Unravelling the therapeutic potential of marine drugs as SARS-CoV-2 inhibitors: An insight from essential dynamics and free energy landscape.

Computers in Biology and Medicine
Shailima RampoguKeun Woo Lee


Coronavirus disease 2019 (COVID-19) is an ongoing pandemic. The virus that causes the disease, severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), predominantly infects the respiratory tract, which may lead to pneumonia and death in severe cases. Many marine compounds have been found to have immense medicinal value and have gained approval from the Food and Drug Administration (FDA), and some are being tested in clinical trials. In the current investigation, we redirected a number of marine compounds toward SARS-CoV-2 by targeting the main protease (Mpro, PDB ID: 6Y2F), subjecting them to several advanced computational techniques using co-crystallised ligand as the reference compound. The results of the binding affinity studies showed that two compounds, eribulin mesylate (eri) and soblidotin (sob), displayed higher docking scores than did the reference compound. When these compounds were assessed using molecular dynamics simulation, it was evident that they demonstrated stable binding at the binding pocket of the target protein. The systems demonstrated stable root mean square deviation and radius of gyration values, while occupying the binding pocket during the simulation run. Furthermore, the essential dynamics and...Continue Reading


Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Oct 8, 2005·Journal of Computational Chemistry·David Van Der SpoelHerman J C Berendsen
Mar 27, 2010·Antiviral Research·Jarred Yasuhara-Bell, Yuanan Lu
Apr 7, 2010·Trends in Pharmacological Sciences·Alejandro M S MayerDale E Shuster
May 5, 2011·Journal of Computational Chemistry·Vincent ZoeteOlivier Michielin
Jan 11, 2013·BMC Bioinformatics·B JayaramVandana Shekhar
May 8, 2013·Bioorganic & Medicinal Chemistry·Ji-Young ParkYoung Bae Ryu
Dec 1, 2004·Drug Discovery Today. Technologies·Christopher A Lipinski
Apr 4, 2015·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Nicholas F Dybdal-HargreavesSusan L Mooberry
Sep 25, 2015·Nucleic Acids Research·Sunghwan KimStephen H Bryant
May 3, 2016·Journal of Pharmacy & Bioallied Sciences·Harshad Malve
Mar 18, 2017·Acta Pharmaceutica Sinica. B·Zongru Guo
Nov 16, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Ashwini Machhindra LondheAe Nim Pae
Jan 19, 2020·International Journal of Infectious Diseases : IJID : Official Publication of the International Society for Infectious Diseases·David S HuiEskild Petersen
Jan 23, 2020·Journal of Medical Virology·Yu ChenDeyin Guo
Apr 1, 2020·International Journal of Biological Sciences·Jun Zheng
Apr 1, 2020·Microbiology Australia·John S Mackenzie, David W Smith
Apr 7, 2020·Life Sciences·Mahmoud Kandeel, Mohammed Al-Nazawi
Apr 16, 2020·International Journal of Molecular Sciences·Yung-Fang TuShih-Hwa Chiou
Apr 18, 2020·Gene Reports·Rozhgar A KhailanyMehmet Ozaslan
May 15, 2020·Nature·Denisa BojkovaChristian Münch
May 16, 2020·Journal of Biomolecular Structure & Dynamics·Muhammad Tahir KhanDong-Qing Wei
May 31, 2020·International Journal of Molecular Sciences·Aleix GimenoSantiago Garcia-Vallvé
Aug 26, 2020·BioRxiv : the Preprint Server for Biology·Catherine Z ChenWei Zheng
Sep 6, 2020·Pharmacological Reports : PR·Thakur Uttam SinghRaj Kumar Singh
Nov 5, 2020·Briefings in Bioinformatics·Serena DotoloRoberto Tagliaferri
Nov 27, 2020·Frontiers in Pharmacology·Janet SultanaGianluca Trifirò
Dec 18, 2020·ACS Pharmacology & Translational Science·Catherine Z ChenGary R Whittaker
Feb 14, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Poonam KalhotraTzayhri Gallardo-Velazquez

❮ Previous
Next ❯


❮ Previous
Next ❯

Software Mentioned

Discovery Studio
visual dynamics ( VMD )
Clean Protein

Related Concepts

Trending Feeds


Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.


Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.


Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.