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da Fonseca AM, Cabongo SQ, Caluaco BJ, Colares RP, Fernandes CFC, Dos Santos HS, de Lima-Neto P, Marinho ES. The search for new efficient inhibitors of SARS-COV-2 through the De novo drug design developed by artificial intelligence. J Biomol Struct Dyn 2023; 41:9890-9906. [PMID: 36420665 DOI: 10.1080/07391102.2022.2148128] [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: 08/11/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022]
Abstract
The pandemic caused by Sars-CoV-2 is a viral infection that has generated one of the most significant health problems worldwide. Previous studies report the main protease (Mpro) as a potential target for this virus, as it is considered a crucial enzyme in mediating replication and viral transcription. This work presented the construction of new bioactive compounds for possible inhibition. The De novo molecular design of drugs method in the incremental construction of a ligant model within a receptor model was used, producing new structures with the help of artificial intelligence. The research algorithm and the scoring function responsible for predicting orientation and affinity in the molecular target at the time of coupling showed, as a result of the simulation, the compound with the highest bioaffinity value, Hit 998, with the energy of -17.62 kcal/mol, and synthetic viability close to 50%. While hit 1103 presented better synthetic viability (80%), its affinity energy of -10.28 kcal/mol. Both were compared with the reference linker N3, with a binding affinity of -7.5 kcal/mol. ADMET tests demonstrated that simulated compounds have a low risk of metabolic activation and do not exert effective distribution in the CNS, suggesting a pharmacokinetic mechanism based on local action, even with high topological polarity, which resulted in low oral bioavailability. In conclusion, MMGBSA, H-bonds, RMSD, SASA, and RMSF values were also obtained through molecular dynamics to verify the stability of the receptor-ligant complex within the active protein site to seek new therapeutic propositions in the fight against the pandemic.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aluísio Marques da Fonseca
- Mestrado Acadêmico em Sociobiodiversidades e Tecnologias Sustentáveis - MASTS, Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Acarape, CE, Brazil
| | - Sadrack Queque Cabongo
- Instituto de Ciências Exatas e da Natureza, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Acarape, CE, Brazil
| | - Bernardino Joaquim Caluaco
- Instituto de Ciências Exatas e da Natureza, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Acarape, CE, Brazil
| | - Regilany Paulo Colares
- Instituto de Ciências Exatas e da Natureza, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Acarape, CE, Brazil
| | | | | | - Pedro de Lima-Neto
- Department of Analytical Chemistry and Physical Chemistry, Science Center, Federal University of Ceara, Fortaleza, CE, Brazil
| | - Emmanuel Silva Marinho
- Grupo de química Teorica e Eletroquimica-GQTE, Universidade Estadual do Ceará, Limoeiro do Norte, CE, Brazil
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Lima JPO, da Fonseca AM, Marinho GS, da Rocha MN, Marinho EM, dos Santos HS, Freire RM, Marinho ES, de Lima-Neto P, Fechine PBA. De novo design of bioactive phenol and chromone derivatives for inhibitors of Spike glycoprotein of SARS-CoV-2 in silico. 3 Biotech 2023; 13:301. [PMID: 37588795 PMCID: PMC10425314 DOI: 10.1007/s13205-023-03695-9] [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: 03/16/2023] [Accepted: 06/29/2023] [Indexed: 08/18/2023] Open
Abstract
This work presents the synthesis of 12 phenol and chromone derivatives, prepared by the analogs, and the possibility of conducting an in silico study of its derivatives as a therapeutic alternative to combat the SARS-CoV-2, pathogen responsible for COVID-19 pandemic, using its S-glycoprotein as a macromolecular target. After the initial screening for the ranking of the products, it was chosen which structure presented the best energy bond with the target. As a result, derivative 4 was submitted to a molecular growth study using artificial intelligence, where 8436 initial structures were obtained that passed through the interaction filters and similarity to the active glycoprotein pocket through the MolAICal computational package. Thus, 557 Hits with active configuration were generated, which is very promising compared to the BLA reference link for inhibiting the biological target. Molecular dynamics also simulated these compounds to verify their stability within the active protein site to seek new therapeutic propositions to fight against the pandemic. The Hit 48 and 250 are the most active compounds against SARS-CoV-2. In summary, the results show that the Hit 250 would be more active than the natural compound, which could be further developed for further testing against SARS-CoV-2. The study employs the de novo approach to design new drugs, combining artificial intelligence and molecular dynamics simulations to create efficient molecular structures. This research aims to contribute to the development of effective therapeutic strategies against the pandemic.
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Affiliation(s)
- Joan Petrus Oliveira Lima
- Advanced Materials Chemistry Group (GQMat)-Department of Analytical Chemistry and Physical Chemistry, Federal University of Ceará, Campus Pici, Fortaleza, Ceará 60455-970 Brazil
| | - Aluísio Marques da Fonseca
- Mestrado Acadêmico em Sociobiodiversidades e Tecnologias Sustentáveis-MASTS, Instituto de Engenharias e Desenvolvimento Sustentável, Universidade da Integração Internacional da Lusofonia Afro-Brasileira, Acarape, CE 62785-000 Brazil
| | - Gabrielle Silva Marinho
- Faculdade de Filosofia Dom Aureliano Matos-FAFIDAM, Universidade Estadual do Ceará, Centro, Limoeiro do Norte, CE 62930-000 Brazil
| | - Matheus Nunes da Rocha
- Faculdade de Filosofia Dom Aureliano Matos-FAFIDAM, Universidade Estadual do Ceará, Centro, Limoeiro do Norte, CE 62930-000 Brazil
| | - Emanuelle Machado Marinho
- Advanced Materials Chemistry Group (GQMat)-Department of Analytical Chemistry and Physical Chemistry, Federal University of Ceará, Campus Pici, Fortaleza, Ceará 60455-970 Brazil
| | | | | | - Emmanuel Silva Marinho
- Faculdade de Filosofia Dom Aureliano Matos-FAFIDAM, Universidade Estadual do Ceará, Centro, Limoeiro do Norte, CE 62930-000 Brazil
| | - Pedro de Lima-Neto
- Advanced Materials Chemistry Group (GQMat)-Department of Analytical Chemistry and Physical Chemistry, Federal University of Ceará, Campus Pici, Fortaleza, Ceará 60455-970 Brazil
| | - Pierre Basílio Almeida Fechine
- Advanced Materials Chemistry Group (GQMat)-Department of Analytical Chemistry and Physical Chemistry, Federal University of Ceará, Campus Pici, Fortaleza, Ceará 60455-970 Brazil
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Mamat A, Lame Y, Sabine Adeline FY, Yvette N, Ndode Herman ON, Arnold Roger BN, Dieudonné N. In vitro nematocidal potential of hydro-ethanolic and aqueous extracts of Calotropis procera (Aiton) W.T. Aiton, 1811 (Apocynaceae) and Faidherbia albida (Delile) A. Chev., 1934 (Fabacae) against Onchocerca ochengi and Caenorhabditiselegans. Heliyon 2023; 9:e16379. [PMID: 37251817 PMCID: PMC10209015 DOI: 10.1016/j.heliyon.2023.e16379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 04/27/2023] [Accepted: 05/15/2023] [Indexed: 05/31/2023] Open
Abstract
Onchocerciasis caused by Onchocerca volvulus Leuckart, 1893 is the second-world infection responsible for human blindness. Except Ivermectin which has as targets the microfilariae of that parasite, specific treatment for this disease does not exist and in developing countries, medicinal plants seem to remedy that health problem. For that, aqueous and hydro-ethanolic leaf, bark, and root extracts of Calotropis procera and Faidherbia albida were evaluated in vitro, against the most popular bovine model, Onchocerca ochengi and the free-resistant nematode Caenorhabditis elegans. O. ochengi microfilariae and adults extracted from the bovine nodules and skins as well as the free strains of C. elegans were exposed to the various concentrations of the plant parts extracts and Ivermectin. In results, all the plant parts extracts were rich in tannins, saponins, alkaloids, flavonoids, phenols, coumarins, and glycosides. Phenols (175.45 ± 0.01 mg EGA/g DM), flavonoids (158.98 ± 0.05 mg EC/g DM), and tannins (89.98 ± 2.56 mg ETA/g DM) contents were high in the bark hydro-ethanolic extract of F. albida. The leaf hydro-ethanolic extract of F. albida induced high activity against O. ochengi microfilariae (CL50 = 0.13 mg/mL). The bark hydro-ethanolic extract of F. albida was also the most effective on O. ochengi adults and particularly on female adults (CL50 = 0.18 mg/mL). Against the parasite strain resistant to Ivermectin, F. albida leaf hydro-ethanolic extract appeared more active with CL50 = 0.13 mg/mL. Similarly, the bark hydro-ethanolic extract of F. albida was the most potent on the wild strain of C. elegans. Thus, this study validates the use of these plants by traditional healers in the management of onchocerciasis and suggests a new source of isolation of the potential plant compounds against Onchocerca.
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Affiliation(s)
- Amina Mamat
- Department of Biological Sciences, Faculty of Science, University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon
- Centre for Research on Medicinal Plants and Traditional Medicine, Institute of Medical Research and Medicinal Plant Studies, P.O. Box 13033, Yaoundé, Cameroon
| | - Younoussa Lame
- Department of Animal Biology and Physiology, Faculty of Science, University of Yaounde 1 P.O. Box 812, Yaoundé, Cameroon
| | - Fanta Yadang Sabine Adeline
- Department of Biological Sciences, Faculty of Science, University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon
- Centre for Research on Medicinal Plants and Traditional Medicine, Institute of Medical Research and Medicinal Plant Studies, P.O. Box 13033, Yaoundé, Cameroon
| | - Nguezeye Yvette
- Department of Biological Sciences, Faculty of Science, University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon
- Centre for Research on Medicinal Plants and Traditional Medicine, Institute of Medical Research and Medicinal Plant Studies, P.O. Box 13033, Yaoundé, Cameroon
| | - Okah-Nnane Ndode Herman
- Institute of Agricultural Research for Development (IRAD), Veterinary Research Laboratory, Wakwa Regional Center, P.O. Box 65, Ngaoundéré, Cameroon
| | - Bitja-Nyom Arnold Roger
- Department of Biological Sciences, Faculty of Science, University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon
| | - Ndjonka Dieudonné
- Department of Biological Sciences, Faculty of Science, University of Ngaoundere, P.O. Box 454, Ngaoundere, Cameroon
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2,4-Bis(2,4-dimethoxyphenyl)-1,3-dithia-2,4-diphosphetane 2,4-disulfide and its derivatives: Syntheses, structural characterizations, anticancer activities, and theoretical studies on some dithiophosphonato Ni(II) complex. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.134197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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5
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Devim M, Akkoç S, Zeyrek CT, Aslan HG, Kökbudak Z. Design, synthesis, in vitro antiproliferative activity properties, quantum chemical and molecular docking studies of novel Schiff bases incorporating pyrimidine nucleus. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132421] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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Elucidating Antiangiogenic Potential of Rauwolfia serpentina: VEGFR-2 Targeting-Based Molecular Docking Study. EVIDENCE-BASED COMPLEMENTARY AND ALTERNATIVE MEDICINE 2022; 2022:6224666. [PMID: 35198035 PMCID: PMC8860507 DOI: 10.1155/2022/6224666] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/17/2022] [Indexed: 12/13/2022]
Abstract
Angiogenesis plays a critical role in tumorigenesis as it provides the necessary blood supply to the newly grown solid tumor. It helps maintain the tumor microenvironment, promotes tumor development, progression, and metastasis. The vascular epithelial growth factor (VEGF), interacting with the tyrosine kinase receptor VEGFR-2 on endothelial cells, exerts its proangiogenic activity. Hence, targeting the VEGFR-2 signaling is considered a promising strategy to inhibit angiogenesis and thus cancer treatment. This study aims to identify the bioactive compounds derived from the medicinal herb Rauwolfia serpentina that effectively binds with VEGFR-2. The bioactive compounds of R. serpentina were first screened for their physicochemical properties using the DataWarrior program (version 5.5.0). Finally, 17 compounds that obeyed Lipinski's rule of five and showed good drug-likeness were selected for molecular docking studies. Molecular docking results showed that the ligands ajmalicidine, 1, 2-dihydrovomilenine, rauwolscine, yohimbine, ajmaline, and papaverine interact strongly with the target VEGFR-2 receptor. Hydrogen bonds and hydrophobic interactions stabilized the interactions of these compounds with VEGFR-2. These compounds showed favourable drug-like properties and possess no significant toxicity. Therefore, the findings of this study indicate that the compounds derived from R. serpentina can be considered for the development of antiangiogenic drug candidates by targeting VEGFR-2.
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Adinortey CA, Kwarko GB, Koranteng R, Boison D, Obuaba I, Wilson MD, Kwofie SK. Molecular Structure-Based Screening of the Constituents of Calotropis procera Identifies Potential Inhibitors of Diabetes Mellitus Target Alpha Glucosidase. Curr Issues Mol Biol 2022; 44:963-987. [PMID: 35723349 PMCID: PMC8928985 DOI: 10.3390/cimb44020064] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 01/07/2022] [Accepted: 01/09/2022] [Indexed: 01/09/2023] Open
Abstract
Diabetes mellitus is a disorder characterized by higher levels of blood glucose due to impaired insulin mechanisms. Alpha glucosidase is a critical drug target implicated in the mechanisms of diabetes mellitus and its inhibition controls hyperglycemia. Since the existing standard synthetic drugs have therapeutic limitations, it is imperative to identify new potent inhibitors of natural product origin which may slow carbohydrate digestion and absorption via alpha glucosidase. Since plant extracts from Calotropis procera have been extensively used in the treatment of diabetes mellitus, the present study used molecular docking and dynamics simulation techniques to screen its constituents against the receptor alpha glucosidase. Taraxasterol, syriogenin, isorhamnetin-3-O-robinobioside and calotoxin were identified as potential novel lead compounds with plausible binding energies of −40.2, −35.1, −34.3 and −34.3 kJ/mol against alpha glucosidase, respectively. The residues Trp481, Asp518, Leu677, Leu678 and Leu680 were identified as critical for binding and the compounds were predicted as alpha glucosidase inhibitors. Structurally similar compounds with Tanimoto coefficients greater than 0.7 were reported experimentally to be inhibitors of alpha glucosidase or antidiabetic. The structures of the molecules may serve as templates for the design of novel inhibitors and warrant in vitro assaying to corroborate their antidiabetic potential.
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Affiliation(s)
- Cynthia A. Adinortey
- Department of Molecular Biology and Biotechnology, School of Biological Sciences, University of Cape Coast, Cape Coast CC 033, Ghana;
| | - Gabriel B. Kwarko
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 54, Ghana;
| | - Russell Koranteng
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana;
| | - Daniel Boison
- Department of Biochemistry, School of Biological Sciences, University of Cape Coast, Cape Coast CC 033, Ghana; (D.B.); (I.O.)
| | - Issaka Obuaba
- Department of Biochemistry, School of Biological Sciences, University of Cape Coast, Cape Coast CC 033, Ghana; (D.B.); (I.O.)
| | - Michael D. Wilson
- Department of Parasitology, Noguchi Memorial Institute for Medical Research (NMIMR), College of Health Sciences (CHS), University of Ghana, Legon, Accra LG 581, Ghana;
| | - Samuel K. Kwofie
- West African Centre for Cell Biology of Infectious Pathogens, Department of Biochemistry, Cell and Molecular Biology, College of Basic and Applied Sciences, University of Ghana, Legon, Accra LG 54, Ghana;
- Department of Biomedical Engineering, School of Engineering Sciences, College of Basic & Applied Sciences, University of Ghana, Legon, Accra LG 77, Ghana;
- Correspondence: ; Tel.: +233-203-797922
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Synthesis, antimicrobial activity, density functional modelling and molecular docking with COVID-19 main protease studies of benzoxazole derivative: 2-(p-chloro-benzyl)-5-[3-(4-ethly-1-piperazynl) propionamido]-benzoxazole. J Mol Struct 2021; 1237:130413. [PMID: 33846658 PMCID: PMC8026219 DOI: 10.1016/j.molstruc.2021.130413] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 02/20/2021] [Accepted: 03/30/2021] [Indexed: 12/28/2022]
Abstract
This study contains synthesis, antimicrobial activity, density functional modelling and molecular docking studies of benzoxazole derivative: 2-(p-chloro-benzyl)-5-[3-(4-ethly-1-piperazynl) propionamido]-benzoxazole. The synthetic procedure of investigated compound is given in detail. The newly synthesized benzoxazole compound and standard drugs were evaluated for their antimicrobial activity against some Gram-positive, Gram-negative bacteria and fungus C. albicans and their drug-resistant isolates. The benzoxazole compound has been characterized by using 1H-NMR, IR and MASS spectrometry and elemental analysis techniques. The molecular structure of the compound in the ground state has been modelling using density functional theory (DFT) with B3LYP/6-311++g(d,p) level. The molecular docking of 2-(p-chloro-benzyl)-5-[3-(4-ethly-1-piperazynl) propionamido]-benzoxazole with COVID-19 main protease has been also performed by using optimized geometry and the experimentally determined dimensional structure of the main protease (M-pro) of COVID-19.
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Adegbola AE, Fadahunsi OS, Alausa A, Abijo AZ, Balogun TA, Aderibigbe TS, Semire B, Adegbola PI. Computational prediction of nimbanal as potential antagonist of respiratory syndrome coronavirus. INFORMATICS IN MEDICINE UNLOCKED 2021; 24:100617. [PMID: 34075339 PMCID: PMC8161736 DOI: 10.1016/j.imu.2021.100617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 05/21/2021] [Accepted: 05/22/2021] [Indexed: 12/19/2022] Open
Abstract
The high pathogenic nature of the Middle East Respiratory coronavirus (MER) and the associated high fatality rate demands an urgent attention from researchers. Because there is currently no approved drug for the management of the disease, research efforts have been intensified towards the discovery of a potent drug for the treatment of the disease. Papain Like protease (PLpro) is one of the key proteins involved in the viral replication. We therefore docked forty-six compounds already characterized from Azadirachta indica, Xylopia aethipica and Allium cepa against MERS-CoV-PLpro. The molecular docking analysis was performed with AutoDock 1.5.6 and compounds which exhibit more negative free energy of binding, and low inhibition constant (Ki) with the protein (MERS-CoV-PLpro) were considered potent. The physicochemical and pharmacokinetic properties of the compounds were predicted using the Swissadme web server. Twenty-two of the compounds showed inhibition potential similar to dexamethasone and remdesvir, which had binding affinity of -6.8 and -6.3 kcal/mol respectively. The binding affinity of the compounds ranged between -3.4 kcal/mol and -7.7 kcal/mol whereas; hydroxychloroquine had a binding affinity of -4.5 kcal/mol. Among all the compounds, nimbanal and verbenone showed drug likeliness, they did not violate the Lipinski rule neither were they inhibitors of drug-metabolizing enzymes. Both nimbanal and verbenone were further post-scored with MM/GBSA and the binding free energy of nimbanal (-25.51 kcal/mol) was comparable to that of dexamethasone (-25.46 kcal/mol). The RMSD, RMSF, torsional angle, and other analysis following simulation further substantiate the efficacy of nimbanal as an effective drug candidate. In conclusion, our study showed that nimbanal is a more promising therapeutic agent and could be a lead for the discovery of a new drug that may be useful in the management of severe respiratory coronavirus syndrome.
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Affiliation(s)
- Aanuoluwa Eunice Adegbola
- Department of Pure and Applied Chemistry, Faculty of Pure and Applied Sciences, Ladoke Akintola University of Technology, Nigeria
| | - Olumide Samuel Fadahunsi
- Department of Biochemistry, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Nigeria
| | - Abdulahi Alausa
- Department of Biochemistry, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Nigeria
| | - Ayodeji Zabdiel Abijo
- Department of Anatomy, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Nigeria
| | | | - Taiwo Sarah Aderibigbe
- Department of Science Laboratory Technology, Biological Sciences, Microbiology Unit, the Oke Ogun Polytechnic Saki, Nigeria
| | - Banjo Semire
- Department of Pure and Applied Chemistry, Faculty of Pure and Applied Sciences, Ladoke Akintola University of Technology, Nigeria
| | - Peter Ifeoluwa Adegbola
- Department of Biochemistry, Faculty of Basic Medical Sciences, Ladoke Akintola University of Technology, Nigeria
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Marinho EM, Batista de Andrade Neto J, Silva J, Rocha da Silva C, Cavalcanti BC, Marinho ES, Nobre Júnior HV. Virtual screening based on molecular docking of possible inhibitors of Covid-19 main protease. Microb Pathog 2020; 148:104365. [PMID: 32619669 PMCID: PMC7834391 DOI: 10.1016/j.micpath.2020.104365] [Citation(s) in RCA: 71] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/22/2020] [Accepted: 06/25/2020] [Indexed: 02/07/2023]
Abstract
Coronavirus (COVID-19) is an enveloped RNA virus that is diversely found in humans and that has now been declared a global pandemic by the World Health Organization. Thus, there is an urgent need to develop effective therapies and vaccines against this disease. In this context, this study aimed to evaluate in silico the molecular interactions of drugs with therapeutic indications for treatment of COVID-19 (Azithromycin, Baricitinib and Hydroxychloroquine) and drugs with similar structures (Chloroquine, Quinacrine and Ruxolitinib) in docking models from the SARS-CoV-2 main protease (M-pro) protein. The results showed that all inhibitors bound to the same enzyme site, more specifically in domain III of the SARS-CoV-2 main protease. Therefore, this study allows proposing the use of baricitinib and quinacrine, in combination with azithromycin; however, these computer simulations are just an initial step for conceiving new projects for the development of antiviral molecules.
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Affiliation(s)
- Emanuelle Machado Marinho
- Department of Analytical Chemistry and Physical Chemistry, Group of Theoretical Chemistry (GQT), Science Center, Federal University of Ceará, Fortaleza, CE, 60.455-760, Brazil
| | - João Batista de Andrade Neto
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil; Christus University Center (UNICHRISTUS), Fortaleza, CE, Brazil; Drug Research and Development Center, Federal University of Ceará, Fortaleza, CE, Brazil
| | - Jacilene Silva
- Department of Chemistry, Group of Theoretical Chemistry and Electrochemistry (GQTE), State University of Ceará, Limoeiro do Norte, Ceará, Brazil
| | - Cecília Rocha da Silva
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil; Drug Research and Development Center, Federal University of Ceará, Fortaleza, CE, Brazil
| | | | - Emmanuel Silva Marinho
- Department of Chemistry, Group of Theoretical Chemistry and Electrochemistry (GQTE), State University of Ceará, Limoeiro do Norte, Ceará, Brazil
| | - Hélio Vitoriano Nobre Júnior
- School of Pharmacy, Laboratory of Bioprospection in Antimicrobial Molecules (LABIMAN), Federal University of Ceara, Fortaleza, CE, Brazil; Drug Research and Development Center, Federal University of Ceará, Fortaleza, CE, Brazil.
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11
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Pathania S, Bansal P, Gupta P, Rawal RK. Genus Calotropis: A Hub of Medicinally Active Phytoconstituents. CURRENT TRADITIONAL MEDICINE 2020. [DOI: 10.2174/2215083805666190619095933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Traditional medicines derived from plant and other natural sources have several
advantages over synthetic drugs when used for the management of pathological conditions.
Natural product based therapies are safer than synthetic drugs-based chemotherapies. One of
such sources of bioactive molecules includes C. procera and C. gigantea, flowering herbal
plants, belonging to the genus Calotropis, family Apocynaceae, which, due to their diverse
pharmacological profile, have been widely employed in Ayurveda, Unani, Siddha and other
traditional systems for the treatment of various diseases. The various parts of this plant are
rich in phytoconstituents such as cardiac glycosides, flavonoids, terpenoids, steroids, phenolic
compounds, proteins etc. Due to the presence of multiple constituents, this plant possess
diverse biological activities such as analgesic, antitumor, antihelmintic, antioxidant, hepatoprotective,
antidiarrhoeal, anticonvulsant, antimicrobial, oestrogenic, antinociceptive, antimalarial
activity etc. The present review provides comprehensive information about various
phytochemical constituents of the plant along with their medicinal importance.
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Affiliation(s)
- Shelly Pathania
- Research Scholar, Department of Pharmaceutical Sciences and Technology, Maharaja Ranjit Singh Punjab Technical University, Bathinda (Punjab) 151001, India
| | - Parveen Bansal
- University Centre of Excellence in Research, Baba Farid University of Health Sciences, Faridkot, Punjab, India
| | - Prasoon Gupta
- Natural Product Chemistry Division, Indian Institute of Integrative Medicine, Canal Road, Jammu-180001, India
| | - Ravindra K. Rawal
- Department of Chemistry, Maharishi Markandeshwar (Deemed to be University), Mullana-133207, Ambala, Haryana, India
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12
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Radaeva M, Dong X, Cherkasov A. The Use of Methods of Computer-Aided Drug Discovery in the Development of Topoisomerase II Inhibitors: Applications and Future Directions. J Chem Inf Model 2020; 60:3703-3721. [DOI: 10.1021/acs.jcim.0c00325] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Mariia Radaeva
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
| | - Xuesen Dong
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
| | - Artem Cherkasov
- Vancouver Prostate Centre, University of British Columbia, 2660 Oak Street, Vancouver, British Columbia V6H 3Z6, Canada
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Gurung AB, Ali MA, Lee J, Al-Hemaid F, Farah MA, Al-Anazi KM. Molecular docking elucidates the plausible mechanisms underlying the anticancer properties of acetyldigitoxigenin from Adenium obesum. Saudi J Biol Sci 2020; 27:1907-1911. [PMID: 32565713 PMCID: PMC7296488 DOI: 10.1016/j.sjbs.2020.04.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Revised: 04/10/2020] [Accepted: 04/12/2020] [Indexed: 12/20/2022] Open
Abstract
Adenium obesum (Forssk.) Roem. & Schult. is a promising medicinal plant belonging to the Apocynaceae family. It is a rich source of various phytochemicals such as cardiac glycosides, flavonoids, terpeniods, pregnanes etc. which have different pharmacological properties such as anticancer, antibacterial, acaricidal etc. While previous reports showed the anticancer activity of the aerial parts of the plant extract of A. obesum, the mechanisms of action of its chemical constituents are not known. The present study is aimed at elucidation of plausible mechanisms of anticancer activity of the plant by evaluating the binding interaction of its nine major selected compounds with macromolecular receptors implicated in the initiation and progression of cancer using various in silico approaches. Molecular docking results showed that the compound Δ16-3-Acetyldigitoxigenin (16-anhydro-3-acetylgitoxigenin) scored the best binding energy scores with the majority of the target proteins. The molecular binding of the compound was stabilized through hydrogen bonds as well as hydrophobic interactions, and also possesses favorable drug-like properties without significant toxicities.
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Affiliation(s)
- Arun Bahadur Gurung
- Department of Basic Sciences and Social Sciences, North-Eastern Hill University, Shillong 793022, Meghalaya, India
| | - Mohammad Ajmal Ali
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Joongku Lee
- Department of Environment and Forest Resources, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
| | - Fahad Al-Hemaid
- Department of Botany and Microbiology, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Mohammad Abul Farah
- Genetics Laboratory, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khalid Mashay Al-Anazi
- Genetics Laboratory, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
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Unravelling lead antiviral phytochemicals for the inhibition of SARS-CoV-2 M pro enzyme through in silico approach. Life Sci 2020; 255:117831. [PMID: 32450166 PMCID: PMC7243810 DOI: 10.1016/j.lfs.2020.117831] [Citation(s) in RCA: 91] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Revised: 05/11/2020] [Accepted: 05/19/2020] [Indexed: 01/21/2023]
Abstract
A new SARS coronavirus (SARS-CoV-2) belonging to the genus Betacoronavirus has caused a pandemic known as COVID-19. Among coronaviruses, the main protease (Mpro) is an essential drug target which, along with papain-like proteases catalyzes the processing of polyproteins translated from viral RNA and recognizes specific cleavage sites. There are no human proteases with similar cleavage specificity and therefore, inhibitors are highly likely to be nontoxic. Therefore, targeting the SARS-CoV-2 Mpro enzyme with small molecules can block viral replication. The present study is aimed at the identification of promising lead molecules for SARS-CoV-2 Mpro enzyme through virtual screening of antiviral compounds from plants. The binding affinity of selected small drug-like molecules to SARS-CoV-2 Mpro, SARS-CoV Mpro and MERS-CoV Mpro were studied using molecular docking. Bonducellpin D was identified as the best lead molecule which shows higher binding affinity (−9.28 kcal/mol) as compared to the control (−8.24 kcal/mol). The molecular binding was stabilized through four hydrogen bonds with Glu166 and Thr190 as well as hydrophobic interactions via eight residues. The SARS-CoV-2 Mpro shows identities of 96.08% and 50.65% to that of SARS-CoV Mpro and MERS-CoV Mpro respectively at the sequence level. At the structural level, the root mean square deviation (RMSD) between SARS-CoV-2 Mpro and SARS-CoV Mpro was found to be 0.517 Å and 0.817 Å between SARS-CoV-2 Mpro and MERS-CoV Mpro. Bonducellpin D exhibited broad-spectrum inhibition potential against SARS-CoV Mpro and MERS-CoV Mpro and therefore is a promising drug candidate, which needs further validations through in vitro and in vivo studies.
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Song IS, Jeong YJ, Kim JE, Shin J, Jang SW. Frugoside Induces Mitochondria-Mediated Apoptotic Cell Death through Inhibition of Sulfiredoxin Expression in Melanoma Cells. Cancers (Basel) 2019; 11:cancers11060854. [PMID: 31248223 PMCID: PMC6627655 DOI: 10.3390/cancers11060854] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Revised: 06/12/2019] [Accepted: 06/18/2019] [Indexed: 01/06/2023] Open
Abstract
Malignant melanoma is the most life-threatening neoplasm of the skin. Despite the increase in incidence, melanoma is becoming more resistant to current therapeutic agents. The bioactive compound frugoside has been recently reported to inhibit growth when used in various cancer cells. However, this effect has not been demonstrated in melanoma. Here, we found that frugoside inhibited the rate of reduction of hyperoxidized peroxiredoxins (Prxs) by downregulating sulfiredoxin (Srx) expression. Furthermore, frugoside increased the accumulation of sulfinic Prxs and reactive oxygen species (ROS) and stimulated p-p38 activation, resulting in the mitochondria-mediated death of M14 and A375 human melanoma cells. The mitochondria-mediated cell death induced by frugoside was inhibited by the overexpression of Srx and antioxidants, such as N-acetyl cysteine and diphenyleneiodonium. In addition, we observed that frugoside inhibited tumor growth without toxicity through a M14 xenograft animal model. Taken together, our findings reveal that frugoside exhibits a novel antitumor effect based on a ROS-mediated cell death in melanoma cells, which may have therapeutic implications.
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Affiliation(s)
- In-Sung Song
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Korea.
| | - Yu Jeong Jeong
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Korea.
- Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Korea.
| | - Ji Eun Kim
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Korea.
- Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Korea.
| | - Jimin Shin
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Korea.
- Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Korea.
| | - Sung-Wuk Jang
- Department of Biomedical Sciences, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Korea.
- Asan Medical Institute of Convergence Science and Technology, Asan Medical Center, University of Ulsan College of Medicine, Seoul 138-736, Korea.
- Department of Biochemistry and Molecular Biology, University of Ulsan College of Medicine, Seoul 138-736, Korea.
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