 2 Å, is 67%, substantially higher than the 40% success rate of conventional methods. The MDO success rate can be increased to 83% if the ONIOM calculations are applied only for the starting poses with ligands inside the binding cavities. CONCLUSION The MDO protocol provides high quality enzyme-ligand binding mode prediction with reasonable computational cost. The MDO protocol is recommended for use in the structure-based drug design.
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Affiliation(s)
- Amar Y Al-Ansi
- Hefei National Laboratory for Physical Sciences at Microscale & CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Department of Physics, University of Science and Technology of China, Hefei 230026, China
- Department of Physics, Sana'a University, Sana'a, Yemen
| | - Zijing Lin
- Hefei National Laboratory for Physical Sciences at Microscale & CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Department of Physics, University of Science and Technology of China, Hefei 230026, China
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Improving Drug Sensitivity of HIV-1 Protease Inhibitors by Restriction of Cellular Efflux System in a Fission Yeast Model. Pathogens 2022; 11:pathogens11070804. [PMID: 35890048 PMCID: PMC9318301 DOI: 10.3390/pathogens11070804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 07/12/2022] [Accepted: 07/14/2022] [Indexed: 12/10/2022] Open
Abstract
Fission yeast can be used as a cell-based system for high-throughput drug screening. However, higher drug concentrations are often needed to achieve the same effect as in mammalian cells. Our goal here was to improve drug sensitivity so reduced drugs could be used. Three different methods affecting drug uptakes were tested using an FDA-approved HIV-1 protease inhibitor (PI) drug Darunavir (DRV). First, we tested whether spheroplasts without cell walls increase the drug sensitivity. Second, we examined whether electroporation could be used. Although small improvements were observed, neither of these two methods showed significant increase in the EC50 values of DRV compared with the traditional method. In contrast, when DRV was tested in a mutant strain PR836 that lacks key proteins regulating cellular efflux, a significant increase in the EC50 was observed. A comparison of nine FDA-approved HIV-1 PI drugs between the wild-type RE294 strain and the mutant PR836 strain showed marked enhancement of the drug sensitivities ranging from an increase of 0.56 log to 2.48 logs. Therefore, restricting cellular efflux through the adaption of the described fission yeast mutant strain enhances the drug sensitivity, reduces the amount of drug used, and increases the chance of success in future drug discovery.
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Combining classical molecular docking with self-consistent charge density-functional tight-binding computations for the efficient and quality prediction of ligand binding structure. JOURNAL OF CHEMICAL RESEARCH 2022. [DOI: 10.1177/17475198221101999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
To improve the successful prediction rate of the existing molecular docking methods, a new docking approach is proposed that consists of three steps: generating an ensemble of docked poses with a conventional docking method, performing clustering analysis of the ensemble to select the representative poses, and optimizing the representative structures with a low-cost quantum mechanics method. Three quantum mechanics methods, self-consistent charge density-functional tight-binding, ONIOM(DFT:PM6), and ONIOM(SCC-DFTB:PM6), are tested on 18 ligand-receptor bio-complexes. The rate of successful binding pose predictions by the proposed self-consistent charge density-functional tight-binding docking method is the highest, at 67%. The self-consistent charge density-functional tight-binding docking method should be useful for the structure-based drug design.
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Robertson MJ, Meyerowitz JG, Skiniotis G. Drug discovery in the era of cryo-electron microscopy. Trends Biochem Sci 2022; 47:124-135. [PMID: 34281791 PMCID: PMC8760134 DOI: 10.1016/j.tibs.2021.06.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/16/2021] [Accepted: 06/29/2021] [Indexed: 02/03/2023]
Abstract
Structure-based drug discovery (SBDD) is an indispensable approach for the design and optimization of new therapeutic agents. Here, we highlight the rapid progress that has turned cryo-electron microscopy (cryoEM) into an exceptional SBDD tool, and the wealth of new structural information it is providing for high-value pharmacological targets. We review key advantages of a technique that directly images vitrified biomolecules without the need for crystallization; both in terms of a broader array of systems that can be studied and the different forms of information it can provide, including heterogeneity and dynamics. We discuss near- and far-future developments, working in concert towards achieving the resolution and throughput necessary for cryoEM to make a widespread impact on the SBDD pipeline.
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Affiliation(s)
- Michael J Robertson
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA
| | - Justin G Meyerowitz
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA; Department of Anesthesiology, Perioperative & Pain Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Georgios Skiniotis
- Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA, USA; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA, USA.
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6
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Single-Agent and Fixed-Dose Combination HIV-1 Protease Inhibitor Drugs in Fission Yeast ( Schizosaccharomyces pombe). Pathogens 2021; 10:pathogens10070804. [PMID: 34202872 PMCID: PMC8308830 DOI: 10.3390/pathogens10070804] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 06/07/2021] [Accepted: 06/18/2021] [Indexed: 11/17/2022] Open
Abstract
Successful combination antiretroviral therapies (cART) eliminate active replicating HIV-1, slow down disease progression, and prolong lives. However, cART effectiveness could be compromised by the emergence of viral multidrug resistance, suggesting the need for new drug discoveries. The objective of this study was to further demonstrate the utility of the fission yeast cell-based systems that we developed previously for the discovery and testing of HIV protease (PR) inhibitors (PIs) against wild-type or multi-PI drug resistant M11PR that we isolated from an infected individual. All thirteen FDA-approved single-agent and fixed-dose combination HIV PI drugs were tested. The effect of these drugs on HIV PR activities was tested in pure compounds or formulation drugs. All FDA-approved PI drugs, except for a prodrug FPV, were able to suppress the wild-type PR-induced cellular and enzymatic activities. Relative drug potencies measured by EC50 in fission yeast were discussed in comparison with those measured in human cells. In contrast, none of the FDA-approved drugs suppressed the multi-PI drug resistant M11PR activities. Results of this study show that fission yeast is a reliable cell-based system for the discovery and testing of HIV PIs and further demonstrate the need for new PI drugs against viral multi-PI resistance.
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Asiri YI, Alsayari A, Muhsinah AB, Mabkhot YN, Hassan MZ. Benzothiazoles as potential antiviral agents. J Pharm Pharmacol 2020; 72:1459-1480. [PMID: 32705690 PMCID: PMC7405065 DOI: 10.1111/jphp.13331] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 06/03/2020] [Accepted: 06/13/2020] [Indexed: 12/11/2022]
Abstract
OBJECTIVES The recent viral pandemic poses a unique challenge for healthcare providers. Despite the remarkable progress, the number of novel antiviral agents in the pipeline is woefully inadequate against the evolving virulence and drug resistance of current viruses. This highlights the urgent need for new and improved vaccines, diagnostics and therapeutic agents to obviate the viral pandemic. KEY FINDINGS Benzothiazole plays a pivotal role in the design and development of antiviral drugs. This is evident from the fact that it comprises many clinically useful agents. The current review is aimed to provide an insight into the recent development of benzothiazole-based antiviral agents, with a special focus on their structure-activity relationships and lead optimisation. One hundred and five articles were initially identified, and from these studies, 64 potential novel lead molecules and main findings were highlighted in this review. SUMMARY We hope this review will provide a logical perspective on the importance of improving the future designs of novel broad-spectrum benzothiazole-based antiviral agents to be used against emerging viral diseases.
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Affiliation(s)
- Yahya I Asiri
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Abdulrhman Alsayari
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Abdullatif B Muhsinah
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Yahia N Mabkhot
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Mohd Z Hassan
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
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Olotu FA, Agoni C, Soremekun O, Soliman MES. The recent application of 3D-QSAR and docking studies to novel HIV-protease inhibitor drug discovery. Expert Opin Drug Discov 2020; 15:1095-1110. [PMID: 32692273 DOI: 10.1080/17460441.2020.1773428] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
INTRODUCTION Despite the availability of FDA approved inhibitors of HIV protease, numerous efforts are still ongoing to achieve 'near-perfect' drugs devoid of characteristic adverse side effects, toxicities, and mutational resistance. While experimental methods have been plagued with huge consumption of time and resources, there has been an incessant shift towards the use of computational simulations in HIV protease inhibitor drug discovery. AREAS COVERED Herein, the authors review the numerous applications of 3D-QSAR modeling methods over recent years relative to the design of new HIV protease inhibitors from a series of experimentally derived compounds. Also, the augmentative contributions of molecular docking are discussed. EXPERT OPINION Efforts to optimize 3D QSAR and molecular docking for HIV-1 drug discovery are ongoing, which could further incorporate inhibitor motions at the active site using molecular dynamics parameters. Also, highly predictive machine learning algorithms such as random forest, K-means, decision trees, linear regression, hierarchical clustering, and Bayesian classifiers could be employed.
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Affiliation(s)
- Fisayo A Olotu
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
| | - Clement Agoni
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
| | - Opeyemi Soremekun
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Laboratory, School of Health Sciences, University of KwaZulu-Natal, Westville Campus , Durban, 4001, South Africa
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9
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Performance of radial distribution function-based descriptors in the chemoinformatic studies of HIV-1 protease. Future Med Chem 2020; 12:299-309. [DOI: 10.4155/fmc-2019-0241] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Aim: This letter investigates the role of radial distribution function-based descriptors for in silico design of new drugs. Methodology: The multiple linear regression models for HIV-1 protease and its complexes with a series of inhibitors were constructed. A detailed analysis of major atomic contributions to the radial distribution function descriptor weighted by the number of valence shell electrons identified residues Arg8, Asp29 and residues of the catalytic triad as crucial for the correlation with the inhibition constant, together with residues Asp30 and Ile50, whose mutations are known to cause an emergence of drug resistant variants. Conclusion: This study demonstrates an easy and fast assessment of the activity of potential drugs and the derivation of structural information of their complexes with the receptor or enzyme.
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10
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Grillo IB, Urquiza‐Carvalho GA, Chaves EJF, Rocha GB. Semiempirical methods do Fukui functions: Unlocking a modeling framework for biosystems. J Comput Chem 2020; 41:862-873. [DOI: 10.1002/jcc.26148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 10/15/2019] [Accepted: 01/01/2020] [Indexed: 01/16/2023]
Affiliation(s)
- Igor Barden Grillo
- Departamento de Química Universidade Federal da Paraíba João Pessoa Brazil
| | | | | | - Gerd Bruno Rocha
- Departamento de Química Universidade Federal da Paraíba João Pessoa Brazil
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11
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Jian-Song, Gao QL, Wu BW, Li D, Shi L, Zhu T, Lou JF, Jin CY, Zhang YB, Zhang SY, Liu HM. Novel tertiary sulfonamide derivatives containing benzimidazole moiety as potent anti-gastric cancer agents: Design, synthesis and SAR studies. Eur J Med Chem 2019; 183:111731. [PMID: 31577977 DOI: 10.1016/j.ejmech.2019.111731] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 09/08/2019] [Accepted: 09/21/2019] [Indexed: 12/30/2022]
Abstract
With the expectation to find out new anti-gastric cancer agents with high efficacy and selectivity, a series of novel tertiary sulfonamide derivatives were synthesized and the anti-cancer activity was studied in three selected cancer cell lines (MGC-803, PC-3, MCF-7) in vitro. Some of the synthesized compounds could significantly inhibit the proliferation of these tested cancer cells and were more potent than the positive control (5-Fu). The structure-activity relationship of tertiary sulfonamide derivatives was explored in this report. Among the tested compounds, compound 13g containing benzimidazole moiety showed the best anti-proliferation activities against MGC-803 cells (IC50 = 1.02 μM), HGC-27 cells (IC50 = 1.61 μM), SGC-7901 (IC50 = 2.30 μM) cells as well as the good selectivity between the cancer and normal cells. Cellular mechanism studies elucidated compound 13g inhibited the colony formation of gastric cancer cell lines. Meanwhile, compound 13g arrested cell cycle at G2/M phase and induced cell apoptosis. Mechanistically, compound 13g markedly decreased p-Akt and p-c-Raf expression, which revealed that compound 13g targeted gastric cancer cell lines via interfering with AKT/mTOR and RAS/Raf/MEK/ERK pathways. All the findings suggest that compound 13g might be a valuable lead compound for the anti-gastric cancer agents.
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Affiliation(s)
- Jian-Song
- School of Pharmaceutical Sciences & Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou, 450001, China; Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, 450001, China
| | - Qiu-Lei Gao
- School of Pharmaceutical Sciences & Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou, 450001, China; Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, 450001, China
| | - Bo-Wen Wu
- School of Pharmaceutical Sciences & Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou, 450001, China; Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, 450001, China
| | - Dong Li
- School of Pharmaceutical Sciences & Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou, 450001, China; Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, 450001, China
| | - Lei Shi
- School of Pharmaceutical Sciences & Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou, 450001, China; Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, 450001, China
| | - Ting Zhu
- School of Pharmaceutical Sciences & Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou, 450001, China; Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, 450001, China
| | - Jian-Feng Lou
- School of Pharmaceutical Sciences & Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou, 450001, China; Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, 450001, China
| | - Cheng-Yun Jin
- School of Pharmaceutical Sciences & Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou, 450001, China; Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, 450001, China
| | - Yan-Bing Zhang
- School of Pharmaceutical Sciences & Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou, 450001, China; Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, 450001, China
| | - Sai-Yang Zhang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou, 450001, China; School of Pharmaceutical Sciences & Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou, 450001, China; Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou, 450001, China.
| | - Hong-Min Liu
- School of Pharmaceutical Sciences & Collaborative Innovation Center of New Drug Research and Safety Evaluation, Zhengzhou University, Zhengzhou, 450001, China; Key Laboratory of Advanced Drug Preparation Technologies (Ministry of Education), Zhengzhou University, Zhengzhou, 450001, China
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12
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Zhao C, Rakesh KP, Ravidar L, Fang WY, Qin HL. Pharmaceutical and medicinal significance of sulfur (S VI)-Containing motifs for drug discovery: A critical review. Eur J Med Chem 2019; 162:679-734. [PMID: 30496988 PMCID: PMC7111228 DOI: 10.1016/j.ejmech.2018.11.017] [Citation(s) in RCA: 283] [Impact Index Per Article: 56.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 10/17/2018] [Accepted: 11/07/2018] [Indexed: 01/04/2023]
Abstract
Sulfur (SVI) based moieties, especially, the sulfonyl or sulfonamide based analogues have showed a variety of pharmacological properties, and its derivatives propose a high degree of structural diversity that has established useful for the finding of new therapeutic agents. The developments of new less toxic, low cost and highly active sulfonamides containing analogues are hot research topics in medicinal chemistry. Currently, more than 150 FDA approved Sulfur (SVI)-based drugs are available in the market, and they are widely used to treat various types of diseases with therapeutic power. This comprehensive review highlights the recent developments of sulfonyl or sulfonamides based compounds in huge range of therapeutic applications such as antimicrobial, anti-inflammatory, antiviral, anticonvulsant, antitubercular, antidiabetic, antileishmanial, carbonic anhydrase, antimalarial, anticancer and other medicinal agents. We believe that, this review article is useful to inspire new ideas for structural design and developments of less toxic and powerful Sulfur (SVI) based drugs against the numerous death-causing diseases.
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Affiliation(s)
- Chuang Zhao
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR, China
| | - K P Rakesh
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR, China.
| | - L Ravidar
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR, China
| | - Wan-Yin Fang
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR, China
| | - Hua-Li Qin
- Department of Pharmaceutical Engineering, School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan, 430070, PR, China.
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13
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Li Y, Tian Y, Qin Z, Yan A. Classification of HIV-1 Protease Inhibitors by Machine Learning Methods. ACS OMEGA 2018; 3:15837-15849. [PMID: 30556015 PMCID: PMC6288788 DOI: 10.1021/acsomega.8b01843] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2018] [Accepted: 10/24/2018] [Indexed: 05/16/2023]
Abstract
HIV-1 protease plays an important role in the processing of virus infection. Protease is an effective therapeutic target for the treatment of HIV-1. Our data set is based on a selection of 4855 HIV-1 protease inhibitors (PIs) from ChEMBL. A series of 15 classification models for predicting the active inhibitors were built by machine learning methods, including k-nearest neighors (K-NN), decision tree (DT), random forest (RF), support vector machine (SVM), and deep neural network (DNN). The molecular structures were characterized by (1) fingerprint descriptors including MACCS fingerprints and PubChem fingerprints and (2) physicochemical descriptors calculated by CORINA Symphony. The prediction accuracies of all of the models are more than 70% on the test set; the best accuracy of 83.07% was obtained by model 4A, which was built by the SVM method based on MACCS fingerprint descriptors. Nine consensus models were built with three kinds of different descriptors, which combined all of the machine learning methods using the "consensus prediction". Model C3a developed with MACCS fingerprint descriptors showed the highest accuracy on both training set (91.96%) and test set (83.15%). An external validation set including 35 989 compounds from DUD database and 239 active inhibitors from the recent literature was used to verify the performance of our model. The best prediction accuracy of 98.37% was obtained by model 3C, which was built by RF based on CORINA Symphony descriptors. In addition, from the analysis of molecular descriptors, it shows that the aromatic system and atoms related to hydrogen bonding provide important contributions to the bioactivity of PIs.
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Affiliation(s)
- Yang Li
- State
Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical
Engineering, Beijing University of Chemical
Technology, P.O. Box 53, 15 BeiSanHuan East Road, Beijing 100029, P. R. China
- Institute
of Science and Technology, Shandong University
of Traditional Chinese Medicine, Ji’nan, Shandong 250355, China
| | - Yujia Tian
- State
Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical
Engineering, Beijing University of Chemical
Technology, P.O. Box 53, 15 BeiSanHuan East Road, Beijing 100029, P. R. China
| | - Zijian Qin
- State
Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical
Engineering, Beijing University of Chemical
Technology, P.O. Box 53, 15 BeiSanHuan East Road, Beijing 100029, P. R. China
| | - Aixia Yan
- State
Key Laboratory of Chemical Resource Engineering, Department of Pharmaceutical
Engineering, Beijing University of Chemical
Technology, P.O. Box 53, 15 BeiSanHuan East Road, Beijing 100029, P. R. China
- E-mail: . Phone: +86-10-64421335 (A.Y.)
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14
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Amin SA, Adhikari N, Bhargava S, Jha T, Gayen S. Structural exploration of hydroxyethylamines as HIV-1 protease inhibitors: new features identified. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2018; 29:385-408. [PMID: 29566580 DOI: 10.1080/1062936x.2018.1447511] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The current study deals with chemometric modelling strategies (Naïve Bayes classification, hologram-based quantitative structure-activity relationship (HQSAR), comparative molecular field analysis (CoMFA) and comparative molecular similarity index analysis (CoMSIA)) to explore the important features of hydroxylamine derivatives for exerting potent human immunodeficiency virus-1 (HIV-1) protease inhibition. Depending on the statistically validated reliable and robust quantitative structure-activity relationship (QSAR) models, important and crucial structural features have been identified that may be responsible for enhancing the activity profile of these hydroxylamine compounds. Arylsulfonamide function along with methoxy or fluoro substitution is important for enhancing activity. Bulky steric substitution at the sulfonamide nitrogen disfavours activity whereas smaller hydrophobic substitution at the same position is found to be favourable. Apart from the crucial oxazolidinone moiety, pyrrolidine, cyclic urea and methyl ester functions are also responsible for increasing the HIV-1 protease inhibitory profile. Observations derived from these modelling studies may be utilized further in designing promising HIV-1 protease inhibitors of this class.
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Affiliation(s)
- S A Amin
- a Natural science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P.O. Box 17020 , Jadavpur University , Kolkata 700032 , West Bengal , India
| | - N Adhikari
- a Natural science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P.O. Box 17020 , Jadavpur University , Kolkata 700032 , West Bengal , India
| | - S Bhargava
- b Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr Hari Singh Gour University , Sagar 470003 , Madhya Pradesh , India
| | - T Jha
- a Natural science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology, P.O. Box 17020 , Jadavpur University , Kolkata 700032 , West Bengal , India
| | - S Gayen
- b Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr Hari Singh Gour University , Sagar 470003 , Madhya Pradesh , India
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15
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Kumar SV, Ma D. Synthesis of N-(Hetero)aryl Carbamates via CuI/MNAO Catalyzed Cross-Coupling of (Hetero)aryl Halides with Potassium Cyanate in Alcohols. J Org Chem 2018; 83:2706-2713. [PMID: 29406714 DOI: 10.1021/acs.joc.7b03175] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An efficient route to N-(hetero)aryl carbamates was developed through CuI/MNAO [2-((2-methylnaphthalen-1-yl)amino)-2-oxoacetic acid] catalyzed cross-coupling of (hetero)aryl chlorides with potassium cyanate in alcohols at 120-130 °C. This method utilizes broadly available substrates to afford various N-(hetero)aryl carbamates in good to excellent yields. Moreover, (hetero)aryl bromides and (hetero)aryl iodides were also reacted at low catalyst loadings and relatively low temperatures to provide N-(hetero)aryl carbamates.
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Affiliation(s)
- S Vijay Kumar
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , 345 Lingling Lu, Shanghai 200032, China
| | - Dawei Ma
- State Key Laboratory of Bioorganic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences , 345 Lingling Lu, Shanghai 200032, China
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16
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Bhargava S, Adhikari N, Amin SA, Das K, Gayen S, Jha T. Hydroxyethylamine derivatives as HIV-1 protease inhibitors: a predictive QSAR modelling study based on Monte Carlo optimization. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2017; 28:973-990. [PMID: 29072112 DOI: 10.1080/1062936x.2017.1388281] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 09/29/2017] [Indexed: 06/07/2023]
Abstract
Application of HIV-1 protease inhibitors (as an anti-HIV regimen) may serve as an attractive strategy for anti-HIV drug development. Several investigations suggest that there is a crucial need to develop a novel protease inhibitor with higher potency and reduced toxicity. Monte Carlo optimized QSAR study was performed on 200 hydroxyethylamine derivatives with antiprotease activity. Twenty-one QSAR models with good statistical qualities were developed from three different splits with various combinations of SMILES and GRAPH based descriptors. The best models from different splits were selected on the basis of statistically validated characteristics of the test set and have the following statistical parameters: r2 = 0.806, Q2 = 0.788 (split 1); r2 = 0.842, Q2 = 0.826 (split 2); r2 = 0.774, Q2 = 0.755 (split 3). The structural attributes obtained from the best models were analysed to understand the structural requirements of the selected series for HIV-1 protease inhibitory activity. On the basis of obtained structural attributes, 11 new compounds were designed, out of which five compounds were found to have better activity than the best active compound in the series.
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Affiliation(s)
- S Bhargava
- a Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr Harisingh Gour University (A Central University) , Madhya Pradesh , India
| | - N Adhikari
- b Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology , Jadavpur University , Kolkata , West Bengal , India
| | - S A Amin
- b Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology , Jadavpur University , Kolkata , West Bengal , India
| | - K Das
- c Department of Chemistry , Dr. Harisingh Gour University (A Central University) , Madhya Pradesh , India
| | - S Gayen
- a Laboratory of Drug Design and Discovery, Department of Pharmaceutical Sciences , Dr Harisingh Gour University (A Central University) , Madhya Pradesh , India
| | - T Jha
- b Natural Science Laboratory, Division of Medicinal and Pharmaceutical Chemistry, Department of Pharmaceutical Technology , Jadavpur University , Kolkata , West Bengal , India
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17
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Zhou H, Hong J, Huang J, Chen Z. Highly Efficient Curtius Rearrangement Approach for the Synthesis of Unsymmetrical Sulfonimidoyl Ureas. ASIAN J ORG CHEM 2017. [DOI: 10.1002/ajoc.201700248] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Hao Zhou
- Key Laboratory of Functional Small Organic Molecules; Ministry of Education; College of Chemistry & Chemical Engineering; Jiangxi Normal University; 99 Ziyang Road Nanchang Jiangxi 330022 P. R. China
| | - Jianquan Hong
- School of Chemical and Material Engineering; Jiangnan University; 1800 Lihu Road Wuxi Jiangsu 214122 P. R. China
| | - Jiapian Huang
- Key Laboratory of Functional Small Organic Molecules; Ministry of Education; College of Chemistry & Chemical Engineering; Jiangxi Normal University; 99 Ziyang Road Nanchang Jiangxi 330022 P. R. China
| | - Zhiyuan Chen
- Key Laboratory of Functional Small Organic Molecules; Ministry of Education; College of Chemistry & Chemical Engineering; Jiangxi Normal University; 99 Ziyang Road Nanchang Jiangxi 330022 P. R. China
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18
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Paulsen JL, Leidner F, Ragland DA, Kurt Yilmaz N, Schiffer CA. Interdependence of Inhibitor Recognition in HIV-1 Protease. J Chem Theory Comput 2017; 13:2300-2309. [PMID: 28358514 PMCID: PMC5425943 DOI: 10.1021/acs.jctc.6b01262] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
![]()
Molecular recognition
is a highly interdependent process. Subsite
couplings within the active site of proteases are most often revealed
through conditional amino acid preferences in substrate recognition.
However, the potential effect of these couplings on inhibition and
thus inhibitor design is largely unexplored. The present study examines
the interdependency of subsites in HIV-1 protease using a focused
library of protease inhibitors, to aid in future inhibitor design.
Previously a series of darunavir (DRV) analogs was designed to systematically
probe the S1′ and S2′ subsites. Co-crystal structures
of these analogs with HIV-1 protease provide the ideal opportunity
to probe subsite interdependency. All-atom molecular dynamics simulations
starting from these structures were performed and systematically analyzed
in terms of atomic fluctuations, intermolecular interactions, and
water structure. These analyses reveal that the S1′ subsite
highly influences other subsites: the extension of the hydrophobic
P1′ moiety results in 1) reduced van der Waals contacts in
the P2′ subsite, 2) more variability in the hydrogen bond frequencies
with catalytic residues and the flap water, and 3) changes in the
occupancy of conserved water sites both proximal and distal to the
active site. In addition, one of the monomers in this homodimeric
enzyme has atomic fluctuations more highly correlated with DRV than
the other monomer. These relationships intricately link the HIV-1
protease subsites and are critical to understanding molecular recognition
and inhibitor binding. More broadly, the interdependency of subsite
recognition within an active site requires consideration in the selection
of chemical moieties in drug design; this strategy is in contrast
to what is traditionally done with independent optimization of chemical
moieties of an inhibitor.
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Affiliation(s)
- Janet L Paulsen
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Florian Leidner
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Debra A Ragland
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
| | - Celia A Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School , Worcester, Massachusetts 01605, United States
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19
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Fast and accurate determination of the relative binding affinities of small compounds to HIV-1 protease using non-equilibrium work. J Comput Chem 2016; 37:2734-2742. [DOI: 10.1002/jcc.24502] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Revised: 08/29/2016] [Accepted: 09/06/2016] [Indexed: 02/06/2023]
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20
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Ghosh AK, Osswald HL, Prato G. Recent Progress in the Development of HIV-1 Protease Inhibitors for the Treatment of HIV/AIDS. J Med Chem 2016; 59:5172-208. [PMID: 26799988 PMCID: PMC5598487 DOI: 10.1021/acs.jmedchem.5b01697] [Citation(s) in RCA: 274] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
HIV-1 protease inhibitors continue to play an important role in the treatment of HIV/AIDS, transforming this deadly ailment into a more manageable chronic infection. Over the years, intensive research has led to a variety of approved protease inhibitors for the treatment of HIV/AIDS. In this review, we outline current drug design and medicinal chemistry efforts toward the development of next-generation protease inhibitors beyond the currently approved drugs.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Heather L. Osswald
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Gary Prato
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
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21
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Miranda WE, Noskov SY, Valiente PA. Improving the LIE Method for Binding Free Energy Calculations of Protein–Ligand Complexes. J Chem Inf Model 2015; 55:1867-77. [DOI: 10.1021/acs.jcim.5b00012] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Williams E. Miranda
- Computational
Biology and Biomolecular Dynamics Laboratory, Center for Protein Studies,
Faculty of Biology, University of Havana, Havana, Cuba
| | - Sergei Yu. Noskov
- Centre
for Molecular Simulations and Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Pedro A. Valiente
- Computational
Biology and Biomolecular Dynamics Laboratory, Center for Protein Studies,
Faculty of Biology, University of Havana, Havana, Cuba
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22
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Islam MA, Pillay TS. Exploration of the structural requirements of HIV-protease inhibitors using pharmacophore, virtual screening and molecular docking approaches for lead identification. J Mol Graph Model 2015; 56:20-30. [DOI: 10.1016/j.jmgm.2014.11.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 11/24/2014] [Accepted: 11/30/2014] [Indexed: 12/19/2022]
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23
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Recent patents and emerging therapeutics for HIV infections: a focus on protease inhibitors. Pharm Pat Anal 2014; 2:513-38. [PMID: 24237127 DOI: 10.4155/ppa.13.33] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
The inclusion of protease inhibitors (PIs) in highly active antiretroviral therapy has significantly improved clinical outcomes in HIV-1-infected patients. To date, PIs are considered to be the most important therapeutic agents for the treatment of HIV infections. Despite high anti-HIV-1 potency, poor oral bioavailability of PIs has been a major concern. For achieving therapeutic concentrations, large doses of PIs are administered, which results in unacceptable systemic toxicities. Such severe and long-term toxicities necessitate the development of safer and potentially promising PIs. Recently, considerable attention has been paid to the development of newer compounds capable of inhibiting wild-type and resistant HIV-1 protease. Some of these PIs have displayed potent HIV-1 protease inhibitory activity. In this review, we have made an attempt to provide an overview on clinically approved and newly developing PIs, and related recent patents in the development of novel PIs.
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24
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Ganguly AK, Alluri SS, Wang CH, Antropow A, White A, Caroccia D, Biswas D, Kang E, Zhang LK, Carroll SS, Burlein C, Fay J, Orth P, Strickland C. Structural optimization of cyclic sulfonamide based novel HIV-1 protease inhibitors to picomolar affinities guided by X-ray crystallographic analysis. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.03.038] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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25
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Li J, Mach P, Koehl P. Measuring the shapes of macromolecules - and why it matters. Comput Struct Biotechnol J 2013; 8:e201309001. [PMID: 24688748 PMCID: PMC3962087 DOI: 10.5936/csbj.201309001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2013] [Revised: 11/22/2013] [Accepted: 11/22/2013] [Indexed: 11/22/2022] Open
Abstract
The molecular basis of life rests on the activity of biological macromolecules, mostly nucleic acids and proteins. A perhaps surprising finding that crystallized over the last handful of decades is that geometric reasoning plays a major role in our attempt to understand these activities. In this paper, we address this connection between geometry and biology, focusing on methods for measuring and characterizing the shapes of macromolecules. We briefly review existing numerical and analytical approaches that solve these problems. We cover in more details our own work in this field, focusing on the alpha shape theory as it provides a unifying mathematical framework that enable the analytical calculations of the surface area and volume of a macromolecule represented as a union of balls, the detection of pockets and cavities in the molecule, and the quantification of contacts between the atomic balls. We have shown that each of these quantities can be related to physical properties of the molecule under study and ultimately provides insight on its activity. We conclude with a brief description of new challenges for the alpha shape theory in modern structural biology.
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Affiliation(s)
- Jie Li
- Genome Center, University of California, Davis, 451 Health Sciences Drive, Davis, CA 95616, United States
| | - Paul Mach
- Graduate Group of Applied Mathematics, University of California, Davis, 1, Shields Ave, Davis, CA, 95616, United States
| | - Patrice Koehl
- Department of Computer Science and Genome Center, University of California, Davis, 1, Shields Ave, Davis, CA, 95616, United States
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26
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Shen Y, Altman MD, Ali A, Nalam MNL, Cao H, Rana TM, Schiffer CA, Tidor B. Testing the substrate-envelope hypothesis with designed pairs of compounds. ACS Chem Biol 2013; 8:2433-41. [PMID: 23952265 PMCID: PMC3833293 DOI: 10.1021/cb400468c] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
![]()
Acquired resistance to therapeutic
agents is a significant barrier to the development of clinically effective
treatments for diseases in which evolution occurs on clinical time
scales, frequently arising from target mutations. We previously reported
a general strategy to design effective inhibitors for rapidly mutating
enzyme targets, which we demonstrated for HIV-1 protease inhibition
[Altman et al. J. Am. Chem. Soc. 2008, 130, 6099–6113]. Specifically, we developed a computational inverse
design procedure with the added constraint that designed inhibitors
bind entirely inside the substrate envelope, a consensus volume occupied
by natural substrates. The rationale for the substrate-envelope constraint
is that it prevents designed inhibitors from making interactions beyond
those required by substrates and thus limits the availability of mutations
tolerated by substrates but not by designed inhibitors. The strategy
resulted in subnanomolar inhibitors that bind robustly across a clinically
derived panel of drug-resistant variants. To further test the substrate-envelope
hypothesis, here we have designed, synthesized, and assayed derivatives
of our original compounds that are larger and extend outside the substrate
envelope. Our designs resulted in pairs of compounds that are very
similar to one another, but one respects and one violates the substrate
envelope. The envelope-respecting inhibitor demonstrates robust binding
across a panel of drug-resistant protease variants, whereas the envelope-violating
one binds tightly to wild type but loses affinity to at least one
variant. This study provides strong support for the substrate-envelope
hypothesis as a design strategy for inhibitors that reduce susceptibility
to resistance mutations.
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Affiliation(s)
| | | | | | | | | | - Tariq M. Rana
- Sanford-Burnham Medical Research Institute, La Jolla, California 92037, United States
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27
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Nalam MN, Ali A, Reddy GKK, Cao H, Anjum SG, Altman MD, Yilmaz NK, Tidor B, Rana TM, Schiffer CA. Substrate envelope-designed potent HIV-1 protease inhibitors to avoid drug resistance. CHEMISTRY & BIOLOGY 2013; 20:1116-24. [PMID: 24012370 PMCID: PMC3934494 DOI: 10.1016/j.chembiol.2013.07.014] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Revised: 07/12/2013] [Accepted: 07/23/2013] [Indexed: 01/07/2023]
Abstract
The rapid evolution of HIV under selective drug pressure has led to multidrug resistant (MDR) strains that evade standard therapies. We designed highly potent HIV-1 protease inhibitors (PIs) using the substrate envelope model, which confines inhibitors within the consensus volume of natural substrates, providing inhibitors less susceptible to resistance because a mutation affecting such inhibitors will simultaneously affect viral substrate processing. The designed PIs share a common chemical scaffold but utilize various moieties that optimally fill the substrate envelope, as confirmed by crystal structures. The designed PIs retain robust binding to MDR protease variants and display exceptional antiviral potencies against different clades of HIV as well as a panel of 12 drug-resistant viral strains. The substrate envelope model proves to be a powerful strategy to develop potent and robust inhibitors that avoid drug resistance.
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Affiliation(s)
- Madhavi N.L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
| | - Akbar Ali
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
| | - G.S. Kiran Kumar Reddy
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
| | - Hong Cao
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
| | - Saima G. Anjum
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
| | - Michael D. Altman
- Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nese Kurt Yilmaz
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
| | - Bruce Tidor
- Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Corresponding Authors: Bruce Tidor: Phone: +1 (617) 253-7258, , Tariq M. Rana: Phone: +1 (858)795-5325, , Celia A. Schiffer: Phone: +1 (508) 856-8008,
| | - Tariq M. Rana
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
- Corresponding Authors: Bruce Tidor: Phone: +1 (617) 253-7258, , Tariq M. Rana: Phone: +1 (858)795-5325, , Celia A. Schiffer: Phone: +1 (508) 856-8008,
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts, Medical School, Worcester, Massachusetts 01605, United States
- Corresponding Authors: Bruce Tidor: Phone: +1 (617) 253-7258, , Tariq M. Rana: Phone: +1 (858)795-5325, , Celia A. Schiffer: Phone: +1 (508) 856-8008,
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28
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Ni Z, Chen H, Qi X, Jin R. Why is Substrate Peptide Binding Unsusceptible to Multidrug-Resistant Mutations in HIV-1 Protease? A Structural and Energetic Analysis. Int J Pept Res Ther 2013. [DOI: 10.1007/s10989-013-9365-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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29
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Sundquist WI, Kräusslich HG. HIV-1 assembly, budding, and maturation. Cold Spring Harb Perspect Med 2013; 2:a006924. [PMID: 22762019 DOI: 10.1101/cshperspect.a006924] [Citation(s) in RCA: 512] [Impact Index Per Article: 46.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A defining property of retroviruses is their ability to assemble into particles that can leave producer cells and spread infection to susceptible cells and hosts. Virion morphogenesis can be divided into three stages: assembly, wherein the virion is created and essential components are packaged; budding, wherein the virion crosses the plasma membrane and obtains its lipid envelope; and maturation, wherein the virion changes structure and becomes infectious. All of these stages are coordinated by the Gag polyprotein and its proteolytic maturation products, which function as the major structural proteins of the virus. Here, we review our current understanding of the mechanisms of HIV-1 assembly, budding, and maturation, starting with a general overview and then providing detailed descriptions of each of the different stages of virion morphogenesis.
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Affiliation(s)
- Wesley I Sundquist
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA.
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30
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Ul-Haq Z, Usmani S, Shamshad H, Mahmood U, Halim SA. A combined 3D-QSAR and docking studies for the In-silico prediction of HIV-protease inhibitors. Chem Cent J 2013; 7:88. [PMID: 23683267 PMCID: PMC3660290 DOI: 10.1186/1752-153x-7-88] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2013] [Accepted: 05/06/2013] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Tremendous research from last twenty years has been pursued to cure human life against HIV virus. A large number of HIV protease inhibitors are in clinical trials but still it is an interesting target for researchers due to the viral ability to get mutated. Mutated viral strains led the drug ineffective but still used to increase the life span of HIV patients. RESULTS In the present work, 3D-QSAR and docking studies were performed on a series of Danuravir derivatives, the most potent HIV- protease inhibitor known so far. Combined study of 3D-QSAR was applied for Danuravir derivatives using ligand-based and receptor-based protocols and generated models were compared. The results were in good agreement with the experimental results. Additionally, docking analysis of most active 32 and least active 46 compounds into wild type and mutated protein structures further verified our results. The 3D-QSAR and docking results revealed that compound 32 bind efficiently to the wild and mutated protein whereas, sufficient interactions were lost in compound 46. CONCLUSION The combination of two computational techniques would helped to make a clear decision that compound 32 with well inhibitory activity bind more efficiently within the binding pocket even in case of mutant virus whereas compound 46 lost its interactions on mutation and marked as least active compound of the series. This is all due to the presence or absence of substituents on core structure, evaluated by 3D-QSAR studies. This set of information could be used to design highly potent drug candidates for both wild and mutated form of viruses.
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Affiliation(s)
- Zaheer Ul-Haq
- Dr, Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi 75270, Pakistan.
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31
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De Marco R, Greco A, Rupiani S, Tolomelli A, Tomasini C, Pieraccini S, Gentilucci L. In-peptide synthesis of di-oxazolidinone and dehydroamino acid–oxazolidinone motifs as β-turn inducers. Org Biomol Chem 2013; 11:4316-26. [DOI: 10.1039/c3ob40357b] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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32
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Yang X, Zhang Y, Ma D. Synthesis of Aryl Carbamates
via
Copper‐Catalyzed Coupling of Aryl Halides with Potassium Cyanate. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201200296] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Xinye Yang
- Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Yihua Zhang
- Center of Drug Discovery, China Pharmaceutical University, Nanjing 210009, People's Republic of China
| | - Dawei Ma
- State Key Laboratory of Bioorganic & Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, 354 Fenglin Lu, Shanghai 200032, People's Republic of China, Fax: (+86)‐21‐6416‐6128
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33
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Bell JA, Ho KL, Farid R. Significant reduction in errors associated with nonbonded contacts in protein crystal structures: automated all-atom refinement with PrimeX. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2012; 68:935-52. [PMID: 22868759 PMCID: PMC3413210 DOI: 10.1107/s0907444912017453] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2012] [Accepted: 04/19/2012] [Indexed: 11/12/2022]
Abstract
All-atom models are essential for many applications in molecular modeling and computational chemistry. Nonbonded atomic contacts much closer than the sum of the van der Waals radii of the two atoms (clashes) are commonly observed in such models derived from protein crystal structures. A set of 94 recently deposited protein structures in the resolution range 1.5-2.8 Å were analyzed for clashes by the addition of all H atoms to the models followed by optimization and energy minimization of the positions of just these H atoms. The results were compared with the same set of structures after automated all-atom refinement with PrimeX and with nonbonded contacts in protein crystal structures at a resolution equal to or better than 0.9 Å. The additional PrimeX refinement produced structures with reasonable summary geometric statistics and similar R(free) values to the original structures. The frequency of clashes at less than 0.8 times the sum of van der Waals radii was reduced over fourfold compared with that found in the original structures, to a level approaching that found in the ultrahigh-resolution structures. Moreover, severe clashes at less than or equal to 0.7 times the sum of atomic radii were reduced 15-fold. All-atom refinement with PrimeX produced improved crystal structure models with respect to nonbonded contacts and yielded changes in structural details that dramatically impacted on the interpretation of some protein-ligand interactions.
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Affiliation(s)
- Jeffrey A. Bell
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
| | - Kenneth L. Ho
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
| | - Ramy Farid
- Schrödinger, 120 West 45th Street, 17th Floor, New York, NY 10036, USA
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34
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Parai MK, Huggins DJ, Cao H, Nalam MNL, Ali A, Schiffer CA, Tidor B, Rana TM. Design, synthesis, and biological and structural evaluations of novel HIV-1 protease inhibitors to combat drug resistance. J Med Chem 2012; 55:6328-41. [PMID: 22708897 PMCID: PMC3409094 DOI: 10.1021/jm300238h] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of new HIV-1 protease inhibitors (PIs) were designed using a general strategy that combines computational structure-based design with substrate-envelope constraints. The PIs incorporate various alcohol-derived P2 carbamates with acyclic and cyclic heteroatomic functionalities into the (R)-hydroxyethylamine isostere. Most of the new PIs show potent binding affinities against wild-type HIV-1 protease and three multidrug resistant (MDR) variants. In particular, inhibitors containing the 2,2-dichloroacetamide, pyrrolidinone, imidazolidinone, and oxazolidinone moieties at P2 are the most potent with K(i) values in the picomolar range. Several new PIs exhibit nanomolar antiviral potencies against patient-derived wild-type viruses from HIV-1 clades A, B, and C and two MDR variants. Crystal structure analyses of four potent inhibitors revealed that carbonyl groups of the new P2 moieties promote extensive hydrogen bond interactions with the invariant Asp29 residue of the protease. These structure-activity relationship findings can be utilized to design new PIs with enhanced enzyme inhibitory and antiviral potencies.
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Affiliation(s)
- Maloy Kumar Parai
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
| | - David J. Huggins
- Department of Biological Engineering and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Hong Cao
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Madhavi N. L. Nalam
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Akbar Ali
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Celia A. Schiffer
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
| | - Bruce Tidor
- Department of Biological Engineering and Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Tariq M. Rana
- Program for RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037
- Chemical Biology Program, Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605
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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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36
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Abedi H, Ebrahimzadeh H, Ghasemi JB. 3D-QSAR, CoMFA, and CoMSIA of new phenyloxazolidinones derivatives as potent HIV-1 protease inhibitors. Struct Chem 2012. [DOI: 10.1007/s11224-012-0092-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Mohammed I, Parai MK, Jiang X, Sharova N, Singh G, Stevenson M, Rana TM. SAR and Lead Optimization of an HIV-1 Vif-APOBEC3G Axis Inhibitor. ACS Med Chem Lett 2012; 3:465-469. [PMID: 24533175 DOI: 10.1021/ml300037k] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
We describe structure-activity relationship and optimization studies of RN-18, an HIV-1 Vif-APOBEC3G axis inhibitor. Targeted modifications of RN-18 ring-C, ring-B, ring-A, bridge A-B, and bridge B-C were performed to identify the crucial structural features, which generated new inhibitors with similar (4g and 4i) and improved (5, 8b, and 11) activities. Two potent water-soluble RN-18 analogues, 17 and 19, are also disclosed, and we describe the results of pharmacological studies with compound 19. The findings described here will be useful in the development of more potent Vif inhibitors and in the design of probes to identify the target protein of RN-18 and its analogues.
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Affiliation(s)
- Idrees Mohammed
- Program for
RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla,
California 92037, United States
| | - Maloy K. Parai
- Program for
RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla,
California 92037, United States
| | - Xinpeng Jiang
- Program for
RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla,
California 92037, United States
| | - Natalia Sharova
- Division of Infectious Diseases,
Miller School of Medicine, University of Miami, Miami, Florida 33136, United States
| | - Gatikrushna Singh
- Program for
RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla,
California 92037, United States
| | - Mario Stevenson
- Division of Infectious Diseases,
Miller School of Medicine, University of Miami, Miami, Florida 33136, United States
| | - Tariq M. Rana
- Program for
RNA Biology, Sanford-Burnham Medical Research Institute, La Jolla,
California 92037, United States
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38
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Chiummiento L, Funicello M, Lupattelli P, Tramutola F, Berti F, Marino-Merlo F. Synthesis and biological evaluation of novel small non-peptidic HIV-1 PIs: The benzothiophene ring as an effective moiety. Bioorg Med Chem Lett 2012; 22:2948-50. [DOI: 10.1016/j.bmcl.2012.02.046] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Revised: 02/10/2012] [Accepted: 02/15/2012] [Indexed: 10/28/2022]
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39
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Synthesis and biological evaluation of novel amprenavir-based P1-substituted bi-aryl derivatives as ultra-potent HIV-1 protease inhibitors. Bioorg Med Chem Lett 2012; 22:1976-9. [DOI: 10.1016/j.bmcl.2012.01.037] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2011] [Revised: 01/11/2012] [Accepted: 01/12/2012] [Indexed: 11/23/2022]
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40
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Guan ZH, Lei H, Chen M, Ren ZH, Bai Y, Wang YY. Palladium-Catalyzed Carbonylation of Amines: Switchable Approaches to Carbamates and N,N′-Disubstituted Ureas. Adv Synth Catal 2012. [DOI: 10.1002/adsc.201100545] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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41
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De Marco R, Tolomelli A, Campitiello M, Rubini P, Gentilucci L. Expedient synthesis of pseudo-Pro-containing peptides: towards constrained peptidomimetics and foldamers. Org Biomol Chem 2012; 10:2307-17. [DOI: 10.1039/c2ob07172j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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42
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Pluripotentialities of a quenched fluorescent peptide substrate library: enzymatic detection, characterization, and isoenzymes differentiation. Anal Biochem 2011; 419:95-105. [DOI: 10.1016/j.ab.2011.08.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2011] [Revised: 07/22/2011] [Accepted: 08/10/2011] [Indexed: 11/22/2022]
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43
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Ghosh AK, Anderson DD. Tetrahydrofuran, tetrahydropyran, triazoles and related heterocyclic derivatives as HIV protease inhibitors. Future Med Chem 2011; 3:1181-97. [PMID: 21806380 PMCID: PMC3164575 DOI: 10.4155/fmc.11.68] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
HIV/AIDS remains a formidable disease with millions of individuals inflicted worldwide. Although treatment regimens have improved considerably, drug resistance brought on by viral mutation continues to erode their effectiveness. Intense research efforts are currently underway in search of new and improved therapies. This review is concerned with the design of novel HIV-1 protease inhibitors that incorporate heterocyclic scaffolds and which have been reported within the recent literature (2005-2010). Various examples in this review showcase the essential role heterocycles play as scaffolds and bioisosteres in HIV-1 protease inhibitor drug development. This review will hopefully stimulate the widespread application of these heterocycles in the design of other therapeutic agents.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, USA.
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