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Das N, Roy J, Patra B, Saunders E, Sarkar D, Goon S, Sinha BP, Roy S, Roy S, Sarif J, Bandopadhyay P, Barik S, Mukherjee S, McNamara N, Varghese S, Simpson K, Baell J, McConville M, Ganguly D, Talukdar A. Hit-to-lead optimization of 2-aminoquinazolines as anti-microbial agents against Leishmania donovani. Eur J Med Chem 2024; 269:116256. [PMID: 38461679 DOI: 10.1016/j.ejmech.2024.116256] [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: 11/09/2023] [Revised: 02/06/2024] [Accepted: 02/16/2024] [Indexed: 03/12/2024]
Abstract
Visceral leishmaniasis is a potentially fatal disease caused by infection by the intracellular protist pathogens Leishmania donovani or Leishmania infantum. Present therapies are ineffective because of high costs, variable efficacy against different species, the requirement for hospitalization, toxicity and drug resistance. Detailed analysis of previously published hit molecules suggested a crucial role of 'guanidine' linkage for their efficacy against L. donovani. Here we report the design of 2-aminoquinazoline heterocycle as a basic pharmacophore-bearing guanidine linkage. The introduction of various groups and functionality at different positions of the quinazoline scaffold results in enhanced antiparasitic potency with modest host cell cytotoxicity using a physiologically relevant THP-1 transformed macrophage infection model. In terms of the ADME profile, the C7 position of quinazoline was identified as a guiding tool for designing better molecules. The good ADME profile of the compounds suggests that they merit further consideration as lead compounds for treating visceral leishmaniasis.
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Affiliation(s)
- Nirmal Das
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Jayasree Roy
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India
| | - Binita Patra
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Eleanor Saunders
- Department of Biochemistry and Pharmacology, Bio21 Institute of Molecular Science and Biotechnology (Bio21), University of Melbourne, Parkville, Victoria 3052, Australia
| | - Dipika Sarkar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Sunny Goon
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Bishnu Prasad Sinha
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India
| | - Shreya Roy
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India
| | - Swarnali Roy
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India
| | - Jafar Sarif
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India
| | - Purbita Bandopadhyay
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India
| | - Subhasis Barik
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India
| | - Suravi Mukherjee
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India
| | - Nicole McNamara
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 2052, Australia
| | - Swapna Varghese
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 2052, Australia
| | - Kaylene Simpson
- Victorian Centre for Functional Genomics, Peter MacCallum Cancer Centre, 305 Grattan St, Melbourne, Victoria 3000, Australia
| | - Jonathan Baell
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University (Parkville Campus), 381 Royal Parade, Parkville, Victoria 2052, Australia
| | - Malcolm McConville
- Department of Biochemistry and Pharmacology, Bio21 Institute of Molecular Science and Biotechnology (Bio21), University of Melbourne, Parkville, Victoria 3052, Australia
| | - Dipyaman Ganguly
- IICB-Translational Research Unit of Excellence, Department of Cancer Biology and Inflammatory Disorders, CSIR-Indian Institute of Chemical Biology, CN6, Sector V, Salt Lake, Kolkata 700091, West Bengal, India.
| | - Arindam Talukdar
- Department of Organic and Medicinal Chemistry, CSIR-Indian Institute of Chemical Biology, 4 Raja S. C. Mullick Road, Kolkata 700032, West Bengal, India.
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2
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Serafim MSM, Kronenberger T, Rocha REO, Rosa ADRA, Mello TLG, Poso A, Ferreira RS, Abrahão JS, Kroon EG, Mota BEF, Maltarollo VG. Aminopyrimidine Derivatives as Multiflavivirus Antiviral Compounds Identified from a Consensus Virtual Screening Approach. J Chem Inf Model 2024; 64:393-411. [PMID: 38194508 DOI: 10.1021/acs.jcim.3c01505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2024]
Abstract
Around three billion people are at risk of infection by the dengue virus (DENV) and potentially other flaviviruses. Worldwide outbreaks of DENV, Zika virus (ZIKV), and yellow fever virus (YFV), the lack of antiviral drugs, and limitations on vaccine usage emphasize the need for novel antiviral research. Here, we propose a consensus virtual screening approach to discover potential protease inhibitors (NS3pro) against different flavivirus. We employed an in silico combination of a hologram quantitative structure-activity relationship (HQSAR) model and molecular docking on characterized binding sites followed by molecular dynamics (MD) simulations, which filtered a data set of 7.6 million compounds to 2,775 hits. Lastly, docking and MD simulations selected six final potential NS3pro inhibitors with stable interactions along the simulations. Five compounds had their antiviral activity confirmed against ZIKV, YFV, DENV-2, and DENV-3 (ranging from 4.21 ± 0.14 to 37.51 ± 0.8 μM), displaying aggregator characteristics for enzymatic inhibition against ZIKV NS3pro (ranging from 28 ± 7 to 70 ± 7 μM). Taken together, the compounds identified in this approach may contribute to the design of promising candidates to treat different flavivirus infections.
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Affiliation(s)
- Mateus Sá Magalhães Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Thales Kronenberger
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- Excellence Cluster "Controlling Microbes to Fight Infections" (CMFI), Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
| | - Rafael Eduardo Oliveira Rocha
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Amanda Del Rio Abreu Rosa
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Thaysa Lara Gonçalves Mello
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Antti Poso
- Institute of Pharmacy, Pharmaceutical/Medicinal Chemistry and Tübingen Center for Academic Drug Discovery (TüCAD2), Eberhard Karls University Tübingen, Auf der Morgenstelle 8, Tübingen 72076, Germany
- School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio 70211, Finland
- Department of Medical Oncology and Pneumology, University Hospital of Tübingen, Tübingen 70211, Germany
| | - Rafaela Salgado Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Jonatas Santos Abrahão
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Erna Geessien Kroon
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Bruno Eduardo Fernandes Mota
- Departamento de Análises Clínicas e Toxicológicas, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
| | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG 31270-901, Brazil
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3
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Exertier C, Salerno A, Antonelli L, Fiorillo A, Ocello R, Seghetti F, Caciolla J, Uliassi E, Masetti M, Fiorentino E, Orsini S, Di Muccio T, Ilari A, Bolognesi ML. Fragment Merging, Growing, and Linking Identify New Trypanothione Reductase Inhibitors for Leishmaniasis. J Med Chem 2024; 67:402-419. [PMID: 38164929 PMCID: PMC10788915 DOI: 10.1021/acs.jmedchem.3c01439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/30/2023] [Accepted: 11/27/2023] [Indexed: 01/03/2024]
Abstract
Trypanothione reductase (TR) is a suitable target for drug discovery approaches against leishmaniasis, although the identification of potent inhibitors is still challenging. Herein, we harnessed a fragment-based drug discovery (FBDD) strategy to develop new TR inhibitors. Previous crystallographic screening identified fragments 1-3, which provided ideal starting points for a medicinal chemistry campaign. In silico investigations revealed critical hotspots in the TR binding site, guiding our structure- and ligand-based structure-actvity relationship (SAR) exploration that yielded fragment-derived compounds 4-14. A trend of improvement in Leishmania infantum TR inhibition was detected along the optimization and confirmed by the crystal structures of 9, 10, and 14 in complex with Trypanosoma brucei TR. Compound 10 showed the best TR inhibitory profile (Ki = 0.2 μM), whereas 9 was the best one in terms of in vitro and ex vivo activity. Although further fine-tuning is needed to improve selectivity, we demonstrated the potentiality of FBDD on a classic but difficult target for leishmaniasis.
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Affiliation(s)
- Cécile Exertier
- Institute of Molecular Biology and Pathology (IBPM) of the National Research Council of Italy (CNR), c/o Department of Biochemical Sciences, Sapienza University of Rome, Piazzale A. Moro 5, Roma 00185, Italy
| | - Alessandra Salerno
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum─University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Lorenzo Antonelli
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Piazzale A. Moro 5, Roma 00185, Italy
| | - Annarita Fiorillo
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Piazzale A. Moro 5, Roma 00185, Italy
| | - Riccardo Ocello
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum─University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
- Computational and Chemical Biology, Istituto Italiano di Tecnologia, via Morego 30, Genova 16163, Italy
| | - Francesca Seghetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum─University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Jessica Caciolla
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum─University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Elisa Uliassi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum─University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Matteo Masetti
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum─University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
| | - Eleonora Fiorentino
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, Roma 00161, Italy
| | - Stefania Orsini
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, Roma 00161, Italy
| | - Trentina Di Muccio
- Department of Infectious Diseases, Istituto Superiore di Sanità, Viale Regina Elena 299, Roma 00161, Italy
| | - Andrea Ilari
- Institute of Molecular Biology and Pathology (IBPM) of the National Research Council of Italy (CNR), c/o Department of Biochemical Sciences, Sapienza University of Rome, Piazzale A. Moro 5, Roma 00185, Italy
| | - Maria Laura Bolognesi
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum─University of Bologna, Via Belmeloro 6, Bologna 40126, Italy
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4
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Animal venoms as a source of antiviral peptides active against arboviruses: a systematic review. Arch Virol 2022; 167:1763-1772. [PMID: 35723756 DOI: 10.1007/s00705-022-05494-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 04/04/2022] [Indexed: 11/02/2022]
Abstract
Arthropod-borne viruses (arboviruses), such as Zika virus (ZIKV), chikungunya virus (CHIKV), dengue virus (DENV), yellow fever virus (YFV), and West Nile virus (WNV), are pathogens of global importance. Therefore, there has been an increasing need for new drugs for the treatment of these viral infections. In this context, antimicrobial peptides (AMPs) obtained from animal venoms stand out as promising compounds because they exhibit strong antiviral activity against emerging arboviral pathogens. Thus, we systematically searched and critically analyzed in vitro and in vivo studies that evaluated the anti-arbovirus effect of peptide derivatives from toxins produced by vertebrates and invertebrates. Thirteen studies that evaluated the antiviral action of 10 peptides against arboviruses were included in this review. The peptides were derived from the venom of scorpions, spiders, wasps, snakes, sea snails, and frogs and were tested against DENV, ZIKV, YFV, WNV, and CHIKV. Despite the high structural variety of the peptides included in this study, their antiviral activity appears to be associated with the presence of positive charges, an excess of basic amino acids (mainly lysine), and a high isoelectric point (above 8). These peptides use different antiviral mechanisms, the most common of which is the inhibition of viral replication, release, entry, or fusion. Moreover, peptides with virucidal and cytoprotective (pre-treatment) effects were also identified. In conclusion, animal-venom-derived peptides stand out as a promising alternative in the search and development of prototype antivirals against arboviruses.
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5
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Nunes DADF, Santos FRDS, da Fonseca STD, de Lima WG, Nizer WSDC, Ferreira JMS, de Magalhães JC. NS2B-NS3 protease inhibitors as promising compounds in the development of antivirals against Zika virus: A systematic review. J Med Virol 2021; 94:442-453. [PMID: 34636434 DOI: 10.1002/jmv.27386] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 10/06/2021] [Accepted: 10/10/2021] [Indexed: 01/18/2023]
Abstract
Zika virus (ZIKV) infections are associated with severe neurological complications and are a global public health concern. There are no approved vaccines or antiviral drugs to inhibit ZIKV replication. NS2B-NS3 protease (NS2B-NS3 pro), which is essential for viral replication, is a promising molecular target for anti-ZIKV drugs. We conducted a systematic review to identify compounds with promising effects against ZIKV; we discussed their pharmacodynamic and pharmacophoric characteristics. The online search, performed using the PubMed/MEDLINE and SCOPUS databases, yielded 56 articles; seven relevant studies that reported nine promising compounds with inhibitory activity against ZIKV NS2B-NS3 pro were selected. Of these, five (niclosamide, nitazoxanide, bromocriptine, temoporfin, and novobiocin) are currently available on the market and have been tested for off-label use against ZIKV. The 50% inhibitory concentration values of these compounds for the inhibition of NS2B-NS3 pro ranged at 0.38-21.6 µM; most compounds exhibited noncompetitive inhibition (66%). All compounds that could inhibit the NS2B-NS3 pro complex showed potent in vitro anti-ZIKV activity with a 50% effective concentration ranging 0.024-50 µM. The 50% cytotoxic concentration of the compounds assayed using A549, Vero, and WRL-69 cell lines ranged at 0.6-1388.02 µM and the selectivity index was 3.07-1698. This review summarizes the most promising antiviral agents against ZIKV that have inhibitory activity against viral proteases.
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Affiliation(s)
- Damiana Antônia de Fátima Nunes
- Department of Health Sciences, Laboratory of Medical Microbiology, Campus Centro Oeste Dona Lindu, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brasil
| | - Felipe Rocha da Silva Santos
- Department of Health Sciences, Laboratory of Medical Microbiology, Campus Centro Oeste Dona Lindu, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brasil
| | - Sara Thamires Dias da Fonseca
- Department of Health Sciences, Laboratory of Medical Microbiology, Campus Centro Oeste Dona Lindu, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brasil
| | - William Gustavo de Lima
- Department of Health Sciences, Laboratory of Medical Microbiology, Campus Centro Oeste Dona Lindu, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brasil
| | | | - Jaqueline Maria Siqueira Ferreira
- Department of Health Sciences, Laboratory of Medical Microbiology, Campus Centro Oeste Dona Lindu, Universidade Federal de São João del-Rei, Divinópolis, Minas Gerais, Brasil
| | - José Carlos de Magalhães
- Laboratory of Virology and Cellular Technology, Department of Chemistry, Biotechnology, and Bioprocess Engineering, Universidade Federal de São João del-Rei, Ouro Branco, Minas Gerais, Brasil
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6
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Kronenberger T, Sá Magalhães Serafim M, Kumar Tonduru A, Gonçalves Maltarollo V, Poso A. Ligand Accessibility Insights to the Dengue Virus NS3-NS2B Protease Assessed by Long-Timescale Molecular Dynamics Simulations. ChemMedChem 2021; 16:2524-2534. [PMID: 33899341 PMCID: PMC8453957 DOI: 10.1002/cmdc.202100246] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Indexed: 11/12/2022]
Abstract
Dengue is a tropical disease caused by the dengue virus (DENV), with an estimate of 300 million new cases every year. Due to the limited vaccine efficiency and absence of effective antiviral treatment, new drug candidates are urgently needed. DENV NS3-NS2B protease complex is essential for viral post-translational processing and maturation, and this enzyme has been extensively studied as a relevant drug target. Crystal structures often underestimate NS3-NS2B flexibility, whereas they can adopt different conformational states depending on the bound substrate. We conducted molecular dynamics simulations (∼30 μs) with a non- and covalently bound inhibitor to understand the conformational changes in the DENV-3 NS3-NS2B complex. Our results show that the open-closing movement of the protease exposes multiple druggable subpockets that can be investigated in later drug discovery efforts.
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Affiliation(s)
- Thales Kronenberger
- Department of Medical Oncology and PneumologyUniversity Hospital of TübingenOtfried-Müller-Strasse 1472076TübingenGermany
- School of PharmacyUniversity of Eastern FinlandKuopio70211Finland
| | - Mateus Sá Magalhães Serafim
- Departamento de MicrobiologiaUniversidade Federal de Minas Gerais (UFMG)Av. Antônio Carlos, 6627PampulhaCEP 31270-901Belo HorizonteBrazil
| | | | - Vinícius Gonçalves Maltarollo
- Departamento de Produtos FarmacêuticosUniversidade Federal de Minas Gerais (UFMG)Av. Antônio Carlos, 6627PampulhaCEP 31270-901Belo HorizonteBrazil
| | - Antti Poso
- Department of Medical Oncology and PneumologyUniversity Hospital of TübingenOtfried-Müller-Strasse 1472076TübingenGermany
- School of PharmacyUniversity of Eastern FinlandKuopio70211Finland
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7
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Kumar N, Sarma H, Sastry GN. Repurposing of approved drug molecules for viral infectious diseases: a molecular modelling approach. J Biomol Struct Dyn 2021; 40:8056-8072. [PMID: 33810775 DOI: 10.1080/07391102.2021.1905558] [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] [Indexed: 12/23/2022]
Abstract
The identification of new viral drugs has become a task of paramount significance due to the frequent occurrence of viral infections and especially during the current pandemic. Despite the recent advancements, the development of antiviral drugs has not made parallel progress. Reduction of time frame and cost of the drug development process is the major advantage of drug repurposing. Therefore, in this study, a drug repurposing strategy using molecular modelling techniques, i.e. biological activity prediction, virtual screening, and molecular dynamics simulation was employed to find promising repurposing candidates for viral infectious diseases. The biological activities of non-redundant (4171) drug molecules were predicted using PASS analysis, and 1401 drug molecules were selected which showed antiviral activities in the analysis. These drug molecules were subjected to virtual screening against the selected non-structural viral proteins. A series of filters, i.e. top 10 drug molecules based on binding affinity, mean value of binding affinity, visual inspection of protein-drug complexes, and number of H-bond between protein and drug molecules were used to narrow down the drug molecules. Molecular dynamics simulation analysis was carried out to validate the intrinsic atomic interactions and binding conformations of protein-drug complexes. The binding free energies of drug molecules were assessed by employing MMPBSA analysis. Finally, nine drug molecules were prioritized, as promising repurposing candidates with the potential to inhibit the selected non-structural viral proteins.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Nandan Kumar
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Hyderabad, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Himakshi Sarma
- Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, India
| | - G Narahari Sastry
- Centre for Molecular Modelling, CSIR-Indian Institute of Chemical Technology, Hyderabad, India.,Advanced Computation and Data Sciences Division, CSIR-North East Institute of Science and Technology, Jorhat, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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8
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Hamdani SS, Khan BA, Hameed S, Batool F, Saleem HN, Mughal EU, Saeed M. Synthesis and evaluation of novel S-benzyl- and S-alkylphthalimide- oxadiazole -benzenesulfonamide hybrids as inhibitors of dengue virus protease. Bioorg Chem 2020; 96:103567. [PMID: 32062063 DOI: 10.1016/j.bioorg.2020.103567] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 01/01/2020] [Accepted: 01/02/2020] [Indexed: 12/18/2022]
Abstract
Direct acting antiviral drugs (DAADs) are becoming therapeutics of choice for the treatment of viral infections. Successful development of anti HIV and HCV drugs by targeting the viral proteases has provided impetus for discovering newer DAADs. Dengue virus (DENV) protease, which is composed of two nonstructural proteins, NS2B and NS3pro, can be likewise exploited for discovering new anti-dengue therapeutics. In this study, we have linked together two pharmaceutically interesting motifs, namely 1,3,4-oxadiazole and benzenesulfonamide in two alternative series to develop novel S-benzylated and S-alkylphthalimidated hybrids. For the first series of hybrids, 4-aminobenzoic acid (1) was reacted with substituted benzenesulfonyl chlorides via its amino group, whereas the carboxylic acid side was elaborated to sulfonamido-1,3,4-oxadiazole-2-thiols (6a/b) in three steps. At this stage, the intermediates 6a/b were bifurcated to either S-alkylphthalimidated (8a-j) or S-benzylated (9a-c) hybrids by reacting with corresponding halides. For the alternative series of hybrids, the carboxylic acid group of probenecid (10) was similarly elaborated to sulfonamido-1,3,4-oxadiazole-2-thiols (13), and diverged to S-alkylphthalimidated (14a-f) and S-benzylated hybrids (15a-e). Bioactivity assays demonstrated that 8g and 8h are the most potent inhibitors among the synthesized analogs, exhibiting the IC50 values of 13.9 μM and 15.1 μM, respectively. Computational assessment predicted the binding of the inhibitors at an allosteric site developed in the open conformation of DENV2 NS2B/NS3pro. Taken together these findings point out that the synthesized hybrid inhibitors possess a great potential for further antiviral drug development.
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Affiliation(s)
- Syeda Shamila Hamdani
- Department of Chemistry, University of Azad Jammu and Kashmir, Muzaffarabad 13100 AJK, Pakistan; Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Bilal Ahmad Khan
- Department of Chemistry, University of Azad Jammu and Kashmir, Muzaffarabad 13100 AJK, Pakistan.
| | - Shahid Hameed
- Department of Chemistry, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Farwa Batool
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore 54792 Pakistan
| | - Hafiza Nosheen Saleem
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore 54792 Pakistan
| | | | - Muhammad Saeed
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore 54792 Pakistan.
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9
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Santos FRS, Lima WG, Maia EHB, Assis LC, Davyt D, Taranto AG, Ferreira JMS. Identification of a Potential Zika Virus Inhibitor Targeting NS5 Methyltransferase Using Virtual Screening and Molecular Dynamics Simulations. J Chem Inf Model 2020; 60:562-568. [PMID: 31985225 DOI: 10.1021/acs.jcim.9b00809] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The NS5 methyltransferase (MTase) has been reported as an attractive molecular target for antivirals discovery against the Zika virus (ZIKV). Here, we report structure-based virtual screening of 42 390 structures from the Development Therapeutics Program (DTP) AIDS Antiviral Screen Database. Among the docked compounds, ZINC1652386 stood out due to its high affinity for MTase in comparison to the cocrystallized ligand MS2042, which interacts with the Asp146 residue in the MTase binding site by hydrogen bonding. Subsequent molecular dynamics simulations predicted that this compound forms a stable complex with MTase within 50 ns. Thus, ZINC1652386 may represent a promising ZIKV methyltransferase inhibitor.
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Affiliation(s)
- Felipe R S Santos
- Laboratório de Microbiologia Médica , Universidade Federal de São João Del-Rei , Divinópolis , Minas Gerais , Brasil
| | - William G Lima
- Departamento de Produtos Farmacêuticos, Faculdade de Farmácia , Universidade Federal de Minas Gerais , Belo Horizonte , Minas Gerais , Brasil
| | - Eduardo H B Maia
- Laboratório de Quı́mica Farmacêutica Medicinal , Universidade Federal de São João Del-Rei , Minas Gerais , Divinópolis , Brasil
| | - Letícia C Assis
- Laboratório de Quı́mica Farmacêutica Medicinal , Universidade Federal de São João Del-Rei , Minas Gerais , Divinópolis , Brasil
| | - Danilo Davyt
- Departamento de Quı́mica Orgánica , Universidad de la República , Montevideo , Uruguay
| | - Alex Gutterres Taranto
- Laboratório de Quı́mica Farmacêutica Medicinal , Universidade Federal de São João Del-Rei , Minas Gerais , Divinópolis , Brasil
| | - Jaqueline M S Ferreira
- Laboratório de Microbiologia Médica , Universidade Federal de São João Del-Rei , Divinópolis , Minas Gerais , Brasil
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10
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Dos Santos M, Teixeira TR, Santos FRDS, Lima WG, Ferraz AC, Silva NL, Leite FJ, Siqueira JM, Luyten W, de Castro AHF, de Magalhães JC, Ferreira JMS. Bauhinia holophylla (Bong.) Steud. leaves-derived extracts as potent anti-dengue serotype 2. Nat Prod Res 2019; 35:2804-2809. [PMID: 31554433 DOI: 10.1080/14786419.2019.1669030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dengue virus (DENV) is the most prevalent mosquito-borne viral pathogen and made the disease a major health concern worldwide. However, specific antiviral drugs against this arbovirose or vaccines are not yet available for treatment or prevention. Thus, here we aimed to study the antiviral activity of hydroethanolic extract, fraction ethyl acetate and subfractions of the leaves of Bauhinia holophylla (Fabaceae:Cercideae), a native plant of the Brazilian Cerrado, against DENV-2 by methylthiazolyldiphenyl-tetrazolium bromide (MTT) method in mammalian cells culture. As results, the hydroethanolic extract showed the most potent effect, with an inhibitory concentration (IC50) of 3.2 μg mL-1 and selectivity index (SI) of 27.6, approximately 16-times higher anti-DENV-2 activity than of the ribavirin (IC50 52.8 μg mL-1). Our results showed in this study appointed that B. holophylla has a promising anti-dengue activity, which was associated mainly with the presence of flavonoids.
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Affiliation(s)
- Michelli Dos Santos
- Laboratório de Microbiologia Médica, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - Thaiz Rodrigues Teixeira
- Laboratório de Química Orgânica do Ambiente Marinho. Departamento de Física e Química da Faculdade de Ciências Farmacêuticas, Universidade de São Paulo, Ribeirão Preto, Brazil
| | | | - William Gustavo Lima
- Laboratório de Radioisótopos, Departamento de Produtos Farmacêuticos, Faculdade de Farmácia, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ariane Coelho Ferraz
- Laboratório de Microbiologia Médica, Universidade Federal de São João del-Rei, Divinópolis, Brazil.,Laboratório de Biologia Molecular e Celular, Departamento de Química, Biotecnologia e Engenharia de Bioprocessos, Universidade Federal de São João del-Rei, Ouro Branco, Brazil
| | - Nathália Lucca Silva
- Laboratório de Química de Produtos Naturais, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - Flávio José Leite
- Laboratório de Química de Produtos Naturais, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | - João Máximo Siqueira
- Laboratório de Química de Produtos Naturais, Universidade Federal de São João del-Rei, Divinópolis, Brazil
| | | | | | - José Carlos de Magalhães
- Laboratório de Biologia Molecular e Celular, Departamento de Química, Biotecnologia e Engenharia de Bioprocessos, Universidade Federal de São João del-Rei, Ouro Branco, Brazil
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11
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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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Gopala Reddy SB, Chin WX, Shivananju NS. Dengue virus NS2 and NS4: Minor proteins, mammoth roles. Biochem Pharmacol 2018; 154:54-63. [PMID: 29674002 DOI: 10.1016/j.bcp.2018.04.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2018] [Accepted: 04/10/2018] [Indexed: 12/11/2022]
Abstract
Despite the ever-increasing global incidence of dengue fever, there are no specific chemotherapy regimens for its treatment. Structural studies on dengue virus (DENV) proteins have revealed potential drug targets. Major DENV proteins such as the envelope protein and non-structural (NS) proteins 3 and 5 have been extensively investigated in antiviral studies, but with limited success in vitro. However, the minor NS proteins NS2 and NS4 have remained relatively underreported. Emerging evidence indicating their indispensable roles in virus propagation and host immunomodulation should encourage us to target these proteins for drug discovery. This review covers current knowledge on DENV NS2 and NS4 proteins from structural and functional perspectives and assesses their potential as targets for antiviral design. Antiviral targets in NS2A include surface-exposed transmembrane regions involved in pathogenesis, while those in NS2B include protease-binding sites in a conserved hydrophilic domain. Ideal drug targets in NS4A include helix α4 and the PEPEKQR sequence, which are essential for NS4A-2K cleavage and NS4A-NS4B association, respectively. In NS4B, the cytoplasmic loop connecting helices α5 and α7 is an attractive target for antiviral design owing to its role in dimerization and NS4B-NS3 interaction. Findings implicating NS2A, NS2B, and NS4A in membrane-modulation and viroporin-like activities indicate an opportunity to target these proteins by disrupting their association with membrane lipids. Despite the lack of 3D structural data, recent topological findings and progress in structure-prediction methods should be sufficient impetus for targeting NS2 and NS4 for drug design.
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Affiliation(s)
- Sindhoora Bhargavi Gopala Reddy
- Department of Biotechnology, Sri Jayachamarajendra College of Engineering, JSS Science and Technology University, JSS TEI Campus, Mysuru 57006, Karnataka, India
| | - Wei-Xin Chin
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117597, Singapore
| | - Nanjunda Swamy Shivananju
- Department of Biotechnology, Sri Jayachamarajendra College of Engineering, JSS Science and Technology University, JSS TEI Campus, Mysuru 57006, Karnataka, India.
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