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Han L, Wang B, Sun K, Sitara M, Li M, Wang P, Chen N, Yu XA, Tian J. A SARS-CoV-2 M pro fluorescent sensor for exploring pharmacodynamic substances from traditional Chinese medicine. Analyst 2024; 149:3585-3595. [PMID: 38767148 DOI: 10.1039/d4an00372a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2024]
Abstract
The main protease of SARS-CoV-2 (SARS-CoV-2 Mpro) plays a critical role in the replication and life cycle of the virus. Currently, how to screen SARS-CoV-2 Mpro inhibitors from complex traditional Chinese medicine (TCM) is the bottleneck for exploring the pharmacodynamic substances of TCM against SARS-CoV-2. In this study, a simple, cost-effective, rapid, and selective fluorescent sensor (TPE-S-TLG sensor) was designed with an AIE (aggregation-induced emission) probe (TPE-Ph-In) and the SARS-CoV-2 Mpro substrate (S-TLG). The TPE-S-TLG sensor was characterized using UV-Vis absorption spectroscopy, fluorescence spectroscopy, dynamic light scattering (DLS), transmission electron microscopy (TEM), zeta potential, and Fourier transform infrared (FTIR) spectroscopy techniques. The limit of detection of this method to detect SARS-CoV-2 Mpro was measured to be 5 ng mL-1. Furthermore, the TPE-S-TLG sensor was also successfully applied to screen Mpro inhibitors from Xuebijing injection using the separation and collection of the HPLC-fully automatic partial fraction collector (HPLC-FC). Six active compounds, including protocatechualdehyde, chlorogenic acid, hydroxysafflower yellow A, caffeic acid, isoquercetin, and pentagalloylglucose, were identified using UHPLC-Q-TOF/MS that could achieve 90% of the Mpro inhibition rate for the Xuebijing injection. Accordingly, the strategy can be broadly applied in the detection of disease-related proteases as well as screening active substances from TCM.
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Affiliation(s)
- Lei Han
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China.
| | - Bing Wang
- NMPA Key Laboratory for Quality Research and Evaluation of Traditional Chinese Medicine, Shenzhen Institute for Drug Control, Shenzhen, 518057, People's Republic of China.
| | - Kunhui Sun
- NMPA Key Laboratory for Quality Research and Evaluation of Traditional Chinese Medicine, Shenzhen Institute for Drug Control, Shenzhen, 518057, People's Republic of China.
| | - Muqadas Sitara
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China.
| | - Meifang Li
- NMPA Key Laboratory for Quality Research and Evaluation of Traditional Chinese Medicine, Shenzhen Institute for Drug Control, Shenzhen, 518057, People's Republic of China.
| | - Ping Wang
- NMPA Key Laboratory for Quality Research and Evaluation of Traditional Chinese Medicine, Shenzhen Institute for Drug Control, Shenzhen, 518057, People's Republic of China.
| | - Ning Chen
- NMPA Key Laboratory for Quality Research and Evaluation of Traditional Chinese Medicine, Shenzhen Institute for Drug Control, Shenzhen, 518057, People's Republic of China.
| | - Xie-An Yu
- NMPA Key Laboratory for Quality Research and Evaluation of Traditional Chinese Medicine, Shenzhen Institute for Drug Control, Shenzhen, 518057, People's Republic of China.
| | - Jiangwei Tian
- State Key Laboratory of Natural Medicines, Jiangsu Key Laboratory of TCM Evaluation and Translational Research, School of Traditional Chinese Pharmacy, China Pharmaceutical University, Nanjing, 211198, People's Republic of China.
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2
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Stewart J, Shawon J, Ali MA, Williams B, Shahinuzzaman ADA, Rupa SA, Al-Adhami T, Jia R, Bourque C, Faddis R, Stone K, Sufian MA, Islam R, McShan AC, Rahman KM, Halim MA. Antiviral peptides inhibiting the main protease of SARS-CoV-2 investigated by computational screening and in vitro protease assay. J Pept Sci 2024; 30:e3553. [PMID: 38031661 DOI: 10.1002/psc.3553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/29/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023]
Abstract
The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays an important role in viral replication and transcription and received great attention as a vital target for drug/peptide development. Therapeutic agents such as small-molecule drugs or peptides that interact with the Cys-His present in the catalytic site of Mpro are an efficient way to inhibit the protease. Although several emergency-approved vaccines showed good efficacy and drastically dropped the infection rate, evolving variants are still infecting and killing millions of people globally. While a small-molecule drug (Paxlovid) received emergency approval, small-molecule drugs have low target specificity and higher toxicity. Besides small-molecule drugs, peptide therapeutics are thus gaining increasing popularity as they are easy to synthesize and highly selective and have limited side effects. In this study, we investigated the therapeutic value of 67 peptides targeting Mpro using molecular docking. Subsequently, molecular dynamics (MD) simulations were implemented on eight protein-peptide complexes to obtain molecular-level information on the interaction between these peptides and the Mpro active site, which revealed that temporin L, indolicidin, and lymphocytic choriomeningitis virus (LCMV) GP1 are the best candidates in terms of stability, interaction, and structural compactness. These peptides were synthesized using the solid-phase peptide synthesis protocol, purified by reversed-phase high-performance liquid chromatography (RP-HPLC), and authenticated by mass spectrometry (MS). The in vitro fluorometric Mpro activity assay was used to validate the computational results, where temporin L and indolicidin were observed to be very active against SARS-CoV-2 Mpro with IC50 values of 38.80 and 87.23 μM, respectively. A liquid chromatography-MS (LC-MS) assay was developed, and the IC50 value of temporin L was measured at 23.8 μM. The solution-state nuclear magnetic resonance (NMR) structure of temporin L was determined in the absence of sodium dodecyl sulfate (SDS) micelles and was compared to previous temporin structures. This combined investigation provides critical insights and assists us to further develop peptide inhibitors of SARS-CoV-2 Mpro through structural guided investigation.
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Affiliation(s)
- James Stewart
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Jakaria Shawon
- Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
| | - Md Ackas Ali
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Blaise Williams
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - A D A Shahinuzzaman
- Pharmaceutical Sciences Research Division, Bangladesh Council of Scientific and Industrial Research (BCSIR), Dhaka, Bangladesh
| | | | - Taha Al-Adhami
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Science, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Ruoqing Jia
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Cole Bourque
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Ryan Faddis
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Kaylee Stone
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
| | - Md Abu Sufian
- School of Pharmacy, Temple University, Philadelphia, PA, USA
| | - Rajib Islam
- Division of Infectious Diseases and Division of Computer-Aided Drug Design, The Red-Green Research Centre, BICCB, Tejgaon, Dhaka, Bangladesh
- Department of Chemistry, Clemson University, Clemson, SC, USA
| | - Andrew C McShan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA, USA
| | - Khondaker Miraz Rahman
- Institute of Pharmaceutical Science, School of Cancer and Pharmaceutical Science, Faculty of Life Sciences and Medicine, King's College London, London, UK
| | - Mohammad A Halim
- Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, GA, USA
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3
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Alshammari SO. Marine Brown Algae-Derived Compounds as Potential Inhibitors of Japanese Encephalitis Virus RNA-Dependent RNA Polymerase. Mar Drugs 2024; 22:92. [PMID: 38393063 PMCID: PMC10890675 DOI: 10.3390/md22020092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 02/07/2024] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
The Japanese encephalitis virus (JEV) is a mosquito-borne flavivirus that primarily affects people in Asia and seriously threatens public health. Considering the rising occurrence rates and lack of targeted antiviral treatments, it is essential to comprehend and tackle obstacles related to JEV in order to lessen its influence on world health. This investigation explores compounds derived from marine brown algae (Phaeophyceae) as potential inhibitors of JEV RNA-dependent RNA polymerase (RdRp), a critical enzyme in the virus's replication cycle. Employing the computational virtual screen approach, four compounds, i.e., CMNPD16749, CMNPD2606, CMNPD27817, and CMNPD23662, with favorable binding energies ranging from -15.7 Kcal/mol to -13.9 kcal/mol were identified. Subsequently, through molecular docking analysis, the interactions responsible for the binding stability between the target protein and hit molecules compared to the reference molecule Galidesvir were studied. Further, through extensive molecular dynamic (MD) simulation studies at 200 ns, it was confirmed that each docked complex showed acceptable dynamic stability compared to the reference molecule. These findings were further validated using MM/PBSA free binding energy calculations, PCA analysis and free energy landscape construction. These computational findings suggested that the brown algae-derived compounds may act as an antiviral drug against JEV infection and lay a crucial foundation for future experimental studies against JEV.
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Affiliation(s)
- Saud O Alshammari
- Department of Pharmacognosy and Alternative Medicine, Faculty of Pharmacy, Northern Border University, Rafha 76321, Saudi Arabia
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4
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Iwaniak A, Minkiewicz P, Darewicz M. Bioinformatics and bioactive peptides from foods: Do they work together? ADVANCES IN FOOD AND NUTRITION RESEARCH 2024; 108:35-111. [PMID: 38461003 DOI: 10.1016/bs.afnr.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2024]
Abstract
We live in the Big Data Era which affects many aspects of science, including research on bioactive peptides derived from foods, which during the last few decades have been a focus of interest for scientists. These two issues, i.e., the development of computer technologies and progress in the discovery of novel peptides with health-beneficial properties, are closely interrelated. This Chapter presents the example applications of bioinformatics for studying biopeptides, focusing on main aspects of peptide analysis as the starting point, including: (i) the role of peptide databases; (ii) aspects of bioactivity prediction; (iii) simulation of peptide release from proteins. Bioinformatics can also be used for predicting other features of peptides, including ADMET, QSAR, structure, and taste. To answer the question asked "bioinformatics and bioactive peptides from foods: do they work together?", currently it is almost impossible to find examples of peptide research with no bioinformatics involved. However, theoretical predictions are not equivalent to experimental work and always require critical scrutiny. The aspects of compatibility of in silico and in vitro results are also summarized herein.
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Affiliation(s)
- Anna Iwaniak
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland.
| | - Piotr Minkiewicz
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland
| | - Małgorzata Darewicz
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland
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5
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Vincenzi M, Mercurio FA, Leone M. Virtual Screening of Peptide Libraries: The Search for Peptide-Based Therapeutics Using Computational Tools. Int J Mol Sci 2024; 25:1798. [PMID: 38339078 PMCID: PMC10855943 DOI: 10.3390/ijms25031798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 01/26/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Over the last few decades, we have witnessed growing interest from both academic and industrial laboratories in peptides as possible therapeutics. Bioactive peptides have a high potential to treat various diseases with specificity and biological safety. Compared to small molecules, peptides represent better candidates as inhibitors (or general modulators) of key protein-protein interactions. In fact, undruggable proteins containing large and smooth surfaces can be more easily targeted with the conformational plasticity of peptides. The discovery of bioactive peptides, working against disease-relevant protein targets, generally requires the high-throughput screening of large libraries, and in silico approaches are highly exploited for their low-cost incidence and efficiency. The present review reports on the potential challenges linked to the employment of peptides as therapeutics and describes computational approaches, mainly structure-based virtual screening (SBVS), to support the identification of novel peptides for therapeutic implementations. Cutting-edge SBVS strategies are reviewed along with examples of applications focused on diverse classes of bioactive peptides (i.e., anticancer, antimicrobial/antiviral peptides, peptides blocking amyloid fiber formation).
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Affiliation(s)
| | | | - Marilisa Leone
- Institute of Biostructures and Bioimaging, Via Pietro Castellino 111, 80131 Naples, Italy; (M.V.); (F.A.M.)
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Khalaj-Hedayati A, Moosavi S, Manta O, Helal MH, Ibrahim MM, El-Bahy ZM, Supriyanto G. Identification and In Silico Characterization of a Conserved Peptide on Influenza Hemagglutinin Protein: A New Potential Antigen for Universal Influenza Vaccine Development. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:2796. [PMID: 37887946 PMCID: PMC10609762 DOI: 10.3390/nano13202796] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 10/28/2023]
Abstract
Antigenic changes in surface proteins of the influenza virus may cause the emergence of new variants that necessitate the reformulation of influenza vaccines every year. Universal influenza vaccine that relies on conserved regions can potentially be effective against all strains regardless of any antigenic changes and as a result, it can bring enormous public health impact and economic benefit worldwide. Here, a conserved peptide (HA288-107) on the stalk domain of hemagglutinin glycoprotein is identified among highly pathogenic influenza viruses. Five top-ranked B-cell and twelve T-cell epitopes were recognized by epitope mapping approaches and the corresponding Human Leukocyte Antigen alleles to T-cell epitopes showed high population coverage (>99%) worldwide. Moreover, molecular docking analysis indicated that VLMENERTL and WTYNAELLV epitopes have high binding affinity to the antigen-binding groove of the HLA-A*02:01 and HLA-A*68:02 molecules, respectively. Theoretical physicochemical properties of the peptide were assessed to ensure its thermostability and hydrophilicity. The results suggest that the HA288-107 peptide can be a promising antigen for universal influenza vaccine design. However, in vitro and in vivo analyses are needed to support and evaluate the effectiveness of the peptide as an immunogen for vaccine development.
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Affiliation(s)
- Atin Khalaj-Hedayati
- Department of Chemistry, Faculty of Science and Technology, Airlangga University, Mulyorejo, Surabaya 60115, Indonesia
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor’s University, Subang Jaya 47500, Malaysia
| | - Seyedehmaryam Moosavi
- Department of Nanotechnology Engineering, Faculty of Advance Technology and Multidiscipline, Airlangga University, Mulyorejo, Surabaya 60115, Indonesia;
| | - Otilia Manta
- Romanian Academy, Victor Slavescu Centre for Financial and Monetary Research, 050731 Bucharest, Romania;
- Romanian Academy, CE-MONT Mountain Economy Center, 725700 Vatra Dornei, Romania
- Research Department, Romanian American University, 012101 Bucharest, Romania
| | - Mohamed H. Helal
- Department of Chemistry, Faculty of Arts and Science, Northern Border University, Rafha 76413, Saudi Arabia;
| | - Mohamed M. Ibrahim
- Department of Chemistry, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Zeinhom M. El-Bahy
- Department of Chemistry, Faculty of Science, Al-Azhar University, Nasr City 11884, Egypt;
| | - Ganden Supriyanto
- Department of Chemistry, Faculty of Science and Technology, Airlangga University, Mulyorejo, Surabaya 60115, Indonesia
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Alguridi HI, Alzahrani F, Almalki S, Zamzami MA, Altayb HN. Identification and molecular docking of novel chikungunya virus NSP4 inhibitory peptides from camel milk proteins. J Biomol Struct Dyn 2023:1-16. [PMID: 37668009 DOI: 10.1080/07391102.2023.2254398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 08/28/2023] [Indexed: 09/06/2023]
Abstract
The chikungunya (CHIK) virus is an arbovirus belonging to the alphavirus (Togaviridae family). Around 85% of infected individuals suffer from symptoms such as high fever and severe joint pain; about 30 to 40% will develop a chronic joint illness. The Nsp4 protease is the most conserved protein in the alphavirus family and serves as an RNA-dependent RNA polymerase (RdRp). Targeting this enzyme might inhibit the CHIKV replication cycle. This work aims to in silico study the CHIKV RdRp inhibitory effect of peptides derived from camel milk protein as antiviral peptides. Various bioinformatics tools were recruited to identify, screen, predict and assess peptides obtained from camel milk as antiviral peptides (AVPs). During this study, CHIKV Nsp4 (polymerase) was used as a target to be inhibited by interaction with peptides derived from camel milk protein. Among 91 putative bioactive peptides, the best predicted 5 were further evaluated. Molecular docking showed that the top 5 AVPs generated better docking scores and interacted well with active sites of Nsp4 by the formation of different hydrogen bonds as well as other bonds. AVP63 and AVP20 showed the best Molecular docking and MD simulation results. The residue 315ASP of the GDD motif (catalytic core) exhibited a favorable interaction with the AVPs. The findings of this study suggest that the AVP20 derived from camel milk protein can be a potential novel CHIKV polymerase inhibitor.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Hassan I Alguridi
- Molecular Biology Department, Jeddah Regional Laboratory, Ministry of Health, Jeddah, Saudi Arabia
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University Jeddah, Saudi Arabia
- Research Unit, Jeddah Regional Laboratory, Ministry of Health, Jeddah, Saudi Arabia
| | - Faisal Alzahrani
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University Jeddah, Saudi Arabia
- Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
- King Fahd Medical Research Center, Embryonic Stem Cells Unit, King Abdulaziz University Jeddah, Saudi Arabia
| | - Safar Almalki
- Molecular Biology Department, Jeddah Regional Laboratory, Ministry of Health, Jeddah, Saudi Arabia
- Laboratories and Blood Banks Administration, Ministry of Health, Jeddah, Saudi Arabia
| | - Mazin A Zamzami
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University Jeddah, Saudi Arabia
- Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hisham N Altayb
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University Jeddah, Saudi Arabia
- Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah, Saudi Arabia
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Kongsompong S, E-kobon T, Taengphan W, Sangkhawasi M, Khongkow M, Chumnanpuen P. Computer-Aided Virtual Screening and In Vitro Validation of Biomimetic Tyrosinase Inhibitory Peptides from Abalone Peptidome. Int J Mol Sci 2023; 24:ijms24043154. [PMID: 36834568 PMCID: PMC9965614 DOI: 10.3390/ijms24043154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/02/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
Hyperpigmentation is a medical and cosmetic problem caused by an excess accumulation of melanin or the overexpression of the enzyme tyrosinase, leading to several skin disorders, i.e., freckles, melasma, and skin cancer. Tyrosinase is a key enzyme in melanogenesis and thus a target for reducing melanin production. Although abalone is a good source of bioactive peptides that have been used for several properties including depigmentation, the available information on the anti-tyrosinase property of abalone peptides remains insufficient. This study investigated the anti-tyrosinase properties of Haliotis diversicolor tyrosinase inhibitory peptides (hdTIPs) based on mushroom tyrosinase, cellular tyrosinase, and melanin content assays. The binding conformation between peptides and tyrosinase was also examined by molecular docking and dynamics study. KNN1 showed a high potent inhibitory effect on mushroom tyrosinase with an IC50 of 70.83 μM. Moreover, our selected hdTIPs could inhibit melanin production through the reductions in tyrosinase activity and reactive oxygen species (ROS) levels by enhancing the antioxidative enzymes. RF1 showed the highest activity on both cellular tyrosinase inhibition and ROS reduction. leading to the lower melanin content in B16F10 murine melanoma cells. Accordingly, it can be assumed that our selected peptides exhibited high potential in medical cosmetology applications.
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Affiliation(s)
- Sasikarn Kongsompong
- Interdisciplinary Graduate Program in Bioscience, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
| | - Teerasak E-kobon
- Department of Genetics, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
| | - Weerasak Taengphan
- Expert Centre of Innovative Herbal Products (InnoHerb), Thailand Institute of Scientific and Technological Research, Techno Polis, Khlong Luang District, Pathum Thani 12120, Thailand
| | - Mattanun Sangkhawasi
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Mattaka Khongkow
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Pramote Chumnanpuen
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
- Correspondence:
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Prasertsuk K, Prongfa K, Suttiwanich P, Harnkit N, Sangkhawasi M, Promta P, Chumnanpuen P. Computer-Aided Screening for Potential Coronavirus 3-Chymotrypsin-like Protease (3CLpro) Inhibitory Peptides from Putative Hemp Seed Trypsinized Peptidome. Molecules 2022; 28:50. [PMID: 36615263 PMCID: PMC9822321 DOI: 10.3390/molecules28010050] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 12/05/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022] Open
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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Affiliation(s)
- Kansate Prasertsuk
- Pibulwitthayalai School, 777 Naraimaharach, Talaychoopsorn, Lopburi District, Lopburi 15000, Thailand
| | - Kasidit Prongfa
- Pibulwitthayalai School, 777 Naraimaharach, Talaychoopsorn, Lopburi District, Lopburi 15000, Thailand
| | - Piyapach Suttiwanich
- Pibulwitthayalai School, 777 Naraimaharach, Talaychoopsorn, Lopburi District, Lopburi 15000, Thailand
| | - Nathaphat Harnkit
- Medicinal Plant Research Institute, Department of Medical Sciences, Ministry of Public Health, Nonthaburi 11000, Thailand
| | - Mattanun Sangkhawasi
- Program in Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok 10330, Thailand
| | - Pongsakorn Promta
- Pibulwitthayalai School, 777 Naraimaharach, Talaychoopsorn, Lopburi District, Lopburi 15000, Thailand
| | - Pramote Chumnanpuen
- Omics Center for Agriculture, Bioresources, Food and Health, Kasetsart University (OmiKU), Bangkok 10900, Thailand
- Department of Zoology, Faculty of Science, Kasetsart University, Bangkok 10900, Thailand
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