Structurally Observed Electrostatic Features of the COVID-19 Coronavirus-Related Experimental Structures inside Protein Data Bank: A Brief Update

Abstract

Since the Coronavirus disease (COVID-19) outbreak at the end of 2019, the past two month has seen an acceleration both in and outside China in the R&D of the diagnostics, vaccines and therapeutics for this novel coronavirus. As one of the molecular forces that determine protein structure, electrostatic effects dominate many aspects of protein behaviour and biological function. Thus, incorporating currently available experimental structures related to COVID-19, this article reports a simple python-based analysis tool and a LaTeX-based editing tool to extract and summarize the electrostatic features from experimentally determined structures, to strengthen our understanding of COVID-19's structure and function and to facilitate machine-learning and structure-based computational design of its neutralizing antibodies and/or small molecule(s) as potential therapeutic candidates. Finally, this article puts forward a brief update of the structurally observed electrostatic features of the COVID-19 coronavirus.

Additional Positive Electric Residues in the Crucial Spike Glycoprotein S Regions of the New SARS-CoV-2 Variants

“… 3 Similarly, electrical features of the structure of COVID-19 coronavirus have aroused interest since the beginning of the pandemic. 4 An adequate concept was presented that special distributions of charged amino acids ( Figure 1 ) can, in an electrostatic manner, facilitate both the SARS-CoV-2 infection of the cells and the interaction with potential drugs. 5 In the area of biochemical research, the electrostatic inhibition of interplaying furin 6 and the electrostatic interactions of therapeutic antibodies with RBD was considered.…”

A Furin Cleavage Site Inserted into the Spike Protein of SARS-CoV-2: A Structural Implication?

“…Finally, of the inserted FCS in the spike protein of SARS-CoV-2, the structural analysis here constitutes a preliminary starting point pointing towards a comprehensive structural and functional understanding of the spike protein of the causative virus of COVID-19 [5][6][7][8][9].…”

“…It has been more than three months since the emergence of the COVID-19 coronavirus disease [1][2][3][4]. The past three months saw a considerable amount of studies of SARS-CoV-2, the causative virus of COVID-19 [5][6][7][8][9]. The membrane of SARS-CoV-2 harbours a trimeric ( [10]) transmembrane spike (S) glycoprotein, which is essential for the entry of virus particles into the cell.…”

A GIBAC-based selectivity strategy for the design of PDE5 inhibitors to minimize visual disturbances

“…As is known, ligand-receptor binding affinity is an essential parameter in computer-assisted drug discovery and structure-based drug design [23]. Thanks to the continued development of experimental structural biology and the half-a-century old Protein Data Bank (PDB) [24][25][26][27][28], a comprehensive structural biophysical analysis becomes possible [29,30] for specific ligand-receptor complex structures deposited in PDB, such that our understanding of the structural and biophysical basis of their interfacial stability is able to help us modify the binding affinity of certain drug target and its interacting partners [31][32][33][34][35]. Take PDE5 as an example here, where the structural key is the design of non-PDE6binding PDE5 inhibitor (abbreviated below as molecule X), ensuring that:…”