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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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Norshidah H, Leow CH, Ezleen KE, Wahab HA, Vignesh R, Rasul A, Lai NS. Assessing the potential of NS2B/NS3 protease inhibitors biomarker in curbing dengue virus infections: In silico vs. In vitro approach. Front Cell Infect Microbiol 2023; 13:1061937. [PMID: 36864886 PMCID: PMC9971573 DOI: 10.3389/fcimb.2023.1061937] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/18/2023] [Indexed: 02/16/2023] Open
Abstract
An increase in the occurrence of viral infectious diseases is a global concern for human health. According to a WHO report, dengue virus (DENV) is one of the most common viral diseases affecting approximately 400 million people annually, with worsening symptoms in nearly 1% of cases. Both academic and industrial researchers have conducted numerous studies on viral epidemiology, virus structure and function, source and route of infection, treatment targets, vaccines, and drugs. The development of CYD-TDV or Dengvaxia® vaccine has been a major milestone in dengue treatment. However, evidence has shown that vaccines have some drawbacks and limitations. Therefore, researchers are developing dengue antivirals to curb infections. DENV NS2B/NS3 protease is a DENV enzyme essential for replication and virus assembly, making it an interesting antiviral target. For faster hit and lead recognition of DENV targets, methods to screen large number of molecules at lower costs are essential. Similarly, an integrated and multidisciplinary approach involving in silico screening and confirmation of biological activity is required. In this review, we discuss recent strategies for searching for novel DENV NS2B/NS3 protease inhibitors from the in silico and in vitro perspectives, either by applying one of the approaches or by integrating both. Therefore, we hope that our review will encourage researchers to integrate the best strategies and encourage further developments in this area.
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Affiliation(s)
- Harun Norshidah
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia,Universiti Kuala Lumpur-Royal College of Medicine Perak, Ipoh, Perak, Malaysia,*Correspondence: Harun Norshidah, ; Ramachandran Vignesh, ; Ngit Shin Lai,
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia
| | | | - Habibah A. Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Ramachandran Vignesh
- Universiti Kuala Lumpur-Royal College of Medicine Perak, Ipoh, Perak, Malaysia,*Correspondence: Harun Norshidah, ; Ramachandran Vignesh, ; Ngit Shin Lai,
| | - Azhar Rasul
- Department of Zoology, Faculty of Life Sciences, Government College University, Faisalabad, Pakistan
| | - Ngit Shin Lai
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, Penang, Malaysia,*Correspondence: Harun Norshidah, ; Ramachandran Vignesh, ; Ngit Shin Lai,
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Design and synthesis of novel substituted indole-acrylamide derivatives and evaluation of their anti-cancer activity as potential tubulin-targeting agents. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Shimu MSS, Mahmud S, Tallei TE, Sami SA, Adam AA, Acharjee UK, Paul GK, Emran TB, Zaman S, Uddin MS, Saleh MA, Alshehri S, Ghoneim MM, Alruwali M, Obaidullah AJ, Jui NR, Kim J, Kim B. Phytochemical Compound Screening to Identify Novel Small Molecules against Dengue Virus: A Docking and Dynamics Study. Molecules 2022; 27:molecules27030653. [PMID: 35163918 PMCID: PMC8840231 DOI: 10.3390/molecules27030653] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/10/2022] [Accepted: 01/14/2022] [Indexed: 02/04/2023] Open
Abstract
The spread of the Dengue virus over the world, as well as multiple outbreaks of different serotypes, has resulted in a large number of deaths and a medical emergency, as no viable medications to treat Dengue virus patients have yet been found. In this paper, we provide an in silico virtual screening and molecular dynamics-based analysis to uncover efficient Dengue infection inhibitors. Based on a Google search and literature mining, a large phytochemical library was generated and employed as ligand molecules. In this investigation, the protein target NS2B/NS3 from Dengue was employed, and around 27 compounds were evaluated in a docking study. Phellodendroside (−63 kcal/mole), quercimeritrin (−59.5 kcal/mole), and quercetin-7-O-rutinoside (−54.1 kcal/mole) were chosen based on their binding free energy in MM-GBSA. The tested compounds generated numerous interactions at Lys74, Asn152, and Gln167 residues in the active regions of NS2B/NS3, which is needed for the protein’s inhibition. As a result, the stable mode of docked complexes is defined by various descriptors from molecular dynamics simulations, such as RMSD, SASA, Rg, RMSF, and hydrogen bond. The pharmacological properties of the compounds were also investigated, and no toxicity was found in computational ADMET properties calculations. As a result, this computational analysis may aid fellow researchers in developing innovative Dengue virus inhibitors.
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Affiliation(s)
| | - Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Trina Ekwati Tallei
- Department of Biology, Faculty of Mathematics and Natural Science, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Saad Ahmed Sami
- Department of Pharmacy, University of Chittagong, Chittagong 4331, Bangladesh;
| | - Ahmad Akroman Adam
- Dentistry Study Program, Faculty of Medicine, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Uzzal Kumar Acharjee
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh;
- Correspondence: (U.K.A.); (M.A.S.); (B.K.)
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh;
| | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Md. Salah Uddin
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
| | - Md. Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi 6205, Bangladesh; (S.M.); (G.K.P.); (S.Z.); (M.S.U.)
- Correspondence: (U.K.A.); (M.A.S.); (B.K.)
| | - Sultan Alshehri
- Department of Pharamaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Mohammed M Ghoneim
- Department of Pharmacy Practice, College of Pharamcy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia; (M.M.G.); (M.A.)
| | - Maha Alruwali
- Department of Pharmacy Practice, College of Pharamcy, AlMaarefa University, Ad Diriyah 13713, Saudi Arabia; (M.M.G.); (M.A.)
| | - Ahmad J. Obaidullah
- Drug Exploration and Development Chair (DEDC), Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Nabilah Rahman Jui
- Department of Biochemistry and Biotechnology, University of Science and Technology, Chittagong 4202, Bangladesh;
| | - Junghwan Kim
- Department of Internal Medicine, College of Korean Medicine, Kyung Hee University, Seoul 02447, Korea;
| | - Bonglee Kim
- Department of Pathology, College of Korean Medicine, Kyung Hee University, Hoegidong Dongdaemungu, Seoul 05253, Korea
- Correspondence: (U.K.A.); (M.A.S.); (B.K.)
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Immunoinformatics based prediction of recombinant multi-epitope vaccine for the control and prevention of SARS-CoV-2. ALEXANDRIA ENGINEERING JOURNAL 2021; 60. [PMCID: PMC7849527 DOI: 10.1016/j.aej.2021.01.046] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
The emergence of SARS-CoV-2 has been reported during December 2019, in the city of Wuhan, China. The transmission of this virus via human to human interaction has already been described. The novel virus has become pandemic and declared as a comprehensive emergency worldwide by World Health Organization due to its exponential spread within and outside China. There is a need of time to create a therapeutic agent and a vaccine to cure and control this lethal SARS-CoV-2. Conventionally, the vaccine development process is time taking, tiresome and requires more economical inputs with manpower. However, bioinformatics offers a key solution to compute the possibilities. The present study focuses on the utilization of bioinformatics platforms to forecast B and T cell epitopes that belong to SARS-CoV-2 spike glycoprotein. The protein is thought to have an involvement in triggering of momentous immune response. NCBI database was explored to collect the surface glycoprotein sequence and was analyzed to determine the immunogenic epitopes. This prediction analysis was carried out using IEDB web based server and the prediction of protein structure was done by homology modeling approach. This study resulted in prediction of 5T cell and 13B cell epitopes. Moreover, GPGPG linker was used to make these predicted epitopes a single peptide prior to further analysis. Afterwards, a 3D model of the final vaccine peptide was constructed, and the structure quality of the final construct was checked by Ramachandran Plot analysis and ProSA-web. Moreover, docking analysis highlighted three interactions of epitope against HLA-B7 including Lys 178, Gol 303 and Thr 31 residues. In conclusion, the predicted multi epitope peptide can be suggested as therapeutic or prophylactic candidate vaccine against SARS-CoV-2 after further confirmation by immunological assays.
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Facile Synthesis and In Vitro Activity of N-Substituted 1,2-Benzisothiazol-3(2 H)-ones against Dengue Virus NS2BNS3 Protease. Pathogens 2021; 10:pathogens10040464. [PMID: 33921368 PMCID: PMC8070447 DOI: 10.3390/pathogens10040464] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 12/02/2022] Open
Abstract
Several new N-substituted 1,2-benzisothiazol-3(2H)-ones (BITs) were synthesised through a facile synthetic route for testing their anti-dengue protease inhibition. Contrary to the conventional multistep synthesis, we achieved structurally diverse BITs with excellent yields using a two-step, one-pot reaction strategy. All the synthesised compounds were prescreened for drug-like properties using the online Swiss Absorption, Distribution, Metabolism and Elimination (SwissADME) model, indicating their favourable pharmaceutical properties. Thus, the synthesised BITs were tested for inhibitory activity against the recombinant dengue virus serotype-2 (DENV-2) NS2BNS3 protease. Dose–response experiments and computational docking analyses revealed that several BITs bind to the protease in the vicinity of the catalytic triad with IC50 values in the micromolar range. The DENV2 infection assay showed that two BITs, 2-(2-chlorophenyl)benzo[d]isothiazol-3(2H)-one and 2-(2,6-dichlorophenyl)benzo[d]isothiazol-3(2H)-one, could suppress DENV replication and virus infectivity. These results indicate the potential of BITs for developing new anti-dengue therapeutics.
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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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Dalle Vedove A, Zonta F, Zanforlin E, Demitri N, Ribaudo G, Cazzanelli G, Ongaro A, Sarno S, Zagotto G, Battistutta R, Ruzzene M, Lolli G. A novel class of selective CK2 inhibitors targeting its open hinge conformation. Eur J Med Chem 2020; 195:112267. [PMID: 32283296 DOI: 10.1016/j.ejmech.2020.112267] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/02/2020] [Accepted: 03/20/2020] [Indexed: 12/16/2022]
Abstract
Protein kinase CK2 sustains cancer growth, especially in hematological malignancies. Its inhibitor SRPIN803, based on a 6-methylene-5-imino-1,3,4-thiadiazolopyrimidin-7-one scaffold, showed notable specificity. Our synthesis of the initially proposed SRPIN803 resulted in its constitutional isomer SRPIN803-revised, where the 2-cyano-2-propenamide group does not cyclise and fuse to the thiadiazole ring. Its crystallographic structure in complex with CK2α identifies the structural determinants of the reported specificity. SRPIN803-revised explores the CK2 open hinge conformation, extremely rare among kinases, also interacting with side chains from this region. Its optimization lead to the more potent compound 4, which inhibits endocellular CK2, significantly affects viability of tumour cells and shows remarkable selectivity on a panel of 320 kinases.
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Affiliation(s)
- Andrea Dalle Vedove
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Francesca Zonta
- Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Enrico Zanforlin
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padua, Italy
| | - Nicola Demitri
- Elettra-Sincrotrone Trieste, S.S. 14 Km 163.5 in Area Science Park, 34149, Basovizza-Trieste, Italy
| | - Giovanni Ribaudo
- Department of Molecular and Translational Medicine, Division of Pharmacology, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Giulia Cazzanelli
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Via Sommarive 9, 38123, Trento, Italy
| | - Alberto Ongaro
- Department of Molecular and Translational Medicine, Division of Pharmacology, University of Brescia, Viale Europa 11, 25123, Brescia, Italy
| | - Stefania Sarno
- Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy
| | - Giuseppe Zagotto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padua, Via F. Marzolo 5, 35131, Padua, Italy.
| | - Roberto Battistutta
- Department of Chemical Sciences and CNR Institute of Biomolecular Chemistry, University of Padua, Via F. Marzolo 1, 35131, Padua, Italy.
| | - Maria Ruzzene
- Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padua, Via U. Bassi 58/B, 35131, Padua, Italy.
| | - Graziano Lolli
- Department of Cellular, Computational and Integrative Biology - CIBIO, University of Trento, Via Sommarive 9, 38123, Trento, Italy.
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Bhowmick S, Alissa SA, Wabaidur SM, Chikhale RV, Islam MA. Structure-guided screening of chemical database to identify NS3-NS2B inhibitors for effective therapeutic application in dengue infection. J Mol Recognit 2020; 33:e2838. [PMID: 32060998 DOI: 10.1002/jmr.2838] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Revised: 01/01/2020] [Accepted: 01/13/2020] [Indexed: 12/14/2022]
Abstract
Dengue infection is the most common arthropod-borne disease caused by dengue viruses, predominantly affecting millions of human beings annually. To find out promising chemical entities for therapeutic application in Dengue, in the current research, a multi-step virtual screening effort was conceived to screen out the entire "screening library" of the Asinex database. Initially, through "Lipinski rule of five" filtration criterion almost 0.6 million compounds were collected and docked with NS3-NS2B protein. Thereby, the chemical space was reduced to about 3500 compounds through the analysis of binding affinity obtained from molecular docking study in AutoDock Vina. Further, the "Virtual Screening Workflow" (VSW) utility of Schrödinger suite was used, which follows a stepwise multiple docking programs such as - high-throughput virtual screening (HTVS), standard precision (SP), and extra precision (XP) docking, and in postprocessing analysis the MM-GBSA based free binding energy calculation. Finally, five potent molecules were proposed as potential inhibitors for the dengue NS3-NS2B protein based on the investigation of molecular interactions map and protein-ligand fingerprint analyses. Different pharmacokinetics and drug-likeness parameters were also checked, which favour the potentiality of selected molecules for being drug-like candidates. The molecular dynamics (MD) simulation analyses of protein-ligand complexes were explained that NS3-NS2B bound with proposed molecules quite stable in dynamic states as observed from the root means square deviation (RMSD) and root means square fluctuation (RMSF) parameters. The binding free energy was calculated using MM-GBSA method from the MD simulation trajectories revealed that all proposed molecules possess such a strong binding affinity towards the dengue NS3-NS2B protein. Therefore, proposed molecules may be potential chemical components for effective inhibition of dengue NS3-NS2B protein subjected to experimental validation.
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Affiliation(s)
- Shovonlal Bhowmick
- Department of Chemical Technology, University of Calcutta, Kolkata, India
| | - Siham A Alissa
- Chemistry Department, College of Science, Princess Nourah bint Abdulrahman University, Riyadh, Saudi Arabia
| | | | | | - Md Ataul Islam
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK.,School of Health Sciences, University of Kwazulu-Natal, Westville Campus, Durban, South Africa.,Department of Chemical Pathology, Faculty of Health Sciences, University of Pretoria, Pretoria, South Africa
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Abdullah AA, Lee YK, Chin SP, Lim SK, Lee VS, Othman R, Othman S, Rahman NA, Yusof R, Heh CH. Discovery of Dengue Virus Inhibitors. Curr Med Chem 2020; 27:4945-5036. [PMID: 30514185 DOI: 10.2174/0929867326666181204155336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 11/11/2018] [Accepted: 11/22/2018] [Indexed: 11/22/2022]
Abstract
To date, there is still no approved anti-dengue agent to treat dengue infection in the market. Although the only licensed dengue vaccine, Dengvaxia is available, its protective efficacy against serotypes 1 and 2 of dengue virus was reported to be lower than serotypes 3 and 4. Moreover, according to WHO, the risk of being hospitalized and having severe dengue increased in seronegative individuals after they received Dengvaxia vaccination. Nevertheless, various studies had been carried out in search of dengue virus inhibitors. These studies focused on the structural (C, prM, E) and non-structural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B and NS5) of dengue virus as well as host factors as drug targets. Hence, this article provides an overall up-to-date review of the discovery of dengue virus inhibitors that are only targeting the structural and non-structural viral proteins as drug targets.
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Affiliation(s)
- Adib Afandi Abdullah
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Yean Kee Lee
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Sek Peng Chin
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - See Khai Lim
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Vannajan Sanghiran Lee
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Rozana Othman
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Shatrah Othman
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Noorsaadah Abdul Rahman
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Rohana Yusof
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
| | - Choon Han Heh
- Drug Design and Development Research Group (DDDRG), University of Malaya, Kuala Lumpur, Malaysia
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Majerová T, Novotný P, Krýsová E, Konvalinka J. Exploiting the unique features of Zika and Dengue proteases for inhibitor design. Biochimie 2019; 166:132-141. [PMID: 31077760 DOI: 10.1016/j.biochi.2019.05.004] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2019] [Accepted: 05/01/2019] [Indexed: 02/07/2023]
Abstract
Zika and Dengue viruses have attracted substantial attention from researchers in light of recent outbreaks of Dengue fever and increases in cases of congenital microcephaly in areas with Zika incidence. This review summarizes the current state of knowledge about Zika and Dengue proteases. These enzymes have several interesting features: 1) NS3 serine protease requires the activating co-factor NS2B, which is anchored in the membrane of the endoplasmic reticulum; 2) NS2B displays extensive conformational dynamics; 3) NS3 is a multidomain protein with proteolytic, NTPase, RNA 5' triphosphatase and helicase activity and has many protein-protein interaction partners; 4) NS3 is autoproteolytically released from its precursor. Attempts to design tight-binding and specific active-site inhibitors are complicated by the facts that the substrate pocket of the NS2B-NS3 protease is flat and the active-site ligands are charged. The ionic character of potential active-site inhibitors negatively influences their cell permeability. Possibilities to block cis-autoprocessing of the protease precursor have recently been considered. Additionally, potential allosteric sites on NS2B-NS3 proteases have been identified and allosteric compounds have been designed to impair substrate binding and/or block the NS2B-NS3 interaction. Such compounds could be specific to viral proteases, without off-target effects on host serine proteases, and could have favorable pharmacokinetic profiles. This review discusses various groups of inhibitors of these proteases according to their mechanisms of action and chemical structures.
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Affiliation(s)
- Taťána Majerová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic
| | - Pavel Novotný
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic
| | - Eliška Krýsová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo Nám. 2, 16610, Prague 6, Czech Republic; Department of Biochemistry, Faculty of Science, Charles University in Prague, 12843, Prague, Czech Republic.
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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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Dengue drug discovery: Progress, challenges and outlook. Antiviral Res 2018; 163:156-178. [PMID: 30597183 DOI: 10.1016/j.antiviral.2018.12.016] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/22/2018] [Accepted: 12/25/2018] [Indexed: 12/14/2022]
Abstract
In the context of the only available vaccine (DENGVAXIA) that was marketed in several countries, but poses higher risks to unexposed individuals, the development of antivirals for dengue virus (DENV), whilst challenging, would bring significant benefits to public health. Here recent progress in the field of DENV drug discovery made in academic laboratories and industry is reviewed. Characteristics of an ideal DENV antiviral molecule, given the specific immunopathology provoked by this acute viral infection, are described. New chemical classes identified from biochemical, biophysical and phenotypic screens that target viral (especially NS4B) and host proteins, offer promising opportunities for further development. In particular, new methodologies ("omics") can accelerate the discovery of much awaited flavivirus specific inhibitors. Challenges and opportunities in lead identification activities as well as the path to clinical development of dengue drugs are discussed. To galvanize DENV drug discovery, collaborative public-public partnerships and open-access resources will greatly benefit both the DENV research community and DENV patients.
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Development of a NS2B/NS3 protease inhibition assay using AlphaScreen ® beads for screening of anti-dengue activities. Heliyon 2018; 4:e01023. [PMID: 30560214 PMCID: PMC6289942 DOI: 10.1016/j.heliyon.2018.e01023] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/27/2018] [Accepted: 12/04/2018] [Indexed: 12/15/2022] Open
Abstract
Background Dengue infection is an endemic infectious disease and it can lead to dengue fever, dengue hemorrhagic fever, and/or dengue shock syndromes. Dengue NS2B/NS3 protease complex is essential for viral replication and is a primary target for anti-dengue drug development. In this study, a NS2B/NS3 protease inhibition assay was developed using AlphaScreen® beads and was used to screen compounds for their protease inhibition activities. Methods The assay system utilized a known NS2B/NS3 peptide substrate, a recombinant of NS2B/NS3 protease with proprietary StrepTactin® donor and nickel chelate acceptor beads in 384-well format. Results The optimized assay to screen for NS2B/NS3 protease inhibitors was demonstrated to be potentially useful with reasonable zʹ factor, coefficient variance and signal to background ratio. However, screening of synthesized thioguanine derivatives using the optimized AlphaScreen® assay revealed weak NS2B/NS3 inhibition activities. Conclusion The AlphaScreen® assay to screen for NS2B/NS3 protease inhibitors is potentially applicable for high throughput screening.
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Chen J, Jiang H, Li F, Hu B, Wang Y, Wang M, Wang J, Cheng M. Computational insight into dengue virus NS2B-NS3 protease inhibition: A combined ligand- and structure-based approach. Comput Biol Chem 2018; 77:261-271. [DOI: 10.1016/j.compbiolchem.2018.09.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 09/10/2018] [Accepted: 09/12/2018] [Indexed: 01/15/2023]
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16
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Coronado MA, Eberle RJ, Bleffert N, Feuerstein S, Olivier DS, de Moraes FR, Willbold D, Arni RK. Zika virus NS2B/NS3 proteinase: A new target for an old drug - Suramin a lead compound for NS2B/NS3 proteinase inhibition. Antiviral Res 2018; 160:118-125. [PMID: 30393012 DOI: 10.1016/j.antiviral.2018.10.019] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2018] [Revised: 09/25/2018] [Accepted: 10/24/2018] [Indexed: 01/15/2023]
Abstract
Zika virus infection is the focus of much research due to the medical and social repercussions. Due the role of the viral NS2B/NS3 proteinase in maturation of the viral proteins, it had become an attractive antiviral target. Numerous investigations on viral epidemiology, structure and function analysis, vaccines, and therapeutic drugs have been conducted around the world. At present, no approved vaccine or even drugs have been reported. Thus, there is an urgent need to develop therapeutic agents to cure this epidemic disease. In the present study, we identified the polyanion suramin, an approved antiparasitic drug with antiviral properties, as a potential inhibitor of Zika virus complex NS2B/NS3 proteinase with IC50 of 47 μM. Using fluorescence spectroscopy results we could determine a kd value of 28 μM and had shown that the ligand does not affect the thermal stability of the protein. STD NMR spectroscopy experiments and molecular docking followed by molecular dynamics simulation identified the binding epitopes of the molecule and shows the mode of interaction, respectively. The computational analysis showed that suramin block the Ser135 residue and interact with the catalytically histidine residue.
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Affiliation(s)
- Monika Aparecida Coronado
- Multiuser Center for Biomolecular Innovation, Department of Physics, Universidade Estadual Paulista (UNESP), São José do Rio Preto SP, 15054-000, Brazil.
| | - Raphael Josef Eberle
- Multiuser Center for Biomolecular Innovation, Department of Physics, Universidade Estadual Paulista (UNESP), São José do Rio Preto SP, 15054-000, Brazil
| | - Nicole Bleffert
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Sophie Feuerstein
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany; Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany
| | - Danilo Silva Olivier
- Multiuser Center for Biomolecular Innovation, Department of Physics, Universidade Estadual Paulista (UNESP), São José do Rio Preto SP, 15054-000, Brazil
| | - Fabio Rogerio de Moraes
- Multiuser Center for Biomolecular Innovation, Department of Physics, Universidade Estadual Paulista (UNESP), São José do Rio Preto SP, 15054-000, Brazil
| | - Dieter Willbold
- Institute of Complex System, Structural Biochemistry (ICS-6), Forchungszentrum Jülich, Germany; Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Universitätsstraße, Germany
| | - Raghuvir Krishnaswamy Arni
- Multiuser Center for Biomolecular Innovation, Department of Physics, Universidade Estadual Paulista (UNESP), São José do Rio Preto SP, 15054-000, Brazil.
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Strategies Towards Protease Inhibitors for Emerging Flaviviruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1062:175-186. [PMID: 29845533 PMCID: PMC7121277 DOI: 10.1007/978-981-10-8727-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Infections with flaviviruses are a continuing public health threat. In addition to vaccine development and vector control, the search for antiviral agents that alleviate symptoms in patients are of considerable interest. Among others, the flaviviral protease NS2B-NS3 is a promising drug target to inhibit viral replication. Flaviviral proteases share a high degree of structural similarity and substrate-recognition profile, which may facilitate a strategy towards development of pan-flaviviral protease inhibitors. However, the success of various drug discovery attempts during the last decade has been limited by the nature of the viral enzyme as well as a lack of robust structural templates. Small-molecular, structurally diverse protease inhibitors have been reported to reach affinities in the lower micromolar range. Peptide-based, substrate-derived compounds are often nanomolar inhibitors, however, with highly compromised drug-likeness. With some exceptions, the antiviral cellular activity of most of the reported compounds have been patchy and insufficient for further development. Recent progress has been made in the elucidation of inhibitor binding using different structural methods. This will hopefully lead to more rational attempts for the identification of various lead compounds that may be successful in cellular assays, animal models and ultimately translated to patients.
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18
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Yao X, Ling Y, Guo S, He S, Wang J, Zhang Q, Wu W, Zou M, Zhang T, Nandakumar KS, Chen X, Liu S. Inhibition of dengue viral infection by diasarone-I is associated with 2'O methyltransferase of NS5. Eur J Pharmacol 2018; 821:11-20. [DOI: 10.1016/j.ejphar.2017.12.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 12/10/2017] [Accepted: 12/11/2017] [Indexed: 02/06/2023]
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19
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Zhao RY. Yeast for virus research. MICROBIAL CELL (GRAZ, AUSTRIA) 2017; 4:311-330. [PMID: 29082230 PMCID: PMC5657823 DOI: 10.15698/mic2017.10.592] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 08/27/2017] [Indexed: 12/25/2022]
Abstract
Budding yeast (Saccharomyces cerevisiae) and fission yeast (Schizosaccharomyces pombe) are two popular model organisms for virus research. They are natural hosts for viruses as they carry their own indigenous viruses. Both yeasts have been used for studies of plant, animal and human viruses. Many positive sense (+) RNA viruses and some DNA viruses replicate with various levels in yeasts, thus allowing study of those viral activities during viral life cycle. Yeasts are single cell eukaryotic organisms. Hence, many of the fundamental cellular functions such as cell cycle regulation or programed cell death are highly conserved from yeasts to higher eukaryotes. Therefore, they are particularly suited to study the impact of those viral activities on related cellular activities during virus-host interactions. Yeasts present many unique advantages in virus research over high eukaryotes. Yeast cells are easy to maintain in the laboratory with relative short doubling time. They are non-biohazardous, genetically amendable with small genomes that permit genome-wide analysis of virologic and cellular functions. In this review, similarities and differences of these two yeasts are described. Studies of virologic activities such as viral translation, viral replication and genome-wide study of virus-cell interactions in yeasts are highlighted. Impacts of viral proteins on basic cellular functions such as cell cycle regulation and programed cell death are discussed. Potential applications of using yeasts as hosts to carry out functional analysis of small viral genome and to develop high throughput drug screening platform for the discovery of antiviral drugs are presented.
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Affiliation(s)
- Richard Yuqi Zhao
- Department of Pathology, Department of Microbiology and Immunology, Institute of Global Health, and Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
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20
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Tambunan USF, Nasution MAF, Azhima F, Parikesit AA, Toepak EP, Idrus S, Kerami D. Modification of S-Adenosyl-l-Homocysteine as Inhibitor of Nonstructural Protein 5 Methyltransferase Dengue Virus Through Molecular Docking and Molecular Dynamics Simulation. Drug Target Insights 2017; 11:1177392817701726. [PMID: 28469408 PMCID: PMC5404899 DOI: 10.1177/1177392817701726] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 03/01/2017] [Indexed: 01/01/2023] Open
Abstract
Dengue fever is still a major threat worldwide, approximately threatening two-fifths of the world's population in tropical and subtropical countries. Nonstructural protein 5 (NS5) methyltransferase enzyme plays a vital role in the process of messenger RNA capping of dengue by transferring methyl groups from S-adenosyl-l-methionine to N7 atom of the guanine bases of RNA and the RNA ribose group of 2'OH, resulting in S-adenosyl-l-homocysteine (SAH). The modification of SAH compound was screened using molecular docking and molecular dynamics simulation, along with computational ADME-Tox (absorption, distribution, metabolism, excretion, and toxicity) test. The 2 simulations were performed using Molecular Operating Environment (MOE) 2008.10 software, whereas the ADME-Tox test was performed using various software. The modification of SAH compound was done using several functional groups that possess different polarities and properties, resulting in 3460 ligands to be docked. After conducting docking simulation, we earned 3 best ligands (SAH-M331, SAH-M2696, and SAH-M1356) based on ΔGbinding and molecular interactions, which show better results than the standard ligands. Moreover, the results of molecular dynamics simulation show that the best ligands are still able to maintain the active site residue interaction with the binding site until the end of the simulation. After a series of molecular docking and molecular dynamics simulation were performed, we concluded that SAH-M1356 ligand is the most potential SAH-based compound to inhibit NS5 methyltransferase enzyme for treating dengue fever.
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Affiliation(s)
- Usman Sumo Friend Tambunan
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
| | | | - Fauziah Azhima
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
| | - Arli Aditya Parikesit
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
| | - Erwin Prasetya Toepak
- Bioinformatics Research Group, Department of Chemistry, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
| | - Syarifuddin Idrus
- Industrial Standardization Laboratory, Ministry of Industrial Affair, Ambon, Indonesia
| | - Djati Kerami
- Mathematics Computation Research Group, Department of Mathematics, Faculty of Mathematics and Natural Science, University of Indonesia, Depok, Indonesia
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Lee H, Ren J, Nocadello S, Rice AJ, Ojeda I, Light S, Minasov G, Vargas J, Nagarathnam D, Anderson WF, Johnson ME. Identification of novel small molecule inhibitors against NS2B/NS3 serine protease from Zika virus. Antiviral Res 2016; 139:49-58. [PMID: 28034741 DOI: 10.1016/j.antiviral.2016.12.016] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/21/2016] [Accepted: 12/22/2016] [Indexed: 01/11/2023]
Abstract
Zika flavivirus infection during pregnancy appears to produce higher risk of microcephaly, and also causes multiple neurological problems such as Guillain-Barré syndrome. The Zika virus is now widespread in Central and South America, and is anticipated to become an increasing risk in the southern United States. With continuing global travel and the spread of the mosquito vector, the exposure is expected to accelerate, but there are no currently approved treatments against the Zika virus. The Zika NS2B/NS3 protease is an attractive drug target due to its essential role in viral replication. Our studies have identified several compounds with inhibitory activity (IC50) and binding affinity (KD) of ∼5-10 μM against the Zika NS2B-NS3 protease from testing 71 HCV NS3/NS4A inhibitors that were initially discovered by high-throughput screening of 40,967 compounds. Competition surface plasmon resonance studies and mechanism of inhibition analyses by enzyme kinetics subsequently determined the best compound to be a competitive inhibitor with a Ki value of 9.5 μM. We also determined the X-ray structure of the Zika NS2B-NS3 protease in a "pre-open conformation", a conformation never observed before for any flavivirus proteases. This provides the foundation for new structure-based inhibitor design.
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Affiliation(s)
- Hyun Lee
- Novalex Therapeutics, Inc., 2242 W Harrison Suite 201, Chicago, IL 60612, USA
| | - Jinhong Ren
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA
| | - Salvatore Nocadello
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - Amy J Rice
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, IL 60612, USA
| | - Isabel Ojeda
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, IL 60612, USA
| | - Samuel Light
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - George Minasov
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - Jason Vargas
- Center for Biomolecular Science, University of Illinois at Chicago, 900 S. Ashland, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, 833 S. Wood Street, IL 60612, USA
| | | | - Wayne F Anderson
- Center for Structural Genomics of Infectious Diseases (CSGID), Dept. of Biochemistry and Molecular Genetics, Northwestern University, Feinberg School of Medicine, 303 E. Chicago Ave., Chicago, IL 60611, USA
| | - Michael E Johnson
- Novalex Therapeutics, Inc., 2242 W Harrison Suite 201, Chicago, IL 60612, USA.
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Identification of fused bicyclic derivatives of pyrrolidine and imidazolidinone as dengue virus-2 NS2B-NS3 protease inhibitors. Eur J Med Chem 2016; 125:751-759. [PMID: 27721158 DOI: 10.1016/j.ejmech.2016.09.063] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2016] [Revised: 09/19/2016] [Accepted: 09/20/2016] [Indexed: 11/23/2022]
Abstract
A series of fused ring derivatives of pyrrolidine and imidazolidinone were designed, synthesized, characterized and assayed against the DENV-2 NS2B-NS3 protease and wild-type DENV-2 virus. The linear dipeptide compound 1 and the non-peptidic fused ring compound 2 show comparable activities against DENV-2 NS2B-NS3 protease and wild-type DENV-2 virus in a viral replication assay. The preliminary SAR reveals that a substituent and its stereochemistry at C-3 position, substitution (X) at N-2 arene and a linker (Y) between C-3 position and its attached arene are important for the fused-ring scaffold of pyrrolidino [1,2-c]imidazolidinone to block the active site of NS2B-NS3 protease. This promising structural core will facilitate the discovery of non-peptidic, potent NS2B-NS3 protease inhibitors to stop dengue virus infections.
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Timiri AK, Sinha BN, Jayaprakash V. Progress and prospects on DENV protease inhibitors. Eur J Med Chem 2016; 117:125-43. [DOI: 10.1016/j.ejmech.2016.04.008] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Revised: 03/28/2016] [Accepted: 04/04/2016] [Indexed: 12/17/2022]
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Abstract
The dengue virus and related flaviviruses are an increasing global health threat. In this perspective, we comment on and review medicinal chemistry efforts aimed at the prevention or treatment of dengue infections. We include target-based approaches aimed at viral or host factors and results from phenotypic screenings in cellular assay systems for viral replication. This perspective is limited to the discussion of results that provide explicit chemistry or structure-activity relationship (SAR), or appear to be of particular interest to the medicinal chemist for other reasons. The discovery and development efforts discussed here may at least partially be extrapolated toward other emerging flaviviral infections, such as West Nile virus. Therefore, this perspective, although not aimed at flaviviruses in general, should also be able to provide an overview of the medicinal chemistry of these closely related infectious agents.
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Affiliation(s)
- Mira A M Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Christoph Nitsche
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Veaceslav Boldescu
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany.,Laboratory of Organic Synthesis, Institute of Chemistry of the Academy of Sciences of Moldova , Academiei 3, 2028 Chisinau, Moldova
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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Discovery of antiviral molecules for dengue: In silico search and biological evaluation. Eur J Med Chem 2016; 110:87-97. [PMID: 26807547 DOI: 10.1016/j.ejmech.2015.12.030] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 11/08/2015] [Accepted: 12/14/2015] [Indexed: 12/24/2022]
Abstract
BACKGROUND Dengue disease is a global disease that has no effective treatment. The dengue virus (DENV) NS2B/NS3 protease complex is a target for designing specific antivirals due to its importance in viral replication and its high degree of conservation. METHODS NS2B/NS3 protease complex structural information was employed to find small molecules that are capable of inhibiting the activity of the enzyme complex. This inhibitory activity was probed with in vitro assays using a fluorescent substrate and the complex NS2B/NS3 obtained by recombinant DNA techniques. HepG2 cells infected with dengue virus serotype 2 were used to test the activity against dengue virus replication. RESULTS A total of 210,903 small molecules from PubChem were docked in silico to the NS2B/NS3 structure (PDB: 2FOM) to find molecules that were capable of inhibiting this protein complex. Five of the best 500 leading compounds, according to their affinity values (-11.6 and -13.5 kcal/mol), were purchased. The inhibitory protease activity on the recombinant protein and antiviral assays was tested. CONCLUSIONS Chemicals CID 54681617, CID 54692801 and CID 54715399 were strong inhibitors of NS2B/NS3, with IC50 values (μM) and percentages of viral titer reductions of 19.9, 79.9%; 17.5, 69.8%; and 9.1, 73.9%, respectively. Multivariate methods applied to the molecular descriptors showed two compounds that were structurally different from other DENV inhibitors. GENERAL SIGNIFICANCE This discovery opens new possibilities for obtaining drug candidates against Dengue virus.
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26
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Ourique GS, Vianna JF, Neto JXL, Oliveira JIN, Mauriz PW, Vasconcelos MS, Caetano EWS, Freire VN, Albuquerque EL, Fulco UL. A quantum chemistry investigation of a potential inhibitory drug against the dengue virus. RSC Adv 2016. [DOI: 10.1039/c6ra10121f] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
The total interaction energy of the inhibitor Bz-nKRR-H bound to a serine protease of the dengue virus is mainly due to the action of Asn152, Met49, Tyr161, Asp129 and Gly151 (Met84, Met75, Asp81, Asp79 and Asp80) residues at the NS3 (NS2B) subunit.
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Affiliation(s)
- G. S. Ourique
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - J. F. Vianna
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - J. X. Lima Neto
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - J. I. N. Oliveira
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - P. W. Mauriz
- Departamento de Física
- Instituto Federal de Educação
- Ciência e Tecnologia do Maranhão
- São Luís
- Brazil
| | - M. S. Vasconcelos
- Escola de Ciência e Tecnologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - E. W. S. Caetano
- Instituto Federal de Educação
- Ciência e Tecnologia do Ceará
- Fortaleza
- Brazil
| | - V. N. Freire
- Departamento de Física
- Universidade Federal do Ceará
- Fortaleza
- Brazil
| | - E. L. Albuquerque
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
| | - U. L. Fulco
- Departamento de Biofísica e Farmacologia
- Universidade Federal do Rio Grande do Norte
- Natal
- Brazil
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Behnam MAM, Graf D, Bartenschlager R, Zlotos DP, Klein CD. Discovery of Nanomolar Dengue and West Nile Virus Protease Inhibitors Containing a 4-Benzyloxyphenylglycine Residue. J Med Chem 2015; 58:9354-70. [PMID: 26562070 DOI: 10.1021/acs.jmedchem.5b01441] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The dengue virus (DENV) and West Nile Virus (WNV) NS2B-NS3 proteases are attractive targets for the development of dual-acting therapeutics against these arboviral pathogens. We present the synthesis and extensive biological evaluation of inhibitors that contain benzyl ethers of 4-hydroxyphenylglycine as non-natural peptidic building blocks synthesized via a copper-complex intermediate. A three-step optimization strategy, beginning with fragment growth of the C-terminal 4-hydroxyphenylglycine to the benzyloxy ether, followed by C- and N-terminal optimization, and finally fragment merging generated compounds with in vitro affinities in the low nanomolar range. The most promising derivative reached Ki values of 12 nM at the DENV-2 and 39 nM at the WNV proteases. Several of the newly discovered protease inhibitors yielded a significant reduction of dengue and West Nile virus titers in cell-based assays of virus replication, with an EC50 value of 3.4 μM at DENV-2 and 15.5 μM at WNV for the most active analogue.
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Affiliation(s)
- Mira A M Behnam
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Dominik Graf
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University , Im Neuenheimer Feld 345, 69120 Heidelberg, Germany.,German Center for Infection Research, Heidelberg University , Im Neuenheimer Feld 345, 69120 Heidelberg, Germany
| | - Darius P Zlotos
- Department of Pharmaceutical Chemistry, The German University in Cairo , New Cairo City, 11835 Cairo, Egypt
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, 69120 Heidelberg, Germany
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Weigel LF, Nitsche C, Graf D, Bartenschlager R, Klein CD. Phenylalanine and Phenylglycine Analogues as Arginine Mimetics in Dengue Protease Inhibitors. J Med Chem 2015; 58:7719-33. [PMID: 26367391 DOI: 10.1021/acs.jmedchem.5b00612] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Dengue virus is an increasingly global pathogen. One of the promising targets for antiviral drug discovery against dengue and related flaviviruses such as West Nile virus is the viral serine protease NS2B-NS3. We here report the synthesis and in vitro characterization of potent peptidic inhibitors of dengue virus protease that incorporate phenylalanine and phenylglycine derivatives as arginine-mimicking groups with modulated basicity. The most promising compounds were (4-amidino)-L-phenylalanine-containing inhibitors, which reached nanomolar affinities against dengue virus protease. The type and position of the substituents on the phenylglycine and phenylalanine side chains has a significant effect on the inhibitory activity against dengue virus protease and selectivity against other proteases. In addition, the non-natural, basic amino acids described here may have relevance for the development of other peptidic and peptidomimetic drugs such as inhibitors of the blood clotting cascade.
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Affiliation(s)
- Lena F Weigel
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Christoph Nitsche
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Dominik Graf
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
| | - Ralf Bartenschlager
- Department of Infectious Diseases, Molecular Virology, Heidelberg University , Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany.,German Centre for Infection Research, Heidelberg University , D-69120 Heidelberg, Germany
| | - Christian D Klein
- Medicinal Chemistry, Institute of Pharmacy and Molecular Biotechnology IPMB, Heidelberg University , Im Neuenheimer Feld 364, D-69120 Heidelberg, Germany
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Policresulen, a novel NS2B/NS3 protease inhibitor, effectively inhibits the replication of DENV2 virus in BHK-21 cells. Acta Pharmacol Sin 2015; 36:1126-36. [PMID: 26279156 DOI: 10.1038/aps.2015.56] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 05/08/2015] [Indexed: 12/17/2022] Open
Abstract
AIM Dengue is a severe epidemic disease caused by dengue virus (DENV) infection, for which no effective treatment is available. The protease complex, consisting of nonstructural protein 3 (NS3) and its cofactor NS2B, plays a pivotal role in the replication of DENV, thus may be a potential target for anti-DENV drugs. Here, we report a novel inhibitor of DENV2 NS2B/NS3 protease and its antiviral action. METHODS An enzymatic inhibition assay was used for screening DENV2 NS2B/NS3 inhibitors. Cytotoxicity to BHK-21 cells was assessed with MTT assay. Antiviral activity was evaluated in BHK-21 cells transfected with Rlu-DENV-Rep. The molecular mechanisms of the antiviral action was analyzed using surface plasmon resonance, ultraviolet-visible spectral analysis and differential scanning calorimetry assays, as well as molecular docking analysis combined with site-directed mutagenesis. RESULTS In our in-house library of old drugs (~1000 compounds), a topical hemostatic and antiseptic 2-hydroxy-3,5-bis[(4-hydroxy-2-methyl-5-sulfophenyl)methyl]-4-methyl-benzene-sulfonic acid (policresulen) was found to be a potent inhibitor of DENV2 NS2B/NS3 protease with IC50 of 0.48 μg/mL. Furthermore, policresulen inhibited DENV2 replication in BHK-21 cells with IC50 of 4.99 μg/mL, whereas its IC50 for cytotoxicity to BHK-21 cells was 459.45 μg/mL. Policresulen acted as a competitive inhibitor of the protease, and slightly affected the protease stability. Using biophysical technology-based assays and molecular docking analysis combined with site-directed mutagenesis, we demonstrated that the residues Gln106 and Arg133 of DENV2 NS2B/NS3 protease directly interacted with policresulen via hydrogen bonding. CONCLUSION Policresulen is a potent inhibitor of DENV2 NS2B/NS3 protease that inhibits DENV2 replication in BHK-21 cells. The binding mode of the protease and policresulen provides useful hints for designing new type of inhibitors against the protease.
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Luo D, Vasudevan SG, Lescar J. The flavivirus NS2B-NS3 protease-helicase as a target for antiviral drug development. Antiviral Res 2015; 118:148-58. [PMID: 25842996 DOI: 10.1016/j.antiviral.2015.03.014] [Citation(s) in RCA: 192] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/20/2015] [Accepted: 03/26/2015] [Indexed: 11/30/2022]
Abstract
The flavivirus NS3 protein is associated with the endoplasmic reticulum membrane via its close interaction with the central hydrophilic region of the NS2B integral membrane protein. The multiple roles played by the NS2B-NS3 protein in the virus life cycle makes it an attractive target for antiviral drug discovery. The N-terminal region of NS3 and its cofactor NS2B constitute the protease that cleaves the viral polyprotein. The NS3 C-terminal domain possesses RNA helicase, nucleoside and RNA triphosphatase activities and is involved both in viral RNA replication and virus particle formation. In addition, NS2B-NS3 serves as a hub for the assembly of the flavivirus replication complex and also modulates viral pathogenesis and the host immune response. Here, we review biochemical and structural advances on the NS2B-NS3 protein, including the network of interactions it forms with NS5 and NS4B and highlight recent drug development efforts targeting this protein. This article forms part of a symposium in Antiviral Research on flavivirus drug discovery.
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Affiliation(s)
- Dahai Luo
- Lee Kong Chian School of Medicine, Nanyang Technological University, 61 Biopolis Drive, Proteos Building, #07-03, Singapore 138673, Singapore.
| | - Subhash G Vasudevan
- Program in Emerging Infectious Diseases, DUKE-NUS Graduate Medical School, 8 College Road, Singapore 169857, Singapore.
| | - Julien Lescar
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; UPMC UMRS CR7 - CNRS ERL 8255-INSERM U1135 Centre d'Immunologie et des Maladies Infectieuses, Centre Hospitalier Universitaire Pitié-Salpêtrière, Faculté de Médecine Pierre et Marie Curie, Paris, France.
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