Identification and in silico molecular modelling study of newly isolated Bacillus subtilis SI-18 strain against S9 protein of Rhizoctonia solani

Islam, Md. Samiul; Mahmud, Shafi; Sultana, Razia; Dong, Wubei

doi:10.1016/j.arabjc.2020.09.044

Cited by 25 publications

(14 citation statements)

References 60 publications

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“…Piperine, an ethanol extract compound of the fruits of Piper longum L. that suppress hemorrhage, and alleviates the lethality of Russell’s viper ( Doboia russelii ) venom in vivo [ 22 , 23 ]. Elderberry extract demonstrates a proficient effect against influenza A and B virus, whereas black soybean extract subdues coxsackievirus B1 and human adenovirus (type 1) [ 24 , 25 , 26 ]. The key antimicrobial compound of Allium sativum extract is allicin and the trypsin-like protease activity (which involves in developing periodontitis disease) of Porphyromonas gingivalis nearly entirely inhibited by allicin [ 27 ].…”

Section: Introductionmentioning

confidence: 99%

Efficacy of Phytochemicals Derived from Avicennia officinalis for the Management of COVID-19: A Combined In Silico and Biochemical Study

et al. 2021

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The recent coronavirus disease 2019 (COVID-19) pandemic is a global threat for healthcare management and the economic system, and effective treatments against the pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus responsible for this disease have not yet progressed beyond the developmental phases. As drug refinement and vaccine progression require enormously broad investments of time, alternative strategies are urgently needed. In this study, we examined phytochemicals extracted from Avicennia officinalis and evaluated their potential effects against the main protease of SARS-CoV-2. The antioxidant activities of A. officinalis leaf and fruit extracts at 150 µg/mL were 95.97% and 92.48%, respectively. Furthermore, both extracts displayed low cytotoxicity levels against Artemia salina. The gas chromatography–mass spectroscopy analysis confirmed the identifies of 75 phytochemicals from both extracts, and four potent compounds, triacontane, hexacosane, methyl linoleate, and methyl palminoleate, had binding free energy values of −6.75, −6.7, −6.3, and −6.3 Kcal/mol, respectively, in complexes with the SARS-CoV-2 main protease. The active residues Cys145, Met165, Glu166, Gln189, and Arg188 in the main protease formed non-bonded interactions with the screened compounds. The root-mean-square difference (RMSD), root-mean-square fluctuations (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen bond data from a molecular dynamics simulation study confirmed the docked complexes′ binding rigidity in the atomistic simulated environment. However, this study′s findings require in vitro and in vivo validation to ensure the possible inhibitory effects and pharmacological efficacy of the identified compounds.

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Section: Introductionmentioning

confidence: 99%

Efficacy of Phytochemicals Derived from Avicennia officinalis for the Management of COVID-19: A Combined In Silico and Biochemical Study

et al. 2021

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“…The time-step of the simulation cell was set as 1.25 fs and each of the trajectories were saved at a 100-ps interval. Finally, the simulation was carried out for 100 ns to analyze the root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent accessible surface area (SASA), and hydrogen bond [ 25 , 26 , 27 , 28 ].…”

Section: Methodsmentioning

confidence: 99%

Drug Repurposing Approach against Novel Coronavirus Disease (COVID-19) through Virtual Screening Targeting SARS-CoV-2 Main Protease

Chowdhury

Mahmud

et al. 2020

Biology

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Novel coronavirus disease (COVID-19) was identified from China in December 2019 and spread rapidly through human-to-human transmission, affecting so many people worldwide. Until now, there has been no specific treatment against the disease and repurposing of the drug. Our investigation aimed to screen potential inhibitors against coronavirus for the repurposing of drugs. Our study analyzed sequence comparison among SARS-CoV, SARS-CoV-2, and MERS-CoV to determine the identity matrix using discovery studio. SARS-CoV-2 Mpro was targeted to generate an E-pharmacophore hypothesis to screen drugs from the DrugBank database having similar features. Promising drugs were used for docking-based virtual screening at several precisions. Best hits from virtual screening were subjected to MM/GBSA analysis to evaluate binding free energy, followed by the analysis of binding interactions. Furthermore, the molecular dynamics simulation approaches were carried out to assess the docked complex’s conformational stability. A total of 33 drug classes were found from virtual screening based on their docking scores. Among them, seven potential drugs with several anticancer, antibiotic, and immunometabolic categories were screened and showed promising MM/GBSA scores. During interaction analysis, these drugs exhibited different types of hydrogen and hydrophobic interactions with amino acid residue. Besides, 17 experimental drugs selected from virtual screening might be crucial for drug discovery against COVID-19. The RMSD, RMSF, SASA, Rg, and MM/PBSA descriptors from molecular dynamics simulation confirmed the complex’s firm nature. Seven promising drugs for repurposing against SARS-CoV-2 main protease (Mpro), namely sapanisertib, ornidazole, napabucasin, lenalidomide, daniquidone, indoximod, and salicylamide, could be vital for the treatment of COVID-19. However, extensive in vivo and in vitro studies are required to evaluate the mentioned drug’s activity.

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“…The simulation was run by using 1.25 fs time step. The trajectories were saved after every 100 ps to analyze the root mean square deviation, root mean square fluctuations, hydrogen bond, radius of gyration, and solvent accessible surface area (Bappy et al, 2020;Khan et al, 2020;Islam et al, 2020;Mahmud et al, 2020a;Mahmud et al, 2020b;Mahmud et al, 2021b;Swargiary et al, 2020;Chowdhury et al, 2021;Rakib et al, 2021;Uddin et al, 2021).…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Prospective Role of Peptide-Based Antiviral Therapy Against the Main Protease of SARS-CoV-2

Mahmud

Paul

Biswas

et al. 2021

Front. Mol. Biosci.

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The recently emerged coronavirus (SARS-CoV-2) has created a crisis in world health, and economic sectors as an effective treatment or vaccine candidates are still developing. Besides, negative results in clinical trials and effective cheap solution against this deadly virus have brought new challenges. The viral protein, the main protease from SARS-CoV-2, can be effectively targeted due to its viral replication and pathogenesis role. In this study, we have enlisted 88 peptides from the AVPdb database. The peptide molecules were modeled to carry out the docking interactions. The four peptides molecules, P14, P39, P41, and P74, had more binding energy than the rest of the peptides in multiple docking programs. Interestingly, the active points of the main protease from SARS-CoV-2, Cys145, Leu141, Ser139, Phe140, Leu167, and Gln189, showed nonbonded interaction with the peptide molecules. The molecular dynamics simulation study was carried out for 200 ns to find out the docked complex’s stability where their stability index was proved to be positive compared to the apo and control complex. Our computational works based on peptide molecules may aid the future development of therapeutic options against SARS-CoV-2.

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Identification and in silico molecular modelling study of newly isolated Bacillus subtilis SI-18 strain against S9 protein of Rhizoctonia solani

Cited by 25 publications

References 60 publications

Efficacy of Phytochemicals Derived from Avicennia officinalis for the Management of COVID-19: A Combined In Silico and Biochemical Study

Efficacy of Phytochemicals Derived from Avicennia officinalis for the Management of COVID-19: A Combined In Silico and Biochemical Study

Drug Repurposing Approach against Novel Coronavirus Disease (COVID-19) through Virtual Screening Targeting SARS-CoV-2 Main Protease

Prospective Role of Peptide-Based Antiviral Therapy Against the Main Protease of SARS-CoV-2

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