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Chongjun Y, Nasr AMS, Latif MAM, Rahman MBA, Marlisah E, Tejo BA. Predicting repurposed drugs targeting the NS3 protease of dengue virus using machine learning-based QSAR, molecular docking, and molecular dynamics simulations. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2024; 35:707-728. [PMID: 39210743 DOI: 10.1080/1062936x.2024.2392677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 08/08/2024] [Indexed: 09/04/2024]
Abstract
Dengue fever, prevalent in Southeast Asian countries, currently lacks effective pharmaceutical interventions for virus replication control. This study employs a strategy that combines machine learning (ML)-based quantitative-structure-activity relationship (QSAR), molecular docking, and molecular dynamics simulations to discover potential inhibitors of the NS3 protease of the dengue virus. We used nine molecular fingerprints from PaDEL to extract features from the NS3 protease dataset of dengue virus type 2 in the ChEMBL database. Feature selection was achieved through the low variance threshold, F-Score, and recursive feature elimination (RFE) methods. Our investigation employed three ML models - support vector machine (SVM), random forest (RF), and extreme gradient boosting (XGBoost) - for classifier development. Our SVM model, combined with SVM-RFE, had the best accuracy (0.866) and ROC_AUC (0.964) in the testing set. We identified potent inhibitors on the basis of the optimal classifier probabilities and docking binding affinities. SHAP and LIME analyses highlighted the significant molecular fingerprints (e.g. ExtFP69, ExtFP362, ExtFP576) involved in NS3 protease inhibitory activity. Molecular dynamics simulations indicated that amphotericin B exhibited the highest binding energy of -212 kJ/mol and formed a hydrogen bond with the critical residue Ser196. This approach enhances NS3 protease inhibitor identification and expedites the discovery of dengue therapeutics.
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Affiliation(s)
- Y Chongjun
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Malaysia
| | - A M S Nasr
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Malaysia
| | - M A M Latif
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Malaysia
- Centre for Foundation Studies in Science, Universiti Putra Malaysia, Serdang, Malaysia
| | - M B A Rahman
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Malaysia
| | - E Marlisah
- Department of Computer Science, Faculty of Computer Science and Information Technology, Universiti Putra Malaysia, Serdang, Malaysia
| | - B A Tejo
- Department of Chemistry, Faculty of Science, Universiti Putra Malaysia, Serdang, Malaysia
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2
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Akram M, Hameed S, Hassan A, Khan KM. Development in the Inhibition of Dengue Proteases as Drug Targets. Curr Med Chem 2024; 31:2195-2233. [PMID: 37723635 DOI: 10.2174/0929867331666230918110144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Revised: 06/24/2023] [Accepted: 08/04/2023] [Indexed: 09/20/2023]
Abstract
BACKGROUND Viral infections continue to increase morbidity and mortality severely. The flavivirus genus has fifty different species, including the dengue, Zika, and West Nile viruses that can infect 40% of individuals globally, who reside in at least a hundred different countries. Dengue, one of the oldest and most dangerous human infections, was initially documented by the Chinese Medical Encyclopedia in the Jin period. It was referred to as "water poison," connected to flying insects, i.e., Aedes aegypti and Aedes albopictus. DENV causes some medical expressions like dengue hemorrhagic fever, acute febrile illness, and dengue shock syndrome. OBJECTIVE According to the World Health Organization report of 2012, 2500 million people are in danger of contracting dengue fever worldwide. According to a recent study, 96 million of the 390 million dengue infections yearly show some clinical or subclinical severity. There is no antiviral drug or vaccine to treat this severe infection. It can be controlled by getting enough rest, drinking plenty of water, and using painkillers. The first dengue vaccine created by Sanofi, called Dengvaxia, was previously approved by the USFDA in 2019. All four serotypes of the DENV1-4 have shown re-infection in vaccine recipients. However, the usage of Dengvaxia has been constrained by its adverse effects. CONCLUSION Different classes of compounds have been reported against DENV, such as nitrogen-containing heterocycles (i.e., imidazole, pyridine, triazoles quinazolines, quinoline, and indole), oxygen-containing heterocycles (i.e., coumarins), and some are mixed heterocyclic compounds of S, N (thiazole, benzothiazine, and thiazolidinediones), and N, O (i.e., oxadiazole). There have been reports of computationally designed compounds to impede the molecular functions of specific structural and non-structural proteins as potential therapeutic targets. This review summarized the current progress in developing dengue protease inhibitors.
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Affiliation(s)
- Muhammad Akram
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Shehryar Hameed
- H.E.J. Research Institute of Chemistry, International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, 75720, Pakistan
| | - Abbas Hassan
- Department of Chemistry, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Khalid Mohammed Khan
- H.E.J. Research Institute of Chemistry, International Centre for Chemical and Biological Sciences, University of Karachi, Karachi, 75720, Pakistan
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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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Evaluation of Melongosides as Potential Inhibitors of NS2B-NS3 Activator-Protease of Dengue Virus (Serotype 2) by Using Molecular Docking and Dynamics Simulation Approach. J Trop Med 2022; 2022:7111786. [PMID: 36051190 PMCID: PMC9427285 DOI: 10.1155/2022/7111786] [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: 04/21/2022] [Accepted: 07/08/2022] [Indexed: 11/18/2022] Open
Abstract
Dengue is a Flavivirus infection transmitted through mosquitoes of the Aedes genus, which is known to occur in over 100 countries of the world. Dengue has no available drugs for treatment; CYD-TDV is the only vaccine thus far approved for use by a few countries in the world. In the absence of drugs and a widely approved vaccine, attention has been focused on plant-derived compounds to the discovery of a potential therapeutic for DENV. The present study aimed to determine, in silico, the binding energies of the steroidal saponins, melongosides, to NS2B-NS3 activator protease of DENV-2, which plays an essential role in the viral replication. The blind molecular docking studies carried out gave binding energies (ΔG = −kcal/mol) of melongosides B, F, G, H, N, O, and P as 7.7, 8.2, 7.6, 7.8, 8.3, 8.0, and 8.0, respectively. All the melongosides interacted with the NS3 protease part of NS2B-NS3. Melongosides B, F, and N showed interactions with His51, while melongoside G interacted with Asp75 of NS3, to be noted, these are important amino acid residues in the catalytic site of the NS3 protease. However, the 200 ns molecular dynamic simulation experiment indicates significant stability of the protein-ligand interactions with the RMSD values of 2.5 Å, thus suggesting a better docking position and no disruption of the protein-ligand structure. Taken together, melongosides need further attention for more scientific studies as a DENV inhibitory agent, which if proven, in vivo and in clinical trials, can be a useful therapeutic agent against at least DENV-2.
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Venkatesan A, Dhanabalan AK, Rajendran S, Shanmugasundharam SG, Gunasekaran K, Febin Prabhu Dass J. Structure-based pharmacophore modeling, virtual screening approaches to identifying the potent hepatitis C viral protease and polymerase novel inhibitors. J Cell Biochem 2022; 123:1366-1380. [PMID: 35726444 DOI: 10.1002/jcb.30298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 11/07/2022]
Abstract
Hepatitis C is an infectious disease that leads to acute and chronic liver illnesses. Currently, there are no effective vaccines against this deadly virus. Direct acting antiviral (DAA) drugs are given in the combination with ribavirin and pegylated interferon which lead to adverse effects. Through in silico analysis, the structure-based docking study was performed against NS3/4A protease and NS5B polymerase proteins of HCV. In the current study, multiple e-pharmacophore-based virtual screening methods such as HTVS, SP, and XP were carried out to screen natural compounds and enamine databases. Our result outcomes revealed that CID AE-848/13196185 and CID AE-848/36959205 compounds show good binding interactions with protease protein. In addition, CID 15081408 and CID 173568 show better binding interactions with the polymerase protein. Further to validate the docking results, we performed molecular dynamics simulation for the top hit compounds bound with protease and polymerase proteins to illustrate conformational differences in the stability compared with the active site of the cocrystal inhibitor. Thus, the current study emphasizes these compounds could be an effective drug to treat HCV.
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Affiliation(s)
- Arthi Venkatesan
- Department of Integrative Biology, School of Bio Sciences and Technology (SBST), VIT, Vellore, India
| | - Anantha Krishnan Dhanabalan
- Centre of Advance study in Crystallography and Biophysics & Bioinformatics Infrastructure Facility, University of Madras, Chennai, India
| | - Selvakumar Rajendran
- Centre of Advance study in Crystallography and Biophysics & Bioinformatics Infrastructure Facility, University of Madras, Chennai, India
| | | | - Krishnasamy Gunasekaran
- Centre of Advance study in Crystallography and Biophysics & Bioinformatics Infrastructure Facility, University of Madras, Chennai, India
| | - J Febin Prabhu Dass
- Department of Integrative Biology, School of Bio Sciences and Technology (SBST), VIT, Vellore, India
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Samrat SK, Xu J, Li Z, Zhou J, Li H. Antiviral Agents against Flavivirus Protease: Prospect and Future Direction. Pathogens 2022; 11:293. [PMID: 35335617 PMCID: PMC8955721 DOI: 10.3390/pathogens11030293] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/15/2022] [Accepted: 02/20/2022] [Indexed: 12/18/2022] Open
Abstract
Flaviviruses cause a significant amount of mortality and morbidity, especially in regions where they are endemic. A recent example is the outbreak of Zika virus throughout the world. Development of antiviral drugs against different viral targets is as important as the development of vaccines. During viral replication, a single polyprotein precursor (PP) is produced and further cleaved into individual proteins by a viral NS2B-NS3 protease complex together with host proteases. Flavivirus protease is one of the most attractive targets for development of therapeutic antivirals because it is essential for viral PP processing, leading to active viral proteins. In this review, we have summarized recent development in drug discovery targeting the NS2B-NS3 protease of flaviviruses, especially Zika, dengue, and West Nile viruses.
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Affiliation(s)
- Subodh K. Samrat
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (S.K.S.); (Z.L.)
| | - Jimin Xu
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; (J.X.); (J.Z.)
| | - Zhong Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (S.K.S.); (Z.L.)
| | - Jia Zhou
- Chemical Biology Program, Department of Pharmacology and Toxicology, University of Texas Medical Branch, Galveston, TX 77555, USA; (J.X.); (J.Z.)
| | - Hongmin Li
- Department of Pharmacology and Toxicology, College of Pharmacy, The University of Arizona, 1703 E Mabel St, Tucson, AZ 85721, USA; (S.K.S.); (Z.L.)
- BIO5 Institute, The University of Arizona, Tucson, AZ 85721, USA
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7
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In Silico Prediction of the Phosphorylation of NS3 as an Essential Mechanism for Dengue Virus Replication and the Antiviral Activity of Quercetin. BIOLOGY 2021; 10:biology10101067. [PMID: 34681164 PMCID: PMC8570334 DOI: 10.3390/biology10101067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 10/09/2021] [Accepted: 10/11/2021] [Indexed: 11/25/2022]
Abstract
Simple Summary Dengue is a mosquito-borne virus that infects up to 400 million people worldwide annually. Dengue infection triggers high fever, severe body aches, rash, low platelet count, and could lead to Dengue hemorrhagic fever (DHF) in some cases. There is currently no cure, nor a broadly effective vaccine. The interaction of two viral proteins, nonstructural Proteins 3 and 5 (NS3 and NS5), is required for viral replication in the infected host’s cells. Our computational modeling of NS3 suggested that phosphorylation of a serine residue at position 137 of NS3 by a specific c-Jun N-terminal kinase (JNK) enhances viral replication by increasing the interaction of NS3 and NS5 through structural changes in amino acid residues 49–95. Experimental studies have shown that inhibition of JNK prevents viral replication and have suggested that the plants’ flavonoid Quercetin, Agathis flavone, and Myricetin inhibit Dengue infection. Our molecular simulations revealed that Quercetin binds NS3 and obstructs serine 137 phosphorylation, which may decrease viral replication. This work offers a molecular mechanism that can be used for anti-Dengue drug development. Abstract Dengue virus infection is a global health problem for which there have been challenges to obtaining a cure. Current vaccines and anti-viral drugs can only be narrowly applied in ongoing clinical trials. We employed computational methods based on structure-function relationships between human host kinases and viral nonstructural protein 3 (NS3) to understand viral replication inhibitors’ therapeutic effect. Phosphorylation at each of the two most evolutionarily conserved sites of NS3, serine 137 and threonine 189, compared to the unphosphorylated state were studied with molecular dynamics and docking simulations. The simulations suggested that phosphorylation at serine 137 caused a more remarkable structural change than phosphorylation at threonine 189, specifically located at amino acid residues 49–95. Docking studies supported the idea that phosphorylation at serine 137 increased the binding affinity between NS3 and nonstructural Protein 5 (NS5), whereas phosphorylation at threonine 189 decreased it. The interaction between NS3 and NS5 is essential for viral replication. Docking studies with the antiviral plant flavonoid Quercetin with NS3 indicated that Quercetin physically occluded the serine 137 phosphorylation site. Taken together, these findings suggested a specific site and mechanism by which Quercetin inhibits dengue and possible other flaviviruses.
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Buendia-Atencio C, Pieffet GP, Montoya-Vargas S, Martínez Bernal JA, Rangel HR, Muñoz AL, Losada-Barragán M, Segura NA, Torres OA, Bello F, Suárez A, Rodríguez AK. Inverse Molecular Docking Study of NS3-Helicase and NS5-RNA Polymerase of Zika Virus as Possible Therapeutic Targets of Ligands Derived from Marcetia taxifolia and Its Implications to Dengue Virus. ACS OMEGA 2021; 6:6134-6143. [PMID: 33718704 PMCID: PMC7948243 DOI: 10.1021/acsomega.0c04719] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 01/29/2021] [Indexed: 06/01/2023]
Abstract
Dengue and Zika are two mosquito-borne diseases of great impact on public health around the world in tropical and subtropical countries. DENV and ZIKV belong to the Flaviviridae family and the Flavivirus genus. Currently, there are no effective therapeutic agents to treat or prevent these pathologies. The main objective of this work was to evaluate potential inhibitors from active compounds obtained from Marcetia taxifolia by performing inverse molecular docking on ZIKV-NS3-helicase and ZIKV-NS5-RNA polymerase as targets. This computational strategy is based on renormalizing the binding scores of the compounds to these two proteins, allowing a direct comparison of the results across the proteins. The crystallographic structures of the ZIKV-NS3-helicase and ZIKV-NS5-RNA-polymerase proteins share a great similarity with DENV homologous proteins. The P-loop active site of the crystallographic structure of ZIKV-NS3-helicase presents a high percentage of homology with the four dengue serotypes. It was found that most ligands of the active compounds (5,3'-dihydroxy-3,6,7,8,4'-pentamethoxyflavone (5DP); 5-hydroxy-3,6,7,8,3',4'-hexamethoxyflavone (5HH); myricetin-3-O-rhamnoside (M3OR)) from Marcetia taxifolia had a better affinity for ZIKV-NS3-helicase than for ZIKV-NS5-RNA polymerase, as indicated by the negative multiple active site correction (MASC) score, except for M3RG that showed a higher affinity for ZIKV-NS5-RNA polymerase. On the other hand, the AutoDock Vina scores showed that M3OR had the highest score value (-9.60 kcal/mol) and the highest normalized score (1.13) against ZIKV-NS3-helicase. These results in silico demonstrated that the nonstructural proteins NS3-helicase and NS5-RNA polymerase, which share similar molecular structures between the selected viruses, could become therapeutic targets for some bioactive compounds derived from Marcetia taxifolia.
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Affiliation(s)
| | - Gilles Paul Pieffet
- Faculty
of Science, Universidad Antonio Nariño
(UAN), Bogotá 110231, Colombia
| | | | | | - Héctor Rafael Rangel
- Laboratory
of Molecular Virology, Instituto Venezolano
de Investigaciones Científicas, Caracas 1204, Venezuela
| | - Ana Luisa Muñoz
- PhD
Program of Health Science, Universidad Antonio
Nariño (UAN), Bogotá 110231, Colombia
| | | | - Nidya Alexandra Segura
- Faculty
of Science, Universidad Pedagógica
y Tecnológica de Colombia, Tunja150003, Colombia
| | - Orlando A. Torres
- Faculty
of
Veterinary Medicine, Universidad Antonio
Nariño (UAN), Bogotá 110231, Colombia
| | - Felio Bello
- Faculty
of Agricultural and Livestock Sciences, Program of Veterinary Medicine, Universidad de La Salle, Bogotá 110131 Colombia
| | - Alírica
Isabel Suárez
- Natural
Products Laboratory, Faculty of Pharmacy, Universidad Central de Venezuela, Caracas 1050, Venezuela
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9
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Identification of Cleavage Sites Proteolytically Processed by NS2B-NS3 Protease in Polyprotein of Japanese Encephalitis Virus. Pathogens 2021; 10:pathogens10020102. [PMID: 33494395 PMCID: PMC7911949 DOI: 10.3390/pathogens10020102] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 12/14/2022] Open
Abstract
Understanding the proteolytic processing of polyprotein mediated by NS2B-NS3 protease contributes to the exploration of the mechanisms underlying infection of Japanese encephalitis virus (JEV), a zoonotic flavivirus. In this study, eukaryotic and prokaryotic cell models were employed to identify the cleavage sites mediated by viral NS2B-NS3 protease in JEV polyprotein. Artificial green fluorescent protein (GFP) substrates that contained the predicted cleavage site sequences of JEV polyprotein were expressed in swine testicle (ST) cells in the presence and absence of JEV infection, or co-expressed in E. coli with the recombinant NS2B-NS3 protease that was generated by fusing the N-terminal protease domain of NS3 to the central hydrophilic domain of NS2B. The cleavage of GFP substrates was examined by western blot. Among twelve artificial GFP substrates containing the cleavage site sequences predictively processed by host cell and/or NS2B-NS3 proteases, all sites were found to be cleaved by host cell proteases with different efficiencies. The sites at internal C, NS2A/NS2B, NS2B/NS3 and NS3/NS4A junctions, but not the sites at internal NS3, internal NS4A and NS4B/NS5 junctions were identified to be cleaved by JEV NS2B-NS3 protease. These data provide insight into the proteolytic processing of polyprotein, which is useful for understanding JEV replication and pathogenesis.
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Pawar R, Patravale V. A Step towards Treating Dengue Viral Infection: An In Silico Approach to Identify Potential Antidengue Phytoconstituents. ChemistrySelect 2020. [DOI: 10.1002/slct.202004137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Rohit Pawar
- Department of Pharmaceutical Sciences and Technology Institute of Chemical Technology Nathalal Parekh Marg, Matunga Mumbai 400019 Maharashtra India
| | - Vandana Patravale
- Department of Pharmaceutical Sciences and Technology Institute of Chemical Technology Nathalal Parekh Marg, Matunga Mumbai 400019 Maharashtra India
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11
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Kumar D, Kumar A, Bhardwaj T, Giri R. Zika virus NS4A N-Terminal region (1-48) acts as a cofactor for inducing NTPase activity of NS3 helicase but not NS3 protease. Arch Biochem Biophys 2020; 695:108631. [DOI: 10.1016/j.abb.2020.108631] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/18/2020] [Accepted: 10/13/2020] [Indexed: 12/20/2022]
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12
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Shanmugam A, Ramakrishnan C, Velmurugan D, Gromiha MM. Identification of Potential Inhibitors for Targets Involved in Dengue Fever. Curr Top Med Chem 2020; 20:1742-1760. [PMID: 32552652 DOI: 10.2174/1568026620666200618123026] [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: 10/20/2019] [Revised: 11/05/2019] [Accepted: 01/10/2020] [Indexed: 01/16/2023]
Abstract
Lethality due to dengue infection is a global threat. Nearly 400 million people are affected every year, which approximately costs 500 million dollars for surveillance and vector control itself. Many investigations on the structure-function relationship of proteins expressed by the dengue virus are being made for more than a decade and had come up with many reports on small molecule drug discovery. In this review, we present a detailed note on viral proteins and their functions as well as the inhibitors discovered/designed so far using experimental and computational methods. Further, the phytoconstituents from medicinal plants, specifically the extract of the papaya leaves, neem and bael, which combat dengue infection via dengue protease, helicase, methyl transferase and polymerase are summarized.
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Affiliation(s)
- Anusuya Shanmugam
- Department of Pharmaceutical Engineering, Vinayaka Mission's Kirupananda Variyar Engineering College, Vinayaka Mission's Research Foundation (Deemed to be University), Salem - 636308, India
| | - Chandrasekaran Ramakrishnan
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai - 600036, India
| | - Devadasan Velmurugan
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai - 600025, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology (IIT) Madras, Chennai - 600036, India
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13
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Kurniawan I, Rosalinda M, Ikhsan N. Implementation of ensemble methods on QSAR Study of NS3 inhibitor activity as anti-dengue agent. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2020; 31:477-492. [PMID: 32546117 DOI: 10.1080/1062936x.2020.1773534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 05/20/2020] [Indexed: 06/11/2023]
Abstract
Dengue fever is a disease transmitted by infected mosquitoes. This disease spreads in several countries, especially those with a tropical climate. To date, there is no specific drug that can be used to treat dengue. Use of clinically investigated drugs, such as Balapiravir, is still not effective in inhibiting the activity of virus replication. The design of a drug candidate can be performed by using the non-structural protein 3 (NS3) as target. This study aimed to develop QSAR models to predict the inhibitory activity class of NS3 inhibitors. The classification was performed by using feature importance analysis for selecting the descriptors and three ensemble methods, i.e. random forest (RF), adaptive boosting (AdaBoost), and extremely randomized trees (ERT), for model design and prediction. Hyperparameter tuning was performed to improve the performance of the models. Based on the results, we found that model 9, developed from ERT produced the best performance with values of accuracy and AUC equal to 0.73 and 0.82, respectively. Use of y-scrambling method allowed us to confirm that the model was not related to the chance correlation.
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Affiliation(s)
- I Kurniawan
- School of Computing, Telkom University , Bandung, Indonesia
- Research Center of Human Centric Engineering, Telkom University , Bandung, Indonesia
| | - M Rosalinda
- Research Center of Human Centric Engineering, Telkom University , Bandung, Indonesia
| | - N Ikhsan
- School of Computing, Telkom University , Bandung, Indonesia
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14
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Dwivedi VD, Bharadwaj S, Afroz S, Khan N, Ansari MA, Yadava U, Tripathi RC, Tripathi IP, Mishra SK, Kang SG. Anti-dengue infectivity evaluation of bioflavonoid from Azadirachta indica by dengue virus serine protease inhibition. J Biomol Struct Dyn 2020; 39:1417-1430. [DOI: 10.1080/07391102.2020.1734485] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Vivek Dhar Dwivedi
- Faculty of Science and Environment, Mahatma Gandhi Chitrakoot Gramodaya Vishwavidyalaya, Chitrakoot, Satna, India
- Center for Bioinformatics, Computational and System Biology, Pathfinder Research and Training Foundation, India
| | - Shiv Bharadwaj
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
| | - Sumbul Afroz
- Department of Biotechnology, School of Life Science, University of Hyderabad, India
| | - Nooruddin Khan
- Department of Biotechnology, School of Life Science, University of Hyderabad, India
| | | | - Umesh Yadava
- Department of Physics, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India
| | - Ramesh Chandra Tripathi
- Faculty of Science and Environment, Mahatma Gandhi Chitrakoot Gramodaya Vishwavidyalaya, Chitrakoot, Satna, India
| | - Indra Prasad Tripathi
- Faculty of Science and Environment, Mahatma Gandhi Chitrakoot Gramodaya Vishwavidyalaya, Chitrakoot, Satna, India
| | - Sarad Kumar Mishra
- Department of Biotechnology, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, India
| | - Sang Gu Kang
- Department of Biotechnology, Institute of Biotechnology, College of Life and Applied Sciences, Yeungnam University, Gyeongsan, Gyeongbuk, Republic of Korea
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15
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Evaluating Drug Resistant Mutations to HCV NS3 Protease Inhibitors in Iranian Naïve Patients. Int J Pept Res Ther 2019. [DOI: 10.1007/s10989-019-09957-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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16
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Rodriguez AK, Muñoz AL, Segura NA, Rangel HR, Bello F. Molecular characteristics and replication mechanism of dengue, zika and chikungunya arboviruses, and their treatments with natural extracts from plants: An updated review. EXCLI JOURNAL 2019; 18:988-1006. [PMID: 31762724 PMCID: PMC6868920 DOI: 10.17179/excli2019-1825] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022]
Abstract
Viruses transmitted by arthropods (arboviruses) are the etiological agents of several human diseases with worldwide distribution; including dengue (DENV), zika (ZIKV), yellow fever (YFV), and chikungunya (CHIKV) viruses. These viruses are especially important in tropical and subtropical regions; where, ZIKV and CHIKV are involved in epidemics worldwide, while the DENV remains as the biggest problem in public health. Factors, such as, environmental conditions promote the distribution of vectors, deficiencies in health services, and lack of effective vaccines, guarantee the presence of these vector-borne diseases. Treatment against these viral diseases is only palliative since available therapies formulated lack to demonstrate specific antiviral activity and vaccine candidates fail to demonstrate enough effectiveness. The use of natural products, as therapeutic tools, is an ancestral practice in different cultures. According to WHO 80 % of the population of some countries from Africa and Asia depend on the use of traditional medicines to deal with some diseases. Molecular characteristics of these viruses are important in determining its cellular pathogenesis, emergence, and dispersion mechanisms, as well as for the development of new antivirals and vaccines to control strategies. In this review, we summarize the current knowledge of the molecular structure and replication mechanisms of selected arboviruses, as well as their mechanism of entry into host cells, and a brief overview about the potential targets accessed to inhibit these viruses in vitro and a summary about their treatment with natural extracts from plants.
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Affiliation(s)
| | - Ana Luisa Muñoz
- Faculty of Science, Universidad Antonio Nariño (UAN), Bogotá, 110231, Colombia
| | - Nidya Alexandra Segura
- Faculty of Science, Universidad Pedagógica y Tecnológica de Colombia, Tunja 150003, Colombia
| | - Héctor Rafael Rangel
- Laboratory of Molecular Virology, Instituto Venezolano de Investigaciones Científicas, Caracas, 1204, Venezuela
| | - Felio Bello
- Faculty of Agricultural and Livestock Sciences, Program of Veterinary Medicine, Universidad de La Salle, Bogotá, 110131, Colombia
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17
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Neutralization of Acidic Intracellular Vesicles by Niclosamide Inhibits Multiple Steps of the Dengue Virus Life Cycle In Vitro. Sci Rep 2019; 9:8682. [PMID: 31213630 PMCID: PMC6582152 DOI: 10.1038/s41598-019-45095-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 05/30/2019] [Indexed: 01/20/2023] Open
Abstract
Dengue fever is one of the most important mosquito-borne viral infections in large parts of tropical and subtropical countries and is a significant public health concern and socioeconomic burden. There is an urgent need to develop antivirals that can effectively reduce dengue virus (DENV) replication and decrease viral load. Niclosamide, an antiparasitic drug approved for human use, has been recently identified as an effective antiviral agent against a number of pH-dependent viruses, including flaviviruses. Here, we reveal that neutralization of low-pH intracellular compartments by niclosamide affects multiple steps of the DENV infectious cycle. Specifically, niclosamide-induced endosomal neutralization not only prevents viral RNA replication but also affects the maturation of DENV particles, rendering them non-infectious. We found that niclosamide-induced endosomal neutralization prevented E glycoprotein conformational changes on the virion surface of flaviviruses, resulting in the release of non-infectious immature virus particles with uncleaved pr peptide from host cells. Collectively, our findings support the potential application of niclosamide as an antiviral agent against flavivirus infection and highlight a previously uncharacterized mechanism of action of the drug.
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18
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Vora J, Patel S, Athar M, Sinha S, Chhabria MT, Jha PC, Shrivastava N. Pharmacophore modeling, molecular docking and molecular dynamics simulation for screening and identifying anti-dengue phytocompounds. J Biomol Struct Dyn 2019; 38:1726-1740. [PMID: 31057055 DOI: 10.1080/07391102.2019.1615002] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Dengue is a fast spreading mosquito borne viral disease that poses a serious threat to human health. Lack of therapeutic drugs and vaccines signify that more resources need to be explored. Accumulated evidence has suggested that plants offer a vast reservoir for antiviral drug discovery which are safe for human consumption. Plant-based drug discovery is a complex and time-consuming process as plants possess rich repository of chemically diverse compounds. Various in silico methods can make this process simple and economic. We, therefore, performed pharmacophore mapping, molecular docking, molecular dynamics (MD) simulations and ADME (absorption, distribution, metabolism, excretion) prediction to screen potential candidates against dengue. In particular, combined pharmacophore mapping and molecular docking were used to prioritize the potentially active ligands from a ligand library. Biological activities of plant based ligands were predicted using 3D-QSAR pharmacophore modeling. Interaction between proteins, namely, envelope G protein, NS2B/NS3 protease, NS5 methyltransferase, NS1, NS5 polymerase and active plant-based ligands (pIC50 > 5.1) were analyzed using molecular docking. Best docked complex, namely, envelope G protein-mulberroside C, NS2B-NS3 protease-curcumin, NS5 methyltransferase-chebulic acid, NS1-mulberroside A, NS5 methyltransferase-punigluconin and NS5 methyltransferase-chebulic acid were further subjected to MD simulations study to assess the fluctuation and conformational changes during protein-ligand interaction. ADME studies were performed to assess their drug-likeness properties. Collectively, these in silico results helped to identify the potential plant-based hits against the various receptors of dengue virus which can be further validated by bioactivity-based experiments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Jaykant Vora
- B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Ahmedabad, India.,Department of Life science, Gujarat University, Ahmedabad, India
| | - Shivani Patel
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Ahmedabad, India
| | - Mohd Athar
- School of Chemical Sciences, Central University of Gujarat, Gandhinagar, India
| | - Sonam Sinha
- B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Ahmedabad, India.,Department of Life science, Gujarat University, Ahmedabad, India
| | - Mahesh T Chhabria
- Department of Pharmaceutical Chemistry, L. M. College of Pharmacy, Ahmedabad, India
| | - Prakash C Jha
- Centre for Applied Chemistry, Central University of Gujarat, Gandhinagar, India
| | - Neeta Shrivastava
- B. V. Patel Pharmaceutical Education and Research Development (PERD) Centre, Ahmedabad, India
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19
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Dighe SN, Ekwudu O, Dua K, Chellappan DK, Katavic PL, Collet TA. Recent update on anti-dengue drug discovery. Eur J Med Chem 2019; 176:431-455. [PMID: 31128447 DOI: 10.1016/j.ejmech.2019.05.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/12/2019] [Accepted: 05/06/2019] [Indexed: 01/27/2023]
Abstract
Dengue is the most important arthropod-borne viral disease of humans, with more than half of the global population living in at-risk areas. Despite the negative impact on public health, there are no antiviral therapies available, and the only licensed vaccine, Dengvaxia®, has been contraindicated in children below nine years of age. In an effort to combat dengue, several small molecules have entered into human clinical trials. Here, we review anti-DENV molecules and their drug targets that have been published within the past five years (2014-2018). Further, we discuss their probable mechanisms of action and describe a role for classes of clinically approved drugs and also an unclassified class of anti-DENV agents. This review aims to enhance our understanding of novel agents and their cognate targets in furthering innovations in the use of small molecules for dengue drug therapies.
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Affiliation(s)
- Satish N Dighe
- Innovative Medicines Group, Institute of Health & Biomedical Innovation, School of Clinical Sciences, Queensland University of Technology, Brisbane, Australia.
| | - O'mezie Ekwudu
- Innovative Medicines Group, Institute of Health & Biomedical Innovation, School of Clinical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Kamal Dua
- Discipline of Pharmacy, Graduate School of Health, University of Technology Sydney, Ultimo, Australia
| | - Dinesh Kumar Chellappan
- Department of Life Sciences, School of Pharmacy, International Medical University (IMU), Bukit Jalil, Kuala Lumpur, 57000, Malaysia
| | - Peter L Katavic
- Innovative Medicines Group, Institute of Health & Biomedical Innovation, School of Clinical Sciences, Queensland University of Technology, Brisbane, Australia
| | - Trudi A Collet
- Innovative Medicines Group, Institute of Health & Biomedical Innovation, School of Clinical Sciences, Queensland University of Technology, Brisbane, Australia
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20
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Hariono M, Choi SB, Roslim RF, Nawi MS, Tan ML, Kamarulzaman EE, Mohamed N, Yusof R, Othman S, Abd Rahman N, Othman R, Wahab HA. Thioguanine-based DENV-2 NS2B/NS3 protease inhibitors: Virtual screening, synthesis, biological evaluation and molecular modelling. PLoS One 2019; 14:e0210869. [PMID: 30677071 PMCID: PMC6345492 DOI: 10.1371/journal.pone.0210869] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 01/03/2019] [Indexed: 12/25/2022] Open
Abstract
Dengue virus Type 2 (DENV-2) is predominant serotype causing major dengue epidemics. There are a number of studies carried out to find its effective antiviral, however to date, there is still no molecule either from peptide or small molecules released as a drug. The present study aims to identify small molecules inhibitor from National Cancer Institute database through virtual screening. One of the hits, D0713 (IC50 = 62 μM) bearing thioguanine scaffold was derivatised into 21 compounds and evaluated for DENV-2 NS2B/NS3 protease inhibitory activity. Compounds 18 and 21 demonstrated the most potent activity with IC50 of 0.38 μM and 16 μM, respectively. Molecular dynamics and MM/PBSA free energy of binding calculation were conducted to study the interaction mechanism of these compounds with the protease. The free energy of binding of 18 calculated by MM/PBSA is -16.10 kcal/mol compared to the known inhibitor, panduratin A (-11.27 kcal/mol), which corroborates well with the experimental observation. Results from molecular dynamics simulations also showed that both 18 and 21 bind in the active site and stabilised by the formation of hydrogen bonds with Asn174.
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Affiliation(s)
- Maywan Hariono
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
- Faculty of Pharmacy, Sanata Dharma University, Maguwoharjo, Sleman, Yogyakarta, Indonesia
| | - Sy Bing Choi
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
- School of Data Sciences, Perdana University, Blok B and d1, MARDI Complex, Jalan MAEPS Perdana, Serdang, Selangor
| | - Ros Fatihah Roslim
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
| | - Mohamed Sufian Nawi
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
- Department of Pharmaceutical Chemistry, Kulliyah of Pharmacy, International Islamic University Malaysia, Kuantan, Pahang, Malaysia
| | - Mei Lan Tan
- Advanced Medical and Dental Institute, Universiti Sains Malaysia, Bertam, Pulau Pinang, Malaysia
| | | | - Nornisah Mohamed
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
| | - Rohana Yusof
- Department of Molecular Medicine, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Shatrah Othman
- Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Noorsaadah Abd Rahman
- Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Rozana Othman
- Department of Pharmacy, Faculty of Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Habibah A. Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Minden, Pulau Pinang, Malaysia
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, Ministry of Science, Technology and Innovation, Halaman Bukit Gambir, Bayan Lepas, Pulau Pinang, Malaysia
- * E-mail: ,
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21
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Qadir A, Riaz M, Saeed M, Shahzad-Ul-Hussan S. Potential targets for therapeutic intervention and structure based vaccine design against Zika virus. Eur J Med Chem 2018; 156:444-460. [PMID: 30015077 DOI: 10.1016/j.ejmech.2018.07.014] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Revised: 06/28/2018] [Accepted: 07/06/2018] [Indexed: 01/01/2023]
Abstract
Continuously increasing number of reports of Zika virus (ZIKV) infections and associated severe clinical manifestations, including autoimmune abnormalities and neurological disorders such as neonatal microcephaly and Guillain-Barré syndrome have created alarming situation in various countries. To date, no specific antiviral therapy or vaccine is available against ZIKV. This review provides a comprehensive insight into the potential therapeutic targets and describes viral epitopes of broadly neutralizing antibodies (bNAbs) in vaccine design perspective. Interactions between ZIKV envelope glycoprotein E and cellular receptors mediate the viral fusion and entry to the target cell. Blocking these interactions by targeting cellular receptors or viral structural proteins mediating these interactions or viral surface glycans can inhibit viral entry to the cell. Similarly, different non-structural proteins of ZIKV and un-translated regions (UTRs) of its RNA play essential roles in viral replication cycle and potentiate for therapeutic interventions. Structure based vaccine design requires identity and structural description of the epitopes of bNAbs. We have described different conserved bNAb epitopes present in the ZIKV envelope as potential targets for structure based vaccine design. This review also highlights successes, unanswered questions and future perspectives in relation to therapeutic and vaccine development against ZIKV.
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Affiliation(s)
- Amina Qadir
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan
| | - Muhammad Riaz
- Department of Chemistry, University of Azad Jammu & Kashmir, Muzaffarabad, Pakistan
| | - Muhammad Saeed
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan.
| | - Syed Shahzad-Ul-Hussan
- Department of Biology, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore, 54792, Pakistan.
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22
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Cloning and Expression of NS3 Gene of Pakistani Isolate Type 2 Dengue Virus. J Vet Res 2018; 62:17-26. [PMID: 29978123 PMCID: PMC5957457 DOI: 10.2478/jvetres-2018-0003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Accepted: 03/08/2018] [Indexed: 11/20/2022] Open
Abstract
Introduction Dengue is one of the major emerging viral diseases in the world, with dramatic increases in reported cases in the last few decades and annual worldwide occurrence of approximately 390 million infections. It is a highly important mosquito-vectored disease and is a problem in tropical and subtropical areas of the world. The major aim of this study was to clone and express the dengue NS3 gene, in service to its therapeutic importance for the development of stable cell lines. Material and Methods Blood samples from dengue fever (DF) patients were collected and subjected to PCR amplification of the NS3 gene of dengue virus serotype-2 (DENV-2). The NS3 gene was amplified using gene specific primers and cloned in the TA cloning vectors. Results The gene was successfully expressed in mammalian expression vector pcDNA3.1. The current finding was different from a previously reported DENV-2 strain replicon constructed in different cells, in which the whole genetic material of the virus was used instead of an active protease gene, and which gave a low yield of replicon expressing cells. Conclusion Recombinant NS3 could be used to produce an antibody that is possibly helpful for developing a single step diagnostic assay to detect the dengue virus NS3 antigen in sera of dengue patients.
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23
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Dwivedi VD, Tripathi IP, Tripathi RC, Bharadwaj S, Mishra SK. Genomics, proteomics and evolution of dengue virus. Brief Funct Genomics 2018; 16:217-227. [PMID: 28073742 DOI: 10.1093/bfgp/elw040] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The genome of a pathogenic organism possesses a specific order of nucleotides that contains not only information about the synthesis and expression of proteomes, which are required for its growth and survival, but also about its evolution. Inhibition of any particular protein, which is required for the survival of that pathogenic organism, can be used as a potential therapeutic target for the development of effective drugs to treat its infections. In this review, the genomics, proteomics and evolution of dengue virus have been discussed, which will be helpful in better understanding of its origin, growth, survival and evolution, and may contribute toward development of new efficient anti-dengue drugs.
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24
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Leonel CA, Lima WG, dos Santos M, Ferraz AC, Taranto AG, de Magalhães JC, dos Santos LL, Ferreira JMS. Pharmacophoric characteristics of dengue virus NS2B/NS3pro inhibitors: a systematic review of the most promising compounds. Arch Virol 2017; 163:575-586. [DOI: 10.1007/s00705-017-3641-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 09/29/2017] [Indexed: 12/18/2022]
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25
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Sittivicharpinyo T, Wonnapinij P, Surat W. Complete coding sequence of dengue virus serotype 4 isolated from field-caught mosquitoes in Thailand. Mem Inst Oswaldo Cruz 2017; 112:580-582. [PMID: 28767984 PMCID: PMC5530551 DOI: 10.1590/0074-02760170022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 03/22/2017] [Indexed: 11/21/2022] Open
Abstract
This report is the first to characterise the complete coding sequence of a dengue virus serotype 4 (DENV-4) genotype I that was isolated from field-caught mosquitoes from an endemic area in Thailand in June 2013. The sequence was assembled from high-throughput sequencing reads generated by Illumina HiSeq. Three out of four observed intra-sample variants caused an amino acid variation in C, NS2B, and NS5 genes. The C4279T variant located in the NS2B gene can indirectly affect the proteolytic activity of the NS3 protein. The sequence provided in this study might be useful for the epidemiological study of DENV-4.
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Affiliation(s)
- Thikhumporn Sittivicharpinyo
- Kasetsart University, Faculty of Science, Department of Genetics, Evolutionary Genetics and Computational Biology Research Unit, Bangkok, Thailand
| | - Passorn Wonnapinij
- Kasetsart University, Faculty of Science, Department of Genetics, Evolutionary Genetics and Computational Biology Research Unit, Bangkok, Thailand.,Kasetsart University, National Research University-Kasetsart, Centre for Advanced Studies in Tropical Natural Resources, Bangkok, Thailand
| | - Wunrada Surat
- Kasetsart University, Faculty of Science, Department of Genetics, Evolutionary Genetics and Computational Biology Research Unit, Bangkok, Thailand.,Kasetsart University, National Research University-Kasetsart, Centre for Advanced Studies in Tropical Natural Resources, Bangkok, Thailand
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26
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Dwivedi VD, Tripathi IP, Bharadwaj S, Kaushik AC, Mishra SK. Identification of new potent inhibitors of dengue virus NS3 protease from traditional Chinese medicine database. Virusdisease 2016; 27:220-225. [PMID: 28466032 DOI: 10.1007/s13337-016-0328-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 07/12/2016] [Indexed: 01/01/2023] Open
Abstract
Dengue virus (DENV) has emerged as an increasing fitness problem in the world for which no specialized drug is available. The non-structural protein NS3 protease of DENV has already been recognized as a potential therapeutic target for the discovery and development of novel antiviral agents against DENV infections. In this study, we employed the virtual screening technique to explore the potent inhibitors of DENV NS2B/NS3pro from Traditional Chinese Medicine (TCM) database. Total 200 inhibitors from TCM against DENV NS3pro were screened and only five TCM compounds like eriodictyol 7-O-glucuronide, luteolin 8-C-beta-glucopyranoside, (-)-epicatechin-3-O-gallate, 6-O-trans-p-coumaroylgeniposide and luteolin-7-O-glucoside were selected for further analysis which showed binding energies, -7.000, -7.380, -7.380, -7.440 and -7.440 kcal/mol, respectively. The findings of this study suggest that these five TCM compounds can be considered as potent inhibitors for DENV NS2B/NS3pro for the development of anti-dengue drugs.
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Affiliation(s)
- Vivek Dhar Dwivedi
- Faculty of Science and Environment, M.G.C.G.Vishwavidyalaya, Chitrakoot, Satna, M. P. India
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, U. P. India
| | - Indra Prasad Tripathi
- Faculty of Science and Environment, M.G.C.G.Vishwavidyalaya, Chitrakoot, Satna, M. P. India
| | - Shiv Bharadwaj
- Nanotechnology Research and Application Center, Sabanci University, Istanbul, Turkey
| | | | - Sarad Kumar Mishra
- Department of Biotechnology, D.D.U. Gorakhpur University, Gorakhpur, U. P. India
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27
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Viswanathan U, Tomlinson SM, Fonner JM, Mock SA, Watowich SJ. Identification of a novel inhibitor of dengue virus protease through use of a virtual screening drug discovery Web portal. J Chem Inf Model 2014; 54:2816-25. [PMID: 25263519 DOI: 10.1021/ci500531r] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
We report the discovery of a novel small-molecule inhibitor of the dengue virus (DENV) protease (NS2B-NS3pro) using a newly constructed Web-based portal (DrugDiscovery@TACC) for structure-based virtual screening. Our drug discovery portal, an extension of virtual screening studies performed using IBM's World Community Grid, facilitated access to supercomputer resources managed by the Texas Advanced Computing Center (TACC) and enabled druglike commercially available small-molecule libraries to be rapidly screened against several high-resolution DENV NS2B-NS3pro crystallographic structures. Detailed analysis of virtual screening docking scores and hydrogen-bonding interactions between each docked ligand and the NS2B-NS3pro Ser135 side chain were used to select molecules for experimental validation. Compounds were ordered from established chemical companies, and compounds with established aqueous solubility were tested for their ability to inhibit DENV NS2B-NS3pro cleavage of a model substrate in kinetic studies. As a proof-of-concept, we validated a small-molecule dihydronaphthalenone hit as a single-digit-micromolar mixed noncompetitive inhibitor of the DENV protease. Since the dihydronaphthalenone was predicted to interact with NS2B-NS3pro residues that are largely conserved between DENV and the related West Nile virus (WNV), we tested this inhibitor against WNV NS2B-NS3pro and observed a similar mixed noncompetitive inhibition mechanism. However, the inhibition constants were ∼10-fold larger against the WNV protease relative to the DENV protease. This novel validated lead had no chemical features or pharmacophores associated with adverse toxicity, carcinogenicity, or mutagenicity risks and thus is attractive for additional characterization and optimization.
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Affiliation(s)
- Usha Viswanathan
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch , Galveston, Texas 77555, United States
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28
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Homology modeling and virtual screening for antagonists of protease from yellow head virus. J Mol Model 2014; 20:2116. [PMID: 24562855 PMCID: PMC7087857 DOI: 10.1007/s00894-014-2116-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2013] [Accepted: 12/14/2013] [Indexed: 11/21/2022]
Abstract
Yellow head virus (YHV) is one of the causative agents of shrimp viral disease. The prevention of YHV infection in shrimp has been developed by various methods, but it is still insufficient to protect the mass mortality in shrimp. New approaches for the antiviral drug development for viral infection have been focused on the inhibition of several potent viral enzymes, and thus the YHV protease is one of the interesting targets for developing antiviral drugs according to the pivotal roles of the enzyme in an early stage of viral propagation. In this study, a theoretical modeling of the YHV protease was constructed based on the folds of several known crystal structures of other viral proteases, and was subsequently used as a target for virtual screening—molecular docking against approximately 1364 NCI structurally diversity compounds. A complex between the protease and the hit compounds was investigated for intermolecular interactions by molecular dynamics simulations. Five best predicted compounds (NSC122819, NSC345647, NSC319990, NSC50650, and NSC5069) were tested against bacterial expressed YHV. The NSC122819 showed the best inhibitory characteristic among the candidates, while others showed more than 50 % of inhibition in the assay condition. These compounds could potentially be inhibitors for curing YHV infection.
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29
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de Almeida H, Bastos IMD, Ribeiro BM, Maigret B, Santana JM. New binding site conformations of the dengue virus NS3 protease accessed by molecular dynamics simulation. PLoS One 2013; 8:e72402. [PMID: 23991109 PMCID: PMC3749139 DOI: 10.1371/journal.pone.0072402] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2013] [Accepted: 07/10/2013] [Indexed: 12/21/2022] Open
Abstract
Dengue fever is caused by four distinct serotypes of the dengue virus (DENV1-4), and is estimated to affect over 500 million people every year. Presently, there are no vaccines or antiviral treatments for this disease. Among the possible targets to fight dengue fever is the viral NS3 protease (NS3PRO), which is in part responsible for viral processing and replication. It is now widely recognized that virtual screening campaigns should consider the flexibility of target protein by using multiple active conformational states. The flexibility of the DENV NS3PRO could explain the relatively low success of previous virtual screening studies. In this first work, we explore the DENV NS3PRO conformational states obtained from molecular dynamics (MD) simulations to take into account protease flexibility during the virtual screening/docking process. To do so, we built a full NS3PRO model by multiple template homology modeling. The model comprised the NS2B cofactor (essential to the NS3PRO activation), a glycine flexible link and the proteolytic domain. MD simulations had the purpose to sample, as closely as possible, the ligand binding site conformational landscape prior to inhibitor binding. The obtained conformational MD sample was clustered into four families that, together with principal component analysis of the trajectory, demonstrated protein flexibility. These results allowed the description of multiple binding modes for the Bz-Nle-Lys–Arg–Arg-H inhibitor, as verified by binding plots and pair interaction analysis. This study allowed us to tackle protein flexibility in our virtual screening campaign against the dengue virus NS3 protease.
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Affiliation(s)
- Hugo de Almeida
- Laboratório de Interação Patógeno-Hospedeiro, Departamento de Biologia Celular, Universidade de Brasília, Brasília, Brasília, Brazil
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Lai H, Dou D, Aravapalli S, Teramoto T, Lushington GH, Mwania TM, Alliston KR, Eichhorn DM, Padmanabhan R, Groutas WC. Design, synthesis and characterization of novel 1,2-benzisothiazol-3(2H)-one and 1,3,4-oxadiazole hybrid derivatives: potent inhibitors of Dengue and West Nile virus NS2B/NS3 proteases. Bioorg Med Chem 2013; 21:102-13. [PMID: 23211969 PMCID: PMC3563426 DOI: 10.1016/j.bmc.2012.10.058] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2012] [Revised: 10/22/2012] [Accepted: 10/31/2012] [Indexed: 12/27/2022]
Abstract
1,2-Benzisothiazol-3(2H)-ones and 1,3,4-oxadiazoles individually have recently attracted considerable interest in drug discovery, including as antibacterial and antifungal agents. In this study, a series of functionalized 1,2-benzisothiazol-3(2H)-one-1,3,4-oxadiazole hybrid derivatives were synthesized and subsequently screened against Dengue and West Nile virus proteases. Ten out of twenty-four compounds showed greater than 50% inhibition against DENV2 and WNV proteases ([I] = 10 μM). The IC(50) values of compound 7n against DENV2 and WNV NS2B/NS3 were found to be 3.75 ± 0.06 and 4.22 ± 0.07 μM, respectively. The kinetics data support a competitive mode of inhibition by compound 7n. Molecular modeling studies were performed to delineate the putative binding mode of this series of compounds. This study reveals that the hybrid series arising from the linking of the two scaffolds provides a suitable platform for conducting a hit-to-lead optimization campaign via iterative structure-activity relationship studies, in vitro screening and X-ray crystallography.
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Affiliation(s)
- Huiguo Lai
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Dengfeng Dou
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Sridhar Aravapalli
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Tadahisa Teramoto
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Gerald H. Lushington
- Molecular Graphics and Modeling Laboratory, The University of Kansas, Lawrence, KS 66045, USA
| | - Tom M. Mwania
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Kevin R. Alliston
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - David M. Eichhorn
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - R. Padmanabhan
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - William C. Groutas
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
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Aravapalli S, Lai H, Teramoto T, Alliston KR, Lushington GH, Ferguson EL, Padmanabhan R, Groutas WC. Inhibitors of Dengue virus and West Nile virus proteases based on the aminobenzamide scaffold. Bioorg Med Chem 2012; 20:4140-8. [PMID: 22632792 PMCID: PMC3563422 DOI: 10.1016/j.bmc.2012.04.055] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 04/19/2012] [Accepted: 04/27/2012] [Indexed: 10/28/2022]
Abstract
Dengue and West Nile viruses (WNV) are mosquito-borne members of flaviviruses that cause significant morbidity and mortality. There is no approved vaccine or antiviral drugs for human use to date. In this study, a series of functionalized meta and para aminobenzamide derivatives were synthesized and subsequently screened in vitro against Dengue virus and West Nile virus proteases. Four active compounds were identified which showed comparable activity toward the two proteases and shared in common a meta or para(phenoxy)phenyl group. The inhibition constants (K(i)) for the most potent compound 7n against Dengue and West Nile virus proteases were 8.77 and 5.55 μM, respectively. The kinetics data support a competitive mode of inhibition of both proteases by compound 7n. This conclusion is further supported by molecular modeling. This study reveals a new chemical scaffold which is amenable to further optimization to yield potent inhibitors of the viral proteases via the combined utilization of iterative medicinal chemistry/structure-activity relationship studies and in vitro screening.
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Affiliation(s)
- Sridhar Aravapalli
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Huiguo Lai
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Tadahisa Teramoto
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Kevin R. Alliston
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Gerald H. Lushington
- Molecular Graphics and Modeling Laboratory, The University of Kansas, Lawrence, KS 66045, USA
| | - Eron L. Ferguson
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - R. Padmanabhan
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - William C. Groutas
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
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Tiew KC, Dou D, Teramoto T, Lai H, Alliston KR, Lushington GH, Padmanabhan R, Groutas WC. Inhibition of Dengue virus and West Nile virus proteases by click chemistry-derived benz[d]isothiazol-3(2H)-one derivatives. Bioorg Med Chem 2012; 20:1213-21. [PMID: 22249124 PMCID: PMC3279297 DOI: 10.1016/j.bmc.2011.12.047] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2011] [Revised: 12/14/2011] [Accepted: 12/21/2011] [Indexed: 11/18/2022]
Abstract
Two click chemistry-derived focused libraries based on the benz[d]isothiazol-3(2H)-one scaffold were synthesized and screened against Dengue virus and West Nile virus NS2B-NS3 proteases. Several compounds (4l, 7j-n) displayed noteworthy inhibitory activity toward Dengue virus NS2B-NS3 protease in the absence and presence of added detergent. These compounds could potentially serve as a launching pad for a hit-to-lead optimization campaign.
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Affiliation(s)
- Kok-Chuan Tiew
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Dengfeng Dou
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Tadahisa Teramoto
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Huiguo Lai
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - Kevin R. Alliston
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
| | - Gerald H. Lushington
- Molecular Graphics and Modeling Laboratory, The University of Kansas, Lawrence, KS 66045, USA
| | - R. Padmanabhan
- Department of Microbiology and Immunology, Georgetown University Medical Center, Washington, DC 20057, USA
| | - William C. Groutas
- Department of Chemistry, Wichita State University, Wichita, Kansas 67260, USA
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Jitendra S, Vinay R. Structure based drug designing of a novel antiflaviviral inhibitor for nonstructural 3 protein. Bioinformation 2011; 6:57-60. [PMID: 21544165 PMCID: PMC3082862 DOI: 10.6026/97320630006057] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2011] [Accepted: 02/28/2011] [Indexed: 11/23/2022] Open
Abstract
UNLABELLED Literature shows that Flaviviruses cause a variety of diseases, including fevers, encephalitis, and hemorrhagic fevers. NS3 is a multifunctional protein with an Nterminal protease domain (NS3pro) that is responsible for proteolytic processing of the viral polyprotein, and a C-terminal region that contains an RNA triphosphatase, RNA helicase and RNA-stimulated NTPase domain that are essential for RNA replication. Therefore, NS3 protein is the preferential choice for inhibition to stop the proteolytic processing. Hence, the 3D structure of NS3 protein was modeled using homology modeling by MODELLER 9v7. Evaluation of the constructed NS3 protein models were done by PROCHECK, VERYFY3D and through ProSA calculations. Ligands for the catalytic triad were designed using LIGBUILDER. The NS3 protein's catalytic triad was explored to find out the critical interactions pattern for inhibitor binding using molecular docking methodology using AUTODOCK Vina. It should be noted that these predicted data should be validated using suitable assays for further consideration. ABBREVIATIONS DOPE - Discrete optimized protein energy, WHO - World Health Organization, ADME/T - Absorption, Distribution, Metabolism, Excretion and Toxicity.
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Affiliation(s)
- Singh Jitendra
- Department of Bioinformatics, Sri Ramachandra University, Porur, Chennai- 600 116, India
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