Targeting SARS-CoV-2 non-structural protein 13 via helicase-inhibitor-repurposing and non-structural protein 16 through pharmacophore-based screening

Abstract

Novel drug compound hunting was carried out for SARS-CoV-2 proteins with low mutation susceptibility. The probability of escape mutation and drug resistance is lower if conserved microbial proteins are targeted by therapeutic drugs. Mutation rate of all SARS-CoV-2 proteins were analyzed via multiple sequence alignment Non-Structural Protein 13 and Non-Structural Protein 16 were selected for the current study due to low mutation rate among viral strains and significant functionality. Cross-species mutation rate analysis for NSP13 and NSP16 showed these are well-conserved proteins among four coronaviral species. Viral helicase inhibitors, identified using literature-mining, were docked against NSP13. Pharmacophore-based screening of 11,375 natural compounds was conducted for NSP16. Stabilities of top compounds inside human body were confirmed via molecular dynamic simulation. ADME properties and LD 50 values of the helicase inhibitors and Ambinter natural compounds were analyzed. Compounds against NSP13 showed binding affinities between −10 and −5.9 kcal/mol whereby ivermectin and scutellarein showed highest binding energies of −10 and −9.9 kcal/mol. Docking of 18 hit compounds against NSP16 yielded binding affinities between −8.9 and −4.1 kcal/mol. Hamamelitannin and deacyltunicamycin were the top compounds with binding affinities of −8.9 kcal/mol and −8.4 kcal/mol. The top compounds showed stable ligand-protein interactions in molecular dynamics simulation. The analyses revealed two hit compounds against each targeted protein displaying stable behavior, high binding affinity and molecular interactions. Conversion of these compounds into drugs after in vitro experimentation can become better treatment options to elevate COVID management.

Biochemical analysis of SARS-CoV-2 Nsp13 helicase implicated in COVID-19 and factors that regulate its catalytic functions

“…The specified concentration of Nsp13 (see Figure Legends ) was pre-incubated with 0.25 nM RNA partial duplex containing the specified number of bp ( 13 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 ) for 5 min at RT in 20 mM HEPES-KOH (pH 7.5), 20 mM NaCl, 1 mM DTT, 100 μg/mL BSA and the indicated concentration of MgCl 2 , as noted in the Figure Legends . Reactions were initiated by the addition of 2 mM ATP, 5 nM unlabeled oligonucleotide (same as radio-labeled oligonucleotide), and 100 nM dT 200 protein trap.…”

“…Nsp13 helicases from SARS-CoV and SARS-CoV-2 differ by just one amino acid at residue 570 (Isoleucine in SARS-CoV and Valine in SARS-CoV-2) ( 17 ). An alignment of Nsp13 from SARS BJ01 and Bat SARS-like coronavirus show over 99% similarity as well ( 18 ). Nsp13 has a low mutation rate with only 23 mutations observed in a sample of 439 SARS-CoV-2 viral strains ( 18 ).…”

“…An alignment of Nsp13 from SARS BJ01 and Bat SARS-like coronavirus show over 99% similarity as well ( 18 ). Nsp13 has a low mutation rate with only 23 mutations observed in a sample of 439 SARS-CoV-2 viral strains ( 18 ). A BLASTp alignment of the MERS (QKF93417.1) and SARS-CoV-2 (YP_009725308.1) Nsp13 amino acid sequences revealed 85% positives and 72% identities over 590 amino acids indicating significant sequence conservation.…”

Therapeutic potential of compounds targeting SARS-CoV-2 helicase

“…The SARS-CoV-2 helicase has been screened, virtually, in many instances ( Supplementary Table S3 ). From our analysis it was observed that most publications have performed virtual screening on commercially available drugs ( Balasubramaniam and Schmookler Reis 2020 ; Borgio et al, 2020 ; Gurung 2020 ; Iftikhar et al, 2020 ; Ugurel et al, 2020 ; Abidi et al, 2021 ; Sundar et al, 2021 ; Alanazi et al, 2022 ; Azmoodeh et al, 2022 ) or natural products ( Kousar et al, 2020 ; Naik et al, 2020 ; Ahmad et al, 2021 ; James et al, 2021 ; Vivek-Ananth et al, 2021 ; Bhargavi et al, 2022 ; Hossain et al, 2022 ; Samdani et al, 2022 ). Other published works make use of fragments ( Freidel and Armen, 2021 ) or publicly available compound libraries ( Mirza and Froeyen, 2020 ; García et al, 2021 ; El Hassab et al, 2022 ; Pitsillou et al, 2022 ).…”

From Hamamelitannin Synthesis to the Study of Enzymatic Acylations of D-Hamamelose

“…The antiviral efficacy against influenza A virus and human papillomavirus of tannins from Hamamelis virginiana bark extract has also been demonstrated [ 32 ]. Gallotannin 1 has also become a relatively successful molecule in various in silico screening models aimed at studying the inhibition of proteins important in the process of carcinogenesis, atherosclerosis, or SARS-CoV-2 disease [ 33 , 34 , 35 , 36 ].…”