TY - JOUR

T1 - Antiviral Potential of Antillogorgia americana and elisabethae Natural Products against nsp16–nsp10 Complex, nsp13, and nsp14 Proteins of SARS-CoV-2: An In Silico Investigation

AU - Pokharkar, Omkar

AU - Lakshmanan, Hariharan

AU - Zyryanov, Grigory V.

AU - Tsurkan, Mikhail V.

N1 - This work was supported by the Ministry of Science and Higher Education of the Russian Federation, Agreement #075-15-2022-1118, dated 29 June 2022.

PY - 2023

Y1 - 2023

N2 - Biomolecules of marine origin have many applications in the field of biotechnology and medicine, but still hold great potential as bioactive substances against different diseases. The purification or total synthesis of marine metabolites is expensive, and requires a reliable selection method to reveal their pharmaceutical potential prior to clinical validation. This study aimed to explore the hidden potential of natural products from the gorgonian genus Antillogorgia as anti-SARS-CoV-2 agents, via binding affinity assessments and molecular dynamics (MDs) simulations. The three-dimensional protein structures of the nsp16–nsp10 complex, nsp13, and nsp14 were acquired from the RCSB PDB database. All 165 natural products (NPs) were discovered using the PubChem, ChemSpider, and CMNPD databases. The freeware Autodock Vina was used to conduct the molecular docking procedure, once the proteins and ligands were prepared using BIOVIA discovery studio and Avogadro software v1.95. Before running MDs simulations using the CABS-flex 2.0 website, the binding affinity assessments and amino acid interactions were carefully examined. Just twelve NPs were selected, and five of those NPs interacted optimally with the catalytic amino acids of proteins. To conclude, pseudopterosin A (−8.0 kcal/mol), seco-pseudopterosin A (−7.2 kcal/mol), sandresolide B (−6.2 kcal/mol), elisabatin A (−7.0 kcal/mol), and elisapterosin A (−10.7 kcal/mol) appeared to be the most promising candidates against the nsp16–nsp10, nsp13, and nsp14 proteins.

AB - Biomolecules of marine origin have many applications in the field of biotechnology and medicine, but still hold great potential as bioactive substances against different diseases. The purification or total synthesis of marine metabolites is expensive, and requires a reliable selection method to reveal their pharmaceutical potential prior to clinical validation. This study aimed to explore the hidden potential of natural products from the gorgonian genus Antillogorgia as anti-SARS-CoV-2 agents, via binding affinity assessments and molecular dynamics (MDs) simulations. The three-dimensional protein structures of the nsp16–nsp10 complex, nsp13, and nsp14 were acquired from the RCSB PDB database. All 165 natural products (NPs) were discovered using the PubChem, ChemSpider, and CMNPD databases. The freeware Autodock Vina was used to conduct the molecular docking procedure, once the proteins and ligands were prepared using BIOVIA discovery studio and Avogadro software v1.95. Before running MDs simulations using the CABS-flex 2.0 website, the binding affinity assessments and amino acid interactions were carefully examined. Just twelve NPs were selected, and five of those NPs interacted optimally with the catalytic amino acids of proteins. To conclude, pseudopterosin A (−8.0 kcal/mol), seco-pseudopterosin A (−7.2 kcal/mol), sandresolide B (−6.2 kcal/mol), elisabatin A (−7.0 kcal/mol), and elisapterosin A (−10.7 kcal/mol) appeared to be the most promising candidates against the nsp16–nsp10, nsp13, and nsp14 proteins.

UR - http://www.scopus.com/inward/record.url?partnerID=8YFLogxK&scp=85172162846

UR - https://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=tsmetrics&SrcApp=tsm_test&DestApp=WOS_CPL&DestLinkType=FullRecord&KeyUT=001076376000001

U2 - 10.3390/microbiolres14030068

DO - 10.3390/microbiolres14030068

M3 - Article

VL - 14

SP - 993

EP - 1019

JO - Microbiology Research

JF - Microbiology Research

SN - 2036-7473

IS - 3

ER -