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Article ; Online: Pinpointing top inhibitors for GSK3β from pool of indirubin derivatives using rigorous computational workflow and their validation using molecular dynamics (MD) simulations.

Pandya, Vamangi / Rao, Priyashi / Prajapati, Jignesh / Rawal, Rakesh M / Goswami, Dweipayan

2024 Volume 14, Issue 1, Page(s) 49

Abstract: Glycogen synthase kinase-3β (GSK3β) is a pivotal protein kinase implicated in a spectrum of debilitating diseases, encompassing cancer, diabetes, and neurodegenerative disorders. While the therapeutic potential of GSK3β inhibition is widely recognized, ... ...

Abstract	Glycogen synthase kinase-3β (GSK3β) is a pivotal protein kinase implicated in a spectrum of debilitating diseases, encompassing cancer, diabetes, and neurodegenerative disorders. While the therapeutic potential of GSK3β inhibition is widely recognized, there remains an unmet need for a rigorous, systematic analysis probing the theoretical inhibition dynamics of a comprehensive library of indirubin derivatives against GSK3β using advanced computational methodologies. Addressing this gap, this study embarked on an ambitious endeavor, leveraging indirubin-a renowned scaffold-as a template to curate a vast library of 1000 indirubin derivatives from PubChem. These were enriched with varied substitutions and modifications, identified via a structure similarity search with a Tanimoto similarity threshold of 85%. Harnessing a robust virtual screening workflow, we meticulously identified the top 10 contenders based on XP docking scores. Delving deeper, we gauged the binding free energy differentials (ΔGBind) of these hits, spotlighting the top three compounds that showcased unparalleled binding prowess. A comparative pharmacophore feature mapping with the reference inhibitor OH8, co-crystallized with GSK3β (PDB ID: 6Y9R), was undertaken. The binding dynamics of these elite compounds were further corroborated with 100 ns molecular dynamics simulations, underlining their stable and potent interactions with GSK3β. Remarkably, our findings unveil that these indirubin derivatives not only match but, in certain scenarios, surpass the binding affinity and specificity of OH8. By bridging this research chasm, our study amplifies the therapeutic promise of indirubin derivatives, positioning them as frontrunners in the quest for groundbreaking GSK3β inhibitors, potentially revolutionizing treatments for a myriad of ailments.
MeSH term(s)	Molecular Dynamics Simulation ; Glycogen Synthase Kinase 3 beta ; Workflow ; Indoles/pharmacology ; Molecular Docking Simulation
Chemical Substances	Glycogen Synthase Kinase 3 beta (EC 2.7.11.1) ; indirubin (V86L8P74GI) ; Indoles
Language	English
Publishing date	2024-01-02
Publishing country	England
Document type	Journal Article
ZDB-ID	2615211-3
ISSN	2045-2322 ; 2045-2322
ISSN (online)	2045-2322
ISSN	2045-2322
DOI	10.1038/s41598-023-50992-7
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Article ; Online: Comprehensive computational investigation for ligand recognition and binding dynamics of SdiA: a degenerate LuxR -type receptor in Klebsiella pneumoniae.

Panchal, Janki / Prajapati, Jignesh / Dabhi, Milan / Patel, Arun / Patel, Sandip / Rawal, Rakesh / Saraf, Meenu / Goswami, Dweipayan

Molecular diversity

2024

Abstract: SdiA is a LuxR-type receptor that controls the virulence of Klebsiella pneumoniae, a Gram-negative bacterium that causes various infections in humans. SdiA senses exogenous acyl-homoserine lactones (AHLs) and autoinducer-2 (AI-2), two types of quorum ... ...

Abstract	SdiA is a LuxR-type receptor that controls the virulence of Klebsiella pneumoniae, a Gram-negative bacterium that causes various infections in humans. SdiA senses exogenous acyl-homoserine lactones (AHLs) and autoinducer-2 (AI-2), two types of quorum sensing signals produced by other bacterial species. However, the molecular details of how SdiA recognizes and binds to different ligands and how this affects its function and regulation in K. pneumoniae still need to be better understood. This study uses computational methods to explore the protein-ligand binding dynamics of SdiA with 11 AHLs and 2 AI-2 ligands. The 3D structure of SdiA was predicted through homology modeling, followed by molecular docking with AHLs and AI-2 ligands. Binding affinities were quantified using MM-GBSA, and complex stability was assessed via Molecular Dynamics (MD) simulations. Results demonstrated that SdiA in Klebsiella pneumoniae exhibits a degenerate binding nature, capable of interacting with multiple AHLs and AI-2. Specific ligands, namely C10-HSL, C8-HSL, 3-oxo-C8-HSL, and 3-oxo-C10-HSL, were found to have high binding affinities and formed critical hydrogen bonds with key amino acid residues of SdiA. This finding aligns with the observed preference of SdiA for AHLs having 8 to 10 carbon-length acyl chains and lacking hydroxyl groups. In contrast, THMF and HMF demonstrated poor binding properties. Furthermore, AI-2 exhibited a low affinity, corroborating the inference that SdiA is not the primary receptor for AI-2 in K. pneumoniae. These findings provide insights into the protein-ligand binding dynamics of SdiA and its role in quorum sensing and virulence of K. pneumoniae.
Language	English
Publishing date	2024-01-12
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-023-10785-6
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Article ; Online: Endophytic fungi: A treasure trove of novel anticancer compounds.

Prajapati, Jignesh / Goswami, Dweipayan / Rawal, Rakesh M

Current research in pharmacology and drug discovery

2021 Volume 2, Page(s) 100050

Abstract: Cancer is a multifactorial disease with a convoluted genesis and progression. The emergence of multidrug resistance to presently be offered drug and relapse is by far, the most critical concern to tackle this deteriorating disease. Henceforth, there is ... ...

Abstract	Cancer is a multifactorial disease with a convoluted genesis and progression. The emergence of multidrug resistance to presently be offered drug and relapse is by far, the most critical concern to tackle this deteriorating disease. Henceforth, there is undeniably an inflated necessity for safe, promising, and less harmful new anticancer drugs. Natural compounds from various sources like plants, animals, and microorganisms have occupied a center stage in drug discovery due to their tremendous chemical diversity and potential as therapeutic agents. Endophytic microbes are symbiotically associated with plants and have been proven to produce novel or analogues of host bioactive metabolites exhibiting a variety of biological activities including anticancer activity. This review emphasizes on structurally diverse unprecedented anticancer natural compounds that have been reported exclusively from endophytic fungi from 2016 to 2020. It covers chemical nature of metabolites, its fungal source associated with terrestrial, as well as marine plants and anticancer activity based on their cytotoxicity profile against various cancer cell lines. Many of these fungal metabolites with promising anticancer activity can be used as lead molecules for
Language	English
Publishing date	2021-09-01
Publishing country	Netherlands
Document type	Journal Article
ISSN	2590-2571
ISSN (online)	2590-2571
DOI	10.1016/j.crphar.2021.100050
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Article ; Online: A Comprehensive in vitro and in silico Assessment on Inhibition of CYP51B and Ergosterol Biosynthesis by Eugenol in Rhizopus oryzae

Prajapati, Jignesh / Rao, Priyashi / Poojara, Lipi / Acharya, Dhaval / Patel, Saumya K. / Goswami, Dweipayan / Rawal, Rakesh M.

Curr Microbiol. 2023 Jan., v. 80, no. 1 p.47-47

2023

Abstract: Mucormycosis, also known as Zygomycosis, is a disease caused by invasive fungi, predominantly Rhizopus species belonging to the Order of Mucorales. Seeing from the chemistry perspective, heterocyclic compounds with an "azole" moiety are widely employed ... ...

Abstract	Mucormycosis, also known as Zygomycosis, is a disease caused by invasive fungi, predominantly Rhizopus species belonging to the Order of Mucorales. Seeing from the chemistry perspective, heterocyclic compounds with an "azole" moiety are widely employed as antifungal agent for minimising the effect of mucormycosis as a prescribed treatment. These azoles serve as non-competitive inhibitors of fungal CYP51B by predominantly binding to its heme moiety, rendering its inhibition. However, long-term usage and abuse of azoles as antifungal medicines has resulted in drug resistance among certain fungal pathogens. Hence, there is an unmet need to find alternative therapeutic compounds. In present study, we used various in vitro tests to investigate the antifungal activity of eugenol against R. oryzae/R. arrhizus, including ergosterol quantification to test inhibition of ergosterol production mediated antifungal action. The minimum inhibitory concentration (MIC) value obtained for eugenol was 512 μg/ml with reduced ergosterol concentration of 77.11 ± 3.25% at MIC/2 concentration. Further, the molecular interactions of eugenol with fungal CYP51B were meticulously studied making use of proteomics in silico study including molecular docking and molecular dynamics simulations that showed eugenol to be strongly interacting with heme in an identical fashion to that shown by azole drugs (in this case, clotrimazole was evaluated). This is the first of a kind study showing the simulation study of eugenol with CYP51B of fungi. This inhibition results in ergosterol synthesis and is also studied and compared with keeping clotrimazole as a reference.
Keywords	Rhizopus oryzae ; antifungal properties ; biosynthesis ; clotrimazole ; computer simulation ; drug resistance ; ergosterol ; eugenol ; fungi ; heme ; minimum inhibitory concentration ; moieties ; molecular dynamics ; proteomics ; therapeutics ; zygomycosis
Language	English
Dates of publication	2023-01
Size	p. 47.
Publishing place	Springer US
Document type	Article ; Online
ZDB-ID	134238-1
ISSN	1432-0991 ; 0343-8651
ISSN (online)	1432-0991
ISSN	0343-8651
DOI	10.1007/s00284-022-03108-9
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Article: An anecdote of mechanics for Fusarium biocontrol by plant growth promoting microbes

Patel, Rohit / Mehta, Krina / Prajapati, Jignesh / Shukla, Arpit / Parmar, Paritosh / Goswami, Dweipayan / Saraf, Meenu

Biological control. 2022 Nov., v. 174

2022

Abstract: Fusariumis a phytopathogenic mold that belongs to ascomycetes group which are frequently associated with a range of plant diseases such as root and stem rots,blights, and wilts. The mycotoxins produced by Fusarium sp. are responsible for its invasion ... ...

Abstract	Fusariumis a phytopathogenic mold that belongs to ascomycetes group which are frequently associated with a range of plant diseases such as root and stem rots,blights, and wilts. The mycotoxins produced by Fusarium sp. are responsible for its invasion into fresh fruits and vegetables during storage, causing various rots and spoilage. Conventional approaches for control of Fusarium include the use of fungicides which leads to disruption of indigenous rhizospheric microflora. Therefore, the need of the hour is to design a strategy that selectively targets the phytopathogens without interfering with the natural functioning of the plant and its rhizosphere. Genome mining has enabled the prediction, prioritization, and identification of effector genes (foa, foc, avr and lys) in Fusarium which has extended the existing understanding of host-pathogen interaction that could pave a path towards sustainable genetic immunization of plant against related phytopathogens. Gene clusters in plant growth promoting microbes such as, ituDABC (Bacillus sp.) and phlACBD (Pseudomonas sp.) are identified to be involved in production of iturin and 2,4 –diacetylphloroglucinol, respectively, to control the proliferation of Fusarium. This review describes the microbiological understanding of Fusarium for phytopathogens along with recent developments in its biocontrol by incorporating molecular and computational biology approaches.
Keywords	Bacillus (bacteria) ; Fusarium ; Pseudomonas ; bioinformatics ; biological control ; host-pathogen relationships ; immunization ; iturin ; mechanics ; microorganisms ; mycotoxins ; plant growth ; plant pathogens ; prediction ; prioritization ; rhizosphere ; spoilage
Language	English
Dates of publication	2022-11
Publishing place	Elsevier Inc.
Document type	Article
ZDB-ID	1149971-0
ISSN	1049-9644
ISSN	1049-9644
DOI	10.1016/j.biocontrol.2022.105012
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Article: Perceiving SARS-CoV-2 Mpro and PLpro dual inhibitors from pool of recognized antiviral compounds of endophytic microbes: an in silico simulation study.

Prajapati, Jignesh / Patel, Rohit / Rao, Priyashi / Saraf, Meenu / Rawal, Rakesh / Goswami, Dweipayan

Structural chemistry

2022 Volume 33, Issue 5, Page(s) 1619–1643

Abstract: Coronavirus disease 2019 (COVID-19) persists and shook the global population where the endgame to this pandemic is brought on by developing vaccines in record-breaking time. Nevertheless, these vaccines are far from perfect where their efficiency ranges ... ...

Abstract	Coronavirus disease 2019 (COVID-19) persists and shook the global population where the endgame to this pandemic is brought on by developing vaccines in record-breaking time. Nevertheless, these vaccines are far from perfect where their efficiency ranges from 65 to 90%; therefore, vaccines are not the one only solution to overcome this situation, and apart from administration of vaccines, the scientific community is at quest for finding alternative solutions to incumber SARS-CoV-2 infection. In this study, our research group is keen on identifying a bioactive molecule that is independent in its mode of action from existing vaccines which can potentially target the SARS-CoV-2 virus replicative efficacy. Papain-like protease (PLpro) and main protease (Mpro) are the most lucrative targets of COVIDs against which the drugs can be developed, as these proteases play a vital role in the replication and development of viral particles. Researchers have modelled a compound such as GRL0617 and X77 as an inhibitor of Mpro and PLpro, respectively, but use of these compounds has several limitations on hosts like toxicity and solubility. Under the current study by deploying rigorous computational assessments, pool of microbial secondary metabolites was screened and handpicked to search a structural or functional analogue of GRL0617 and X77, with an idea to identify a compound that can serve as dual inhibitor for both PLpro and Mpro. From the manually curated database of known antiviral compounds from fungal origin, we found cytonic acids A and B to potentially serve as dual inhibitor of PLpro and Mpro.
Language	English
Publishing date	2022-04-08
Publishing country	United States
Document type	Journal Article
ZDB-ID	2018832-8
ISSN	1572-9001 ; 1040-0400
ISSN (online)	1572-9001
ISSN	1040-0400
DOI	10.1007/s11224-022-01932-0
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Article ; Online: Potential dual inhibition of SE and CYP51 by eugenol conferring inhibition of Candida albicans: Computationally curated study with experimental validation.

Prajapati, Jignesh / Goswami, Dweipayan / Dabhi, Milan / Acharya, Dhaval / Rawal, Rakesh M

Computers in biology and medicine

2022 Volume 151, Issue Pt A, Page(s) 106237

Abstract: Ergosterol is the key sterol component in the cell membrane of fungi including moulds and yeasts. Any decrease in the levels of ergosterol in the cell membrane of fungi render them venerable to cell membrane damage and even its death. Majority of ... ...

Abstract	Ergosterol is the key sterol component in the cell membrane of fungi including moulds and yeasts. Any decrease in the levels of ergosterol in the cell membrane of fungi render them venerable to cell membrane damage and even its death. Majority of antifungal drug targets the key enzymes involved in ergosterol biosynthesis pathway. The biochemical pathway for the synthesis of Ergosterol is a complex one, though the reactions carried by Squalene Epoxidase (SE) and 14α-demethylase (CYP51- a member of Cytochrome P450 family) serves to the key rate limiting reactions that can impact the overall production of Ergosterol. Allylamines class of antifungal drug target SE while Azoles target the CYP51. Currently advancement in the drug development is focused to introduce newer drugs that can simultaneously inhibit both this rate limiting enzymes. However, natural compounds established to possess antifungal activity but the major loophole about their understanding lies in the fact that their mode of action are severely unstudied. One such well-established antifungal natural phytochemical is Eugenol, and in current manuscript we investigated its efficacy to interact with both, SE and CYP51 of Candida albicans using molecular Docking, Free energy change calculations and Molecular Dynamics (MD) simulation, showing promising outcomes. For experimental studies, terbinafine, clotrimazole and eugenol showed 4 μg/ml, 2 μg/ml, and 512 μg/ml MIC
MeSH term(s)	Candida albicans ; Squalene Monooxygenase ; Antifungal Agents/pharmacology ; Antifungal Agents/chemistry ; Eugenol/pharmacology ; Eugenol/chemistry ; Molecular Docking Simulation ; Ergosterol
Chemical Substances	Squalene Monooxygenase (EC 1.14.14.17) ; Antifungal Agents ; Eugenol (3T8H1794QW) ; Ergosterol (Z30RAY509F)
Language	English
Publishing date	2022-10-26
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2022.106237
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Article ; Online: Interactive bioinformatics analysis for the screening of hub genes and molecular docking of phytochemicals present in kitchen spices to inhibit CDK1 in cervical cancer.

Vaghasia, Harsha / Sakaria, Shiralee / Prajapati, Jignesh / Saraf, Meenu / Rawal, Rakesh M

Computers in biology and medicine

2022 Volume 149, Page(s) 105994

Abstract: Cervical cancer (CC) is the world's fourth most prevalent cancer among women. The mortality rate of cervical cancer increases each year due to a lack of early diagnosis. Our study aims to find potential genes linked to cervical cancer and validate the ... ...

Abstract	Cervical cancer (CC) is the world's fourth most prevalent cancer among women. The mortality rate of cervical cancer increases each year due to a lack of early diagnosis. Our study aims to find potential genes linked to cervical cancer and validate the findings using docking analysis. The microarray datasets (GSE6791, GSE7803, GSE9750, GSE39001, GSE52903, GSE63514, and GSE75132) were downloaded from the GEO (Gene Expression Omnibus) database. A total of 1160 Differentially Expressed Genes (DEGs) were discovered using the R statistical language, including 825 up-regulated and 335 down-regulated genes. STRING, which predicts the potential interaction between genes at the protein level, was used to build the PPI network of these DEGs. Moreover, hub gene expression analysis was carried out by CytoHubba plugin Cytoscape. CDK1 was considered for subsequent molecular docking because of its frequent appearance throughout the analysis. CDK1 was docked with the 399 phytochemicals of Indian kitchen spices. The top three compounds namely, Vicenin 2, 2-O,3-O,4-O,6-O-Tetragalloyl-d-glucopyranose and Pentagalloylglucose, were chosen based on their docking scores and their interactions with the key amino acids present in the ATP binding pocket, like the positive control Dinaciclib. In conclusion, the findings of this study may lead to new insights on CC diagnosis, aetiology, and treatment options. In the future, it may be possible to develop particular diagnostics and therapies for CC by identifying hub genes and studying overexpressed proteins as therapeutic targets.
MeSH term(s)	Adenosine Triphosphate ; Amino Acids ; CDC2 Protein Kinase/genetics ; Computational Biology ; Early Detection of Cancer ; Female ; Gene Expression Profiling ; Gene Expression Regulation, Neoplastic ; Gene Regulatory Networks ; Humans ; Molecular Docking Simulation ; Phytochemicals ; Uterine Cervical Neoplasms/drug therapy ; Uterine Cervical Neoplasms/genetics
Chemical Substances	Amino Acids ; Phytochemicals ; Adenosine Triphosphate (8L70Q75FXE) ; CDC2 Protein Kinase (EC 2.7.11.22) ; CDK1 protein, human (EC 2.7.11.22)
Language	English
Publishing date	2022-08-19
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2022.105994
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Article ; Online: Repurposing the antibacterial drugs for inhibition of SARS-CoV2-PLpro using molecular docking, MD simulation and binding energy calculation.

Patel, Rohit / Prajapati, Jignesh / Rao, Priyashi / Rawal, Rakesh M / Saraf, Meenu / Goswami, Dweipayan

Molecular diversity

2021 Volume 26, Issue 4, Page(s) 2189–2209

Abstract: Papain-like protease (nsp-3; non-structural protein) of novel corona virus is an ideal target for developing drugs as it plays multiple important functions for viral growth and replication. For instance, role of nsp-3 has been recognized in cleavage of ... ...

Abstract	Papain-like protease (nsp-3; non-structural protein) of novel corona virus is an ideal target for developing drugs as it plays multiple important functions for viral growth and replication. For instance, role of nsp-3 has been recognized in cleavage of viral polyprotein; furthermore, in infected host it weakens the immune system via downregulating the production of type I interferon. This downregulation is promoted by removal of ubiquitin-like interferon-stimulated gene 15 protein (ISG15) from interferon-responsive factor 3 (IRF3) protein. Among known inhibitors of SARS-CoV-PLpro GRL0617 is by far the most effective inhibitor. As PLpro of SARS-CoV2 is having more than 80% similarity with SARS-CoV-PLpro, GRL0617 is reported to be effective even against SARS-CoV2. Owing to this similarity, certain key amino acids remain the same/conserved in both proteins. Among conserved amino acids Tyr268 for SARS-CoV2 and Tyr269 for SARS-CoV produce important hydrophobic interactions with aromatic rings of GRL0617. Here, in this study antibacterial compounds were collected from ZINC database, and they were filtered to select compounds that are having similar structural features as GRL0617. This filtered library of compound was then docked with SARS-CoV and CoV2-PLpro. Five hits were noted that were able to interact with Tyr268 (SARS-CoV2) and Tyr269 (SARS-CoV). Further, best hit 2-(2-((benzofuran-2-carboxamido)methyl)-5-methoxy-1H-indol-1-yl)acetic acid (ZINC44459905) was studied using molecular dynamic simulation where stability of protein-ligand complex as well as stability of produced interactions was noted.
MeSH term(s)	Amino Acids ; Aniline Compounds/pharmacology ; Anti-Bacterial Agents ; Benzamides/pharmacology ; COVID-19/drug therapy ; Coronavirus Papain-Like Proteases/antagonists & inhibitors ; Drug Repositioning ; Humans ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Naphthalenes/pharmacology ; RNA, Viral ; SARS-CoV-2/drug effects ; Ubiquitins/chemistry ; Ubiquitins/metabolism
Chemical Substances	5-amino-2-methyl-N-((R)-1-(1-naphthyl)ethyl)benzamide ; Amino Acids ; Aniline Compounds ; Anti-Bacterial Agents ; Benzamides ; Naphthalenes ; RNA, Viral ; Ubiquitins ; Coronavirus Papain-Like Proteases (EC 3.4.22.2) ; papain-like protease, SARS-CoV-2 (EC 3.4.22.2)
Language	English
Publishing date	2021-09-30
Publishing country	Netherlands
Document type	Journal Article
ZDB-ID	1376507-3
ISSN	1573-501X ; 1381-1991
ISSN (online)	1573-501X
ISSN	1381-1991
DOI	10.1007/s11030-021-10325-0
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Article ; Online: Sterenin M as a potential inhibitor of SARS-CoV-2 main protease identified from MeFSAT database using molecular docking, molecular dynamics simulation and binding free energy calculation.

Prajapati, Jignesh / Patel, Rohit / Goswami, Dweipayan / Saraf, Meenu / Rawal, Rakesh M

Computers in biology and medicine

2021 Volume 135, Page(s) 104568

Abstract: The disease outbreak of Coronavirus disease-19 (COVID-19), caused by the novel SARS-CoV-2 virus, remains a public health concern. COVID-19 is spreading rapidly with a high mortality rate due to unavailability of effective treatment or vaccine for the ... ...

Abstract	The disease outbreak of Coronavirus disease-19 (COVID-19), caused by the novel SARS-CoV-2 virus, remains a public health concern. COVID-19 is spreading rapidly with a high mortality rate due to unavailability of effective treatment or vaccine for the disease. The high rate of mutation and recombination in SARS-CoV2 makes it difficult for scientist to develop specific anti-CoV2 drugs and vaccines. SARS-CoV-2-Mpro cleaves the viral polyprotein to produce a variety of non-structural proteins, but in human host it also cleaves the nuclear transcription factor kappa B (NF-κB) essential modulator (NEMO), which suppresses the activation of the NF-κB pathway and weakens the immune response. Since the main protease (Mpro) is required for viral gene expression and replication, it is a promising target for antagonists to treat novel coronavirus disease and discovery of high resolution crystal structure of SARS-CoV-2-Mpro provide an opportunity for in silico identification of its possible inhibitors. In this study we intend to find novel and potential Mpro inhibitors from around 1830 chemically diverse and therapeutically important secondary metabolites available in the MeFSAT database by performing molecular docking against the Mpro structure of SARS-CoV-2 (PDB ID: 6LZE). After ADMET (absorption, distribution, metabolism, excretion, and toxicity) profile and binding energy calculation through MM-GBSA for top five hits, Sterenin M was proposed as a SARS-CoV2-Mpro inhibitor with validation of molecular dynamics (MD) simulation study. Sterenin M seems to have the potential to be a promising ligand against SARS-CoV-2, and thus it requires further validation by in vitro and in vivo studies.
MeSH term(s)	Coronavirus 3C Proteases/antagonists & inhibitors ; Indoles/pharmacology ; Molecular Docking Simulation ; Molecular Dynamics Simulation ; Protease Inhibitors/pharmacology ; RNA, Viral ; SARS-CoV-2/drug effects
Chemical Substances	Indoles ; Protease Inhibitors ; RNA, Viral ; 3C-like proteinase, SARS-CoV-2 (EC 3.4.22.-) ; Coronavirus 3C Proteases (EC 3.4.22.28)
Language	English
Publishing date	2021-06-12
Publishing country	United States
Document type	Journal Article
ZDB-ID	127557-4
ISSN	1879-0534 ; 0010-4825
ISSN (online)	1879-0534
ISSN	0010-4825
DOI	10.1016/j.compbiomed.2021.104568
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