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Computer-Aided Screening for Potential Coronavirus 3-Chymotrypsin-like Protease (3CLpro) Inhibitory Peptides from Putative Hemp Seed Trypsinized Peptidome.
Prasertsuk, Kansate; Prongfa, Kasidit; Suttiwanich, Piyapach; Harnkit, Nathaphat; Sangkhawasi, Mattanun; Promta, Pongsakorn; Chumnanpuen, Pramote.
  • Prasertsuk K; Pibulwitthayalai School, 777 Naraimaharach, Talaychoopsorn, Lopburi District, Lopburi 15000, Thailand.
  • Prongfa K; Pibulwitthayalai School, 777 Naraimaharach, Talaychoopsorn, Lopburi District, Lopburi 15000, Thailand.
  • Suttiwanich P; Pibulwitthayalai School, 777 Naraimaharach, Talaychoopsorn, Lopburi District, Lopburi 15000, Thailand.
  • Harnkit N; Medicinal Plant Research Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand.
  • Sangkhawasi M; Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand.
  • Promta P; Pibulwitthayalai School, 777 Naraimaharach, Talaychoopsorn, Lopburi District, Lopburi 15000, Thailand.
  • Chumnanpuen P; Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand.
Molecules ; 28(1)2022 Dec 21.
Article in English | MEDLINE | ID: covidwho-2244344
ABSTRACT
To control the COVID-19 pandemic, antivirals that specifically target the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are urgently required. The 3-chymotrypsin-like protease (3CLpro) is a promising drug target since it functions as a catalytic dyad in hydrolyzing polyprotein during the viral life cycle. Bioactive peptides, especially food-derived peptides, have a variety of functional activities, including antiviral activity, and also have a potential therapeutic effect against COVID-19. In this study, the hemp seed trypsinized peptidome was subjected to computer-aided screening against the 3CLpro of SARS-CoV-2. Using predictive trypsinized products of the five major proteins in hemp seed (i.e., edestin 1, edestin 2, edestin 3, albumin, and vicilin), the putative hydrolyzed peptidome was established and used as the input dataset. To select the Cannabis sativa antiviral peptides (csAVPs), a predictive bioinformatic analysis was performed by three webserver screening programs iAMPpred, AVPpred, and Meta-iAVP. The amino acid composition profile comparison was performed by COPid to screen for the non-toxic and non-allergenic candidates, ToxinPred and AllerTOP and AllergenFP, respectively. GalaxyPepDock and HPEPDOCK were employed to perform the molecular docking of all selected csAVPs to the 3CLpro of SARS-CoV-2. Only the top docking-scored candidate (csAVP4) was further analyzed by molecular dynamics simulation for 150 nanoseconds. Molecular docking and molecular dynamics revealed the potential ability and stability of csAVP4 to inhibit the 3CLpro catalytic domain with hydrogen bond formation in domain 2 with short bonding distances. In addition, these top ten candidate bioactive peptides contained hydrophilic amino acid residues and exhibited a positive net charge. We hope that our results may guide the future development of alternative therapeutics against COVID-19.
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Full text: Available Collection: International databases Database: MEDLINE Main subject: Peptides / Cannabis / Coronavirus Protease Inhibitors / SARS-CoV-2 / COVID-19 Drug Treatment Type of study: Prognostic study / Reviews Limits: Humans Language: English Journal subject: Biology Year: 2022 Document Type: Article Affiliation country: Molecules28010050

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Full text: Available Collection: International databases Database: MEDLINE Main subject: Peptides / Cannabis / Coronavirus Protease Inhibitors / SARS-CoV-2 / COVID-19 Drug Treatment Type of study: Prognostic study / Reviews Limits: Humans Language: English Journal subject: Biology Year: 2022 Document Type: Article Affiliation country: Molecules28010050