Open Access
How Does the Novel Coronavirus Interact with the Human ACE2 Enzyme? A Thermodynamic Answer
TLDR
This work presents a chemical reason for the difficulty in treating the SARS-CoV-2 virus using drugs targeting its Spike Protein, as well as helps to explain its infectivity, while defining a minimum free energy of binding for new drugs to be designed against this disease.Citations
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Dual nature of human ACE2 glycosylation in binding to SARS-CoV-2 spike
TL;DR: Using atomistic molecular dynamics simulations, it is found that the glycosylation of the human ACE2 receptor contributes substantially to the binding of the virus and the targeted development of neutralizing antibodies and SARS-CoV-2 fusion inhibitors.
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Molecular Basis of SARS-CoV-2 Infection and Rational Design of Potential Antiviral Agents: Modeling and Simulation Approaches.
Antonio Francés-Monerris,Cécilia Hognon,Tom Miclot,Tom Miclot,Cristina García-Iriepa,Isabel Iriepa,Alessio Terenzi,Stéphanie Grandemange,Giampaolo Barone,Marco Marazzi,Antonio Monari +10 more
TL;DR: This Review focuses on how in silico studies have contributed to the understanding of the SARS-CoV-2 infection mechanism and the proposal of novel and original agents to inhibit the viral key functioning, and demonstrates that molecular modeling and simulation represent an effective approach to gather information on key biological processes and thus guide rational molecular design strategies.
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In silico analysis of the interactions of certain flavonoids with the receptor-binding domain of 2019 novel coronavirus and cellular proteases and their pharmacokinetic properties.
Erman Salih Istifli,Paulo A. Netz,Arzuhan Sihoglu Tepe,Mehmet Tahir Husunet,Cengiz Sarikurkcu,Bektas Tepe +5 more
TL;DR: Although this molecule is not capable of crossing the blood-brain barrier (BBB), (-)-epicatechin gallate can be evaluated as a candidate molecule in drug development studies against 2019-nCoV since it was not the substrate of P-gp, did not inhibit any of the cytochrome Ps, and did not show AMES toxicity or hepatotoxicity on eukaryotic cells.
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Beyond COVID-19: Do biothermodynamic properties allow predicting the future evolution of SARS-CoV-2 variants?
TL;DR: In this paper , an attempt was made to predict the development of the SARS-CoV-2 pandemic, based on biothermodynamic parameters: Gibbs energy energy of binding and Gibbs energy of growth.
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ROS/RNS balancing, aerobic fermentation regulation and cell cycle control a complex early trait ('CoV-MAC-TED') for combating SARS-CoV-2-induced cell reprogramming
José Hélio Costa,Gunasekharan Mohanapriya,Bharadwaj Revuru,Carlos Noceda,Karine Leitão Lima Thiers,Shahid Aziz,Shivani Srivatsava,Manuela Oliveira,Kapuganti Jagadis Gupta,Aparajita Kumari,Debabrata Sircar,Sarma Rajeev Kumar,Arvind Achra,Ramalingam Sathishkumar,Alok Adhloeya,Birgit Arnholdt-Schmitt +15 more
TL;DR: In this paper, a standard profile of selected genes named ReprogVirus was proposed for in vitro-scanning of early virus-induced reprogramming in critical primary infected cells/tissues as target trait.
References
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The COVID-19 vaccine development landscape.
Tung Thanh Le,Zacharias Andreadakis,Arun Kumar,Raúl Gómez Román,Stig Tollefsen,Melanie Saville,Stephen Mayhew +6 more
TL;DR: The Coalition for Epidemic Preparedness Innovations has developed and is continuously maintaining an overview of the global landscape of COVID-19 vaccine development activity, which includes vaccine development programmes reported through the WHO's authoritative and continually updated list, along with other projects identified from publicly available and proprietary sources.
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A generalized reaction field method for molecular dynamics simulations
TL;DR: In this paper, an analytical solution of the linearized Poisson-Boltzmann (PB) equation valid in a spherical region is obtained, which can be used for evaluating the electrostatic potential and its derivative at the origin of the sphere.
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Potent Neutralizing Antibodies against SARS-CoV-2 Identified by High-Throughput Single-Cell Sequencing of Convalescent Patients' B Cells.
Y Cao,Bin Su,Xianghua Guo,Wenjie Sun,Yong-Qiang Deng,Linlin Bao,Qinyu Zhu,Xu Zhang,Yinghui Zheng,Chenyang Geng,Xiaoran Chai,Runsheng He,Xiaofeng Li,Qi Lv,Hua Zhu,Wei Deng,Yanfeng Xu,Yanjun Wang,Luxin Qiao,Yafang Tan,Liyang Song,Guopeng Wang,Xiao-Xia Du,Ning Gao,Jiangning Liu,Junyu Xiao,Xiao-Dong Su,Zongmin Du,Yingmei Feng,Chuan Qin,Cheng-Feng Qin,Ronghua Jin,X. Sunney Xie +32 more
TL;DR: It is shown that human neutralizing antibodies could be efficiently discovered by high-throughput single B-cell sequencing in response to pandemic infectious diseases.
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Structure-based design of antiviral drug candidates targeting the SARS-CoV-2 main protease.
Wenhao Dai,Wenhao Dai,Bing Zhang,Xia Ming Jiang,Haixia Su,Jian Li,Jian Li,Yao Zhao,Xiong Xie,Zhenming Jin,Jingjing Peng,Fengjiang Liu,Chunpu Li,You Li,Fang Bai,Haofeng Wang,Xi Cheng,Xiaobo Cen,Shulei Hu,Xiuna Yang,Jiang Wang,Xiang Liu,Gengfu Xiao,Hualiang Jiang,Zihe Rao,Lei Ke Zhang,Yechun Xu,Haitao Yang,Hong Liu +28 more
TL;DR: Two peptidomimetic aldehydes were designed, synthesized, and evaluated as antiviral drug candidates, and both exhibited excellent inhibitory activity and potent anti-SARS-CoV-2 infection activity.
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An orally bioavailable broad-spectrum antiviral inhibits SARS-CoV-2 in human airway epithelial cell cultures and multiple coronaviruses in mice.
Timothy P. Sheahan,Amy C. Sims,Shuntai Zhou,Rachel L. Graham,Andrea J. Pruijssers,Maria L. Agostini,Sarah R. Leist,Alexandra Schäfer,Kenneth H. Dinnon,Laura J. Stevens,James D. Chappell,Xiaotao Lu,Tia M. Hughes,Amelia S. George,Collin S. Hill,Stephanie A. Montgomery,Ariane J. Brown,Gregory R. Bluemling,Michael G. Natchus,Manohar Saindane,Alexander A. Kolykhalov,George R. Painter,Jennifer L Harcourt,Azaibi Tamin,Natalie J. Thornburg,Ronald Swanstrom,Mark R. Denison,Ralph S. Baric +27 more
TL;DR: It is shown that the ribonucleoside analog β-d-N4-hydroxycytidine (NHC; EIDD-1931) has broad-spectrum antiviral activity against SARS- coV-2, MERS-CoV, SARS, and related zoonotic group 2b or 2c bat-CoVs, as well as increased potency against a CoV bearing resistance mutations to the nucleosid analog inhibitor remdesivir