Das, Tanushree Mukhopadhyay, Chaitali
Published in
Chemical physics letters
Coarse-grained molecular dynamics simulations of the lipid bilayer mixture of POPC and cholesterol were carried out in the presence and absence of ganglioside monosialo 1 (GM1) with N - terminal domain (NTD) of SARS-CoV-2 spike glycoprotein. The interactions of GM1 with two different NTD orientations were compared. NTD orientation I compactly bind ...
Du, Jianbin Yao, Ning Ma, Xiangyun Wang, Huijie Li, Qifeng Feng, Zhifang
Published in
Chemical Physics Letters
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has spread around the world rapidly, which seriously threatens to human health and safety. The rapid detection of the virus in the early stage is very important to prevent the cross infection and transmission. It is also a key link in the post-treatment examination. This paper has explore...
Ni, Shuang Yang, Qiang Huang, Jinling Zhou, Minjie Wei, Lai Yang, Yue Wen, Jiaxin Mo, Wenbo Le, Wei Qi, Daojian
...
Published in
Chemical physics letters
In order to control COVID-19, rapid and accurate detection of the pathogenic, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an urgent task. The target spike proteins of SARS-CoV-2 have been detected experimentally via Raman spectroscopy. However, there lacks high-accuracy theoretical Raman spectra of the spike proteins to as a st...
Arba, Muhammad Paradis, Nicholas Wahyudi, Setyanto T Brunt, Dylan J Hausman, Katherine R Lakernick, Phillip M Singh, Mursalin Wu, Chun
Published in
Chemical physics letters
The binding of the active form of Remdesivir (RTP) to RNA-dependent RNA Polymerase (RdRp) of SARS-CoV-2 was studied using molecular dynamics simulation. The RTP maintained the interactions observed in the experimental cryo-EM structure. Next, we designed new analogues of RTP, which not only binds to the RNA primer strand in a similar pose as that o...
Ono, Junichi Koshimizu, Uika Fukunishi, Yoshifumi Nakai, Hiromi
Published in
Chemical physics letters
The main protease (Mpro) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) catalyzes the cleavage of polyproteins for viral replication. Here, large-scale quantum molecular dynamics and metadynamics simulations for ligand-free Mpro were performed, where all the atoms were treated quantum-mechanically, focusing on elucidation of the co...
Liang, Julia J Pitsillou, Eleni Ververis, Katherine Guallar, Victor Hung, Andrew Karagiannis, Tom C
Published in
Chemical physics letters
The SARS-CoV-2 papain-like (PLpro) protease is essential for viral replication. We investigated potential antiviral effects of hypericin relative to the well-known noncovalent PLpro inhibitor GRL-0617. Molecular dynamics and PELE Monte Carlo simulations highlight favourable binding of hypericin and GRL-0617 to the naphthalene binding pocket of PLpr...
Tumskiy, Roman S Tumskaia, Anastasiia V
Published in
Chemical physics letters
The main protease (3CLpro) of SARS-CoV and SARS-CoV-2 is a promising target for discovery of novel antiviral agents. In this paper, new possible inhibitors of 3CLpro with high predicted binding affinity were detected through multistep computer-aided molecular design and bioisosteric replacements. For discovery of prospective 3CLpro binders several ...
Pitsillou, Eleni Liang, Julia Yu Meng Huang, Helen Hung, Andrew Karagiannis, Tom C
Published in
Chemical physics letters
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA-dependent RNA polymerase (RdRp) is a promising target for antiviral drugs. In this study, a chemical library (n = 300) was screened against the nidovirus RdRp-associated nucleotidyltransferase (NiRAN) domain. Blind docking was performed using a selection of 30 compounds and nine l...
Itoh, Satoru G Tanimoto, Shoichi Okumura, Hisashi
Published in
Chemical physics letters
One of the promising drug targets against COVID-19 is an RNA-dependent RNA polymerase (RdRp) of SARS-CoV-2. The tertiary structures of the SARS-CoV-2 and SARS-CoV RdRps are almost the same. However, the RNA-synthesizing activity of the SARS-CoV RdRp is higher than that of the SARS-CoV-2 RdRp. We performed molecular dynamics simulations and found di...
Liang, Julia Pitsillou, Eleni Burbury, Lucy Hung, Andrew Karagiannis, Tom C
Published in
Chemical physics letters
The COVID-19 pandemic caused by SARS-CoV-2 has resulted in an international health emergency. The SARS-CoV-2 nsp16 is an S-adenosyl-L-methionine (SAM)-dependent methyltransferase, and with its cofactor nsp10, is responsible for RNA cap formation. This study aimed to identify small molecules binding to the SAM-binding site of the nsp10-nsp16 heterod...
