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Le VT, Zhan ZJ, Vu TTP, Malik MS, Ou YY. ProtTrans and multi-window scanning convolutional neural networks for the prediction of protein-peptide interaction sites. J Mol Graph Model 2024; 130:108777. [PMID: 38642500 DOI: 10.1016/j.jmgm.2024.108777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 03/28/2024] [Accepted: 04/16/2024] [Indexed: 04/22/2024]
Abstract
This study delves into the prediction of protein-peptide interactions using advanced machine learning techniques, comparing models such as sequence-based, standard CNNs, and traditional classifiers. Leveraging pre-trained language models and multi-view window scanning CNNs, our approach yields significant improvements, with ProtTrans standing out based on 2.1 billion protein sequences and 393 billion amino acids. The integrated model demonstrates remarkable performance, achieving an AUC of 0.856 and 0.823 on the PepBCL Set_1 and Set_2 datasets, respectively. Additionally, it attains a Precision of 0.564 in PepBCL Set 1 and 0.527 in PepBCL Set 2, surpassing the performance of previous methods. Beyond this, we explore the application of this model in cancer therapy, particularly in identifying peptide interactions for selective targeting of cancer cells, and other fields. The findings of this study contribute to bioinformatics, providing valuable insights for drug discovery and therapeutic development.
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Affiliation(s)
- Van-The Le
- Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, 32003, Taiwan
| | - Zi-Jun Zhan
- Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, 32003, Taiwan
| | - Thi-Thu-Phuong Vu
- Graduate Program in Biomedical Informatics, Yuan Ze University, Chung-Li, 32003, Taiwan
| | - Muhammad-Shahid Malik
- Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, 32003, Taiwan; Department of Computer Science and Engineering, Karakoram International University, Pakistan
| | - Yu-Yen Ou
- Department of Computer Science and Engineering, Yuan Ze University, Chung-Li, 32003, Taiwan; Graduate Program in Biomedical Informatics, Yuan Ze University, Chung-Li, 32003, Taiwan.
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2
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Yu X, He Q, Kong Q. Multidisciplinary approaches to combat emerging viruses: diagnostics, therapeutic gene and vaccine delivery, and nanotherapeutics. Front Microbiol 2024; 15:1387623. [PMID: 38966392 PMCID: PMC11222566 DOI: 10.3389/fmicb.2024.1387623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Accepted: 04/08/2024] [Indexed: 07/06/2024] Open
Abstract
Emerging viruses, such as filoviruses (Ebola, Marburg), SARS and MERS coronaviruses, and Zika, pose significant threats to global public health, particularly for individuals with co-morbidities. To address these challenges, this review article explores multidisciplinary strategies for combatting emerging viruses. We emphasize the importance of developing accurate diagnostics, innovative therapeutic gene and vaccine delivery systems, and long-acting nanotherapeutics. These approaches are designed to enhance the safety and efficacy of treatments against these deadly pathogens. We discuss the collaborative efforts of virologists, geneticists, formulation scientists, clinicians, immunologists, and medicinal chemists in advancing these therapeutic modalities.
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Affiliation(s)
- Xianqiang Yu
- Medical College of Qingdao University, Qingdao, China
| | - Qing He
- School of Basic Medicine and Forensics, Key Laboratory of Bio-tech Vaccine of Zhejiang Province, Engineering Research Center of Novel Vaccine of Zhejiang Province, Hangzhou Medical College, Hangzhou, China
| | - Qingming Kong
- School of Basic Medicine and Forensics, Key Laboratory of Bio-tech Vaccine of Zhejiang Province, Engineering Research Center of Novel Vaccine of Zhejiang Province, Hangzhou Medical College, Hangzhou, China
- Key Laboratory of Biomarkers and In Vitro Diagnosis Translation of Zhejiang province, School of Laboratory Medicine and Bioengineering, Hangzhou Medical College, Hangzhou, China
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3
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Essa RZ, Wu YS, Batumalaie K, Sekar M, Poh CL. Antiviral peptides against SARS-CoV-2: therapeutic targets, mechanistic antiviral activity, and efficient delivery. Pharmacol Rep 2022; 74:1166-1181. [PMID: 36401119 PMCID: PMC9676828 DOI: 10.1007/s43440-022-00432-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 11/19/2022]
Abstract
The global pandemic of COVID-19 is a serious public health concern. Over 625 million confirmed cases and more than 6 million deaths have been recorded worldwide. Although several vaccines and antiviral medications have been developed, their efficacy is limited by the emerging new SARS-CoV-2 strains. Peptide-based therapeutics is a fast-growing class of new drugs and have unique advantages over large proteins and small molecules. Antiviral peptides (AVPs) are short polycationic antivirals with broad-spectrum effects, which have been shown to exert both prophylactic and therapeutic actions against reported coronaviruses. The potential therapeutic targets of AVPs are located either on the virus (e.g., E-protein and S-protein) to prohibit viral binding or host cells, particularly, those present on the cell surface (e.g., ACE2 and TMPRSS2). Despite AVPs having promising antiviral effects, their efficacy is limited by low bioavailability. Thus, nanoformulation is a prerequisite for prolonged bioavailability and efficient delivery. This review aimed to present an insight into the therapeutic AVP targets on both virus and host cells by discussing their antiviral activities and associated molecular mechanisms. Besides, it described the technique for discovering and developing possible AVPs based on their targets, as well as the significance of using nanotechnology for their efficient delivery against SARS-CoV-2.
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Affiliation(s)
- Raahilah Zahir Essa
- Department of Medical Sciences, School of Medical and Life Sciences, Sunway University, 47500 Selangor, Malaysia
| | - Yuan-seng Wu
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, 47500 Selangor, Malaysia ,Department of Biological Sciences, School of Medical and Life Sciences, Sunway University, 47500 Selangor, Malaysia
| | - Kalaivani Batumalaie
- Department of Biomedical Sciences, Faculty of Health Sciences, Asia Metropolitan University, 81750 Johor, Malaysia
| | - Mahendran Sekar
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Health Sciences, Royal College of Medicine Perak, Universiti Kuala Lumpur, 30450 Ipoh, Perak Malaysia
| | - Chit-laa Poh
- Centre for Virus and Vaccine Research, School of Medical and Life Sciences, Sunway University, 47500 Selangor, Malaysia
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4
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Vishwakarma P, Yadav N, Rizvi ZA, Khan NA, Chiranjivi AK, Mani S, Bansal M, Dwivedi P, Shrivastava T, Kumar R, Awasthi A, Ahmed S, Samal S. Severe Acute Respiratory Syndrome Coronavirus 2 Spike Protein Based Novel Epitopes Induce Potent Immune Responses in vivo and Inhibit Viral Replication in vitro. Front Immunol 2021; 12:613045. [PMID: 33841395 PMCID: PMC8032902 DOI: 10.3389/fimmu.2021.613045] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 02/09/2021] [Indexed: 11/13/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) initiates infection by attachment of the surface-exposed spike glycoprotein to the host cell receptors. The spike glycoprotein (S) is a promising target for inducing immune responses and providing protection; thus the ongoing efforts for the SARS-CoV-2 vaccine and therapeutic developments are mostly spiraling around S glycoprotein. The matured functional spike glycoprotein is presented on the virion surface as trimers, which contain two subunits, such as S1 (virus attachment) and S2 (virus fusion). The S1 subunit harbors the N-terminal domain (NTD) and the receptor-binding domain (RBD). The RBD is responsible for binding to host-cellular receptor angiotensin-converting enzyme 2 (ACE2). The NTD and RBD of S1, and the S2 of S glycoprotein are the major structural moieties to design and develop spike-based vaccine candidates and therapeutics. Here, we have identified three novel epitopes (20-amino acid peptides) in the regions NTD, RBD, and S2 domains, respectively, by structural and immunoinformatic analysis. We have shown as a proof of principle in the murine model, the potential role of these novel epitopes in-inducing humoral and cellular immune responses. Further analysis has shown that RBD and S2 directed epitopes were able to efficiently inhibit the replication of SARS-CoV-2 wild-type virus in vitro suggesting their role as virus entry inhibitors. Structural analysis revealed that S2-epitope is a part of the heptad repeat 2 (HR2) domain which might have plausible inhibitory effects on virus fusion. Taken together, this study discovered novel epitopes that might have important implications in the development of potential SARS-CoV-2 spike-based vaccine and therapeutics.
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Affiliation(s)
- Preeti Vishwakarma
- Translational Health Science & Technology Institute, National Capital Region (NCR) Biotech Science Cluster, Faridabad, India
| | - Naveen Yadav
- Translational Health Science & Technology Institute, National Capital Region (NCR) Biotech Science Cluster, Faridabad, India
| | - Zaigham Abbas Rizvi
- Translational Health Science & Technology Institute, National Capital Region (NCR) Biotech Science Cluster, Faridabad, India
| | - Naseem Ahmed Khan
- Translational Health Science & Technology Institute, National Capital Region (NCR) Biotech Science Cluster, Faridabad, India
| | - Adarsh Kumar Chiranjivi
- Translational Health Science & Technology Institute, National Capital Region (NCR) Biotech Science Cluster, Faridabad, India
| | - Shailendra Mani
- Translational Health Science & Technology Institute, National Capital Region (NCR) Biotech Science Cluster, Faridabad, India
| | - Manish Bansal
- Translational Health Science & Technology Institute, National Capital Region (NCR) Biotech Science Cluster, Faridabad, India
| | - Prabhanjan Dwivedi
- Translational Health Science & Technology Institute, National Capital Region (NCR) Biotech Science Cluster, Faridabad, India
| | - Tripti Shrivastava
- Translational Health Science & Technology Institute, National Capital Region (NCR) Biotech Science Cluster, Faridabad, India
| | - Rajesh Kumar
- Translational Health Science & Technology Institute, National Capital Region (NCR) Biotech Science Cluster, Faridabad, India
| | - Amit Awasthi
- Translational Health Science & Technology Institute, National Capital Region (NCR) Biotech Science Cluster, Faridabad, India
| | - Shubbir Ahmed
- Translational Health Science & Technology Institute, National Capital Region (NCR) Biotech Science Cluster, Faridabad, India
| | - Sweety Samal
- Translational Health Science & Technology Institute, National Capital Region (NCR) Biotech Science Cluster, Faridabad, India
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Sharma A, Pant K, Pande A, Sinha S, Pant B. Modeling novel Anti-Viral peptides (AVPs) with in-silico docking simulations against corona virus. ACTA ACUST UNITED AC 2021; 46:11169-11176. [PMID: 33680868 PMCID: PMC7914030 DOI: 10.1016/j.matpr.2021.02.377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 11/25/2022]
Abstract
The havoc created by Corona virus has been dealt with using various integrative approaches adopted by laboratories through-out the world. Use of anti-viral peptides (AVPs) although new but has shown tremendous potential against many pathogens. Previously AVPs have been designed against spike protein of corona virus which is the major entry mediating molecule. Using various in-silico strategies, in this research work AVPs have been modeled against lesser studied viral proteins namely ORF7a protein, Envelope protein (E), Nucleoprotein (N), and Non-Structural protein (Nsp1 and Nsp2). The predicted AVPs have been docked against various host as well as viral proteins. The interaction of small AVPs seems capable of interfering with binding between viral protein and its host counterpart. Therefore, these AVPs can act as a deterrent against novel corona virus, which requires further validation through laboratory techniques.
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Affiliation(s)
- Aditi Sharma
- Deparment of Life Sciences, Graphic Era Deemed to be University, Dehradun, Uttarakhand, India
| | - Kumud Pant
- Department of Biotechnology, Graphic Era Deemed to be University, Dehradun, Uttarakhand, India
| | - Akshara Pande
- Department of Computer Sciences, Graphic Era Hill University, Dehradun, Uttarakhand, India
| | - Somya Sinha
- Department of Biotechnology, Graphic Era Deemed to be University, Dehradun, Uttarakhand, India
| | - Bhasker Pant
- Department of Computer Sciences, Graphic Era Hill University, Dehradun, Uttarakhand, India
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Vilas Boas LCP, Campos ML, Berlanda RLA, de Carvalho Neves N, Franco OL. Antiviral peptides as promising therapeutic drugs. Cell Mol Life Sci 2019; 76:3525-3542. [PMID: 31101936 PMCID: PMC7079787 DOI: 10.1007/s00018-019-03138-w] [Citation(s) in RCA: 168] [Impact Index Per Article: 33.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 05/04/2019] [Accepted: 05/07/2019] [Indexed: 01/28/2023]
Abstract
While scientific advances have led to large-scale production and widespread distribution of vaccines and antiviral drugs, viruses still remain a major cause of human diseases today. The ever-increasing reports of viral resistance and the emergence and re-emergence of viral epidemics pressure the health and scientific community to constantly find novel molecules with antiviral potential. This search involves numerous different approaches, and the use of antimicrobial peptides has presented itself as an interesting alternative. Even though the number of antimicrobial peptides with antiviral activity is still low, they already show immense potential to become pharmaceutically available antiviral drugs. Such peptides can originate from natural sources, such as those isolated from mammals and from animal venoms, or from artificial sources, when bioinformatics tools are used. This review aims to shed some light on antimicrobial peptides with antiviral activities against human viruses and update the data about the already well-known peptides that are still undergoing studies, emphasizing the most promising ones that may become medicines for clinical use.
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Affiliation(s)
| | - Marcelo Lattarulo Campos
- Centro de Análises Bioquímicas e Proteômicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, 70790-160, Brazil
- Departamento de Botânica e Ecologia, Instituto de Biociências, Universidade Federal de Mato Grosso, Cuiabá, MT, 78060-900, Brazil
| | - Rhayfa Lorrayne Araujo Berlanda
- Centro de Análises Bioquímicas e Proteômicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, 70790-160, Brazil
| | - Natan de Carvalho Neves
- Centro de Análises Bioquímicas e Proteômicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, 70790-160, Brazil
| | - Octávio Luiz Franco
- Universidade de Brasília, Pós-Graduação em Patologia Molecular, Campus Darcy Ribeiro, Brasília, DF, 70910-900, Brazil.
- Centro de Análises Bioquímicas e Proteômicas, Pós-graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, 70790-160, Brazil.
- S-Inova Biotech, Pós-graduação em Biotecnologia Universidade Católica Dom Bosco, Campo Grande, MS, 79117-900, Brazil.
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7
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Sterpone F, Melchionna S, Tuffery P, Pasquali S, Mousseau N, Cragnolini T, Chebaro Y, St-Pierre JF, Kalimeri M, Barducci A, Laurin Y, Tek A, Baaden M, Nguyen PH, Derreumaux P. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem Soc Rev 2014; 43:4871-93. [PMID: 24759934 PMCID: PMC4426487 DOI: 10.1039/c4cs00048j] [Citation(s) in RCA: 120] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The OPEP coarse-grained protein model has been applied to a wide range of applications since its first release 15 years ago. The model, which combines energetic and structural accuracy and chemical specificity, allows the study of single protein properties, DNA-RNA complexes, amyloid fibril formation and protein suspensions in a crowded environment. Here we first review the current state of the model and the most exciting applications using advanced conformational sampling methods. We then present the current limitations and a perspective on the ongoing developments.
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Affiliation(s)
- Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.
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8
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Inhibition of influenza A virus infection in vitro by peptides designed in silico. PLoS One 2013; 8:e76876. [PMID: 24146939 PMCID: PMC3795628 DOI: 10.1371/journal.pone.0076876] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Accepted: 08/26/2013] [Indexed: 11/19/2022] Open
Abstract
Influenza A viruses are enveloped, segmented negative single-stranded RNA viruses, capable of causing severe human respiratory infections. Currently, only two types of drugs are used to treat influenza A infections, the M2 H+ ion channel blockers (amantadine and rimantadine) and the neuraminidase inhibitors (NAI) (oseltamivir and zanamivir). Moreover, the emergence of drug-resistant influenza A virus strains has emphasized the need to develop new antiviral agents to complement or replace the existing drugs. Influenza A virus has on the surface a glycoprotein named hemagglutinin (HA) which due to its important role in the initial stage of infection: receptor binding and fusion activities of viral and endosomal membranes, is a potential target for new antiviral drugs. In this work we designed nine peptides using several bioinformatics tools. These peptides were derived from the HA1 and HA2 subunits of influenza A HA with the aim to inhibit influenza A virus infection. The peptides were synthetized and their antiviral activity was tested in vitro against several influenza A viral strains: Puerto Rico/916/34 (H1N1), (H1N1)pdm09, swine (H1N1) and avian (H5N2). We found these peptides were able to inhibit the influenza A viral strains tested, without showing any cytotoxic effect. By docking studies we found evidence that all the peptides were capable to bind to the viral HA, principally to important regions on the viral HA stalk, thus could prevent the HA conformational changes required to carry out its membranes fusion activity.
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9
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Teixeira LD, Silva ON, Migliolo L, Fensterseifer ICM, Franco OL. In vivo antimicrobial evaluation of an alanine-rich peptide derived from Pleuronectes americanus. Peptides 2013; 42:144-8. [PMID: 23416023 DOI: 10.1016/j.peptides.2013.02.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/04/2013] [Revised: 02/04/2013] [Accepted: 02/04/2013] [Indexed: 11/18/2022]
Abstract
In several organisms, the first barrier against microbial infections consists of antimicrobial peptides (AMPs) which are molecules that act as components of the innate immune system. Recent studies have demonstrated that AMPs can perform various functions in different tissues or physiological conditions. In this view, this study was carried out in order to evaluate the multifunctional activity in vivo of an alanine-rich peptide, known as Pa-MAP, derived from the polar fish Pleuronectes americanus. Pa-MAP was evaluated in intraperitoneally infected mice with a sub-lethal concentration of Escherichia coli at standard concentrations of 1 and 5 mg kg(-1). At both concentrations, Pa-MAPs exhibited an ability to prevent E. coli infection and increase mice survival, similar to the result observed in mice treated with ampicillin at 2 mg kg(-1). In addition, mice were monitored for weight loss. The results showed that mice treated with Pa-MAPs at 1 mg kg(-1) gained 0.8% of body weight during the 72 h of experiment. The same was observed with Pa-MAP at 5 mg kg(-1), which had a gain of 0.5% in body weight during the treatment. Mice treated with ampicillin at 2 mg kg(-1) show a significant weight loss of 5.6% of body weight. The untreated group exhibited a 5.5% loss of body weight. The immunomodulatory effects were also evaluated by the quantification of IL-10, IL-12, TNF-α, IFN-γ and nitric oxide cytokines in serum, but no immunomodulatory activity was observed. Data presented here suggest that Pa-MAP should be used as a novel antibiotic against infection control.
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Affiliation(s)
- Leandro D Teixeira
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília, DF, Brazil
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Galdiero S, Falanga A, Tarallo R, Russo L, Galdiero E, Cantisani M, Morelli G, Galdiero M. Peptide inhibitors against herpes simplex virus infections. J Pept Sci 2013; 19:148-58. [PMID: 23389903 DOI: 10.1002/psc.2489] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 11/07/2022]
Abstract
Herpes simplex virus (HSV) is a significant human pathogen causing mucocutaneous lesions primarily in the oral or genital mucosa. Although acyclovir (ACV) and related nucleoside analogs provide successful treatment, HSV remains highly prevalent worldwide and is a major cofactor for the spread of human immunodeficiency virus. Encephalitis, meningitis, and blinding keratitis are among the most severe diseases caused by HSV. ACV resistance poses an important problem for immunocompromised patients and highlights the need for new safe and effective agents; therefore, the development of novel strategies to eradicate HSV is a global public health priority. Despite the continued global epidemic of HSV and extensive research, there have been few major breakthroughs in the treatment or prevention of the virus since the introduction of ACV in the 1980s. A therapeutic strategy at the moment not fully addressed is the use of small peptide molecules. These can be either modeled on viral proteins or derived from antimicrobial peptides. Any peptide that interrupts protein-protein or viral protein-host cell membrane interactions is potentially a novel antiviral drug and may be a useful tool for elucidating the mechanisms of viral entry. This review summarizes current knowledge and strategies in the development of synthetic and natural peptides to inhibit HSV infectivity.
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Affiliation(s)
- Stefania Galdiero
- Department of Pharmacy, University of Naples Federico II, Via Mezzocannone 16, 80134, Napoli, Italy.
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