Dataset Information

Virtual Screening for SARS-CoV-2 Main Protease Inhibitory Peptides from the Putative Hydrolyzed Peptidome of Rice Bran.

ABSTRACT: The Coronavirus Disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the loss of life and has affected the life quality, economy, and lifestyle. The SARS-CoV-2 main protease (Mpro), which hydrolyzes the polyprotein, is an interesting antiviral target to inhibit the spreading mechanism of COVID-19. Through predictive digestion, the peptidomes of the four major proteins in rice bran, albumin, glutelin, globulin, and prolamin, with three protease enzymes (pepsin, trypsin, and chymotrypsin), the putative hydrolyzed peptidome was established and used as the input dataset. Then, the prediction of the antiviral peptides (AVPs) was performed by online bioinformatics tools, i.e., AVPpred, Meta-iAVP, AMPfun, and ENNAVIA programs. The amino acid composition and cytotoxicity of candidate AVPs were analyzed by COPid and ToxinPred, respectively. The ten top-ranked antiviral peptides were selected and docked to the SARS-CoV-2 main protease using GalaxyPepDock. Only the top docking scored candidate (AVP4) was further analyzed by molecular dynamics simulation for one nanosecond. According to the bioinformatic analysis results, the candidate SARS-CoV-2 main protease inhibitory peptides were 7-33 amino acid residues and formed hydrogen bonds at Thr22-24, Glu154, and Thr178 in domain 2 with short bonding distances. In addition, these top-ten candidate bioactive peptides contain hydrophilic amino acid residues and have a positive net charge. We hope that this study will provide a potential starting point for peptide-based therapeutic agents against COVID-19.

SUBMITTER: Harnkit N

PROVIDER: S-EPMC9598432 | biostudies-literature | 2022 Sep

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Virtual Screening for SARS-CoV-2 Main Protease Inhibitory Peptides from the Putative Hydrolyzed Peptidome of Rice Bran.

Harnkit Nathaphat N Khongsonthi Thanakamol T Masuwan Noprada N Prasartkul Pornpinit P Noikaew Tipanart T Chumnanpuen Pramote P

Antibiotics (Basel, Switzerland) 20220927 10

The Coronavirus Disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has led to the loss of life and has affected the life quality, economy, and lifestyle. The SARS-CoV-2 main protease (Mpro), which hydrolyzes the polyprotein, is an interesting antiviral target to inhibit the spreading mechanism of COVID-19. Through predictive digestion, the peptidomes of the four major proteins in rice bran, albumin, glutelin, globulin, and prolamin, with three prot ...[more]

PMID: 36289976

Similar Datasets

Project description:De-oiled rice bran (DORB) is a potentially useful by-product of the rice bran oil industry. DORB may prove to be an important protein source, and also contains many other micronutrients. This study has the principal aim of optimizing the process of DORB protein hydrolysate preparation, and then testing the hydrolysate to determine its lipase inhibitory activity. DORB underwent hydrolysis using Alcalase® and response surface methodology (RSM). The resulting degree of hydrolysis (DH) was then monitored along with the extent of any lipase inhibitory activity. The optimum levels of lipase inhibition were obtained at a temperature of 49.88 °C, a duration of 150.43 minutes, and 1.53% Alcalase® used for the sample 5% (w/v) solution. In these conditions, the DH value was 35.65%, and the IC50 value for lipase inhibitory activity was 2.84 μg mL-1. Five ranges of different molecular weights were obtained via fractionation, whereupon it was determined that the highest level of inhibitory activity was achieved by the <0.65 kDa fraction. This fraction was then further purified via RP-HPLC, and the resulting peak had a retention time of 21.75 minutes (F 2 sub-fraction) and exhibited high lipase inhibitory activity. Mass spectrometry was used to determine the amino acid sequence for this peak, identified as FYLGYCDY. This particular peptide is categorized as bitter, with a non-toxic profile, and having poor water solubility. The synthesized form of this peptide showed lipase inhibitory activity measured by an IC50 value of 0.47 ± 0.02 μM. The Lineweaver-Burk plot revealed that FYLGYCDY is a non-competitive inhibitor, while analysis of the docking results provided details of the FYLGYCDY peptide binding site with the porcine pancreatic lipase (PPL) complex, which is a competitive type. It can be inferred from these findings that DORB may prove a useful raw material source for the production of anti-obesity peptides which might enhance the therapeutic and commercial performance of functional foods and healthcare products.

Dataset Information

Virtual Screening for SARS-CoV-2 Main Protease Inhibitory Peptides from the Putative Hydrolyzed Peptidome of Rice Bran.

Publications

Virtual Screening for SARS-CoV-2 Main Protease Inhibitory Peptides from the Putative Hydrolyzed Peptidome of Rice Bran.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets