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Kant R, Tilford H, Freitas CS, Ferreira DAS, Ng J, Rucinski G, Watkins J, Pemberton R, Abramyan TM, Contreras SC, Vera A, Christodoulides M. Antimicrobial activity of compounds identified by artificial intelligence discovery engine targeting enzymes involved in Neisseria gonorrhoeae peptidoglycan metabolism. Biol Res 2024; 57:62. [PMID: 39238057 PMCID: PMC11375863 DOI: 10.1186/s40659-024-00543-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 08/27/2024] [Indexed: 09/07/2024] Open
Abstract
BACKGROUND Neisseria gonorrhoeae (Ng) causes the sexually transmitted disease gonorrhoea. There are no vaccines and infections are treated principally with antibiotics. However, gonococci rapidly develop resistance to every antibiotic class used and there is a need for developing new antimicrobial treatments. In this study we focused on two gonococcal enzymes as potential antimicrobial targets, namely the serine protease L,D-carboxypeptidase LdcA (NgO1274/NEIS1546) and the lytic transglycosylase LtgD (NgO0626/NEIS1212). To identify compounds that could interact with these enzymes as potential antimicrobials, we used the AtomNet virtual high-throughput screening technology. We then did a computational modelling study to examine the interactions of the most bioactive compounds with their target enzymes. The identified compounds were tested against gonococci to determine minimum inhibitory and bactericidal concentrations (MIC/MBC), specificity, and compound toxicity in vitro. RESULTS AtomNet identified 74 compounds that could potentially interact with Ng-LdcA and 84 compounds that could potentially interact with Ng-LtgD. Through MIC and MBC assays, we selected the three best performing compounds for both enzymes. Compound 16 was the most active against Ng-LdcA, with a MIC50 value < 1.56 µM and MBC50/90 values between 0.195 and 0.39 µM. In general, the Ng-LdcA compounds showed higher activity than the compounds directed against Ng-LtgD, of which compound 45 had MIC50 values of 1.56-3.125 µM and MBC50/90 values between 3.125 and 6.25 µM. The compounds were specific for gonococci and did not kill other bacteria. They were also non-toxic for human conjunctival epithelial cells as judged by a resazurin assay. To support our biological data, in-depth computational modelling study detailed the interactions of the compounds with their target enzymes. Protein models were generated in silico and validated, the active binding sites and amino acids involved elucidated, and the interactions of the compounds interacting with the enzymes visualised through molecular docking and Molecular Dynamics Simulations for 50 ns and Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA). CONCLUSIONS We have identified bioactive compounds that appear to target the N. gonorrhoeae LdcA and LtgD enzymes. By using a reductionist approach involving biological and computational data, we propose that compound Ng-LdcA-16 and Ng-LtgD-45 are promising anti-gonococcal compounds for further development.
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Affiliation(s)
- Ravi Kant
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
- Medical Biotechnology Laboratory, Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi, North Campus, Delhi, 110007, India
| | - Hannah Tilford
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
| | - Camila S Freitas
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
- Programa de Pós-Graduação em Ciências da Saúde: Infectologia e Medicina Tropical, Faculdade de Medicina, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, 30130-100, Brazil
| | - Dayana A Santos Ferreira
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
- Laboratory of Pathophysiology, Butantan Institute, Av. Vital Brazil, 1500, São Paulo, SP, 05503-900, Brazil
| | - James Ng
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
| | - Gwennan Rucinski
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
| | - Joshua Watkins
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD
| | - Ryan Pemberton
- ATOMWISE, 717 Market Street, Suite 800, San Francisco, CA, 94103, USA
| | - Tigran M Abramyan
- ATOMWISE, 717 Market Street, Suite 800, San Francisco, CA, 94103, USA
| | | | - Alejandra Vera
- Laboratorio de Bacteriología, Escuela de Medicina, Universidad de Valparaíso, Valparaíso, Chile
| | - Myron Christodoulides
- Neisseria Research Group, Molecular Microbiology, School of Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton, England, SO16 6YD.
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Khalili NSD, Khawory MH, Salin NH, Zakaria II, Hariono M, Mikhaylov AA, Kamarulzaman EE, A Wahab H, Supratman U, Nurul Azmi M. Synthesis and biological activity of imidazole phenazine derivatives as potential inhibitors for NS2B-NS3 dengue protease. Heliyon 2024; 10:e24202. [PMID: 38293469 PMCID: PMC10825487 DOI: 10.1016/j.heliyon.2024.e24202] [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: 10/03/2023] [Revised: 01/04/2024] [Accepted: 01/04/2024] [Indexed: 02/01/2024] Open
Abstract
A series of new imidazole-phenazine derivatives were synthesized via a two-step process. The condensation of 2,3-diaminophenazine and benzaldehyde derivatives proceeds with intermediate formation of an aniline Schiff base, which undergoes subsequent cyclodehydrogenation in situ. The structures of the synthesized compounds were characterized by 1D and 2D NMR, FTIR and HRMS. A total of thirteen imidazole phenazine derivatives were synthesized and validated for their inhibitory activity as anti-dengue agents by an in vitro DENV2 NS2B-NS3 protease assay using a fluorogenic Boc-Gly-Arg-Arg-AMC substrate. Two para-substituted imidazole phenazines, 3e and 3k, were found to be promising lead molecules for novel NS2B-NS3 protease inhibitors with IC50 of 54.8 μM and 71.9 μM, respectively, compared to quercetin as a control (IC50 104.8 μM). The in silico study was performed using AutoDock Vina to identify the binding energy and conformation of 3e and 3k with the active site of the DENV2 NS2B-NS3 protease Wichapong model. The results indicate better binding properties of 3e and 3k with calculated binding energies of -8.5 and -8.4 kcal mol-1, respectively, compared to the binding energy of quercetin of -7.2 kcal mol-1, which corroborates well with the experimental observations.
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Affiliation(s)
- Nur Sarah Dyana Khalili
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
- Natural Products and Synthesis Organic Research Laboratory (NPSO), School of Chemical Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Muhammad Hidhir Khawory
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
| | - Nurul Hanim Salin
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
| | - Iffah Izzati Zakaria
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, 43000 Kajang, Selangor, Malaysia
| | - Maywan Hariono
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Andrey A. Mikhaylov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, 16/10 Miklukho-Maklaya St., Moscow, 117997, Russia
| | - Ezatul Ezleen Kamarulzaman
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Habibah A Wahab
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Pulau Pinang, Malaysia
| | - Unang Supratman
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, Universitas Padjadjaran, 45363 Jatinangor, Indonesia
| | - Mohamad Nurul Azmi
- Natural Products and Synthesis Organic Research Laboratory (NPSO), School of Chemical Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
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3
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Salin NH, Hariono M, Khalili NSD, Zakaria II, Saqallah FG, Mohamad Taib MNA, Kamarulzaman EE, Wahab HA, Khawory MH. Computational study of nitro-benzylidene phenazine as dengue virus-2 NS2B-NS3 protease inhibitor. Front Mol Biosci 2022; 9:875424. [PMID: 36465554 PMCID: PMC9715268 DOI: 10.3389/fmolb.2022.875424] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 10/06/2022] [Indexed: 08/17/2023] Open
Abstract
According to the World Health Organisation (WHO), as of week 23 of 2022, there were more than 1,311 cases of dengue in Malaysia, with 13 deaths reported. Furthermore, there was an increase of 65.7% during the same period in 2021. Despite the increase in cumulative dengue incidence, there is no effective antiviral drug available for dengue treatment. This work aimed to evaluate several nitro-benzylidene phenazine compounds, especially those that contain 4-hydroxy-3,5-bis((2-(4-nitrophenyl)hydrazinylidene)-methyl)benzoate through pharmacophore queries selection method as potential dengue virus 2 (DENV2) NS2B-NS3 protease inhibitors. Herein, molecular docking was employed to correlate the energies of selected hits' free binding and their binding affinities. Pan assay interference compounds (PAINS) filter was also adopted to identify and assess the drug-likeness, toxicity, mutagenicity potentials, and pharmacokinetic profiles to select hit compounds that can be considered as lead DENV2 NS2B-NS3 protease inhibitors. Molecular dynamics assessment of two nitro-benzylidene phenazine derivatives bearing dinitro and hydroxy groups at the benzylidene ring showed their stability at the main binding pocket of DENV2 protease, where their MM-PBSA binding energies were between -22.53 and -17.01 kcal/mol. This work reports those two nitro-benzylidene phenazine derivatives as hits with 52-55% efficiency as antiviral candidates. Therefore, further optimisation is required to minimise the lead compounds' toxicity and mutagenicity.
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Affiliation(s)
- Nurul Hanim Salin
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Pulau Pinang, Malaysia
| | - Maywan Hariono
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Pulau Pinang, Malaysia
| | - Nur Sarah Dyana Khalili
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
- School of Chemical Sciences, Universiti Sains Malaysia, Gelugor, Pulau Pinang, Malaysia
| | - Iffah Izzati Zakaria
- Malaysia Genome and Vaccine Institute, National Institutes of Biotechnology Malaysia, Kajang, Selangor, Malaysia
| | - Fadi G. Saqallah
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Pulau Pinang, Malaysia
| | | | | | - Habibah A. Wahab
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, Gelugor, Pulau Pinang, Malaysia
| | - Muhammad Hidhir Khawory
- Malaysian Institute of Pharmaceuticals and Nutraceuticals, National Institutes of Biotechnology Malaysia, Gelugor, Pulau Pinang, Malaysia
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Wahaab A, Mustafa BE, Hameed M, Stevenson NJ, Anwar MN, Liu K, Wei J, Qiu Y, Ma Z. Potential Role of Flavivirus NS2B-NS3 Proteases in Viral Pathogenesis and Anti-flavivirus Drug Discovery Employing Animal Cells and Models: A Review. Viruses 2021; 14:44. [PMID: 35062249 PMCID: PMC8781031 DOI: 10.3390/v14010044] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 02/07/2023] Open
Abstract
Flaviviruses are known to cause a variety of diseases in humans in different parts of the world. There are very limited numbers of antivirals to combat flavivirus infection, and therefore new drug targets must be explored. The flavivirus NS2B-NS3 proteases are responsible for the cleavage of the flavivirus polyprotein, which is necessary for productive viral infection and for causing clinical infections; therefore, they are a promising drug target for devising novel drugs against different flaviviruses. This review highlights the structural details of the NS2B-NS3 proteases of different flaviviruses, and also describes potential antiviral drugs that can interfere with the viral protease activity, as determined by various studies. Moreover, optimized in vitro reaction conditions for studying the NS2B-NS3 proteases of different flaviviruses may vary and have been incorporated in this review. The increasing availability of the in silico and crystallographic/structural details of flavivirus NS2B-NS3 proteases in free and drug-bound states can pave the path for the development of promising antiflavivirus drugs to be used in clinics. However, there is a paucity of information available on using animal cells and models for studying flavivirus NS2B-NS3 proteases, as well as on the testing of the antiviral drug efficacy against NS2B-NS3 proteases. Therefore, on the basis of recent studies, an effort has also been made to propose potential cellular and animal models for the study of flavivirus NS2B-NS3 proteases for the purposes of exploring flavivirus pathogenesis and for testing the efficacy of possible drugs targets, in vitro and in vivo.
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Affiliation(s)
- Abdul Wahaab
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Bahar E Mustafa
- Sub Campus Toba Tek Singh, University of Agriculture, Faisalabad 36050, Pakistan;
| | - Muddassar Hameed
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
- Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute, State University, Fralin Life Sciences Building, 360 W Campus Blacksburg, Blacksburg, VA 24061, USA
| | - Nigel J. Stevenson
- Royal College of Surgeons in Ireland, Medical University of Bahrain, Busaiteen, Adliya 15503, Bahrain;
- Viral Immunology Group, School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, D02 R590 Dublin, Ireland
| | - Muhammad Naveed Anwar
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Ke Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Jianchao Wei
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Yafeng Qiu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
| | - Zhiyong Ma
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Science, Shanghai 200241, China; (A.W.); (M.H.); (M.N.A.); (K.L.); (J.W.)
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5
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Khodadadi E, Maroufi P, Khodadadi E, Esposito I, Ganbarov K, Espsoito S, Yousefi M, Zeinalzadeh E, Kafil HS. Study of combining virtual screening and antiviral treatments of the Sars-CoV-2 (Covid-19). Microb Pathog 2020; 146:104241. [PMID: 32387389 PMCID: PMC7199731 DOI: 10.1016/j.micpath.2020.104241] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 02/07/2023]
Abstract
The recent epidemic outbreak of a novel human coronavirus called SARS-CoV-2 and causing the respiratory tract disease COVID-19 has reached worldwide resonance and a global effort is being undertaken to characterize the molecular features and evolutionary origins of this virus. Therefore, rapid and accurate identification of pathogenic viruses plays a vital role in selecting appropriate treatments, saving people's lives and preventing epidemics. Additionally, general treatments, coronavirus-specific treatments, and antiviral treatments useful in fighting COVID-19 are addressed. This review sets out to shed light on the SARS-CoV-2 and host receptor recognition, a crucial factor for successful virus infection and taking immune-informatics approaches to identify B- and T-cell epitopes for surface glycoprotein of SARS-CoV-2. A variety of improved or new approaches also have been developed. It is anticipated that this will assist researchers and clinicians in developing better techniques for timely and effective detection of coronavirus infection. Moreover, the genomic sequence of the virus responsible for COVID-19, as well as the experimentally determined three-dimensional structure of the Main protease (Mpro) is available. The reported structure of the target Mpro was described in this review to identify potential drugs for COVID-19 using virtual high throughput screening.
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Affiliation(s)
- Ehsaneh Khodadadi
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Parham Maroufi
- Department of Orthopedy, School of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Ehsan Khodadadi
- Department of Biology, Tabriz Branch, Islamic Azad University, Tabriz, Iran.
| | | | | | | | - Mehdi Yousefi
- Stem Cell Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Elham Zeinalzadeh
- Hematology and Oncology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Srinivasan S, Cui H, Gao Z, Liu M, Lu S, Mkandawire W, Narykov O, Sun M, Korkin D. Structural Genomics of SARS-CoV-2 Indicates Evolutionary Conserved Functional Regions of Viral Proteins. Viruses 2020; 12:v12040360. [PMID: 32218151 PMCID: PMC7232164 DOI: 10.3390/v12040360] [Citation(s) in RCA: 160] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 03/15/2020] [Accepted: 03/20/2020] [Indexed: 12/22/2022] Open
Abstract
During its first two and a half months, the recently emerged 2019 novel coronavirus, SARS-CoV-2, has already infected over one-hundred thousand people worldwide and has taken more than four thousand lives. However, the swiftly spreading virus also caused an unprecedentedly rapid response from the research community facing the unknown health challenge of potentially enormous proportions. Unfortunately, the experimental research to understand the molecular mechanisms behind the viral infection and to design a vaccine or antivirals is costly and takes months to develop. To expedite the advancement of our knowledge, we leveraged data about the related coronaviruses that is readily available in public databases and integrated these data into a single computational pipeline. As a result, we provide comprehensive structural genomics and interactomics roadmaps of SARS-CoV-2 and use this information to infer the possible functional differences and similarities with the related SARS coronavirus. All data are made publicly available to the research community.
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Affiliation(s)
- Suhas Srinivasan
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
| | - Hongzhu Cui
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA; (H.C.); (Z.G.); (M.L.); (S.L.); (W.M.); (D.K.)
| | - Ziyang Gao
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA; (H.C.); (Z.G.); (M.L.); (S.L.); (W.M.); (D.K.)
| | - Ming Liu
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA; (H.C.); (Z.G.); (M.L.); (S.L.); (W.M.); (D.K.)
| | - Senbao Lu
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA; (H.C.); (Z.G.); (M.L.); (S.L.); (W.M.); (D.K.)
| | - Winnie Mkandawire
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA; (H.C.); (Z.G.); (M.L.); (S.L.); (W.M.); (D.K.)
| | - Oleksandr Narykov
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
| | - Mo Sun
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA; (H.C.); (Z.G.); (M.L.); (S.L.); (W.M.); (D.K.)
| | - Dmitry Korkin
- Data Science Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01609, USA; (H.C.); (Z.G.); (M.L.); (S.L.); (W.M.); (D.K.)
- Computer Science Department, Worcester Polytechnic Institute, Worcester, MA 01609, USA;
- Correspondence:
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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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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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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: 10] [Impact Index Per Article: 1.7] [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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10
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Balasubramani S, Sabapathi G, Moola AK, Solomon RV, Venuvanalingam P, Bollipo Diana RK. Evaluation of the Leaf Essential Oil from Artemisia vulgaris and Its Larvicidal and Repellent Activity against Dengue Fever Vector Aedes aegypti-An Experimental and Molecular Docking Investigation. ACS OMEGA 2018; 3:15657-15665. [PMID: 30556010 PMCID: PMC6288777 DOI: 10.1021/acsomega.8b01597] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Accepted: 10/31/2018] [Indexed: 06/09/2023]
Abstract
Aedes aegypti is a mosquito vector that spreads dengue fever and yellow fever worldwide in tropical and subtropical countries. Essential oil isolated from Artemisia vulgaris is found to have larvicidal and repellent action against this vector. The dried leaves were subjected to hydrodistillation using a clevenger-type apparatus for 4 h. The isolated essential oil was analyzed by using gas chromatography-mass spectrometry, and the major insecticidal compounds were identified as α-humulene (0.72%), β-caryophyllene (0.81%), and caryophyllene oxide (15.87%). Larvicidal activity results revealed that the essential oil exposure for 24 h period against the third stage larvae was LC50 = 6.87, LC90 = 59.197 ppm and for the fourth stage larvae LC50 = 4.269, LC90 = 50.363 ppm. Highest mortality rates were observed at 24 h exposure period of third and fourth stages, and the exposed A. aegypti larvae were subjected to histo chemical studies, and the studies revealed that larvae cells got totally damaged (midgut and cortex). The repellent activity results revealed that at 50% concentration of the essential oil showed the highest repellent activity at 60 min protection time against the A. aegypti female mosquitoes. To gain further insights into the insecticidal activity, density functional theory and molecular docking calculations were performed with the active components of this essential oil as the ligand and NS3 protease domain (PDB ID: 2FOM) as a receptor. Molecular docking calculation results show that (E)-β-caryophyllene strongly binds with NS3 protease domain than (Z)-β-caryophyllene, α-humulene, and β-caryophyllene oxide and is the major active component for the insecticidal action. It primarily interacts with the receptor through hydrophobic and ionic forces and using water bridges between the amino acid residues in the binding pocket and (E)-β-caryophyllene.
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Affiliation(s)
- Sundararajan Balasubramani
- Department
of Botany and Theoretical and Computational Chemistry Laboratory,
School of Chemistry, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Gopal Sabapathi
- Department
of Botany and Theoretical and Computational Chemistry Laboratory,
School of Chemistry, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Anil Kumar Moola
- Department
of Botany and Theoretical and Computational Chemistry Laboratory,
School of Chemistry, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Rajadurai Vijay Solomon
- Department
of Chemistry, Madras Christian College (Autonomous), Chennai 600059, Tamil Nadu, India
| | - Ponnambalam Venuvanalingam
- Department
of Botany and Theoretical and Computational Chemistry Laboratory,
School of Chemistry, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
| | - Ranjitha Kumari Bollipo Diana
- Department
of Botany and Theoretical and Computational Chemistry Laboratory,
School of Chemistry, Bharathidasan University, Tiruchirappalli 620024, Tamil Nadu, India
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11
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Kumar V, Sobhia ME. Molecular Dynamics Assisted Mechanistic Study of Isoniazid-Resistance against Mycobacterium tuberculosis InhA. PLoS One 2015; 10:e0144635. [PMID: 26658674 PMCID: PMC4682841 DOI: 10.1371/journal.pone.0144635] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2015] [Accepted: 11/21/2015] [Indexed: 12/20/2022] Open
Abstract
Examination of InhA mutants I16T, I21V, I47T, S94A, and I95P showed that direct and water mediated H-bond interactions between NADH and binding site residues reduced drastically. It allowed conformational flexibility to NADH, particularly at the pyrophosphate region, leading to weakening of its binding at dinucleotide binding site. The highly scattered distribution of pyrophosphate dihedral angles and chi1 side chain dihedral angles of corresponding active site residues therein confirmed weak bonding between InhA and NADH. The average direct and water mediated bridged H-bond interactions between NADH and mutants were observed weaker as compared to wild type. Further, estimated NADH binding free energy in mutants supported the observed weakening of InhA-NADH interactions. Similarly, per residue contribution to NADH binding was also found little less as compared to corresponding residues in wild type. This investigation clearly depicted and supported the effect of mutations on NADH binding and can be accounted for isoniazid resistance as suggested by previous biochemical and mutagenic studies. Further, structural analysis of InhA provided the crucial points to enhance the NADH binding affinity towards InhA mutants in the presence of direct InhA inhibitors to combat isoniazid drug resistance. This combination could be a potential alternative for treatment of drug resistant tuberculosis.
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Affiliation(s)
- Vivek Kumar
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar- 160 062, Punjab, India
| | - M. Elizabeth Sobhia
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar- 160 062, Punjab, India
- * E-mail:
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12
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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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13
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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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14
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Enzymatic analysis of recombinant Japanese encephalitis virus NS2B(H)-NS3pro protease with fluorogenic model peptide substrates. PLoS One 2012; 7:e36872. [PMID: 22615830 PMCID: PMC3352935 DOI: 10.1371/journal.pone.0036872] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2012] [Accepted: 04/09/2012] [Indexed: 01/29/2023] Open
Abstract
Background Japanese encephalitis virus (JEV), a member of the Flaviviridae family, causes around 68,000 encephalitis cases annually, of which 20–30% are fatal, while 30–50% of the recovered cases develop severe neurological sequelae. Specific antivirals for JEV would be of great importance, particularly in those cases where the infection has become persistent. Being indispensable for flaviviral replication, the NS2B-NS3 protease is a promising target for design of anti-flaviviral inhibitors. Contrary to related flaviviral proteases, the JEV NS2B-NS3 protease is structurally and mechanistically much less characterized. Here we aimed at establishing a straightforward procedure for cloning, expression, purification and biochemical characterization of JEV NS2B(H)-NS3pro protease. Methodology/Principal Findings The full-length sequence of JEV NS2B-NS3 genotype III strain JaOArS 982 was obtained as a synthetic gene. The sequence of NS2B(H)-NS3pro was generated by splicing by overlap extension PCR (SOE-PCR) and cloned into the pTrcHisA vector. Hexahistidine-tagged NS2B(H)-NS3pro, expressed in E. coli as soluble protein, was purified to >95% purity by a single-step immobilized metal affinity chromatography. SDS-PAGE and immunoblotting of the purified enzyme demonstrated NS2B(H)-NS3pro precursor and its autocleavage products, NS3pro and NS2B(H), as 36, 21, and 10 kDa bands, respectively. Kinetic parameters, Km and kcat, for fluorogenic protease model substrates, Boc-GRR-amc, Boc-LRR-amc, Ac-nKRR-amc, Bz-nKRR-amc, Pyr-RTKR-amc and Abz-(R)4SAG-nY-amide, were obtained using inner filter effect correction. The highest catalytic efficiency kcat/Km was found for Pyr-RTKR-amc (kcat/Km: 1962.96±85.0 M−1 s−1) and the lowest for Boc-LRR-amc (kcat/Km: 3.74±0.3 M−1 s−1). JEV NS3pro is inhibited by aprotinin but to a lesser extent than DEN and WNV NS3pro. Conclusions/Significance A simplified procedure for the cloning, overexpression and purification of the NS2B(H)-NS3pro was established which is generally applicable to other flaviviral proteases. Kinetic parameters obtained for a number of model substrates and inhibitors, are useful for the characterization of substrate specificity and eventually for the design of high-throughput assays aimed at antiviral inhibitor discovery.
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15
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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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Abstract
Dengue is a mosquito-borne viral hemorrhagic disease that is a major threat to human health in tropical and subtropical regions. Here we report crystal structures of a peptide covalently bound to dengue virus serotype 3 (DENV-3) protease as well as the serine-protease inhibitor aprotinin bound to the same enzyme. These structures reveal, for the first time, a catalytically active, closed conformation of the DENV protease. In the presence of the peptide, the DENV-3 protease forms the closed conformation in which the hydrophilic β-hairpin region of NS2B wraps around the NS3 protease core, in a manner analogous to the structure of West Nile virus (WNV) protease. Our results confirm that flavivirus proteases form the closed conformation during proteolysis, as previously proposed for WNV. The current DENV-3 protease structures reveal the detailed interactions at the P4' to P3 sites of the substrate. The new structural information explains the sequence preference, particularly for long basic residues in the nonprime side, as well as the difference in substrate specificity between the WNV and DENV proteases at the prime side. Structural analysis of the DENV-3 protease-peptide complex revealed a pocket that is formed by residues from NS2B and NS3; this pocket also exists in the WNV NS2B/NS3 protease structure and could be targeted for potential antivirus development. The structural information presented in the current study is invaluable for the design of specific inhibitors of DENV protease.
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Shiryaev SA, Cheltsov AV, Gawlik K, Ratnikov BI, Strongin AY. Virtual ligand screening of the National Cancer Institute (NCI) compound library leads to the allosteric inhibitory scaffolds of the West Nile Virus NS3 proteinase. Assay Drug Dev Technol 2010; 9:69-78. [PMID: 21050032 DOI: 10.1089/adt.2010.0309] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Viruses of the genus Flavivirus are responsible for significant human disease and mortality. The N-terminal domain of the flaviviral nonstructural (NS)3 protein codes for the serine, chymotrypsin-fold proteinase (NS3pro). The presence of the nonstructural (NS)2B cofactor, which is encoded by the upstream gene in the flaviviral genome, is necessary for NS3pro to exhibit its proteolytic activity. The two-component NS2B-NS3pro functional activity is essential for the viral polyprotein processing and replication. Both the structure and the function of NS2B-NS3pro are conserved in the Flavivirus family. Because of its essential function in the posttranslational processing of the viral polyprotein precursor, NS2B-NS3pro is a promising target for anti-flavivirus drugs. To identify selective inhibitors with the reduced cross-reactivity and off-target effects, we focused our strategy on the allosteric inhibitors capable of targeting the NS2B-NS3pro interface rather than the NS3pro active site. Using virtual ligand screening of the diverse, ∼275,000-compound library and the catalytic domain of the two-component West Nile virus (WNV) NS2B-NS3pro as a receptor, we identified a limited subset of the novel inhibitory scaffolds. Several of the discovered compounds performed as allosteric inhibitors and exhibited a nanomolar range potency in the in vitro cleavage assays. The inhibitors were also potent in cell-based assays employing the sub-genomic, luciferase-tagged WNV and Dengue viral replicons. The selectivity of the inhibitors was confirmed using the in vitro cleavage assays with furin, a human serine proteinase, the substrate preferences of which are similar to those of WNV NS2B-NS3pro. Conceptually, the similar in silico drug discovery strategy may be readily employed for the identification of inhibitors of other flaviviruses.
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Affiliation(s)
- Sergey A Shiryaev
- Inflammatory and Infectious Disease Center, Sanford-Burnham Medical Research Institute, 10901 N. Torrey Pines Road, La Jolla, CA 92037, USA
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Novel dengue virus-specific NS2B/NS3 protease inhibitor, BP2109, discovered by a high-throughput screening assay. Antimicrob Agents Chemother 2010; 55:229-38. [PMID: 20937790 DOI: 10.1128/aac.00855-10] [Citation(s) in RCA: 94] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Dengue virus (DENV) causes disease globally, with an estimated 25 to 100 million new infections per year. At present, no effective vaccine is available, and treatment is supportive. In this study, we identified BP2109, a potent and selective small-molecule inhibitor of the DENV NS2B/NS3 protease, by a high-throughput screening assay using a recombinant protease complex consisting of the central hydrophilic portion of NS2B and the N terminus of the protease domain. BP2109 inhibited DENV (serotypes 1 to 4), but not Japanese encephalitis virus (JEV), replication and viral RNA synthesis without detectable cytotoxicity. The compound inhibited recombinant DENV-2 NS2B/NS3 protease with a 50% inhibitory concentration (IC(50)) of 15.43 ± 2.12 μM and reduced the reporter expression of the DENV-2 replicon with a 50% effective concentration (EC(50)) of 0.17 ± 0.01 μM. Sequencing analyses of several individual clones derived from BP2109-resistant DENV-2 RNAs revealed that two amino acid substitutions (R55K and E80K) are found in the region of NS2B, a cofactor of the NS2B/NS3 protease complex. The introduction of R55K and E80K double mutations into the dengue virus NS2B/NS3 protease and a dengue virus replicon construct conferred 10.3- and 73.8-fold resistance to BP2109, respectively. The E80K mutation was further determined to be the key mutation conferring dengue virus replicon resistance (61.3-fold) to BP2109, whereas the R55K mutation alone did not affect resistance to BP2109. Both the R55K and E80K mutations are located in the central hydrophilic portion of the NS2B cofactor, where extensive interactions with the NS3pro domain exist. Thus, our data provide evidence that BP2109 likely inhibits DENV by a novel mechanism.
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