2022
DOI: 10.3390/metabo12100982
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Cheminformatics Bioprospection of Broad Spectrum Plant Secondary Metabolites Targeting the Spike Proteins of Omicron Variant and Wild-Type SARS-CoV-2

Abstract: The spike protein (SP) of SARS-CoV-2 (SC-2) is susceptible to high mutation and has contributed to the multiple waves of COVID-19 being experienced. Hence, targeting the SP remains a logical approach in the development of potent therapeutics against SARS-CoV-2. Here, a computational technique was adopted to identify broad-spectrum plant secondary metabolites with indigenous relevance in the management of respiratory infections against the SPs of the SC-2 wild- type (SC-2WT) and omicron variants. Following 100 … Show more

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Cited by 11 publications
(7 citation statements)
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“…The RMSF quantifies the average position of protein residues over time from their reference position 29 , 30 . As a result, it analyzes the structural parts that vary most or least within a protein, thereby providing information on the stability of formed intra-molecular and inter-molecular bonds.…”
Section: Resultsmentioning
confidence: 99%
See 1 more Smart Citation
“…The RMSF quantifies the average position of protein residues over time from their reference position 29 , 30 . As a result, it analyzes the structural parts that vary most or least within a protein, thereby providing information on the stability of formed intra-molecular and inter-molecular bonds.…”
Section: Resultsmentioning
confidence: 99%
“…Numerous thermodynamic factors, such as flexibility, stability, compactness, and the interactions of proteins with their key amino acids, affect the capacity of ligands to bind to and inactivate the target protein 30 , 35 , 36 . Consequently, the study analyzed the length, number, and type of binding interactions formed by the best compounds with CviR at various periods (Supplementary Figs.…”
Section: Resultsmentioning
confidence: 99%
“…These structures were optimised by removing water molecules and non-standard naming protein residue connectivity [ 23 ]. Molecular docking of the structures: SARS-CoV-2 spike protein (target) and furin protease (ligand), or SARS-CoV-2 spike protein (target) and A. fumigatus alkaline protease 1 (ligand), were performed using the open-source computational tool known as the high ambiguity driven protein-protein docking (HADDOCK) ( https://haddock.science.uu.nl ) [ 24 ].…”
Section: Methodsmentioning
confidence: 99%
“…Data Science, machine learning and data-driven science have emerged as the 4 th paradigm of science (38), Hence, DS and ML has gaining importance not only in chemistry, but also in correlated disciplines such as Materials Science (39), Biology (40,41) and Health Sciences (42)(43)(44). Despite the growing interest and research in ML tools for chemistry, data collection and storage is a critical step in ML model design and validation, since the size of dataset is of utmost importance in ML.…”
Section: Outlook and Perspective Of Data Science And Machine Learning...mentioning
confidence: 99%