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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] [What about the content of this article? (0)] [Affiliation(s)] [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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2
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Guan J, Yao L, Xie P, Chung CR, Huang Y, Chiang YC, Lee TY. A two-stage computational framework for identifying antiviral peptides and their functional types based on contrastive learning and multi-feature fusion strategy. Brief Bioinform 2024; 25:bbae208. [PMID: 38706321 DOI: 10.1093/bib/bbae208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2024] [Revised: 03/14/2024] [Accepted: 04/17/2024] [Indexed: 05/07/2024] Open
Abstract
Antiviral peptides (AVPs) have shown potential in inhibiting viral attachment, preventing viral fusion with host cells and disrupting viral replication due to their unique action mechanisms. They have now become a broad-spectrum, promising antiviral therapy. However, identifying effective AVPs is traditionally slow and costly. This study proposed a new two-stage computational framework for AVP identification. The first stage identifies AVPs from a wide range of peptides, and the second stage recognizes AVPs targeting specific families or viruses. This method integrates contrastive learning and multi-feature fusion strategy, focusing on sequence information and peptide characteristics, significantly enhancing predictive ability and interpretability. The evaluation results of the model show excellent performance, with accuracy of 0.9240 and Matthews correlation coefficient (MCC) score of 0.8482 on the non-AVP independent dataset, and accuracy of 0.9934 and MCC score of 0.9869 on the non-AMP independent dataset. Furthermore, our model can predict antiviral activities of AVPs against six key viral families (Coronaviridae, Retroviridae, Herpesviridae, Paramyxoviridae, Orthomyxoviridae, Flaviviridae) and eight viruses (FIV, HCV, HIV, HPIV3, HSV1, INFVA, RSV, SARS-CoV). Finally, to facilitate user accessibility, we built a user-friendly web interface deployed at https://awi.cuhk.edu.cn/∼dbAMP/AVP/.
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Affiliation(s)
- Jiahui Guan
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Road, 518172 Shenzhen, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, 2001 Longxiang Road, 518172 Shenzhen, China
| | - Lantian Yao
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Road, 518172 Shenzhen, China
- School of Science and Engineering, The Chinese University of Hong Kong, 2001 Longxiang Road, 518172 Shenzhen, China
| | - Peilin Xie
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, 2001 Longxiang Road, 518172 Shenzhen, China
| | - Chia-Ru Chung
- Department of Computer Science and Information Engineering, National Central University, 320317 Taoyuan, Taiwan
| | - Yixian Huang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Road, 518172 Shenzhen, China
| | - Ying-Chih Chiang
- School of Medicine, The Chinese University of Hong Kong, Shenzhen, 2001 Longxiang Road, 518172 Shenzhen, China
- Kobilka Institute of Innovative Drug Discovery, School of Medicine, The Chinese University of Hong Kong, 2001 Longxiang Road, 518172 Shenzhen, China
| | - Tzong-Yi Lee
- Institute of Bioinformatics and Systems Biology, National Yang Ming Chiao Tung University, 300093 Hsinchu, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang Ming Chiao Tung University, 300093 Hsinchu, Taiwan
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3
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Quagliata M, Papini AM, Rovero P. Chemically modified antiviral peptides against SARS-CoV-2. J Pept Sci 2024; 30:e3541. [PMID: 37699615 DOI: 10.1002/psc.3541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 07/31/2023] [Accepted: 08/22/2023] [Indexed: 09/14/2023]
Abstract
To date, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) COVID-19 pandemic continues to be a potentially lethal disease. Although both vaccines and specific antiviral drugs have been approved, the search for more specific therapeutic approaches is still ongoing. The infection mechanism of SARS-CoV-2 consists of several stages, and each one can be selectively blocked to disrupt viral infection. Peptides are a promising class of antiviral compounds, which may be suitably modified to be more stable, more effective, and more selective towards a specific viral replication step. The latter two goals might be obtained by increasing the specificity and/or the affinity of the interaction with a specific target and often imply the stabilization of the secondary structure of the active peptide. This review is focused on modified antiviral peptides against SARS-CoV-2 acting at different stages of virus replication, including ACE2-RBD interaction, membrane fusion mechanism, and the proteolytic cleavage by different viral proteases. Therefore, the landscape presented herein provides a useful springboard for the design of new and powerful antiviral therapeutics.
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Affiliation(s)
- Michael Quagliata
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino, Italy
| | - Paolo Rovero
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino, Italy
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Bess A, Berglind F, Mukhopadhyay S, Brylinski M, Alvin C, Fattah F, Wasan KM. Identification of oral therapeutics using an AI platform against the virus responsible for COVID-19, SARS-CoV-2. Front Pharmacol 2023; 14:1297924. [PMID: 38186640 PMCID: PMC10770831 DOI: 10.3389/fphar.2023.1297924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 11/29/2023] [Indexed: 01/09/2024] Open
Abstract
Purpose: This study introduces a sophisticated computational pipeline, eVir, designed for the discovery of antiviral drugs based on their interactions within the human protein network. There is a pressing need for cost-effective therapeutics for infectious diseases (e.g., COVID-19), particularly in resource-limited countries. Therefore, our team devised an Artificial Intelligence (AI) system to explore repurposing opportunities for currently used oral therapies. The eVir system operates by identifying pharmaceutical compounds that mirror the effects of antiviral peptides (AVPs)-fragments of human proteins known to interfere with fundamental phases of the viral life cycle: entry, fusion, and replication. eVir extrapolates the probable antiviral efficacy of a given compound by analyzing its established and predicted impacts on the human protein-protein interaction network. This innovative approach provides a promising platform for drug repurposing against SARS-CoV-2 or any virus for which peptide data is available. Methods: The eVir AI software pipeline processes drug-protein and protein-protein interaction networks generated from open-source datasets. eVir uses Node2Vec, a graph embedding technique, to understand the nuanced connections among drugs and proteins. The embeddings are input a Siamese Network (SNet) and MLPs, each tailored for the specific mechanisms of entry, fusion, and replication, to evaluate the similarity between drugs and AVPs. Scores generated from the SNet and MLPs undergo a Platt probability calibration and are combined into a unified score that gauges the potential antiviral efficacy of a drug. This integrated approach seeks to boost drug identification confidence, offering a potential solution for detecting therapeutic candidates with pronounced antiviral potency. Once identified a number of compounds were tested for efficacy and toxicity in lung carcinoma cells (Calu-3) infected with SARS-CoV-2. A lead compound was further identified to determine its efficacy and toxicity in K18-hACE2 mice infected with SARS-CoV-2. Computational Predictions: The SNet confidently differentiated between similar and dissimilar drug pairs with an accuracy of 97.28% and AUC of 99.47%. Key compounds identified through these networks included Zinc, Mebendazole, Levomenol, Gefitinib, Niclosamide, and Imatinib. Notably, Mebendazole and Zinc showcased the highest similarity scores, while Imatinib, Levemenol, and Gefitinib also ranked within the top 20, suggesting their significant pharmacological potentials. Further examination of protein binding analysis using explainable AI focused on reverse engineering the causality of the networks. Protein interaction scores for Mebendazole and Imatinib revealed their effects on notable proteins such as CDPK1, VEGF2, ABL1, and several tyrosine protein kinases. Laboratory Studies: This study determined that Mebendazole, Gefitinib, Topotecan and to some extent Carfilzomib showed conventional drug-response curves, with IC50 values near or below that of Remdesivir with excellent confidence all above R2>0.91, and no cytotoxicity at the IC50 concentration in Calu-3 cells. Cyclosporine A showed antiviral activity, but also unconventional drug-response curves and low R2 which are explained by the non-dose dependent toxicity of the compound. Additionally, Niclosamide demonstrated a conventional drug-response curve with high confidence; however, its inherent cytotoxicity may be a confounding element that misrepresents true antiviral efficacy, by reflecting cellular damage rather than a genuine antiviral action. Remdesivir was used as a control compound and was evaluated in parallel with the submitted test article and had conventional drug-response curves validating the overall results of the assay. Mebendazole was identified from the cell studies to have efficacy at non-toxic concentrations and were further evaluated in mice infected with SARS-CoV-2. Mebendazole administered to K18-hACE2 mice infected with SARS-CoV-2, resulted in a 44.2% reduction in lung viral load compared to non-treated placebo control respectively. There were no significant differences in body weight and all clinical chemistry determinations evaluated (i.e., kidney and liver enzymes) between the different treatment groups. Conclusion: This research underscores the potential of repurposing existing compounds for treating COVID-19. Our preliminary findings underscore the therapeutic promise of several compounds, notably Mebendazole, in both in vitro and in vivo settings against SARS-CoV-2. Several of the drugs explored, especially Mebendazole, are off-label medication; their cost-effectiveness position them as economical therapies against SARS-CoV-2.
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Affiliation(s)
- Adam Bess
- Department of Computer Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Frej Berglind
- Department of Computer Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Supratik Mukhopadhyay
- Department of Environmental Sciences, Center for Computation & Technology, Coastal Studies Institute, Louisiana State University, Baton Rouge, LA, United States
| | - Michal Brylinski
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA, United States
| | - Chris Alvin
- Department of Computer Science, Furman University, Greenville, SC, United States
| | - Fanan Fattah
- Department of Urologic Sciences, Faculty of Medicine and the Neglected Global Diseases Initiative, University of British Columbia, Vancouver, BC, Canada
| | - Kishor M. Wasan
- Department of Urologic Sciences, Faculty of Medicine and the Neglected Global Diseases Initiative, University of British Columbia, Vancouver, BC, Canada
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6
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Cao R, Hu W, Wei P, Ding Y, Bin Y, Zheng C. FFMAVP: a new classifier based on feature fusion and multitask learning for identifying antiviral peptides and their subclasses. Brief Bioinform 2023; 24:bbad353. [PMID: 37861174 DOI: 10.1093/bib/bbad353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/25/2023] [Accepted: 09/06/2023] [Indexed: 10/21/2023] Open
Abstract
Antiviral peptides (AVPs) are widely found in animals and plants, with high specificity and strong sensitivity to drug-resistant viruses. However, due to the great heterogeneity of different viruses, most of the AVPs have specific antiviral activities. Therefore, it is necessary to identify the specific activities of AVPs on virus types. Most existing studies only identify AVPs, with only a few studies identifying subclasses by training multiple binary classifiers. We develop a two-stage prediction tool named FFMAVP that can simultaneously predict AVPs and their subclasses. In the first stage, we identify whether a peptide is AVP or not. In the second stage, we predict the six virus families and eight species specifically targeted by AVPs based on two multiclass tasks. Specifically, the feature extraction module in the two-stage task of FFMAVP adopts the same neural network structure, in which one branch extracts features based on amino acid feature descriptors and the other branch extracts sequence features. Then, the two types of features are fused for the following task. Considering the correlation between the two tasks of the second stage, a multitask learning model is constructed to improve the effectiveness of the two multiclass tasks. In addition, to improve the effectiveness of the second stage, the network parameters trained through the first-stage data are used to initialize the network parameters in the second stage. As a demonstration, the cross-validation results, independent test results and visualization results show that FFMAVP achieves great advantages in both stages.
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Affiliation(s)
- Ruifen Cao
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Computer Science and Technology, Anhui University
| | - Weiling Hu
- Information Materials and Intelligent Sensing Laboratory of Anhui Province, School of Computer Science and Technology, Anhui University
| | - Pijing Wei
- Institutes of Physical Science and Information Technology, Anhui University
| | - Yun Ding
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University
| | - Yannan Bin
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education and Information Materials and Intelligent Sensing Laboratory of Anhui Province, Institutes of Physical Science and Information Technology, Anhui University
| | - Chunhou Zheng
- Key Laboratory of Intelligent Computing and Signal Processing of Ministry of Education, School of Artificial Intelligence, Anhui University
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7
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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8
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Liu Y, Zhu Y, Sun X, Ma T, Lao X, Zheng H. DRAVP: A Comprehensive Database of Antiviral Peptides and Proteins. Viruses 2023; 15:v15040820. [PMID: 37112801 PMCID: PMC10141206 DOI: 10.3390/v15040820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 03/18/2023] [Accepted: 03/22/2023] [Indexed: 04/29/2023] Open
Abstract
Viruses with rapid replication and easy mutation can become resistant to antiviral drug treatment. With novel viral infections emerging, such as the recent COVID-19 pandemic, novel antiviral therapies are urgently needed. Antiviral proteins, such as interferon, have been used for treating chronic hepatitis C infections for decades. Natural-origin antimicrobial peptides, such as defensins, have also been identified as possessing antiviral activities, including direct antiviral effects and the ability to induce indirect immune responses to viruses. To promote the development of antiviral drugs, we constructed a data repository of antiviral peptides and proteins (DRAVP). The database provides general information, antiviral activity, structure information, physicochemical information, and literature information for peptides and proteins. Because most of the proteins and peptides lack experimentally determined structures, AlphaFold was used to predict each antiviral peptide's structure. A free website for users (http://dravp.cpu-bioinfor.org/, accessed on 30 August 2022) was constructed to facilitate data retrieval and sequence analysis. Additionally, all the data can be accessed from the web interface. The DRAVP database aims to be a useful resource for developing antiviral drugs.
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Affiliation(s)
- Yanchao Liu
- School of Life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Youzhuo Zhu
- School of Life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Xin Sun
- School of Life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Tianyue Ma
- School of Life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Xingzhen Lao
- School of Life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
| | - Heng Zheng
- School of Life Science and Technology, China Pharmaceutical University, 24 Tongjiaxiang, Nanjing 210009, China
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9
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Carfagno A, Lin SC, Chafran L, Akhrymuk I, Callahan V, Po M, Zhu Y, Altalhi A, Durkin DP, Russo P, Vliet KA, Webb-Robertson BJ, Kehn-Hall K, Bishop B. Bioprospecting the American Alligator Peptidome for antiviral peptides against Venezuelan equine encephalitis virus. Proteomics 2023; 23:e2200237. [PMID: 36480152 DOI: 10.1002/pmic.202200237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Revised: 11/30/2022] [Accepted: 12/05/2022] [Indexed: 12/13/2022]
Abstract
The innate immune protection provided by cationic antimicrobial peptides (CAMPs) has been shown to extend to antiviral activity, with putative mechanisms of action including direct interaction with host cells or pathogen membranes. The lack of therapeutics available for the treatment of viruses such as Venezuelan equine encephalitis virus (VEEV) underscores the urgency of novel strategies for antiviral discovery. American alligator plasma has been shown to exhibit strong in vitro antibacterial activity, and functionalized hydrogel particles have been successfully employed for the identification of specific CAMPs from alligator plasma. Here, a novel bait strategy in which particles were encapsulated in membranes from either healthy or VEEV-infected cells was implemented to identify peptides preferentially targeting infected cells for subsequent evaluation of antiviral activity. Statistical analysis of peptide identification results was used to select five candidate peptides for testing, of which one exhibited a dose-dependent inhibition of VEEV and also significantly inhibited infectious titers. Results suggest our bioprospecting strategy provides a versatile platform that may be adapted for antiviral peptide identification from complex biological samples.
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Affiliation(s)
- Amy Carfagno
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, USA
| | - Shih-Chao Lin
- School of Systems Biology, George Mason University, Manassas, Virginia, USA.,National Taiwan Ocean University, Keelung City, Taiwan
| | - Liana Chafran
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, USA
| | - Ivan Akhrymuk
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Victoria Callahan
- School of Systems Biology, George Mason University, Manassas, Virginia, USA
| | - Marynet Po
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, USA
| | - Yaling Zhu
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, USA
| | - Amaal Altalhi
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, USA
| | - David P Durkin
- Chemistry Department, U.S. Naval Academy, Annapolis, Maryland, USA
| | - Paul Russo
- Center for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia, USA
| | - Kent A Vliet
- Department of Biology, University of Florida, Gainesville, Florida, USA
| | | | - Kylene Kehn-Hall
- Department of Biomedical Sciences and Pathobiology, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA.,Center for Emerging, Zoonotic, and Arthropod-borne Pathogens, Virginia Polytechnic Institute and State University, Blacksburg, Virginia, USA
| | - Barney Bishop
- Department of Chemistry and Biochemistry, George Mason University, Manassas, Virginia, USA
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10
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Xu Q, Wang F, Jiao W, Zhang M, Xing G, Feng H, Sun X, Hu M, Zhang G. Virtual Screening-Based Peptides Targeting Spike Protein to Inhibit Porcine Epidemic Diarrhea Virus (PEDV) Infection. Viruses 2023; 15:v15020381. [PMID: 36851595 PMCID: PMC9965349 DOI: 10.3390/v15020381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 01/14/2023] [Accepted: 01/21/2023] [Indexed: 01/31/2023] Open
Abstract
Due to the rapid mutation of porcine epidemic diarrhea virus (PEDV), existing vaccines cannot provide sufficient immune protection for pigs. Therefore, it is urgent to design the affinity peptides for the prevention and control of this disease. In this study, we made use of a molecular docking technology for virtual screening of affinity peptides that specifically recognized the PEDV S1 C-terminal domain (CTD) protein for the first time. Experimentally, the affinity, cross-reactivity and sensitivity of the peptides were identified by an enzyme-linked immunosorbent assay (ELISA) and a surface plasmon resonance (SPR) test, separately. Subsequently, Cell Counting Kit-8 (CCK-8), quantitative real-time PCR (qRT-PCR), Western blot and indirect immunofluorescence were used to further study the antiviral effect of different concentrations of peptide 110766 in PEDV. Our results showed that the P/N value of peptide 110766 at 450 nm reached 167, with a KD value of 216 nM. The cytotoxic test indicated that peptide 110766 was not toxic to vero cells. Results of the absolute quantitative PCR revealed that different concentrations (3.125 μM, 6.25 μM, 12.5 μM, 25 μM, 50 μM, 100 μM, 200 μM) of peptide 110766 could significantly reduce the viral load of PEDV compared with the virus group (p < 0.0001). Similarly, results of Western blot and indirect immunofluorescence also suggested that the antiviral effect of peptide 110766 at 3.125 is still significant. Based on the above research, high-affinity peptide 110766 binding to the PEDV S1-CTD protein was attained by a molecular docking technology. Therefore, designing, screening, and identifying affinity peptides can provide a new method for the development of antiviral drugs for PEDV.
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Affiliation(s)
- Qian Xu
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yang ling, Xianyang 712100, China
- Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, 116# Huayuan Road, Zhengzhou 450002, China
| | - Fangyu Wang
- Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, 116# Huayuan Road, Zhengzhou 450002, China
| | - Wenqiang Jiao
- Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, 116# Huayuan Road, Zhengzhou 450002, China
| | - Mengting Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yang ling, Xianyang 712100, China
- Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, 116# Huayuan Road, Zhengzhou 450002, China
| | - Guangxu Xing
- Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, 116# Huayuan Road, Zhengzhou 450002, China
| | - Hua Feng
- Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, 116# Huayuan Road, Zhengzhou 450002, China
| | - Xuefeng Sun
- Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, 116# Huayuan Road, Zhengzhou 450002, China
| | - Man Hu
- Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, 116# Huayuan Road, Zhengzhou 450002, China
| | - Gaiping Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northwest A&F University, Yang ling, Xianyang 712100, China
- Key Laboratory for Animal Immunology, Henan Academy of Agricultural Sciences, 116# Huayuan Road, Zhengzhou 450002, China
- Longhu Modern Immunology Laboratory, Zhengzhou 450046, China
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou 225009, China
- Correspondence:
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11
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Aleebrahim-Dehkordi E, Soveyzi F, Saberianpour S, Rafieian-Kopaei M. Are Herbal-peptides Effective as Adjunctive Therapy in Coronavirus Disease COVID-19? Curr Drug Res Rev 2023; 15:29-34. [PMID: 36029074 DOI: 10.2174/2589977514666220826155013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 02/16/2022] [Accepted: 02/16/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Plant antiviral peptides (AVP) are macromolecules that can inhibit the pathogenesis of viruses by affecting their pathogenic mechanism, but most of these peptides can bind to cell membranes, inhibit viral receptors, and prevent viruses. Recently, due to the coronavirus pandemic, the availability of appropriate drugs with low side effects is needed. In this article, the importance of plant peptides in viral inhibition, especially viral inhibition of the coronavirus family, will be discussed. METHODS By searching the databases of PubMed, Scopus, Web of Science, the latest articles on plant peptides effective on the COVID-19 virus were collected and reviewed. RESULTS Some proteins can act against the COVID-19 virus by blocking sensitive receptors in COVID-19, such as angiotensin-converting enzyme 2 (ACE2). The 23bp sequence of the ACE2 alpha receptor chain can be considered as a target for therapeutic peptides. Protease and RNAP inhibitors and other important receptors that are active against COVID-19 should also be considered. CONCLUSION Herbal medicines with AVP, especially those with a long history of antiviral effects, might be a good choice in complement therapy against the COVID-19 virus.
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Affiliation(s)
- Elahe Aleebrahim-Dehkordi
- Systematic Review and Meta-Analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Nutritional Health Team (NHT), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
| | - Faezeh Soveyzi
- Systematic Review and Meta-Analysis Expert Group (SRMEG), Universal Scientific Education and Research Network (USERN), Tehran, Iran
- Department of Medicine, Tehran University of Medical Sciences, Tehran, Iran
| | - Shirin Saberianpour
- Department of Molecular Medicine, Vascular and Endovascular Surgery Research Center, Mashhad University of Medical Science, Mashhad, Iran
| | - Mahmoud Rafieian-Kopaei
- Medical Plants Research Center, Basic Health Sciences Institute, Shahrekord University of Medical Sciences, Shahrekord, Iran
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12
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Feyzyab H, Fathi N, Bolhassani A. Antiviral Peptides Derived from Plants: Their Designs and Functions. Protein Pept Lett 2023; 30:975-985. [PMID: 38013436 DOI: 10.2174/0109298665278148231106052509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 09/22/2023] [Accepted: 10/03/2023] [Indexed: 11/29/2023]
Abstract
In recent years, plant-derived bioactive compounds have been developed as antiviral agents. Plants synthesize a variety of compounds, especially peptides, which possess antimicrobial activity. Current studies have shown that some antimicrobial peptides have antiviral activity against a wide range of human DNA and RNA viruses and play an effective role in the treatment of human viral diseases. These peptides act through different mechanisms. They can integrate into the envelope of the target virus or cell membrane of the host, resulting in an unstable membrane. For instance, some peptides prevent the attachment of viral spike proteins to host cells. On the other hand, some peptides may alter the cellular pathways, including DNA replication or protein synthesis, leading to the suppression of viral infection. However, the antiviral activity of peptides can be affected by their chemical and structural properties. In several studies, the properties of antimicrobial (antiviral) peptides were altered by minor modifications, but these changes require tools to predict. Recently, computational approaches have been introduced to analyze the effects of structural modifications on the physicochemical properties, mechanism of action, stability, and activity of peptides. In this mini-review, we will describe the design and function of antiviral peptides derived from plants.
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Affiliation(s)
- Haleh Feyzyab
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Nikoo Fathi
- Department of Genetics, Faculty of Advanced Science and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
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13
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Ramirez-Acosta K, Rosales-Fuerte IA, Perez-Sanchez JE, Nuñez-Rivera A, Juarez J, Cadena-Nava RD. Design and selection of peptides to block the SARS-CoV-2 receptor binding domain by molecular docking. Beilstein J Nanotechnol 2022; 13:699-711. [PMID: 35957673 PMCID: PMC9344557 DOI: 10.3762/bjnano.13.62] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 07/12/2022] [Indexed: 05/05/2023]
Abstract
The novel Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) is currently one of the most contagious viruses in existence and the cause of the worst pandemic in this century, COVID-19. SARS-CoV-2 infection begins with the recognition of the cellular receptor angiotensin converting enzyme-2 by its spike glycoprotein receptor-binding domain (RBD). Thus, the use of small peptides to neutralize the infective mechanism of SARS-CoV-2 through the RBD is an interesting strategy. The binding ability of 104 peptides (University of Nebraska Medical Center's Antimicrobial Peptide Database) to the RBD was assessed using molecular docking. Based on the molecular docking results, peptides with great affinity to the RBD were selected. The most common amino acids involved in the recognition of the RBD were identified to design novel peptides based on the number of hydrogen bonds that were formed. At physiological pH, these peptides are almost neutral and soluble in aqueous media. Interestingly, several peptides showed the capability to bind to the active surface area of the RBD of the Wuhan strain, as well as to the RBD of the Delta variant and other SARS-Cov-2 variants. Therefore, these peptides have promising potential in the treatment of the COVID-19 disease caused by different variants of SARS-CoV-2. This research work will be focused on the molecular docking of peptides by molecular dynamics, in addition to an analysis of the possible interaction of these peptides with physiological proteins. This methodology could be extended to design peptides that are active against other viruses.
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Affiliation(s)
- Kendra Ramirez-Acosta
- Centro de Nanociencias y Nanotecnología - Universidad Nacional Autónoma de México (UNAM) – Ensenada, Baja California, México
- Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, (CICESE), Ensenada, Baja California, México
| | - Ivan A Rosales-Fuerte
- Centro de Nanociencias y Nanotecnología - Universidad Nacional Autónoma de México (UNAM) – Ensenada, Baja California, México
- Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, (CICESE), Ensenada, Baja California, México
| | - J Eduardo Perez-Sanchez
- Centro de Nanociencias y Nanotecnología - Universidad Nacional Autónoma de México (UNAM) – Ensenada, Baja California, México
- Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, (CICESE), Ensenada, Baja California, México
| | - Alfredo Nuñez-Rivera
- Centro de Nanociencias y Nanotecnología - Universidad Nacional Autónoma de México (UNAM) – Ensenada, Baja California, México
- Centro de Investigación Científica y de Educación Superior de Ensenada, Baja California, (CICESE), Ensenada, Baja California, México
| | - Josue Juarez
- Departamento de Física, Universidad de Sonora, Blvd. Luis Encinas y Rosales, Hermosillo, Sonora, México
| | - Ruben D Cadena-Nava
- Centro de Nanociencias y Nanotecnología - Universidad Nacional Autónoma de México (UNAM) – Ensenada, Baja California, México
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14
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Sukmarini L. Antiviral Peptides (AVPs) of Marine Origin as Propitious Therapeutic Drug Candidates for the Treatment of Human Viruses. Molecules 2022; 27:molecules27092619. [PMID: 35565968 PMCID: PMC9101517 DOI: 10.3390/molecules27092619] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/03/2022] [Accepted: 04/18/2022] [Indexed: 12/13/2022]
Abstract
The marine environment presents a favorable avenue for potential therapeutic agents as a reservoir of new bioactive natural products. Due to their numerous potential pharmacological effects, marine-derived natural products—particularly marine peptides—have gained considerable attention. These peptides have shown a broad spectrum of biological functions, such as antimicrobial, antiviral, cytotoxic, immunomodulatory, and analgesic effects. The emergence of new virus strains and viral resistance leads to continuing efforts to develop more effective antiviral drugs. Interestingly, antimicrobial peptides (AMPs) that possess antiviral properties and are alternatively regarded as antiviral peptides (AVPs) demonstrate vast potential as alternative peptide-based drug candidates available for viral infection treatments. Hence, AVPs obtained from various marine organisms have been evaluated. This brief review features recent updates of marine-derived AVPs from 2011 to 2021. Moreover, the biosynthesis of this class of compounds and their possible mechanisms of action are also discussed. Selected peptides from various marine organisms possessing antiviral activities against important human viruses—such as human immunodeficiency viruses, herpes simplex viruses, influenza viruses, hepatitis C virus, and coronaviruses—are highlighted herein.
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Affiliation(s)
- Linda Sukmarini
- Research Center for Applied Microbiology, National Research and Innovation Agency (BRIN), Jl. Raya Bogor Km. 46, Cibinong 16911, West Java, Indonesia
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15
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Manavalan B, Basith S, Lee G. Comparative analysis of machine learning-based approaches for identifying therapeutic peptides targeting SARS-CoV-2. Brief Bioinform 2022; 23:bbab412. [PMID: 34595489 PMCID: PMC8500067 DOI: 10.1093/bib/bbab412] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/27/2021] [Accepted: 09/07/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) has impacted public health as well as societal and economic well-being. In the last two decades, various prediction algorithms and tools have been developed for predicting antiviral peptides (AVPs). The current COVID-19 pandemic has underscored the need to develop more efficient and accurate machine learning (ML)-based prediction algorithms for the rapid identification of therapeutic peptides against severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). Several peptide-based ML approaches, including anti-coronavirus peptides (ACVPs), IL-6 inducing epitopes and other epitopes targeting SARS-CoV-2, have been implemented in COVID-19 therapeutics. Owing to the growing interest in the COVID-19 field, it is crucial to systematically compare the existing ML algorithms based on their performances. Accordingly, we comprehensively evaluated the state-of-the-art IL-6 and AVP predictors against coronaviruses in terms of core algorithms, feature encoding schemes, performance evaluation metrics and software usability. A comprehensive performance assessment was then conducted to evaluate the robustness and scalability of the existing predictors using well-constructed independent validation datasets. Additionally, we discussed the advantages and disadvantages of the existing methods, providing useful insights into the development of novel computational tools for characterizing and identifying epitopes or ACVPs. The insights gained from this review are anticipated to provide critical guidance to the scientific community in the rapid design and development of accurate and efficient next-generation in silico tools against SARS-CoV-2.
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Affiliation(s)
| | - Shaherin Basith
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Korea
| | - Gwang Lee
- Department of Physiology, Ajou University School of Medicine, Suwon 16499, Korea
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16
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Efaz FM, Islam S, Talukder SA, Akter S, Tashrif MZ, Ali MA, Sufian MA, Parves MR, Islam MJ, Halim MA. Repurposing fusion inhibitor peptide against SARS-CoV-2. J Comput Chem 2021; 42:2283-2293. [PMID: 34591335 DOI: 10.1002/jcc.26758] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 08/03/2021] [Accepted: 09/19/2021] [Indexed: 11/08/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously evolving. Although several vaccines were approved, this pandemic is still a major threat to public life. Till date, no established therapies are available against SARS-CoV-2. Peptide inhibitors hold great promise for this viral pathogen due to their efficacy, safety, and specificity. In this study, seventeen antiviral peptides which were known to inhibit SARS-CoV-1 are collected and computationally screened against heptad repeat 1 (HR1) of the SARS-CoV-2 spike protein (S2). Out of 17 peptides, Fp13 and Fp14 showed better binding affinity toward HR1 compared to a control peptide EK1 (a modified pan-coronavirus fusion inhibitor) in molecular docking. To explore the time-dependent interactions of the fusion peptide with HR1, molecular dynamics simulation was performed incorporating lipid membrane. During 100 ns MD simulation, structural and energy parameters of Fp13-HR1 and Fp14-HR1 complexes demonstrated lower fluctuations compared to the control EK1-HR1 complex. Furthermore, principal component analysis and free energy landscape study revealed that these two peptides (Fp13 and Fp14) strongly bind to the HR1 with higher affinity than that of control EK1. Tyr917, Asn919, Gln926, lys933, and Gln949 residues in HR1 protein were found to be crucial residues for peptide interaction. Notably, Fp13, Fp14 showed reasonably better binding free energy and hydrogen bond contribution than that of EK1. Taken together, Fp13 and Fp14 peptides may be highly specific for HR1 which can potentially prevent the formation of the fusion core and could be further developed as therapeutics for treatment or prophylaxis of SARS-CoV-2 infection.
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Affiliation(s)
- Faiyaz Md Efaz
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Shafiqul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Shafi Ahmad Talukder
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Shaila Akter
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Zakaria Tashrif
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Ackas Ali
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Abu Sufian
- School of Pharmacy, Temple University, Philadelphia, Pennsylvania, USA
| | - Md Rimon Parves
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Md Jahirul Islam
- Division of Infectious disease and Division of Computer Aided Drug Design, The Red-Green Research Centre, Dhaka, Bangladesh
| | - Mohammad A Halim
- Department of Physical Sciences, University of Arkansas-Fort Smith, Fort Smith, Arkansas, USA.,Department of Chemistry and Biochemistry, Kennesaw State University, Kennesaw, Georgia, USA
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17
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Gao B, Zhao D, Li L, Cheng Z, Guo Y. Antiviral Peptides with in vivo Activity: Development and Modes of Action. Chempluschem 2021; 86:1547-1558. [PMID: 34755499 DOI: 10.1002/cplu.202100351] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 10/28/2021] [Indexed: 12/25/2022]
Abstract
The viral pandemic has resulted in a growing demand for antiviral drugs. The existing small-molecule antiviral drugs are limited, due to their incidence of drug resistance and adverse side effects. As potential drugs, antiviral peptides have the benefits of high activity, high stability, and few side effects. Furthermore, the diversity of acquisition methods allows antiviral peptides to be quickly designed and yielded. The drug properties (such as high bioavailability and in vivo stability) of antiviral peptides can be improved by the developed modifications. Currently, two peptide antiviral drugs have been approved for the treatment of acquired immunodeficiency syndrome (AIDS). Many antiviral peptides have entered clinical trials for the treatment of diseases caused by viruses. In addition, new antiviral peptides are continuously being identified and validated against virus infections. Given the benefits of antiviral peptides, they will become major antiviral drugs to combat new outbreaks caused by unknown viruses in the future. This review provides an overview of recent developments in antiviral peptides with in vivo activity.
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Affiliation(s)
- Bing Gao
- School of Public Health, Baotou Medical College, Baotou, 31 Construction Road, Donghe District, Baotou, Inner Mongolia, P. R. China
| | - Dongdong Zhao
- School of Pharmacy, Baotou Medical College, Baotou, 31 Construction Road, Donghe District, Baotou, Inner Mongolia, P. R. China
| | - Lingmu Li
- School of Pharmacy, Baotou Medical College, Baotou, 31 Construction Road, Donghe District, Baotou, Inner Mongolia, P. R. China
| | - Zhigang Cheng
- School of Pharmacy, Baotou Medical College, Baotou, 31 Construction Road, Donghe District, Baotou, Inner Mongolia, P. R. China
| | - Ye Guo
- School of Pharmacy, Baotou Medical College, Baotou, 31 Construction Road, Donghe District, Baotou, Inner Mongolia, P. R. China
- Inner Mongolia Key Laboratory of Disease-Related Biomarkers, Baotou Medical College, Baotou, 31 Construction Road, Donghe District, Baotou, Inner Mongolia, P. R. China
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18
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Mammari N, Krier Y, Albert Q, Devocelle M, Varbanov M. Plant-Derived Antimicrobial Peptides as Potential Antiviral Agents in Systemic Viral Infections. Pharmaceuticals (Basel) 2021; 14:ph14080774. [PMID: 34451871 PMCID: PMC8400714 DOI: 10.3390/ph14080774] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/30/2021] [Accepted: 07/30/2021] [Indexed: 12/26/2022] Open
Abstract
Numerous studies have led to a better understanding of the mechanisms of action of viruses in systemic infections for the development of prevention strategies and very promising antiviral therapies. Viruses still remain one of the main causes of human diseases, mainly because the development of new vaccines is usually challenging and drug resistance has become an increasing concern in recent decades. Therefore, the development of potential antiviral agents remains crucial and is an unmet clinical need. One abundant source of potential therapeutic molecules are plants: they biosynthesize a myriad of compounds, including peptides which can have antimicrobial activity. Our objective is to summarize the literature on peptides with antiviral properties derived from plants and to identify key features of these peptides and their application in systemic viral infections. This literature review highlights studies including clinical trials which demonstrated that plant cyclotides have the ability to inhibit the growth of viruses causing human diseases, defensin-like peptides possess anti-HIV-1 activity, and lipid transfer proteins and some lectins exhibit a varied antimicrobial profile. To conclude, plant peptides remain interesting to explore in the context of emerging and re-emerging infectious diseases.
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Affiliation(s)
- Nour Mammari
- L2CM, Université de Lorraine, CNRS, F-54000 Nancy, France;
| | - Ysaline Krier
- Faculté de Pharmacie, 7 Avenue de la Foret de Haye, 54505 Vandoeuvre-Les-Nancy, France;
| | - Quentin Albert
- Fungal Biodiversity and Biotechnology, INRAE/Aix-Marseille University, UMR1163, 13009 Marseille, France;
- CIRM-CF, INRAE/Aix Marseille University, UMR1163, 13009 Marseille, France
| | - Marc Devocelle
- SSPC (SFI Research Centre for Pharmaceuticals), V94T9PX Limerick, Ireland;
- Department of Chemistry, Royal College of Surgeons in Ireland, RCSI University of Medicine and Health Sciences, 123, St. Stephen’s Green, D02 YN77 Dublin 2, Ireland
| | - Mihayl Varbanov
- L2CM, Université de Lorraine, CNRS, F-54000 Nancy, France;
- Correspondence:
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19
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F Nahhas A, F Nahhas A, J Webster T. Nanoscale pathogens treated with nanomaterial-like peptides: a platform technology appropriate for future pandemics. Nanomedicine (Lond) 2021; 16:1237-1254. [PMID: 33988037 PMCID: PMC8120868 DOI: 10.2217/nnm-2020-0447] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/29/2021] [Indexed: 01/13/2023] Open
Abstract
Viral infections are historically very difficult to treat. Although imperfect and time-consuming to develop, we do have some conventional vaccine and therapeutic approaches to stop viral spreading. Most importantly, all of this takes significant time while viruses continue to wreak havoc on our healthcare system. Furthermore, viral infections are accompanied by a weakened immune system which is often overlooked in antiviral drug strategies and requires additional drug development. In this review, for the first time, we touch on some promising alternative approaches to treat viral infections, specifically those focused on the use of platform nanomaterials with antiviral peptides. In doing so, this review presents a timely discussion of how we need to change our old way of treating viruses into one that can quickly meet the demands of COVID-19, as well as future pandemic-causing viruses, which will come.
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Affiliation(s)
- Alaa F Nahhas
- Biochemistry Department, College of Science, King Abdulaziz University, Jeddah 21589, KSA
| | - Alrayan F Nahhas
- Biochemistry Department, College of Science, King Abdulaziz University, Jeddah 21589, KSA
| | - Thomas J Webster
- Department of Chemical Engineering, College of Engineering, Northeastern University, Boston, MA 02115, USA
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20
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Tonk M, Růžek D, Vilcinskas A. Compelling Evidence for the Activity of Antiviral Peptides against SARS-CoV-2. Viruses 2021; 13:v13050912. [PMID: 34069206 PMCID: PMC8156787 DOI: 10.3390/v13050912] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/09/2021] [Accepted: 05/12/2021] [Indexed: 12/20/2022] Open
Abstract
Multiple outbreaks of epidemic and pandemic viral diseases have occurred in the last 20 years, including those caused by Ebola virus, Zika virus, and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The emergence or re-emergence of such diseases has revealed the deficiency in our pipeline for the discovery and development of antiviral drugs. One promising solution is the extensive library of antimicrobial peptides (AMPs) produced by all eukaryotic organisms. AMPs are widely known for their activity against bacteria, but many possess additional antifungal, antiparasitic, insecticidal, anticancer, or antiviral activities. AMPs could therefore be suitable as leads for the development of new peptide-based antiviral drugs. Sixty therapeutic peptides had been approved by the end of 2018, with at least another 150 in preclinical or clinical development. Peptides undergoing clinical trials include analogs, mimetics, and natural AMPs. The advantages of AMPs include novel mechanisms of action that hinder the evolution of resistance, low molecular weight, low toxicity toward human cells but high specificity and efficacy, the latter enhanced by the optimization of AMP sequences. In this opinion article, we summarize the evidence supporting the efficacy of antiviral AMPs and discuss their potential to treat emerging viral diseases including COVID-19.
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Affiliation(s)
- Miray Tonk
- Institute for Insect Biotechnology, Justus Liebig University of Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany;
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany
| | - Daniel Růžek
- Department of Virology, Veterinary Research Institute, Hudcova 70, CZ-62100 Brno, Czech Republic;
- Biology Centre of the Czech Academy of Sciences, Institute of Parasitology, Branisovska 31, 37005 Ceske Budejovice, Czech Republic
| | - Andreas Vilcinskas
- Institute for Insect Biotechnology, Justus Liebig University of Giessen, Heinrich-Buff-Ring 26-32, 35392 Giessen, Germany;
- LOEWE Centre for Translational Biodiversity Genomics (LOEWE-TBG), Senckenberganlage 25, 60325 Frankfurt, Germany
- Department of Bioresources, Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany
- Correspondence:
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21
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Padhi S, Sanjukta S, Chourasia R, Labala RK, Singh SP, Rai AK. A Multifunctional Peptide From Bacillus Fermented Soybean for Effective Inhibition of SARS-CoV-2 S1 Receptor Binding Domain and Modulation of Toll Like Receptor 4: A Molecular Docking Study. Front Mol Biosci 2021; 8:636647. [PMID: 33869283 PMCID: PMC8044374 DOI: 10.3389/fmolb.2021.636647] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/05/2021] [Indexed: 12/25/2022] Open
Abstract
Fermented soybean products are traditionally consumed and popular in many Asian countries and the northeastern part of India. To search for potential agents for the interruption of the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Spike glycoprotein 1 (S1) and human angiotensin-converting enzyme 2 (ACE2) receptor interactions, the in silico antiviral prospective of peptides identified from the proteome of kinema was investigated. Soybean was fermented using Bacillus licheniformis KN1G, Bacillus amyloliquefaciens KN2G and two different strains of Bacillus subtilis (KN2B and KN2M). The peptides were screened in silico for possible antiviral activity using two different web servers (AVPpred and meta-iAVP), and binding interactions of selected 44 peptides were further explored against the receptor-binding domain (RBD) of the S1 protein (PDB ID: 6M0J) by molecular docking using ZDOCK. The results showed that a peptide ALPEEVIQHTFNLKSQ (P13) belonging to B. licheniformis KN1G fermented kinema was able to make contacts with the binding motif of RBD by blocking specific residues designated as critical (GLN493, ASN501) in the binding of human angiotensin-converting enzyme 2 (ACE2) cell receptor. The selected peptide was also observed to have a significant affinity towards human toll like receptor 4 (TLR4)/Myeloid Differentiation factor 2 (MD2) (PDB ID: 3FXI) complex known for its essential role in cytokine storm. The energy properties of the docked complexes were analyzed through the Generalized Born model and Solvent Accessibility method (MM/GBSA) using HawkDock server. The results showed peptidyl amino acids GLU5, GLN8, PHE11, and LEU13 contributed most to P13-RBD binding. Similarly, ARG90, PHE121, LEU61, PHE126, and ILE94 were appeared to be significant in P13-TLR4/MD2 complex. The findings of the study suggest that the peptides from fermented soy prepared using B. licheniformis KN1G have better potential to be used as antiviral agents. The specific peptide ALPEEVIQHTFNLKSQ could be synthesized and used in combination with experimental studies to validate its effect on SARS-CoV-2-hACE2 interaction and modulation of TLR4 activity. Subsequently, the protein hydrolysate comprising these peptides could be used as prophylaxis against viral diseases, including COVID-19.
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Affiliation(s)
- Srichandan Padhi
- Institute of Bioresources and Sustainable Development, Regional Centre, Gangtok, India
| | | | - Rounak Chourasia
- Institute of Bioresources and Sustainable Development, Regional Centre, Gangtok, India
| | | | - Sudhir P. Singh
- Centre of Innovative and Applied Bioprocessing, Mohali, India
| | - Amit K. Rai
- Institute of Bioresources and Sustainable Development, Regional Centre, Gangtok, India
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22
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Manna S, Chowdhury T, Baindara P, Mandal SM. Fusion Protein Targeted Antiviral Peptides: Fragment-Based Drug Design (FBDD) Guided Rational Design of Dipeptides Against SARS-CoV-2. Curr Protein Pept Sci 2021; 21:938-947. [PMID: 32901582 DOI: 10.2174/1389203721666200908164641] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 11/22/2022]
Abstract
Infectious diseases caused by viruses have become a serious public health issue in the recent past, including the current pandemic situation of COVID-19. Enveloped viruses are most commonly known to cause emerging and recurring infectious diseases. Viral and cell membrane fusion is the major key event in the case of enveloped viruses that is required for their entry into the cell. Viral fusion proteins play an important role in the fusion process and in infection establishment. Because of this, the fusion process targeting antivirals become an interest to fight against viral diseases caused by the enveloped virus. Lower respiratory tract infections casing viruses like influenza, respiratory syncytial virus (RSV), and severe acute respiratory syndrome coronavirus (SARS-CoV) are examples of such enveloped viruses that are at the top in public health issues. Here, we summarized the viral fusion protein targeted antiviral peptides along with their mechanism and specific design to combat the viral fusion process. The pandemic COVID-19, severe respiratory syndrome disease is an outbreak worldwide. There are no definitive drugs yet, but few are in on-going trials. Here, an approach of fragmentbased drug design (FBDD) methodology is used to identify the broad spectrum agent target to the conserved region of fusion protein of SARS CoV-2. Three dipeptides (DL, LQ and ID) were chosen from the library and designed by the systematic combination along with their possible modifications of amino acids to the target sites. Designed peptides were docked with targeted fusion protein after energy minimization. Results show strong and significant binding affinity (DL = -60.1 kcal/mol; LQ = - 62.8 kcal/mol; ID= -71.5 kcal/mol) during interaction. Anyone of the active peptides from the developed libraries may help to block the target sites competitively to successfully control COVID-19.
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Affiliation(s)
- Sounik Manna
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Trinath Chowdhury
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Piyush Baindara
- Department of Molecular Microbiology and Immunology, University of Missouri, Columbia 65212, MO, United States
| | - Santi M Mandal
- Central Research Facility, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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23
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Arumugam AC, Agharbaoui FE, Khazali AS, Yusof R, Abd Rahman N, Ahmad Fuaad AAH. Computational-aided design: minimal peptide sequence to block dengue virus transmission into cells. J Biomol Struct Dyn 2020; 40:5026-5035. [PMID: 33382015 DOI: 10.1080/07391102.2020.1866074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Dengue virus (DV) infection is one of the main public health concerns, affecting approximately 390 million people worldwide, as reported by the World Health Organization. Yet, there is no antiviral treatment for DV infection. Therefore, the development of potent and nontoxic anti-DV, as a complement for the existing treatment strategies, is urgently needed. Herein, we investigate a series of small peptides inhibitors of DV antiviral activity targeting the entry process as the promising strategy to block DV infection. The peptides were designed based on our previously reported peptide sequence, DN58opt (TWWCFYFCRRHHPFWFFYRHN), to identify minimal effective inhibitory sequence through molecular docking and dynamics studies. The in silico designed peptides were synthesized using conventional Fmoc solid-phase peptide synthesis chemistry, purified by RP-HPLC and characterized using LCMS. Later, they were screened for their antiviral activity. One of the peptides, AC 001, was able to reduce about 40% of DV plaque formation. This observation correlates well with the molecular mechanics-Poisson-Boltzmann surface area (MM-PBSA) analysis - AC 001 showed the most favorable binding affinity through 60 ns simulations. Pairwise residue decomposition analysis has revealed four key residues that contributed to the binding of these peptides into the DV2 E protein pocket. This work identifies the minimal peptide sequence required to inhibit DV replication and explains the behavior observed on an atomic level using computational study.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Aathe Cangaree Arumugam
- Faculty of Science, Department of Chemistry, DDDRG, Universiti Malaya, Kuala Lumpur, Malaysia
| | | | - Ahmad Suhail Khazali
- Faculty of Medicine, Department of Molecular Medicine, Universiti Malaya, Kuala Lumpur, Malaysia.,Faculty of Applied Sciences, Universiti Teknologi Mara, Arau, Perlis, Malaysia
| | - Rohana Yusof
- Faculty of Medicine, Department of Molecular Medicine, Universiti Malaya, Kuala Lumpur, Malaysia
| | - Noorsaadah Abd Rahman
- Faculty of Science, Department of Chemistry, DDDRG, Universiti Malaya, Kuala Lumpur, Malaysia
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24
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Mahendran ASK, Lim YS, Fang CM, Loh HS, Le CF. The Potential of Antiviral Peptides as COVID-19 Therapeutics. Front Pharmacol 2020; 11:575444. [PMID: 33041819 PMCID: PMC7522797 DOI: 10.3389/fphar.2020.575444] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 08/28/2020] [Indexed: 01/05/2023] Open
Affiliation(s)
- Arun Suria Karnan Mahendran
- School of Biosciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Malaysia
| | - Yin Sze Lim
- School of Biosciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Malaysia
| | - Chee-Mun Fang
- Division of Biomedical Sciences, School of Pharmacy, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Malaysia
| | - Hwei-San Loh
- School of Biosciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Malaysia
| | - Cheng Foh Le
- School of Biosciences, Faculty of Science and Engineering, University of Nottingham Malaysia, Semenyih, Malaysia
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25
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Feng M, Fei S, Xia J, Labropoulou V, Swevers L, Sun J. Antimicrobial Peptides as Potential Antiviral Factors in Insect Antiviral Immune Response. Front Immunol 2020; 11:2030. [PMID: 32983149 PMCID: PMC7492552 DOI: 10.3389/fimmu.2020.02030] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 07/27/2020] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial peptides (AMPs) with antiviral activity (antiviral peptides: AVPs) have become a research hotspot and already show immense potential to become pharmaceutically available antiviral drugs. AVPs have exhibited huge potential in inhibiting viruses by targeting various stages of their life cycle. Insects are the most speciose group of animals that inhabit almost all ecosystems and habitats on the land and are a rich source of natural AMPs. However, insect AVP mining, functional research, and drug development are still in their infancy. This review aims to summarize the currently validated insect AVPs, explore potential new insect AVPs and to discuss their possible mechanism of synthesis and action, with a view to providing clues to unravel the mechanisms of insect antiviral immunity and to develop insect AVP-derived antiviral drugs.
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Affiliation(s)
- Min Feng
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China.,Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research Demokritos, Athens, Greece
| | - Shigang Fei
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Junming Xia
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Vassiliki Labropoulou
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research Demokritos, Athens, Greece
| | - Luc Swevers
- Insect Molecular Genetics and Biotechnology, Institute of Biosciences and Applications, National Centre for Scientific Research Demokritos, Athens, Greece
| | - Jingchen Sun
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, Guangzhou, China
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26
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Câmara GA, Nishiyama-Jr MY, Kitano ES, Oliveira UC, da Silva PI, Junqueira-de-Azevedo IL, Tashima AK. A Multiomics Approach Unravels New Toxins With Possible In Silico Antimicrobial, Antiviral, and Antitumoral Activities in the Venom of Acanthoscurria rondoniae. Front Pharmacol 2020; 11:1075. [PMID: 32774304 PMCID: PMC7388414 DOI: 10.3389/fphar.2020.01075] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022] Open
Abstract
The Araneae order is considered one of the most successful groups among venomous animals in the world. An important factor for this success is the production of venoms, a refined biological fluid rich in proteins, short peptides and cysteine-rich peptides (CRPs). These toxins may present pharmacologically relevant biological actions, as antimicrobial, antiviral and anticancer activities, for instance. Therefore, there is an increasing interest in the exploration of venom toxins for therapeutic reasons, such as drug development. However, the process of peptide sequencing and mainly the evaluation of potential biological activities of these peptides are laborious, considering the low yield of venom extraction and the high variability of toxins present in spider venoms. Here we show a robust methodology for identification, sequencing, and initial screening of potential bioactive peptides found in the venom of Acanthoscurria rondoniae. This methodology consists in a multiomics approach involving proteomics, peptidomics and transcriptomics analyses allied to in silico predictions of antibacterial, antifungal, antiviral, and anticancer activities. Through the application of this strategy, a total of 92,889 venom gland transcripts were assembled and 84 novel toxins were identified at the protein level, including seven short peptides and 10 fully sequenced CRPs (belonging to seven toxin families). In silico analysis suggests that seven CRPs families may have potential antimicrobial or antiviral activities, while two CRPs and four short peptides are potentially anticancer. Taken together, our results demonstrate an effective multiomics strategy for the discovery of new toxins and in silico screening of potential bioactivities. This strategy may be useful in toxin discovery, as well as in the screening of possible activities for the vast diversity of molecules produced by venomous animals.
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Affiliation(s)
- Guilherme A Câmara
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Milton Y Nishiyama-Jr
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo, Brazil
| | - Eduardo S Kitano
- Laboratory of Immunology, Heart Institute (InCor), Faculty of Medicine, University of Sao Paulo, Sao Paulo, Brazil
| | - Ursula C Oliveira
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo, Brazil
| | - Pedro I da Silva
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo, Brazil
| | - Inácio L Junqueira-de-Azevedo
- Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo, Brazil
| | - Alexandre K Tashima
- Departamento de Bioquímica, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil.,Laboratório Especial de Toxinologia Aplicada, Center of Toxins, Immune-Response and Cell Signaling, Instituto Butantan, São Paulo, Brazil
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27
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Shilovskiy IP, Andreev SM, Kozhikhova KV, Nikolskii AA, Khaitov MR. [Prospects For the Use of Peptides against Respiratory Syncytial Virus]. Mol Biol (Mosk) 2019; 53:541-560. [PMID: 31397431 DOI: 10.1134/s002689841904013x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 03/13/2019] [Indexed: 11/23/2022]
Abstract
The human respiratory syncytial virus (RSV) is one of the most common viral pathogens that affects the lower respiratory tract and could be a reason of bronchiolitis and/or pneumonia. Currently, there are no available effective ways of treating the RSV infection. Attempts to develop preventive vaccine have been unsuccessful. The only therapeutic agent used for RSV treatment is virazole (ribavirin); however, it induces adverse effects. Medications based on neutralizing monoclonal antibodies, such as IGIV (Respigam), palivizumab (Synagis), and MEDI-524 (Numab), are under clinical trials; however, their use will be limited by their high cost. One of the promising approaches for antiviral therapy is the use of natural peptides (defensins and cathelicidins), or their synthetic analogs. The majority of currently described antiviral peptides are developed against the human immunodeficiency virus, the herpes simplex virus, and the influenza virus. At the same time, a body of experimental data evidencing anti-RSV activity of peptides has been accumulated. The main advantages of peptide drugs are their wide spectrum of antiviral activity and low toxicity. However, there are obstacles in implementing peptide-based drugs in clinical practice. Due to their low resistance to the action of serum proteases, most authors consider peptides promising only for local application. Given that RSV affects the epithelium of the respiratory tract, where the protease activity is lower than in the systemic circulation, it is possible to develop locally active peptide drugs, for example, as inhalation forms. Their stability could also be increased by the synthesis of dendrimer peptides and by the development of recombinant peptides as precursor proteins. Anti-RSV peptides can be divided into several groups: (1) attachment and/or fusion blockers; (2) peptides displaying direct virucidal activity, disrupting the viral envelope. Such peptides, which suppress early stages of the viral life cycle, are considered prophylactic agents. However, for several peptides, their immunoregulatory properties have been described, which opens the possibility for therapeutic use. This review summarizes the information on the antiviral properties of such peptides and mechanisms of their action and describes the prospects of the future development of antiviral peptides.
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Affiliation(s)
- I P Shilovskiy
- National Research Center-Institute of Immunology, Federal Medical-Biological Agency.,
| | - S M Andreev
- National Research Center-Institute of Immunology, Federal Medical-Biological Agency
| | - K V Kozhikhova
- National Research Center-Institute of Immunology, Federal Medical-Biological Agency
| | - A A Nikolskii
- National Research Center-Institute of Immunology, Federal Medical-Biological Agency
| | - M R Khaitov
- National Research Center-Institute of Immunology, Federal Medical-Biological Agency
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28
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Jackson JW, Hancock TJ, Dogra P, Patel R, Arav-Boger R, Williams AD, Kennel SJ, Wall JS, Sparer TE. Anticytomegalovirus Peptides Point to New Insights for CMV Entry Mechanisms and the Limitations of In Vitro Screenings. mSphere 2019; 4:e00586-18. [PMID: 30760613 DOI: 10.1128/mSphere.00586-18] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In the absence of an effective vaccine to prevent HCMV infections, alternative interventions must be developed. Prevention of viral entry into susceptible cells is an attractive alternative strategy. Here we report that heparan sulfate-binding peptides effectively inhibit entry into fibroblasts of in vitro-derived CMVs and partially inhibit in vivo-derived CMVs. This includes the inhibition of urine-derived HCMV (uCMV), which is highly resistant to antibody neutralization. While these antiviral peptides are highly effective at inhibiting cell-free virus, they do not inhibit MCMV cell-to-cell spread. This underscores the need to understand the mechanism of cell-to-cell spread and differences between in vivo-derived versus in vitro-derived CMV entry to effectively prevent CMV’s spread. Human cytomegalovirus (HCMV) is a ubiquitous betaherpesvirus that can cause severe disease following in utero exposure, during primary infection, or latent virus reactivation in immunocompromised populations. These complications lead to a 1- to 2-billion-dollar economic burden, making vaccine development and/or alternative treatments a high priority. Current treatments for HCMV include nucleoside analogues such as ganciclovir (GCV), foscarnet, and cidofovir. Recently, letermovir, a terminase complex inhibitor, was approved for prophylaxis after stem cell transplantation. These treatments have unwanted side effects, and HCMV is becoming resistant to them. Therefore, we sought to develop an alternative treatment that targets a different stage in viral infection. Currently, small antiviral peptides are being investigated as anti-influenza and anti-HIV treatments. We have developed heparan sulfate-binding peptides as tools for preventing CMV infections. These peptides are highly effective at stopping infection of fibroblasts with in vitro-derived HCMV and murine cytomegalovirus (MCMV). However, they do not prevent MCMV infection in vivo. Interestingly, these peptides inhibit infectivity of in vivo-derived CMVs, albeit not as well as tissue culture-grown CMVs. We further demonstrate that this class of heparan sulfate-binding peptides is incapable of inhibiting MCMV cell-to-cell spread, which is independent of heparan sulfate usage. These data indicate that inhibition of CMV infection can be achieved using synthetic polybasic peptides, but cell-to-cell spread and in vivo-grown CMVs require further investigation to design appropriate anti-CMV peptides. IMPORTANCE In the absence of an effective vaccine to prevent HCMV infections, alternative interventions must be developed. Prevention of viral entry into susceptible cells is an attractive alternative strategy. Here we report that heparan sulfate-binding peptides effectively inhibit entry into fibroblasts of in vitro-derived CMVs and partially inhibit in vivo-derived CMVs. This includes the inhibition of urine-derived HCMV (uCMV), which is highly resistant to antibody neutralization. While these antiviral peptides are highly effective at inhibiting cell-free virus, they do not inhibit MCMV cell-to-cell spread. This underscores the need to understand the mechanism of cell-to-cell spread and differences between in vivo-derived versus in vitro-derived CMV entry to effectively prevent CMV’s spread.
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29
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Alghrair ZK, Fernig DG, Ebrahimi B. Enhanced inhibition of influenza virus infection by peptide-noble-metal nanoparticle conjugates. Beilstein J Nanotechnol 2019; 10:1038-1047. [PMID: 31165030 PMCID: PMC6541353 DOI: 10.3762/bjnano.10.104] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 04/30/2019] [Indexed: 05/21/2023]
Abstract
The influenza ("flu") type-A virus is a major medical and veterinary health concern and causes global pandemics. The peptide "FluPep" is an established inhibitor of influenza virus infectivity in model systems. We have explored the potential for noble-metal nanoparticle conjugates of FluPep to enhance its antiviral activity and to determine their potential as a delivery platform for FluPep. FluPep ligand is FluPep extended at its N-terminus with the sequence CVVVTAAA, to allow for its incorporation into a mixed-matrix ligand shell of a peptidol and an alkanethiol ethylene glycol consisting of 70% CVVVTol and 30% HS(CH2)11(OC2H4)4OH (mol/mol). Gold and silver nanoparticles (ca. 10 nm diameter) with up to 5% (mol/mol) FluPep ligand remained as stable as the control of mixed-matrix-passivated nanoparticles in a variety of tests, including ligand exchange with dithiothreitol. The free FluPep ligand peptide was found to inhibit viral plaque formation in canine MDCK cells (IC50 = 2.1 nM), but was less potent than FluPep itself (IC50 = 140 pM). Nanoparticles functionalised with FluPep ligand showed enhanced antiviral activity compared to the free peptides. The IC50 value of the FluPep-functionalised nanoparticles decreased as the grafting density of FluPep ligand increased from 0.03% to 5% (both mol/mol), with IC50 values down to about 10% of that of the corresponding free peptide. The data demonstrate that conjugation of FluPep to gold and silver nanoparticles enhances its antiviral potency; the antimicrobial activity of silver ions may enable the design of even more potent antimicrobial inhibitors, capable of targeting both influenza and bacterial co-infections.
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Affiliation(s)
- Zaid K Alghrair
- Department of Biochemistry Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - David G Fernig
- Department of Biochemistry Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Bahram Ebrahimi
- Department of Functional and Comparative Genomics, Institute of Integrative Biology, Biosciences Building, Crown Street, University of Liverpool, Liverpool, L69 7ZB, UK
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30
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Vilas Boas LCP, de Lima LMP, Migliolo L, Mendes GDS, de Jesus MG, Franco OL, Silva PA. Linear antimicrobial peptides with activity against herpes simplex virus 1 and Aichi virus. Biopolymers 2017; 108. [PMID: 27161201 DOI: 10.1002/bip.22871] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 04/30/2016] [Accepted: 05/04/2016] [Indexed: 01/01/2023]
Abstract
Viruses are the major cause of disease and mortality worldwide. Nowadays there are treatments based on antivirals or prophylaxis with vaccines. However, the rising number of reports of viral resistance to current antivirals and the emergence of new types of virus has concerned the scientific community. In this scenario, the search for alternative treatments has led scientists to the discovery of antimicrobial peptides (AMPs) derived from many different sources. Since some of them have shown antiviral activities, here we challenged 10 synthetic peptides from different animal and plant sources against, herpes simplex virus 1 (HSV-1), and Aichi virus. Among them, the highlight was Pa-MAP from the polar fish Pleuronectes americanus, which caused around 90% of inhibition of the HSV with a selectivity index of 5 and a virucidal mechanism of action. Moreover, LL-37 from human neutrophils showed 96% of inhibition against the Aichi virus, showing a selectivity index of 3.4. The other evaluated peptides did not show significant antiviral activity. In conclusion, the present study demonstrated that Pa-MAP seems to be a reliable candidate for a possible alternative drug to treat HSV-1 infections. © 2016 Wiley Periodicals, Inc. Biopolymers (Pept Sci) 108: 1-6, 2017.
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Affiliation(s)
- Liana Costa Pereira Vilas Boas
- Centro De Análises Proteômicas E Bioquímicas: Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Distrito Federal, Brazil
| | - Lídia Maria Pinto de Lima
- Centro De Análises Proteômicas E Bioquímicas: Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Distrito Federal, Brazil
| | - Ludovico Migliolo
- Centro De Análises Proteômicas E Bioquímicas: Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Distrito Federal, Brazil.,S-Inova Biotech, Pós-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Gabriele Dos Santos Mendes
- Centro De Análises Proteômicas E Bioquímicas: Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Distrito Federal, Brazil
| | - Maianne Gonçalves de Jesus
- Centro De Análises Proteômicas E Bioquímicas: Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Distrito Federal, Brazil
| | - Octávio Luiz Franco
- Centro De Análises Proteômicas E Bioquímicas: Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Distrito Federal, Brazil.,S-Inova Biotech, Pós-Graduação Em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil
| | - Paula Andréia Silva
- Centro De Análises Proteômicas E Bioquímicas: Programa De Pós-Graduação Em Ciências Genômicas E Biotecnologia, Universidade Católica De Brasília, Distrito Federal, Brazil
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Gordts SC, Renders M, Férir G, Huskens D, Van Damme EJM, Peumans W, Balzarini J, Schols D. NICTABA and UDA, two GlcNAc-binding lectins with unique antiviral activity profiles. J Antimicrob Chemother 2015; 70:1674-85. [PMID: 25700718 PMCID: PMC7537945 DOI: 10.1093/jac/dkv034] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Revised: 01/18/2015] [Accepted: 01/25/2015] [Indexed: 01/25/2023] Open
Abstract
OBJECTIVES This study aimed to assess the antiviral properties of a unique lectin (NICTABA) produced by the tobacco plant, Nicotiana tabacum. METHODS Cellular assays were used to investigate the antiviral activity of NICTABA and Urtica dioica agglutinin (UDA). Surface plasmon resonance (SPR) studies were performed to study the sugar specificity and the interactions of both lectins with the envelope glycoproteins of HIV-1. RESULTS The N-acetyl-d-glucosamine (GlcNAc)-binding lectins exhibited broad-spectrum activity against several families of enveloped viruses including influenza A/B, Dengue virus type 2, herpes simplex virus types 1 and 2 and HIV-1/2. The IC50 of NICTABA for various HIV-1 strains, clinical isolates and HIV-2 assessed in PBMCs ranged from 5 to 30 nM. Furthermore, NICTABA inhibited syncytium formation between persistently HIV-1-infected T cells and uninfected CD4+ T lymphocytes and prevented DC-SIGN-mediated HIV-1 transmission to CD4+ target T lymphocytes. However, unlike many other antiviral carbohydrate-binding agents (CBAs) described so far, NICTABA did not block HIV-1 capture to DC-SIGN+ cells and it did not interfere with the binding of the human monoclonal antibody 2G12 to gp120. SPR studies with HIV-1 envelope glycoproteins showed that the affinity of NICTABA for gp120 and gp41 was in the low nanomolar range. The specific binding of NICTABA to gp120 could be prevented in the presence of a GlcNAc trimer, but not in the presence of mannose trimers. NICTABA displayed no antiviral activity against non-enveloped viruses. CONCLUSIONS Since CBAs possess a high genetic barrier for the development of viral resistance and NICTABA shows a broad antiviral activity profile, this CBA may qualify as a potential antiviral candidate with a pleiotropic mode of action aimed at targeting the entry of enveloped viruses.
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Affiliation(s)
- Stephanie C Gordts
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Marleen Renders
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium Laboratory of Medicinal Chemistry, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Geoffrey Férir
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Dana Huskens
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Els J M Van Damme
- Laboratory of Biochemistry and Glycobiology, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Willy Peumans
- Laboratory of Biochemistry and Glycobiology, Ghent University, Coupure links 653, 9000 Gent, Belgium
| | - Jan Balzarini
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
| | - Dominique Schols
- Laboratory of Virology and Chemotherapy, Rega Institute for Medical Research, KU Leuven, Minderbroedersstraat 10, 3000 Leuven, Belgium
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