Ilimaquinone (marine sponge metabolite) as a novel inhibitor of SARS-CoV-2 key target proteins in comparison with suggested COVID-19 drugs: designing, docking and molecular dynamics simulation study

Abstract

Inhibitory potential of ilimaquinone (marine sponge metabolite) against nine essential SARS-CoV-2 target proteins, employing a molecular interaction and dynamics simulation approach.

Strong Inhibitory Activity and Action Modes of Synthetic Maslinic Acid Derivative on Highly Pathogenic Coronaviruses: COVID-19 Drug Candidate

“…Oleanolic acid (1) and maslinic acid (2), isolated from pomace olive oil, and a series of their synthesized structural analogues (3)(4)(5)(6)(7)(8)(9)(10)(11)(12)(13)(14)(15)(16)(17) were first evaluated using molecular docking for their proposed expected inhibitory activities against SARS-CoV-2 main protease, and then were screened for the same activity. Most of the tested compounds showed promising affinities towards SARS-CoV-2 main protease, especially for the most active member (17).…”

“…Therefore, a lot of FDA approved drugs have been tested or repositioned to act as anti-SARS-CoV-2 [2,3]. In parallel, several trials to virtually recommend or practically test the anti-SARS-CoV-2 activity of synthetic compounds, natural extracts and immunomodulatory agents have been attempted [4][5][6][7].…”

An in-silico evaluation of different bioactive molecules of tea for their inhibition potency against non structural protein-15 of SARS-CoV-2

“…CDOCKER follows a grid based approach towards docking ( Puratchikody et al, 2016 , Wu et al, 2003 ), thus we defined a grid box with a grid angle of 90° and spacing of 0.50. The co-ordinates of the ligand binding site of the input sphere were 10.959, −0.514, 20.8275, 12, with the ligand molecule (citric acid) as the center point ( Chandra et al, 2020 , Kim et al, 2020 , Surti et al, 2020 ). The number of starting random conformations and the number of rotated ligand orientations to refine for each of the conformations for 1000 dynamics steps were set to ten.…”

“…Currently, there are no treatment measures or vaccination against SARS-CoV2, and the requirement of a prophylactic and therapeutic intervention technique is critical ( Shannon et al, 2020 , Sinha et al, 2020 , Walls et al, 2020 ). Targeting the conserved Nsp15 active site via potent inhibitor molecules will not only hinder its involvement in virus replication activity but also prohibit the protein from interfering with the host’s innate immune response, enabling it to fight the viral invasion ( Chandra et al, 2020 , Khan et al, 2020 , Surti et al, 2020 ). The current investigation was performed with the aim of finding potent inhibitor molecules that could strongly bind to the active site of Nsp15.…”

Biflavonoids from Rhus succedanea as probable natural inhibitors against SARS-CoV-2: a molecular docking and molecular dynamics approach

“…Recently, several studies have revealed that many bioactive compounds from different medicinal plants act as promising inhibitors against coronavirus (in review, Siddiqui et al, 2020aSiddiqui et al, , 2020b. Recently, Surti and coworkers have discovered that Ilimaquinone (marine sponge metabolite) as a novel inhibitor of SARS-CoV-2 key target proteins in comparison with suggested COVID-19 drugs (hydroxychloroquine, azithromycin, favipiravir, ivermectin and remdesivir) (Surti et al, 2020). In addition, many antiviral phytocompounds from green tea (catechins or polyphenols); from Indian spices (Rosmanol, Carnosol and Arjunglucoside-I); from buriti oil (Mauritia flexuosa L.) are proposed to be promising against SARS-CoV-2 Mpro protease (Costa et al, 2020;Das et al, 2020;Ghosh et al, 2020;Umesh et al, 2020) R. succedanea (formerly Toxicodendron succedaneum) also known as 'japanese tallow or wax tree' belonging to the Anacardiaceae family is one of the plants with many medicinal properties.…”