| dc.description.abstract | Severe acute respiratory syndrome 2 (SARS-CoV-2) has been recognized
as a deadly epidemic since it was first detected in the end of 2019 at Wuhan fish
market, China. Recently, three SARS-CoV-2 variants of concern, B.1.1.7,
B.1.351, and B.1.1.248, among many developing variants are known to carry
several mutations within the spike protein which introduce an emergent of
mutant escape. In the context of fast transmission, optimizing antibody
therapeutic strategies to target specific epitopes of multiple mutant viral strains
remains challenging. Herein, we performed in silico molecular docking of two
broad-spectrum nanobodies targeting the Receptor-Binding Domain of different
SARS-CoV-2 variants of concern. In this study, four protein-protein docking
applications ZDOCK 3.0.2, MEGADOCK 4.0, Cluspro and HADDOCK, were utilized
to investigate the molecular interaction of nanobodies binding to targeted-RBD
on S spikes across SARS-CoV-2 variants. To evaluate neutralization ability of
nanobody comparing to in vitro activity, nanobody structures were
computationally grafted from complementarity-determining regions (CDRs) of
synthetic construct nanobodies that were involved in experimentally against the
RBD of SARS-CoV-2. Nanobody structures were computationally grafted from
complementarity-determining regions (CDRs) of synthetic build nanobodies that
were involved experimentally against the RBD of SARS-CoV-2 in order to
evaluate neutralizing ability relative to in vitro activity. Considering four docking
tools, our results show that HADDOCK and Cluspro are most capable of offering
dependable results. However, ZDOCK 3.0.2 and MEGADOCK 4.0 failed to achieve
the desired results using multiple assessment methods. According to our
understanding, the purpose of this research is to contribute to the docking
validation of various protein-protein docking techniques in order to get a
trustworthy outcome in the current SARS-CoV-2 pandemic challenge, which has
a restricted crystallographic structure. To our knowledge, this research aims to
contribute to the docking validation of different protein-protein docking tools in
present SARS-CoV-2 pandemic challenge, which has a restricted availability of
crystallographic structure. | en_US |
