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Rezaei, R.

Publications and source records attributed to Rezaei, R..

2 recordsLinked to original sources

Characterization of Critical Determinants of ACE2-RBD Interaction

Despite sequence similarity to SARS-CoV-1, SARS-CoV-2 has demonstrated greater widespread virulence and unique challenges to researchers aiming to study its pathogenicity in humans. The interaction of the viral receptor binding domain (RBD) with its main host cell receptor, angiotensin-converting enzyme 2 (ACE2), has emerged as a critical focal point for the development of anti-viral therapeutics and vaccines. Utilizing our recently developed NanoBiT technology-based biosensor, we selectively identify and characterize the impact of mutating certain amino acid residues in the RBD of SARS-CoV-2 and in ACE2. Specifically, we examine the mutational effects on RBD-ACE2 binding ability, before and after the addition of competitive inhibitors, as well as neutralizing antibody activity. These critical determinants of virus-host interactions may provide more effective targets for ongoing vaccines, drug development, and potentially pave the way for determining the genetic variation underlying disease severity.

microbiology

Optimizing Consensus Generation Algorithms for Highly Variable Amino Acid Sequence Clusters

Producing a functional consensus sequence is a preliminary bioinformatics task, which is a necessity for many research purposes. However, the existence of hypervariable regions in the input multiple sequence alignment files causes complications in generating a useful consensus sequence. The current methods for consensus generation, Threshold, and majority algorithms, have several problems, which exclude them as applicable algorithms for such highly variable sequence clusters. Hence, we designed a novel alternative algorithm for the same purpose. The algorithm was explained both using a mathematical formula and a practical implementation in Python programming language. A sequence set from HCV genotype 1b E2 protein has been utilized as a practical example for evaluating the algorithms performance. A few in silico tests have been performed on the output sequence and the results have been compared to results from other algorithms. Epitope-mapping analysis indicates the functionality of this algorithm, by preserving the hotspot residues in the consensus sequence, and the antigenicity index shows significant antigenicity of the consensus sequence. Moreover, phylogenetic analysis shows no significant change in the placement of the new consensus sequence on the phylogenetic tree compared to other algorithms. This approach will have several implications in designing a new vaccine for highly variable viruses such as HIV-1, Influenza, and Hepatitis C Viruses (HCV).

bioinformatics