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Giugliano G, Gajo M, Marforio TD, Zerbetto F, Mattioli EJ, Calvaresi M. Identification of Potential Drug Targets of Calix[4]arene by Reverse Docking. Chemistry 2024; 30:e202400871. [PMID: 38777795 DOI: 10.1002/chem.202400871] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 05/25/2024]
Abstract
Calixarenes are displaying great potential for the development of new drug delivery systems, diagnostic imaging, biosensing devices and inhibitors of biological processes. In particular, calixarene derivatives are able to interact with many different enzymes and function as inhibitors. By screening of the potential drug target database (PDTD) with a reverse docking procedure, we identify and discuss a selection of 100 proteins that interact strongly with calix[4]arene. We also discover that leucine (23.5 %), isoleucine (11.3 %), phenylalanines (11.3 %) and valine (9.5 %) are the most frequent binding residues followed by hydrophobic cysteines and methionines and aromatic histidines, tyrosines and tryptophanes. Top binders are peroxisome proliferator-activated receptors that already are targeted by commercial drugs, demonstrating the practical interest in calix[4]arene. Nuclear receptors, potassium channel, several carrier proteins, a variety of cancer-related proteins and viral proteins are prominent in the list. It is concluded that calix[4]arene, which is characterized by facile access, well-defined conformational characteristics, and ease of functionalization at both the lower and higher rims, could be a potential lead compound for the development of enzyme inhibitors and theranostic platforms.
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Affiliation(s)
- Giulia Giugliano
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Margherita Gajo
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Tainah Dorina Marforio
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Francesco Zerbetto
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Edoardo Jun Mattioli
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
| | - Matteo Calvaresi
- Dipartimento di Chimica "Giacomo Ciamician", Alma Mater Studiorum - Università di Bologna, Via Francesco Selmi 2, 40126, Bologna, Italy E-Mail
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2
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Ghosh AK, Lee D, Sharma A, Johnson ME, Ghosh AK, Wang YF, Agniswamy J, Amano M, Hattori SI, Weber IT, Mitsuya H. Design of substituted tetrahydrofuran derivatives for HIV-1 protease inhibitors: synthesis, biological evaluation, and X-ray structural studies. Org Biomol Chem 2024. [PMID: 38973505 DOI: 10.1039/d4ob00506f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/09/2024]
Abstract
Substituted tetrahydrofuran derivatives were designed and synthesized to serve as the P2 ligand for a series of potent HIV-1 protease inhibitors. Both enantiomers of the tetrahydrofuran derivatives were synthesized stereoselectivity in optically active forms using lipase-PS catalyzed enzymatic resolution as the key step. These tetrahydrofuran derivatives are designed to promote hydrogen bonding and van der Waals interactions with the backbone atoms in the S2 subsite of the HIV-1 protease active site. Several inhibitors displayed very potent HIV-1 protease inhibitory activity. A high-resolution X-ray crystal structure of an inhibitor-bound HIV-1 protease provided important insight into the ligand binding site interactions in the active site.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA.
- Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA
| | - Daniel Lee
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA.
| | - Ashish Sharma
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA.
| | - Megan E Johnson
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA.
| | - Ajay K Ghosh
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, USA.
| | - Yuan-Fang Wang
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA
| | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA
| | - Masayuki Amano
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto 860-8556, Japan
| | - Shin-Ichiro Hattori
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Irene T Weber
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, USA
| | - Hiroaki Mitsuya
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto 860-8556, Japan
- Center for Clinical Sciences, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
- Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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3
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Herman RA, Ayepa E, Zhang WX, Li ZN, Zhu X, Ackah M, Yuan SS, You S, Wang J. Molecular modification and biotechnological applications of microbial aspartic proteases. Crit Rev Biotechnol 2024; 44:388-413. [PMID: 36842994 DOI: 10.1080/07388551.2023.2171850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 12/13/2022] [Accepted: 01/07/2023] [Indexed: 02/28/2023]
Abstract
The growing preference for incorporating microbial aspartic proteases in industries is due to their high catalytic function and high degree of substrate selectivity. These properties, however, are attributable to molecular alterations in their structure and a variety of other characteristics. Molecular tools, functional genomics, and genome editing technologies coupled with other biotechnological approaches have aided in improving the potential of industrially important microbial proteases by addressing some of their major limitations, such as: low catalytic efficiency, low conversion rates, low thermostability, and less enzyme yield. However, the native folding within their full domain is dependent on a surrounding structure which challenges their functionality in substrate conversion, mainly due to their mutual interactions in the context of complex systems. Hence, manipulating their structure and controlling their expression systems could potentially produce enzymes with high selectivity and catalytic functions. The proteins produced by microbial aspartic proteases are industrially capable and far-reaching in regulating certain harmful distinctive industrial processes and the benefits of being eco-friendly. This review provides: an update on current trends and gaps in microbial protease biotechnology, exploring the relevant recombinant strategies and molecular technologies widely used in expression platforms for engineering microbial aspartic proteases, as well as their potential industrial and biotechnological applications.
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Affiliation(s)
- Richard Ansah Herman
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
- School of Materials Science and Engineering, Jiangsu University of Science and Technology, Zhenjiang, P. R. China
| | - Ellen Ayepa
- Oil Palm Research Institute, Council for Scientific and Industrial Research, Kusi, Ghana
| | - Wen-Xin Zhang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
| | - Zong-Nan Li
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
| | - Xuan Zhu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
| | - Michael Ackah
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
| | - Shuang-Shuang Yuan
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
| | - Shuai You
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, P.R. China
| | - Jun Wang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, P.R. China
- Key Laboratory of Silkworm and Mulberry Genetic Improvement, Ministry of Agricultural and Rural Affairs, Sericultural Research Institute, Chinese Academy of Agricultural Sciences, Zhenjiang, P.R. China
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4
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Verma SK, Rangappa S, Verma R, Xue F, Verma S, Sharath Kumar KS, Rangappa KS. Sulfur (S Ⅵ)-containing heterocyclic hybrids as antibacterial agents against methicillin-resistant Staphylococcus aureus (MRSA) and its SAR. Bioorg Chem 2024; 145:107241. [PMID: 38437761 DOI: 10.1016/j.bioorg.2024.107241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/16/2024] [Accepted: 02/23/2024] [Indexed: 03/06/2024]
Abstract
The discovery of new small molecule-based inhibitors is an attractive field in medicinal chemistry. Structurally diversified heterocyclic derivatives have been investigated to combat multi-drug resistant bacterial infections and they offers several mechanism of action. Methicillin-resistant Staphylococcus aureus (MRSA) is becoming more and more deadly to humans because of its simple method of transmission, quick development of antibiotic resistance, and ability to cause hard-to-treat skin and filmy diseases. The sulfur (SVI) particularly sulfonyl and sulfonamide based heterocyclic moieties, have found to be good anti-MRSA agents. The development of new nontoxic, economical and highly active sulfur (SVI) containing derivatives has become hot research topics in drug discovery research. Presently, 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 different therapeutic potential. The present collective data provides the latest advancements in Sulfur (SVI)-hybrid compounds as antibacterial agents against MRSA. It also examines the outcomes of in-vitro and in-vivo investigations, exploring potential mechanisms of action and offering alternative perspectives on the structure-activity relationship (SAR). Sulfur (SVI)-hybrids exhibits synergistic effects with existing drugs to provide antibacterial action against MRSA.
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Affiliation(s)
| | - Shobith Rangappa
- Adichunchanagiri Institute for Molecular Medicine, Adichunchanagiri Institute of Medical Sciences, Adichunchanagiri University, B. G. Nagar 571448, India
| | - Rameshwari Verma
- School of New Energy, Yulin University, Yulin 719000, Shaanxi, PR China.
| | - Fan Xue
- Shaanxi Key Laboratory of Low Metamorphic Coal Clean Utilization, Yulin University, Yulin 719000, PR China
| | - Shekhar Verma
- Department of Pharmacy, Guru Ghasidas Central University, Bilaspur 495009, Chhattisgarh, India
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5
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Manna S, Das K, Santra S, Nosova EV, Zyryanov GV, Halder S. Structural and Synthetic Aspects of Small Ring Oxa- and Aza-Heterocyclic Ring Systems as Antiviral Activities. Viruses 2023; 15:1826. [PMID: 37766233 PMCID: PMC10536032 DOI: 10.3390/v15091826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 08/17/2023] [Accepted: 08/21/2023] [Indexed: 09/29/2023] Open
Abstract
Antiviral properties of different oxa- and aza-heterocycles are identified and properly correlated with their structural features and discussed in this review article. The primary objective is to explore the activity of such ring systems as antiviral agents, as well as their synthetic routes and biological significance. Eventually, the structure-activity relationship (SAR) of the heterocyclic compounds, along with their salient characteristics are exhibited to build a suitable platform for medicinal chemists and biotechnologists. The synergistic conclusions are extremely important for the introduction of a newer tool for the future drug discovery program.
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Affiliation(s)
- Sibasish Manna
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur 440010, India
| | - Koushik Das
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur 440010, India
| | - Sougata Santra
- Department of Organic and Biomolecular Chemistry, Chemical Engineering Institute, Ural Federal University, 19 Mira Street, 620002 Yekaterinburg, Russia; (S.S.); (E.V.N.); (G.V.Z.)
| | - Emily V. Nosova
- Department of Organic and Biomolecular Chemistry, Chemical Engineering Institute, Ural Federal University, 19 Mira Street, 620002 Yekaterinburg, Russia; (S.S.); (E.V.N.); (G.V.Z.)
- I. Ya. Postovskiy Institute of Organic Synthesis, Ural Division of the Russian Academy of Sciences, 22 S. Kovalevskoy Street, 620219 Yekaterinburg, Russia
| | - Grigory V. Zyryanov
- Department of Organic and Biomolecular Chemistry, Chemical Engineering Institute, Ural Federal University, 19 Mira Street, 620002 Yekaterinburg, Russia; (S.S.); (E.V.N.); (G.V.Z.)
- I. Ya. Postovskiy Institute of Organic Synthesis, Ural Division of the Russian Academy of Sciences, 22 S. Kovalevskoy Street, 620219 Yekaterinburg, Russia
| | - Sandipan Halder
- Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur 440010, India
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6
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Zhou S, Liu Y, Wang S, Wang L. Chemical features and machine learning assisted predictions of protein-ligand short hydrogen bonds. Sci Rep 2023; 13:13741. [PMID: 37612311 PMCID: PMC10447522 DOI: 10.1038/s41598-023-40614-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023] Open
Abstract
There are continuous efforts to elucidate the structure and biological functions of short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms reside more than 0.3 Å closer than the sum of their van der Waals radii. In this work, we evaluate 1070 atomic-resolution protein structures and characterize the common chemical features of SHBs formed between the side chains of amino acids and small molecule ligands. We then develop a machine learning assisted prediction of protein-ligand SHBs (MAPSHB-Ligand) model and reveal that the types of amino acids and ligand functional groups as well as the sequence of neighboring residues are essential factors that determine the class of protein-ligand hydrogen bonds. The MAPSHB-Ligand model and its implementation on our web server enable the effective identification of protein-ligand SHBs in proteins, which will facilitate the design of biomolecules and ligands that exploit these close contacts for enhanced functions.
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Affiliation(s)
| | - Yuanhao Liu
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA
| | - Sijian Wang
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA.
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ, 08854, USA.
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7
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Brzeski J, Ciesielska A, Makowski M. Theoretical Study on the Alkylimino-Substituted Sulfonamides with Potential Biological Activity. J Phys Chem B 2023; 127:6620-6627. [PMID: 37478052 PMCID: PMC10405214 DOI: 10.1021/acs.jpcb.3c01965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/14/2023] [Indexed: 07/23/2023]
Abstract
Antibiotics play a key role in the fight against bacterial diseases. However, bacteria quickly learn how to minimize the effects of antibiotics and strengthen their resistance. Thus, the fight against them becomes more and more difficult and there is a constant search for new bactericidal compounds. It is important in this type of search to determine the basic properties of compounds such as pKa, hydrogen bond formation, or hydrophobicity. Here, we present the results of our in silico study of five sulfonamide derivatives differing in alkylamine substituent length. Based on our results, we propose a model of three possible pKa values for each of the studied compounds. Interestingly, the use of Muckerman's approach for pKa determination exhibits that theoretical and experimental results are in very good agreement. Intramolecular hydrogen bond formation affects pKa. The strength of the H-bond interaction increases from ethyl to butylamine and then decreases with the elongation of the alkylamine chain. The obtained partition coefficients (expressed here in the value of log P) increase with the number of carbon atoms in the alkylamine chain following Lipinski's rule of five. The presented results provide important structural, physicochemical, and thermodynamic information that allows for the understanding of the influence of some sulfonamides and their possible activity.
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Affiliation(s)
- Jakub Brzeski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
| | | | - Mariusz Makowski
- Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, 80-308 Gdańsk, Poland
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8
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Ghosh AK, Mishevich JL, Kovela S, Shaktah R, Ghosh AK, Johnson M, Wang YF, Wong-Sam A, Agniswamy J, Amano M, Takamatsu Y, Hattori SI, Weber IT, Mitsuya H. Exploration of imatinib and nilotinib-derived templates as the P2-Ligand for HIV-1 protease inhibitors: Design, synthesis, protein X-ray structural studies, and biological evaluation. Eur J Med Chem 2023; 255:115385. [PMID: 37150084 PMCID: PMC10759558 DOI: 10.1016/j.ejmech.2023.115385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 04/13/2023] [Accepted: 04/14/2023] [Indexed: 05/09/2023]
Abstract
Structure-based design, synthesis, X-ray structural studies, and biological evaluation of a new series of potent HIV-1 protease inhibitors are described. These inhibitors contain various pyridyl-pyrimidine, aryl thiazole or alkylthiazole derivatives as the P2 ligands in combination with darunavir-like hydroxyethylamine sulfonamide isosteres. These heterocyclic ligands are inherent to kinase inhibitor drugs, such as nilotinib and imatinib. These ligands are designed to make hydrogen bonding interactions with the backbone atoms in the S2 subsite of HIV-1 protease. Various benzoic acid derivatives have been synthesized and incorporation of these ligands provided potent inhibitors that exhibited subnanomolar level protease inhibitory activity and low nanomolar level antiviral activity. Two high resolution X-ray structures of inhibitor-bound HIV-1 protease were determined. These structures provided important ligand-binding site interactions for further optimization of this class of protease inhibitors.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, United States.
| | - Jennifer L Mishevich
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, United States
| | - Satish Kovela
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, United States
| | - Ryan Shaktah
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, United States
| | - Ajay K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, United States
| | - Megan Johnson
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, United States
| | - Yuan-Fang Wang
- Department of Biology, Georgia State University, Atlanta, GA, 30303, United States
| | - Andres Wong-Sam
- Department of Biology, Georgia State University, Atlanta, GA, 30303, United States
| | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, GA, 30303, United States
| | - Masayuki Amano
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto, 860-8556, Japan
| | - Yuki Takamatsu
- Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan
| | - Shin-Ichiro Hattori
- Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan
| | - Irene T Weber
- Department of Biology, Georgia State University, Atlanta, GA, 30303, United States
| | - Hiroaki Mitsuya
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto, 860-8556, Japan; Refractory Viral Diseases, National Center for Global Health and Medicine Research Institute, Tokyo, 162-8655, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, United States
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9
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Zhou S, Liu Y, Wang S, Wang L. Chemical Features and Machine Learning Assisted Predictions of Protein-Ligand Short Hydrogen Bonds. RESEARCH SQUARE 2023:rs.3.rs-2895170. [PMID: 37292822 PMCID: PMC10246099 DOI: 10.21203/rs.3.rs-2895170/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
There are continuous efforts to elucidate the structure and biological functions of short hydrogen bonds (SHBs), whose donor and acceptor heteroatoms reside more than 0.3 A closer than the sum of their van der Waals radii. In this work, we evaluate 1070 atomic-resolution protein structures and characterize the common chemical features of SHBs formed between the side chains of amino acids and small molecule ligands. We then develop a machine learning assisted prediction of protein-ligand SHBs (MAPSHB-Ligand) model and reveal that the types of amino acids and ligand functional groups as well as the sequence of neighboring residues are essential factors that determine the class of protein-ligand hydrogen bonds. The MAPSHB-Ligand model and its implementation on our web server enable the effective identification of protein-ligand SHBs in proteins, which will facilitate the design of biomolecules and ligands that exploit these close contacts for enhanced functions.
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Affiliation(s)
| | - Yuanhao Liu
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Sijian Wang
- Department of Statistics, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, Piscataway, NJ 08854, USA
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10
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Deepa P, Thirumeignanam D. Understanding the impact of halogen functional group (Br, Cl, F, OH) in amprenavir ligand of the HIV protease. J Biomol Struct Dyn 2023; 41:12157-12170. [PMID: 36645135 DOI: 10.1080/07391102.2023.2166121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 01/01/2023] [Indexed: 01/17/2023]
Abstract
We focused our attention towards the most dreadful disease that threatens the mankind of 20th century - Acquired immunodeficiency syndrome (AIDS), caused through the human immunodeficiency virus (HIV) and a sexually transmitted infection (STI). In this study, our foremost interest was to identify the potency and stability of HIV ligand- Amprenavir (APV) and its modelled functional group (Br, Cl, F, CF3, CH3, NH2) ligands through halogen and hydrogen bond contact, which will have a clear portrait on the structure activity of protein ligand interactions. This will assist chemist in synthesizing novel APV ligands, which are expected to inhibit the activity of HIV-1 protease enzyme. The binding strength of Amprenavir ligand with interacting hinge region amino acid side chains: Isoleucine (ILE 147, 150, 184), Valine (VAL 82), Alanine (ALA 28), Aspartic acid (25, 30, 125, 130) and Glycine (GLY 127, 149) were understood through interaction energy calculations at HF, B3LYP, M052X, MP2 level of theories for different basis set (6-311 G**, LANL2DZ). The present work will reveal an understandable picture about the halogen and hydrogen bond interaction that grip the contact of ligand and amino acids in the hinge region. Overall the Halogen atom (Br, Cl, F) functional groups improved the binding strength of APV in HIV protease; which provide a new novel path for the functional group preference on the ligand that enclose perfectly with the amino acid in the hinge region.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Palanisamy Deepa
- Department of Physics, Manonmaniam Sundaranar University, Tirunelveli, India
| | - Duraisamy Thirumeignanam
- Department of Animal Nutrition, Veterinary College and Research Institute, Tamil Nadu Veterinary and Animal Sciences University, Tirunelveli, India
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11
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Wong-Sam A, Wang YF, Kneller DW, Kovalevsky AY, Ghosh AK, Harrison RW, Weber IT. HIV-1 protease with 10 lopinavir and darunavir resistance mutations exhibits altered inhibition, structural rearrangements and extreme dynamics. J Mol Graph Model 2022; 117:108315. [PMID: 36108568 PMCID: PMC10091457 DOI: 10.1016/j.jmgm.2022.108315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 08/17/2022] [Accepted: 08/21/2022] [Indexed: 01/14/2023]
Abstract
Antiretroviral drug resistance is a therapeutic obstacle for people with HIV. HIV protease inhibitors darunavir and lopinavir are recommended for resistant infections. We characterized a protease mutant (PR10x) derived from a highly resistant clinical isolate including 10 mutations associated with resistance to lopinavir and darunavir. Compared to the wild-type protease, PR10x exhibits ∼3-fold decrease in catalytic efficiency and Ki values of 2-3 orders of magnitude worse for darunavir, lopinavir, and potent investigational inhibitor GRL-519. Crystal structures of the mutant were solved in a ligand-free form and in complex with GRL-519. The structures show altered interactions in the active site, flap-core interface, hydrophobic core, hinge region, and 80s loop compared to the corresponding wild-type protease structures. The ligand-free crystal structure exhibits a highly curled flap conformation which may amplify drug resistance. Molecular dynamics simulations performed for 1 μs on ligand-free dimers showed extremely large fluctuations in the flaps for PR10x compared to equivalent simulations on PR with a single L76V mutation or wild-type protease. This analysis offers insight about the synergistic effects of mutations in highly resistant variants.
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Affiliation(s)
- Andres Wong-Sam
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Yuan-Fang Wang
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA
| | - Daniel W Kneller
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Andrey Y Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Arun K Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN, 47907, USA
| | - Robert W Harrison
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA; Department of Computer Science, Georgia State University, Atlanta, GA, 30303, USA
| | - Irene T Weber
- Department of Biology, Georgia State University, Atlanta, GA, 30303, USA; Department of Chemistry, Georgia State University, Atlanta, GA, 30303, USA.
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12
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Tukulula M, Olasupo IA, Mugumbate GC, Lobb KA, Klein R, Sayed Y, Tshiwawa T, Kaye PT. Synthesis, stereochemistry and in vitro STD NMR and in silico HIV-1 PR enzyme-binding potential of MBH-derived inhibitors. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Kaur N, Sharma K, Ahlawat N. Synthesis of heterocycles by use of thioureas as chiral auxiliaries and as reactants. PHOSPHORUS SULFUR 2022. [DOI: 10.1080/10426507.2022.2134375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Affiliation(s)
- Navjeet Kaur
- Department of Chemistry & Division of Research and Development, Lovely Professional University, Phagwara, India
- Department of Physical Sciences, Chemistry, Banasthali Vidyapith, Jaipur, India
| | - Khushi Sharma
- Department of Physical Sciences, Chemistry, Banasthali Vidyapith, Jaipur, India
| | - Neha Ahlawat
- Department of Physical Sciences, Chemistry, Banasthali Vidyapith, Jaipur, India
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14
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Yu YX, Wang W, Sun HB, Zhang LL, Wang LF, Yin YY. Decoding drug resistant mechanism of V32I, I50V and I84V mutations of HIV-1 protease on amprenavir binding by using molecular dynamics simulations and MM-GBSA calculations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2022; 33:805-831. [PMID: 36322686 DOI: 10.1080/1062936x.2022.2140708] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/20/2022] [Indexed: 06/16/2023]
Abstract
Mutations V32I, I50V and I84V in the HIV-1 protease (PR) induce drug resistance towards drug amprenavir (APV). Multiple short molecular dynamics (MSMD) simulations and molecular mechanics generalized Born surface area (MM-GBSA) method were utilized to investigate drug-resistant mechanism of V32I, I50V and I84V towards APV. Dynamic information arising from MSMD simulations suggest that V32I, I50V and I84V highly affect structural flexibility, motion modes and conformational behaviours of two flaps in the PR. Binding free energies calculated by MM-GBSA method suggest that the decrease in binding enthalpy and the increase in binding entropy induced by mutations V32I, I50V and I84V are responsible for drug resistance of the mutated PRs on APV. The energetic contributions of separate residues on binding of APV to the PR show that V32I, I50V and I84V highly disturb the interactions of two flaps with APV and mostly drive the decrease in binding ability of APV to the PR. Thus, the conformational changes of two flaps in the PR caused by V32I, I50V and I84V play key roles in drug resistance of three mutated PR towards APV. This study can provide useful dynamics information for the design of potent inhibitors relieving drug resistance.
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Affiliation(s)
- Y X Yu
- School of Science, Shandong Jiaotong University, Jinan, China
| | - W Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - H B Sun
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L L Zhang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - L F Wang
- School of Science, Shandong Jiaotong University, Jinan, China
| | - Y Y Yin
- School of Science, Shandong Jiaotong University, Jinan, China
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15
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Bilen E, Özdemir Özmen Ü, Çete S, Alyar S, Yaşar A. Bioactive sulfonyl hydrazones with alkyl derivative: Characterization, ADME properties, molecular docking studies and investigation of inhibition on choline esterase enzymes for the diagnosis of Alzheimer's disease. Chem Biol Interact 2022; 360:109956. [PMID: 35452634 DOI: 10.1016/j.cbi.2022.109956] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 04/10/2022] [Accepted: 04/14/2022] [Indexed: 01/24/2023]
Abstract
In this work, new sulfonylhydrazone compounds with alkyl derivatives (SH1- SH4 series) were synthesized via a green chemistry method, and their inhibition effects on acetylcholinesterase and butyrylcholinesterase (AChE, BChE) were determined in vitro. This work was designed in two stages; in the first stage, using compounds that contain both sulfonamide and hydrazine groups which have important pharmacological properties, a series of sulfonyl hydrazone with alkyl derivatives (SH1- SH4) were synthesized with a method that is less time-consuming and more environmentalist that was by using different substitute groups containing aldehyde and ketone compounds. The structures of the synthesized compounds were characterized by elemental analyses, 1H NMR, 13C NMR, FT-IR methods. In the second stage, the effects of the synthesized sulfonyl hydrazones with alkyl derivatives on acetylcholinesterase and butyrylcholinesterase enzymes were examined. According to the results, all the synthesized compounds inhibited AChE and BChE enzymes. When the IC50 values were compared, SH2-3 (IC50 = 5.27 ± 0.05 μM) and SH3-3 (IC50 = 12.29 ± 1.47 μM) compounds which are containing the butyl group have the best inhibition effect on the AChE enzyme and BChE enzyme, respectively. In addition, the predictive properties of all compounds in terms of drug similarity were scanned using five Lipinski rules and ADME estimations. In silico ADME studies play an important role in improving and predicting drug compounds. In the ADME study; The absorption, distribution, metabolism, elimination, and properties of the molecules given below were theoretically calculated. Also, to evaluate the binding interactions between the sulfonylhydrazone compounds and enzymes, molecular docking studies were performed and the compounds with the best inhibition effect SH2-3 (for AChE enzyme) and SH3-3 (for BChE enzyme) were tested. Both in vitro and silico the results showed that two compounds could act as potent inhibitors of AChE, BChE.
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Affiliation(s)
- Esra Bilen
- Department of Chemistry, Faculty of Science, Gazi University, 06500, Ankara, Turkey
| | - Ümmühan Özdemir Özmen
- Department of Chemistry, Faculty of Science, Gazi University, 06500, Ankara, Turkey.
| | - Servet Çete
- Department of Chemistry, Faculty of Science, Gazi University, 06500, Ankara, Turkey
| | - Saliha Alyar
- Department of Chemistry, Faculty of Science, Karatekin University, 18100, Çankırı, Turkey
| | - Ahmet Yaşar
- Department of Chemistry, Faculty of Science, Gazi University, 06500, Ankara, Turkey
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16
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Ghosh AK, Kovela S, Sharma A, Shahabi D, Ghosh AK, Hopkins DR, Yadav M, Johnson ME, Agniswamy J, Wang YF, Aoki M, Amano M, Weber IT, Mitsuya H. Design, Synthesis and X-ray Structural Studies of Potent HIV-1 Protease Inhibitors Containing C-4 Substituted Tricyclic Hexahydro-furofuran derivatives as P2 ligands. ChemMedChem 2022; 17:e202200058. [PMID: 35170223 PMCID: PMC9081228 DOI: 10.1002/cmdc.202200058] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Indexed: 11/06/2022]
Abstract
The design, synthesis, X-ray structural, and biological evaluation of a series of highly potent HIV-1 protease inhibitors are reported herein. These inhibitors incorporated novel cyclohexane-fused tricyclic bis -tetrahydrofuran as P2 ligands in combination with a variety of P1 and P2'-ligands. Compound 4d with a difluoromethylphenyl P1 ligand and a cyclopropylaminobenzothiazole P2' ligand exhibited the most potent antiviral activity. Also, it maintained highly potent antiviral activity against a panel of highly multidrug-resistant HIV-1 variants. The corresponding inhibitor 5d with an enantiomeric ligand was significantly less potent in these antiviral assays. The new P2 ligands were synthesized in optically active form using enzymatic desymmetrization of meso -diols as the key step. To obtain molecular insight, high resolution X-ray structures of inhibitors 4b and 5d -bound HIV-1 protease were determined and structural analyses are highlighted here.
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Affiliation(s)
- Arun K Ghosh
- Purdue University, Departments of Chemistry and Medicinal Chemistry, 560 Oval Drive, 47907, West Lafayette, UNITED STATES
| | | | | | | | | | | | | | | | - Johnson Agniswamy
- Georgia State University Department of Biology, Biology and Chemistry, UNITED STATES
| | - Yuan-Fang Wang
- Georgia State University Department of Biology, Biology and Chemistry, UNITED STATES
| | - Manabu Aoki
- Kumamoto University: Kumamoto Daigaku, Department of Hematology and Infectious Disease, JAPAN
| | - Masayuki Amano
- Kumamoto University: Kumamoto Daigaku, Department of Hematology and Infectious Disease, JAPAN
| | - Irene T Weber
- Georgia State University Department of Biology, Biology and Chemistry, UNITED STATES
| | - Hiroaki Mitsuya
- National Center for Global Health and Medicine: Kokuritsu Kenkyu Kaihatsu Hojin Kokuritsu Kokusai Iryo Kenkyu Center, Center for Clinical Sciences, JAPAN
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17
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Synthesis of and molecular docking studies of azomethine- tethered sulfonamides as carbonic anhydrase II & 15-lipoxygenase inhibitors. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130821] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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18
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Mahmudpour M, Nabipour I, Keshavarz M, Farrokhnia M. Virtual Screening on Marine Natural Products for Discovering TMPRSS2 Inhibitors. Front Chem 2021; 9:722633. [PMID: 34712648 PMCID: PMC8545810 DOI: 10.3389/fchem.2021.722633] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 09/17/2021] [Indexed: 01/08/2023] Open
Abstract
Although SARS-CoV-2 entry to cells strictly depends on angiotensin-converting enzyme 2 (ACE2), the virus also needs transmembrane serine protease 2 (TMPRSS2) for its spike protein priming. It has been shown that the entrance of SARS-CoV-2 through ACE2 can be blocked by cellular TMPRSS2 blockers. The main aim of this study was to find potential inhibitor(s) of TMPRSS2 through virtual screening against a homology model of TMPRSS2 using the library of marine natural products (MNPs). The homology modeling technique for generating a three-dimensional structure of TMPRSS2 was applied. Molecular docking, MM-GBSA and absorption, distribution, metabolism, excretion (ADME) evaluations were performed to investigate the inhibitory activity of marine natural products (MNPs) against TMPRSS2 and their pharmacokinetic properties. Camostat and nafamostat mesylate were used as the standard inhibitory molecules. Seven MNPs were able to inhibit TMPRSS2 better than the standard compounds. MNP 10 with CAS number 107503-09-3, called Watasenia β-D- Preluciferyl glucopyrasoiuronic acid, was found to be the best inhibitor of TMPRSS2 with acceptable pharmacokinetic properties. Herein, for the first time, a new marine natural product was introduced with potent inhibitory effects against TMPRSS2. MNP 10 exhibited favorable drug-like pharmacokinetic properties and it promises a novel TMPRSS2 blocker to combat SARS-CoV-2.
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Affiliation(s)
- Mehdi Mahmudpour
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Iraj Nabipour
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Mohsen Keshavarz
- The Persian Gulf Tropical Medicine Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
| | - Maryam Farrokhnia
- The Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, Iran
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19
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Sherry D, Worth R, Sayed Y. Elasticity-Associated Functionality and Inhibition of the HIV Protease. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1371:79-108. [PMID: 34351572 DOI: 10.1007/5584_2021_655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
HIV protease plays a critical role in the life cycle of the virus through the generation of mature and infectious virions. Detailed knowledge of the structure of the enzyme and its substrate has led to the development of protease inhibitors. However, the development of resistance to all currently available protease inhibitors has contributed greatly to the decreased success of antiretroviral therapy. When therapy failure occurs, multiple mutations are found within the protease sequence starting with primary mutations, which directly impact inhibitor binding, which can also negatively impact viral fitness and replicative capacity by decreasing the binding affinity of the natural substrates to the protease. As such, secondary mutations which are located outside of the active site region accumulate to compensate for the recurrently deleterious effects of primary mutations. However, the resistance mechanism of these secondary mutations is not well understood, but what is known is that these secondary mutations contribute to resistance in one of two ways, either through increasing the energetic penalty associated with bringing the protease into the closed conformation, or, through decreasing the stability of the protein/drug complex in a manner that increases the dissociation rate of the drug, leading to diminished inhibition. As a result, the elasticity of the enzyme-substrate complex has been implicated in the successful recognition and catalysis of the substrates which may be inferred to suggest that the elasticity of the enzyme/drug complex plays a role in resistance. A realistic representation of the dynamic nature of the protease may provide a more powerful tool in structure-based drug design algorithms.
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Affiliation(s)
- Dean Sherry
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Roland Worth
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa
| | - Yasien Sayed
- Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand, Johannesburg, South Africa.
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20
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Ota R, So K, Tsuda M, Higuchi Y, Yamashita F. Prediction of HIV drug resistance based on the 3D protein structure: Proposal of molecular field mapping. PLoS One 2021; 16:e0255693. [PMID: 34347839 PMCID: PMC8336827 DOI: 10.1371/journal.pone.0255693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 07/21/2021] [Indexed: 11/19/2022] Open
Abstract
A method for predicting HIV drug resistance by using genotypes would greatly assist in selecting appropriate combinations of antiviral drugs. Models reported previously have had two major problems: lack of information on the 3D protein structure and processing of incomplete sequencing data in the modeling procedure. We propose obtaining the 3D structural information of viral proteins by using homology modeling and molecular field mapping, instead of just their primary amino acid sequences. The molecular field potential parameters reflect the physicochemical characteristics associated with the 3D structure of the proteins. We also introduce the Bayesian conditional mutual information theory to estimate the probabilities of occurrence of all possible protein candidates from an incomplete sequencing sample. This approach allows for the effective use of uncertain information for the modeling process. We applied these data analysis techniques to the HIV-1 protease inhibitor dataset and developed drug resistance prediction models with reasonable performance.
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Affiliation(s)
- Ryosaku Ota
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Kanako So
- Department of Applied Pharmaceutics and Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Masahiro Tsuda
- Department of Applied Pharmaceutics and Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Yuriko Higuchi
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
| | - Fumiyoshi Yamashita
- Department of Drug Delivery Research, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
- Department of Applied Pharmaceutics and Pharmacokinetics, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
- * E-mail:
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21
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Korie NPU, Tandoh KZ, Kwofie SK, Quaye O. Therapeutic potential of HIV-1 entry inhibitor peptidomimetics. Exp Biol Med (Maywood) 2021; 246:1060-1068. [PMID: 33596698 PMCID: PMC8113741 DOI: 10.1177/1535370221990870] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Human immunodeficiency virus 1 (HIV-1) infection remains a public health concern globally. Although great strides in the management of HIV-1 have been achieved, current highly active antiretroviral therapy is limited by multidrug resistance, prolonged use-related effects, and inability to purge the HIV-1 latent pool. Even though novel therapeutic options with HIV-1 broadly neutralizing antibodies (bNAbs) are being explored, the scalability of bNAbs is limited by economic cost of production and obligatory requirement for parenteral administration. However, these limitations can be addressed by antibody mimetics/peptidomimetics of HIV-1 bNAbs. In this review we discuss the limitations of HIV-1 bNAbs as HIV-1 entry inhibitors and explore the potential therapeutic use of antibody mimetics/peptidomimetics of HIV-1 entry inhibitors as an alternative for HIV-1 bNAbs. We highlight the reduced cost of production, high specificity, and oral bioavailability of peptidomimetics compared to bNAbs to demonstrate their suitability as candidates for novel HIV-1 therapy and conclude with some perspectives on future research toward HIV-1 novel drug discovery.
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Affiliation(s)
- Nneka PU Korie
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra 00233, Ghana
| | - Kwesi Z Tandoh
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra 00233, Ghana
| | - Samuel K Kwofie
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic and Applied Sciences, University of Ghana, Accra 00233, Ghana
| | - Osbourne Quaye
- Department of Biochemistry, Cell and Molecular Biology, West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra 00233, Ghana
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22
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Laville P, Petitjean M, Regad L. Structural Impacts of Drug-Resistance Mutations Appearing in HIV-2 Protease. Molecules 2021; 26:molecules26030611. [PMID: 33503916 PMCID: PMC7865771 DOI: 10.3390/molecules26030611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/15/2021] [Accepted: 01/19/2021] [Indexed: 11/16/2022] Open
Abstract
The use of antiretroviral drugs is accompanied by the emergence of HIV-2 resistances. Thus, it is important to elucidate the mechanisms of resistance to antiretroviral drugs. Here, we propose a structural analysis of 31 drug-resistant mutants of HIV-2 protease (PR2) that is an important target against HIV-2 infection. First, we modeled the structures of each mutant. We then located structural shifts putatively induced by mutations. Finally, we compared wild-type and mutant inhibitor-binding pockets and interfaces to explore the impacts of these induced structural deformations on these two regions. Our results showed that one mutation could induce large structural rearrangements in side-chain and backbone atoms of mutated residue, in its vicinity or further. Structural deformations observed in side-chain atoms are frequent and of greater magnitude, that confirms that to fight drug resistance, interactions with backbone atoms should be favored. We showed that these observed structural deformations modify the conformation, volume, and hydrophobicity of the binding pocket and the composition and size of the PR2 interface. These results suggest that resistance mutations could alter ligand binding by modifying pocket properties and PR2 stability by impacting its interface. Our results reinforce the understanding of the effects of mutations that occurred in PR2 and the different mechanisms of PR2 resistance.
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23
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Affiliation(s)
- Mark Aldren M. Feliciano
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
| | - Brian Gold
- Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico 87131, United States
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24
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Dogan B, Durdagi S. Drug Re-positioning Studies for Novel HIV-1 Inhibitors Using Binary QSAR Models and Multi-target-driven In Silico Studies. Mol Inform 2020; 40:e2000012. [PMID: 33405326 DOI: 10.1002/minf.202000012] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 08/16/2020] [Indexed: 12/20/2022]
Abstract
Current antiretroviral therapies against HIV involve the usage of at least two drugs that target different stages of HIV life cycle. However, potential drug interactions and side effects pose a problem. A promising concept for complex disease treatment is 'one molecule-multiple target' approach to overcome undesired effects of multiple drugs. Additionally, it is beneficial to consider drug re-purposing due to the cost of taking a drug into the market. Taking these into account, here potential anti-HIV compounds are suggested by virtually screening small approved drug molecules and clinical candidates. Initially, binary QSAR models are used to predict the therapeutic activity of around 7900 compounds against HIV and to predict the toxicity of molecules with high therapeutic activities. Selected compounds are considered for molecular docking studies against two targets, HIV-1 protease enzyme, and chemokine co-receptor CCR5. The top docking poses for all 549 molecules are then subjected to short (1 ns) individual molecular dynamics (MD) simulations and they are ranked based on their calculated relative binding free energies. Finally, 25 molecules are selected for long (200 ns) MD simulations, and 5 molecules are suggested as promising multi-target HIV agents. The results of this study may open new avenues for the designing of new dual HIV-1 inhibitor scaffolds.
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Affiliation(s)
- Berna Dogan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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25
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Kneller DW, Agniswamy J, Harrison RW, Weber IT. Highly drug-resistant HIV-1 protease reveals decreased intra-subunit interactions due to clusters of mutations. FEBS J 2020; 287:3235-3254. [PMID: 31920003 PMCID: PMC7343616 DOI: 10.1111/febs.15207] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/16/2019] [Accepted: 01/08/2020] [Indexed: 01/07/2023]
Abstract
Drug-resistance is a serious problem for treatment of the HIV/AIDS pandemic. Potent clinical inhibitors of HIV-1 protease show several orders of magnitude worse inhibition of highly drug-resistant variants. Hence, the structure and enzyme activities were analyzed for HIV protease mutant HIV-1 protease (EC 3.4.23.16) (PR) with 22 mutations (PRS5B) from a clinical isolate that was selected by machine learning to represent high-level drug-resistance. PRS5B has 22 mutations including only one (I84V) in the inhibitor binding site; however, clinical inhibitors had poor inhibition of PRS5B activity with kinetic inhibition value (Ki ) values of 4-1000 nm or 18- to 8000-fold worse than for wild-type PR. High-resolution crystal structures of PRS5B complexes with the best inhibitors, amprenavir (APV) and darunavir (DRV) (Ki ~ 4 nm), revealed only minor changes in protease-inhibitor interactions. Instead, two distinct clusters of mutations in distal regions induce coordinated conformational changes that decrease favorable internal interactions across the entire protein subunit. The largest structural rearrangements are described and compared to other characterized resistant mutants. In the protease hinge region, the N83D mutation eliminates a hydrogen bond connecting the hinge and core of the protease and increases disorder compared to highly resistant mutants PR with 17 mutations and PR with 20 mutations with similar hinge mutations. In a distal β-sheet, mutations G73T and A71V coordinate with accessory mutations to bring about shifts that propagate throughout the subunit. Molecular dynamics simulations of ligand-free dimers show differences consistent with loss of interactions in mutant compared to wild-type PR. Clusters of mutations exhibit both coordinated and antagonistic effects, suggesting PRS5B may represent an intermediate stage in the evolution of more highly resistant variants. DATABASES: Structural data are available in Protein Data Bank under the accession codes 6P9A and 6P9B for PRS5B/DRV and PRS5B/APV, respectively.
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Affiliation(s)
- Daniel W. Kneller
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States of America
| | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States of America
| | - Robert W. Harrison
- Department of Computer Science, Georgia State University, Atlanta, Georgia 30303, United States of America
| | - Irene T. Weber
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States of America,Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, United States of America,Author of correspondence:
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26
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Peng C, Wang J, Xu Z, Cai T, Zhu W. Accurate prediction of relative binding affinities of a series of HIV-1 protease inhibitors using semi-empirical quantum mechanical charge. J Comput Chem 2020; 41:1773-1780. [PMID: 32352193 DOI: 10.1002/jcc.26218] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 04/03/2020] [Accepted: 04/18/2020] [Indexed: 11/05/2022]
Abstract
A major challenge in computer-aided drug design is the accurate estimation of ligand binding affinity. Here, a new approach that combines the adaptive steered molecular dynamics (ASMD) and partial atomic charges calculated by semi-empirical quantum mechanics (SQMPC), namely ASMD-SQMPC, is suggested to predict the ligand binding affinities, with 24 HIV-1 protease inhibitors as testing examples. In the ASMD-SQMPC, the relative binding free energy (ΔG) is reflected by the average maximum potential of mean force (<PMF>max ) between bound and unbound states. The correlation coefficient (R2 ) between the <PMF>max and experimentally determined ΔG is 0.86, showing a significant improvement compared with the conventional ASMD (R2 = 0.52). Therefore, this study provides an efficient approach to predict the relative ΔG and reveals the significance of precise partial atomic charges in the theoretical simulations.
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Affiliation(s)
- Cheng Peng
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, China
| | - Jinan Wang
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, China
| | - Tingting Cai
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research; Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai, China.,University of Chinese Academy of Sciences, No. 19A Yuquan Road, Beijing, China.,Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao, China
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27
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Sahin K. Investigation of novel indole-based HIV-1 protease inhibitors using virtual screening and text mining. J Biomol Struct Dyn 2020; 39:3638-3648. [PMID: 32496942 DOI: 10.1080/07391102.2020.1775121] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Human immunodeficiency virus type 1 protease (HIV-1 PR) inhibitors have been used as possible therapeutic agents for HIV-1 infection in clinical study. Most of the HIV therapy-related problems usually stem from long-term opioid usage. The rapid development of drug-resistant variants limits the long-term effectiveness of current inhibitors as therapeutic agents. In addition, different side effects were reported. Further drug development is required to design new compounds which have similar efficacy as the drugs currently used in HIV infection but without having undesirable side effects. Indole derivatives were considered as one of the effective HIV inhibitors. Indole is an important fragment used in many FDAapproved medicines and used in various diseases. For this purpose, in this study the molecules containing" indole" keywords in their fragments are taken from the Specs-SC database which includes 212520 small molecules. 5194 molecules that include indole keywords are selected. These selected molecules are then screened against HIV-1 PR target protein using molecular docking simulations. Then the molecules are ranked according to the their docking scores. Top docking poses of ten ligands and FDA approved drug Amprenavir are subjected to 100 ns Molecular Dynamics (MD) simulations. Thus, by using combination of text mining and integrated molecular modeling approaches, we identified novel indole-based hits against HIV-1 PR.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kader Sahin
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
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28
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Lawal MM, Sanusi ZK, Govender T, Maguire GE, Honarparvar B, Kruger HG. From Recognition to Reaction Mechanism: An Overview on the Interactions between HIV-1 Protease and its Natural Targets. Curr Med Chem 2020; 27:2514-2549. [DOI: 10.2174/0929867325666181113122900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 11/04/2018] [Accepted: 11/07/2018] [Indexed: 12/28/2022]
Abstract
Current investigations on the Human Immunodeficiency Virus Protease (HIV-1
PR) as a druggable target towards the treatment of AIDS require an update to facilitate further
development of promising inhibitors with improved inhibitory activities. For the past two
decades, up to 100 scholarly reports appeared annually on the inhibition and catalytic mechanism
of HIV-1 PR. A fundamental literature review on the prerequisite of HIV-1 PR action
leading to the release of the infectious virion is absent. Herein, recent advances (both computationally
and experimentally) on the recognition mode and reaction mechanism of HIV-1 PR
involving its natural targets are provided. This review features more than 80 articles from
reputable journals. Recognition of the natural Gag and Gag-Pol cleavage junctions by this
enzyme and its mutant analogs was first addressed. Thereafter, a comprehensive dissect of
the enzymatic mechanism of HIV-1 PR on its natural polypeptide sequences from literature
was put together. In addition, we highlighted ongoing research topics in which in silico
methods could be harnessed to provide deeper insights into the catalytic mechanism of the
HIV-1 protease in the presence of its natural substrates at the molecular level. Understanding
the recognition and catalytic mechanism of HIV-1 PR leading to the release of an infective
virion, which advertently affects the immune system, will assist in designing mechanismbased
inhibitors with improved bioactivity.
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Affiliation(s)
- Monsurat M. Lawal
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Zainab K. Sanusi
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Glenn E.M. Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
| | - Hendrik G. Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban 4041, South Africa
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29
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Bastys T, Gapsys V, Walter H, Heger E, Doncheva NT, Kaiser R, de Groot BL, Kalinina OV. Non-active site mutants of HIV-1 protease influence resistance and sensitisation towards protease inhibitors. Retrovirology 2020; 17:13. [PMID: 32430025 PMCID: PMC7236880 DOI: 10.1186/s12977-020-00520-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/04/2020] [Indexed: 02/07/2023] Open
Abstract
Background HIV-1 can develop resistance to antiretroviral drugs, mainly through mutations within the target regions of the drugs. In HIV-1 protease, a majority of resistance-associated mutations that develop in response to therapy with protease inhibitors are found in the protease’s active site that serves also as a binding pocket for the protease inhibitors, thus directly impacting the protease-inhibitor interactions. Some resistance-associated mutations, however, are found in more distant regions, and the exact mechanisms how these mutations affect protease-inhibitor interactions are unclear. Furthermore, some of these mutations, e.g. N88S and L76V, do not only induce resistance to the currently administered drugs, but contrarily induce sensitivity towards other drugs. In this study, mutations N88S and L76V, along with three other resistance-associated mutations, M46I, I50L, and I84V, are analysed by means of molecular dynamics simulations to investigate their role in complexes of the protease with different inhibitors and in different background sequence contexts. Results Using these simulations for alchemical calculations to estimate the effects of mutations M46I, I50L, I84V, N88S, and L76V on binding free energies shows they are in general in line with the mutations’ effect on \documentclass[12pt]{minimal}
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\begin{document}$$IC_{50}$$\end{document}IC50 values. For the primary mutation L76V, however, the presence of a background mutation M46I in our analysis influences whether the unfavourable effect of L76V on inhibitor binding is sufficient to outweigh the accompanying reduction in catalytic activity of the protease. Finally, we show that L76V and N88S changes the hydrogen bond stability of these residues with residues D30/K45 and D30/T31/T74, respectively. Conclusions We demonstrate that estimating the effect of both binding pocket and distant mutations on inhibitor binding free energy using alchemical calculations can reproduce their effect on the experimentally measured \documentclass[12pt]{minimal}
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\begin{document}$$IC_{50}$$\end{document}IC50 values. We show that distant site mutations L76V and N88S affect the hydrogen bond network in the protease’s active site, which offers an explanation for the indirect effect of these mutations on inhibitor binding. This work thus provides valuable insights on interplay between primary and background mutations and mechanisms how they affect inhibitor binding.
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Affiliation(s)
- Tomas Bastys
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany.,Saarbrücken Graduate School of Computer Science, University of Saarland, 66123, Saarbrücken, Germany
| | - Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Hauke Walter
- Medizinisches Labor Stendal, 39576, Stendal, Germany
| | - Eva Heger
- Institute of Virology, University of Cologne, 50935, Cologne, Germany
| | - Nadezhda T Doncheva
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany.,Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Rolf Kaiser
- Institute of Virology, University of Cologne, 50935, Cologne, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics, Max Planck Institute for Biophysical Chemistry, 37077, Göttingen, Germany
| | - Olga V Kalinina
- Department for Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123, Saarbrücken, Germany. .,Helmholtz Institute for Pharmaceutical Research Saarland (HIPS), Helmholtz Centre for Infection Research (HZI), 66123, Saarbrücken, Germany. .,Faculty of Medicine, Saarland University, 66421, Homburg, Germany.
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30
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Vazquez J, Deplano A, Herrero A, Gibert E, Herrero E, Luque FJ. Assessing the Performance of Mixed Strategies To Combine Lipophilic Molecular Similarity and Docking in Virtual Screening. J Chem Inf Model 2020; 60:4231-4245. [PMID: 32364713 DOI: 10.1021/acs.jcim.9b01191] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The accuracy of structure-based (SB) virtual screening (VS) is heavily affected by the scoring function used to rank a library of screened compounds. Even in cases where the docked pose agrees with the experimental binding mode of the ligand, the limitations of current scoring functions may lead to sensible inaccuracies in the ability to discriminate between actives and inactives. In this context, the combination of SB and ligand-based (LB) molecular similarity may be a promising strategy to increase the hit rates in VS. This study explores different strategies that aim to exploit the synergy between LB and SB methods in order to mitigate the limitations of these techniques, and to enhance the performance of VS studies by means of a balanced combination between docking scores and three-dimensional (3D) similarity. Particularly, attention is focused to the use of measurements of molecular similarity with PharmScreen, which exploits the 3D distribution of atomic lipophilicity determined from quantum mechanical-based continuum solvation calculations performed with the MST model, in conjunction with three docking programs: Glide, rDock, and GOLD. Different strategies have been explored to combine the information provided by docking and similarity measurements for re-ranking the screened ligands. For a benchmarking of 44 datasets, including 41 targets, the hybrid methods increase the identification of active compounds, according to the early (ROCe%) and total (AUC) enrichment metrics of VS, compared to pure LB and SB methods. Finally, the hybrid approaches are also more effective in enhancing the chemical diversity of active compounds. The datasets employed in this work are available in https://github.com/Pharmacelera/Molecular-Similarity-and-Docking.
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Affiliation(s)
- Javier Vazquez
- Pharmacelera, Plaça Pau Vila, 1, Sector C 2a, Edificio Palau de Mar, Barcelona 08039, Spain.,Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB), and Institute of Theoretical and Computational Chemistry (IQTC-UB), University of Barcelona, Av. Prat de la Riba 171, Santa Coloma de Gramanet E-08921, Spain
| | - Alessandro Deplano
- Pharmacelera, Plaça Pau Vila, 1, Sector C 2a, Edificio Palau de Mar, Barcelona 08039, Spain
| | - Albert Herrero
- Pharmacelera, Plaça Pau Vila, 1, Sector C 2a, Edificio Palau de Mar, Barcelona 08039, Spain
| | - Enric Gibert
- Pharmacelera, Plaça Pau Vila, 1, Sector C 2a, Edificio Palau de Mar, Barcelona 08039, Spain
| | - Enric Herrero
- Pharmacelera, Plaça Pau Vila, 1, Sector C 2a, Edificio Palau de Mar, Barcelona 08039, Spain
| | - F Javier Luque
- Department of Nutrition, Food Science and Gastronomy, Faculty of Pharmacy and Food Sciences, Institute of Biomedicine (IBUB), and Institute of Theoretical and Computational Chemistry (IQTC-UB), University of Barcelona, Av. Prat de la Riba 171, Santa Coloma de Gramanet E-08921, Spain
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31
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Ghosh AK, Kovela S, Osswald HL, Amano M, Aoki M, Agniswamy J, Wang YF, Weber IT, Mitsuya H. Structure-Based Design of Highly Potent HIV-1 Protease Inhibitors Containing New Tricyclic Ring P2-Ligands: Design, Synthesis, Biological, and X-ray Structural Studies. J Med Chem 2020; 63:4867-4879. [PMID: 32348139 PMCID: PMC7425579 DOI: 10.1021/acs.jmedchem.0c00202] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We describe here design, synthesis, and biological evaluation of a series of highly potent HIV-1 protease inhibitors containing stereochemically defined and unprecedented tricyclic furanofuran derivatives as P2 ligands in combination with a variety of sulfonamide derivatives as P2' ligands. These inhibitors were designed to enhance the ligand-backbone binding and van der Waals interactions in the protease active site. A number of inhibitors containing the new P2 ligand, an aminobenzothiazole as the P2' ligand and a difluorophenylmethyl as the P1 ligand, displayed very potent enzyme inhibitory potency and also showed excellent antiviral activity against a panel of highly multidrug-resistant HIV-1 variants. The tricyclic P2 ligand has been synthesized efficiently in an optically active form using enzymatic desymmetrization of meso-1,2-(dihydroxymethyl)cyclohex-4-ene as the key step. We determined high-resolution X-ray structures of inhibitor-bound HIV-1 protease. These structures revealed extensive interactions with the backbone atoms of HIV-1 protease and provided molecular insights into the binding properties of these new inhibitors.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry, Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Satish Kovela
- Department of Chemistry, Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Heather L. Osswald
- Department of Chemistry, Department of Medicinal Chemistry and Molecular Pharmacology, Purdue University, West Lafayette, Indiana 47907, United States
| | - Masayuki Amano
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto 860-8556, Japan
| | - Manabu Aoki
- Department of Medical Technology, Kumamoto Health Science University, Kumamoto 861-5598, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States; Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto 860-8556, Japan
| | - Johnson Agniswamy
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | - Yuan-Fang Wang
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | - Irene T. Weber
- Department of Biology, Georgia State University, Atlanta, Georgia 30303, United States
| | - Hiroaki Mitsuya
- Department of Refractory Viral Infection, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States; Department of Clinical Sciences, Kumamoto University Hospital, Kumamoto 860-8556, Japan
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32
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Melo R, Lemos A, Preto AJ, Bueschbell B, Matos-Filipe P, Barreto C, Almeida JG, Silva RDM, Correia JDG, Moreira IS. An Overview of Antiretroviral Agents for Treating HIV Infection in Paediatric Population. Curr Med Chem 2020; 27:760-794. [PMID: 30182840 DOI: 10.2174/0929867325666180904123549] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 07/11/2018] [Accepted: 07/11/2018] [Indexed: 12/19/2022]
Abstract
Paediatric Acquired ImmunoDeficiency Syndrome (AIDS) is a life-threatening and infectious disease in which the Human Immunodeficiency Virus (HIV) is mainly transmitted through Mother-To- Child Transmission (MTCT) during pregnancy, labour and delivery, or breastfeeding. This review provides an overview of the distinct therapeutic alternatives to abolish the systemic viral replication in paediatric HIV-1 infection. Numerous classes of antiretroviral agents have emerged as therapeutic tools for downregulation of different steps in the HIV replication process. These classes encompass Non- Nucleoside Analogue Reverse Transcriptase Inhibitors (NNRTIs), Nucleoside/Nucleotide Analogue Reverse Transcriptase Inhibitors (NRTIs/NtRTIs), INtegrase Inhibitors (INIs), Protease Inhibitors (PIs), and Entry Inhibitors (EIs). Co-administration of certain antiretroviral drugs with Pharmacokinetic Enhancers (PEs) may boost the effectiveness of the primary therapeutic agent. The combination of multiple antiretroviral drug regimens (Highly Active AntiRetroviral Therapy - HAART) is currently the standard therapeutic approach for HIV infection. So far, the use of HAART offers the best opportunity for prolonged and maximal viral suppression, and preservation of the immune system upon HIV infection. Still, the frequent administration of high doses of multiple drugs, their inefficient ability to reach the viral reservoirs in adequate doses, the development of drug resistance, and the lack of patient compliance compromise the complete HIV elimination. The development of nanotechnology-based drug delivery systems may enable targeted delivery of antiretroviral agents to inaccessible viral reservoir sites at therapeutic concentrations. In addition, the application of Computer-Aided Drug Design (CADD) approaches has provided valuable tools for the development of anti-HIV drug candidates with favourable pharmacodynamics and pharmacokinetic properties.
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Affiliation(s)
- Rita Melo
- Centro de Ciencias e Tecnologias Nucleares, Instituto Superior Tecnico, Universidade de Lisboa, CTN, Estrada Nacional 10 (km 139,7), Bobadela LRS 2695-066, Portugal.,CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Agostinho Lemos
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal.,GIGA Cyclotron Research Centre In Vivo Imaging, University of Liège, Liège 4000, Belgium
| | - António J Preto
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Beatriz Bueschbell
- Pharmaceutical Chemistry I, PharmaCenter, Pharmaceutical Institute, University of Bonn, Bonn, Germany
| | - Pedro Matos-Filipe
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Carlos Barreto
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - José G Almeida
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal
| | - Rúben D M Silva
- Centro de Ciencias e Tecnologias Nucleares, Instituto Superior Tecnico, Universidade de Lisboa, CTN, Estrada Nacional 10 (km 139,7), Bobadela LRS 2695-066, Portugal
| | - João D G Correia
- Centro de Ciencias e Tecnologias Nucleares, Instituto Superior Tecnico, Universidade de Lisboa, CTN, Estrada Nacional 10 (km 139,7), Bobadela LRS 2695-066, Portugal
| | - Irina S Moreira
- CNC - Center for Neuroscience and Cell Biology; Rua Larga, FMUC, Polo I, 1ºandar, Universidade de Coimbra, Coimbra 3004-517, Portugal.,Bijvoet Center for Biomolecular Research, Faculty of Science - Chemistry, Utrecht University, Utrecht 3584CH, Netherland
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33
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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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34
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Kovalevsky A, Gerlits O, Beltran K, Weiss KL, Keen DA, Blakeley MP, Louis JM, Weber IT. Proton transfer and drug binding details revealed in neutron diffraction studies of wild-type and drug resistant HIV-1 protease. Methods Enzymol 2020; 634:257-279. [PMID: 32093836 DOI: 10.1016/bs.mie.2019.12.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
HIV-1 protease is an essential therapeutic target for the design and development of antiviral inhibitors to treat AIDS. We used room temperature neutron crystallography to accurately determine hydrogen atom positions in several protease complexes with clinical drugs, amprenavir and darunavir. Hydrogen bonding interactions were carefully mapped to provide an unprecedented picture of drug binding to the protease target. We demonstrate that hydrogen atom positions within the enzyme catalytic site can be altered by introducing drug resistant mutations and by protonating surface residues that trigger proton transfer reactions between the catalytic Asp residues and the hydroxyl group of darunavir. When protein perdeuteration is not feasible, we validate the use of initial H/D exchange with unfolded protein and partial deuteration in pure D2O with hydrogenous glycerol to maximize deuterium incorporation into the protein, with no detrimental effects on the growth of quality crystals suitable for neutron diffraction experiments.
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Affiliation(s)
- Andrey Kovalevsky
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States.
| | - Oksana Gerlits
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, United States
| | - Kaira Beltran
- Department of Natural Sciences, Tennessee Wesleyan University, Athens, TN, United States
| | - Kevin L Weiss
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
| | - David A Keen
- ISIS Facility, Rutherford Appleton Laboratory, Harwell Campus, Didcot, United Kingdom
| | | | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, DHHS, Bethesda, MD, United States
| | - Irene T Weber
- Department of Biology, Georgia State University, Atlanta, GA, United States; Department of Chemistry, Georgia State University, Atlanta, GA, United States
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35
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Ngo ST, Hong ND, Quynh Anh LH, Hiep DM, Tung NT. Effective estimation of the inhibitor affinity of HIV-1 protease via a modified LIE approach. RSC Adv 2020; 10:7732-7739. [PMID: 35492181 PMCID: PMC9049864 DOI: 10.1039/c9ra09583g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 02/06/2020] [Indexed: 01/07/2023] Open
Abstract
The inhibition of the Human Immunodeficiency Virus Type 1 Protease (HIV-1 PR) can prevent the synthesis of new viruses. Computer-aided drug design (CADD) would enhance the discovery of new therapies, through which the estimation of ligand-binding affinity is critical to predict the most efficient inhibitor. A time-consuming binding free energy method would reduce the usefulness of CADD. The modified linear interaction energy (LIE) approach emerges as an appropriate protocol that performs this task. In particular, the polar interaction free energy, which is obtained via numerically resolving the linear Poisson–Boltzmann equation, plays as an important role in driving the binding mechanism of the HIV-1 PR + inhibitor complex. The electrostatic interaction energy contributes to the attraction between two molecules, but the vdW interaction acts as a repulsive factor between the ligand and the HIV-1 PR. Moreover, the ligands were found to adopt a very strong hydrophobic interaction with the HIV-1 PR. Furthermore, the results obtained corroborate the high accuracy and precision of computational studies with a large correlation coefficient value R = 0.83 and a small RMSE δRMSE = 1.25 kcal mol−1. This method is less time-consuming than the other end-point methods, such as the molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and free energy perturbation (FEP) approaches. Overall, the modified LIE approach would provide ligand-binding affinity with HIV-1 PR accurately, precisely, and rapidly, resulting in a more efficient design of new inhibitors. The inhibition of the Human Immunodeficiency Virus Type 1 Protease (HIV-1 PR) can prevent the synthesis of new viruses.![]()
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Affiliation(s)
- Son Tung Ngo
- Laboratory of Theoretical and Computational Biophysics
- Ton Duc Thang University
- Ho Chi Minh City
- Vietnam
- Faculty of Applied Sciences
| | - Nam Dao Hong
- University of Medicine and Pharmacy at Ho Chi Minh City
- Ho Chi Minh City
- Vietnam
| | - Le Huu Quynh Anh
- Department of Climate Change and Renewable Energy
- Ho Chi Minh City University of Natural Resources and Environment
- Ho Chi Minh City
- Vietnam
| | | | - Nguyen Thanh Tung
- Institute of Materials Science & Graduate University of Science and Technology
- Vietnam Academy of Science and Technology
- Hanoi
- Vietnam
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36
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Triki D, Kermarrec M, Visseaux B, Descamps D, Flatters D, Camproux AC, Regad L. Exploration of the effects of sequence variations between HIV-1 and HIV-2 proteases on their three-dimensional structures. J Biomol Struct Dyn 2019; 38:5014-5026. [PMID: 31830870 DOI: 10.1080/07391102.2019.1704877] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
HIV protease inhibitors (PIs) approved by the FDA (US Food and Drug Administration) are a major class of antiretroviral. HIV-2 protease (PR2) is naturally resistant to most of them as PIs were designed for HIV-1 protease (PR1). In this study, we explored the impact of amino-acid substitutions between PR1 and PR2 on the structure of protease (PR) by comparing the structural variability of 13 regions using 24 PR1 and PR2 structures complexed with diverse ligands. Our analyses confirmed structural rigidity of the catalytic region and highlighted the important role of three regions in the conservation of the catalytic region conformation. Surprisingly, we showed that the flap region, corresponding to a flexible region, exhibits similar conformations in PR1 and PR2. Furthermore, we identified regions exhibiting different conformations in PR1 and PR2, which could be explained by the intrinsic flexibility of these regions, by crystal packing, or by PR1 and PR2 substitutions. Some substitutions induce structural changes in the R2 and R4 regions that could have an impact on the properties of PI-binding site and could thus modify PI binding mode. Substitutions involved in structural changes in the elbow region could alter the flexibility of the PR2 flap regions relative to PR1, and thus play a role in the transition from the semi-open form to the closed form, and have an impact on ligand binding. These results improve the understanding of the impact of sequence variations between PR1 and PR2 on the natural resistance of HIV-2 to commercially available PIs.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Dhoha Triki
- Department of Chemistry, Bioinformatics Research Center, College of Science, North Carolina State University, Raleigh, North Carolina, USA.,Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, Paris, France
| | - Maxime Kermarrec
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, Paris, France
| | - Benoît Visseaux
- Université de Paris, IAME, UMR 1137, INSERM, AP-HP, Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - Diane Descamps
- Université de Paris, IAME, UMR 1137, INSERM, AP-HP, Laboratoire de Virologie, Hôpital Bichat-Claude Bernard, Paris, France
| | - Delphine Flatters
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, Paris, France
| | | | - Leslie Regad
- Université de Paris, BFA, UMR 8251, CNRS, ERL U1133, Inserm, Paris, France
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37
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Ghosh AK, Xia Z, Kovela S, Robinson WL, Johnson ME, Kneller DW, Wang YF, Aoki M, Takamatsu Y, Weber IT, Mitsuya H. Potent HIV-1 Protease Inhibitors Containing Carboxylic and Boronic Acids: Effect on Enzyme Inhibition and Antiviral Activity and Protein-Ligand X-ray Structural Studies. ChemMedChem 2019; 14:1863-1872. [PMID: 31549492 PMCID: PMC6842059 DOI: 10.1002/cmdc.201900508] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 09/18/2019] [Indexed: 01/07/2023]
Abstract
We report the synthesis and biological evaluation of phenylcarboxylic acid and phenylboronic acid containing HIV-1 protease inhibitors and their functional effect on enzyme inhibition and antiviral activity in MT-2 cell lines. Inhibitors bearing bis-THF ligand as P2 ligand and phenylcarboxylic acids and carboxamide as the P2' ligands, showed very potent HIV-1 protease inhibitory activity. However, carboxylic acid containing inhibitors showed very poor antiviral activity relative to carboxamide-derived inhibitors which showed good antiviral IC50 value. Boronic acid derived inhibitor with bis-THF as the P2 ligand showed very potent enzyme inhibitory activity, but it showed lower antiviral activity than darunavir in the same assay. Boronic acid containing inhibitor with a P2-Crn-THF ligand also showed potent enzyme Ki but significantly decreased antiviral activity. We have evaluated antiviral activity against a panel of highly drug-resistant HIV-1 variants. One of the inhibitors maintained good antiviral activity against HIVDRVRP20 and HIVDRVRP30 viruses. We have determined high resolution X-ray structures of two synthetic inhibitors bound to HIV-1 protease and obtained molecular insight into the ligand-binding site interactions.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Zilei Xia
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Satish Kovela
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - William L. Robinson
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Megan E. Johnson
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907
| | - Daniel W. Kneller
- Departments of Biology and Chemistry, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303
| | - Yuan-Fang Wang
- Departments of Biology and Chemistry, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303
| | - Manabu Aoki
- Experimental Retrovirology Section, HIV and AIDS Malignancy, Branch, National Cancer Institute, Bethesda, MD 20892,Department of Refractory Viral Infections, National Center for Global Heath and Medicine Research Institute, Shinjuku, Tokyo 162-8655, Japan
| | - Yuki Takamatsu
- Department of Refractory Viral Infections, National Center for Global Heath and Medicine Research Institute, Shinjuku, Tokyo 162-8655, Japan
| | - Irene T. Weber
- Departments of Biology and Chemistry, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303
| | - Hiroaki Mitsuya
- Departments of Hematology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556, Japan,Experimental Retrovirology Section, HIV and AIDS Malignancy, Branch, National Cancer Institute, Bethesda, MD 20892,Department of Refractory Viral Infections, National Center for Global Heath and Medicine Research Institute, Shinjuku, Tokyo 162-8655, Japan
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38
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Wang Y, Liu BY, Yang G, Chai Z. Synthesis of 2-Aminophosphates via S N2-Type Ring Openings of Aziridines with Organophosphoric Acids. Org Lett 2019; 21:4475-4479. [PMID: 31184161 DOI: 10.1021/acs.orglett.9b01302] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of 2-aminophosphates is achieved by a SN2-type ring opening reaction of various N-protected or free aziridines with phosphoric acids in a regiospecific and/or enantiospecific way. A one-pot, two-step procedure is also developed enabling direct access to 2-aminophosphates from olefins without isolation of the aziridine intermediates.
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Affiliation(s)
- Yang Wang
- MOE Key Laboratory of Functionalized Molecular Solids, Anhui Key Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base), College of Chemistry and Materials Science , Anhui Normal University , Wuhu , Anhui 241002 , China
| | - Bing-Yi Liu
- MOE Key Laboratory of Functionalized Molecular Solids, Anhui Key Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base), College of Chemistry and Materials Science , Anhui Normal University , Wuhu , Anhui 241002 , China
| | - Gaosheng Yang
- MOE Key Laboratory of Functionalized Molecular Solids, Anhui Key Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base), College of Chemistry and Materials Science , Anhui Normal University , Wuhu , Anhui 241002 , China
| | - Zhuo Chai
- MOE Key Laboratory of Functionalized Molecular Solids, Anhui Key Laboratory of Molecule-Based Materials (State Key Laboratory Cultivation Base), College of Chemistry and Materials Science , Anhui Normal University , Wuhu , Anhui 241002 , China
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39
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Structural studies of antiviral inhibitor with HIV-1 protease bearing drug resistant substitutions of V32I, I47V and V82I. Biochem Biophys Res Commun 2019; 514:974-978. [PMID: 31092330 DOI: 10.1016/j.bbrc.2019.05.064] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 05/07/2019] [Indexed: 12/23/2022]
Abstract
HIV-1 protease inhibitors are effective in HIV/AIDS therapy, although drug resistance is a severe problem. This study examines the effects of four investigational inhibitors against HIV-1 protease with drug resistant mutations of V32I, I47V and V82I (PRTri) that model the inhibitor-binding site of HIV-2 protease. These inhibitors contain diverse chemical modifications on the darunavir scaffold and form new interactions with wild type protease, however, the measured inhibition constants for PRTri mutant range from 17 to 40 nM or significantly worse than picomolar values reported for wild type enzyme. The X-ray crystal structure of PRTri mutant in complex with inhibitor 1 at 1.5 Å resolution shows minor changes in interactions with inhibitor compared with the corresponding wild type PR complex. Instead, the basic amine at P2 of inhibitor together with mutation V82I induces two alternate conformations for the side chain of Arg8 with new interactions with inhibitor and Leu10. Hence, inhibition is influenced by small coordinated changes in hydrophobic interactions.
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40
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Gadiyaram V, Vishveshwara S, Vishveshwara S. From Quantum Chemistry to Networks in Biology: A Graph Spectral Approach to Protein Structure Analyses. J Chem Inf Model 2019; 59:1715-1727. [DOI: 10.1021/acs.jcim.9b00002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vasundhara Gadiyaram
- IISc Mathematics Initiative (IMI), Indian Institute of Science, C V Raman Road, Bengaluru, Karnataka 560012, India
| | - Smitha Vishveshwara
- Department of Physics, University of Illinois at Urbana−Champaign, Urbana, Illinois 61801-3080, United States
| | - Saraswathi Vishveshwara
- Molecular Biophysics Unit, Indian Institute of Science, C V Raman Road, Bengaluru, Karnataka 560012, India
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41
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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: 288] [Impact Index Per Article: 57.6] [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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42
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Characterizing early drug resistance-related events using geometric ensembles from HIV protease dynamics. Sci Rep 2018; 8:17938. [PMID: 30560871 PMCID: PMC6298995 DOI: 10.1038/s41598-018-36041-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 11/14/2018] [Indexed: 02/07/2023] Open
Abstract
The use of antiretrovirals (ARVs) has drastically improved the life quality and expectancy of HIV patients since their introduction in health care. Several millions are still afflicted worldwide by HIV and ARV resistance is a constant concern for both healthcare practitioners and patients, as while treatment options are finite, the virus constantly adapts via complex mutation patterns to select for resistant strains under the pressure of drug treatment. The HIV protease is a crucial enzyme for viral maturation and has been a game changing drug target since the first application. Due to similarities in protease inhibitor designs, drug cross-resistance is not uncommon across ARVs of the same class. It is known that resistance against protease inhibitors is associated with a wider active site, but results from our large scale molecular dynamics simulations combined with statistical tests and network analysis further show, for the first time, that there are regions of local expansions and compactions associated with high levels of resistance conserved across eight different protease inhibitors visible in their complexed form within closed receptor conformations. The observed conserved expansion sites may provide an alternative drug-targeting site. Further, the method developed here is novel, supplementary to methods of variation analysis at sequence level, and should be applicable in analysing the structural consequences of mutations in other contexts using molecular ensembles.
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43
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Design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors incorporating aminothiochromane and aminotetrahydronaphthalene carboxamide derivatives as the P2 ligands. Eur J Med Chem 2018; 160:171-182. [PMID: 30340140 PMCID: PMC6237192 DOI: 10.1016/j.ejmech.2018.09.046] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 09/13/2018] [Accepted: 09/14/2018] [Indexed: 01/07/2023]
Abstract
We describe the design, synthesis, and biological evaluation of a series of novel HIV-1 protease inhibitors with carboxamide derivatives as the P2 ligands. We have specifically designed aminothiochromane and aminotetrahydronaphthalene-based carboxamide ligands to promote hydrogen bonding and van der Waals interactions in the active site of HIV-1 protease. Inhibitors 4e and 4j have shown potent enzyme inhibitory and antiviral activity. High resolution X-ray crystal structures of 4d- and 4k-bound HIV-1 protease revealed molecular insights into the ligand-binding site interactions.
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44
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Hanane T, Abbaz T, Bendjeddou A, Villemin D. Synthesis, Characterization and Theoretical Study of the Chemical Reactivity of New Cyclic Sulfamides Linked to Tetrathiafulvalene. PHOSPHORUS SULFUR 2018. [DOI: 10.1080/10426507.2018.1490282] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Tabbi Hanane
- Laboratory of Aquatic and Terrestrial Ecosystems, Org. and Bio-org. Chem. Group, University of Mohamed-Cherif Messaadia, Souk Ahras, Algeria
| | - Tahar Abbaz
- Laboratory of Aquatic and Terrestrial Ecosystems, Org. and Bio-org. Chem. Group, University of Mohamed-Cherif Messaadia, Souk Ahras, Algeria
| | - Amel Bendjeddou
- Laboratory of Aquatic and Terrestrial Ecosystems, Org. and Bio-org. Chem. Group, University of Mohamed-Cherif Messaadia, Souk Ahras, Algeria
| | - Didier Villemin
- Laboratory of Molecular and Thio-Organic Chemistry, UMR CNRS 6507, INC3M, FR 3038, Labex EMC3, ensicaen & University of Caen, Caen, France
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45
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Ghosh AK, Williams JN, Ho RY, Simpson HM, Hattori SI, Hayashi H, Agniswamy J, Wang YF, Weber IT, Mitsuya H. Design and Synthesis of Potent HIV-1 Protease Inhibitors Containing Bicyclic Oxazolidinone Scaffold as the P2 Ligands: Structure-Activity Studies and Biological and X-ray Structural Studies. J Med Chem 2018; 61:9722-9737. [PMID: 30354121 PMCID: PMC6541917 DOI: 10.1021/acs.jmedchem.8b01227] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
We have designed, synthesized, and evaluated a new class of potent HIV-1 protease inhibitors with novel bicyclic oxazolidinone derivatives as the P2 ligand. We have developed an enantioselective synthesis of these bicyclic oxazolidinones utilizing a key o-iodoxybenzoic acid mediated cyclization. Several inhibitors displayed good to excellent activity toward HIV-1 protease and significant antiviral activity in MT-4 cells. Compound 4k has shown an enzyme Ki of 40 pM and antiviral IC50 of 31 nM. Inhibitors 4k and 4l were evaluated against a panel of highly resistant multidrug-resistant HIV-1 variants, and their fold-changes in antiviral activity were similar to those observed with darunavir. Additionally, two X-ray crystal structures of the related inhibitors 4a and 4e bound to HIV-1 protease were determined at 1.22 and 1.30 Å resolution, respectively, and revealed important interactions in the active site that have not yet been explored.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States,Corresponding Author Phone: (765) 494-5323. Fax: (765) 496-1612.
| | - Jacqueline N. Williams
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Rachel Y. Ho
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Hannah M. Simpson
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, United States
| | - Shin-ichiro Hattori
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
| | - Hironori Hayashi
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan
| | - Johnson Agniswamy
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, United States
| | - Yuan-Fang Wang
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, United States
| | - Irene T. Weber
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, United States
| | - Hiroaki Mitsuya
- Department of Refractory Viral Infections, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan, Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto 860-8556, Japan, Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, United States
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46
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Ezeokonkwo MA, Eze CC, Okafor SN, Onoabedje EA, Godwin-Nwakwasi EU, Ibeanu FN. Diazabenzo[a]phenoxazone sulphonamides: synthesis, in-silico and in-vitro antimicrobial studies. Med Chem Res 2018. [DOI: 10.1007/s00044-018-2251-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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47
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Bastys T, Gapsys V, Doncheva NT, Kaiser R, de Groot BL, Kalinina OV. Consistent Prediction of Mutation Effect on Drug Binding in HIV-1 Protease Using Alchemical Calculations. J Chem Theory Comput 2018; 14:3397-3408. [PMID: 29847122 DOI: 10.1021/acs.jctc.7b01109] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Despite a large number of antiretroviral drugs targeting HIV-1 protease for inhibition, mutations in this protein during the course of patient treatment can render them inefficient. This emerging resistance inspired numerous computational studies of the HIV-1 protease aimed at predicting the effect of mutations on drug binding in terms of free binding energy Δ G, as well as in mechanistic terms. In this study, we analyze ten different protease-inhibitor complexes carrying major resistance-associated mutations (RAMs) G48V, I50V, and L90M using molecular dynamics simulations. We demonstrate that alchemical free energy calculations can consistently predict the effect of mutations on drug binding. By explicitly probing different protonation states of the catalytic aspartic dyad, we reveal the importance of the correct choice of protonation state for the accuracy of the result. We also provide insight into how different mutations affect drug binding in their specific ways, with the unifying theme of how all of them affect the crucial drug binding regions of the protease.
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Affiliation(s)
- Tomas Bastys
- Department for Computational Biology and Applied Algorithmics , Max Planck Institute for Informatics , D-66123 Saarbrücken , Germany.,Saarbrücken Graduate School of Computer Science , University of Saarland , D-66123 Saarbrücken , Germany
| | - Vytautas Gapsys
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics , Max Planck Institute for Biophysical Chemistry , D-37077 Göttingen , Germany
| | - Nadezhda T Doncheva
- Department for Computational Biology and Applied Algorithmics , Max Planck Institute for Informatics , D-66123 Saarbrücken , Germany.,Faculty of Health and Medical Sciences , University of Copenhagen , 2200 Copenhagen , Denmark
| | - Rolf Kaiser
- Institute for Virology , University Clinic of Cologne , D-50935 Köln , Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Department of Theoretical and Computational Biophysics , Max Planck Institute for Biophysical Chemistry , D-37077 Göttingen , Germany
| | - Olga V Kalinina
- Department for Computational Biology and Applied Algorithmics , Max Planck Institute for Informatics , D-66123 Saarbrücken , Germany
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48
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Ghosh AK, Nyalapatla PR, Kovela S, Rao KV, Brindisi M, Osswald HL, Amano M, Aoki M, Agniswamy J, Wang YF, Weber IT, Mitsuya H. Design and Synthesis of Highly Potent HIV-1 Protease Inhibitors Containing Tricyclic Fused Ring Systems as Novel P2 Ligands: Structure-Activity Studies, Biological and X-ray Structural Analysis. J Med Chem 2018; 61:4561-4577. [PMID: 29763303 PMCID: PMC6044451 DOI: 10.1021/acs.jmedchem.8b00298] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The design, synthesis, and biological evaluation of a new class of HIV-1 protease inhibitors containing stereochemically defined fused tricyclic polyethers as the P2 ligands and a variety of sulfonamide derivatives as the P2' ligands are described. A number of ring sizes and various substituent effects were investigated to enhance the ligand-backbone interactions in the protease active site. Inhibitors 5c and 5d containing this unprecedented fused 6-5-5 ring system as the P2 ligand, an aminobenzothiazole as the P2' ligand, and a difluorophenylmethyl as the P1 ligand exhibited exceptional enzyme inhibitory potency and maintained excellent antiviral activity against a panel of highly multidrug-resistant HIV-1 variants. The umbrella-like P2 ligand for these inhibitors has been synthesized efficiently in an optically active form using a Pauson-Khand cyclization reaction as the key step. The racemic alcohols were resolved efficiently using a lipase catalyzed enzymatic resolution. Two high resolution X-ray structures of inhibitor-bound HIV-1 protease revealed extensive interactions with the backbone atoms of HIV-1 protease and provided molecular insight into the binding properties of these new inhibitors.
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Affiliation(s)
- Arun K. Ghosh
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA,The corresponding author: Department of Chemistry and Department of Medicinal Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN 47907, Phone: (765)-494-5323; Fax: (765)-496-1612,
| | - Prasanth R. Nyalapatla
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Satish Kovela
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Kalapala Venkateswara Rao
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Margherita Brindisi
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Heather L. Osswald
- Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Masayuki Amano
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto 860-8556, Japan,Department of Medical Technology, Kumamoto Health Science University, Kumamoto 861-5598, Japan
| | - Manabu Aoki
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto 860-8556, Japan,Department of Medical Technology, Kumamoto Health Science University, Kumamoto 861-5598, Japan,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Johnson Agniswamy
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, USA
| | - Yuan-Fang Wang
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, USA
| | - Irene T. Weber
- Department of Biology, Molecular Basis of Disease, Georgia State University, Atlanta, Georgia 30303, USA
| | - Hiroaki Mitsuya
- Departments of Infectious Diseases and Hematology, Kumamoto University Graduate School of Biomedical Sciences, Kumamoto 860-8556, Japan,Department of Refractory Viral Infection, National Center for Global Health and Medicine Research Institute, Tokyo 162-8655, Japan,Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
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49
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Ghosh AK, Rao KV, Nyalapatla PR, Kovela S, Brindisi M, Osswald HL, Reddy BS, Agniswamy J, Wang YF, Aoki M, Hattori SI, Weber IT, Mitsuya H. Design of Highly Potent, Dual-Acting and Central-Nervous-System-Penetrating HIV-1 Protease Inhibitors with Excellent Potency against Multidrug-Resistant HIV-1 Variants. ChemMedChem 2018; 13:803-815. [PMID: 29437300 PMCID: PMC5912973 DOI: 10.1002/cmdc.201700824] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 02/09/2018] [Indexed: 01/07/2023]
Abstract
Herein we report the design, synthesis, X-ray structural, and biological studies of an exceptionally potent HIV-1 protease inhibitor, compound 5 ((3S,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl ((2S,3R)-4-((2-(cyclopropylamino)-N-isobutylbenzo[d]thiazole)-6-sulfonamido)-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl)carbamate). Using structure-based design, we incorporated an unprecedented 6-5-5-ring-fused crown-like tetrahydropyranofuran as the P2-ligand, a cyclopropylaminobenzothiazole as the P2'-ligand, and a 3,5-difluorophenylmethyl group as the P1-ligand. The resulting inhibitor 5 exhibited exceptional HIV-1 protease inhibitory and antiviral potency at the picomolar level. Furthermore, it displayed antiviral IC50 values in the picomolar range against a wide panel of highly multidrug-resistant HIV-1 variants. The inhibitor shows an extremely high genetic barrier against the emergence of drug-resistant variants. It also showed extremely potent inhibitory activity toward dimerization as well as favorable central nervous system penetration. We determined a high-resolution X-ray crystal structure of the complex between inhibitor 5 and HIV-1 protease, which provides molecular insight into the unprecedented activity profiles observed.
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Affiliation(s)
- Arun K. Ghosh
- Prof. Dr. A. K. Ghosh, Dr. K. V. Rao, Dr. P. R. Nyalapatla, Dr. S. Kovela, Dr. M. Brindisi, Dr. H. L. Osswald, Dr. B. Sekhara Reddy Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA),
| | - Kalapala Venkateswara Rao
- Prof. Dr. A. K. Ghosh, Dr. K. V. Rao, Dr. P. R. Nyalapatla, Dr. S. Kovela, Dr. M. Brindisi, Dr. H. L. Osswald, Dr. B. Sekhara Reddy Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Prasanth R. Nyalapatla
- Prof. Dr. A. K. Ghosh, Dr. K. V. Rao, Dr. P. R. Nyalapatla, Dr. S. Kovela, Dr. M. Brindisi, Dr. H. L. Osswald, Dr. B. Sekhara Reddy Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Satish Kovela
- Prof. Dr. A. K. Ghosh, Dr. K. V. Rao, Dr. P. R. Nyalapatla, Dr. S. Kovela, Dr. M. Brindisi, Dr. H. L. Osswald, Dr. B. Sekhara Reddy Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Margherita Brindisi
- Prof. Dr. A. K. Ghosh, Dr. K. V. Rao, Dr. P. R. Nyalapatla, Dr. S. Kovela, Dr. M. Brindisi, Dr. H. L. Osswald, Dr. B. Sekhara Reddy Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Heather L. Osswald
- Prof. Dr. A. K. Ghosh, Dr. K. V. Rao, Dr. P. R. Nyalapatla, Dr. S. Kovela, Dr. M. Brindisi, Dr. H. L. Osswald, Dr. B. Sekhara Reddy Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Bhavanam Sekhara Reddy
- Prof. Dr. A. K. Ghosh, Dr. K. V. Rao, Dr. P. R. Nyalapatla, Dr. S. Kovela, Dr. M. Brindisi, Dr. H. L. Osswald, Dr. B. Sekhara Reddy Department of Chemistry and Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907 (USA)
| | - Johnson Agniswamy
- Dr. J. Agniswamy, Y.-F. Wang, Prof. Dr. I. T. Weber Departments of Biology and Chemistry, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303 (USA)
| | - Yuan-Fang Wang
- Dr. J. Agniswamy, Y.-F. Wang, Prof. Dr. I. T. Weber Departments of Biology and Chemistry, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303 (USA)
| | - Manabu Aoki
- Dr. M. Aoki, Prof. Dr. H. Mitsuya Departments of Hematology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556 (Japan),Dr. M. Aoki, Prof. Dr. H. Mitsuya Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD 20892 (USA),Dr. M. Aoki, S.-i. Hattori, Prof. Dr. H. Mitsuya Center for Clinical Sciences, National Center for Global Heath and Medicine, Shinjuku, Tokyo 162-8655 (Japan)
| | - Shin-ichiro Hattori
- Dr. M. Aoki, S.-i. Hattori, Prof. Dr. H. Mitsuya Center for Clinical Sciences, National Center for Global Heath and Medicine, Shinjuku, Tokyo 162-8655 (Japan)
| | - Irene T. Weber
- Dr. J. Agniswamy, Y.-F. Wang, Prof. Dr. I. T. Weber Departments of Biology and Chemistry, Molecular Basis of Disease, Georgia State University, Atlanta, GA 30303 (USA)
| | - Hiroaki Mitsuya
- Dr. M. Aoki, Prof. Dr. H. Mitsuya Departments of Hematology and Infectious Diseases, Kumamoto University School of Medicine, Kumamoto 860-8556 (Japan),Dr. M. Aoki, Prof. Dr. H. Mitsuya Experimental Retrovirology Section, HIV and AIDS Malignancy Branch, National Cancer Institute, Bethesda, MD 20892 (USA),Dr. M. Aoki, S.-i. Hattori, Prof. Dr. H. Mitsuya Center for Clinical Sciences, National Center for Global Heath and Medicine, Shinjuku, Tokyo 162-8655 (Japan)
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Maffucci I, Hu X, Fumagalli V, Contini A. An Efficient Implementation of the Nwat-MMGBSA Method to Rescore Docking Results in Medium-Throughput Virtual Screenings. Front Chem 2018; 6:43. [PMID: 29556494 PMCID: PMC5844977 DOI: 10.3389/fchem.2018.00043] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 02/19/2018] [Indexed: 01/05/2023] Open
Abstract
Nwat-MMGBSA is a variant of MM-PB/GBSA based on the inclusion of a number of explicit water molecules that are the closest to the ligand in each frame of a molecular dynamics trajectory. This method demonstrated improved correlations between calculated and experimental binding energies in both protein-protein interactions and ligand-receptor complexes, in comparison to the standard MM-GBSA. A protocol optimization, aimed to maximize efficacy and efficiency, is discussed here considering penicillopepsin, HIV1-protease, and BCL-XL as test cases. Calculations were performed in triplicates on both classic HPC environments and on standard workstations equipped by a GPU card, evidencing no statistical differences in the results. No relevant differences in correlation to experiments were also observed when performing Nwat-MMGBSA calculations on 4 or 1 ns long trajectories. A fully automatic workflow for structure-based virtual screening, performing from library set-up to docking and Nwat-MMGBSA rescoring, has then been developed. The protocol has been tested against no rescoring or standard MM-GBSA rescoring within a retrospective virtual screening of inhibitors of AmpC β-lactamase and of the Rac1-Tiam1 protein-protein interaction. In both cases, Nwat-MMGBSA rescoring provided a statistically significant increase in the ROC AUCs of between 20 and 30%, compared to docking scoring or to standard MM-GBSA rescoring.
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Affiliation(s)
- Irene Maffucci
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "Alessandro Marchesini," Università degli Studi di Milano, Milan, Italy
| | - Xiao Hu
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "Alessandro Marchesini," Università degli Studi di Milano, Milan, Italy
| | - Valentina Fumagalli
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "Alessandro Marchesini," Università degli Studi di Milano, Milan, Italy
| | - Alessandro Contini
- Dipartimento di Scienze Farmaceutiche, Sezione di Chimica Generale e Organica "Alessandro Marchesini," Università degli Studi di Milano, Milan, Italy
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