Interface-based design of the favipiravir-binding site in SARS-CoV-2 RNA-dependent RNA polymerase reveals mutations conferring resistance to chain termination.
TLDR
In this article, the authors used high-throughput interface-based protein design to generate >100k designs of the favipiravir-binding site of RdRp and identify mutational hotspots.About:
This article is published in FEBS Letters.The article was published on 2021-09-01 and is currently open access. It has received 19 citations till now. The article focuses on the topics: Favipiravir & RNA-dependent RNA polymerase.read more
Citations
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Genomic Variations in the Structural Proteins of SARS-CoV-2 and Their Deleterious Impact on Pathogenesis: A Comparative Genomics Approach.
Taj Mohammad,Arunabh Choudhury,Insan Habib,Purva Asrani,Yash Mathur,Mohd Umair,Farah Anjum,Alaa Shafie,Dharmendra Kumar Yadav,Md. Imtaiyaz Hassan +9 more
TL;DR: In this paper, a comparative genomics analysis of the structural proteins of SARS-CoV-2 has been performed to get deeper insights into the mechanism of pathogenesis, structure-function relationships and development of modern therapeutic approaches.
Journal ArticleDOI
Oral antiviral treatments for COVID-19: opportunities and challenges
Laila Rahmah,Sunny O. Abarikwu,Amanuel Godana Arero,Aliyu Tijani Jibril,Andrzej M Fal,Robert Flisiak,Rangarirai Makuku,Leander Marquez,Kawthar Mohamed,Lamin Ndow,Dorota Zarębska-Michaluk,Nima Rezaei,Piotr Rzymski +12 more
TL;DR: In this paper , the authors present the potential pharmaceutical antiviral targets, including various host-based targets and viral based targets, and characterizes the first-generation anti-SARS-CoV-2 oral drugs (nirmatrelvir/ritonavir and molnupiravir).
Journal ArticleDOI
Identification of broad anti-coronavirus chemical agents for repurposing against SARS-CoV-2 and variants of concern
TL;DR: In this paper , an image-based multicycle infection procedure with α-coronavirus hCoV-229E-eGFP was performed in an arrayed chemical library screen of 5440 clinical and preclinical compounds.
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Lethal Mutagenesis of RNA Viruses and Approved Drugs with Antiviral Mutagenic Activity
TL;DR: Among approved nucleoside analogs, experiments with polioviruses and other RNA viruses suggested that ribavirin can be mutagenic, although its mechanism of action is not clear.
Journal ArticleDOI
Hotspot residues and resistance mutations in the nirmatrelvir-binding site of SARS-CoV-2 main protease: Design, identification, and correlation with globally circulating viral genomes
Aditya K. Padhi,Timir Tripathi +1 more
TL;DR: In this article , a high-throughput protein design technique, the hotspot residues, and signatures of adaptation of Mpro having the highest probability of mutating and rendering nirmatrelvir ineffective were identified.
References
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WebLogo: A Sequence Logo Generator
TL;DR: WebLogo generates sequence logos, graphical representations of the patterns within a multiple sequence alignment that provide a richer and more precise description of sequence similarity than consensus sequences and can rapidly reveal significant features of the alignment otherwise difficult to perceive.
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A new coronavirus associated with human respiratory disease in China.
Fan Wu,Su Zhao,Bin Yu,Yan-Mei Chen,Wen Wang,Zhi gang Song,Yi Hu,Zhao Wu Tao,Jun Hua Tian,Yuan Yuan Pei,Ming Li Yuan,Yu Ling Zhang,Fa Hui Dai,Yi Liu,Qi Min Wang,Jiao Jiao Zheng,Lin Xu,Edward C. Holmes,Edward C. Holmes,Yong-Zhen Zhang,Yong-Zhen Zhang +20 more
TL;DR: Phylogenetic and metagenomic analyses of the complete viral genome of a new coronavirus from the family Coronaviridae reveal that the virus is closely related to a group of SARS-like coronaviruses found in bats in China.
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Tracking Changes in SARS-CoV-2 Spike: Evidence that D614G Increases Infectivity of the COVID-19 Virus.
Bette T. Korber,Will Fischer,Sandrasegaram Gnanakaran,Hyejin Yoon,James Theiler,Werner Abfalterer,Nick Hengartner,Elena E. Giorgi,Tanmoy Bhattacharya,Brian T. Foley,Kathryn M. Hastie,Matthew Parker,David G Partridge,Cariad Evans,Timothy M. Freeman,Thushan I de Silva,Adrienne Angyal,Rebecca Brown,Laura Carrilero,Luke R. Green,Luke R. Green,Luke R. Green,Danielle C. Groves,Katie Johnson,Alexander J Keeley,Benjamin B Lindsey,Paul J. Parsons,Mohammad Raza,Sarah Rowland-Jones,Nikki Smith,Rachel Tucker,Dennis Wang,Matthew Wyles,Charlene McDanal,Lautaro G. Perez,Haili Tang,Alex Moon-Walker,Alex Moon-Walker,Alex Moon-Walker,Sean P. J. Whelan,Celia C. LaBranche,Erica Ollmann Saphire,David C. Montefiori +42 more
TL;DR: A SARS-CoV-2 variant carrying the Spike protein amino acid change D614G has become the most prevalent form in the global pandemic, and it is found that the G614 variant grows to higher titer as pseudotyped virions.
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Spike mutation D614G alters SARS-CoV-2 fitness.
Jessica A. Plante,Yang Liu,Jianying Liu,Hongjie Xia,Bryan A. Johnson,Kumari G. Lokugamage,Xianwen Zhang,Antonio E. Muruato,Jing Zou,Camila R. Fontes-Garfias,Divya Mirchandani,Dionna Scharton,John P. Bilello,Zhiqiang Ku,Zhiqiang An,Birte Kalveram,Alexander N. Freiberg,Vineet D. Menachery,Xuping Xie,Kenneth S. Plante,Scott C. Weaver,Pei Yong Shi +21 more
TL;DR: Hamsters infected with SARS-CoV-2 expressing spike D614G (G614 virus) produced higher infectious titres in nasal washes and the trachea, but not in the lungs, supporting clinical evidence showing that the mutation enhances viral loads in the upper respiratory tract of COVID-19 patients and may increase transmission.
Journal ArticleDOI
Structure of the RNA-dependent RNA polymerase from COVID-19 virus.
Yan Gao,Yan Gao,Liming Yan,Yucen Huang,Fengjiang Liu,Yao Zhao,Lin Cao,Tao Wang,Qianqian Sun,Zhenhua Ming,Lianqi Zhang,Ji Ge,Litao Zheng,Ying Zhang,Haofeng Wang,Haofeng Wang,Yan Zhu,Chen Zhu,Tianyu Hu,Tian Hua,Bing Zhang,Xiuna Yang,Jun Li,Haitao Yang,Zhi-Jie Liu,Wenqing Xu,Luke W. Guddat,Quan Wang,Zhiyong Lou,Zihe Rao +29 more
TL;DR: The structure of the COVID-19 virus polymerase essential for viral replication provides a basis for the design of new antiviral drugs that target viral RdRp, also named nsp12, and it appears to be a primary target for the antiviral drug remdesivir.