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Nagavarapu S, Kumar J, Biswal PK. Molecular docking based comparative study of antiviral compounds on SARS-CoV-2 spike protein. Nat Prod Res 2024:1-9. [PMID: 38759218 DOI: 10.1080/14786419.2024.2355589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Accepted: 05/09/2024] [Indexed: 05/19/2024]
Abstract
The urgent need for effective therapeutic interventions against SARS-CoV-2 has prompted extensive exploration of potential drug candidates. Among the viral proteins, the spike (S) protein presents an attractive target due to its critical role in viral entry and infection. In this study, we employed molecular docking techniques to investigate the binding affinities and interaction profiles of a panel of active compounds against the SARS-CoV-2 spike protein. Utilising computational simulations, we assessed the binding properties of these compounds within the receptor-binding domain (RBD) and other key regions of the spike protein. Our comparative analysis elucidates the differential binding patterns and identifies promising lead compounds with high binding affinity and favourable interaction profiles. Furthermore, we discuss the implications of these findings for the development of potential therapeutics targeting the SARS-CoV-2 spike protein. Using molecular docking and the Lipinski five rule, this study illustrates possible compounds with strong binding affinities, their molecular interactions, for both naturally occurring and man-made drugs. Computational approach is applied, and it is concluded that, drugs like Withanolide, Dihydroergocristine, Fenebrutinib, and Ergotamine shows binding energies between -8.3 and -9.1 kcal/mol, and are possible candidate for anti covid drug.
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Affiliation(s)
- Sowmya Nagavarapu
- Department of Electronics and Communication Engineering, GIET University Gunupur, Odisha, India
| | - Jitendra Kumar
- Department of Electronics and Communication Engineering, GIET University Gunupur, Odisha, India
| | - Pradyut K Biswal
- Department of Electronics and Communication Engineering, IIIT Bhubaneswar, Odisha, India
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Niaei N, Hassanpour S, Petr J. Chiral resolution of cationic piperazine derivatives by capillary electrophoresis using sulfated β-cyclodextrin. Electrophoresis 2024. [PMID: 38576224 DOI: 10.1002/elps.202300271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/06/2024]
Abstract
This research focuses on the development and validation of a capillary electrophoresis (CE) method for the chiral separation of three H1-antihistamine drugs chlorcyclizine, norchlorcyclizine, and neobenodine using sulfated β-cyclodextrin (S-β-CD) as the chiral selector. The study explores various factors influencing the separation efficiency, including CD concentration, organic modifier content, voltage application, and buffer pH. Optimal conditions were identified as a 100 mM phosphate buffer (pH 6.0) with 34 mg mL-1 S-β-CD and 40% (v/v) methanol. The method demonstrated excellent linearity in calibration curves, with coefficients of determination exceeding 0.99 for each enantiomer. Precision studies revealed good intra- and inter-day precision for migration times and peak areas. The limits of detection and quantification for the analytes were within the ranges of 5.9-11.4 and 18-34.6 µmol L-1, respectively. Overall, the developed CE method offers a robust and precise approach for the chiral separation of H1-antihistamine drugs, holding promise for pharmaceutical applications.
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Affiliation(s)
- Navid Niaei
- Department of Analytical Chemistry, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Soodabeh Hassanpour
- Department of Analytical Chemistry, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jan Petr
- Department of Analytical Chemistry, Faculty of Science, Palacký University Olomouc, Olomouc, Czech Republic
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3
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Mushtaq M, Naz S, Ashraf S, Doerksen RJ, Nur-e-Alam M, Ul-Haq Z. Exploring the viral protease inhibitor space driven by consensus scoring-based virtual screening. In Silico Pharmacol 2023; 12:2. [PMID: 38050479 PMCID: PMC10693542 DOI: 10.1007/s40203-023-00174-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 10/26/2023] [Indexed: 12/06/2023] Open
Abstract
Dengue fever presents a major health concern, and the lack of an effective vaccine or definite therapeutic regimen has led the research community to identify safe-by-design potential targets for drug discovery. Since the association of the NS2B co-factor with the protease domain of NS3 is imperative for the catalytic activity of the enzyme complex, inhibitors blocking their interaction could provide an alternative strategy to combat the dengue virus. In this context, the present study is aimed at exploring computer-assisted modeling of significant physicochemical features required for the inhibition of the dengue virus protease complex. First of all, alanine scanning was utilized to map hot spot residues critical for the association of the two subunits, NS2B and NS3pro, by studying their energy profiles. Then, consensus score-based virtual screening was performed to search through the commercially available chemical datasets. After screening, 1,575 small molecules were moved forward into docking studies to investigate their interactions with crucial interfacial residues (i.e., Tyr23, Lys26, Phe46, and Leu58), with only 233 molecules passing that stage. The top 30 molecules were selected based on a detailed profile of intermolecular interactions. After that, the top five molecules were selected for detailed mechanistic studies via molecular dynamics simulations followed by subsequent binding free energy calculations, principal component analysis in conjunction with free energy landscape. To the best of our knowledge, this is the first systematic and comprehensive investigation to identify protein-protein interaction blockers against the target protein at such a large scale, using integrated computational tools. Our results highlight the enhanced stability and good binding affinities towards the target protein of these compounds, which might act as new scaffolds for NS2B-NS3 protease inhibition. Future studies will be directed to explore the detailed atomistic-based structural and energetic framework of the mutation-induced affinity change between the protease domain of the DENV-2 NS3 protein and its cofactor NS2B. The detailed insight in turn might suggest precise and focused targeted points for the structure-based drug design but the computational cost may be a challenge. Graphical abstract Supplementary Information The online version contains supplementary material available at 10.1007/s40203-023-00174-0.
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Affiliation(s)
- Mamona Mushtaq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Sehrish Naz
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Sajda Ashraf
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
| | - Robert J. Doerksen
- Department of BioMolecular Sciences, University of Mississippi, Oxford, MS 38677 USA
| | - Mohammad Nur-e-Alam
- Department of Pharmacognosy, College of Pharmacy, King Saud University, 11451 Riyadh, Saudi Arabia
| | - Zaheer Ul-Haq
- Dr. Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270 Pakistan
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Pant S, Jena NR. Repurposing of antiparasitic drugs against the NS2B-NS3 protease of the Zika virus. J Biomol Struct Dyn 2023:1-13. [PMID: 37747074 DOI: 10.1080/07391102.2023.2255648] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 08/28/2023] [Indexed: 09/26/2023]
Abstract
To date, no approved drugs are available to treat the Zika virus (ZIKV) infection. Therefore, it is necessary to urgently identify potential drugs against the ZIKV infection. Here, the repurposing of 30 antiparasitic drugs against the NS2B-NS3 protease of the ZIKV has been carried out by using combined docking and molecular dynamics- (MD) simulations. Based on the docking results, 5 drugs, such as Amodiaquine, Primaquine, Paromomycin, Dichlorophene, and Ivermectin were screened for further analysis by MD simulations and free energy calculations. Among these drugs, Amodiaquine and Dichlorophen are found to produce the most stable complexes and possess relative binding free energies of about -44.3 ± 3.7 kcal/mol and -41.1 ± 5.3 kcal/mol respectively. Therefore, they would act as potent small-molecule inhibitors of the ZIKV protease.However, evaluations of biological and safety activities of these drugs against the ZIKV protease are required before their clinical use.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- S Pant
- Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - N R Jena
- Discipline of Natural Sciences, Indian Institute of Information Technology, Design and Manufacturing, Jabalpur, India
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Santos LH, Rocha REO, Dias DL, Ribeiro BMRM, Serafim MSM, Abrahão JS, Ferreira RS. Evaluating Known Zika Virus NS2B-NS3 Protease Inhibitor Scaffolds via In Silico Screening and Biochemical Assays. Pharmaceuticals (Basel) 2023; 16:1319. [PMID: 37765127 PMCID: PMC10537087 DOI: 10.3390/ph16091319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/04/2023] [Accepted: 09/11/2023] [Indexed: 09/29/2023] Open
Abstract
The NS2B-NS3 protease (NS2B-NS3pro) is regarded as an interesting molecular target for drug design, discovery, and development because of its essential role in the Zika virus (ZIKV) cycle. Although no NS2B-NS3pro inhibitors have reached clinical trials, the employment of drug-like scaffolds can facilitate the screening process for new compounds. In this study, we performed a combination of ligand-based and structure-based in silico methods targeting two known non-peptide small-molecule scaffolds with micromolar inhibitory activity against ZIKV NS2B-NS3pro by a virtual screening (VS) of promising compounds. Based on these two scaffolds, we selected 13 compounds from an initial library of 509 compounds from ZINC15's similarity search. These compounds exhibited structural modifications that are distinct from previously known compounds yet keep pertinent features for binding. Despite promising outcomes from molecular docking and initial enzymatic assays against NS2B-NS3pro, confirmatory assays with a counter-screening enzyme revealed an artifactual inhibition of the assessed compounds. However, we report two compounds, 9 and 11, that exhibited antiviral properties at a concentration of 50 μM in cellular-based assays. Overall, this study provides valuable insights into the ongoing research on anti-ZIKV compounds to facilitate and improve the development of new inhibitors.
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Affiliation(s)
- Lucianna H. Santos
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Rafael E. O. Rocha
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Diego L. Dias
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil (M.S.M.S.)
| | - Beatriz M. R. M. Ribeiro
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
| | - Mateus Sá M. Serafim
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil (M.S.M.S.)
| | - Jônatas S. Abrahão
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil (M.S.M.S.)
| | - Rafaela S. Ferreira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte 31270-901, Brazil
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Structural Insights into Plasticity and Discovery of Flavonoid Allosteric Inhibitors of Flavivirus NS2B–NS3 Protease. BIOPHYSICA 2023. [DOI: 10.3390/biophysica3010006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Flaviviruses are among the most critical pathogens in tropical regions; they cause various severe diseases in developing countries but are not restricted to these countries. The development of antiviral therapeutics is crucial for managing flavivirus outbreaks. Ten proteins are encoded in the flavivirus RNA. The N2B–NS3pro protein complex plays a fundamental role in flavivirus replication and is a promising drug target; however, no flavivirus protease inhibitors have progressed to the preclinical stage. This study analyzed the structural models and plasticity of the NS2B–NS3pro protein complex of five medically important non-dengue flaviviruses (West Nile, Rocio, Ilhéus, yellow fever, and Saint Louis encephalitis). The flavonoids amentoflavone, tetrahydrorobustaflavone, and quercetin were selected for their exceptional binding energies as potential inhibitors of the NS2B–NS3pro protein complex. AutoDock Vina results ranged from −7.0 kcal/mol to −11.5 kcal/mol and the compounds preferentially acted non-competitively. Additionally, the first structural model for the NS2B–NS3pro protein complex was proposed for Ilhéus and Rocio viruses. The NS2B–NS3pro protease is an attractive molecular target for drug development. The three identified natural flavonoids showed great inhibitory potential against the viral species. Nevertheless, further in silico and in vitro studies are required to obtain more information regarding NS2B–NS3pro inhibition by these flavonoids and their therapeutic potential.
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Kandagalla S, Novak J, Shekarappa SB, Grishina MA, Potemkin VA, Kumbar B. Exploring potential inhibitors against Kyasanur forest disease by utilizing molecular dynamics simulations and ensemble docking. J Biomol Struct Dyn 2022; 40:13547-13563. [PMID: 34662258 DOI: 10.1080/07391102.2021.1990131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Kyasanur forest disease (KFD) is a tick-borne, neglected tropical disease, caused by KFD virus (KFDV) which belongs to Flavivirus (Flaviviridae family). This emerging viral disease is a major threat to humans. Currently, vaccination is the only controlling method against the KFDV, and its effectiveness is very low. An effective control strategy is required to combat this emerging tropical disease using the existing resources. In this regard, in silico drug repurposing method offers an effective strategy to find suitable antiviral drugs against KFDV proteins. Drug repurposing is an effective strategy to identify new use for approved or investigational drugs that are outside the scope of their initial usage and the repurposed drugs have lower risk and higher safety compared to de novo developed drugs, because their toxicity and safety issues are profoundly investigated during the preclinical trials in human/other models. In the present work, we evaluated the effectiveness of the FDA approved and natural compounds against KFDV proteins using in silico molecular docking and molecular simulations. At present, no experimentally solved 3D structures for the KFD viral proteins are available in Protein Data Bank and hence their homology model was developed and used for the analysis. The present analysis successfully developed the reliable homology model of NS3 of KFDV, in terms of geometry and energy contour. Further, in silico molecular docking and molecular dynamics simulations successfully presented four FDA approved drugs and one natural compound against the NS3 homology model of KFDV. Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shivananda Kandagalla
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Jurica Novak
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Sharath Belenahalli Shekarappa
- Department of PG Studies and Research in Biotechnology and Bioinformatics, Kuvempu University, Shivamogga, Karnataka, India
| | - Maria A Grishina
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Vladimir A Potemkin
- Laboratory of Computational Modeling of Drugs, Higher Medical and Biological School, South Ural State University, Chelyabinsk, Russia
| | - Bhimanagoud Kumbar
- Department of PG Studies and Research in Biotechnology and Bioinformatics, Kuvempu University, Shivamogga, Karnataka, India.,ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
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Thirumoorthy G, Tarachand SP, Nagella P, Veerappa Lakshmaiah V. Identification of potential ZIKV NS2B-NS3 protease inhibitors from Andrographis paniculata: An insilico approach. J Biomol Struct Dyn 2022; 40:11203-11215. [PMID: 34319220 DOI: 10.1080/07391102.2021.1956592] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Andrographis paniculata is a widely used medicinal plant for treating a variety of human infections. The plant's bioactives have been shown to have a variety of biological activities in various studies, including potential antiviral, anticancer, and anti-inflammatory effects in a variety of experimental models. The present investigation identifies a potent antiviral compound from the phytochemicals of Andrographis paniculata against Zika virus using computational docking simulation. The ZIKV NS2B-NS3 protease, which is involved in viral replication, has been considered as a promising target for Zika virus drug development. The bioactives from Andrographis paniculata, along with standard drugs as control were screened for their binding energy using AutoDock 4.2 against the viral protein. Based on the higher binding affinity the phytocompounds Bisandrographolide A (-11.7), Andrographolide (-10.2) and Andrographiside (-9.7) have convenient interactions at the binding site of target protein (ZIKV NS2B-NS3 protease) in comparison with the control drug. In addition, using insilico tools, the selected high-scoring molecules were analysed for pharmacological properties such as ADME (Absorption, Distribution, Metabolism, and Excretion profile) and toxicity. Andrographolide was reported to have strong pharmacodynamics properties and target accuracy based on the Lipinski rule and lower binding energy. The selected bioactives showed lower AMES toxicity and has potent antiviral activity against zika virus targets. Further, MD simulation studies validated Bisandrographolide A & Andrographolide as a potential hit compound by exhibiting good binding with the target protein. The compounds exhibited good hydrogen bonds with ZIKV NS2B-NS3 protease. As a result, bioactives from the medicinal plant Andrographis paniculata can be studied in vitro and in vivo to develop an antiviral phytopharmaceutical for the successful treatment of zika virus.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Sharma Pooja Tarachand
- Department of Life Sciences, CHRIST (Deemed to be University), Bengaluru, Karnataka, India
| | - Praveen Nagella
- Department of Life Sciences, CHRIST (Deemed to be University), Bengaluru, Karnataka, India
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Dos Santos Nascimento IJ, da Silva Rodrigues ÉE, da Silva MF, de Araújo-Júnior JX, de Moura RO. Advances in Computational Methods to Discover New NS2B-NS3 Inhibitors Useful Against Dengue and Zika Viruses. Curr Top Med Chem 2022; 22:2435-2462. [PMID: 36415099 DOI: 10.2174/1568026623666221122121330] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/20/2022] [Accepted: 09/27/2022] [Indexed: 11/24/2022]
Abstract
The Flaviviridae virus family consists of the genera Hepacivirus, Pestivirus, and Flavivirus, with approximately 70 viral types that use arthropods as vectors. Among these diseases, dengue (DENV) and zika virus (ZIKV) serotypes stand out, responsible for thousands of deaths worldwide. Due to the significant increase in cases, the World Health Organization (WHO) declared DENV a potential threat for 2019 due to being transmitted by infected travelers. Furthermore, ZIKV also has a high rate of transmissibility, highlighted in the outbreak in 2015, generating consequences such as Guillain-Barré syndrome and microcephaly. According to clinical outcomes, those infected with DENV can be asymptomatic, and in other cases, it can be lethal. On the other hand, ZIKV has severe neurological symptoms in newborn babies and adults. More serious symptoms include microcephaly, brain calcifications, intrauterine growth restriction, and fetal death. Despite these worrying data, no drug or vaccine is approved to treat these diseases. In the drug discovery process, one of the targets explored against these diseases is the NS2B-NS3 complex, which presents the catalytic triad His51, Asp75, and Ser135, with the function of cleaving polyproteins, with specificity for basic amino acid residues, Lys- Arg, Arg-Arg, Arg-Lys or Gln-Arg. Since NS3 is highly conserved in all DENV serotypes and plays a vital role in viral replication, this complex is an excellent drug target. In recent years, computer-aided drug discovery (CADD) is increasingly essential in drug discovery campaigns, making the process faster and more cost-effective, mainly explained by discovering new drugs against DENV and ZIKV. Finally, the main advances in computational methods applied to discover new compounds against these diseases will be presented here. In fact, molecular dynamics simulations and virtual screening is the most explored approach, providing several hit and lead compounds that can be used in further optimizations. In addition, fragment-based drug design and quantum chemistry/molecular mechanics (QM/MM) provides new insights for developing anti-DENV/ZIKV drugs. We hope that this review offers further helpful information for researchers worldwide and stimulates the use of computational methods to find a promising drug for treating DENV and ZIKV.
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Affiliation(s)
- Igor José Dos Santos Nascimento
- Department of Pharmacy, Estácio of Alagoas College, Maceió, Brazil.,Department of Pharmacy, Cesmac University Center, Maceió, Brazil.,Department of Pharmacy, Drug Development and Synthesis Laboratory, State University of Paraíba, Campina Grande, Brazil
| | | | - Manuele Figueiredo da Silva
- Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió, Brazil
| | - João Xavier de Araújo-Júnior
- Laboratory of Medicinal Chemistry, Pharmaceutical Sciences Institute, Federal University of Alagoas, Maceió, Brazil
| | - Ricardo Olimpio de Moura
- Department of Pharmacy, Drug Development and Synthesis Laboratory, State University of Paraíba, Campina Grande, Brazil
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Rational designing of peptide-ligand conjugates-based immunotherapy for the treatment of complicated malaria. Life Sci 2022; 311:121121. [DOI: 10.1016/j.lfs.2022.121121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 10/19/2022] [Accepted: 10/20/2022] [Indexed: 11/05/2022]
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Liu J, Zhang L, Gao J, Zhang B, Liu X, Yang N, Liu X, Liu X, Cheng Y. Discovery of genistein derivatives as potential SARS-CoV-2 main protease inhibitors by virtual screening, molecular dynamics simulations and ADMET analysis. Front Pharmacol 2022; 13:961154. [PMID: 36091808 PMCID: PMC9452787 DOI: 10.3389/fphar.2022.961154] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 08/03/2022] [Indexed: 11/13/2022] Open
Abstract
Background: Due to the constant mutation of virus and the lack of specific therapeutic drugs, the coronavirus disease 2019 (COVID-19) pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) still poses a huge threat to the health of people, especially those with underlying diseases. Therefore, drug discovery against the SARS-CoV-2 remains of great significance. Methods: With the main protease of virus as the inhibitor target, 9,614 genistein derivatives were virtually screened by LeDock and AutoDock Vina, and the top 20 compounds with highest normalized scores were obtained. Molecular dynamics simulations were carried out for studying interactions between these 20 compounds and the target protein. The drug-like properties, activity, and ADMET of these compounds were also evaluated by DruLiTo software or online server. Results: Twenty compounds, including compound 11, were screened by normalized molecular docking, which could bind to the target through multiple non-bonding interactions. Molecular dynamics simulation results showed that compounds 2, 4, 5, 11, 13, 14, 17, and 18 had the best binding force with the target protein of SARS-CoV-2, and the absolute values of binding free energies all exceeded 50 kJ/mol. The drug-likeness properties indicated that a variety of compounds including compound 11 were worthy of further study. The results of bioactivity score prediction found that compounds 11 and 12 had high inhibitory activities against protease, which indicated that these two compounds had the potential to be further developed as COVID-19 inhibitors. Finally, compound 11 showed excellent predictive ADMET properties including high absorption and low toxicity. Conclusion: These in silico work results show that the preferred compound 11 (ZINC000111282222), which exhibited strong binding to SARS-CoV-2 main protease, acceptable drug-like properties, protease inhibitory activity and ADMET properties, has great promise for further research as a potential therapeutic agent against COVID-19.
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Affiliation(s)
- Jiawei Liu
- Center for Drug Innovation and Discovery, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Ling Zhang
- School of Chemical Technology, Shijiazhuang University, Shijiazhuang, China
| | - Jian Gao
- College of Plant Protection, Southwest University, Chongqing, China
| | - Baochen Zhang
- Center for Drug Innovation and Discovery, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Xiaoli Liu
- Center for Drug Innovation and Discovery, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Ninghui Yang
- Center for Drug Innovation and Discovery, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Xiaotong Liu
- Center for Drug Innovation and Discovery, College of Life Science, Hebei Normal University, Shijiazhuang, China
| | - Xifu Liu
- Center for Drug Innovation and Discovery, College of Life Science, Hebei Normal University, Shijiazhuang, China
- *Correspondence: Xifu Liu, ; Yu Cheng,
| | - Yu Cheng
- Center for Drug Innovation and Discovery, College of Life Science, Hebei Normal University, Shijiazhuang, China
- *Correspondence: Xifu Liu, ; Yu Cheng,
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12
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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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Mirza MU, Alanko I, Vanmeert M, Muzzarelli KM, Salo-Ahen OMH, Abdullah I, Kovari IA, Claes S, De Jonghe S, Schols D, Schinazi RF, Kovari LC, Trant JF, Ahmad S, Froeyen M. The discovery of Zika virus NS2B-NS3 inhibitors with antiviral activity via an integrated virtual screening approach. Eur J Pharm Sci 2022; 175:106220. [PMID: 35618201 DOI: 10.1016/j.ejps.2022.106220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 05/18/2022] [Accepted: 05/23/2022] [Indexed: 11/15/2022]
Abstract
With expanding recent outbreaks and a lack of treatment options, the Zika virus (ZIKV) poses a severe health concern. The availability of ZIKV NS2B-NS3 co-crystallized structures paved the way for rational drug discovery. A computer-aided structure-based approach was used to screen a diverse library of compounds against ZIKV NS2B-NS3 protease. The top hits were selected based on various binding free energy calculations followed by per-residue decomposition analysis. The selected hits were then evaluated for their biological potential with ZIKV protease inhibition assay and antiviral activity. Among 26 selected compounds, 8 compounds showed promising activity against ZIKV protease with a percentage inhibition of greater than 25 and 3 compounds displayed ∼50% at 10 µM, which indicates an enrichment rate of approximately 36% (threshold IC50 < 10 µM) in the ZIKV-NS2B-NS3 protease inhibition assay. Of these, only one compound (23) produced whole-cell anti-ZIKV activity, and the binding mode of 23 was extensively analyzed through long-run molecular dynamics simulations. The current study provides a promising starting point for the further development of novel compounds against ZIKV.
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Affiliation(s)
- Muhammad Usman Mirza
- KU Leuven, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, Medicinal Chemistry, Herestraat 49, box 1041, Leuven 3000, Belgium; Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, ON, Canada
| | - Ida Alanko
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Michiel Vanmeert
- KU Leuven, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, Medicinal Chemistry, Herestraat 49, box 1041, Leuven 3000, Belgium
| | - Kendall M Muzzarelli
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit 48201, MI, USA
| | - Outi M H Salo-Ahen
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Iskandar Abdullah
- Drug Design Development Research Group, Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Iulia A Kovari
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit 48201, MI, USA
| | - Sandra Claes
- KU Leuven, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Herestraat 49, box 1043, Leuven, Belgium
| | - Steven De Jonghe
- KU Leuven, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Herestraat 49, box 1043, Leuven, Belgium
| | - Dominique Schols
- KU Leuven, Rega Institute for Medical Research, Department of Microbiology, Immunology and Transplantation, Laboratory of Virology and Chemotherapy, Herestraat 49, box 1043, Leuven, Belgium
| | - Raymond F Schinazi
- Center for AIDS Research, Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta 30322, GA, USA
| | - Ladislau C Kovari
- Department of Biochemistry, Microbiology, and Immunology, Wayne State University School of Medicine, Detroit 48201, MI, USA
| | - John F Trant
- Department of Chemistry and Biochemistry, University of Windsor, Windsor N9B 3P4, ON, Canada
| | - Sarfraz Ahmad
- Drug Design Development Research Group, Department of Chemistry, Faculty of Science, Universiti Malaya, Kuala Lumpur 50603, Malaysia
| | - Matheus Froeyen
- KU Leuven, Rega Institute for Medical Research, Department of Pharmaceutical and Pharmacological Sciences, Medicinal Chemistry, Herestraat 49, box 1041, Leuven 3000, Belgium.
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Sundar S, Piramanayagam S, Natarajan J. A review on structural genomics approach applied for drug discovery against three vector-borne viral diseases: Dengue, Chikungunya and Zika. Virus Genes 2022; 58:151-171. [PMID: 35394596 DOI: 10.1007/s11262-022-01898-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 03/22/2022] [Indexed: 12/22/2022]
Abstract
Structural genomics involves the advent of three-dimensional structures of the genome encoded proteins through various techniques available. Numerous structural genomics research groups have been developed across the globe and they contribute enormously to the identification of three-dimensional structures of various proteins. In this review, we have discussed the applications of the structural genomics approach towards the discovery of potential lead-like molecules against the genomic drug targets of three vector-borne diseases, namely, Dengue, Chikungunya and Zika. Currently, all these three diseases are associated with the most important global public health problems and significant economic burden in tropical countries. Structural genomics has accelerated the identification of novel drug targets and inhibitors for the treatment of these diseases. We start with the current development status of the drug targets and antiviral drugs against these three diseases and conclude by describing challenges that need to be addressed to overcome the shortcomings in the process of drug discovery.
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Affiliation(s)
- Shobana Sundar
- Computational Biology Lab, Department of Bioinformatics, Bharathiar University, Coimbatore, India
| | | | - Jeyakumar Natarajan
- Data Mining and Text Mining Laboratory, Department of Bioinformatics, Bharathiar University, Coimbatore, Tamil Nadu, India.
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15
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Zhang Y, Zhang H, Gao K. Borane-Trimethylamine Complex as a Reducing Agent for Selective Methylation and Formylation of Amines with CO 2. Org Lett 2021; 23:8282-8286. [PMID: 34622655 DOI: 10.1021/acs.orglett.1c03023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report herein that a borane-trimethylamine complex worked as an efficient reducing agent for the selective methylation and formylation of amines with 1 atm CO2 under metal-free conditions. 6-Amino-2-picoline serves as a highly efficient catalyst for the methylation of various secondary amines, whereas in its absence, the formylation of primary and secondary amines was achieved in high yield with high chemoselectivity. Mechanistic studies suggest that the 6-amino-2-picoline-borane catalytic system operates like an intramolecular frustrated Lewis pair to activate CO2.
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Affiliation(s)
- Yanmeng Zhang
- Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, P. R. China
| | - He Zhang
- Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, P. R. China
| | - Ke Gao
- Hubei International Scientific and Technological Cooperation Base of Pesticide and Green Synthesis, Key Laboratory of Pesticide & Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, 152 Luoyu Road, Wuhan, Hubei 430079, P. R. China
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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: 13] [Impact Index Per Article: 4.3] [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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17
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Mukhi M, Vishwanathan AS. Identifying potential inhibitors of biofilm-antagonistic proteins to promote biofilm formation: a virtual screening and molecular dynamics simulations approach. Mol Divers 2021; 26:2135-2147. [PMID: 34546549 DOI: 10.1007/s11030-021-10320-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022]
Abstract
Microbial biofilms play a critical role in environmental biotechnology and associated applications. Biofilm production can be enhanced by inhibiting the function of proteins that negatively regulate their formation. With this objective, an in silico approach was adopted to identify competitive inhibitors of eight biofilm-antagonistic proteins, namely AbrB and SinR (from Bacillus subtilis) and AmrZ, PDE (EAL), PslG, RetS, ShrA and TpbA (from Pseudomonas aeruginosa). Fifteen inhibitors that structurally resembled the natural ligand of each protein were shortlisted using ligand-based and structure-based virtual screening. The top four inhibitors obtained from molecular docking using Autodock Vina were further docked using SwissDock and DOCK 6.9 to obtain a consensus hit for each protein based on different scoring functions. Further analysis of the protein-ligand complexes revealed that these top inhibitors formed significant non-covalent interactions with their respective protein binding sites. The eight protein-ligand complexes were then subjected to molecular dynamics simulations for 30 ns using GROMACS. RMSD and radius of gyration values of 0.1-0.4 nm and 1.0-3.5 nm, respectively, along with hydrogen bond formation throughout the trajectory indicated that all the complexes remained stable, compact and intact during the simulation period. Binding energy values between -20 and -77 kJ/mol obtained from MM-PBSA calculations further confirmed the high affinities of the eight inhibitors for their respective receptors. The outcome of this study holds great promise to enhance biofilms that are central to biotechnological processes associated with microbial electrochemical technologies, wastewater treatment, bioremediation and the industrial production of value-added products.
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Affiliation(s)
- Mayur Mukhi
- WATER Laboratory, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, 515134, India
| | - A S Vishwanathan
- WATER Laboratory, Department of Biosciences, Sri Sathya Sai Institute of Higher Learning, Prasanthi Nilayam, Puttaparthi, Andhra Pradesh, 515134, India.
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Rahman S, Das AK. Integrated Multi-omics, Virtual Screening and Molecular Docking Analysis of Methicillin-Resistant Staphylococcus aureus USA300 for the Identification of Potential Therapeutic Targets: An In-Silico Approach. Int J Pept Res Ther 2021; 27:2735-2755. [PMID: 34548853 PMCID: PMC8446483 DOI: 10.1007/s10989-021-10287-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/10/2021] [Indexed: 11/28/2022]
Abstract
Staphylococcus aureus infection is a leading cause of mortality and morbidity in community, hospital and live-stock sectors, especially with the widespread emergence of methicillin-resistant S. aureus (MRSA) strains. To identify new drug molecules to treat MRSA patients, we have undertaken to search essential proteins that are indispensable for their survival but non-homologous to human host proteins. The current study utilizes a subtractive genome and proteome approach to screen the possible therapeutic targets against S. aureus USA300. Bacterial essential genes are obtained from the DEG database and are compared to avoid cross-reactivity with human host genes. In silico analysis shows 198 proteins that may be considered as therapeutic candidates. Depending on their sub-cellular localization, proteins are grouped as either vaccine or drug targets or both. Extracellular proteins such as cell division proteins (Q2FZ91, Q2FZ95), penicillin-binding proteins (Q2FZ94, Q2FYI0) of the bacterial cell wall, phosphoglucomutase (Q2FE11) and lipoteichoic acid synthase (Q2FIS2) are considered as vaccine targets, and their epitopes have been mapped. Altogether, 53 drug targets are identified, which have shown similarity with the drug targets available in the DrugBank database. Predicted drug targets belong to the common metabolic pathways of MRSA, such as fatty acid biosynthesis, folate biosynthesis, peptidoglycan biosynthesis, ribosome, etc. Protein-protein interaction analysis emphasizing peptidoglycan biosynthesis reveals the connection between penicillin-binding proteins, mur-family proteins and FemXAB proteins. In this study, staphylococcal FemA protein (P0A0A5) is subjected to structure-based virtual screening for the drug repurposing approach. There are 20 residues missing in the crystal structure of FemA, and 12 of these residues are located at the catalytic site. The missing residues are modelled, and stereochemistry is checked. FDA approved drugs available in the DrugBank database have been used in virtual screening with FemA in search of potential repurposed molecules. This approach provides us with 10 drugs that may be used in the treatment of methicillin-resistant staphylococcal mediated diseases. AutoDock 4.2 is used for in silico screening and shows a comparable inhibition constant (Ki) for all 10 FDA-approved drugs towards FemA. Most of these drugs are used in the treatment of various cancers, migraines and leukaemia. Protein-drug interaction analysis shows that the drugs mostly interact with hydrophobic residues of FemA. Moreover, Tyr328 and Lys383 contribute largely to hydrogen bondings during interactions. All interacting amino acids that bind to the drugs are part of the active site cavity of FemA. Supplementary Information The online version contains supplementary material available at 10.1007/s10989-021-10287-9.
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Affiliation(s)
- Shakilur Rahman
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302 India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, West Bengal 721302 India
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Structure and Dynamics of Zika Virus Protease and Its Insights into Inhibitor Design. Biomedicines 2021; 9:biomedicines9081044. [PMID: 34440248 PMCID: PMC8394600 DOI: 10.3390/biomedicines9081044] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/04/2021] [Accepted: 08/16/2021] [Indexed: 12/16/2022] Open
Abstract
Zika virus (ZIKV)—a member of the Flaviviridae family—is an important human pathogen. Its genome encodes a polyprotein that can be further processed into structural and non-structural proteins. ZIKV protease is an important target for antiviral development due to its role in cleaving the polyprotein to release functional viral proteins. The viral protease is a two-component protein complex formed by NS2B and NS3. Structural studies using different approaches demonstrate that conformational changes exist in the protease. The structures and dynamics of this protease in the absence and presence of inhibitors were explored to provide insights into the inhibitor design. The dynamic nature of residues binding to the enzyme cleavage site might be important for the function of the protease. Due to the charges at the protease cleavage site, it is challenging to develop small-molecule compounds acting as substrate competitors. Developing small-molecule compounds to inhibit protease activity through an allosteric mechanism is a feasible strategy because conformational changes are observed in the protease. Herein, structures and dynamics of ZIKV protease are summarized. The conformational changes of ZIKV protease and other proteases in the same family are discussed. The progress in developing allosteric inhibitors is also described. Understanding the structures and dynamics of the proteases are important for designing potent inhibitors.
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Pindi C, Chirasani VR, Senapati S. Identifying crucial E-protein residues responsible for unusual stability of Zika virus envelope. Biophys J 2021; 120:4041-4054. [PMID: 34390684 DOI: 10.1016/j.bpj.2021.08.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/28/2021] [Accepted: 08/06/2021] [Indexed: 11/30/2022] Open
Abstract
An outbreak of Zika virus (ZIKV) infections in 2015-16 that caused microcephaly and other congenital abnormalities in newborns prompted intense research across the globe. These studies have suggested that ZIKV can survive high temperatures and harsh physiological conditions, unlike the other flaviviruses such as dengue virus (DENV). In contrast, recent cryo-electron microscopy studies have shown very similar architecture of the ZIKV and DENV envelopes that constitute the primary level of viral protection. Encouraged by these findings, here we attempt to identify the crucial protein residues that make the ZIKV envelope so robust by employing coarse-grained and all-atomic molecular dynamics simulations and computational mutagenesis studies. In accordance with more recent cryo-electron microscopy findings, our simulation results exhibited stable ZIKV envelope protein shell both at 29oC and 40°C, whereas the DENV2 shell loosened up significantly at 40°C. Subsequently, we simulated a series of ZIKV variants to identify the specific domain and residues involved in maintaining the structural integrity of the viral protein shell at high temperatures. Our results suggest that the DIII domain-more specifically, the CD- and FG-loop residues of the ZIKV protein shell-play a crucial role in making the virus envelope thermostable by inducing strong raft-raft interactions. These findings can accelerate the rational design of ZIKV therapeutics.
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Affiliation(s)
- Chinmai Pindi
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Venkat R Chirasani
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai, India
| | - Sanjib Senapati
- Department of Biotechnology and BJM School of Biosciences, Indian Institute of Technology Madras, Chennai, India.
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21
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Dos Santos Nascimento IJ, de Aquino TM, da Silva-Júnior EF. Drug Repurposing: A Strategy for Discovering Inhibitors against Emerging Viral Infections. Curr Med Chem 2021; 28:2887-2942. [PMID: 32787752 DOI: 10.2174/0929867327666200812215852] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 11/22/2022]
Abstract
BACKGROUND Viral diseases are responsible for several deaths around the world. Over the past few years, the world has seen several outbreaks caused by viral diseases that, for a long time, seemed to possess no risk. These are diseases that have been forgotten for a long time and, until nowadays, there are no approved drugs or vaccines, leading the pharmaceutical industry and several research groups to run out of time in the search for new pharmacological treatments or prevention methods. In this context, drug repurposing proves to be a fast and economically viable technique, considering the fact that it uses drugs that have a well-established safety profile. Thus, in this review, we present the main advances in drug repurposing and their benefit for searching new treatments against emerging viral diseases. METHODS We conducted a search in the bibliographic databases (Science Direct, Bentham Science, PubMed, Springer, ACS Publisher, Wiley, and NIH's COVID-19 Portfolio) using the keywords "drug repurposing", "emerging viral infections" and each of the diseases reported here (CoV; ZIKV; DENV; CHIKV; EBOV and MARV) as an inclusion/exclusion criterion. A subjective analysis was performed regarding the quality of the works for inclusion in this manuscript. Thus, the selected works were those that presented drugs repositioned against the emerging viral diseases presented here by means of computational, high-throughput screening or phenotype-based strategies, with no time limit and of relevant scientific value. RESULTS 291 papers were selected, 24 of which were CHIKV; 52 for ZIKV; 43 for DENV; 35 for EBOV; 10 for MARV; and 56 for CoV and the rest (72 papers) related to the drugs repurposing and emerging viral diseases. Among CoV-related articles, most were published in 2020 (31 papers), updating the current topic. Besides, between the years 2003 - 2005, 10 articles were created, and from 2011 - 2015, there were 7 articles, portraying the outbreaks that occurred at that time. For ZIKV, similar to CoV, most publications were during the period of outbreaks between the years 2016 - 2017 (23 articles). Similarly, most CHIKV (13 papers) and DENV (14 papers) publications occur at the same time interval. For EBOV (13 papers) and MARV (4 papers), they were between the years 2015 - 2016. Through this review, several drugs were highlighted that can be evolved in vivo and clinical trials as possible used against these pathogens showed that remdesivir represent potential treatments against CoV. Furthermore, ribavirin may also be a potential treatment against CHIKV; sofosbuvir against ZIKV; celgosivir against DENV, and favipiravir against EBOV and MARV, representing new hopes against these pathogens. CONCLUSION The conclusions of this review manuscript show the potential of the drug repurposing strategy in the discovery of new pharmaceutical products, as from this approach, drugs could be used against emerging viral diseases. Thus, this strategy deserves more attention among research groups and is a promising approach to the discovery of new drugs against emerging viral diseases and also other diseases.
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Kiriwan D, Choowongkomon K. In silico structural elucidation of the rabies RNA-dependent RNA polymerase (RdRp) toward the identification of potential rabies virus inhibitors. J Mol Model 2021; 27:183. [PMID: 34031746 PMCID: PMC8143072 DOI: 10.1007/s00894-021-04798-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 05/17/2021] [Indexed: 11/25/2022]
Abstract
The rabies virus (RABV) is a non-segmented, negative single-stranded RNA virus which causes acute infection of the central nervous system in humans. Once symptoms appear, the result is nearly always death, and to date, post-exposure prophylaxis (PEP) is the only treatment applicable only immediately after an exposure. Previous studies have identified viral RNA-dependent RNA polymerase (RdRp) as a potential drug target due to its significant role in viral replication and transcription. Herein we generated an energy-minimized homology model of RABIES-RdRp and used it for virtual screening against 2045 NCI Diversity Set III library. The best five ligand-RdRp complexes were picked for further energy minimization via molecular dynamics (MDs) where the complex with ligand Z01690699 shows a minimum score characterized with stable hydrogen bonds and hydrophobic interactions with the catalytic site residues. Our study identified an important ligand for development of remedial approach for treatment of rabies infection.
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Affiliation(s)
- Duangnapa Kiriwan
- Interdisciplinary Program in Genetic Engineering, Graduate School, Kasetsart University, Chatuchak, Bangkok, Thailand
| | - Kiattawee Choowongkomon
- Department of Biochemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand. .,Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand.
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23
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Bolz SN, Adasme MF, Schroeder M. Toward an Understanding of Pan-Assay Interference Compounds and Promiscuity: A Structural Perspective on Binding Modes. J Chem Inf Model 2021; 61:2248-2262. [PMID: 33899463 DOI: 10.1021/acs.jcim.0c01227] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Pan-assay interference compounds (PAINS) are promiscuous compound classes that produce false positive hits in high-throughput screenings. Yet, the mechanisms of PAINS activity are poorly understood. Although PAINS are often associated with protein reactivity, several recent studies have shown that they also mediate noncovalent interactions. Aiming at a deep understanding of PAINS promiscuity, we performed an analysis of the Protein Data Bank to characterize the binding modes of PAINS. We explored the binding mode conservation of 34 PAINS classes present in 871 ligands and among 517 protein targets. The two major findings of this work are the following: First, different PAINS classes exhibit different levels of binding mode conservation. Our novel classification of PAINS based on binding mode similarity enables a rational assessment of PAINS from a structural perspective. Second, PAINS classes with variable binding modes can bind with high affinity. The evaluation of noncovalent binding modes of PAINS-like compounds sheds light on the mechanisms of promiscuous binding. Our findings could facilitate the decisions on how to deal with PAINS and help scientists to understand why PAINS produce hits in their screenings.
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Affiliation(s)
- Sarah Naomi Bolz
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
| | - Melissa F Adasme
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
| | - Michael Schroeder
- Biotechnology Center (BIOTEC), Technische Universität Dresden, 01307 Dresden, Germany
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Designs, Synthesis, Docking Studies, and Biological Evaluation of Novel Berberine Derivatives Targeting Zika Virus. J CHEM-NY 2021. [DOI: 10.1155/2021/5567111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The World Health Organization has designated Zika virus (ZIKV) as a dangerous, mosquito-borne flaviviral pathogen that was recently found to be responsible for a dramatically increased number of microcephaly cases and other congenital abnormalities in fetuses and newborns. There is neither a vaccine to prevent nor a drug to treat ZIKA virus infections, at the present time. Berberine (BBR) is a promising drug approved by FDA against flaviviral dengue virus, and BBR derivatives are of great interest in antiviral drug development. In this study, we synthesized eight BBR derivatives by introducing benzyl groups at the C-13 position of BBR and converting to respective 8-oxoberberine derivatives, performed molecular docking analysis, and evaluated their anti-Zika virus activity utilizing a cell‐based phenotypic assay. Binding mode analysis, absolute binding free energy calculation, and structure-activity relationship studies of these compounds with ZIKV NS3 receptor were collected. Amongst these studied compounds, compound 4d with a structure of 13-(2,6-difluoro)-benzylberberine showed high binding affinity (docking score of −7.31 kcal/mol) towards ZIKV NS2B-NS3 protease with critical binding formed within the active site. In the cell-based assay, compound 4d displayed the highest antiviral efficacy against ZIKV with a selective index (SI) of 15.3, with 3.7-fold greater than that of berberine. Together, our study suggests that the potential ZIKV NS2B-NS3 protease inhibitor, compound 4d, is the best alternative to BBR and, further, extends an assuring platform for developing antiviral competitive inhibitors against ZIKV infection.
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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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26
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Structure-Based Virtual Screening: Identification of a Novel NS2B-NS3 Protease Inhibitor with Potent Antiviral Activity against Zika and Dengue Viruses. Microorganisms 2021; 9:microorganisms9030545. [PMID: 33800763 PMCID: PMC8000814 DOI: 10.3390/microorganisms9030545] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 02/25/2021] [Accepted: 03/02/2021] [Indexed: 11/16/2022] Open
Abstract
Zika virus (ZIKV), which is associated with severe diseases in humans, has spread rapidly and globally since its emergence. ZIKV and dengue virus (DENV) are closely related, and antibody-dependent enhancement (ADE) of infection between cocirculating ZIKV and DENV may exacerbate disease. Despite these serious threats, there are currently no approved antiviral drugs against ZIKV and DENV. The NS2B-NS3 viral protease is an attractive antiviral target because it plays a pivotal role in polyprotein cleavage, which is required for viral replication. Thus, we sought to identify novel inhibitors of the NS2B-NS3 protease. To that aim, we performed structure-based virtual screening using 467,000 structurally diverse chemical compounds. Then, a fluorescence-based protease inhibition assay was used to test whether the selected candidates inhibited ZIKV protease activity. Among the 123 candidate inhibitors selected from virtual screening, compound 1 significantly inhibited ZIKV NS2B-NS3 protease activity in vitro. In addition, compound 1 effectively inhibited ZIKV and DENV infection of human cells. Molecular docking analysis suggested that compound 1 binds to the NS2B-NS3 protease of ZIKV and DENV. Thus, compound 1 could be used as a new therapeutic option for the development of more potent antiviral drugs against both ZIKV and DENV, reducing the risks of ADE.
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27
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Identification of Novel SARS-CoV-2 Inhibitors: A Structure-Based Virtual Screening Approach. J CHEM-NY 2021. [DOI: 10.1155/2021/1901484] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The recent outbreak of the coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) in the last few months raised global health concern. Previous research described that remdesivir and ritonavir can be used as effective drugs against COVID-19. In this study, we applied the structure-based virtual screening (SBVS) on the high similar remdesivir- and ritonavir-approved drugs, selected from the DrugBank database as well as on a series of ritonavir derivatives, selected from the literature. The aim was to provide new potent SARS-CoV-2 main protease (Mpro) inhibitors with high stability. The analysis was performed using AutoDock VINA implicated in the PyRx 0.8 tool. Based on the ligand binding energy, 20 compounds were selected and then analyzed by AutoDock tools. Among the 20 compounds, 3 compounds were selected as high-potent anti-COVID-19.
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G Viveiros Rosa S, Fierro IM, C Santos W. Repositioning and investigational drugs for Zika virus infection treatment: a patent review. Expert Opin Ther Pat 2020; 30:847-862. [PMID: 32842803 DOI: 10.1080/13543776.2020.1811854] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Zika virus (ZIKV) is transmitted to humans throughout bites of Aedes mosquitoes. ZIKV infection may be asymptomatic in most cases, but it may cause fever, headache, muscle pain, and rash. Guillain-Barré syndrome also may be associated with the infection. Furthermore, the Pan American Health Organization informed 3,715 cases of the congenital ZIKV syndrome (CZS) in the Americas from 2015 - 2017, which may include microcephaly and other craniofacial deformities. AREAS COVERED This review identifies patent documents on repositioning for ZIKV infection treatment of already approved drugs or phases II/III investigated drugs for other diseases. Thirty-six patents were found reporting compounds with anti-ZIKV activity with application dates ranging from 2015 to 2019. EXPERT OPINION The main drugs claimed in patents were ribavirin, sofosbuvir, and alpha interferons. Preventing CZS is one of the most significant challenges in ZIKV infection. Therefore, repositioning sofosbuvir and niclosamide, that pose no danger for pregnant women, is a particular issue to be considered for clinical tests involving ZIKV disease. Given the substantial costs and developing time of new a drug, repositioning of old drugs is becoming an attractive alternative for diseases with neglected treatments.
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Affiliation(s)
- Sandro G Viveiros Rosa
- Diretoria de Patentes, Divisão De Farmácia - Instituto Nacional Da Propriedade Industrial , Rio de Janeiro, Brasil.,Programa De Pós-Graduação Em Ciências Aplicadas a Produtos Para Saúde, Faculdade De Farmácia, Universidade Federal Fluminense , Brasil
| | - Iolanda M Fierro
- cAcademia De Propriedade Intelectual - Instituto Nacional Da Propriedade Industrial , Rio de Janeiro, Niteroi City, Rio de Janeiro, Brazil
| | - Wilson C Santos
- Programa De Pós-Graduação Em Ciências Aplicadas a Produtos Para Saúde, Faculdade De Farmácia, Universidade Federal Fluminense , Brasil.,Instituto Teófilo Hernando, Departamento De Farmacología, Facultad De Medicina, Universidad Autónoma De Madrid , Madrid, Spain
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29
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Mirza MU, Saadabadi A, Vanmeert M, Salo-Ahen OMH, Abdullah I, Claes S, De Jonghe S, Schols D, Ahmad S, Froeyen M. Discovery of HIV entry inhibitors via a hybrid CXCR4 and CCR5 receptor pharmacophore-based virtual screening approach. Eur J Pharm Sci 2020; 155:105537. [PMID: 32890663 PMCID: PMC7467125 DOI: 10.1016/j.ejps.2020.105537] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/10/2020] [Accepted: 08/30/2020] [Indexed: 12/30/2022]
Abstract
Chemokine receptors are key regulators of cell migration in terms of immunity and inflammation. Among these, CCR5 and CXCR4 play pivotal roles in cancer metastasis and HIV-1 transmission and infection. They act as essential co-receptors for HIV and furnish a route to the cell entry. In particular, inhibition of either CCR5 or CXCR4 leads very often the virus to shift to a more virulent dual-tropic strain. Therefore, dual receptor inhibition might improve the therapeutic strategies against HIV. In this study, we aimed to discover selective CCR5, CXCR4, and dual CCR5/CXCR4 antagonists using both receptor- and ligand-based computational methods. We employed this approach to fully incorporate the interaction attributes of the binding pocket together with molecular dynamics (MD) simulations and binding free energy calculations. The best hits were evaluated for their anti-HIV-1 activity against CXCR4- and CCR5-specific NL4.3 and BaL strains. Moreover, the Ca2+ mobilization assay was used to evaluate their antagonistic activity. From the 27 tested compounds, three were identified as inhibitors: compounds 27 (CCR5), 6 (CXCR4) and 3 (dual) with IC50 values ranging from 10.64 to 64.56 μM. The binding mode analysis suggests that the active compounds form a salt bridge with the glutamates and π-stacking interactions with the aromatic side chains binding site residues of the respective co-receptor. The presented hierarchical virtual screening approach provides essential aspects in identifying potential antagonists in terms of selectivity against a specific co-receptor. The compounds having multiple heterocyclic nitrogen atoms proved to be relatively more specific towards CXCR4 inhibition as compared to CCR5. The identified compounds serve as a starting point for further development of HIV entry inhibitors through synthesis and quantitative structure-activity relationship studies.
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Affiliation(s)
- Muhammad Usman Mirza
- Medicinal Chemistry, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Atefeh Saadabadi
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Michiel Vanmeert
- Medicinal Chemistry, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Outi M H Salo-Ahen
- Pharmaceutical Sciences Laboratory, Faculty of Science and Engineering, Pharmacy, Åbo Akademi University, FI-20520 Turku, Finland; Structural Bioinformatics Laboratory, Faculty of Science and Engineering, Biochemistry, Åbo Akademi University, FI-20520 Turku, Finland
| | - Iskandar Abdullah
- Department of Chemistry, Faculty of Sciences, University Malaya, Kuala Lumpur 59100, Malaysia
| | - Sandra Claes
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Steven De Jonghe
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Department of Microbiology, Immunology and Transplantation, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium
| | - Sarfraz Ahmad
- Department of Chemistry, Faculty of Sciences, University Malaya, Kuala Lumpur 59100, Malaysia
| | - Matheus Froeyen
- Medicinal Chemistry, Department of Pharmaceutical and Pharmacological Sciences, Rega Institute for Medical Research, KU Leuven, B-3000 Leuven, Belgium.
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30
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Yuan S, Chan CCY, Chik KKH, Tsang JOL, Liang R, Cao J, Tang K, Cai JP, Ye ZW, Yin F, To KKW, Chu H, Jin DY, Hung IFN, Yuen KY, Chan JFW. Broad-Spectrum Host-Based Antivirals Targeting the Interferon and Lipogenesis Pathways as Potential Treatment Options for the Pandemic Coronavirus Disease 2019 (COVID-19). Viruses 2020; 12:E628. [PMID: 32532085 PMCID: PMC7354423 DOI: 10.3390/v12060628] [Citation(s) in RCA: 45] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/08/2020] [Accepted: 06/08/2020] [Indexed: 01/14/2023] Open
Abstract
The ongoing Coronavirus Disease 2019 (COVID-19) pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) signals an urgent need for an expansion in treatment options. In this study, we investigated the anti-SARS-CoV-2 activities of 22 antiviral agents with known broad-spectrum antiviral activities against coronaviruses and/or other viruses. They were first evaluated in our primary screening in VeroE6 cells and then the most potent anti-SARS-CoV-2 antiviral agents were further evaluated using viral antigen expression, viral load reduction, and plaque reduction assays. In addition to remdesivir, lopinavir, and chloroquine, our primary screening additionally identified types I and II recombinant interferons, 25-hydroxycholesterol, and AM580 as the most potent anti-SARS-CoV-2 agents among the 22 antiviral agents. Betaferon (interferon-β1b) exhibited the most potent anti-SARS-CoV-2 activity in viral antigen expression, viral load reduction, and plaque reduction assays among the recombinant interferons. The lipogenesis modulators 25-hydroxycholesterol and AM580 exhibited EC50 at low micromolar levels and selectivity indices of >10.0. Combinational use of these host-based antiviral agents with virus-based antivirals to target different processes of the SARS-CoV-2 replication cycle should be evaluated in animal models and/or clinical trials.
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Affiliation(s)
- Shuofeng Yuan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (S.Y.); (C.C.-Y.C.); (K.K.-H.C.); (J.O.-L.T.); (R.L.); (J.C.); (K.T.); (J.-P.C.); (Z.-W.Y.); (K.K.-W.T.); (H.C.)
| | - Chris Chun-Yiu Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (S.Y.); (C.C.-Y.C.); (K.K.-H.C.); (J.O.-L.T.); (R.L.); (J.C.); (K.T.); (J.-P.C.); (Z.-W.Y.); (K.K.-W.T.); (H.C.)
| | - Kenn Ka-Heng Chik
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (S.Y.); (C.C.-Y.C.); (K.K.-H.C.); (J.O.-L.T.); (R.L.); (J.C.); (K.T.); (J.-P.C.); (Z.-W.Y.); (K.K.-W.T.); (H.C.)
| | - Jessica Oi-Ling Tsang
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (S.Y.); (C.C.-Y.C.); (K.K.-H.C.); (J.O.-L.T.); (R.L.); (J.C.); (K.T.); (J.-P.C.); (Z.-W.Y.); (K.K.-W.T.); (H.C.)
| | - Ronghui Liang
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (S.Y.); (C.C.-Y.C.); (K.K.-H.C.); (J.O.-L.T.); (R.L.); (J.C.); (K.T.); (J.-P.C.); (Z.-W.Y.); (K.K.-W.T.); (H.C.)
| | - Jianli Cao
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (S.Y.); (C.C.-Y.C.); (K.K.-H.C.); (J.O.-L.T.); (R.L.); (J.C.); (K.T.); (J.-P.C.); (Z.-W.Y.); (K.K.-W.T.); (H.C.)
| | - Kaiming Tang
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (S.Y.); (C.C.-Y.C.); (K.K.-H.C.); (J.O.-L.T.); (R.L.); (J.C.); (K.T.); (J.-P.C.); (Z.-W.Y.); (K.K.-W.T.); (H.C.)
| | - Jian-Piao Cai
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (S.Y.); (C.C.-Y.C.); (K.K.-H.C.); (J.O.-L.T.); (R.L.); (J.C.); (K.T.); (J.-P.C.); (Z.-W.Y.); (K.K.-W.T.); (H.C.)
| | - Zi-Wei Ye
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (S.Y.); (C.C.-Y.C.); (K.K.-H.C.); (J.O.-L.T.); (R.L.); (J.C.); (K.T.); (J.-P.C.); (Z.-W.Y.); (K.K.-W.T.); (H.C.)
| | - Feifei Yin
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong, China;
| | - Kelvin Kai-Wang To
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (S.Y.); (C.C.-Y.C.); (K.K.-H.C.); (J.O.-L.T.); (R.L.); (J.C.); (K.T.); (J.-P.C.); (Z.-W.Y.); (K.K.-W.T.); (H.C.)
| | - Hin Chu
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (S.Y.); (C.C.-Y.C.); (K.K.-H.C.); (J.O.-L.T.); (R.L.); (J.C.); (K.T.); (J.-P.C.); (Z.-W.Y.); (K.K.-W.T.); (H.C.)
| | - Dong-Yan Jin
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China;
| | - Ivan Fan-Ngai Hung
- Division of Infectious Diseases, Department of Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong, China;
| | - Kwok-Yung Yuen
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (S.Y.); (C.C.-Y.C.); (K.K.-H.C.); (J.O.-L.T.); (R.L.); (J.C.); (K.T.); (J.-P.C.); (Z.-W.Y.); (K.K.-W.T.); (H.C.)
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong, China;
| | - Jasper Fuk-Woo Chan
- State Key Laboratory of Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong, China; (S.Y.); (C.C.-Y.C.); (K.K.-H.C.); (J.O.-L.T.); (R.L.); (J.C.); (K.T.); (J.-P.C.); (Z.-W.Y.); (K.K.-W.T.); (H.C.)
- Hainan Medical University-The University of Hong Kong Joint Laboratory of Tropical Infectious Diseases, The University of Hong Kong, Pokfulam, Hong Kong, China;
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Naik B, Gupta N, Ojha R, Singh S, Prajapati VK, Prusty D. High throughput virtual screening reveals SARS-CoV-2 multi-target binding natural compounds to lead instant therapy for COVID-19 treatment. Int J Biol Macromol 2020; 160:1-17. [PMID: 32470577 PMCID: PMC7250083 DOI: 10.1016/j.ijbiomac.2020.05.184] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 05/21/2020] [Accepted: 05/22/2020] [Indexed: 12/21/2022]
Abstract
The present-day world is severely suffering from the recently emerged SARS-CoV-2. The lack of prescribed drugs for the deadly virus has stressed the likely need to identify novel inhibitors to alleviate and stop the pandemic. In the present high throughput virtual screening study, we used in silico techniques like receptor-ligand docking, Molecular dynamic (MD), and ADME properties to screen natural compounds. It has been documented that many natural compounds display antiviral activities, including anti–SARS-CoV effect. The present study deals with compounds of Natural Product Activity and Species Source (NPASS) database with known biological activity that probably impedes the activity of six essential enzymes of the virus. Promising drug-like compounds were identified, demonstrating better docking score and binding energy for each druggable targets. After an extensive screening analysis, three novel multi-target natural compounds were predicted to subdue the activity of three/more major drug targets simultaneously. Concerning the utility of natural compounds in the formulation of many therapies, we propose these compounds as excellent lead candidates for the development of therapeutic drugs against SARS-CoV-2.
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Affiliation(s)
- Biswajit Naik
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India
| | - Nidhi Gupta
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India
| | - Rupal Ojha
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India
| | - Satyendra Singh
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India
| | - Vijay Kumar Prajapati
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India
| | - Dhaneswar Prusty
- Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, NH-8, Bandarsindri, Kishangarh, 305817 Ajmer, Rajasthan, India.
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Soares TA, Wahab HA. Outlook on the Development and Application of Molecular Simulations in Latin America. J Chem Inf Model 2020; 60:435-438. [PMID: 32009389 DOI: 10.1021/acs.jcim.0c00112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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