molecular docking study and mapping the binding site of some antiviral nanobodies against receptor binding domains (rbds) of sars-cov-2 b.1.617

The b.1.617 lineage of severe acute respiratory syndrome coronavirus 2 (sars-cov-2), has spread throughout india, displacing other pre-existing lineages [1]. the sars-cov-2 b.1.617 is case of delta variant pandemic of coronavirus which there is no country in the worldwide is safe from its harm and consequences [2]. the nautralization ability of 51 antiviral nanobody toward rbds of sars-cov 2 b.1.617 against the human angiotensin coverting enzyme 2 (ace2) was repurposed using cluspro server [3].the candidate vhh selected from 1196 nanobodies that was available in structural antibody database (sabdab) [4]. the 21 selected vhh experimentally was neutralized the member glycoprotein of severe acute respiratory syndrome coronavirus 1 (sars-cov-1), middle east respiratory syndrome (mers), human immunodeficiency viruses 1 (hiv-1) or respiratory syncytial virus (rsv). also, 15 candidate nanobodies were blocking the nef and capsid protein p24 of human immunodeficiency viruses 1 (hiv-1) or capsid protein vp3 of poliovirus. moreover, different conformations of nanobodies that are experimentally involved in the rbd of sars-cov 2 were adapted from pdb. regarless of the synthetic nanobodies blocking of spike glycoproteins rbd of sars-cov 2, other natural vhh occurring in lama glama, vicugna pacos or camelus dromedaries. the crystallography structure of rbd-ace2 of sars-cov 2 (6lzg) as well as delta variant mutant rbds of sars-cov-2, t478k (7ora) and l452r (7orb) was taken from protein data bank (pdb). it was seen, sb23, sr4, vhh pvss8a, vhh 17b, vhh pvsp29f, sdab19, vhh pvsp19b, vhh-55, vhh a12, and vhh pvsp6a respectively was proposed for neutralization of t478k rbd with an estimated binding energy greater than -792.4 (kcal/mol) for ace2. also, vhh pvsp6a, sb23, vhh pvsp29f, sr4, vhh-55, and vhh pvsp19b are others proposed nanobodies according the estimated binding energy greater than -812.3 (kcal/mol) for ace2- l452r. overall, sb23, vhh pvsp29f, sr4, vhh-55, and vhh pvsp19b are repurposing nanobodies for based on the censuses decision making for both against both t478k and l452r rbds of sars-cov-2 b.1.617 strain.