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Rabelo VWH, de Palmer Paixão ICN, Abreu PA. Structural insights into the inhibition of the nsP2 protease from Chikungunya virus by molecular modeling approaches. J Mol Model 2022; 28:311. [PMID: 36097090 DOI: 10.1007/s00894-022-05316-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 09/05/2022] [Indexed: 11/24/2022]
Abstract
Chikungunya virus (CHIKV) is the etiological agent of the Chikungunya fever which has spread worldwide. Clinically, this disease may lead to prolonged incapacitating joint pain that can compromise remarkably the patients' quality of life. However, there are no licensed vaccines or specific drugs to fight this infection yet, making the search for novel therapies an imperative need. In this scenario, the CHIKV nsP2 protease emerged as an attractive therapeutic target once this protein plays a pivotal role in viral replication and pathogenesis. Hence, we investigated the structural basis for the inhibition of this enzyme by using molecular docking and dynamics simulations. Compounds with inhibitory activities against CHIKV nsP2 protease determined experimentally were selected from the literature. Docking studies with a set of stereoisomers showed that trans isomers, but not cis ones, bound close to the catalytic dyad which may explain isomerism requirements to the enzyme's inhibition. Further, binding mode analyses of other known inhibitors revealed highly conserved contacts between inhibitors and enzyme residues like N1011, C1013, A1046, Y1079, N1082, W1084, L1205, and M1242. Molecular dynamics simulations reinforced the importance of some of these interactions and pointed to nonpolar interactions as the main forces for inhibitors' binding. Finally, we observed that true inhibitors exhibited lower structural fluctuation, higher ligand efficiency and did not induce significant changes in protein correlated motions. Collectively, our findings might allow discerning true inhibitors from false ones and can guide drug development efforts targeting the nsP2 protease to fight CHIKV infections in the future.
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Affiliation(s)
- Vitor Won-Held Rabelo
- Instituto de Biologia, Programa de Pós-Graduação em Ciências e Biotecnologia, Universidade Federal Fluminense, Niterói, RJ, 24210-201, Brazil
| | - Izabel Christina Nunes de Palmer Paixão
- Instituto de Biologia, Programa de Pós-Graduação em Ciências e Biotecnologia, Universidade Federal Fluminense, Niterói, RJ, 24210-201, Brazil.,Departamento de Biologia Celular e Molecular, Instituto de Biologia, Universidade Federal Fluminense, Niterói, RJ, 24210-201, Brazil
| | - Paula Alvarez Abreu
- Instituto de Biodiversidade e Sustentabilidade (NUPEM), Universidade Federal do Rio de Janeiro, Macaé, RJ, 27965-045, Brazil.
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2
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Sundar S, Piramanayagam S, Natarajan J. A review on structural genomics approach applied for drug discovery against three vector-borne viral diseases: Dengue, Chikungunya and Zika. Virus Genes 2022; 58:151-171. [PMID: 35394596 DOI: 10.1007/s11262-022-01898-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/22/2022] [Indexed: 12/22/2022]
Abstract
Structural genomics involves the advent of three-dimensional structures of the genome encoded proteins through various techniques available. Numerous structural genomics research groups have been developed across the globe and they contribute enormously to the identification of three-dimensional structures of various proteins. In this review, we have discussed the applications of the structural genomics approach towards the discovery of potential lead-like molecules against the genomic drug targets of three vector-borne diseases, namely, Dengue, Chikungunya and Zika. Currently, all these three diseases are associated with the most important global public health problems and significant economic burden in tropical countries. Structural genomics has accelerated the identification of novel drug targets and inhibitors for the treatment of these diseases. We start with the current development status of the drug targets and antiviral drugs against these three diseases and conclude by describing challenges that need to be addressed to overcome the shortcomings in the process of drug discovery.
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Affiliation(s)
- Shobana Sundar
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India
| | | | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India.
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3
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Zhang M, Wang N, Liu J, Wang C, Xu Y, Ma L. A review on biomass-derived levulinic acid for application in drug synthesis. Crit Rev Biotechnol 2021; 42:220-253. [DOI: 10.1080/07388551.2021.1939261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Mingyue Zhang
- Key Laboratory of Renewable Energy, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Nan Wang
- Key Laboratory of Renewable Energy, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, PR China
- School of Environmental Science and Engineering, Tianjin University, Tianjin, PR China
| | - Jianguo Liu
- Key Laboratory of Renewable Energy, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Chenguang Wang
- Key Laboratory of Renewable Energy, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Ying Xu
- Key Laboratory of Renewable Energy, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
| | - Longlong Ma
- Key Laboratory of Renewable Energy, Guangzhou Institute of Energy Conversion, Chinese Academy of Sciences, Guangzhou, PR China
- University of Chinese Academy of Sciences, Beijing, PR China
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Battisti V, Urban E, Langer T. Antivirals against the Chikungunya Virus. Viruses 2021; 13:1307. [PMID: 34372513 PMCID: PMC8310245 DOI: 10.3390/v13071307] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 06/28/2021] [Accepted: 06/30/2021] [Indexed: 01/20/2023] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that has re-emerged in recent decades, causing large-scale epidemics in many parts of the world. CHIKV infection leads to a febrile disease known as chikungunya fever (CHIKF), which is characterised by severe joint pain and myalgia. As many patients develop a painful chronic stage and neither antiviral drugs nor vaccines are available, the development of a potent CHIKV inhibiting drug is crucial for CHIKF treatment. A comprehensive summary of current antiviral research and development of small-molecule inhibitor against CHIKV is presented in this review. We highlight different approaches used for the identification of such compounds and further discuss the identification and application of promising viral and host targets.
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Affiliation(s)
| | | | - Thierry Langer
- Department of Pharmaceutical Sciences, Pharmaceutical Chemistry Division, University of Vienna, A-1090 Vienna, Austria; (V.B.); (E.U.)
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5
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Mandrekar KS, Tilve SG. Molecular iodine mediated oxidative cleavage of the C–N bond of aryl and heteroaryl (dimethylamino)methyl groups into aldehydes. NEW J CHEM 2021. [DOI: 10.1039/d0nj05832g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An efficient iodine mediated conversion of aryl or heteroaryl (dimethylamino)methyl compunds to aryl or heteroaryl aldehydes is achieved via cleavage of C-N bond.
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Small-Molecule Inhibitors of Chikungunya Virus: Mechanisms of Action and Antiviral Drug Resistance. Antimicrob Agents Chemother 2020; 64:AAC.01788-20. [PMID: 32928738 PMCID: PMC7674028 DOI: 10.1128/aac.01788-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that has spread to more than 60 countries worldwide. CHIKV infection leads to a febrile illness known as chikungunya fever (CHIKF), which is characterized by long-lasting and debilitating joint and muscle pain. CHIKV can cause large-scale epidemics with high attack rates, which substantiates the need for development of effective therapeutics suitable for outbreak containment. In this review, we highlight the different strategies used for developing CHIKV small-molecule inhibitors, ranging from high-throughput cell-based screening to in silico screens and enzymatic assays with purified viral proteins. Chikungunya virus (CHIKV) is a mosquito-transmitted alphavirus that has spread to more than 60 countries worldwide. CHIKV infection leads to a febrile illness known as chikungunya fever (CHIKF), which is characterized by long-lasting and debilitating joint and muscle pain. CHIKV can cause large-scale epidemics with high attack rates, which substantiates the need for development of effective therapeutics suitable for outbreak containment. In this review, we highlight the different strategies used for developing CHIKV small-molecule inhibitors, ranging from high-throughput cell-based screening to in silico screens and enzymatic assays with purified viral proteins. We further discuss the current status of the most promising molecules, including in vitro and in vivo findings. In particular, we focus on describing host and/or viral targets, mode of action, and mechanisms of antiviral drug resistance and associated mutations. Knowledge of the key molecular determinants of drug resistance will aid selection of the most promising antiviral agent(s) for clinical use. For these reasons, we also summarize the available information about drug-resistant phenotypes in Aedes mosquito vectors. From this review, it is evident that more of the active molecules need to be evaluated in preclinical and clinical models to address the current lack of antiviral treatment for CHIKF.
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Rabelo VWH, Paixão ICNDP, Abreu PA. Targeting Chikungunya virus by computational approaches: from viral biology to the development of therapeutic strategies. Expert Opin Ther Targets 2020; 24:63-78. [DOI: 10.1080/14728222.2020.1712362] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Vitor Won-Held Rabelo
- Programa de Pós-graduação em Ciências e Biotecnologia, Instituto de Biologia,Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Izabel Christina Nunes de Palmer Paixão
- Programa de Pós-graduação em Ciências e Biotecnologia, Instituto de Biologia,Universidade Federal Fluminense, Niterói, RJ, Brazil
- Departamento de Biologia Celular e Molecular, Instituto de Biologia,Universidade Federal Fluminense, Niterói, RJ, Brazil
| | - Paula Alvarez Abreu
- Instituto de Biodiversidade e Sustentabilidade (NUPEM), Universidade Federal do Rio de Janeiro, Macaé, RJ, Brazil
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Decuyper L, Magdalenić K, Verstraete M, Jukič M, Sosič I, Sauvage E, Amoroso AM, Verlaine O, Joris B, Gobec S, D'hooghe M. α-Unsaturated 3-Amino-1-carboxymethyl-β-lactams as Bacterial PBP Inhibitors: Synthesis and Biochemical Assessment. Chemistry 2019; 25:16128-16140. [PMID: 31596974 DOI: 10.1002/chem.201904139] [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: 09/09/2019] [Revised: 10/08/2019] [Indexed: 01/24/2023]
Abstract
Innovative monocyclic β-lactam entities create opportunities in the battle against resistant bacteria because of their PBP acylation potential, intrinsically high β-lactamase stability and compact scaffold. α-Benzylidene-substituted 3-amino-1-carboxymethyl-β-lactams were recently shown to be potent PBP inhibitors and constitute eligible anchor points for synthetic elaboration of the chemical space around the central β-lactam ring. The present study discloses a 12-step synthesis of ten α-arylmethylidenecarboxylates using a microwave-assisted Wittig olefination as the crucial reaction step. The library was designed aiming at enhanced β-lactam electrophilicity and extended electron flow after enzymatic attack. Additionally, increased β-lactamase stability and intermolecular target interaction were envisioned by tackling both the substitution pattern of the aromatic ring and the β-lactam C4-position. The significance of α-unsaturation was validated and the R39/PBP3 inhibitory potency shown to be augmented the most through decoration of the aromatic ring with electron-withdrawing groups. Furthermore, ring cleavage by representative β-lactamases was ruled out, providing new insights in the SAR landscape of monocyclic β-lactams as eligible PBP or β-lactamase inhibitors.
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Affiliation(s)
- Lena Decuyper
- SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Katarina Magdalenić
- SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Marie Verstraete
- SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
| | - Marko Jukič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Izidor Sosič
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Eric Sauvage
- Centre for Protein Engineering, Faculty of Sciences, University of Liège, Quartier Agora, Allée du 6 Août 13, Bât B6a, 4000, Liège Sart-Tilman, Belgium
| | - Ana Maria Amoroso
- Centre for Protein Engineering, Faculty of Sciences, University of Liège, Quartier Agora, Allée du 6 Août 13, Bât B6a, 4000, Liège Sart-Tilman, Belgium
| | - Olivier Verlaine
- Centre for Protein Engineering, Faculty of Sciences, University of Liège, Quartier Agora, Allée du 6 Août 13, Bât B6a, 4000, Liège Sart-Tilman, Belgium
| | - Bernard Joris
- Centre for Protein Engineering, Faculty of Sciences, University of Liège, Quartier Agora, Allée du 6 Août 13, Bât B6a, 4000, Liège Sart-Tilman, Belgium
| | - Stanislav Gobec
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva 7, 1000, Ljubljana, Slovenia
| | - Matthias D'hooghe
- SynBioC Research Group, Department of Green Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, 9000, Ghent, Belgium
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9
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Sotriffer C. Docking of Covalent Ligands: Challenges and Approaches. Mol Inform 2018; 37:e1800062. [PMID: 29927068 DOI: 10.1002/minf.201800062] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 06/01/2018] [Indexed: 01/08/2023]
Abstract
Covalent ligands have recently regained considerable attention in drug discovery. The rational design of such ligands, however, is still faced with particular challenges, mostly related to the fact that covalent bond formation is a quantum mechanical phenomenon which cannot adequately be handled by the force fields or empirical approaches typically used for noncovalent protein-ligand interactions. Although the necessity for quantum chemical approaches is clear, they cannot yet routinely be applied on large data sets of ligands or for a broader exploration of binding modes in docking calculations. On the other hand, technical solutions for performing docking calculations with covalent ligands are available, but their scope is normally quite limited. Scoring functions typically neglect the contribution from covalent bond formation completely. In this situation, the question arises how to approach covalent ligands and which methods to choose for their docking and design.
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Affiliation(s)
- Christoph Sotriffer
- Institute of Pharmacy and Food Chemistry, Julius-Maximilians-Universität Würzburg, Am Hubland, D-, 97074, Würzburg, Germany
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10
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Ching KC, F P Ng L, Chai CLL. A compendium of small molecule direct-acting and host-targeting inhibitors as therapies against alphaviruses. J Antimicrob Chemother 2018; 72:2973-2989. [PMID: 28981632 PMCID: PMC7110243 DOI: 10.1093/jac/dkx224] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Alphaviruses were amongst the first arboviruses to be isolated, characterized and assigned a taxonomic status. They are globally widespread, infecting a large variety of terrestrial animals, birds, insects and even fish. Moreover, they are capable of surviving and circulating in both sylvatic and urban environments, causing considerable human morbidity and mortality. The re-emergence of Chikungunya virus (CHIKV) in almost every part of the world has caused alarm to many health agencies throughout the world. The mosquito vector for this virus, Aedes, is globally distributed in tropical and temperate regions and capable of thriving in both rural and urban landscapes, giving the opportunity for CHIKV to continue expanding into new geographical regions. Despite the importance of alphaviruses as human pathogens, there is currently no targeted antiviral treatment available for alphavirus infection. This mini-review discusses some of the major features in the replication cycle of alphaviruses, highlighting the key viral targets and host components that participate in alphavirus replication and the molecular functions that were used in drug design. Together with describing the importance of these targets, we review the various direct-acting and host-targeting inhibitors, specifically small molecules that have been discovered and developed as potential therapeutics as well as their reported in vitro and in vivo efficacies.
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Affiliation(s)
- Kuan-Chieh Ching
- NUS Graduate School for Integrative Sciences and Engineering, Centre for Life Sciences, #05-01, 28 Medical Drive, Singapore 117456.,Department of Pharmacy, Faculty of Science, National University of Singapore, Block S4A, Level 3, 18 Science Drive 4, Singapore 117543
| | - Lisa F P Ng
- Singapore Immunology Network, A*STAR, 8A Biomedical Grove, Immunos Building, #04-06, Singapore 138648.,Department of Biochemistry, Yong Loo Lin School of Medicine, National University of Singapore, Block MD6, Centre for Translational Medicine, 14 Medical Drive, #14-01T, Singapore 117599.,Institute of Infection and Global Health, University of Liverpool, Ronald Ross Building, 8 West Derby Street, Liverpool L697BE, UK
| | - Christina L L Chai
- NUS Graduate School for Integrative Sciences and Engineering, Centre for Life Sciences, #05-01, 28 Medical Drive, Singapore 117456.,Department of Pharmacy, Faculty of Science, National University of Singapore, Block S4A, Level 3, 18 Science Drive 4, Singapore 117543
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11
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Li TR, Maliszewski ML, Xiao WJ, Tunge JA. Stereospecific Decarboxylative Benzylation of Enolates: Development and Mechanistic Insight. Org Lett 2018. [PMID: 29533071 DOI: 10.1021/acs.orglett.8b00169] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A palladium-catalyzed decarboxylative coupling of enol carbonates with diarylmethyl electrophiles that are derived from secondary benzylic alcohols has been developed. This method allows the generation of a variety of β-diaryl ketones through an efficient and highly stereospecific coupling. In addition, detailed mechanistic insight into the coupling suggests that the reaction is a rare example of an intramolecular decarboxylative coupling that proceeds without crossover between reactants.
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Affiliation(s)
- Tian-Ren Li
- Department of Chemistry , The University of Kansas , 2010 Malott Hall, 1251 Wescoe Hall Drive , Lawrence , Kansas 66045 , United States.,The KU Chemical Methodologies and Library Development Center of Excellence , 2034 Becker Drive , Lawrence , Kansas 66047 , United States.,Key Laboratory of Pesticide & Chemical Biology Ministry of Education, College of Chemistry , Central China Normal University , 152 Luoyu Road , Wuhan , Hubei 430079 , China
| | - Mary L Maliszewski
- Department of Chemistry , The University of Kansas , 2010 Malott Hall, 1251 Wescoe Hall Drive , Lawrence , Kansas 66045 , United States.,The KU Chemical Methodologies and Library Development Center of Excellence , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
| | - Wen-Jing Xiao
- Key Laboratory of Pesticide & Chemical Biology Ministry of Education, College of Chemistry , Central China Normal University , 152 Luoyu Road , Wuhan , Hubei 430079 , China
| | - Jon A Tunge
- Department of Chemistry , The University of Kansas , 2010 Malott Hall, 1251 Wescoe Hall Drive , Lawrence , Kansas 66045 , United States.,The KU Chemical Methodologies and Library Development Center of Excellence , 2034 Becker Drive , Lawrence , Kansas 66047 , United States
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13
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Ganesan A, Barakat K. Applications of computer-aided approaches in the development of hepatitis C antiviral agents. Expert Opin Drug Discov 2017; 12:407-425. [PMID: 28164720 DOI: 10.1080/17460441.2017.1291628] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
INTRODUCTION Hepatitis C virus (HCV) is a global health problem that causes several chronic life-threatening liver diseases. The numbers of people affected by HCV are rising annually. Since 2011, the FDA has approved several anti-HCV drugs; while many other promising HCV drugs are currently in late clinical trials. Areas covered: This review discusses the applications of different computational approaches in HCV drug design. Expert opinion: Molecular docking and virtual screening approaches have emerged as a low-cost tool to screen large databases and identify potential small-molecule hits against HCV targets. Ligand-based approaches are useful for filtering-out compounds with rich physicochemical properties to inhibit HCV targets. Molecular dynamics (MD) remains a useful tool in optimizing the ligand-protein complexes and understand the ligand binding modes and drug resistance mechanisms in HCV. Despite their varied roles, the application of in-silico approaches in HCV drug design is still in its infancy. A more mature application should aim at modelling the whole HCV replicon in its active form and help to identify new effective druggable sites within the replicon system. With more technological advancements, the roles of computer-aided methods are only going to increase several folds in the development of next-generation HCV drugs.
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Affiliation(s)
- Aravindhan Ganesan
- a Faculty of Pharmacy and Pharmaceutical Sciences , University of Alberta , Edmonton , Canada
| | - Khaled Barakat
- a Faculty of Pharmacy and Pharmaceutical Sciences , University of Alberta , Edmonton , Canada
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14
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Design and Validation of Novel Chikungunya Virus Protease Inhibitors. Antimicrob Agents Chemother 2016; 60:7382-7395. [PMID: 27736770 DOI: 10.1128/aac.01421-16] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 09/20/2016] [Indexed: 11/20/2022] Open
Abstract
Chikungunya virus (CHIKV; genus Alphavirus) is the causative agent of chikungunya fever. CHIKV replication can be inhibited by some broad-spectrum antiviral compounds; in contrast, there is very little information about compounds specifically inhibiting the enzymatic activities of CHIKV replication proteins. These proteins are translated in the form of a nonstructural (ns) P1234 polyprotein precursor from the CHIKV positive-strand RNA genome. Active forms of replicase enzymes are generated using the autoproteolytic activity of nsP2. The available three-dimensional (3D) structure of nsP2 protease has made it a target for in silico drug design; however, there is thus far little evidence that the designed compounds indeed inhibit the protease activity of nsP2 and/or suppress CHIKV replication. In this study, a set of 12 compounds, predicted to interact with the active center of nsP2 protease, was designed using target-based modeling. The majority of these compounds were shown to inhibit the ability of nsP2 to process recombinant protein and synthetic peptide substrates. Furthermore, all compounds found to be active in these cell-free assays also suppressed CHIKV replication in cell culture, the 50% effective concentration (EC50) of the most potent inhibitor being ∼1.5 μM. Analysis of stereoisomers of one compound revealed that inhibition of both the nsP2 protease activity and CHIKV replication depended on the conformation of the inhibitor. Combining the data obtained from different assays also indicates that some of the analyzed compounds may suppress CHIKV replication using more than one mechanism.
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Chikungunya virus infectivity, RNA replication and non-structural polyprotein processing depend on the nsP2 protease's active site cysteine residue. Sci Rep 2016; 6:37124. [PMID: 27845418 PMCID: PMC5109220 DOI: 10.1038/srep37124] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Accepted: 10/24/2016] [Indexed: 11/23/2022] Open
Abstract
Chikungunya virus (CHIKV), genus Alphavirus, family Togaviridae, has a positive-stand RNA genome approximately 12 kb in length. In infected cells, the genome is translated into non-structural polyprotein P1234, an inactive precursor of the viral replicase, which is activated by cleavages carried out by the non-structural protease, nsP2. We have characterized CHIKV nsP2 using both cell-free and cell-based assays. First, we show that Cys478 residue in the active site of CHIKV nsP2 is indispensable for P1234 processing. Second, the substrate requirements of CHIKV nsP2 are quite similar to those of nsP2 of related Semliki Forest virus (SFV). Third, substitution of Ser482 residue, recently reported to contribute to the protease activity of nsP2, with Ala has almost no negative effect on the protease activity of CHIKV nsP2. Fourth, Cys478 to Ala as well as Trp479 to Ala mutations in nsP2 completely abolished RNA replication in CHIKV and SFV trans-replication systems. In contrast, trans-replicases with Ser482 to Ala mutation were similar to wild type counterparts. Fifth, Cys478 to Ala as well as Trp479 to Ala mutations in nsP2 abolished the rescue of infectious virus from CHIKV RNA transcripts while Ser482 to Ala mutation had no effect. Thus, CHIKV nsP2 is a cysteine protease.
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16
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Byler KG, Collins JT, Ogungbe IV, Setzer WN. Alphavirus protease inhibitors from natural sources: A homology modeling and molecular docking investigation. Comput Biol Chem 2016; 64:163-184. [DOI: 10.1016/j.compbiolchem.2016.06.005] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 05/08/2016] [Accepted: 06/20/2016] [Indexed: 12/11/2022]
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