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Borges PHO, Ferreira SB, Silva FP. Recent Advances on Targeting Proteases for Antiviral Development. Viruses 2024; 16:366. [PMID: 38543732 PMCID: PMC10976044 DOI: 10.3390/v16030366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Revised: 02/21/2024] [Accepted: 02/24/2024] [Indexed: 05/23/2024] Open
Abstract
Viral proteases are an important target for drug development, since they can modulate vital pathways in viral replication, maturation, assembly and cell entry. With the (re)appearance of several new viruses responsible for causing diseases in humans, like the West Nile virus (WNV) and the recent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), understanding the mechanisms behind blocking viral protease's function is pivotal for the development of new antiviral drugs and therapeutical strategies. Apart from directly inhibiting the target protease, usually by targeting its active site, several new pathways have been explored to impair its activity, such as inducing protein aggregation, targeting allosteric sites or by inducing protein degradation by cellular proteasomes, which can be extremely valuable when considering the emerging drug-resistant strains. In this review, we aim to discuss the recent advances on a broad range of viral proteases inhibitors, therapies and molecular approaches for protein inactivation or degradation, giving an insight on different possible strategies against this important class of antiviral target.
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Affiliation(s)
- Pedro Henrique Oliveira Borges
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
| | - Sabrina Baptista Ferreira
- Laboratory of Organic Synthesis and Biological Prospecting, Chemistry Institute, Federal University of Rio de Janeiro, Rio de Janeiro 21941-909, Brazil;
| | - Floriano Paes Silva
- Laboratory of Experimental and Computational Biochemistry of Drugs, Oswaldo Cruz Institute, Fiocruz, Rio de Janeiro 21040-900, Brazil
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2
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Ahmad MF, A. Alsayegh A, Ahmad FA, Akhtar MS, Alavudeen SS, Bantun F, Wahab S, Ahmed A, Ali M, Elbendary EY, Raposo A, Kambal N, H. Abdelrahman M. Ganoderma lucidum: Insight into antimicrobial and antioxidant properties with development of secondary metabolites. Heliyon 2024; 10:e25607. [PMID: 38356540 PMCID: PMC10865332 DOI: 10.1016/j.heliyon.2024.e25607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Revised: 12/15/2023] [Accepted: 01/30/2024] [Indexed: 02/16/2024] Open
Abstract
Ganoderma lucidum is a versatile mushroom. Polysaccharides and triterpenoids are the major bioactive compounds and have been used as traditional medicinal mushrooms since ancient times. They are currently used as nutraceuticals and functional foods. G. lucidum extracts and their bioactive compounds have been used as an alternative to antioxidants and antimicrobial agents. Secondary metabolites with many medicinal properties make it a possible substitute that could be applied as immunomodulatory, anticancer, antimicrobial, anti-oxidant, anti-inflammatory, and anti-diabetic. The miraculous properties of secondary metabolites fascinate researchers for their development and production. Recent studies have paid close attention to the different physical, genetic, biochemical, and nutritional parameters that potentiate the production of secondary metabolites. This review is an effort to collect biologically active constituents from G. lucidum that reveal potential actions against diseases with the latest improvement in a novel technique to get maximum production of secondary metabolites. Studies are going ahead to determine the efficacy of numerous compounds and assess the valuable properties achieved by G. lucidum in favor of antimicrobial and antioxidant outcomes.
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Affiliation(s)
- Md Faruque Ahmad
- Department of Clinical Nutrition, College of Applied Medical Science, Jazan University, Jazan, 45142, Saudi Arabia
| | - Abdulrahman A. Alsayegh
- Department of Clinical Nutrition, College of Applied Medical Science, Jazan University, Jazan, 45142, Saudi Arabia
| | - Fakhruddin Ali Ahmad
- Department of Basic and Applied Science, School of Engineering and Science, G.D Goenka University, Gru Gram, 122103, Haryana, India
| | - Md Sayeed Akhtar
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University, AlFara, Abha, 62223, Saudi Arabia
| | - Sirajudeen S. Alavudeen
- Department of Clinical Pharmacy, College of Pharmacy, King Khalid University, AlFara, Abha, 62223, Saudi Arabia
| | - Farkad Bantun
- Department of Microbiology and Parasitology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Shadma Wahab
- Department of Pharmacognosy, College of Pharmacy, King Khalid University, Abha, 62529, Saudi Arabia
| | - Awais Ahmed
- Department of Management, Shri JJT University, Rajasthan, Post code; 333010, India
| | - M. Ali
- Department of Pharmacognosy, CBS College of Pharmacy & Technology (Pt. B. D. Sharma University of Health Sciences), Chandpur, Faridabad, Haryana, 121101, India
| | - Ehab Y. Elbendary
- Department of Clinical Nutrition, College of Applied Medical Science, Jazan University, Jazan, 45142, Saudi Arabia
| | - António Raposo
- CBIOS (Research Center for Biosciences and Health Technologies), Universidade Lusófona de Humanidades Tecnologias, Campo Grande 376, 1749-024, Lisboa, Portugal
| | - Nahla Kambal
- Department of Clinical Nutrition, College of Applied Medical Science, Jazan University, Jazan, 45142, Saudi Arabia
| | - Mohamed H. Abdelrahman
- College of Applied Medical Sciences, Medical Laboratory Sciences, Jazan University, Jazan, 45142, Saudi Arabia
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3
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Hisamuddin M, Rizvi I, Malik A, Nabi F, Hassan MN, Ali SM, Khan JM, Khan TH, Khan RH. Characterization of pH-induced conformational changes in recombinant DENV NS2B-NS3pro. Int J Biol Macromol 2023; 253:126823. [PMID: 37703975 DOI: 10.1016/j.ijbiomac.2023.126823] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 09/07/2023] [Accepted: 09/07/2023] [Indexed: 09/15/2023]
Abstract
The increasing frequency of Dengue is a cause of severe epidemics and therefore demands strategies for effective prevention, diagnosis, and treatment. DENV-protease is being investigated as a potential therapeutic target. However, due to the flat and highly charged active site of the DENV-protease, designing orthosteric medicines is very difficult. In this study, we have done a thorough analysis of pH-dependent conformational changes in recombinantly expressed DENV protease using various spectroscopic techniques. Our spectroscopic study of DENV protease (NS2B-NS3pro) at different pH conditions gives important insights into the dynamicity of structural conformation. At physiological pH, the DENV-protease exists in a random-coiled state. Lowering the pH promotes the formation of alpha-helical and beta-sheet structures i.e. gain of secondary structure as shown by Far-UV CD. The light scattering and Thioflavin T (ThT)-binding assay proved the aggregation-prone tendency of DENV-protease at pH 4.0. Further, the confocal microscopy image intensity showed the amorphous aggregate formation of DENV protease at pH 4.0. Thus, the DENV protease acquires different conformations with changes in pH conditions. Together, these results have the potential to facilitate the design of a conformation destabilizer-based therapeutic strategy for dengue fever.
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Affiliation(s)
- Malik Hisamuddin
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, UP, India
| | - Irum Rizvi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, UP, India
| | - Ajamaluddin Malik
- Department of Biochemistry, College of Science, King Saud University, P.O. Box 2455, Riyadh, Saudi Arabia
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, UP, India
| | - Md Nadir Hassan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, UP, India
| | - Syed Moasfar Ali
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, UP, India
| | - Javed Masood Khan
- Department of Food Science and Nutrition, Faculty of Food and Agricultural Sciences, King Saud University, 2460, Riyadh 11451, Saudi Arabia
| | - Tabish H Khan
- Department of Pathology and Immunology, Washington University in St. Louis School of Medicine, MO, USA
| | - Rizwan H Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University Aligarh, UP, India.
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4
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Viral proteases as therapeutic targets. Mol Aspects Med 2022; 88:101159. [PMID: 36459838 PMCID: PMC9706241 DOI: 10.1016/j.mam.2022.101159] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 11/30/2022]
Abstract
Some medically important viruses-including retroviruses, flaviviruses, coronaviruses, and herpesviruses-code for a protease, which is indispensable for viral maturation and pathogenesis. Viral protease inhibitors have become an important class of antiviral drugs. Development of the first-in-class viral protease inhibitor saquinavir, which targets HIV protease, started a new era in the treatment of chronic viral diseases. Combining several drugs that target different steps of the viral life cycle enables use of lower doses of individual drugs (and thereby reduction of potential side effects, which frequently occur during long term therapy) and reduces drug-resistance development. Currently, several HIV and HCV protease inhibitors are routinely used in clinical practice. In addition, a drug including an inhibitor of SARS-CoV-2 main protease, nirmatrelvir (co-administered with a pharmacokinetic booster ritonavir as Paxlovid®), was recently authorized for emergency use. This review summarizes the basic features of the proteases of human immunodeficiency virus (HIV), hepatitis C virus (HCV), and SARS-CoV-2 and discusses the properties of their inhibitors in clinical use, as well as development of compounds in the pipeline.
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5
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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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6
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Panda M, Purohit P, Meher BR. Structure-based virtual screening, ADMET profiling, and molecular dynamics simulation studies on HIV-1 protease for identification of active phytocompounds as potential anti-HIV agents. MOLECULAR SIMULATION 2022. [DOI: 10.1080/08927022.2022.2060968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Madhusmita Panda
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Priyanka Purohit
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
| | - Biswa Ranjan Meher
- Computational Biology and Bioinformatics Laboratory, PG Department of Botany, Berhampur University, Berhampur, India
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7
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Mótyán JA, Mahdi M, Hoffka G, Tőzsér J. Potential Resistance of SARS-CoV-2 Main Protease (Mpro) against Protease Inhibitors: Lessons Learned from HIV-1 Protease. Int J Mol Sci 2022; 23:3507. [PMID: 35408866 PMCID: PMC8998604 DOI: 10.3390/ijms23073507] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/16/2022] [Accepted: 03/22/2022] [Indexed: 02/06/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome 2 (SARS-CoV-2), has been one of the most devastating pandemics of recent times. The lack of potent novel antivirals had led to global health crises; however, emergence and approval of potent inhibitors of the viral main protease (Mpro), such as Pfizer's newly approved nirmatrelvir, offers hope not only in the therapeutic front but also in the context of prophylaxis against the infection. By their nature, RNA viruses including human immunodeficiency virus (HIV) have inherently high mutation rates, and lessons learnt from previous and currently ongoing pandemics have taught us that these viruses can easily escape selection pressure through mutation of vital target amino acid residues in monotherapeutic settings. In this paper, we review nirmatrelvir and its binding to SARS-CoV-2 Mpro and draw a comparison to inhibitors of HIV protease that were rendered obsolete by emergence of resistance mutations, emphasizing potential pitfalls in the design of inhibitors that may be of important relevance to the long-term use of novel inhibitors against SARS-CoV-2.
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Affiliation(s)
- János András Mótyán
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (J.A.M.); (M.M.); (G.H.)
| | - Mohamed Mahdi
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (J.A.M.); (M.M.); (G.H.)
| | - Gyula Hoffka
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (J.A.M.); (M.M.); (G.H.)
- Doctoral School of Molecular Cell and Immune Biology, University of Debrecen, 4032 Debrecen, Hungary
| | - József Tőzsér
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (J.A.M.); (M.M.); (G.H.)
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8
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Liu Q, Wei Y, Hao Y, Yang J, Pan B, Yang X, Zhou Y, Wang X. Synthesis and Evaluation of Acylated Derivatives of Hederagenin as Inhibitors of HIV-1 and HCV NS3/4A Proteases. Nat Prod Commun 2022. [DOI: 10.1177/1934578x221075083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Viral infection imposes a major threat to human health. To develop new potent antiviral agents, Hederagenin (HE), a known inhibitor of HIV-1 and HCV NS3/4A proteases, was used as a starting material to synthesize 4 types of HE derivatives, HE-3,23-diacyl, HES-3,23-diacyl, HES-3-acyl, and HES-3-oxo-23-acyl. We evaluated the in vitro inhibitory activities of the derivatives against HIV-1 and HCV NS3/4A proteases. (3 β,23)-Di- O-diglutaryl-hederagenin (1b) and (3 β,23)-di- O-(3′,3′-dimethylsuccinyl-hederagenin ethyl ester (2b) exhibited potent inhibitory activities against the HIV-1 and/or HCV NS3/4A proteases with IC50 values < 10 μM, but did not appreciably inhibit general human proteases renin and trypsin. The SARs showed that dicarboxylic acid hemiesters of HE significantly enhance the antiviral activities when C3 or C23 are linked with 6 carbon acyl chains.
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Affiliation(s)
- Qing Liu
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Ying Wei
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Yongjia Hao
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Jian Yang
- College of Pharmacy and Nutrition, University of Saskatchewan, Saskatoon, SK, Canada
| | - Bowen Pan
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Xiaosheng Yang
- The Key Laboratory of Chemistry for Natural Products of Guizhou Province and Chinese Academy of Sciences, Guiyang, Guizhou, China
| | - Ying Zhou
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
| | - Xia Wang
- Department of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, Guizhou, China
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9
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Aggarwal S, Balaji S, Madhumathi J, Bhargava A, Singh T, Mahajan N, Ambalkar D. Patterns of human immunodeficiency virus drug resistance mutations in people living with human immunodeficiency virus in India: A scoping review. Indian J Sex Transm Dis AIDS 2022; 43:13-19. [PMID: 35846552 PMCID: PMC9282713 DOI: 10.4103/ijstd.ijstd_2_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 06/03/2021] [Accepted: 06/04/2021] [Indexed: 11/04/2022] Open
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10
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Kamboj S, Singh R. Chromanone-A Prerogative Therapeutic Scaffold: An Overview. ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2022; 47:75-111. [PMID: 34226859 PMCID: PMC8244469 DOI: 10.1007/s13369-021-05858-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 06/09/2021] [Indexed: 02/06/2023]
Abstract
Chromanone or Chroman-4-one is the most important and interesting heterobicyclic compound and acts as a building block in medicinal chemistry for isolation, designing and synthesis of novel lead compounds. Structurally, absence of a double bond in chromanone between C-2 and C-3 shows a minor difference from chromone but exhibits significant variations in biological activities. In the present review, various studies published on synthesis, pharmacological evaluation on chroman-4-one analogues are addressed to signify the importance of chromanone as a versatile scaffold exhibiting a wide range of pharmacological activities. But, due to poor yield in the case of chemical synthesis and expensive isolation procedure from natural compounds, more studies are required to provide the most effective and cost-effective methods to synthesize novel chromanone analogs to give leads to chemistry community. Considering the versatility of chromanone, this review is designed to impart comprehensive, critical and authoritative information about chromanone template in drug designing and development.
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Affiliation(s)
- Sonia Kamboj
- Maharishi Markandeshwar College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Haryana 133203 India ,Ch. Devi Lal College of Pharmacy, Jagadhri, Haryana 135003 India
| | - Randhir Singh
- Maharishi Markandeshwar College of Pharmacy, Maharishi Markandeshwar (Deemed to be University), Mullana, Haryana 133203 India
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11
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Dražić T, Kühl N, Gottscheber N, Hacker CN, Klein CD. The spectrum between substrates and inhibitors: Pinpointing the binding mode of dengue protease ligands with modulated basicity and hydrophobicity. Bioorg Med Chem 2021; 48:116412. [PMID: 34592636 DOI: 10.1016/j.bmc.2021.116412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/06/2021] [Accepted: 09/09/2021] [Indexed: 10/20/2022]
Abstract
Peptides can be inhibitors and substrates of proteases. The present study describes the inhibitor- vs. substrate-like properties of peptidic ligands of dengue protease which were designed to provide insight into their binding modes. Of particular interest was the localization of the cleavable peptide bond and the placement of hydrophobic elements in the binding site. The findings provide clues for the design of covalent inhibitors in which electrophilic functional groups bind to the catalytic serine, and in addition for the development of inhibitors that are less basic than the natural substrate and therefore have an improved pharmacokinetic profile. We observed a tendency of basic elements to favor a substrate-like binding mode, whereas hydrophobic elements decrease or eliminate enzymatic cleavage. This indicates a necessity to include basic elements which closely mimic the natural substrates into covalent inhibitors, posing a challenge from the chemical and pharmacokinetic perspective. However, hydrophobic elements may offer opportunities to develop non-covalent inhibitors with a favorable ADME profile and potentially improved target-binding kinetics.
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Affiliation(s)
- Tonko Dražić
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Nikos Kühl
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Nicole Gottscheber
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Christina N Hacker
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University, Im Neuenheimer Feld 364, 69120 Heidelberg, Germany.
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12
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Precursors of Viral Proteases as Distinct Drug Targets. Viruses 2021; 13:v13101981. [PMID: 34696411 PMCID: PMC8537868 DOI: 10.3390/v13101981] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/25/2021] [Accepted: 09/28/2021] [Indexed: 12/16/2022] Open
Abstract
Viral proteases are indispensable for successful virion maturation, thus making them a prominent drug target. Their enzyme activity is tightly spatiotemporally regulated by expression in the precursor form with little or no activity, followed by activation via autoprocessing. These cleavage events are frequently triggered upon transportation to a specific compartment inside the host cell. Typically, precursor oligomerization or the presence of a co-factor is needed for activation. A detailed understanding of these mechanisms will allow ligands with non-canonical mechanisms of action to be designed, which would specifically modulate the initial irreversible steps of viral protease autoactivation. Binding sites exclusive to the precursor, including binding sites beyond the protease domain, can be exploited. Both inhibition and up-regulation of the proteolytic activity of viral proteases can be detrimental for the virus. All these possibilities are discussed using examples of medically relevant viruses including herpesviruses, adenoviruses, retroviruses, picornaviruses, caliciviruses, togaviruses, flaviviruses, and coronaviruses.
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13
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Sohraby F, Aryapour H. Comparative analysis of the unbinding pathways of antiviral drug Indinavir from HIV and HTLV1 proteases by supervised molecular dynamics simulation. PLoS One 2021; 16:e0257916. [PMID: 34570822 PMCID: PMC8476009 DOI: 10.1371/journal.pone.0257916] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
Determining the unbinding pathways of potential small molecule compounds from their target proteins is of great significance for designing efficacious treatment solutions. One of these potential compounds is the approved HIV-1 protease inhibitor, Indinavir, which has a weak effect on the HTLV-1 protease. In this work, by employing the SuMD method, we reconstructed the unbinding pathways of Indinavir from HIV and HTLV-1 proteases to compare and understand the mechanism of the unbinding and to discover the reasons for the lack of inhibitory activity of Indinavir against the HTLV-1 protease. We achieved multiple unbinding events from both HIV and HTLV-1 proteases in which the RMSD values of Indinavir reached over 40 Å. Also, we found that the mobility and fluctuations of the flap region are higher in the HTLV-1 protease, making the drug less stable. We realized that critically positioned aromatic residues such as Trp98/Trp98' and Phe67/Phe67' in the HTLV-1 protease could make strong π-Stacking interactions with Indinavir in the unbinding pathway, which are unfavorable for the stability of Indinavir in the active site. The details found in this study can make a reasonable explanation for the lack of inhibitory activity of this drug against HTLV-1 protease. We believe the details discovered in this work can help design more effective and selective inhibitors for the HTLV-1 protease.
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Affiliation(s)
- Farzin Sohraby
- Faculty of Science, Department of Biology, Golestan University, Gorgan, Iran
| | - Hassan Aryapour
- Faculty of Science, Department of Biology, Golestan University, Gorgan, Iran
- * E-mail:
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14
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More GV, Malekar PV, Kalshetti RG, Shinde MH, Ramana CV. Ru-catalyzed asymmetric transfer hydrogenation of α-acyl butyrolactone via dynamic kinetic resolution: Asymmetric synthesis of bis-THF alcohol intermediate of darunavir. Tetrahedron Lett 2021. [DOI: 10.1016/j.tetlet.2021.152831] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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15
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Lanman T, Letendre S, Ma Q, Bang A, Ellis R. CNS Neurotoxicity of Antiretrovirals. J Neuroimmune Pharmacol 2021; 16:130-143. [PMID: 31823251 PMCID: PMC7282963 DOI: 10.1007/s11481-019-09886-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Accepted: 10/01/2019] [Indexed: 12/20/2022]
Abstract
The development of novel antiretroviral treatments has led to a significant turning point in the fight against HIV. Although therapy leads to virologic suppression and prolonged life expectancies, HIV-associated neurocognitive disorder (HAND) remains prevalent. While various hypotheses have been proposed to explain this phenomenon, a growing body of literature explores the neurotoxic effects of antiretroviral therapy. Research to date brings into question the potential role of such medications in neurocognitive and neuropsychiatric impairment seen in HIV-positive patients. This review highlights recent findings and controversies in cellular, molecular, and clinical neurotoxicity of antiretrovirals. It explores the pathogenesis of such toxicity and relates it to clinical manifestations in each medication class. The concept of accelerated aging in persons living with HIV (PLWH) as well as potential treatments for HAND are also discussed. Ultimately, this article hopes to educate clinicians and basic scientists about the neurotoxic effects of antiretrovirals and spur future scientific investigation into this important topic. Graphical Abstract.
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Affiliation(s)
- Tyler Lanman
- Department of Neurosciences, University of California San Diego School of Medicine, 200 W Arbor Dr, San Diego, La Jolla, CA, 92103, USA
| | - Scott Letendre
- Department of Infectious Diseases, University of California San Diego School of Medicine, La Jolla, CA, USA
| | - Qing Ma
- Pharmacotherapy Research Center, University of Buffalo, School of Pharmacy & Pharmaceutical Sciences, Buffalo, NY, USA
| | - Anne Bang
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Ronald Ellis
- Department of Neurosciences, University of California San Diego School of Medicine, 200 W Arbor Dr, San Diego, La Jolla, CA, 92103, USA.
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16
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Pal M, Musib D, Roy M. Transition metal complexes as potential tools against SARS-CoV-2: an in silicoapproach. NEW J CHEM 2021. [DOI: 10.1039/d0nj04578k] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Screening of selected transition metal-based antiviral agents,in silico, predicted the potential inhibition of RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2 which emerged as the potential drug candidate for COVID-19.
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Affiliation(s)
- Maynak Pal
- Department of Chemistry
- National Institute of Technology Manipur
- Imphal
- India
| | - Dulal Musib
- Department of Chemistry
- National Institute of Technology Manipur
- Imphal
- India
| | - Mithun Roy
- Department of Chemistry
- National Institute of Technology Manipur
- Imphal
- India
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17
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Trindade GG, Caxito SMC, Xavier AREO, Xavier MAS, BrandÃo F. COVID-19: therapeutic approaches description and discussion. AN ACAD BRAS CIENC 2020; 92:e20200466. [PMID: 32556054 DOI: 10.1590/0001-3765202020200466] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 05/28/2020] [Indexed: 02/06/2023] Open
Abstract
COVID-19 emerged in December 2019 in China, and since then, has disrupted global public health and changed economic paradigms. In dealing with the new Coronavirus, SARS-CoV-2, the world has not faced such extreme global fragility since the "Spanish flu" pandemic in 1918. Researchers globally are dedicating efforts to the search for an effective treatment for COVID-19. Drugs already used in a clinical setting for other pathologies have been tested as a new therapeutic approach against SARS-CoV-2, setting off a frenzy over the preliminary data of different studies. This work aims to compile and discuss the data published thus far. Despite the potential effects of some antivirals and antiparasitic against COVID-19, clinical studies must confirm real effectiveness. However, non-pharmacological approaches have proven to be the most efficient strategy to date.
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Affiliation(s)
- Guilherme G Trindade
- University of Brasília, Laboratory of Clinical Microbiology and Immunology, Campus Darcy Ribeiro, Asa Norte, 70910-900 Brasília, DF, Brazil
| | - Samyra M C Caxito
- AMIL/United Health Group (UHG), 6580, SMAS Trecho 1, Guará, 70211-970 Brasília, DF, Brazil.,Institute of Management and Health of the Federal District (IGES-DF), Department of Nursing, Quadra 400-600, s/n, Área Especial, Recanto das Emas, 72630-250 Brasília, DF, Brazil
| | - Alessandra Rejane E O Xavier
- State University of Montes Claros, Center of Biological and Health Sciences, Microbiology Laboratory, Av. Prof. Rui Braga, 39401-089 Montes Claros, MG, Brazil
| | - Mauro A S Xavier
- State University of Montes Claros, Center of Biological and Health Sciences, Microbiology Laboratory, Av. Prof. Rui Braga, 39401-089 Montes Claros, MG, Brazil
| | - Fabiana BrandÃo
- University of Brasília, Department of Pharmacy, Laboratory of Clinical Microbiology and Immunology. Campus Darcy Ribeiro, Asa Norte, 70910-900 Brasília, DF, Brazil.,University of Brasília, Nucleus of Tropical Medicine, Campus Darcy Ribeiro, Asa Norte, 70910-900 Brasília, DF, Brazil
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18
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Cherian SS, Agrawal M, Basu A, Abraham P, Gangakhedkar RR, Bhargava B. Perspectives for repurposing drugs for the coronavirus disease 2019. Indian J Med Res 2020; 151:160-171. [PMID: 32317408 PMCID: PMC7357399 DOI: 10.4103/ijmr.ijmr_585_20] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The newly emerged 2019 novel coronavirus (CoV), named as severe acute respiratory syndrome CoV-2 (SARS-CoV-2), like SARS-CoV (now, SARS-CoV-1) and Middle East respiratory syndrome CoV (MERS-CoV), has been associated with high infection rates with over 36,405 deaths. In the absence of approved marketed drugs against coronaviruses, the treatment and management of this novel CoV disease (COVID-19) worldwide is a challenge. Drug repurposing that has emerged as an effective drug discovery approach from earlier approved drugs could reduce the time and cost compared to de novo drug discovery. Direct virus-targeted antiviral agents target specific nucleic acid or proteins of the virus while host-based antivirals target either the host innate immune responses or the cellular machineries that are crucial for viral infection. Both the approaches necessarily interfere with viral pathogenesis. Here we summarize the present status of both virus-based and host-based drug repurposing perspectives for coronaviruses in general and the SARS-CoV-2 in particular.
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Affiliation(s)
- Sarah S Cherian
- Bioinformatic Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Megha Agrawal
- Bioinformatic Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Atanu Basu
- Electron Microscopy & Histopathology Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Priya Abraham
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Raman R Gangakhedkar
- Division of Epidemiology & Communicable Diseases, Indian Council of Medical Research & Family Welfare, New Delhi, India
| | - Balram Bhargava
- Department of Health Research (ICMR), Ministry of Health & Family Welfare, New Delhi, India
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19
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Fojt L, Grüner B, Šícha V, Nekvinda J, Vespalec R, Fojta M. Electrochemistry of icosahedral cobalt bis(dicarbollide) ions and their carbon and boron substituted derivatives in aqueous phosphate buffers. Electrochim Acta 2020. [DOI: 10.1016/j.electacta.2020.136112] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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20
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Suwannarach N, Kumla J, Sujarit K, Pattananandecha T, Saenjum C, Lumyong S. Natural Bioactive Compounds from Fungi as Potential Candidates for Protease Inhibitors and Immunomodulators to Apply for Coronaviruses. Molecules 2020; 25:E1800. [PMID: 32295300 PMCID: PMC7221821 DOI: 10.3390/molecules25081800] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 04/08/2020] [Accepted: 04/10/2020] [Indexed: 12/11/2022] Open
Abstract
The inhibition of viral protease is an important target in antiviral drug discovery and development. To date, protease inhibitor drugs, especially HIV-1 protease inhibitors, have been available for human clinical use in the treatment of coronaviruses. However, these drugs can have adverse side effects and they can become ineffective due to eventual drug resistance. Thus, the search for natural bioactive compounds that were obtained from bio-resources that exert inhibitory capabilities against HIV-1 protease activity is of great interest. Fungi are a source of natural bioactive compounds that offer therapeutic potential in the prevention of viral diseases and for the improvement of human immunomodulation. Here, we made a brief review of the current findings on fungi as producers of protease inhibitors and studies on the relevant candidate fungal bioactive compounds that can offer immunomodulatory activities as potential therapeutic agents of coronaviruses in the future.
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Affiliation(s)
- Nakarin Suwannarach
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (K.S.); (S.L.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jaturong Kumla
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (K.S.); (S.L.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Kanaporn Sujarit
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (K.S.); (S.L.)
- Division of Biology, Faculty of Science and Technology, Rajamangala University of Technology Thanyaburi, Thanyaburi, Pathumthani 12110, Thailand
| | - Thanawat Pattananandecha
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand; (T.P.); (C.S.)
| | - Chalermpong Saenjum
- Department of Pharmaceutical Sciences, Faculty of Pharmacy, Chiang Mai University, Chiang Mai 50200, Thailand; (T.P.); (C.S.)
| | - Saisamorn Lumyong
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai 50200, Thailand; (J.K.); (K.S.); (S.L.)
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
- Academy of Science, The Royal Society of Thailand, Bangkok 10300, Thailand
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21
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22
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Wang X, Wei Y, Tian WY, Sakharkar MK, Liu Q, Yang X, Zhou YZ, Mou CL, Cai GL, Yang J. Characterization of Nine Compounds Isolated from the Acid Hydrolysate of Lonicera fulvotomentosa Hsu et S. C. Cheng and Evaluation of Their In Vitro Activity towards HIV Protease. Molecules 2019; 24:molecules24244526. [PMID: 31835661 PMCID: PMC6943440 DOI: 10.3390/molecules24244526] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 12/07/2019] [Accepted: 12/09/2019] [Indexed: 01/24/2023] Open
Abstract
In this study, we isolated nine compounds from the acid hydrolysate of the flower buds of Lonicera fulvotomentosa Hsu et S. C. Cheng and characterized their chemical structures using 1H-NMR, 13C-NMR, and electron ionization mass spectroscopy (EI-MS). These compounds were identified as β-sitosterol (1), 5,5′-dibutoxy-2,2′-bifuran (2), nonacosane-10-ol (3), ethyl (3β)-3,23-dihydroxyolean-12-en-28-oate (4), oleanolic acid (5), ethyl caffeate (6), caffeic acid (7), isovanillin (8), and hederagenin (9), with 4 as a new triterpene compound. Inhibitory activity against human immunodeficiency virus (HIV) protease was also evaluated for the compounds, and only ethyl caffeate, caffeic acid, and isovanillin (6, 7, and 8) exhibited inhibitory effects, with IC50 values of 1.0 μM, 1.5 μM, and 3.5 μM, respectively. Molecular docking with energy minimization and subsequent molecular dynamic (MD) simulation showed that ethyl caffeate and caffeic acid bound to the active site of HIV protease, while isovanillin drifted out from the active site and dissociated into bulk water during MD simulations, and most of the binding residues of HIV protease have been previously identified for HIV protease inhibitors. These results suggest that caffeic acid derivatives may possess inhibitory activities towards HIV protease other than previously reported inhibitory activities against HIV integrase, and thus ethyl caffeate and caffeic acid could be used as lead compounds in developing potential HIV protease inhibitors, and possibly even dual-function inhibitors against HIV.
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Affiliation(s)
- Xia Wang
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, South of Dongqing Road, Guiyang 550025, Guizhou Province, China; (X.W.); (W.-Y.T.); (Q.L.); (X.Y.); (C.-L.M.); (G.-L.C.)
| | - Ying Wei
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, South of Dongqing Road, Guiyang 550025, Guizhou Province, China; (X.W.); (W.-Y.T.); (Q.L.); (X.Y.); (C.-L.M.); (G.-L.C.)
- Correspondence: (Y.W.); (J.Y.)
| | - Wei-Yi Tian
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, South of Dongqing Road, Guiyang 550025, Guizhou Province, China; (X.W.); (W.-Y.T.); (Q.L.); (X.Y.); (C.-L.M.); (G.-L.C.)
| | - Meena Kishore Sakharkar
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada;
| | - Qing Liu
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, South of Dongqing Road, Guiyang 550025, Guizhou Province, China; (X.W.); (W.-Y.T.); (Q.L.); (X.Y.); (C.-L.M.); (G.-L.C.)
| | - Xin Yang
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, South of Dongqing Road, Guiyang 550025, Guizhou Province, China; (X.W.); (W.-Y.T.); (Q.L.); (X.Y.); (C.-L.M.); (G.-L.C.)
| | - Yan-Zi Zhou
- Laboratory of Mesoscopic Chemistry, Institute of Theoretical and Computational Chemistry, Nanjing University, Nanjing 210093, Jiangsu Province, China;
| | - Cheng-Li Mou
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, South of Dongqing Road, Guiyang 550025, Guizhou Province, China; (X.W.); (W.-Y.T.); (Q.L.); (X.Y.); (C.-L.M.); (G.-L.C.)
| | - Gui-Lan Cai
- College of Pharmacy, Guizhou University of Traditional Chinese Medicine, South of Dongqing Road, Guiyang 550025, Guizhou Province, China; (X.W.); (W.-Y.T.); (Q.L.); (X.Y.); (C.-L.M.); (G.-L.C.)
| | - Jian Yang
- Drug Discovery and Development Research Group, College of Pharmacy and Nutrition, University of Saskatchewan, 107 Wiggins Road, Saskatoon, SK S7N 5E5, Canada;
- Correspondence: (Y.W.); (J.Y.)
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23
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Voshavar C. Protease Inhibitors for the Treatment of HIV/AIDS: Recent Advances and Future Challenges. Curr Top Med Chem 2019; 19:1571-1598. [PMID: 31237209 DOI: 10.2174/1568026619666190619115243] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 05/22/2019] [Accepted: 05/27/2019] [Indexed: 02/07/2023]
Abstract
Acquired Immunodeficiency Syndrome (AIDS) is a chronic disease characterized by multiple life-threatening illnesses caused by a retro-virus, Human Immunodeficiency Virus (HIV). HIV infection slowly destroys the immune system and increases the risk of various other infections and diseases. Although, there is no immediate cure for HIV infection/AIDS, several drugs targeting various cruxes of HIV infection are used to slow down the progress of the disease and to boost the immune system. One of the key therapeutic strategies is Highly Active Antiretroviral Therapy (HAART) or ' AIDS cocktail' in a general sense, which is a customized combination of anti-retroviral drugs designed to combat the HIV infection. Since HAART's inception in 1995, this treatment was found to be effective in improving the life expectancy of HIV patients over two decades. Among various classes of HAART treatment regimen, Protease Inhibitors (PIs) are known to be widely used as a major component and found to be effective in treating HIV infection/AIDS. For the past several years, a variety of protease inhibitors have been reported. This review outlines the drug design strategies of PIs, chemical and pharmacological characteristics of some mechanism-based inhibitors, summarizes the recent developments in small molecule based drug discovery with HIV protease as a drug target. Further discussed are the pharmacology, PI drug resistance on HIV PR, adverse effects of HIV PIs and challenges/impediments in the successful application of HIV PIs as an important class of drugs in HAART regimen for the effective treatment of AIDS.
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Affiliation(s)
- Chandrashekhar Voshavar
- College of Pharmacy and Pharmaceutical Sciences, Florida A&M University, Tallahassee, FL 32307, United States
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24
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Liu W, Caglar MU, Mao Z, Woodman A, Arnold JJ, Wilke CO, Cameron CE. More than efficacy revealed by single-cell analysis of antiviral therapeutics. SCIENCE ADVANCES 2019; 5:eaax4761. [PMID: 31692968 PMCID: PMC6821460 DOI: 10.1126/sciadv.aax4761] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 09/16/2019] [Indexed: 05/11/2023]
Abstract
Because many aspects of viral infection dynamics and inhibition are governed by stochastic processes, single-cell analysis should provide more information than approaches using population averaging. We have developed a microfluidic device composed of ~6000 wells, with each well containing a microstructure to capture single, infected cells replicating an enterovirus expressing a fluorescent reporter protein. We have used this system to characterize enterovirus inhibitors with distinct mechanisms of action. Single-cell analysis reveals that each class of inhibitor interferes with the viral infection cycle in a manner that can be distinguished by principal component analysis. Single-cell analysis of antiviral candidates not only reveals efficacy but also facilitates clustering of drugs with the same mechanism of action and provides some indication of the ease with which resistance will develop.
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Affiliation(s)
- Wu Liu
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16801, USA
- Corresponding author. (W.L.); (C.E.C.)
| | - Mehmet U. Caglar
- Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, and Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Zhangming Mao
- Department of Engineering Science and Mechanics, The Pennsylvania State University, University Park, PA 16802, USA
| | - Andrew Woodman
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16801, USA
| | - Jamie J. Arnold
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16801, USA
| | - Claus O. Wilke
- Center for Computational Biology and Bioinformatics, Institute for Cellular and Molecular Biology, and Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Craig E. Cameron
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16801, USA
- Corresponding author. (W.L.); (C.E.C.)
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25
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Agrawal N, Rowe J, Lan J, Yu Q, Hrycyna CA, Chmielewski J. Potential Tools for Eradicating HIV Reservoirs in the Brain: Development of Trojan Horse Prodrugs for the Inhibition of P-Glycoprotein with Anti-HIV-1 Activity. J Med Chem 2019; 63:2131-2138. [PMID: 31505928 PMCID: PMC7073916 DOI: 10.1021/acs.jmedchem.9b00779] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
![]()
Combination
antiretroviral therapy is the mainstay of HIV treatment,
lowering plasma viral levels below detection. However, eradication
of HIV is a major challenge due to cellular and anatomical viral reservoirs
that are often protected from treatment by efflux transporters, such
as P-glycoprotein (P-gp) at the blood–brain barrier (BBB).
Herein we described a Trojan horse approach to therapeutic evasion
of P-gp based on a reversibly linked combination of HIV reverse transcriptase
and protease inhibitors. Potent inhibition of P-gp efflux in cells,
including human brain endothelial cells, was observed with the linked
heterodimeric compounds. In vitro regeneration of active monomeric
drugs was observed in a reducing environment with these dimeric prodrugs,
with the superior leaving group promoting more facile release from
the tether. These release trends were mirrored in the efficacy of
the in cyto anti-HIV-1 activity of the Trojan horse heterodimers.
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Affiliation(s)
- Neha Agrawal
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Jennifer Rowe
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Jie Lan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Qigui Yu
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
| | - Christine A Hrycyna
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Jean Chmielewski
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
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26
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Ghosh AK, Williams JN, Kovela S, Takayama J, Simpson HM, Walters DE, Hattori SI, Aoki M, Mitsuya H. Potent HIV-1 protease inhibitors incorporating squaramide-derived P2 ligands: Design, synthesis, and biological evaluation. Bioorg Med Chem Lett 2019; 29:2565-2570. [PMID: 31416666 PMCID: PMC6711809 DOI: 10.1016/j.bmcl.2019.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/31/2019] [Accepted: 08/04/2019] [Indexed: 02/04/2023]
Abstract
We describe the design, synthesis, and biological evaluation of novel HIV-1 protease inhibitors containing a squaramide-derived scaffold as the P2 ligand in combination with a (R)-hydroxyethylamine sulfonamide isostere. Inhibitor 3h with an N-methyl-3-(R)-aminotetrahydrofuranyl squaramide P2-ligand displayed an HIV-1 protease inhibitory Ki value of 0.51 nM. An energy minimized model of 3h revealed the major molecular interactions between HIV-1 protease active site and the tetrahydrofuranyl squaramide scaffold that may be responsible for its potent activity.
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Affiliation(s)
- Arun K Ghosh
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA.
| | - Jacqueline N Williams
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Satish Kovela
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Jun Takayama
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - Hannah M Simpson
- Department of Chemistry, Purdue University, West Lafayette, IN 47907, USA; Department of Medicinal Chemistry, Purdue University, West Lafayette, IN 47907, USA
| | - D Eric Walters
- Department of Pharmaceutical Sciences, Rosalind Franklin University of Medicine and Science, North Chicago, IL 60064, USA
| | - Shin-Ichiro Hattori
- Department of Refractory Viral Infections, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655, Japan
| | - Manabu Aoki
- Department of Refractory Viral Infections, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch National Cancer Institute, Bethesda, MD 20892, USA
| | - Hiroaki Mitsuya
- Department of Refractory Viral Infections, National Center for Global Health and Medicine, Shinjuku, Tokyo 162-8655, Japan; Experimental Retrovirology Section, HIV and AIDS Malignancy Branch National Cancer Institute, Bethesda, MD 20892, USA; Division of Clinical Sciences, Kumamoto University Hospital, Kumamoto 860-8556, Japan
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27
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Maseko S, Padayachee E, Maphumulo S, Govender T, Sayed Y, Maguire G, Lin J, Naicker T, Baijnath S, Gerhardus KH. Kinetic and thermodynamic characterisation of HIV-protease inhibitors against E35D↑G↑S mutant in the South African HIV-1 subtype C protease. J Enzyme Inhib Med Chem 2019; 34:1451-1456. [PMID: 31409143 PMCID: PMC6713120 DOI: 10.1080/14756366.2019.1636234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Herein, we report the effect of nine FDA approved protease inhibitor drugs against a new HIV-1 subtype C mutant protease, E35D↑G↑S. The mutant has five mutations, E35D, two insertions, position 36 (G and S), and D60E. Kinetics, inhibition constants, vitality, Gibbs free binding energies are reported. The variant showed a decreased affinity for substrate and low catalytic efficiency compared to the wild type. There was a significant decrease in the binding of seven FDA approved protease inhibitors against the mutant (p < .0001). Amprenavir and ritonavir showed the least decrease, but still significant reduced activity in comparison to the wildtype (4 and 5 folds, respectively, p = .0021 and .003, respectively). Nelfinavir and atazanavir were the worst inhibitors against the variant as seen from the IC50, with values of 1401 ± 3.0 and 685 ± 3.0 nM, respectively. Thermodynamics data showed less favourable Gibbs free binding energies for the protease inhibitors to the mutant.
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Affiliation(s)
- Sibusiso Maseko
- a Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal , Durban , South Africa
| | - Eden Padayachee
- a Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal , Durban , South Africa
| | - Siyabonga Maphumulo
- a Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal , Durban , South Africa
| | - Thavendran Govender
- a Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal , Durban , South Africa
| | - Yasien Sayed
- b Protein Structure-Function Research Unit, School of Molecular and Cell Biology, University of the Witwatersrand , Wits , South Africa
| | - Glenn Maguire
- a Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal , Durban , South Africa.,c School of Chemistry and Physics, University of KwaZulu-Natal , Durban , South Africa
| | - Johnson Lin
- d School of Life Sciences, University of KwaZulu-Natal , Durban , South Africa
| | - Tricia Naicker
- a Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal , Durban , South Africa
| | - Sooraj Baijnath
- a Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal , Durban , South Africa
| | - Kruger Hendrik Gerhardus
- a Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal , Durban , South Africa
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28
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Karnati KR, Wang Y. Structural and binding insights into HIV-1 protease and P2-ligand interactions through molecular dynamics simulations, binding free energy and principal component analysis. J Mol Graph Model 2019; 92:112-122. [PMID: 31351319 DOI: 10.1016/j.jmgm.2019.07.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/16/2019] [Accepted: 07/17/2019] [Indexed: 12/15/2022]
Abstract
HIV-1 protease (HIV-1-pr) plays an important role in viral replication and maturation, making it one of the most attractive targets for anti-retroviral therapy. To design new effective inhibitors able to combat drug resistance in mutant HIV-1-pr variants, it is essential to gain further understanding about the mechanisms by which the recently proposed inhibitors deactivate the mutant HIV-1-pr variants. In the present work, we explored the interactions between two P2-ligands (DRV, and one new derivative, 4UY) with wild type (WT) and two multiple mutant HIV-1-pr variants (p20 and p51) with all atom molecular dynamics (MD) simulations, binding free energy calculations, and principal component analysis (PCA). The trajectories of MD simulations show that both 4UY and DRV primarily bind with the active sites, flap and 80s loop regions of HIV-1-pr variants through either hydrogen bonds or hydrophobic interactions. More hydrogen bonds and hydrophobic interactions were located for 4UY/HIV-1-pr complexes than for DRV/HIV-1-pr counterparts. More importantly, 4UY was found to have an extra hydrogen bond with the backbone of Gly48' in the flap region of the HIV-1-prs. The flap tip-tip distance (I50-I50') and flap tip-active site distance (I50-D25 and I50'-D25') indicate that the flaps turn more closed in 4UY bound HIV-1-prs than DRV bound ones, and the former also have more compact hydrophobic cavities than the latter. Further, the vector projections from PCA indicate that 4UY/DRV inhibitor binding projects the closing of flap in HIV-1-pr variants. In line with the above trajectory analysis, the thermodynamics calculation with MM-PBSA method suggests much stronger binding affinity for 4UY/HIV-1-pr than DRV/HIV-1-pr by 4.3-6.4 kcal/mol. Although p20 and p51 also induce weaker binding due to multiple mutants for 4UY inhibitor by 1.9-1.8 kcal/mol, their bindings to the new P2 ligand (4UY) are indeed significantly enhanced as compared to DRV. The thermodynamic components responsible for the binding differences and the contribution from key residues to the binding were also discussed in detail.
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Affiliation(s)
- Konda Reddy Karnati
- Department of Chemistry and Forensic Science, Albany State University, Albany, GA, 31705, USA
| | - Yixuan Wang
- Department of Chemistry and Forensic Science, Albany State University, Albany, GA, 31705, USA.
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29
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Maphumulo SI, Halder AK, Govender T, Maseko S, Maguire GEM, Honarparvar B, Kruger HG. Exploring the flap dynamics of the South African HIV subtype C protease in presence of FDA-approved inhibitors: MD study. Chem Biol Drug Des 2018; 92:1899-1913. [PMID: 30003668 DOI: 10.1111/cbdd.13364] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Accepted: 07/09/2018] [Indexed: 01/01/2023]
Abstract
HIV-1 protease (HIV PR) is considered as one of the most attractive targets for the treatment of HIV and the impact of flap dynamics of HIV PR on the binding affinities of protease inhibitors (PIs) is a crucial ongoing research field. Recently, our research group evaluated the binding affinities of different FDA approved PIs against the South African HIV-1 subtype C (C-SA) protease (PR). The CSA-HIV PR displayed weaker binding affinity for most of the clinical PIs compared to HIV-1 B subtype for West and Central Europe, the Americas. In the current work, the flap dynamics of four different systems of HIV-1 C-SA PR complexed to FDA approved second generation PIs and its impact on binding was explored over the molecular dynamic trajectories. It was observed that the interactions of the selected drugs with the binding site residues of the protease may not be the major contributor for affinity towards PIs. Various post-MD analyses were performed, also entropic contributions, solvation free energies and hydrophobic core formation interactions were studied to assess how the flap dynamics of C-SA PR which is affected by such factors. From these contributions, large van der Waals interactions and low solvation free energies were found to be major factors for the higher activity of ATV against C-SA HIV PR. Furthermore, a comparatively stable hydrophobic core may be responsible for higher stability of the PR flaps of the ATV complex. The outcome of this study provides significant guidance to how the flap dynamics of C-SA PR is affected by various factors as a result of the binding affinity of various protease inhibitors. It will also assist with the design of potent inhibitors against C-SA HIV PR that apart from binding in the active site of PR can interacts with the flaps to prevent opening of the flaps resulting in inactivation of the protease.
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Affiliation(s)
- Siyabonga I Maphumulo
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Amit K Halder
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Sibusiso Maseko
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,School of Chemistry and Physics, University of KwaZulu-Natal, Durban, South Africa
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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30
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Nonstructural Proteins of Alphavirus-Potential Targets for Drug Development. Viruses 2018; 10:v10020071. [PMID: 29425115 PMCID: PMC5850378 DOI: 10.3390/v10020071] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2018] [Revised: 02/02/2018] [Accepted: 02/06/2018] [Indexed: 12/31/2022] Open
Abstract
Alphaviruses are enveloped, positive single-stranded RNA viruses, typically transmitted by arthropods. They often cause arthralgia or encephalitic diseases in infected humans and there is currently no targeted antiviral treatment available. The re-emergence of alphaviruses in Asia, Europe, and the Americas over the last decade, including chikungunya and o'nyong'nyong viruses, have intensified the search for selective inhibitors. In this review, we highlight key molecular determinants within the alphavirus replication complex that have been identified as viral targets, focusing on their structure and functionality in viral dissemination. We also summarize recent structural data of these viral targets and discuss how these could serve as templates to facilitate structure-based drug design and development of small molecule inhibitors.
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31
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Agbowuro AA, Huston WM, Gamble AB, Tyndall JDA. Proteases and protease inhibitors in infectious diseases. Med Res Rev 2017; 38:1295-1331. [PMID: 29149530 DOI: 10.1002/med.21475] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/10/2017] [Accepted: 10/17/2017] [Indexed: 12/31/2022]
Abstract
There are numerous proteases of pathogenic organisms that are currently targeted for therapeutic intervention along with many that are seen as potential drug targets. This review discusses the chemical and biological makeup of some key druggable proteases expressed by the five major classes of disease causing agents, namely bacteria, viruses, fungi, eukaryotes, and prions. While a few of these enzymes including HIV protease and HCV NS3-4A protease have been targeted to a clinically useful level, a number are yet to yield any clinical outcomes in terms of antimicrobial therapy. A significant aspect of this review discusses the chemical and pharmacological characteristics of inhibitors of the various proteases discussed. A total of 25 inhibitors have been considered potent and safe enough to be trialed in humans and are at different levels of clinical application. We assess the mechanism of action and clinical performance of the protease inhibitors against infectious agents with their developmental strategies and look to the next frontiers in the use of protease inhibitors as anti-infective agents.
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Affiliation(s)
| | - Wilhelmina M Huston
- School of Life Sciences, University of Technology Sydney, Ultimo, NSW, Australia
| | - Allan B Gamble
- School of Pharmacy, University of Otago, Dunedin, New Zealand
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32
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Padariya M, Kalathiya U, Baginski M. Molecular basis and potential activity of HIV-1 reverse transcriptase toward trimethylamine-based compounds. Biotechnol Appl Biochem 2017; 64:810-826. [DOI: 10.1002/bab.1543] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2016] [Accepted: 10/31/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Monikaben Padariya
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
| | - Umesh Kalathiya
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
| | - Maciej Baginski
- Department of Pharmaceutical Technology and Biochemistry; Faculty of Chemistry; Gdansk University of Technology; Gdansk Poland
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33
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Midde NM, Gong Y, Cory TJ, Li J, Meibohm B, Li W, Kumar S. Influence of Ethanol on Darunavir Hepatic Clearance and Intracellular PK/PD in HIV-Infected Monocytes, and CYP3A4-Darunavir Interactions Using Inhibition and in Silico Binding Studies. Pharm Res 2017; 34:1925-1933. [PMID: 28616684 DOI: 10.1007/s11095-017-2203-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/05/2017] [Indexed: 02/08/2023]
Abstract
PURPOSE Although the prevalence of alcohol consumption is higher in HIV+ people than general public, limited information is available on how alcohol affects the metabolism and bioavailability of darunavir (DRV). METHODS DRV was quantified by using LC-MS/MS method. All in vitro experiments were performed using human liver microsomes and HIV-infected monocytic cells. CYP3A4 and DRV/Ritonavir (RTV) docking was performed using GOLD suite 5.8. RESULTS Ethanol (20 mM) significantly decreased apparent half-life and increased degradation rate constant of RTV-boosted DRV but not for DRV alone. Similarly, ethanol exposure increased hepatic intrinsic clearance for RTV-boosted DRV with no significant influence on DRV alone. Ethanol showed a limited influence on intracellular total DRV exposure in the presence of RTV without altering maximum concentration (Cmax) values in HIV-infected monocytic cells. Ethanol alone elevated HIV replication but this effect was nullified with the addition of DRV or DRV + RTV. Additionally, inhibitory potency of DRV was significantly reduced in the presence of ethanol. Our docking results projected that ethanol increases the average distance between DRV and CYP3A4 heme, and alter the orientation of DRV-CYP3A4 binding. CONCLUSIONS Collectively these findings suggest that DRV metabolism is primarily influenced by ethanol in the liver, but has minor effect in HIV-residing monocytes.
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Affiliation(s)
- Narasimha M Midde
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Ave, Rm 456, Memphis, TN, 38163, USA.
| | - Yuqing Gong
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Ave, Rm 456, Memphis, TN, 38163, USA
| | - Theodore J Cory
- Department of Clinical Pharmacy, College of Pharmacy, University of Tennessee Health Science Center,, Memphis, TN, 38163, USA
| | - Junhao Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology,, Shanghai, 200237, China
| | - Bernd Meibohm
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Ave, Rm 456, Memphis, TN, 38163, USA
| | - Weihua Li
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology,, Shanghai, 200237, China
| | - Santosh Kumar
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Tennessee Health Science Center, 881 Madison Ave, Rm 456, Memphis, TN, 38163, USA.
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34
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Gerlits O, Keen DA, Blakeley MP, Louis JM, Weber IT, Kovalevsky A. Room Temperature Neutron Crystallography of Drug Resistant HIV-1 Protease Uncovers Limitations of X-ray Structural Analysis at 100 K. J Med Chem 2017; 60:2018-2025. [PMID: 28195728 DOI: 10.1021/acs.jmedchem.6b01767] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
HIV-1 protease inhibitors are crucial for treatment of HIV-1/AIDS, but their effectiveness is thwarted by rapid emergence of drug resistance. To better understand binding of clinical inhibitors to resistant HIV-1 protease, we used room-temperature joint X-ray/neutron (XN) crystallography to obtain an atomic-resolution structure of the protease triple mutant (V32I/I47V/V82I) in complex with amprenavir. The XN structure reveals a D+ ion located midway between the inner Oδ1 oxygen atoms of the catalytic aspartic acid residues. Comparison of the current XN structure with our previous XN structure of the wild-type HIV-1 protease-amprenavir complex suggests that the three mutations do not significantly alter the drug-enzyme interactions. This is in contrast to the observations in previous 100 K X-ray structures of these complexes that indicated loss of interactions by the drug with the triple mutant protease. These findings, thus, uncover limitations of structural analysis of drug binding using X-ray structures obtained at 100 K.
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Affiliation(s)
- Oksana Gerlits
- UT/ORNL Joint Institute of Biological Sciences, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - David A Keen
- ISIS Facility, Rutherford Appleton Laboratory , Harwell Campus, Didcot, OX11 0QX, U.K
| | - Matthew P Blakeley
- Large-Scale Structures Group, Institut Laue Langevin , 71 avenue des Martyrs, 38000 Grenoble, France
| | - John M Louis
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health , DHHS, Bethesda, Maryland 20892-0520, United States
| | - Irene T Weber
- Departments of Chemistry and Biology, Georgia State University , Atlanta, Georgia 30302, United States
| | - Andrey Kovalevsky
- Biology and Soft Matter Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
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35
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Duan LL, Zhu T, Li YC, Zhang QG, Zhang JZH. Effect of polarization on HIV-1protease and fluoro-substituted inhibitors binding energies by large scale molecular dynamics simulations. Sci Rep 2017; 7:42223. [PMID: 28155907 PMCID: PMC5290483 DOI: 10.1038/srep42223] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 01/06/2017] [Indexed: 01/01/2023] Open
Abstract
Molecular dynamics simulations in explicit water are carried out to study the binding of six inhibitors to HIV-1 protease (PR) for up to 700 ns using the standard AMBER force field and polarized protein-specific charge (PPC). PPC is derived from quantum mechanical calculation for protein in solution and therefore it includes electronic polarization effect. Our results show that in all six systems, the bridging water W301 drifts away from the binding pocket in AMBER simulation. However, it is very stable in all six complexes systems using PPC. Especially, intra-protease, protease-inhibitor hydrogen bonds are dynamic stabilized in MD simulation. The computed binding free energies of six complexes have a significantly linear correlation with those experiment values and the correlation coefficient is found to be 0.91 in PPC simulation. However, the result from AMBER simulation shows a weaker correlation with the correlation coefficient of −0.51 due to the lack of polarization effect. Detailed binding interactions of W301, inhibitors with PR are further analyzed and discussed. The present study provides important information to quantitative understanding the interaction mechanism of PR-inhibitor and PR-W301 and these data also emphasizes the importance of both the electronic polarization and the bridging water molecule in predicting precisely binding affinities.
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Affiliation(s)
- Li L Duan
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - T Zhu
- Department of Chemistry, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Yu C Li
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - Qing G Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250014, China
| | - John Z H Zhang
- Department of Chemistry, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
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36
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Sevenich A, Liu GQ, Arduengo AJ, Gupton BF, Opatz T. Asymmetric One-Pot Synthesis of (3R,3aS,6aR)-Hexahydrofuro[2,3-b]furan-3-ol: A Key Component of Current HIV Protease Inhibitors. J Org Chem 2017; 82:1218-1223. [DOI: 10.1021/acs.joc.6b02588] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Adrian Sevenich
- Institute
of Organic Chemistry, Johannes Gutenberg University, Duesbergweg 10−14, 55128 Mainz, Germany
| | - Gong-Qing Liu
- Institute
of Organic Chemistry, Johannes Gutenberg University, Duesbergweg 10−14, 55128 Mainz, Germany
| | - Anthony J. Arduengo
- Department
of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - B. Frank Gupton
- Department
of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, United States
| | - Till Opatz
- Institute
of Organic Chemistry, Johannes Gutenberg University, Duesbergweg 10−14, 55128 Mainz, Germany
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37
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Shi S, Nguyen PK, Cabral HJ, Diez-Barroso R, Derry PJ, Kanahara SM, Kumar VA. Development of peptide inhibitors of HIV transmission. Bioact Mater 2016; 1:109-121. [PMID: 29744399 PMCID: PMC5883972 DOI: 10.1016/j.bioactmat.2016.09.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Revised: 08/18/2016] [Accepted: 09/07/2016] [Indexed: 12/26/2022] Open
Abstract
Treatment of HIV has long faced the challenge of high mutation rates leading to rapid development of resistance, with ongoing need to develop new methods to effectively fight the infection. Traditionally, early HIV medications were designed to inhibit RNA replication and protein production through small molecular drugs. Peptide based therapeutics are a versatile, promising field in HIV therapy, which continues to develop as we expand our understanding of key protein-protein interactions that occur in HIV replication and infection. This review begins with an introduction to HIV, followed by the biological basis of disease, current clinical management of the disease, therapeutics on the market, and finally potential avenues for improved drug development.
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Key Words
- AIDS, acquired immunodeficiency syndrome
- ART, antiretroviral therapy
- CDC, Centers for Disease Control and Prevention
- Drug development
- FDA, US Food and Drug Administration
- FY, fiscal year
- HAART, highly active antiretroviral therapy
- HCV, hepatitis C Virus
- HIV
- HIV treatment
- HIV, human immunodeficiency virus
- INSTI, Integrase strand transfer inhibitors
- LEDGF, lens epithelium-derived growth factor
- NNRTI, Non-nucleoside reverse transcriptase inhibitors
- NRTI, Nucleoside/Nucleotide Reverse Transcriptase Inhibitors
- Peptide inhibitor
- Peptide therapeutic
- R&D, research and development
- RT, reverse transcriptase
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Affiliation(s)
- Siyu Shi
- Department of Chemistry, Rice University, Houston, TX 77030, USA
| | - Peter K. Nguyen
- Department of Biomedical Engineering, New Jersey Institute of Technology, University Heights, Newark, NJ 07102, USA
- Department of Chemical, Biological and Pharmaceutical Engineering, New Jersey Institute of Technology, University Heights, Newark, NJ 07102, USA
| | - Henry J. Cabral
- Department of Biomedical Engineering, New Jersey Institute of Technology, University Heights, Newark, NJ 07102, USA
- Department of Chemical, Biological and Pharmaceutical Engineering, New Jersey Institute of Technology, University Heights, Newark, NJ 07102, USA
| | | | - Paul J. Derry
- Department of Chemistry, Rice University, Houston, TX 77030, USA
| | | | - Vivek A. Kumar
- Department of Biomedical Engineering, New Jersey Institute of Technology, University Heights, Newark, NJ 07102, USA
- Department of Chemical, Biological and Pharmaceutical Engineering, New Jersey Institute of Technology, University Heights, Newark, NJ 07102, USA
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38
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Developing HIV-1 Protease Inhibitors through Stereospecific Reactions in Protein Crystals. Molecules 2016; 21:molecules21111458. [PMID: 27809253 PMCID: PMC6273989 DOI: 10.3390/molecules21111458] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 10/26/2016] [Accepted: 10/26/2016] [Indexed: 11/30/2022] Open
Abstract
Protease inhibitors are key components in the chemotherapy of HIV infection. However, the appearance of viral mutants routinely compromises their clinical efficacy, creating a constant need for new and more potent inhibitors. Recently, a new class of epoxide-based inhibitors of HIV-1 protease was investigated and the configuration of the epoxide carbons was demonstrated to play a crucial role in determining the binding affinity. Here we report the comparison between three crystal structures at near-atomic resolution of HIV-1 protease in complex with the epoxide-based inhibitor, revealing an in-situ epoxide ring opening triggered by a pH change in the mother solution of the crystal. Increased pH in the crystal allows a stereospecific nucleophile attack of an ammonia molecule onto an epoxide carbon, with formation of a new inhibitor containing amino-alcohol functions. The described experiments open a pathway for the development of new stereospecific protease inhibitors from a reactive lead compound.
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39
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Molecular dynamics at the receptor level of immunodominant myelin oligodendrocyte glycoprotein 35-55 epitope implicated in multiple sclerosis. J Mol Graph Model 2016; 68:78-86. [PMID: 27388119 DOI: 10.1016/j.jmgm.2016.06.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 06/09/2016] [Accepted: 06/10/2016] [Indexed: 11/24/2022]
Abstract
Multiple Sclerosis (MS) is a common autoimmune disease whereby myelin is destroyed by the immune system. The disease is triggered by the stimulation of encephalitogenic T-cells via the formation of a trimolecular complex between the Human Leukocyte Antigen (HLA), an immunodominant epitope of myelin proteins and T-cell Receptor (TCR). Myelin Oligodendrocyte Glycoprotein (MOG) is located on the external surface of myelin and has been implicated in MS induction. The immunodominant 35-55 epitope of MOG is widely used for in vivo biological evaluation and immunological studies that are related with chronic Experimental Autoimmune Encephalomyelitis (EAE, animal model of MS), inflammatory diseases and MS. In this report, Molecular Dynamics (MD) simulations were used to explore the interactions of MOG35-55 at the receptor level. A detailed mapping of the developed interactions during the creation of the trimolecular complex is reported. This is the first attempt to gain an understanding of the molecular recognition of the MOG35-55 epitope by the HLA and TCR receptors. During the formation of the trimolecular complex, the residues Arg(41) and Arg(46) of MOG35-55 have been confirmed to serve as TCR anchors while Tyr(40) interacts with HLA. The present structural findings indicate that the Arg at positions 41 and 46 is a key residue for the stimulation of the encephalitogenic T-cells.
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40
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Mahanti M, Bhakat S, Nilsson UJ, Söderhjelm P. Flap Dynamics in Aspartic Proteases: A Computational Perspective. Chem Biol Drug Des 2016; 88:159-77. [PMID: 26872937 DOI: 10.1111/cbdd.12745] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Recent advances in biochemistry and drug design have placed proteases as one of the critical target groups for developing novel small-molecule inhibitors. Among all proteases, aspartic proteases have gained significant attention due to their role in HIV/AIDS, malaria, Alzheimer's disease, etc. The binding cleft is covered by one or two β-hairpins (flaps) which need to be opened before a ligand can bind. After binding, the flaps close to retain the ligand in the active site. Development of computational tools has improved our understanding of flap dynamics and its role in ligand recognition. In the past decade, several computational approaches, for example molecular dynamics (MD) simulations, coarse-grained simulations, replica-exchange molecular dynamics (REMD) and metadynamics, have been used to understand flap dynamics and conformational motions associated with flap movements. This review is intended to summarize the computational progress towards understanding the flap dynamics of proteases and to be a reference for future studies in this field.
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Affiliation(s)
- Mukul Mahanti
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Soumendranath Bhakat
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden
| | - Ulf J Nilsson
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, PO Box 124, SE-221 00, Lund, Sweden
| | - Pär Söderhjelm
- Division of Biophysical Chemistry, Department of Chemistry, Lund University, PO Box 124, SE-22100, Lund, Sweden
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41
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Machara A, Lux V, Kožíšek M, Grantz Šašková K, Štěpánek O, Kotora M, Parkan K, Pávová M, Glass B, Sehr P, Lewis J, Müller B, Kräusslich HG, Konvalinka J. Specific Inhibitors of HIV Capsid Assembly Binding to the C-Terminal Domain of the Capsid Protein: Evaluation of 2-Arylquinazolines as Potential Antiviral Compounds. J Med Chem 2016; 59:545-58. [PMID: 26685880 DOI: 10.1021/acs.jmedchem.5b01089] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Assembly of human immunodeficiency virus (HIV-1) represents an attractive target for antiretroviral therapy which is not exploited by currently available drugs. We established high-throughput screening for assembly inhibitors based on competition of small molecules for the binding of a known dodecapeptide assembly inhibitor to the C-terminal domain of HIV-1 CA (capsid). Screening of >70000 compounds from different libraries identified 2-arylquinazolines as low micromolecular inhibitors of HIV-1 capsid assembly. We prepared focused libraries of modified 2-arylquinazolines and tested their capacity to bind HIV-1 CA to compete with the known peptide inhibitor and to prevent the replication of HIV-1 in tissue culture. Some of the compounds showed potent binding to the C-terminal domain of CA and were found to block viral replication at low micromolar concentrations.
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Affiliation(s)
- Aleš Machara
- Department of Organic Chemistry, Faculty of Science, Charles University , 128 43 Prague 2, Czech Republic
| | - Vanda Lux
- Department of Infectious Diseases, Virology, University Hospital Heidelberg , Im Neuenheimer Feld 324, 691 20 Heidelberg, Germany
| | - Milan Kožíšek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center , Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Klára Grantz Šašková
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center , Flemingovo n. 2, 166 10 Prague 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University , 128 43 Prague 2, Czech Republic
| | - Ondřej Štěpánek
- Department of Organic Chemistry, Faculty of Science, Charles University , 128 43 Prague 2, Czech Republic
| | - Martin Kotora
- Department of Organic Chemistry, Faculty of Science, Charles University , 128 43 Prague 2, Czech Republic
| | - Kamil Parkan
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center , Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Marcela Pávová
- Department of Infectious Diseases, Virology, University Hospital Heidelberg , Im Neuenheimer Feld 324, 691 20 Heidelberg, Germany.,Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center , Flemingovo n. 2, 166 10 Prague 6, Czech Republic
| | - Bärbel Glass
- Department of Infectious Diseases, Virology, University Hospital Heidelberg , Im Neuenheimer Feld 324, 691 20 Heidelberg, Germany
| | - Peter Sehr
- Chemical Biology Core Facility, European Molecular Biology Laboratory , 691 17 Heidelberg, Germany
| | - Joe Lewis
- Chemical Biology Core Facility, European Molecular Biology Laboratory , 691 17 Heidelberg, Germany
| | - Barbara Müller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg , Im Neuenheimer Feld 324, 691 20 Heidelberg, Germany
| | - Hans-Georg Kräusslich
- Department of Infectious Diseases, Virology, University Hospital Heidelberg , Im Neuenheimer Feld 324, 691 20 Heidelberg, Germany
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Gilead Sciences and IOCB Research Center , Flemingovo n. 2, 166 10 Prague 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University , 128 43 Prague 2, Czech Republic
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42
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Pietrucci F, Vargiu AV, Kranjc A. HIV-1 Protease Dimerization Dynamics Reveals a Transient Druggable Binding Pocket at the Interface. Sci Rep 2015; 5:18555. [PMID: 26692118 PMCID: PMC4686983 DOI: 10.1038/srep18555] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 11/19/2015] [Indexed: 12/30/2022] Open
Abstract
The binding mechanism of HIV-1 protease monomers leading to the catalytically competent dimeric enzyme has been investigated by means of state-of-the-art atomistic simulations. The emerging picture allows a deeper understanding of experimental observations and reveals that water molecules trapped at the interface have an important role in slowing down the kinetics of the association process. Unexpectedly, a cryptic binding pocket is identified at the interface of the complex, corresponding to a partially bound dimer that lacks enzymatic function. The pocket has a transient nature with a lifetime longer than 1 μs, and it displays very favorable druggability features. Docking as well as MM-GBSA free-energy calculations further support the possibility to target the new binding site by means of inhibitors able to prevent the complete dimerization by capturing the inactive conformation. This discovery could open the way to the rational design of a new class of anti-HIV drugs.
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Affiliation(s)
- Fabio Pietrucci
- Sorbonne Universités, UPMC University Paris 6, CNRS - UMR 7590, IMPMC, F-75005 Paris, France
| | | | - Agata Kranjc
- School of Pharmaceutical Sciences, University of Geneva, CH-1211 Geneva, Switzerland
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43
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Oral Lopinavir Use and Human Papillomavirus Infection in HIV-Positive Women. J Acquir Immune Defic Syndr 2015; 70:e63-6. [PMID: 26181819 DOI: 10.1097/qai.0000000000000752] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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44
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45
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Quantum dots-fluorescence resonance energy transfer-based nanosensors and their application. Biosens Bioelectron 2015; 74:562-74. [DOI: 10.1016/j.bios.2015.06.076] [Citation(s) in RCA: 185] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 01/02/2023]
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46
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Mahdi M, Szojka Z, Mótyán JA, Tőzsér J. Inhibition Profiling of Retroviral Protease Inhibitors Using an HIV-2 Modular System. Viruses 2015; 7:6152-62. [PMID: 26633459 PMCID: PMC4690855 DOI: 10.3390/v7122931] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 11/11/2015] [Accepted: 11/13/2015] [Indexed: 12/13/2022] Open
Abstract
Retroviral protease inhibitors (PIs) are fundamental pillars in the treatment of HIV infection and acquired immunodeficiency syndrome (AIDS). Currently used PIs are designed against HIV-1, and their effect on HIV-2 is understudied. Using a modular HIV-2 protease cassette system, inhibition profiling assays were carried out for protease inhibitors both in enzymatic and cell culture assays. Moreover, the treatment-associated resistance mutations (I54M, L90M) were introduced into the modular system, and comparative inhibition assays were performed to determine their effect on the susceptibility of the protease. Our results indicate that darunavir, saquinavir, indinavir and lopinavir were very effective HIV-2 protease inhibitors, while tipranavir, nelfinavir and amprenavir showed a decreased efficacy. I54M, L90M double mutation resulted in a significant reduction in the susceptibility to most of the inhibitors with the exception of tipranavir. To our knowledge, this modular system constitutes a novel approach in the field of HIV-2 protease characterization and susceptibility testing.
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Affiliation(s)
- Mohamed Mahdi
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4010 Debrecen, Hungary.
| | - Zsófia Szojka
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4010 Debrecen, Hungary.
| | - János András Mótyán
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4010 Debrecen, Hungary.
| | - József Tőzsér
- Laboratory of Retroviral Biochemistry, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, H-4010 Debrecen, Hungary.
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47
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Chauhan J, Chen SE, Fenstermacher KJ, Naser-Tavakolian A, Reingewertz T, Salmo R, Lee C, Williams E, Raje M, Sundberg E, DeStefano JJ, Freire E, Fletcher S. Synthetic, structural mimetics of the β-hairpin flap of HIV-1 protease inhibit enzyme function. Bioorg Med Chem 2015; 23:7095-109. [PMID: 26474665 DOI: 10.1016/j.bmc.2015.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/20/2015] [Accepted: 09/03/2015] [Indexed: 01/11/2023]
Abstract
Small-molecule mimetics of the β-hairpin flap of HIV-1 protease (HIV-1 PR) were designed based on a 1,4-benzodiazepine scaffold as a strategy to interfere with the flap-flap protein-protein interaction, which functions as a gated mechanism to control access to the active site. Michaelis-Menten kinetics suggested our small-molecules are competitive inhibitors, which indicates the mode of inhibition is through binding the active site or sterically blocking access to the active site and preventing flap closure, as designed. More generally, a new bioactive scaffold for HIV-1PR inhibition has been discovered, with the most potent compound inhibiting the protease with a modest K(i) of 11 μM.
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Affiliation(s)
- Jay Chauhan
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA
| | - Shen-En Chen
- Department of Biology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Katherine J Fenstermacher
- Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Aurash Naser-Tavakolian
- Department of Biology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Tali Reingewertz
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 725 West Lombard St., Baltimore, MD 21201, USA
| | - Rosene Salmo
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA
| | - Christian Lee
- PharmD Program, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA
| | - Emori Williams
- Vivien T Thomas Medical Arts Academy, 100 N Calhoun St., Baltimore, MD 21223, USA
| | - Mithun Raje
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA
| | - Eric Sundberg
- Department of Microbiology and Immunology, University of Maryland School of Medicine, 725 West Lombard St., Baltimore, MD 21201, USA
| | - Jeffrey J DeStefano
- Department of Cell Biology & Molecular Genetics, University of Maryland, College Park, MD 20742, USA
| | - Ernesto Freire
- Department of Biology, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD 21218, USA
| | - Steven Fletcher
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 N. Pine St., Baltimore, MD 21201, USA; University of Maryland Greenebaum Cancer Center, 22 S. Greene St., Baltimore, MD 21201, USA.
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Herpoldt KL, Artzy-Schnirman A, Christofferson AJ, Makarucha AJ, de la Rica R, Yarovsky I, Stevens MM. Designing Fluorescent Peptide Sensors with Dual Specificity for the Detection of HIV-1 Protease. CHEMISTRY OF MATERIALS : A PUBLICATION OF THE AMERICAN CHEMICAL SOCIETY 2015; 27:7187-7195. [PMID: 28479671 PMCID: PMC5419500 DOI: 10.1021/acs.chemmater.5b03651] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
HIV-1 protease is a key enzyme in the life cycle of HIV/AIDS, as it is responsible for the formation of the mature virus particle. We demonstrate here that phage-display peptides raised against this enzyme can be used as peptide sensors for the detection of HIV-1 protease in a simple, one-pot assay. The presence of the enzyme is detected through an energy transfer between two peptide sensors when simultaneously complexed with the target protein. The multivalent nature of this assay increases the specificity of the detection by requiring all molecules to be interacting in order for there to be a FRET signal. We also perform molecular dynamics simulations to explore the interaction between the protease and the peptides in order to guide the design of these peptide sensors and to understand the mechanisms which cause these simultaneous binding events. This approach aims to facilitate the development of new assays for enzymes that are not dependent on the cleavage of a substrate and do not require multiple washing steps.
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Affiliation(s)
- Karla-Luise Herpoldt
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
| | - Arbel Artzy-Schnirman
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
| | | | - Adam J. Makarucha
- Health Innovations Research Institute, RMIT University, GPO Box 2476, Victoria 3001, Australia
| | - Roberto de la Rica
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
| | - Irene Yarovsky
- Health Innovations Research Institute, RMIT University, GPO Box 2476, Victoria 3001, Australia
| | - Molly M. Stevens
- Department of Materials, Department of Bioengineering, Institute of Biomedical Engineering, Imperial College London, Prince Consort Road, London, SW7 2AZ, UK
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49
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Effects of drug-resistant mutations on the dynamic properties of HIV-1 protease and inhibition by Amprenavir and Darunavir. Sci Rep 2015; 5:10517. [PMID: 26012849 PMCID: PMC4444956 DOI: 10.1038/srep10517] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Accepted: 04/16/2015] [Indexed: 12/20/2022] Open
Abstract
Molecular dynamics simulations are performed to investigate the dynamic properties of wild-type HIV-1 protease and its two multi-drug-resistant variants (Flap + (L10I/G48V/I54V/V82A) and Act (V82T/I84V)) as well as their binding with APV and DRV inhibitors. The hydrophobic interactions between flap and 80 s (80’s) loop residues (mainly I50-I84’ and I50’-I84) play an important role in maintaining the closed conformation of HIV-1 protease. The double mutation in Act variant weakens the hydrophobic interactions, leading to the transition from closed to semi-open conformation of apo Act. APV or DRV binds with HIV-1 protease via both hydrophobic and hydrogen bonding interactions. The hydrophobic interactions from the inhibitor is aimed to the residues of I50 (I50’), I84 (I84’), and V82 (V82’) which create hydrophobic core clusters to further stabilize the closed conformation of flaps, and the hydrogen bonding interactions are mainly focused with the active site of HIV-1 protease. The combined change in the two kinds of protease-inhibitor interactions is correlated with the observed resistance mutations. The present study sheds light on the microscopic mechanism underlying the mutation effects on the dynamics of HIV-1 protease and the inhibition by APV and DRV, providing useful information to the design of more potent and effective HIV-1 protease inhibitors.
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50
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Papanagnou P, Baltopoulos P, Tsironi M. Marketed nonsteroidal anti-inflammatory agents, antihypertensives, and human immunodeficiency virus protease inhibitors: as-yet-unused weapons of the oncologists' arsenal. Ther Clin Risk Manag 2015; 11:807-19. [PMID: 26056460 PMCID: PMC4445694 DOI: 10.2147/tcrm.s82049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Experimental data indicate that several pharmacological agents that have long been used for the management of various diseases unrelated to cancer exhibit profound in vitro and in vivo anticancer activity. This is of major clinical importance, since it would possibly aid in reassessing the therapeutic use of currently used agents for which clinicians already have experience. Further, this would obviate the time-consuming process required for the development and the approval of novel antineoplastic drugs. Herein, both pre-clinical and clinical data concerning the antineoplastic function of distinct commercially available pharmacological agents that are not currently used in the field of oncology, ie, nonsteroidal anti-inflammatory drugs, antihypertensive agents, and anti-human immunodeficiency virus agents inhibiting viral protease, are reviewed. The aim is to provide integrated information regarding not only the molecular basis of the antitumor function of these agents but also the applicability of the reevaluation of their therapeutic range in the clinical setting.
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Affiliation(s)
- Panagiota Papanagnou
- Department of Nursing, Faculty of Human Movement and Quality of Life Sciences, University of Peloponnese, Sparta, Greece
| | - Panagiotis Baltopoulos
- Department of Sports Medicine and Biology of Physical Activity, Faculty of Physical Education and Sport Science, National and Kapodistrian University of Athens, Athens, Greece
| | - Maria Tsironi
- Department of Nursing, Faculty of Human Movement and Quality of Life Sciences, University of Peloponnese, Sparta, Greece
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