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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 PMCID: PMC11070730 DOI: 10.1093/bib/bbae208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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2
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Bharadwaj A, Kaur R, Gupta S. Emerging Treatment Approaches for COVID-19 Infection: A Critical Review. Curr Mol Med 2024; 24:435-448. [PMID: 37070448 DOI: 10.2174/1566524023666230417112543] [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: 09/02/2022] [Revised: 02/04/2023] [Accepted: 02/07/2023] [Indexed: 04/19/2023]
Abstract
In the present scenario, the SARS-CoV-2 virus has imposed enormous damage on human survival and the global financial system. It has been estimated that around 111 million people all around the world have been infected, and about 2.47 million people died due to this pandemic. The major symptoms were sneezing, coughing, cold, difficulty breathing, pneumonia, and multi-organ failure associated 1with SARS-CoV-2. Currently, two key problems, namely insufficient attempts to develop drugs against SARSCoV-2 and the lack of any biological regulating process, are mostly responsible for the havoc caused by this virus. Henceforth, developing a few novel drugs is urgently required to cure this pandemic. It has been noticed that the pathogenesis of COVID-19 is caused by two main events: infection and immune deficiency, that occur during the pathological process. Antiviral medication can treat both the virus and the host cells. Therefore, in the present review, the major approaches for the treatment have been divided into "target virus" and "target host" groups. These two mechanisms primarily rely on drug repositioning, novel approaches, and possible targets. Initially, we discussed the traditional drugs per the physicians' recommendations. Moreover, such therapeutics have no potential to fight against COVID-19. After that, detailed investigation and analysis were conducted to find some novel vaccines and monoclonal antibodies and conduct a few clinical trials to check their effectiveness against SARSCoV- 2 and mutant strains. Additionally, this study presents the most successful methods for its treatment, including combinatorial therapy. Nanotechnology was studied to build efficient nanocarriers to overcome the traditional constraints of antiviral and biological therapies.
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Affiliation(s)
- Alok Bharadwaj
- Department of Biotechnology, GLA University, Mathura, 281406, UP, India
| | - Rasanpreet Kaur
- Department of Biotechnology, GLA University, Mathura, 281406, UP, India
| | - Saurabh Gupta
- Department of Biotechnology, GLA University, Mathura, 281406, UP, India
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3
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Nath A. Physicochemical and sequence determinants of antiviral peptides. Biol Futur 2023; 74:489-506. [PMID: 37889451 DOI: 10.1007/s42977-023-00188-x] [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: 04/22/2023] [Accepted: 10/06/2023] [Indexed: 10/28/2023]
Abstract
Antiviral peptides (AVPs) open new possibilities as an effective antiviral therapeutic in the current scenario of evolving drug-resistant viruses. Knowledge about the sequence and structure activity relationship in AVPs is still largely unknown. AVPs and antimicrobial peptides (AMPs) share several common features but as they target different life forms (living organisms and viruses), exploring the differential sequence features may facilitate in designing specific AVPs. The current work developed accurate prediction models for discriminating (a) AVPs from AMPs, (b) Coronaviridae AVPs from other virus family specific AVPs and (c) highly active AVPs (HAA) from lowly active AVPs (LAA). Further explainable machine learning methods (using model agnostic global interpretable methods) are utilized for exploring and interpreting the physicochemical spaces of AVPs, Coronaviridae AVPs and highly active AVPs. To further understand the association of physicochemical space distribution with pIC50 values, regression models were developed and analyzed using accumulated local effects and interaction strength analysis. An independent sample t-test is used to filter out the significant compositional differences between the smaller length HAA and longer length HAA groups. AVPs prefer lower charge/length ratio and basic residues in comparison with AMPs. Coronaviridae family-specific AVPs have lower propensities for basic amino acids, charge and preference for aspartic acid. Further there is prevalence for basic residues in lowly active AVPs as compared to highly active AVPs. Sequence order effects captured in terms of average amino acid pair distances proved to be more constructive in deciphering the sequences of AVPs.
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Affiliation(s)
- Abhigyan Nath
- Department of Biochemistry, Pt. Jawahar Lal Nehru Memorial Medical College, Raipur, 492001, India.
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4
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Rossino G, Marchese E, Galli G, Verde F, Finizio M, Serra M, Linciano P, Collina S. Peptides as Therapeutic Agents: Challenges and Opportunities in the Green Transition Era. Molecules 2023; 28:7165. [PMID: 37894644 PMCID: PMC10609221 DOI: 10.3390/molecules28207165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/05/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Peptides are at the cutting edge of contemporary research for new potent, selective, and safe therapeutical agents. Their rise has reshaped the pharmaceutical landscape, providing solutions to challenges that traditional small molecules often cannot address. A wide variety of natural and modified peptides have been obtained and studied, and many others are advancing in clinical trials, covering multiple therapeutic areas. As the demand for peptide-based therapies grows, so does the need for sustainable and environmentally friendly synthesis methods. Traditional peptide synthesis, while effective, often involves environmentally draining processes, generating significant waste and consuming vast resources. The integration of green chemistry offers sustainable alternatives, prioritizing eco-friendly processes, waste reduction, and energy conservation. This review delves into the transformative potential of applying green chemistry principles to peptide synthesis by discussing relevant examples of the application of such approaches to the production of active pharmaceutical ingredients (APIs) with a peptide structure and how these efforts are critical for an effective green transition era in the pharmaceutical field.
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Affiliation(s)
- Giacomo Rossino
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Emanuela Marchese
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
- Department of Health Sciences, University “Magna Graecia”, Viale Europa, 88100 Catanzaro, Italy
| | - Giovanni Galli
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Francesca Verde
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Matteo Finizio
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Massimo Serra
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Pasquale Linciano
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
| | - Simona Collina
- Department of Drug Sciences, University of Pavia, Viale Taramelli 12, 27100 Pavia, Italy; (G.R.); (E.M.); (M.S.); (P.L.)
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Stincarelli MA, Quagliata M, Di Santo A, Pacini L, Fernandez FR, Arvia R, Rinaldi S, Papini AM, Rovero P, Giannecchini S. SARS-CoV-2 inhibitory activity of a short peptide derived from internal fusion peptide of S2 subunit of spike glycoprotein. Virus Res 2023; 334:199170. [PMID: 37422270 PMCID: PMC10384657 DOI: 10.1016/j.virusres.2023.199170] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 07/01/2023] [Accepted: 07/06/2023] [Indexed: 07/10/2023]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) has posed a great concern in human population. To fight coronavirus emergence, we have dissected the conserved amino acid region of the internal fusion peptide in the S2 subunit of Spike glycoprotein of SARS-CoV-2 to design new inhibitory peptides. Among the 11 overlapping peptides (9-23-mer), PN19, a 19-mer peptide, exhibited a powerful inhibitory activity against different SARS-CoV-2 clinical isolate variants in absence of cytotoxicity. The PN19 inhibitory activity was found to be dependent on conservation of the central Phe and C-terminal Tyr residues in the peptide sequence. Circular dichroism spectra of the active peptide exhibited an alpha-helix propensity, confirmed by secondary structure prediction analysis. The PN19 inhibitory activity, exerted in the first step of virus infection, was reduced after peptide adsorption treatment with virus-cell substrate during fusion interaction. Additionally, PN19 inhibitory activity was reduced by adding S2 membrane-proximal region derived peptides. PN19 showed binding ability to the S2 membrane proximal region derived peptides, confirmed by molecular modelling, playing a role in the mechanism of action. Collectively, these results confirm that the internal fusion peptide region is a good candidate on which develop peptidomimetic anti SARS-CoV-2 antivirals.
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Affiliation(s)
- Maria Alfreda Stincarelli
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, Florence 50134, Italy
| | - Michael Quagliata
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Andrea Di Santo
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino 50019, Italy
| | - Lorenzo Pacini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Feliciana Real Fernandez
- CNR - Istituto di Chimica dei Composti Organometallici (CNR-ICCOM), Via Madonna del Piano 10, Sesto Fiorentino I-50019, Italy
| | - Rosaria Arvia
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, Florence 50134, Italy
| | - Silvia Rinaldi
- CNR - Istituto di Chimica dei Composti Organometallici (CNR-ICCOM), Via Madonna del Piano 10, Sesto Fiorentino I-50019, Italy
| | - Anna Maria Papini
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of Chemistry "Ugo Schiff", University of Florence, Sesto Fiorentino 50019, Italy
| | - Paolo Rovero
- Interdepartmental Research Unit of Peptide and Protein Chemistry and Biology, Department of NeuroFarBa, University of Florence, Sesto Fiorentino 50019, Italy
| | - Simone Giannecchini
- Department of Experimental and Clinical Medicine, University of Florence, Viale Morgagni 48, Florence 50134, Italy.
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6
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Mali A, Franci G, Zannella C, Chianese A, Anthiya S, López-Estévez AM, Monti A, De Filippis A, Doti N, Alonso MJ, Galdiero M. Antiviral Peptides Delivered by Chitosan-Based Nanoparticles to Neutralize SARS-CoV-2 and HCoV-OC43. Pharmaceutics 2023; 15:1621. [PMID: 37376070 DOI: 10.3390/pharmaceutics15061621] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/29/2023] [Accepted: 04/07/2023] [Indexed: 06/29/2023] Open
Abstract
The COVID-19 pandemic has made it clear that there is a crucial need for the design and development of antiviral agents that can efficiently reduce the fatality rate caused by infectious diseases. The fact that coronavirus mainly enters through the nasal epithelial cells and spreads through the nasal passage makes the nasal delivery of antiviral agents a promising strategy not only to reduce viral infection but also its transmission. Peptides are emerging as powerful candidates for antiviral treatments, showing not only a strong antiviral activity, but also improved safety, efficacy, and higher specificity against viral pathogens. Based on our previous experience on the use of chitosan-based nanoparticles to deliver peptides intra-nasally the current study aimed to explore the delivery of two-novel antiviral peptides making use of nanoparticles consisting of HA/CS and DS/CS. The antiviral peptides were chemically synthesized, and the optimal conditions for encapsulating them were selected through a combination of physical entrapment and chemical conjugation using HA/CS and DS/CS nanocomplexes. Finally, we evaluated the in vitro neutralization capacity against SARS-CoV-2 and HCoV-OC43 for potential use as prophylaxis or therapy.
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Affiliation(s)
- Avinash Mali
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Gianluigi Franci
- Department of Medicine, Surgery and Dentistry, "Scuola Medica Salernitana", University of Salerno, 84081 Baronissi, Italy
| | - Carla Zannella
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Annalisa Chianese
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Shubaash Anthiya
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), Department of Pharmacy and Pharmaceutical Technology, School of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Ana M López-Estévez
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), Department of Pharmacy and Pharmaceutical Technology, School of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Naples, Italy
- CIRPEB, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, 80134 Naples, Italy
| | - Anna De Filippis
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB), National Research Council (CNR), 80131 Naples, Italy
- CIRPEB, Centro Interuniversitario di Ricerca sui Peptidi Bioattivi, 80134 Naples, Italy
| | - María José Alonso
- Center for Research in Molecular Medicine and Chronic Diseases (CIMUS), Health Research Institute of Santiago de Compostela (IDIS), Department of Pharmacy and Pharmaceutical Technology, School of Pharmacy, University of Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Massimiliano Galdiero
- Department of Experimental Medicine, University of Campania "Luigi Vanvitelli", 80138 Naples, Italy
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7
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Siebert HC, Eckert T, Bhunia A, Klatte N, Mohri M, Siebert S, Kozarova A, Hudson JW, Zhang R, Zhang N, Li L, Gousias K, Kanakis D, Yan M, Jiménez-Barbero J, Kožár T, Nifantiev NE, Vollmer C, Brandenburger T, Kindgen-Milles D, Haak T, Petridis AK. Blood pH Analysis in Combination with Molecular Medical Tools in Relation to COVID-19 Symptoms. Biomedicines 2023; 11:biomedicines11051421. [PMID: 37239092 DOI: 10.3390/biomedicines11051421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 05/02/2023] [Accepted: 05/03/2023] [Indexed: 05/28/2023] Open
Abstract
The global outbreak of SARS-CoV-2/COVID-19 provided the stage to accumulate an enormous biomedical data set and an opportunity as well as a challenge to test new concepts and strategies to combat the pandemic. New research and molecular medical protocols may be deployed in different scientific fields, e.g., glycobiology, nanopharmacology, or nanomedicine. We correlated clinical biomedical data derived from patients in intensive care units with structural biology and biophysical data from NMR and/or CAMM (computer-aided molecular modeling). Consequently, new diagnostic and therapeutic approaches against SARS-CoV-2 were evaluated. Specifically, we tested the suitability of incretin mimetics with one or two pH-sensitive amino acid residues as potential drugs to prevent or cure long-COVID symptoms. Blood pH values in correlation with temperature alterations in patient bodies were of clinical importance. The effects of biophysical parameters such as temperature and pH value variation in relation to physical-chemical membrane properties (e.g., glycosylation state, affinity of certain amino acid sequences to sialic acids as well as other carbohydrate residues and lipid structures) provided helpful hints in identifying a potential Achilles heel against long COVID. In silico CAMM methods and in vitro NMR experiments (including 31P NMR measurements) were applied to analyze the structural behavior of incretin mimetics and SARS-CoV fusion peptides interacting with dodecylphosphocholine (DPC) micelles. These supramolecular complexes were analyzed under physiological conditions by 1H and 31P NMR techniques. We were able to observe characteristic interaction states of incretin mimetics, SARS-CoV fusion peptides and DPC membranes. Novel interaction profiles (indicated, e.g., by 31P NMR signal splitting) were detected. Furthermore, we evaluated GM1 gangliosides and sialic acid-coated silica nanoparticles in complex with DPC micelles in order to create a simple virus host cell membrane model. This is a first step in exploring the structure-function relationship between the SARS-CoV-2 spike protein and incretin mimetics with conserved pH-sensitive histidine residues in their carbohydrate recognition domains as found in galectins. The applied methods were effective in identifying peptide sequences as well as certain carbohydrate moieties with the potential to protect the blood-brain barrier (BBB). These clinically relevant observations on low blood pH values in fatal COVID-19 cases open routes for new therapeutic approaches, especially against long-COVID symptoms.
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Affiliation(s)
- Hans-Christian Siebert
- RI-B-NT-Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr. 116, 24118 Kiel, Germany
| | - Thomas Eckert
- Department of Chemistry and Biology, University of Applied Sciences Fresenius, Limburger Str. 2, 65510 Idstein, Germany
- RISCC-Research Institute for Scientific Computing and Consulting, Ludwig-Schunk-Str. 15, 35452 Heuchelheim, Germany
- Institut für Veterinärphysiologie und Biochemie, Fachbereich Veterinärmedizin, Justus-Liebig Universität Gießen, Frankfurter Str. 100, 35392 Gießen, Germany
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Nele Klatte
- Department of Chemistry and Biology, University of Applied Sciences Fresenius, Limburger Str. 2, 65510 Idstein, Germany
| | - Marzieh Mohri
- RI-B-NT-Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr. 116, 24118 Kiel, Germany
| | - Simone Siebert
- RI-B-NT-Research Institute of Bioinformatics and Nanotechnology, Schauenburgerstr. 116, 24118 Kiel, Germany
| | - Anna Kozarova
- Department of Biomedical Sciences, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - John W Hudson
- Department of Biomedical Sciences, University of Windsor, Windsor, ON N9B 3P4, Canada
| | - Ruiyan Zhang
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, China
| | - Ning Zhang
- Institute of BioPharmaceutical Research, Liaocheng University, Liaocheng 252059, China
| | - Lan Li
- Klinik für Neurochirurgie, Alfried Krupp Krankenhaus, Rüttenscheid, Alfried-Krupp-Straße 21, 45131 Essen, Germany
| | - Konstantinos Gousias
- Klinik für Neurochirurgie, Klinikum Lünen, St.-Marien-Hospital, Akad. Lehrkrankenhaus der Westfälische Wilhelms-Universität Münster, 44534 Lünen, Germany
| | - Dimitrios Kanakis
- Institute of Pathology, University of Nicosia Medical School, 2408 Egkomi, Cyprus
| | - Mingdi Yan
- Department of Chemistry, University of Massachusetts Lowell, 1 University Avenue, Lowell, MA 01854, USA
| | | | - Tibor Kožár
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Šafárik University, Jesenná 5, 04001 Košice, Slovakia
| | - Nikolay E Nifantiev
- Laboratory of Glycoconjugate Chemistry, N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospect 47, 119991 Moscow, Russia
| | - Christian Vollmer
- Department of Anesthesiology, University Hospital Düsseldorf, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Timo Brandenburger
- Department of Anesthesiology, University Hospital Düsseldorf, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Detlef Kindgen-Milles
- Department of Anesthesiology, University Hospital Düsseldorf, Heinrich-Heine University Duesseldorf, Moorenstr. 5, 40225 Düsseldorf, Germany
| | - Thomas Haak
- Diabetes Klinik Bad Mergentheim, Theodor-Klotzbücher-Str. 12, 97980 Bad Mergentheim, Germany
| | - Athanasios K Petridis
- Medical School, Heinrich-Heine-Universität Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
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8
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Bhandu P, Verma H, Raju B, Narendra G, Choudhary S, Singh M, Singh PK, Silakari O. Identification of natural peptides from "PlantPepDB" database as anti-SARS-CoV-2 agents: A protein-protein docking approach. PHYTOMEDICINE PLUS : INTERNATIONAL JOURNAL OF PHYTOTHERAPY AND PHYTOPHARMACOLOGY 2023; 3:100446. [PMID: 37033295 PMCID: PMC10065049 DOI: 10.1016/j.phyplu.2023.100446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
BACKGROUND A global pandemic owing to COVID-19 infection has created havoc in the entire world. The etiological agent responsible for this viral outbreak is classified as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Still, there's no specific drug or preventive medication to treat SARS-CoV-2. This study was designed to demonstrate the efficacy of some anti-viral peptides obtained from a plant database i.e., PlantPepDB as potential ACE-2-Spike (S) protein complex neutralizers using a structure-based drug designing approach. METHOD A total of 83 anti-viral plant peptides were screened from a peptide database i.e. PlantPepDB based on their reported anti-viral activities against various viral strains. In order to screen peptides that may potentially interfere with ACE-2 and S complex formation, molecular docking studies were conducted using the flare module of Cresset software and subsequently, analysed the crucial interactions between the peptides and S complexes and ACE-2/S complex. Herein, the interactions and docking scores obtained for ACE-2/S complex were considered as references. The S-peptides complexes which displayed superior interactions and docking scores than reference complex i.e., ACE2-S were considered as final hits. The Molecular dynamics studies were conducted for a period of 30 ns for each of the final hit/S complex to understand the interaction stability and binding mechanism of designed peptides. RESULTS The molecular docking results revealed that five peptides including Cycloviolacin Y3, Cycloviolacin Y1, White cloud bean defensin, Putative defensin 3.1, and Defensin D1 showed superior docking scores (i.e. -1372.5 kJ/mol to -1232.6 kJ/mol) when docked at the ACE2 binding site of S-protein than score obtained for the complex of ACE-2 and S protein i.e. -1183.4 kJ/mol. Moreover, these top five peptides manifested key interactions required to prevent the binding of S protein with ACE2. The molecular dynamics simulation study revealed that two of these five peptides i.e. Cycloviolacin Y3 and Cycloviolacin Y1 displayed minimal RMSD fluctuations. CONCLUSIONS The current structure-based drug-designing approach shows the possible role of anti-viral plant peptides as potential molecules to be explored at the initial stage of viral pathogenesis.
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Affiliation(s)
- Priyanka Bhandu
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Himanshu Verma
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Baddipadige Raju
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Gera Narendra
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Shalki Choudhary
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Manmeet Singh
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
| | - Pankaj Kumar Singh
- Faculty of Medicine, Integrative Physiology and Pharmacology, Institute of Biomedicine, University of Turku, Turku, FI-20014, Finland
| | - Om Silakari
- Molecular Modeling Lab (MML), Department of Pharmaceutical Sciences and Drug Research, Punjabi University, Patiala, Punjab, 147002, India
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9
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Pashmforoosh N, Baradaran M. Peptides with Diverse Functions from Scorpion Venom: A Great Opportunity for the Treatment of a Wide Variety of Diseases. IRANIAN BIOMEDICAL JOURNAL 2023; 27:84-99. [PMID: 37070616 PMCID: PMC10314758 DOI: 10.61186/ibj.3863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 12/21/2022] [Indexed: 12/17/2023]
Abstract
Toxicology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran The venom glands are a rich source of biologically important peptides with pharmaceutical properties. Scorpion venoms have been identified as a reservoir for components that might be considered as great candidates for drug development. Pharmacological properties of the venom compounds have been confirmed in the treatment of different disorders. Ion channel blockers and AMPs are the main groups of scorpion venom components. Despite the existence of several studies about scorpion peptides, there are still valuable components to be discovered. Additionally, owing to the improvement of proteomics and transcriptomics, the number of peptide drugs is steadily increasing, which reflects the importance of these medications. This review evaluates available literatures on some important scorpion venom peptides with pharmaceutical activities. Given that the last three years have been dominated by the COVID-19 from the medical/pharmaceutical perspective, scorpion compounds with the potential against the coronavirus 2 (SARS-CoV-2) are discussed in this review.
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Affiliation(s)
| | - Masoumeh Baradaran
- Corresponding Author: Masoumeh Baradaran Toxicology Research Center, Medical Basic Sciences Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran; E-mail:
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10
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Recent Patents and FDA-Approved Drugs Based on Antiviral Peptides and Other Peptide-Related Antivirals. Int J Pept Res Ther 2023; 29:5. [PMID: 36466430 PMCID: PMC9702942 DOI: 10.1007/s10989-022-10477-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/16/2022] [Indexed: 11/27/2022]
Abstract
In spite of existing cases of severe viral infections with a high mortality rate, there are not enough antiviral drugs and vaccines available for the prevention and treatment of such diseases. In addition, the increasing reports of the emergence of viral epidemics highlight, the need for novel molecules with antiviral potential. Antimicrobial peptides (AMPs) with antiviral activity or antiviral peptides (AVPs) have turned into a research hotspot and already show tremendous potential to become pharmaceutically available antiviral medicines. AMPs, a diverse group of bioactive peptides act as a part of our first line of defense against pathogen inactivation. Although most of the currently reported AMPs are either antibacterial or antifungal peptides, the number of antiviral peptides is gradually increasing. Some of the AMPs that are shown as effective antivirals have been deployed against viruses such as influenza A virus, severe acute respiratory syndrome coronavirus (SARS-CoV), HIV, HSV, West Nile Virus (WNV), and other viruses. This review offers an overview of AVPs that have been approved within the past few years and will set out a few of the most essential patents and their usage within the context mentioned above during 2000-2020. Moreover, the present study will explain some of the progress in antiviral drugs based on peptides and peptide-related antivirals.
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11
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Khater I, Nassar A. Potential antiviral peptides targeting the SARS-CoV-2 spike protein. BMC Pharmacol Toxicol 2022; 23:91. [PMID: 36461109 PMCID: PMC9716172 DOI: 10.1186/s40360-022-00627-w] [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: 05/17/2022] [Accepted: 11/15/2022] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND The coronavirus disease caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection became an international pandemic and created a public health crisis. The binding of the viral Spike glycoprotein to the human cell receptor angiotensin-converting enzyme 2 (ACE2) initiates viral infection. The development of efficient treatments to combat coronavirus disease is considered essential. METHODS An in silico approach was employed to design amino acid peptide inhibitor against the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. The designed inhibitor (SARS-CoV-2 PEP 49) consists of amino acids with the α1 helix and the β4 - β5 sheets of ACE2. The PEP-FOLD3 web tool was used to create the 3D structures of the peptide amino acids. Analyzing the interaction between ACE2 and the RBD of the Spike protein for three protein data bank entries (6M0J, 7C8D, and 7A95) indicated that the interacting amino acids were contained inside two regions of ACE2: the α1 helical protease domain (PD) and the β4 - β5 sheets. RESULTS Molecular docking analysis of the designed inhibitor demonstrated that SARS-CoV-2 PEP 49 attaches directly to the ACE2 binding site of the Spike protein with a binding affinity greater than the ACE2, implying that the SARS-CoV-2 PEP 49 model may be useful as a potential RBD binding blocker.
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Affiliation(s)
- Ibrahim Khater
- grid.7776.10000 0004 0639 9286Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Aaya Nassar
- grid.7776.10000 0004 0639 9286Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt ,grid.253615.60000 0004 1936 9510Department of Clinical Research and Leadership, School of Medicine and Health Sciences, George Washington University, Washington DC, USA
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12
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Diakou I, Papakonstantinou E, Papageorgiou L, Pierouli K, Dragoumani K, Spandidos DA, Bacopoulou F, Chrousos GP, Eliopoulos E, Vlachakis D. Novel computational pipelines in antiviral structure‑based drug design (Review). Biomed Rep 2022; 17:97. [PMID: 36382260 PMCID: PMC9634337 DOI: 10.3892/br.2022.1580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 10/05/2022] [Indexed: 11/22/2022] Open
Abstract
Viral infections constitute a fundamental and continuous challenge for the global scientific and medical community, as highlighted by the ongoing COVID-19 pandemic. In combination with prophylactic vaccines, the development of safe and effective antiviral drugs remains a pressing need for the effective management of rare and common pathogenic viruses. The design of potent antivirals can be informed by the study of the three-dimensional structure of viral protein targets. Structure-based design of antivirals in silico provides a solution to the arduous and costly process of conventional drug development pipelines. Furthermore, rapid advances in high-throughput computing, along with the growth of available biomolecular and biochemical data, enable the development of novel computational pipelines in the hunt of antivirals. The incorporation of modern methods, such as deep-learning and artificial intelligence, has the potential to revolutionize the structure-based design and repurposing of antiviral compounds, with minimal side effects and high efficacy. The present review aims to provide an outline of both traditional computational drug design and emerging, high-level computing strategies.
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Affiliation(s)
- Io Diakou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Eleni Papakonstantinou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Louis Papageorgiou
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Katerina Pierouli
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Konstantina Dragoumani
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Demetrios A. Spandidos
- Laboratory of Clinical Virology, School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Flora Bacopoulou
- University Research Institute of Maternal and Child Health and Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, ‘Aghia Sophia’ Children's Hospital, 11527 Athens, Greece
| | - George P. Chrousos
- University Research Institute of Maternal and Child Health and Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, ‘Aghia Sophia’ Children's Hospital, 11527 Athens, Greece
| | - Elias Eliopoulos
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
| | - Dimitrios Vlachakis
- Laboratory of Genetics, Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 11855 Athens, Greece
- University Research Institute of Maternal and Child Health and Precision Medicine, and UNESCO Chair on Adolescent Health Care, National and Kapodistrian University of Athens, ‘Aghia Sophia’ Children's Hospital, 11527 Athens, Greece
- Division of Endocrinology and Metabolism, Center of Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of The Academy of Athens, 11527 Athens, Greece
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13
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Lin TT, Sun YY, Wang CT, Cheng WC, Lu IH, Lin CY, Chen SH. AI4AVP: an antiviral peptides predictor in deep learning approach with generative adversarial network data augmentation. BIOINFORMATICS ADVANCES 2022; 2:vbac080. [PMID: 36699402 PMCID: PMC9710571 DOI: 10.1093/bioadv/vbac080] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 09/14/2022] [Accepted: 10/25/2022] [Indexed: 11/05/2022]
Abstract
Motivation Antiviral peptides (AVPs) from various sources suggest the possibility of developing peptide drugs for treating viral diseases. Because of the increasing number of identified AVPs and the advances in deep learning theory, it is reasonable to experiment with peptide drug design using in silico methods. Results We collected the most up-to-date AVPs and used deep learning to construct a sequence-based binary classifier. A generative adversarial network was employed to augment the number of AVPs in the positive training dataset and enable our deep learning convolutional neural network (CNN) model to learn from the negative dataset. Our classifier outperformed other state-of-the-art classifiers when using the testing dataset. We have placed the trained classifiers on a user-friendly web server, AI4AVP, for the research community. Availability and implementation AI4AVP is freely accessible at http://axp.iis.sinica.edu.tw/AI4AVP/; codes and datasets for the peptide GAN and the AVP predictor CNN are available at https://github.com/lsbnb/amp_gan and https://github.com/LinTzuTang/AI4AVP_predictor. Supplementary information Supplementary data are available at Bioinformatics Advances online.
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Affiliation(s)
- Tzu-Tang Lin
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Yih-Yun Sun
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan.,Graduate Institute of Biomedical Electronics and Bioinformatics, College of Electrical Engineering and Computer Science, National Taiwan University, Taipei 106, Taiwan
| | - Ching-Tien Wang
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Wen-Chih Cheng
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - I-Hsuan Lu
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan
| | - Chung-Yen Lin
- Institute of Information Science, Academia Sinica, Taipei 115, Taiwan.,Institute of Fisheries Science, National Taiwan University, Taipei 106, Taiwan.,Genome and Systems Biology Degree Program, National Taiwan University, Taipei 106, Taiwan
| | - Shu-Hwa Chen
- TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei 110, Taiwan
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14
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Saini J, Kaur P, Malik N, Lakhawat SS, Sharma PK. Antimicrobial peptides: A promising tool to combat multidrug resistance in SARS CoV2 era. Microbiol Res 2022; 265:127206. [PMID: 36162150 PMCID: PMC9491010 DOI: 10.1016/j.micres.2022.127206] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/26/2022] [Accepted: 09/16/2022] [Indexed: 10/25/2022]
Abstract
COVID-19 (Coronavirus Disease 2019), a life-threatening viral infection, is caused by a highly pathogenic virus named SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2). Currently, no treatment is available for COVID-19; hence there is an urgent need to find effective therapeutic drugs to combat COVID-19 pandemic. Considering the fact that the world is facing a major issue of antimicrobial drug resistance, naturally occurring compounds have the potential to achieve this goal. Antimicrobial peptides (AMPs) are naturally occurring antimicrobial agents which are effective against a wide variety of microbial infections. Therefore, the use of AMPs is an attractive therapeutic strategy for the treatment of SARS-CoV-2 infection. This review sheds light on the potential of antimicrobial peptides as antiviral agents followed by a comprehensive description of effective antiviral peptides derived from various natural sources found to be effective against SARS-CoV and other respiratory viruses. It also highlights the mechanisms of action of antiviral peptides with special emphasis on their effectiveness against SARS-CoV-2 infection.
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Affiliation(s)
- Jasleen Saini
- Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Pritpal Kaur
- Department of Biotechnology, Sri Guru Granth Sahib World University, Fatehgarh Sahib, Punjab, India
| | - Naveen Malik
- Amity Institute of Biotechnology, Amity University Rajasthan, Jaipur, India
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15
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Zupin L, dos Santos-Silva CA, Al Mughrbi ARH, Vilela LMB, Benko-Iseppon AM, Crovella S. Bioactive Antimicrobial Peptides: A New Weapon to Counteract Zoonosis. Microorganisms 2022; 10:microorganisms10081591. [PMID: 36014009 PMCID: PMC9414035 DOI: 10.3390/microorganisms10081591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/29/2022] [Accepted: 08/03/2022] [Indexed: 11/16/2022] Open
Abstract
Zoonoses have recently become the center of attention of the general population and scientific community. Notably, more than 30 new human pathogens have been identified in the last 30 years, 75% of which can be classified as zoonosis. The complete eradication of such types of infections is far out of reach, considering the limited understanding of animal determinants in zoonoses and their causes of emergence. Therefore, efforts must be doubled in examining the spread, persistence, and pathogenicity of zoonosis and studying possible clinical interventions and antimicrobial drug development. The search for antimicrobial bioactive compounds has assumed great emphasis, considering the emergence of multi-drug-resistant microorganisms. Among the biomolecules of emerging scientific interest are antimicrobial peptides (AMPs), potent biomolecules that can potentially act as important weapons against infectious diseases. Moreover, synthetic AMPs are easily tailored (bioinformatically) to target specific features of the pathogens to hijack, inducing no or very low resistance. Although very promising, previous studies on SAMPs’ efficacy are still at their early stages. Indeed, further studies and better characterization on their mechanism of action with in vitro and in vivo assays are needed so as to proceed to their clinical application on human beings.
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Affiliation(s)
- Luisa Zupin
- Institute for Maternal and Child Health—IRCCS Burlo Garofolo, 34137 Trieste, Italy
- Correspondence: (L.Z.); (S.C.)
| | | | | | - Livia Maria Batista Vilela
- Centro de Biociências, Departamento de Genética, Universidade Federal de Pernambuco, Recife 50670-420, Brazil
| | - Ana Maria Benko-Iseppon
- Centro de Biociências, Departamento de Genética, Universidade Federal de Pernambuco, Recife 50670-420, Brazil
| | - Sergio Crovella
- Biological Science Program, Department of Biological and Environmental Sciences, College of Arts and Sciences, Qatar University, Doha 2713, Qatar
- Correspondence: (L.Z.); (S.C.)
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16
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Anurans against SARS-CoV-2: A review of the potential antiviral action of anurans cutaneous peptides. Virus Res 2022; 315:198769. [PMID: 35430319 PMCID: PMC9008983 DOI: 10.1016/j.virusres.2022.198769] [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: 01/12/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/17/2023]
Abstract
At the end of 2019, in China, clinical signs and symptoms of unknown etiology have been reported in several patients whose sample sequencing revealed pneumonia caused by the SARS-CoV-2 virus. COVID-19 is a disease triggered by this virus, and in 2020, the World Health Organization declared it a pandemic. Since then, efforts have been made to find effective therapeutic agents against this disease. Identifying novel natural antiviral drugs can be an alternative to treatment. For this reason, antimicrobial peptides secreted by anurans' skin have gained attention for showing a promissory antiviral effect. Hence, this review aimed to elucidate how and which peptides secreted by anurans' skin can be considered therapeutic agents to treat or prevent human viral infectious diseases. Through a literature review, we attempted to identify potential antiviral frogs' peptides to combat COVID-19. As a result, the Magainin-1 and -2 peptides, from the Magainin family, the Dermaseptin-S9, from the Dermaseptin family, and Caerin 1.6 and 1.10, from the Caerin family, are molecules that already showed antiviral effects against SARS-CoV-2 in silico. In addition to these peptides, this review suggests that future studies should use other families that already have antiviral action against other viruses, such as Brevinins, Maculatins, Esculentins, Temporins, and Urumins. To apply these peptides as therapeutic agents, experimental studies with peptides already tested in silico and new studies with other families not tested yet should be considered.
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17
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Li X, Zuo S, Wang B, Zhang K, Wang Y. Antimicrobial Mechanisms and Clinical Application Prospects of Antimicrobial Peptides. Molecules 2022; 27:2675. [PMID: 35566025 PMCID: PMC9104849 DOI: 10.3390/molecules27092675] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Revised: 04/14/2022] [Accepted: 04/19/2022] [Indexed: 12/16/2022] Open
Abstract
Antimicrobial peptides are a type of small-molecule peptide that widely exist in nature and are components of the innate immunity of almost all living things. They play an important role in resisting foreign invading microorganisms. Antimicrobial peptides have a wide range of antibacterial activities against bacteria, fungi, viruses and other microorganisms. They are active against traditional antibiotic-resistant strains and do not easily induce the development of drug resistance. Therefore, they have become a hot spot of medical research and are expected to become a new substitute for fighting microbial infection and represent a new method for treating drug-resistant bacteria. This review briefly introduces the source and structural characteristics of antimicrobial peptides and describes those that have been used against common clinical microorganisms (bacteria, fungi, viruses, and especially coronaviruses), focusing on their antimicrobial mechanism of action and clinical application prospects.
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Affiliation(s)
- Xin Li
- Department of Infectious Diseases, First Hospital of Jilin University, Changchun 130021, China; (X.L.); (B.W.)
| | - Siyao Zuo
- Department of Dermatology and Venereology, First Hospital of Jilin University, Changchun 130021, China;
| | - Bin Wang
- Department of Infectious Diseases, First Hospital of Jilin University, Changchun 130021, China; (X.L.); (B.W.)
| | - Kaiyu Zhang
- Department of Infectious Diseases, First Hospital of Jilin University, Changchun 130021, China; (X.L.); (B.W.)
| | - Yang Wang
- Department of Infectious Diseases, First Hospital of Jilin University, Changchun 130021, China; (X.L.); (B.W.)
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18
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Sukmarini L. Antiviral Peptides (AVPs) of Marine Origin as Propitious Therapeutic Drug Candidates for the Treatment of Human Viruses. MOLECULES (BASEL, SWITZERLAND) 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] [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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19
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Bagwe PV, Bagwe PV, Ponugoti SS, Joshi SV. Peptide-Based Vaccines and Therapeutics for COVID-19. Int J Pept Res Ther 2022; 28:94. [PMID: 35463185 PMCID: PMC9017722 DOI: 10.1007/s10989-022-10397-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/21/2022] [Indexed: 12/20/2022]
Affiliation(s)
- Pritam V. Bagwe
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, Maharashtra 400019 India
| | - Priyal V. Bagwe
- Vaccine Nanotechnology Laboratory, Center for Drug Delivery and Research, College of Pharmacy, Mercer University, Atlanta, GA 30341 USA
| | - Sai Srinivas Ponugoti
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, Maharashtra 400019 India
| | - Shreerang V. Joshi
- Department of Pharmaceutical Sciences and Technology, Institute of Chemical Technology, Mumbai, Maharashtra 400019 India
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20
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Rani P, Kapoor B, Gulati M, Atanasov AG, Alzahrani Q, Gupta R. Antimicrobial peptides: A plausible approach for COVID-19 treatment. Expert Opin Drug Discov 2022; 17:473-487. [PMID: 35255763 PMCID: PMC8935455 DOI: 10.1080/17460441.2022.2050693] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Coronavirus disease 2019 (COVID-19), which emerged as a major public health threat, has affected >400 million people globally leading to >5 million mortalities to date. Treatments of COVID-19 are still to be developed as the available therapeutic approaches are not able to combat the virus causing the disease (severe acute respiratory syndrome coronavirus-2; SARS-CoV-2) satisfactorily. However, antiviral peptides (AVPs) have demonstrated prophylactic and therapeutic effects against many coronaviruses (CoVs). AREAS COVERED This review critically discusses various types of AVPs evaluated for the treatment of COVID-19 along with their mechanisms of action. Furthermore, the peptides inhibiting the entry of the virus by targeting its binding to angiotensin-converting enzyme 2 (ACE2) or integrins, fusion mechanism as well as activation of proteolytic enzymes (cathepsin L, transmembrane serine protease 2 (TMPRSS2), or furin) are also discussed. EXPERT OPINION Although extensively investigated, successful treatment of COVID-19 is still a challenge due to emergence of virus mutants. Antiviral peptides are anticipated to be blockbuster drugs for the management of this serious infection because of their formulation and therapeutic advantages. Although they may act on different pathways, AVPs having a multi-targeted approach are considered to have the upper hand in the management of this infection.
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Affiliation(s)
- Pooja Rani
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Bhupinder Kapoor
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Monica Gulati
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
| | - Atanas G Atanasov
- Ludwig Boltzmann Institute for Digital Health and Patient Safety, Medical University of Vienna, Vienna, Austria.,Institute of Genetics and Animal Biotechnology of the Polish Academy of Sciences, Magdalenka, Poland.,Department of Pharmaceutical Sciences, University of Vienna, Vienna, Austria
| | - Qushmua Alzahrani
- Department of Pharmacy/Nursing/Medicine Health and Environment, University of the Region of Joinville (UNIVILLE) volunteer researcher, Joinville, Brazil
| | - Reena Gupta
- School of Pharmaceutical Sciences, Lovely Professional University, Phagwara, India
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21
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Enayathullah MG, Parekh Y, Banu S, Ram S, Nagaraj R, Kumar BK, Idris MM. Gramicidin S and melittin: potential anti-viral therapeutic peptides to treat SARS-CoV-2 infection. Sci Rep 2022; 12:3446. [PMID: 35236909 PMCID: PMC8891299 DOI: 10.1038/s41598-022-07341-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 02/16/2022] [Indexed: 01/02/2023] Open
Abstract
The COVID19 pandemic has led to multipronged approaches for treatment of the disease. Since de novo discovery of drugs is time consuming, repurposing of molecules is now considered as one of the alternative strategies to treat COVID19. Antibacterial peptides are being recognized as attractive candidates for repurposing to treat viral infections. In this study, we describe the anti-SARS-CoV-2 activity of the well-studied antibacterial peptides gramicidin S and melittin obtained from Bacillus brevis and bee venom respectively. The EC50 values for gramicidin S and melittin were 1.571 µg and 0.656 µg respectively based on in vitro antiviral assay. Significant decrease in the viral load as compared to the untreated group with no/very less cytotoxicity was observed. Both the peptides treated to the SARS-CoV-2 infected Vero cells showed viral clearance from 12 h onwards with a maximal viral clearance after 24 h post infection. Proteomics analysis indicated that more than 250 proteins were differentially regulated in the gramicidin S and melittin treated SARS-CoV-2 infected Vero cells against control SARS-CoV-2 infected Vero cells after 24 and 48 h post infection. The identified proteins were found to be associated in the metabolic and mRNA processing of the Vero cells post-treatment and infection. Both these peptides could be attractive candidates for repurposing to treat SARS-CoV-2 infection.
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Affiliation(s)
| | - Yash Parekh
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Sarena Banu
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Sushma Ram
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Ramakrishnan Nagaraj
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - Bokara Kiran Kumar
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India.
| | - Mohammed M Idris
- CSIR-Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India.
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22
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Theta-Defensins to Counter COVID-19 as Furin Inhibitors: In Silico Efficiency Prediction and Novel Compound Design. COMPUTATIONAL AND MATHEMATICAL METHODS IN MEDICINE 2022; 2022:9735626. [PMID: 35154362 PMCID: PMC8829439 DOI: 10.1155/2022/9735626] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/28/2021] [Accepted: 01/21/2022] [Indexed: 12/13/2022]
Abstract
Coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), was characterized as a pandemic by the World Health Organization (WHO) in Dec. 2019. SARS-CoV-2 binds to the cell membrane through spike proteins on its surface and infects the cell. Furin, a host-cell enzyme, possesses a binding site for the spike protein. Thus, molecules that block furin could potentially be a therapeutic solution. Defensins are antimicrobial peptides that can hypothetically inhibit furin because of their arginine-rich structure. Theta-defensins, a subclass of defensins, have attracted attention as drug candidates due to their small size, unique structure, and involvement in several defense mechanisms. Theta-defensins could be a potential treatment for COVID-19 through furin inhibition and an anti-inflammatory mechanism. Note that inflammatory events are a significant and deadly condition that could happen at the later stages of COVID-19 infection. Here, the potential of theta-defensins against SARS-CoV-2 infection was investigated through in silico approaches. Based on docking analysis results, theta-defensins can function as furin inhibitors. Additionally, a novel candidate peptide against COVID-19 with optimal properties regarding antigenicity, stability, electrostatic potential, and binding strength was proposed. Further in vitro/in vivo investigations could verify the efficiency of the designed novel peptide.
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23
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Sureram S, Arduino I, Ueoka R, Rittà M, Francese R, Srivibool R, Darshana D, Piel J, Ruchirawat S, Muratori L, Lembo D, Kittakoop P, Donalisio M. The Peptide A-3302-B Isolated from a Marine Bacterium Micromonospora sp. Inhibits HSV-2 Infection by Preventing the Viral Egress from Host Cells. Int J Mol Sci 2022; 23:947. [PMID: 35055133 PMCID: PMC8778767 DOI: 10.3390/ijms23020947] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 02/04/2023] Open
Abstract
Herpesviruses are highly prevalent in the human population, and frequent reactivations occur throughout life. Despite antiviral drugs against herpetic infections, the increasing appearance of drug-resistant viral strains and their adverse effects prompt the research of novel antiherpetic drugs for treating lesions. Peptides obtained from natural sources have recently become of particular interest for antiviral therapy applications. In this work, we investigated the antiviral activity of the peptide A-3302-B, isolated from a marine bacterium, Micromonospora sp., strain MAG 9-7, against herpes simplex virus type 1, type 2, and human cytomegalovirus. Results showed that the peptide exerted a specific inhibitory activity against HSV-2 with an EC50 value of 14 μM. Specific antiviral assays were performed to investigate the mechanism of action of A-3302-B. We demonstrated that the peptide did not affect the expression of viral proteins, but it inhibited the late events of the HSV-2 replicative cycle. In detail, it reduced the cell-to-cell virus spread and the transmission of the extracellular free virus by preventing the egress of HSV-2 progeny from the infected cells. The dual antiviral and previously reported anti-inflammatory activities of A-3302-B, and its effect against an acyclovir-resistant HSV-2 strain are attractive features for developing a therapeutic to reduce the transmission of HSV-2 infections.
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Affiliation(s)
- Sanya Sureram
- Chulabhorn Research Institute, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand; (S.S.); (S.R.)
| | - Irene Arduino
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043 Orbassano, Italy; (I.A.); (M.R.); (R.F.); (D.L.)
| | - Reiko Ueoka
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland; (R.U.); (J.P.)
| | - Massimo Rittà
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043 Orbassano, Italy; (I.A.); (M.R.); (R.F.); (D.L.)
| | - Rachele Francese
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043 Orbassano, Italy; (I.A.); (M.R.); (R.F.); (D.L.)
| | | | - Dhanushka Darshana
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand;
| | - Jörn Piel
- Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, 8093 Zurich, Switzerland; (R.U.); (J.P.)
| | - Somsak Ruchirawat
- Chulabhorn Research Institute, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand; (S.S.); (S.R.)
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand;
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, Ministry of Higher Education, Science, Research and Innovation, Bangkok 10210, Thailand
| | - Luisa Muratori
- Department of Clinical and Biological Sciences, Neuroscience Institute of the “Cavalieri Ottolenghi” Foundation (NICO), University of Turin, 10043 Orbassano, Italy;
| | - David Lembo
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043 Orbassano, Italy; (I.A.); (M.R.); (R.F.); (D.L.)
| | - Prasat Kittakoop
- Chulabhorn Research Institute, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand; (S.S.); (S.R.)
- Program in Chemical Sciences, Chulabhorn Graduate Institute, Chulabhorn Royal Academy, Kamphaeng Phet 6 Road, Laksi, Bangkok 10210, Thailand;
- Center of Excellence on Environmental Health and Toxicology (EHT), OPS, Ministry of Higher Education, Science, Research and Innovation, Bangkok 10210, Thailand
| | - Manuela Donalisio
- Department of Clinical and Biological Sciences, University of Turin, Regione Gonzole 10, 10043 Orbassano, Italy; (I.A.); (M.R.); (R.F.); (D.L.)
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24
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Vanzolini T, Bruschi M, Rinaldi AC, Magnani M, Fraternale A. Multitalented Synthetic Antimicrobial Peptides and Their Antibacterial, Antifungal and Antiviral Mechanisms. Int J Mol Sci 2022; 23:545. [PMID: 35008974 PMCID: PMC8745555 DOI: 10.3390/ijms23010545] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/22/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023] Open
Abstract
Despite the great strides in healthcare during the last century, some challenges still remained unanswered. The development of multi-drug resistant bacteria, the alarming growth of fungal infections, the emerging/re-emerging of viral diseases are yet a worldwide threat. Since the discovery of natural antimicrobial peptides able to broadly hit several pathogens, peptide-based therapeutics have been under the lenses of the researchers. This review aims to focus on synthetic peptides and elucidate their multifaceted mechanisms of action as antiviral, antibacterial and antifungal agents. Antimicrobial peptides generally affect highly preserved structures, e.g., the phospholipid membrane via pore formation or other constitutive targets like peptidoglycans in Gram-negative and Gram-positive bacteria, and glucan in the fungal cell wall. Additionally, some peptides are particularly active on biofilm destabilizing the microbial communities. They can also act intracellularly, e.g., on protein biosynthesis or DNA replication. Their intracellular properties are extended upon viral infection since peptides can influence several steps along the virus life cycle starting from viral receptor-cell interaction to the budding. Besides their mode of action, improvements in manufacturing to increase their half-life and performances are also taken into consideration together with advantages and impairments in the clinical usage. Thus far, the progress of new synthetic peptide-based approaches is making them a promising tool to counteract emerging infections.
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Affiliation(s)
- Tania Vanzolini
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, PU, Italy; (T.V.); (M.M.); (A.F.)
| | - Michela Bruschi
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, PU, Italy; (T.V.); (M.M.); (A.F.)
| | - Andrea C. Rinaldi
- Department of Biomedical Sciences, University of Cagliari, 09042 Monserrato, CA, Italy;
| | - Mauro Magnani
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, PU, Italy; (T.V.); (M.M.); (A.F.)
| | - Alessandra Fraternale
- Department of Biomolecular Sciences, University of Urbino Carlo Bo, 61029 Urbino, PU, Italy; (T.V.); (M.M.); (A.F.)
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25
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Rudden LSP, Hijazi M, Barth P. Deep learning approaches for conformational flexibility and switching properties in protein design. Front Mol Biosci 2022; 9:928534. [PMID: 36032687 PMCID: PMC9399439 DOI: 10.3389/fmolb.2022.928534] [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: 04/25/2022] [Accepted: 07/15/2022] [Indexed: 11/30/2022] Open
Abstract
Following the hugely successful application of deep learning methods to protein structure prediction, an increasing number of design methods seek to leverage generative models to design proteins with improved functionality over native proteins or novel structure and function. The inherent flexibility of proteins, from side-chain motion to larger conformational reshuffling, poses a challenge to design methods, where the ideal approach must consider both the spatial and temporal evolution of proteins in the context of their functional capacity. In this review, we highlight existing methods for protein design before discussing how methods at the forefront of deep learning-based design accommodate flexibility and where the field could evolve in the future.
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Affiliation(s)
| | | | - Patrick Barth
- *Correspondence: Lucas S. P. Rudden, ; Patrick Barth,
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26
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Dutta K, Elmezayen AD, Al-Obaidi A, Zhu W, Morozova OV, Shityakov S, Khalifa I. Seq12, Seq12m, and Seq13m, peptide analogues of the spike glycoprotein shows antiviral properties against SARS-CoV-2: An in silico study through molecular docking, molecular dynamics simulation, and MM-PB/GBSA calculations. J Mol Struct 2021; 1246:131113. [PMID: 34305174 PMCID: PMC8283670 DOI: 10.1016/j.molstruc.2021.131113] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 07/10/2021] [Accepted: 07/12/2021] [Indexed: 02/07/2023]
Abstract
At the very beginning of the new decade, the COVID-19 pandemic has badly hit modern human societies. SARS-CoV-2, the causative agent of COVID-19 acquiring mutations and circulating as new variants. Herein, we have found three new antiviral peptides (AVPs) against the SARS-CoV-2. These AVPs are analogous to the spike glycoprotein of the SARS-CoV-2. Antiviral peptides, i.e., Seq12, Seq12m, and Seq13m, can block the receptor-binding domain (RBD) of the SARS-CoV-2, which is necessary for communicating with the angiotensin-converting enzyme 2 (ACE2). Also, these AVPs sustain their antiviral properties, even after the insertion of 25 mutations in the RBD (Rosetta and FoldX based). Further, Seq12 and Seq12m showed negligible cytotoxicity. Besides, the binding free energies calculated using MM-PB/GBSA method are also in agreement with the molecular docking studies. The molecular interactions between AVPs and the viral membrane protein (M) also showed a favorable interaction suggesting it could inhibit the viral re-packaging process. In conclusion, this study suggests Seq12, Seq12m, and Seq13m could be helpful to fight against SARS-CoV-2. These AVPs could also aid virus diagnostic tools and nasal spray against SARS-CoV-2 in the future.
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Affiliation(s)
- Kunal Dutta
- Department of Human Physiology, Vidyasagar University, Midnapore 721102, West Bengal, India
| | - Ammar D Elmezayen
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Cibali 34083, Istanbul, Turkey
| | - Anas Al-Obaidi
- Department of Bioinformatics and Genetics, Faculty of Engineering and Natural Sciences, Kadir Has University, Cibali 34083, Istanbul, Turkey
| | - Wei Zhu
- College of Food Science and Technology, Huazhong Agricultural University, Key Laboratory of Environment Correlative Food Science, Ministry of Education, Wuhan 430070, China
| | - Olga V Morozova
- I.N. Blokhina Nizhny Novgorod Research Institute of Epidemiology and Microbiology, 71 Malaya Yamskaya Str., Nizhny Novgorod 603950, Russian Federation
| | - Sergey Shityakov
- Laboratory of Chemoinformatics, Infochemistry Scientific Center, ITMO University, 191002 Saint-Petersburg, Russian Federation
| | - Ibrahim Khalifa
- Food Technology Department, Faculty of Agriculture, Moshtohor 13736, Benha University, Egypt
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27
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G Yathisha U, Srinivasa MG, Siddappa Bc R, P Mandal S, Dixit SR, Pujar GV, Bangera Sheshappa M. Isolation and characterization of ACE-I inhibitory peptides from ribbonfish for a potential inhibitor of the main protease of SARS-CoV-2: An in silico analysis. Proteins 2021; 90:982-992. [PMID: 34877713 DOI: 10.1002/prot.26291] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/02/2021] [Accepted: 12/02/2021] [Indexed: 12/23/2022]
Abstract
Recently, multifunctional fish peptides (FWPs) have gained a lot of attention because of their different biological activities. In the present study, three angiotensin-I converting enzyme (ACE-I) inhibitory peptides [Ala-Pro-Asp-Gly (APDG), Pro-Thr-Arg (PTR), and Ala-Asp (AD)] were isolated and characterized from ribbonfish protein hydrolysate (RFPH) and described their mechanism of action on ACE activity. As per the results, peptide PTR showed ≈ 2 and 2.5-fold higher enzyme inhibitory activity (IC50 = 0.643 ± 0.0011 μM) than APDG (IC50 = 1.061 ± 0.0127 μM) and AD (IC50 = 2.046 ± 0.0130 μM). Based on experimental evidence, peptides were used for in silico analysis to check the inhibitory activity of the main protease (PDB: 7BQY) of SARS-CoV-2. The results of the study reveal that PTR (-46.16 kcal/mol) showed higher binding affinity than APDG (-36.80 kcal/mol) and AD (-30.24 kcal/mol) compared with remdesivir (-30.64 kcal/mol). Additionally, physicochemical characteristics of all the isolated peptides exhibited appropriate pharmacological properties and were found to be nontoxic. Besides, 20 ns molecular dynamic simulation study confirms the rigid nature, fewer confirmation variations, and binding stiffness of the peptide PTR with the main protease of SARS-CoV-2. Therefore, the present study strongly suggested that PTR is the perfect substrate for inhibiting the main protease of SARS-CoV-2 through the in silico study, and this potential drug candidate may promote the researcher for future wet lab experiments.
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Affiliation(s)
- Undiganalu G Yathisha
- Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Paneer Campus, Mangalore, India
| | - Mahendra Gowdru Srinivasa
- Department of Pharmaceutical Chemistry, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, India
| | - Revana Siddappa Bc
- Department of Pharmaceutical Chemistry, NGSM Institute of Pharmaceutical Sciences (NGSMIPS), Nitte (Deemed to be University), Mangalore, India
| | - Subankar P Mandal
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Mysuru, India
| | - Sheshagiri R Dixit
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Mysuru, India
| | - G V Pujar
- Department of Pharmaceutical Chemistry, JSS College of Pharmacy, JSS Academy of Higher Education and Research, Mysuru, India
| | - Mamatha Bangera Sheshappa
- Nitte University Centre for Science Education and Research, Nitte (Deemed to be University), Paneer Campus, Mangalore, India
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28
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Martell EM, González-Garcia M, Ständker L, Otero-González AJ. Host defense peptides as immunomodulators: The other side of the coin. Peptides 2021; 146:170644. [PMID: 34464592 DOI: 10.1016/j.peptides.2021.170644] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 08/27/2021] [Accepted: 08/27/2021] [Indexed: 12/13/2022]
Abstract
Host defense peptides (HDPs) exhibit a broad range of antimicrobial and immunomodulatory activities. In this sense, both functions are like different sides of the same coin. The direct antimicrobial side was discovered first, and widely studied for the development of anti-infective therapies. In contrast, the immunomodulatory side was recognized later and in the last 20 years the interest in this field has been continuously growing. Different to their antimicrobial activities, the immunomodulatory activities of host defense peptides are more effective in vivo. They offer a great opportunity for new therapeutic applications in the fields of anti-infective therapy, chronic inflammatory diseases treatment, novel vaccine adjuvants development and anticancer immunotherapy. These immune related functions of HDPs includes chemoattraction of leukocytes, modulation of inflammation, enhancement of antigen presentation and polarization of adaptive immune responses. Our attempt with this review is to make a careful evaluation of different aspects of the less explored, but attractive immunomodulatory side of the HDP functional coin.
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Affiliation(s)
- Ernesto M Martell
- Center for Protein Studies, Faculty of Biology, Havana University, Cuba
| | | | - Ludger Ständker
- Core Facility Functional Peptidomics (CFP), Ulm University Medical Center, Ulm, Germany
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29
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Kuroki A, Tay J, Lee GH, Yang YY. Broad-Spectrum Antiviral Peptides and Polymers. Adv Healthc Mater 2021; 10:e2101113. [PMID: 34599850 DOI: 10.1002/adhm.202101113] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 09/13/2021] [Indexed: 12/18/2022]
Abstract
As the human cost of the pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is still being witnessed worldwide, the development of broad-spectrum antiviral agents against emerging and re-emerging viruses is seen as a necessity to hamper the spread of infections. Various targets during the viral life-cycle can be considered to inhibit viral infection, from viral attachment to viral fusion or replication. Macromolecules represent a particularly attractive class of therapeutics due to their multivalency and versatility. Although several antiviral macromolecules hold great promise in clinical applications, the emergence of resistance after prolonged exposure urges the need for improved solutions. In the present article, the recent advancement in the discovery of antiviral peptides and polymers with diverse structural features and antiviral mechanisms is reviewed. Future perspectives, such as, the development of virucidal peptides/polymers and their coatings against SARS-CoV-2 infection, standardization of antiviral testing protocols, and use of artificial intelligence or machine learning as a tool to accelerate the discovery of antiviral macromolecules, are discussed.
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Affiliation(s)
- Agnès Kuroki
- Yong Loo Lin School of Medicine National University of Singapore Singapore 117597 Singapore
- Institute of Bioengineering and Bioimaging 31 Biopolis Ways, The Nanos Singapore 138669 Singapore
| | - Joyce Tay
- Institute of Bioengineering and Bioimaging 31 Biopolis Ways, The Nanos Singapore 138669 Singapore
| | - Guan Huei Lee
- Yong Loo Lin School of Medicine National University of Singapore Singapore 117597 Singapore
| | - Yi Yan Yang
- Institute of Bioengineering and Bioimaging 31 Biopolis Ways, The Nanos Singapore 138669 Singapore
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30
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Jhong JH, Yao L, Pang Y, Li Z, Chung CR, Wang R, Li S, Li W, Luo M, Ma R, Huang Y, Zhu X, Zhang J, Feng H, Cheng Q, Wang C, Xi K, Wu LC, Chang TH, Horng JT, Zhu L, Chiang YC, Wang Z, Lee TY. dbAMP 2.0: updated resource for antimicrobial peptides with an enhanced scanning method for genomic and proteomic data. Nucleic Acids Res 2021; 50:D460-D470. [PMID: 34850155 PMCID: PMC8690246 DOI: 10.1093/nar/gkab1080] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/16/2021] [Accepted: 10/25/2021] [Indexed: 12/26/2022] Open
Abstract
The last 18 months, or more, have seen a profound shift in our global experience, with many of us navigating a once-in-100-year pandemic. To date, COVID-19 remains a life-threatening pandemic with little to no targeted therapeutic recourse. The discovery of novel antiviral agents, such as vaccines and drugs, can provide therapeutic solutions to save human beings from severe infections; however, there is no specifically effective antiviral treatment confirmed for now. Thus, great attention has been paid to the use of natural or artificial antimicrobial peptides (AMPs) as these compounds are widely regarded as promising solutions for the treatment of harmful microorganisms. Given the biological significance of AMPs, it was obvious that there was a significant need for a single platform for identifying and engaging with AMP data. This led to the creation of the dbAMP platform that provides comprehensive information about AMPs and facilitates their investigation and analysis. To date, the dbAMP has accumulated 26 447 AMPs and 2262 antimicrobial proteins from 3044 organisms using both database integration and manual curation of >4579 articles. In addition, dbAMP facilitates the evaluation of AMP structures using I-TASSER for automated protein structure prediction and structure-based functional annotation, providing predictive structure information for clinical drug development. Next-generation sequencing (NGS) and third-generation sequencing have been applied to generate large-scale sequencing reads from various environments, enabling greatly improved analysis of genome structure. In this update, we launch an efficient online tool that can effectively identify AMPs from genome/metagenome and proteome data of all species in a short period. In conclusion, these improvements promote the dbAMP as one of the most abundant and comprehensively annotated resources for AMPs. The updated dbAMP is now freely accessible at http://awi.cuhk.edu.cn/dbAMP.
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Affiliation(s)
- Jhih-Hua Jhong
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Lantian Yao
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Yuxuan Pang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Zhongyan Li
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Chia-Ru Chung
- Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan
| | - Rulan Wang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Shangfu Li
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Wenshuo Li
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Mengqi Luo
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Renfei Ma
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Yuqi Huang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Xiaoning Zhu
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Jiahong Zhang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Hexiang Feng
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Qifan Cheng
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Chunxuan Wang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Kun Xi
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Li-Ching Wu
- Department of Biomedical Sciences and Engineering, National Central University, Taoyuan 32001, Taiwan
| | - Tzu-Hao Chang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei 10675, Taiwan
| | - Jorng-Tzong Horng
- Department of Computer Science and Information Engineering, National Central University, Taoyuan 32001, Taiwan
| | - Lizhe Zhu
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Ying-Chih Chiang
- School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Zhuo Wang
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China
| | - Tzong-Yi Lee
- Warshel Institute for Computational Biology, The Chinese University of Hong Kong, Shenzhen 518172, China.,School of Life and Health Sciences, The Chinese University of Hong Kong, Shenzhen 518172, China
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31
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Timmons PB, Hewage CM. ENNAVIA is a novel method which employs neural networks for antiviral and anti-coronavirus activity prediction for therapeutic peptides. Brief Bioinform 2021; 22:bbab258. [PMID: 34297817 PMCID: PMC8575049 DOI: 10.1093/bib/bbab258] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Revised: 06/09/2021] [Accepted: 06/18/2021] [Indexed: 11/14/2022] Open
Abstract
Viruses represent one of the greatest threats to human health, necessitating the development of new antiviral drug candidates. Antiviral peptides often possess excellent biological activity and a favourable toxicity profile, and therefore represent a promising field of novel antiviral drugs. As the quantity of sequencing data grows annually, the development of an accurate in silico method for the prediction of peptide antiviral activities is important. This study leverages advances in deep learning and cheminformatics to produce a novel sequence-based deep neural network classifier for the prediction of antiviral peptide activity. The method outperforms the existent best-in-class, with an external test accuracy of 93.9%, Matthews correlation coefficient of 0.87 and an Area Under the Curve of 0.93 on the dataset of experimentally validated peptide activities. This cutting-edge classifier is available as an online web server at https://research.timmons.eu/ennavia, facilitating in silico screening and design of peptide antiviral drugs by the wider research community.
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Affiliation(s)
- Patrick Brendan Timmons
- UCD School of Biomolecular and Biomedical Science, UCD Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Chandralal M Hewage
- UCD School of Biomolecular and Biomedical Science, UCD Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
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32
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Guo Y, Wang B, Gao H, Gao L, Hua R, Xu JD. ACE2 in the Gut: The Center of the 2019-nCoV Infected Pathology. Front Mol Biosci 2021; 8:708336. [PMID: 34631794 PMCID: PMC8493804 DOI: 10.3389/fmolb.2021.708336] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/11/2021] [Indexed: 12/25/2022] Open
Abstract
The 2019-nCoV is a rapidly contagious pneumonia caused by the recently discovered coronavirus. Although generally the most noticeable symptoms are concentrated in the lungs, the disorders in the gastrointestinal tract are of great importance in the diagnosis of 2019-nCoV. The angiotensin-converting enzyme 2 (ACE2), an important regulator of many physiological functions, including blood pressure and nutrients absorption, is recently identified as a vital entry for 2019-nCoV to enter host cells. In this review, we summarize its functions both physiologically and pathologically. We also elaborate its conflicting roles from the clews of contemporary researches, which may provide significant indications for pharmacological investigations and clinical uses.
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Affiliation(s)
- Yuexin Guo
- Department of Oral Medicine "5+3" Program, Basic Medical College, Capital Medical University, Beijing, China
| | - Boya Wang
- Undergraduate Student of 2018 Eight Program of Clinical Medicine, Peking University Health Science Center, Beijing, China
| | - Han Gao
- Department of Physiology and Pathophysiology, Basic Medical College, Capital Medical University, Beijing, China
| | - Lei Gao
- Department of Bioinformatics, School of Biomedical Engineering, Capital Medical University, Beijing, China
| | - Rongxuan Hua
- Department of Clinical Medicine "5+3" Program, Basic Medical College, Capital Medical University, Beijing, China
| | - Jing-Dong Xu
- Department of Physiology and Pathophysiology, Basic Medical College, Capital Medical University, Beijing, China
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Almehdi AM, Khoder G, Alchakee AS, Alsayyid AT, Sarg NH, Soliman SSM. SARS-CoV-2 spike protein: pathogenesis, vaccines, and potential therapies. Infection 2021; 49:855-876. [PMID: 34339040 PMCID: PMC8326314 DOI: 10.1007/s15010-021-01677-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/26/2021] [Indexed: 12/12/2022]
Abstract
PURPOSE COVID-19 pandemic has emerged as a result of infection by the deadly pathogenic severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), causing enormous threats to humans. Coronaviruses are distinguished by a clove-like spike (S) protein, which plays a key role in viral pathogenesis, evolutions, and transmission. The objectives of this study are to investigate the distinctive structural features of SARS-CoV-2 S protein, its essential role in pathogenesis, and its use in the development of potential therapies and vaccines. METHODOLOGY A literature review was conducted to summarize, analyze, and interpret the available scientific data related to SARS-CoV-2 S protein in terms of characteristics, vaccines development and potential therapies. RESULTS The data indicate that S protein subunits and their variable conformational states significantly affect the virus pathogenesis, infectivity, and evolutionary mutation. A considerable number of potential natural and synthetic therapies were proposed based on S protein. Additionally, neutralizing antibodies were recently approved for emergency use. Furthermore, several vaccines utilizing the S protein were developed. CONCLUSION A better understanding of S protein features, structure and mutations facilitate the recognition of the importance of SARS-CoV-2 S protein in viral infection, as well as the development of therapies and vaccines. The efficacy and safety of these therapeutic compounds and vaccines are still controversial. However, they may potentially reduce or prevent SARS-CoV-2 infection, leading to a significant reduction of the global health burden of this pandemic.
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Affiliation(s)
- Ahmed M Almehdi
- College of Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Ghalia Khoder
- College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, UAE
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Aminah S Alchakee
- College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Azizeh T Alsayyid
- College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Nadin H Sarg
- College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, UAE
| | - Sameh S M Soliman
- College of Pharmacy, University of Sharjah, P.O. Box 27272, Sharjah, UAE.
- Research Institute for Medical and Health Sciences, University of Sharjah, P.O. Box 27272, Sharjah, UAE.
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Rima M, Rima M, Fajloun Z, Sabatier JM, Bechinger B, Naas T. Antimicrobial Peptides: A Potent Alternative to Antibiotics. Antibiotics (Basel) 2021; 10:1095. [PMID: 34572678 PMCID: PMC8466391 DOI: 10.3390/antibiotics10091095] [Citation(s) in RCA: 105] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/02/2021] [Accepted: 09/06/2021] [Indexed: 01/07/2023] Open
Abstract
Antimicrobial peptides constitute one of the most promising alternatives to antibiotics since they could be used to treat bacterial infections, especially those caused by multidrug-resistant pathogens. Many antimicrobial peptides, with various activity spectra and mechanisms of actions, have been described. This review focuses on their use against ESKAPE bacteria, especially in biofilm treatments, their synergistic activity, and their application as prophylactic agents. Limitations and challenges restricting therapeutic applications are highlighted, and solutions for each challenge are evaluated to analyze whether antimicrobial peptides could replace antibiotics in the near future.
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Affiliation(s)
- Mariam Rima
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, 94270 Le Kremlin-Bicetre, France;
| | - Mohamad Rima
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, EDST, Lebanese University, Tripoli 1300, Lebanon; (M.R.); (Z.F.)
| | - Ziad Fajloun
- Laboratory of Applied Biotechnology, Azm Center for Research in Biotechnology and Its Applications, EDST, Lebanese University, Tripoli 1300, Lebanon; (M.R.); (Z.F.)
- Department of Biology, Faculty of Sciences III, Lebanese University, Tripoli 1300, Lebanon
| | - Jean-Marc Sabatier
- Institut de Neuro Physiopathologie, UMR7051, Aix-Marseille Université, Faculté de Pharmacie, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Burkhard Bechinger
- Institut de Chimie de Strasbourg, CNRS, UMR7177, University of Strasbourg, 67008 Strasbourg, France;
- Institut Universitaire de France (IUF), 75005 Paris, France
| | - Thierry Naas
- Team ReSIST, INSERM U1184, School of Medicine Université Paris-Saclay, 94270 Le Kremlin-Bicetre, France;
- Bacteriology-Hygiene Unit, Assistance Publique/Hôpitaux de Paris, Bicêtre Hospital, 94270 Le Kremlin-Bicetre, France
- French National Reference Centre for Antibiotic Resistance: Carbapenemase-Producing Enterobacterales, 94270 Le Kremlin-Bicetre, France
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El Hidan MA, Laaradia MA, El Hiba O, Draoui A, Aimrane A, Kahime K. Scorpion-Derived Antiviral Peptides with a Special Focus on Medically Important Viruses: An Update. BIOMED RESEARCH INTERNATIONAL 2021; 2021:9998420. [PMID: 34527748 PMCID: PMC8437663 DOI: 10.1155/2021/9998420] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/07/2021] [Accepted: 08/23/2021] [Indexed: 11/17/2022]
Abstract
The global burden of viral infection, especially the current pandemics of SARS-CoV-2, HIV/AIDS, and hepatitis, is a very risky one. Additionally, HCV expresses the necessity for antiviral therapeutic elements. Venoms are known to contain an array of bioactive peptides that are commonly used in the treatment of various medical issues. Several peptides isolated from scorpion venom have recently been proven to possess an antiviral activity against several viral families. The aim of this review is to provide an up-to-date overview of scorpion antiviral peptides and to discuss their modes of action and potential biomedical application against different viruses.
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Affiliation(s)
- Moulay Abdelmonaim El Hidan
- Laboratory of Biotechnology and Valorization of Natural Resources, Faculty of Applied Sciences, Ibn Zohr University, Agadir, Morocco
| | | | - Omar El Hiba
- Nutritional Physiopathology Team, Faculty of Sciences, Chouaib Doukkali University, El Jadida 24000, Morocco
| | - Ahmed Draoui
- Laboratory of Clinical and Experimental Neurosciences and Environment, Faculty of Medicine and Pharmacy, Cadi Ayyad University, Morocco
| | - Abdelmohcine Aimrane
- Nutritional Physiopathology Team, Faculty of Sciences, Chouaib Doukkali University, El Jadida 24000, Morocco
- Metabolic Platform, Biochemistry Laboratory, Faculty of Medicine, Cadi Ayad University, Marrakech, Morocco
| | - Kholoud Kahime
- SAEDD Laboratory, School of Technology Essaouira, Cadi Ayyad University of Marrakesh, Morocco
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Sumon TA, Hussain MA, Hasan M, Rashid A, Abualreesh MH, Jang WJ, Sharifuzzaman SM, Brown CL, Lee EW, Hasan MT. Antiviral peptides from aquatic organisms: Functionality and potential inhibitory effect on SARS-CoV-2. AQUACULTURE (AMSTERDAM, NETHERLANDS) 2021; 541:736783. [PMID: 33883784 PMCID: PMC8049179 DOI: 10.1016/j.aquaculture.2021.736783] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Revised: 02/26/2021] [Accepted: 04/14/2021] [Indexed: 05/06/2023]
Abstract
Several antiviral peptides (AVPs) from aquatic organisms have been effective in interfering with the actions of infectious viruses, such as Human Immunodeficiency Virus-1 and Herpes Simplex Virus-1 and 2. AVPs are able to block viral attachment or entry into host cells, inhibit internal fusion or replication events by suppressing viral gene transcription, and prevent viral infections by modulating host immunity. Therefore, as promising therapeutics, the potential of aquatic AVPs for use against the COVID-19 pandemic caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is considered. At present no therapeutic drugs are yet available. A total of 32 AVPs derived from fish and shellfish species are discussed in this review paper with notes on their properties and mechanisms of action in the inhibition of viral diseases both in humans and animals, emphasizing on SARS-CoV-2. The molecular structure of novel SARS-CoV-2 with its entry mechanisms, clinical signs and symptoms are also discussed. In spite of only a few study of these AVPs against SARS-CoV-2, aquatic AVPs properties and infection pathways (entry, replication and particle release) into coronaviruses are linked in this paper to postulate an analysis of their potential but unconfirmed actions to impair SARS-CoV-2 infection in humans.
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Affiliation(s)
- Tofael Ahmed Sumon
- Department of Fish Health Management, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Md Ashraf Hussain
- Department of Fisheries Technology and Quality Control, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Mahmudul Hasan
- Department of Pharmaceuticals and Industrial Biotechnology, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Aminur Rashid
- Department of Aquaculture, Sylhet Agricultural University, Sylhet 3100, Bangladesh
| | - Muyassar Hamid Abualreesh
- Department of Marine Biology, Faculty of Marine Science, King Abdulaziz University, P.O. Box 80207, Jeddah 21589, Saudi Arabia
| | - Won Je Jang
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan 47340, Republic of Korea
| | - S M Sharifuzzaman
- Institute of Marine Sciences, University of Chittagong, Chittagong 4331, Bangladesh
| | - Christopher Lyon Brown
- FAO World Fisheries University Pilot Programme, Pukyong National University, Busan, South Korea
| | - Eun-Woo Lee
- Biopharmaceutical Engineering Major, Division of Applied Bioengineering, Dong-Eui University, Busan 47340, Republic of Korea
| | - Md Tawheed Hasan
- Department of Aquaculture, Sylhet Agricultural University, Sylhet 3100, Bangladesh
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Exploring peptide studies related to SARS-CoV to accelerate the development of novel therapeutic and prophylactic solutions against COVID-19. J Infect Public Health 2021; 14:1106-1119. [PMID: 34280732 PMCID: PMC8253661 DOI: 10.1016/j.jiph.2021.06.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 06/18/2021] [Accepted: 06/27/2021] [Indexed: 01/18/2023] Open
Abstract
Recent advances in peptide research revolutionized therapeutic discoveries for various infectious diseases. In view of the ongoing threat of the COVID-19 pandemic, there is an urgent need to develop potential therapeutic options. Intense and accomplishing research is being carried out to develop broad-spectrum vaccines and treatment options for corona viruses, due to the risk of recurrent infection by the existing strains or pandemic outbreaks by new mutant strains. Developing a novel medicine is costly and time consuming, which increases the value of repurposing existing therapies. Since, SARS-CoV-2 shares significant genomic homology with SARS-CoV, we have summarized various peptides identified against SARS-CoV using in silico and molecular studies and also the peptides effective against SARS-CoV-2. Dissecting the molecular mechanisms underlying viral infection could yield fundamental insights in the discovery of new antiviral agents, targeting viral proteins or host factors. We postulate that these peptides can serve as effective components for therapeutic options against SARS-CoV-2, supporting clinical scientists globally in selectively identifying and testing the therapeutic and prophylactic agents for COVID-19 treatment. In addition, we also summarized the latest updates on peptide therapeutics against SARS-CoV-2.
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Anand U, Jakhmola S, Indari O, Jha HC, Chen ZS, Tripathi V, Pérez de la Lastra JM. Potential Therapeutic Targets and Vaccine Development for SARS-CoV-2/COVID-19 Pandemic Management: A Review on the Recent Update. Front Immunol 2021; 12:658519. [PMID: 34276652 PMCID: PMC8278575 DOI: 10.3389/fimmu.2021.658519] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 06/07/2021] [Indexed: 01/08/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) is a highly pathogenic novel virus that has caused a massive pandemic called coronavirus disease 2019 (COVID-19) worldwide. Wuhan, a city in China became the epicenter of the outbreak of COVID-19 in December 2019. The disease was declared a pandemic globally by the World Health Organization (WHO) on 11 March 2020. SARS-CoV-2 is a beta CoV of the Coronaviridae family which usually causes respiratory symptoms that resemble common cold. Multiple countries have experienced multiple waves of the disease and scientific experts are consistently working to find answers to several unresolved questions, with the aim to find the most suitable ways to contain the virus. Furthermore, potential therapeutic strategies and vaccine development for COVID-19 management are also considered. Currently, substantial efforts have been made to develop successful and safe treatments and SARS-CoV-2 vaccines. Some vaccines, such as inactivated vaccines, nucleic acid-based, and vector-based vaccines, have entered phase 3 clinical trials. Additionally, diverse small molecule drugs, peptides and antibodies are being developed to treat COVID-19. We present here an overview of the virus interaction with the host and environment and anti-CoV therapeutic strategies; including vaccines and other methodologies, designed for prophylaxis and treatment of SARS-CoV-2 infection with the hope that this integrative analysis could help develop novel therapeutic approaches against COVID-19.
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Affiliation(s)
- Uttpal Anand
- Department of Life Sciences, National Institute for Biotechnology in the Negev, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Shweta Jakhmola
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Omkar Indari
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Hem Chandra Jha
- Discipline of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, India
| | - Zhe-Sheng Chen
- Department of Pharmaceutical Sciences, College of Pharmacy and Health Sciences, St. John’s University, Queens, NY, United States
| | - Vijay Tripathi
- Department of Molecular and Cellular Engineering, Jacob Institute of Biotechnology and Bioengineering, Sam Higginbottom University of Agriculture, Technology and Sciences, Prayagraj, India
| | - José M. Pérez de la Lastra
- Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones científicas (CSIS), Santa Cruz de Tenerife, Spain
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Fundamental and Advanced Therapies, Vaccine Development against SARS-CoV-2. Pathogens 2021; 10:pathogens10060636. [PMID: 34064300 PMCID: PMC8224379 DOI: 10.3390/pathogens10060636] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/11/2021] [Accepted: 05/19/2021] [Indexed: 01/08/2023] Open
Abstract
Coronavirus disease (COVID-19) caused by the SARS-CoV-2 virus has been affecting the world since the end of 2019. The severity of the disease can range from an asymptomatic or mild course to acute respiratory distress syndrome (ARDS) with respiratory failure, which may lead to death. Since the outbreak of the pandemic, scientists around the world have been studying the genome and molecular mechanisms of SARS-CoV-2 infection to develop effective therapies and prevention. In this review, we summarize the progressive development of various treatments and vaccines as they have emerged, a year after the outbreak of the pandemic. Initially for COVID-19, patients were recommended drugs with presumed antiviral, anti-inflammatory, and antimicrobial effects that were previously used to treat other diseases. Thereafter, therapeutic interventions were supplemented with promising approaches based on antibodies, peptides, and stem cells. However, licensed COVID-19 vaccines remain the most effective weapon in combating the pandemic. While there is an enormous effort to enhance the vaccination rate to increase the entire population immunity, the production and delivery of vaccines is becoming limited in several countries. In this regard, there are new challenges needing to be addressed by combining non-pharmacological intervention with effective therapies until vaccination is accessible to all.
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Agouram N, El Hadrami EM, Bentama A. 1,2,3-Triazoles as Biomimetics in Peptide Science. Molecules 2021; 26:2937. [PMID: 34069302 PMCID: PMC8156386 DOI: 10.3390/molecules26102937] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/05/2021] [Accepted: 05/05/2021] [Indexed: 01/10/2023] Open
Abstract
Natural peptides are an important class of chemical mediators, essential for most vital processes. What limits the potential of the use of peptides as drugs is their low bioavailability and enzymatic degradation in vivo. To overcome this limitation, the development of new molecules mimicking peptides is of great importance for the development of new biologically active molecules. Therefore, replacing the amide bond in a peptide with a heterocyclic bioisostere, such as the 1,2,3-triazole ring, can be considered an effective solution for the synthesis of biologically relevant peptidomimetics. These 1,2,3-triazoles may have an interesting biological activity, because they behave as rigid link units, which can mimic the electronic properties of amide bonds and show bioisosteric effects. Additionally, triazole can be used as a linker moiety to link peptides to other functional groups.
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Affiliation(s)
- Naima Agouram
- Laboratory of Applied Organic Chemistry, Faculty of Science and Technology, Sidi Mohammed Ben Abdellah University, Immouzer Road, Fez 30050, Morocco; (E.M.E.H.); (A.B.)
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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] [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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Abstract
INTRODUCTION Proteomics, i.e. the study of the set of proteins produced in a cell, tissue, organism, or biological entity, has made possible analyses and contextual comparisons of proteomes/proteins and biological functions among the most disparate entities, from viruses to the human being. In this way, proteomic scrutiny of tumor-associated proteins, autoantigens, and pathogen antigens offers the tools for fighting cancer, autoimmunity, and infections. AREAS COVERED Comparative proteomics and immunoproteomics, the new scientific disciplines generated by proteomics, are the main themes of the present review that describes how comparative analyses of pathogen and human proteomes led to re-modulate the molecular mimicry concept of the pre-proteomic era. I.e. before proteomics, molecular mimicry - the sharing of peptide sequences between two biological entities - was considered as intrinsically endowed with immunologic properties and was related to cross-reactivity. Proteomics allowed to redefine such an assumption using physicochemical parameters according to which frequency and hydrophobicity preferentially confer an immunologic potential to shared peptide sequences. EXPERT OPINION Proteomics is outlining peptide platforms to be used for the diagnostics and management of human diseases. A Molecular Medicine targeted to obtain healing without paying the price for adverse events is on the horizon. The next step is to take up the challenge and operate the paradigm shift that the current proteomic era requires.
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Affiliation(s)
- Darja Kanduc
- Department of Biosciences, Biotechnologies, and Biopharmaceutics, University of Bari, Bari, Italy
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Wong FC, Ong JH, Kumar DT, Chai TT. In Silico Identification of Multi-target Anti-SARS-CoV-2 Peptides from Quinoa Seed Proteins. Int J Pept Res Ther 2021; 27:1837-1847. [PMID: 33867899 PMCID: PMC8034280 DOI: 10.1007/s10989-021-10214-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2021] [Indexed: 12/23/2022]
Abstract
Peptides are promising antagonists against severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). To expedite drug discovery, a computational approach is widely employed for the initial screening of anti-SARS-CoV-2 candidates. This study aimed to investigate the potential of peptides from quinoa seed proteins as multi-target antagonists against SARS-CoV-2 spike glycoprotein receptor-binding domain, main protease, and papain-like protease. Five quinoa proteins were hydrolyzed in silico by papain and subtilisin. Among the 1465 peptides generated, seven could interact stably with the key binding residues and catalytic residues of the viral targets, mainly via hydrogen bonds and hydrophobic interactions. The seven peptides were comparable or superior to previously reported anti-SARS-CoV-2 peptides based on docking scores. Key residues in the seven peptides contributing to binding to viral targets were determined by computational alanine scanning. The seven peptides were predicted in silico to be non-toxic and non-allergenic. The peptides ranged between 546.66 and 3974.87 g/mol in molecular mass, besides exhibiting basic and cationic properties (isoelectric points: 8.26-12.10; net charges: 0.1-4.0). Among the seven peptides, VEDKGMMHQQRMMEKAMNIPRMCGTMQRKCRMS was found to bind the largest number of key residues on the targets. In conclusion, seven putative non-toxic, non-allergenic, multi-target anti-SARS-CoV-2 peptides were identified from quinoa seed proteins. The in vitro and in vivo efficacies of the seven peptides against SARS-CoV-2 deserve attention in future bench-top testing. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10989-021-10214-y.
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Affiliation(s)
- Fai-Chu Wong
- Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman, 31900 Kampar, Malaysia
- Center for Agriculture and Food Research, Universiti Tunku Abdul Rahman, 31900 Kampar, Malaysia
| | - Joe-Hui Ong
- Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman, 31900 Kampar, Malaysia
| | - D. Thirumal Kumar
- Department of Bioinformatics, Saveetha School of Engineering, Saveetha Institute of Medical and Technical Sciences, Chennai, 602 105 Tamil Nadu India
| | - Tsun-Thai Chai
- Department of Chemical Science, Faculty of Science, Universiti Tunku Abdul Rahman, 31900 Kampar, Malaysia
- Center for Agriculture and Food Research, Universiti Tunku Abdul Rahman, 31900 Kampar, Malaysia
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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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Bakovic A, Risner K, Bhalla N, Alem F, Chang TL, Weston WK, Harness JA, Narayanan A. Brilacidin Demonstrates Inhibition of SARS-CoV-2 in Cell Culture. Viruses 2021; 13:271. [PMID: 33572467 PMCID: PMC7916214 DOI: 10.3390/v13020271] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 01/28/2021] [Accepted: 02/05/2021] [Indexed: 12/17/2022] Open
Abstract
Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the newly emergent causative agent of coronavirus disease-19 (COVID-19), has resulted in more than two million deaths worldwide since it was first detected in 2019. There is a critical global need for therapeutic intervention strategies that can be deployed to safely treat COVID-19 disease and reduce associated morbidity and mortality. Increasing evidence shows that both natural and synthetic antimicrobial peptides (AMPs), also referred to as Host Defense Proteins/Peptides (HDPs), can inhibit SARS-CoV-2, paving the way for the potential clinical use of these molecules as therapeutic options. In this manuscript, we describe the potent antiviral activity exerted by brilacidin-a de novo designed synthetic small molecule that captures the biological properties of HDPs-on SARS-CoV-2 in a human lung cell line (Calu-3) and a monkey cell line (Vero). These data suggest that SARS-CoV-2 inhibition in these cell culture models is likely to be a result of the impact of brilacidin on viral entry and its disruption of viral integrity. Brilacidin demonstrated synergistic antiviral activity when combined with remdesivir. Collectively, our data demonstrate that brilacidin exerts potent inhibition of SARS-CoV-2 against different strains of the virus in cell culture.
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Affiliation(s)
- Allison Bakovic
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA 20110, USA; (A.B.); (K.R.); (N.B.); (F.A.)
| | - Kenneth Risner
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA 20110, USA; (A.B.); (K.R.); (N.B.); (F.A.)
| | - Nishank Bhalla
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA 20110, USA; (A.B.); (K.R.); (N.B.); (F.A.)
| | - Farhang Alem
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA 20110, USA; (A.B.); (K.R.); (N.B.); (F.A.)
| | - Theresa L. Chang
- Public Health Research Institute, Rutgers, New Jersey Medical School, The State University of New Jersey, Newark, NJ 07103, USA;
| | - Warren K. Weston
- Innovation Pharmaceuticals Inc., Wakefield, MA 01880, USA; (W.K.W.); (J.A.H.)
| | - Jane A. Harness
- Innovation Pharmaceuticals Inc., Wakefield, MA 01880, USA; (W.K.W.); (J.A.H.)
| | - Aarthi Narayanan
- National Center for Biodefense and Infectious Diseases, George Mason University, Manassas, VA 20110, USA; (A.B.); (K.R.); (N.B.); (F.A.)
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Chakraborty C, Bhattacharya M, Mallick B, Sharma AR, Lee SS, Agoramoorthy G. SARS-CoV-2 protein drug targets landscape: a potential pharmacological insight view for the new drug development. Expert Rev Clin Pharmacol 2021; 14:225-238. [PMID: 33423554 DOI: 10.1080/17512433.2021.1874348] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Introduction: Protein drug targets play a significant choice in different stages of the drug discovery process. There is an urgent need to understand the drug discovery approaches and protein drug targets (PDT) of SARS-CoV-2, with structural insights for the development of SARS-CoV-2 drugs through targeted therapeutic approach.Areas covered: We have described the protein as a drug target class and also discussed various drug discovery approaches for SARS-CoV-2 involving the protein drug targets such as drug repurposing study, designing of viral entry inhibitors, viral replication inhibitors, and different enzymes of the virus. We have performed comprehensive literature search from the popular databases such as PubMed Google scholar, Web of Science, and Scopus. Finally, we have illustrated the structural landscape of different significant viral proteins (3 CLpro or Mpro, PLpro, RdRp, helicase, S protein) and host proteins as drug targets (cathepsin L, furin, TMPRSS2, ACE2).Expert opinion: The structural landscape of PDT with their binding pockets, and significant residues involved in binding has been discussed further to better understand the PDT and the structure-based drug discovery for SARS-CoV-2. This attempt will increase more therapeutic options, and combination therapies with a multi-target strategy.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, West Bengal India.,Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Gangwon-do, Republic of Korea
| | | | - Bidyut Mallick
- Department of Applied Science, Galgotias College of Engineering and Technology, Greater Noida, Uttar Pradesh, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Gangwon-do, Republic of Korea
| | - Sang-Soo Lee
- Institute for Skeletal Aging & Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Gangwon-do, Republic of Korea
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Kurpe SR, Grishin SY, Surin AK, Panfilov AV, Slizen MV, Chowdhury SD, Galzitskaya OV. Antimicrobial and Amyloidogenic Activity of Peptides. Can Antimicrobial Peptides Be Used against SARS-CoV-2? Int J Mol Sci 2020; 21:E9552. [PMID: 33333996 PMCID: PMC7765370 DOI: 10.3390/ijms21249552] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/07/2020] [Accepted: 12/12/2020] [Indexed: 02/07/2023] Open
Abstract
At present, much attention is paid to the use of antimicrobial peptides (AMPs) of natural and artificial origin to combat pathogens. AMPs have several points that determine their biological activity. We analyzed the structural properties of AMPs, as well as described their mechanism of action and impact on pathogenic bacteria and viruses. Recently published data on the development of new AMP drugs based on a combination of molecular design and genetic engineering approaches are presented. In this article, we have focused on information on the amyloidogenic properties of AMP. This review examines AMP development strategies from the perspective of the current high prevalence of antibiotic-resistant bacteria, and the potential prospects and challenges of using AMPs against infection caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2).
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Affiliation(s)
- Stanislav R. Kurpe
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.R.K.); (S.Y.G.); (A.K.S.); (A.V.P.); (M.V.S.)
| | - Sergei Yu. Grishin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.R.K.); (S.Y.G.); (A.K.S.); (A.V.P.); (M.V.S.)
| | - Alexey K. Surin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.R.K.); (S.Y.G.); (A.K.S.); (A.V.P.); (M.V.S.)
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Alexander V. Panfilov
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.R.K.); (S.Y.G.); (A.K.S.); (A.V.P.); (M.V.S.)
| | - Mikhail V. Slizen
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.R.K.); (S.Y.G.); (A.K.S.); (A.V.P.); (M.V.S.)
| | - Saikat D. Chowdhury
- Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur 741246, West Bengal, India;
| | - Oxana V. Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.R.K.); (S.Y.G.); (A.K.S.); (A.V.P.); (M.V.S.)
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
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Ghosh S, Malik YS. Drawing Comparisons between SARS-CoV-2 and the Animal Coronaviruses. Microorganisms 2020; 8:E1840. [PMID: 33238451 PMCID: PMC7700164 DOI: 10.3390/microorganisms8111840] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 11/01/2020] [Accepted: 11/19/2020] [Indexed: 12/19/2022] Open
Abstract
The COVID-19 pandemic, caused by a novel zoonotic coronavirus (CoV), SARS-CoV-2, has infected 46,182 million people, resulting in 1,197,026 deaths (as of 1 November 2020), with devastating and far-reaching impacts on economies and societies worldwide. The complex origin, extended human-to-human transmission, pathogenesis, host immune responses, and various clinical presentations of SARS-CoV-2 have presented serious challenges in understanding and combating the pandemic situation. Human CoVs gained attention only after the SARS-CoV outbreak of 2002-2003. On the other hand, animal CoVs have been studied extensively for many decades, providing a plethora of important information on their genetic diversity, transmission, tissue tropism and pathology, host immunity, and therapeutic and prophylactic strategies, some of which have striking resemblance to those seen with SARS-CoV-2. Moreover, the evolution of human CoVs, including SARS-CoV-2, is intermingled with those of animal CoVs. In this comprehensive review, attempts have been made to compare the current knowledge on evolution, transmission, pathogenesis, immunopathology, therapeutics, and prophylaxis of SARS-CoV-2 with those of various animal CoVs. Information on animal CoVs might enhance our understanding of SARS-CoV-2, and accordingly, benefit the development of effective control and prevention strategies against COVID-19.
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Affiliation(s)
- Souvik Ghosh
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre 334, Saint Kitts and Nevis
| | - Yashpal S. Malik
- College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana 141004, India;
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