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. 2022 Oct 28;23(21):13082.
doi: 10.3390/ijms232113082.

The Spike Mutants Website: A Worldwide Used Resource against SARS-CoV-2

Isabella Romeo  1   2 , Ingrid Guarnetti Prandi  3 , Emanuela Giombini  4 , Cesare Ernesto Maria Gruber  4 , Daniele Pietrucci  3   5 , Stefano Borocci  3   6 , Nabil Abid  6   7 , Anna Fava  8 , Andrea R Beccari  8 , Giovanni Chillemi  3 , Carmine Talarico  8
Affiliations

The Spike Mutants Website: A Worldwide Used Resource against SARS-CoV-2

Isabella Romeo et al. Int J Mol Sci. .

Abstract

A large number of SARS-CoV-2 mutations in a short period of time has driven scientific research related to vaccines, new drugs, and antibodies to combat the new variants of the virus. Herein, we present a web portal containing the structural information, the tridimensional coordinates, and the molecular dynamics trajectories of the SARS-CoV-2 spike protein and its main variants. The Spike Mutants website can serve as a rapid online tool for investigating the impact of novel mutations on virus fitness. Taking into account the high variability of SARS-CoV-2, this application can help the scientific community when prioritizing molecules for experimental assays, thus, accelerating the identification of promising drug candidates for COVID-19 treatment. Below we describe the main features of the platform and illustrate the possible applications for speeding up the drug discovery process and hypothesize new effective strategies to overcome the recurrent mutations in SARS-CoV-2 genome.

Keywords: COVID-19; SARS-CoV-2; molecular dynamics; mutations; spike; variants.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 5
Figure 5
Per-residue RMSF in SARS-CoV-2 (A) Kappa, (B) Alpha, (C) Ihu, (D) Delta, (E) WT, (F) Zeta, (G) Iota1, (H) Iota2, (I) Epsilon systems. The three S monomers are colored in black, red, and green, respectively. Monomer 2 is in an up conformation (see Section 4). The NTD and RBD regions are highlighted with dashed lines. The S1/S2 boundary at residue 681 is highlighted with a dotted line.
Figure 1
Figure 1
Snapshot of the upper portion of the Spike Mutants portal from where the 3D structure of the spike trimeric protein in glycosylated form and its corresponding MD trajectory 100 ns long can be freely downloaded.
Figure 2
Figure 2
Snapshot of the Spike Mutants portal portions where the 3D structures of the spike protein unglycosylated variants can be freely downloaded. (A) “Variants of Concern” section; (B) “Variants of Interest” section; (C) “Variants under Monitoring” section; (D) virtual reality video of a 3D model of the S protein in interaction with the human receptor ACE2 embedded in a membrane bilayer.
Figure 3
Figure 3
Graphical representation of the phylogenetic tree, included in the Spike Mutants portal constructed by the maximum likelihood method based on whole genome SARS-CoV-2 sequences.
Figure 4
Figure 4
Snapshot of part of the Spike Mutants portal portions where the 3D structures of the spike protein glycosylated variants can be freely downloaded together with their respective MD trajectory, 100 ns long.
Figure 6
Figure 6
Registered users of the Spike Mutants website. (A) Country of origin of the users; (B) First seven countries by number of users. (C) Declared the main research objective of the users.
See this image and copyright information in PMC

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