Binding Possibilities of Cro-, λ-, and Gal-Repressor Proteins With SARS-CoV-2 Genomes: a Computational Approach for Potential Drug/Vaccine Design

Abstract

Binding possibilities of Cro-, λ- and Gal- repressor proteins with different variants of SARS-CoV-2 genome have been predicted for the first time. Calculations of their binding energy differences with respect to the corresponding wild-type bindings were done. For λ- and Cro- proteins, a large number of binding sites within the genome was observed having binding affinity of varying strengths. Cro-repressor has been found to have higher binding possibility than the λ-repressor. For Gal-repressor no binding site having higher affinity than that for any of its naturally occurring operators was predicted. Binding possibilities with different variants have been found to be mostly similar. Most of the high affinity binding sites have been found to be located within three genes, viz., S, ORF3a and ORF1ab. Binding of repressor proteins with these genes may interrupt their transcription/translation. The gene-products being vitally important for pathogen-activity, this interruption may restrict the infection process. An analysis for efficacy of future drug/vaccine (basically Cro-based peptides) has also been presented. The probability of prospective drug/vaccine being ineffective due to virus mutations in next 50 years is estimated to be negligibly small.