1
|
Murdocca M, Romeo I, Citro G, Latini A, Centofanti F, Bugatti A, Caccuri F, Caruso A, Ortuso F, Alcaro S, Sangiuolo F, Novelli G. A Dynamic and Effective Peptide-Based Strategy for Promptly Addressing Emerging SARS-CoV-2 Variants of Concern. Pharmaceuticals (Basel) 2024; 17:891. [PMID: 39065742 PMCID: PMC11279616 DOI: 10.3390/ph17070891] [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: 05/20/2024] [Revised: 06/25/2024] [Accepted: 07/02/2024] [Indexed: 07/28/2024] Open
Abstract
Genomic surveillance based on sequencing the entire genetic code of SARS-CoV-2 involves monitoring and studying genetic changes and variations in disease-causing organisms such as viruses and bacteria. By tracing the virus, it is possible to prevent epidemic spread in the community, ensuring a 'precision public health' strategy. A peptide-based design was applied to provide an efficacious strategy that is able to counteract any emerging viral variant of concern dynamically and promptly to affect the outcomes of a pandemic at an early stage while waiting for the production of the anti-variant-specific vaccine, which require longer times. The inhibition of the interaction between the receptor-binding domain (RBD) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and one of the cellular receptors (DPP4) that its receptors routinely bind to infect human cells is an intriguing therapeutic approach to prevent the virus from entering human cells. Among the other modalities developed for this purpose, peptides surely offer unique advantages, including ease of synthesis, serum stability, low immunogenicity and toxicity, and small production and distribution chain costs. Here, we obtained a potent new inhibitor based on the rearrangement of a previously identified peptide that has been rationally designed on a cell dipeptidyl peptidase 4 (DPP4) sequence, a ubiquitous membrane protein known to bind the RBD-SPIKE domain of the virus. This novel peptide (named DPP4-derived), conceived as an endogenous "drug", is capable of targeting the latest tested variants with a high affinity, reducing the VSV* DG-Fluc pseudovirus Omicron's infection capacity by up to 14%, as revealed by in vitro testing in human Calu-3 cells. Surface plasmon resonance (SPR) confirmed the binding affinity of the new DPP4-derived peptide with Omicron variant RBD.
Collapse
Affiliation(s)
- Michela Murdocca
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.M.); (G.C.); (A.L.); (F.C.); (G.N.)
| | - Isabella Romeo
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (I.R.); (F.O.); (S.A.)
- Net4Science Srl Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Gennaro Citro
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.M.); (G.C.); (A.L.); (F.C.); (G.N.)
| | - Andrea Latini
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.M.); (G.C.); (A.L.); (F.C.); (G.N.)
| | - Federica Centofanti
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.M.); (G.C.); (A.L.); (F.C.); (G.N.)
| | - Antonella Bugatti
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.C.); (A.C.)
| | - Francesca Caccuri
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.C.); (A.C.)
| | - Arnaldo Caruso
- Section of Microbiology, Department of Molecular and Translational Medicine, University of Brescia, 25123 Brescia, Italy; (A.B.); (F.C.); (A.C.)
| | - Francesco Ortuso
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (I.R.); (F.O.); (S.A.)
- Net4Science Srl Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Stefano Alcaro
- Dipartimento di Scienze della Salute, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy; (I.R.); (F.O.); (S.A.)
- Net4Science Srl Academic Spin-Off, Università “Magna Græcia” di Catanzaro, Campus “S. Venuta”, Viale Europa, 88100 Catanzaro, Italy
| | - Federica Sangiuolo
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.M.); (G.C.); (A.L.); (F.C.); (G.N.)
| | - Giuseppe Novelli
- Department of Biomedicine and Prevention, University of Rome Tor Vergata, Via Montpellier 1, 00133 Rome, Italy; (M.M.); (G.C.); (A.L.); (F.C.); (G.N.)
- IRCCS Neuromed Mediterranean Neurological Institute, 86077 Pozzilli, Italy
- Department of Pharmacology, School of Medicine, University of Nevada, Reno, NV 89557, USA
| |
Collapse
|
2
|
Saadi S, Makhlouf C, Nacer NE, Halima B, Faiza A, Kahina H, Wahiba F, Afaf K, Rabah K, Saoudi Z. Whey proteins as multifunctional food materials: Recent advancements in hydrolysis, separation, and peptidomimetic approaches. Compr Rev Food Sci Food Saf 2024; 23:e13288. [PMID: 38284584 DOI: 10.1111/1541-4337.13288] [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: 07/21/2023] [Revised: 10/23/2023] [Accepted: 12/11/2023] [Indexed: 01/30/2024]
Abstract
Whey protein derived bioactives, including α-lactalbumin, ß-lactoglobulin, bovine serum albumin, lactoferrin, transferrin, and proteose-peptones, have exhibited wide ranges of functional, biological and therapeutic properties varying from anticancer, antihypertensive, and antimicrobial effects. In addition, their functional properties involve gelling, emulsifying, and foaming abilities. For these reasons, this review article is framed to understand the relationship existed in between those compound levels and structures with their main functional, biological, and therapeutic properties exhibited either in vitro or in vivo. The impacts of hydrolysis mechanism and separation techniques in enhancing those properties are likewise discussed. Furthermore, special emphasize is given to multifunctional effects of whey derived bioactives and their future trends in ameliorating further food, pharmaceutical, and nutraceutical products. The underlying mechanism effects of those properties are still remained unclear in terms of activity levels, efficacy, and targeted effectiveness. For these reasons, some important models linking to functional properties, thermal properties and cell circumstances are established. Moreover, the coexistence of radical trapping groups, chelating groups, sulfhydryl groups, inhibitory groups, and peptide bonds seemed to be the key elements in triggering those functions and properties. Practical Application: Whey proteins are the byproducts of cheese processing and usually the exploitation of these food waste products has increasingly getting acceptance in many countries, especially European countries. Whey proteins share comparable nutritive values to milk products, particularly on their richness on important proteins that can serve immune protection, structural, and energetic roles. The nutritive profile of whey proteins shows diverse type of bioactive molecules like α-lactalbumin, ß-lactoglobulin, lactoferrin, transferrin, immunoglobulin, and proteose peptones with wide biological importance to the living system, such as in maintaining immunological, neuronal, and signaling roles. The diversification of proteins of whey products prompted scientists to exploit the real mechanisms behind of their biological and therapeutic effects, especially in declining the risk of cancer, tumor, and further complications like diabetes type 2 and hypertension risk effects. For these reasons, profiling these types of proteins using different proteomic and peptidomic approaches helps in determining their biological and therapeutic targets along with their release into gastrointestinal tract conditions and their bioavailabilities into portal circulation, tissue, and organs. The wide applicability of those protein fractions and their derivative bioactive products showed significant impacts in the field of emulsion and double emulsion stabilization by playing roles as emulsifying, surfactant, stabilizing, and foaming agents. Their amphoteric properties helped them to act as excellent encapsulating agents, particularly as vehicle for delivering important vitamins and bioactive compounds. The presence of ferric elements increased their transportation to several metal-ions in the same time increased their scavenging effects to metal-transition and peroxidation of lipids. Their richness with almost essential and nonessential amino acids makes them as selective microbial starters, in addition their richness in sulfhydryl amino acids allowed them to act a cross-linker in conjugating further biomolecules. For instance, conjugating gold-nanoparticles and fluorescent materials in targeting diseases like cancer and tumors in vivo is considered the cutting-edges strategies for these versatile molecules due to their active diffusion across-cell membrane and the presence of specific transporters to these therapeutic molecules.
Collapse
Affiliation(s)
- Sami Saadi
- Institut de la Nutrition, de l'Alimentation et des Technologies Agroalimentaires (INATAA), Université Frères Mentouri Constantine 1, Constantine, Algeria
- Laboratoire de Génie Agro-alimentaire, équipe Génie des Procédés Alimentaires, Biodiversité et Agro environnement, INATAA, Université Frères Mentouri Constantine 1 (UFC1), Constantine, Algeria
| | - Chaalal Makhlouf
- Institut de la Nutrition, de l'Alimentation et des Technologies Agroalimentaires (INATAA), Université Frères Mentouri Constantine 1, Constantine, Algeria
- Laboratory of Biotechnology and Food Quality, Institute of Nutrition, Food and Agro-Food Technologies, University of Constantine 1, Constantine, Algeria
- Laboratory of Applied Biochemistry, Faculty of Nature and Life Science, University of Bejaia, Bejaia, Algeria
| | - Nor Elhouda Nacer
- Department of Biology of Organisms, Faculty of Natural and Life Sciences, University of Batna 2, Batna, Algeria
| | - Boughellout Halima
- Institut de la Nutrition, de l'Alimentation et des Technologies Agroalimentaires (INATAA), Université Frères Mentouri Constantine 1, Constantine, Algeria
- Laboratoire de Génie Agro-alimentaire, équipe Génie des Procédés Alimentaires, Biodiversité et Agro environnement, INATAA, Université Frères Mentouri Constantine 1 (UFC1), Constantine, Algeria
| | - Adoui Faiza
- Institut de la Nutrition, de l'Alimentation et des Technologies Agroalimentaires (INATAA), Université Frères Mentouri Constantine 1, Constantine, Algeria
- Laboratoire de Génie Agro-alimentaire, équipe Génie des Procédés Alimentaires, Biodiversité et Agro environnement, INATAA, Université Frères Mentouri Constantine 1 (UFC1), Constantine, Algeria
| | - Hafid Kahina
- Institut de la Nutrition, de l'Alimentation et des Technologies Agroalimentaires (INATAA), Université Frères Mentouri Constantine 1, Constantine, Algeria
- Equipe MaQuaV, Laboratoire Bioqual INATAA, Université des Frères Mentouri-Constantine 1, Constantine, Algeria
| | - Falek Wahiba
- Institut de la Nutrition, de l'Alimentation et des Technologies Agroalimentaires (INATAA), Université Frères Mentouri Constantine 1, Constantine, Algeria
- Laboratoire de Génie Agro-alimentaire, équipe Génie des Procédés Alimentaires, Biodiversité et Agro environnement, INATAA, Université Frères Mentouri Constantine 1 (UFC1), Constantine, Algeria
| | - Kheroufi Afaf
- Institut de la Nutrition, de l'Alimentation et des Technologies Agroalimentaires (INATAA), Université Frères Mentouri Constantine 1, Constantine, Algeria
- Laboratoire de Génie Agro-alimentaire, équipe Génie des Procédés Alimentaires, Biodiversité et Agro environnement, INATAA, Université Frères Mentouri Constantine 1 (UFC1), Constantine, Algeria
| | - Kezih Rabah
- Institut de la Nutrition, de l'Alimentation et des Technologies Agroalimentaires (INATAA), Université Frères Mentouri Constantine 1, Constantine, Algeria
- Laboratory of Biotechnology and Food Quality, Institute of Nutrition, Food and Agro-Food Technologies, University of Constantine 1, Constantine, Algeria
| | - Zineddine Saoudi
- Institut de la Nutrition, de l'Alimentation et des Technologies Agroalimentaires (INATAA), Université Frères Mentouri Constantine 1, Constantine, Algeria
- Laboratoire de Génie Agro-alimentaire, équipe Génie des Procédés Alimentaires, Biodiversité et Agro environnement, INATAA, Université Frères Mentouri Constantine 1 (UFC1), Constantine, Algeria
| |
Collapse
|
3
|
Waring AJ, Jung GCL, Sharma SK, Walther FJ. Lung Surfactant Protein B Peptide Mimics Interact with the Human ACE2 Receptor. Int J Mol Sci 2023; 24:10837. [PMID: 37446012 DOI: 10.3390/ijms241310837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2023] [Revised: 06/24/2023] [Accepted: 06/27/2023] [Indexed: 07/15/2023] Open
Abstract
Lung surfactant is a complex mixture of phospholipids and surfactant proteins that is produced in alveolar type 2 cells. It prevents lung collapse by reducing surface tension and is involved in innate immunity. Exogenous animal-derived and, more recently, synthetic lung surfactant has shown clinical efficacy in surfactant-deficient premature infants and in critically ill patients with acute respiratory distress syndrome (ARDS), such as those with severe COVID-19 disease. COVID-19 pneumonia is initiated by the binding of the viral receptor-binding domain (RBD) of SARS-CoV-2 to the cellular receptor angiotensin-converting enzyme 2 (ACE2). Inflammation and tissue damage then lead to loss and dysfunction of surface activity that can be relieved by treatment with an exogenous lung surfactant. Surfactant protein B (SP-B) is pivotal for surfactant activity and has anti-inflammatory effects. Here, we study the binding of two synthetic SP-B peptide mimics, Super Mini-B (SMB) and B-YL, to a recombinant human ACE2 receptor protein construct using molecular docking and surface plasmon resonance (SPR) to evaluate their potential as antiviral drugs. The SPR measurements confirmed that both the SMB and B-YL peptides bind to the rhACE2 receptor with affinities like that of the viral RBD-ACE2 complex. These findings suggest that synthetic lung surfactant peptide mimics can act as competitive inhibitors of the binding of viral RBD to the ACE2 receptor.
Collapse
Affiliation(s)
- Alan J Waring
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Grace C-L Jung
- Department of Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| | - Shantanu K Sharma
- Materials and Process Simulation Center, California Institute of Technology, Pasadena, CA 91125, USA
| | - Frans J Walther
- The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA 90095, USA
| |
Collapse
|
4
|
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.
Collapse
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
| |
Collapse
|
5
|
Shanmugam A, Venkattappan A, Gromiha MM. Structure based Drug Designing Approaches in SARS-CoV-2 Spike Inhibitor Design. Curr Top Med Chem 2023; 22:2396-2409. [PMID: 36330617 DOI: 10.2174/1568026623666221103091658] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 09/14/2022] [Accepted: 10/06/2022] [Indexed: 11/06/2022]
Abstract
The COVID-19 outbreak and the pandemic situation have hastened the research community to design a novel drug and vaccine against its causative organism, the SARS-CoV-2. The spike glycoprotein present on the surface of this pathogenic organism plays an immense role in viral entry and antigenicity. Hence, it is considered an important drug target in COVID-19 drug design. Several three-dimensional crystal structures of this SARS-CoV-2 spike protein have been identified and deposited in the Protein DataBank during the pandemic period. This accelerated the research in computer- aided drug designing, especially in the field of structure-based drug designing. This review summarizes various structure-based drug design approaches applied to this SARS-CoV-2 spike protein and its findings. Specifically, it is focused on different structure-based approaches such as molecular docking, high-throughput virtual screening, molecular dynamics simulation, drug repurposing, and target-based pharmacophore modelling and screening. These structural approaches have been applied to different ligands and datasets such as FDA-approved drugs, small molecular chemical compounds, chemical libraries, chemical databases, structural analogs, and natural compounds, which resulted in the prediction of spike inhibitors, spike-ACE-2 interface inhibitors, and allosteric inhibitors.
Collapse
Affiliation(s)
- Anusuya Shanmugam
- Department of Pharmaceutical Engineering, Vinayaka Mission's Kirupananda Variyar Engineering College, Vinayaka Mission's Research Foundation (Deemed to be University), Salem, 636308, Tamil Nadu, India.,Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology ,Madras, Chennai, 600036, Tamil Nadu, India
| | - Anbazhagan Venkattappan
- Department of Chemistry, Vinayaka Mission's Kirupananda Variyar Arts and Science College, Vinayaka Mission's Research Foundation (Deemed to be University), Salem, 636308, Tamil Nadu, India
| | - M Michael Gromiha
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology ,Madras, Chennai, 600036, Tamil Nadu, India
| |
Collapse
|
6
|
Liu X, Shi J, Wang D, Su Y, Xing Z, Sun F, Chen F. Therapeutic Polypeptides and Peptidomimetics: Powerful Tools for COVID-19 Treatment. Clin Drug Investig 2023; 43:13-22. [PMID: 36462104 PMCID: PMC9734822 DOI: 10.1007/s40261-022-01231-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/17/2022] [Indexed: 12/04/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has swept the whole world and brought about a public health crisis of unprecedented proportions. To combat the rapid transmission and possible deaths due to the disease, researchers and companies around the world are developing all possible strategies. Due to the advantages of safety, specificity, and fewer adverse effects, polypeptide and peptidomimetic drugs are considered promising strategies. This review comprehensively summarizes and discusses the progress in development of peptide drugs for use in the treatment of COVID-19. Based on the latest results in this field, we divided them into clinically approved drugs, clinical trial drugs, and clinically ineffective drugs, and outlined the molecular targets and mechanisms of action one by one to reveal their feasibility as promising therapeutic agents for COVID-19. Notably, monoclonal antibodies have shown beneficial effects in the early stages of infection, while Paxlovid can significantly reduce hospitalization and mortality among non-vaccinated patients. Among clinical experimental drugs, both the interleukin-1 receptor antagonist anakinra and the bradykinin B2 receptor antagonist icatibant are well tolerated and effective in patients with COVID-19, but long-term trials are needed to confirm the durability of efficacy.
Collapse
Affiliation(s)
- Xinyu Liu
- grid.449428.70000 0004 1797 7280Department of Physiology, Jining Medical University, 133 Hehua Rd, Jining, 272067 China
| | - Jian Shi
- grid.449428.70000 0004 1797 7280Department of Physiology, Jining Medical University, 133 Hehua Rd, Jining, 272067 China
| | - Deyang Wang
- grid.449428.70000 0004 1797 7280Department of Physiology, Jining Medical University, 133 Hehua Rd, Jining, 272067 China
| | - Ying Su
- grid.411634.50000 0004 0632 4559Dongping County People’s Hospital, Tai-an, China
| | - Zhen Xing
- grid.411634.50000 0004 0632 4559Dongping County People’s Hospital, Tai-an, China
| | - Fei Sun
- Qilu Medical University, Zibo, China
| | - Fei Chen
- grid.449428.70000 0004 1797 7280Department of Physiology, Jining Medical University, 133 Hehua Rd, Jining, 272067 China
| |
Collapse
|
7
|
Altiti A, He M, VanPatten S, Cheng KF, Ahmed U, Chiu PY, Mughrabi IT, Jabari BA, Burch RM, Manogue KR, Tracey KJ, Diamond B, Metz CN, Yang H, Hudson LK, Zanos S, Son M, Sherry B, Coleman TR, Al-Abed Y. Thiocarbazate building blocks enable the construction of azapeptides for rapid development of therapeutic candidates. Nat Commun 2022; 13:7127. [PMID: 36443291 PMCID: PMC9705435 DOI: 10.1038/s41467-022-34712-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 11/03/2022] [Indexed: 11/29/2022] Open
Abstract
Peptides, polymers of amino acids, comprise a vital and expanding therapeutic approach. Their rapid degradation by proteases, however, represents a major limitation to their therapeutic utility and chemical modifications to native peptides have been employed to mitigate this weakness. Herein, we describe functionalized thiocarbazate scaffolds as precursors of aza-amino acids, that, upon activation, can be integrated in a peptide sequence to generate azapeptides using conventional peptide synthetic methods. This methodology facilitates peptide editing-replacing targeted amino acid(s) with aza-amino acid(s) within a peptide-to form azapeptides with preferred therapeutic characteristics (extending half-life/bioavailability, while at the same time typically preserving structural features and biological activities). We demonstrate the convenience of this azapeptide synthesis platform in two well-studied peptides with short half-lives: FSSE/P5779, a tetrapeptide inhibitor of HMGB1/MD-2/TLR4 complex formation, and bradykinin, a nine-residue vasoactive peptide. This bench-stable thiocarbazate platform offers a robust and universal approach to optimize peptide-based therapeutics.
Collapse
Affiliation(s)
- Ahmad Altiti
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA.
| | - Mingzhu He
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Sonya VanPatten
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Kai Fan Cheng
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Umair Ahmed
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Pui Yan Chiu
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Ibrahim T Mughrabi
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Bayan Al Jabari
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | | | - Kirk R Manogue
- Center for Molecular Innovation, Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Kevin J Tracey
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Betty Diamond
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Christine N Metz
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Huan Yang
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - LaQueta K Hudson
- Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, Hempstead, NY, USA
| | - Stavros Zanos
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Myoungsun Son
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Barbara Sherry
- Institute of Molecular Medicine, Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Thomas R Coleman
- Center for Molecular Innovation, Feinstein Institutes for Medical Research, Manhasset, NY, USA
| | - Yousef Al-Abed
- Institute of Bioelectronic Medicine, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA.
- Center for Molecular Innovation, Feinstein Institutes for Medical Research, Manhasset, NY, USA.
| |
Collapse
|
8
|
Mousavi Maleki MS, Sardari S, Ghandehari Alavijeh A, Madanchi H. Recent Patents and FDA-Approved Drugs Based on Antiviral Peptides and Other Peptide-Related Antivirals. Int J Pept Res Ther 2022; 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.
Collapse
Affiliation(s)
| | - Soroush Sardari
- Drug Design and Bioinformatics Unit, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Ali Ghandehari Alavijeh
- Drug Design and Bioinformatics Unit, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| | - Hamid Madanchi
- Department of Medical Biotechnology, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
- Drug Design and Bioinformatics Unit, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
9
|
Chavda VP, Redwan EM. SARS-CoV-2: Immunopeptidomics and Other Immunological Studies. Vaccines (Basel) 2022; 10:vaccines10111975. [PMID: 36423070 PMCID: PMC9694091 DOI: 10.3390/vaccines10111975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 11/23/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has produced a significant continuing epidemic worldwide [...]
Collapse
Affiliation(s)
- Vivek P. Chavda
- Department of Pharmaceutics and Pharmaceutical Technology, L M College of Pharmacy, Ahmedabad 380008, India
- Correspondence: (V.P.C.); (E.M.R.); Tel.: +91-7030-919-407 (V.P.C.)
| | - Elrashdy M. Redwan
- Biological Science Department, Faculty of Science, King Abdulaziz University, P.O. Box 80203, Jeddah 21589, Saudi Arabia
- Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA City), Alexandria 21934, Egypt
- Correspondence: (V.P.C.); (E.M.R.); Tel.: +91-7030-919-407 (V.P.C.)
| |
Collapse
|
10
|
Ssenyange G, Kerfoot M, Zhao M, Farhadian S, Chen S, Peng L, Ren P, Dela Cruz CS, Gupta S, Sutton RE. Development of an efficient reproducible cell-cell transmission assay for rapid quantification of SARS-CoV-2 spike interaction with hACE2. CELL REPORTS METHODS 2022; 2:100252. [PMID: 35757815 PMCID: PMC9213030 DOI: 10.1016/j.crmeth.2022.100252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/28/2022] [Accepted: 06/14/2022] [Indexed: 06/15/2023]
Abstract
Efficient quantitative assays for measurement of viral replication and infectivity are indispensable for future endeavors to develop prophylactic or therapeutic antiviral drugs or vaccines against SARS-CoV-2. We developed a SARS-CoV-2 cell-cell transmission assay that provides a rapid and quantitative readout to assess SARS-CoV-2 spike hACE2 interaction in the absence of pseudotyped particles or live virus. We established two well-behaved stable cell lines, which demonstrated a remarkable correlation with standard cell-free viral pseudotyping for inhibition by convalescent sera, small-molecule drugs, and murine anti-spike monoclonal antibodies. The assay is rapid, reliable, and highly reproducible, without a requirement for any specialized research reagents or laboratory equipment and should be easy to adapt for use in most investigative and clinical settings. It can be effectively used or modified for high-throughput screening for compounds and biologics that interfere with virus-cell binding and entry to complement other neutralization assays currently in use.
Collapse
Affiliation(s)
- George Ssenyange
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06510, USA
| | - Maya Kerfoot
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06510, USA
| | - Min Zhao
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06510, USA
| | - Shelli Farhadian
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06510, USA
| | - Sidi Chen
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Lei Peng
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Ping Ren
- Department of Genetics, Yale School of Medicine, New Haven, CT 06510, USA
| | - Charles S. Dela Cruz
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Shaili Gupta
- Department of Medicine, Section of General Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Medicine, Veterans Affairs Healthcare Systems of Connecticut, West Haven, CT 06516, USA
| | - Richard E. Sutton
- Department of Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06510, USA
- Department of Medicine, Veterans Affairs Healthcare Systems of Connecticut, West Haven, CT 06516, USA
| |
Collapse
|
11
|
Krut' VG, Chuvpilo SA, Astrakhantseva IV, Kozlovskaya LI, Efimov GA, Kruglov AA, Drutskaya MS, Nedospasov SA. Will Peptides Help to Stop COVID-19? BIOCHEMISTRY (MOSCOW) 2022; 87:590-604. [PMID: 36154880 PMCID: PMC9282900 DOI: 10.1134/s0006297922070021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Peptides are widely used for the diagnostics, prevention, and therapy of certain human diseases. How useful can they be for the disease caused by the SARS-CoV-2 coronavirus? In this review, we discuss the possibility of using synthetic and recombinant peptides and polypeptides for prevention of COVID-19 via blocking the interaction between the virus and its main receptor ACE2, as well as components of antiviral vaccines, in particular, against new emerging virus variants.
Collapse
Affiliation(s)
- Viktoriya G Krut'
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
| | - Sergei A Chuvpilo
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
| | - Irina V Astrakhantseva
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
| | - Liubov I Kozlovskaya
- Chumakov Federal Scientific Center for Research and Development of Immunobiological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Institute of Translational Medicine and Biotechnology, Sechenov Moscow State Medical University, Moscow, 119991, Russia
| | - Grigory A Efimov
- National Medical Research Center of Hematology, Ministry of Health of the Russian Federation, Moscow, 125167, Russia
| | - Andrei A Kruglov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- German Rheumatism Research Center (DRFZ), Leibniz Institute, Berlin, 10117, Germany
| | - Marina S Drutskaya
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Sergei A Nedospasov
- Sirius University of Science and Technology, Federal Territory Sirius, Krasnodar Krai, 354340, Russia.
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Faculty of Biology, Lomonosov Moscow State University, Moscow, 119234, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 119991, Russia
| |
Collapse
|
12
|
Rational Discovery of Antiviral Whey Protein-Derived Small Peptides Targeting the SARS-CoV-2 Main Protease. Biomedicines 2022; 10:biomedicines10051067. [PMID: 35625804 PMCID: PMC9139167 DOI: 10.3390/biomedicines10051067] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 04/30/2022] [Accepted: 04/30/2022] [Indexed: 11/17/2022] Open
Abstract
In the present work, and for the first time, three whey protein-derived peptides (IAEK, IPAVF, MHI), endowed with ACE inhibitory activity, were examined for their antiviral activity against the SARS-CoV-2 3C-like protease (3CLpro) and Human Rhinovirus 3C protease (3Cpro) by employing molecular docking. Computational studies showed reliable binding poses within 3CLpro for the three investigated small peptides, considering docking scores as well as the binding free energy values. Validation by in vitro experiments confirmed these results. In particular, IPAVF exhibited the highest inhibitory activity by returning an IC50 equal to 1.21 μM; it was followed by IAEK, which registered an IC50 of 154.40 μM, whereas MHI was less active with an IC50 equal to 2700.62 μM. On the other hand, none of the assayed peptides registered inhibitory activity against 3Cpro. Based on these results, the herein presented small peptides are introduced as promising molecules to be exploited in the development of “target-specific antiviral” agents against SARS-CoV-2.
Collapse
|
13
|
Song L, Liu C, Tian G, Van Meervelt L, Van der Eycken J, Van der Eycken EV. Late-stage diversification of peptidomimetics and oligopeptides via gold-catalyzed post-Ugi cyclization. MOLECULAR CATALYSIS 2022. [DOI: 10.1016/j.mcat.2022.112240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
14
|
Zarei O, Kleine-Weber H, Hoffmann M, Hamzeh-Mivehroud M. Development and evaluation of peptidomimetic compounds against SARS-CoV-2 spike protein: an in silico and in vitro study. Mol Inform 2022; 41:e2100231. [PMID: 35068079 PMCID: PMC9015386 DOI: 10.1002/minf.202100231] [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] [Accepted: 01/16/2022] [Indexed: 11/08/2022]
Abstract
Background: Coronavirus disease 2019 (COVID‐19) as global pandemic disease has been adversely affecting public health and social life with considerable loss of human life worldwide. Therefore, there is an urgent need for developing novel therapeutics to combat COVID‐19. The causative agent of COVID‐19 is SARS‐CoV‐2 which targets human angiotensin converting enzyme 2 (ACE2) as cellular receptor via its spike (S) protein. In this context, interfering with the binding of SARS‐CoV‐2 S protein to target molecules could provide a promising strategy to find novel therapeutic agents against SARS‐CoV‐2. The purpose of the current study was to identify potential peptidomimetics against S protein with a combination of structure‐based virtual screening methods and in vitro assays. Methods: The candidates were inspected in terms of ADME properties, drug‐likeness, as well as toxicity profiles. Additionally, molecular docking and dynamics simulations were performed to predict binding of the studied ligands to spike protein. Results: Biological evaluation of the compounds revealed that PM2 molecule exhibits some antiviral activity. Conclusion: In summary, this study highlights the importance of combining in silico and in vitro techniques in order to identify antiviral compound to tackle COVID‐19 and presents a new scaffold that may be structurally optimized for improved antiviral activity.
Collapse
Affiliation(s)
- Omid Zarei
- Kurdistan University of Medical Sciences, IRAN (THE ISLAMIC REPUBLIC OF)
| | | | - Markus Hoffmann
- German Primate Centre Leibniz Institute for Primate Research, GERMANY
| | | |
Collapse
|
15
|
Ortega-Berlanga B, Pniewski T. Plant-Based Vaccines in Combat against Coronavirus Diseases. Vaccines (Basel) 2022; 10:138. [PMID: 35214597 PMCID: PMC8876659 DOI: 10.3390/vaccines10020138] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/06/2022] [Accepted: 01/14/2022] [Indexed: 02/07/2023] Open
Abstract
Coronavirus (CoV) diseases, including Middle East Respiratory Syndrome (MERS) and Severe Acute Respiratory Syndrome (SARS) have gained in importance worldwide, especially with the current COVID-19 pandemic caused by SARS-CoV-2. Due to the huge global demand, various types of vaccines have been developed, such as more traditional attenuated or inactivated viruses, subunit and VLP-based vaccines, as well as novel DNA and RNA vaccines. Nonetheless, emerging new COVID-19 variants are necessitating continuous research on vaccines, including these produced in plants, either via stable expression in transgenic or transplastomic plants or transient expression using viral vectors or agroinfection. Plant systems provide low cost, high scalability, safety and capacity to produce multimeric or glycosylated proteins. To date, from among CoVs antigens, spike and capsid proteins have been produced in plants, mostly using transient expression systems, at the additional advantage of rapid production. Immunogenicity of plant-produced CoVs proteins was positively evaluated after injection of purified antigens. However, this review indicates that plant-produced CoVs proteins or their carrier-fused immunodominant epitopes can be potentially applied also as mucosal vaccines, either after purification to be administered to particular membranes (nasal, bronchus mucosa) associated with the respiratory system, or as oral vaccines obtained from partly processed plant tissue.
Collapse
Affiliation(s)
- Benita Ortega-Berlanga
- Institute of Plant Genetics, Polish Academy of Sciences, Strzeszyńska 34, 60-479 Poznań, Poland;
| | | |
Collapse
|
16
|
Jawad B, Adhikari P, Cheng K, Podgornik R, Ching WY. Computational Design of Miniproteins as SARS-CoV-2 Therapeutic Inhibitors. Int J Mol Sci 2022; 23:838. [PMID: 35055023 PMCID: PMC8776159 DOI: 10.3390/ijms23020838] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/11/2022] [Accepted: 01/11/2022] [Indexed: 12/20/2022] Open
Abstract
A rational therapeutic strategy is urgently needed for combating SARS-CoV-2 infection. Viral infection initiates when the SARS-CoV-2 receptor-binding domain (RBD) binds to the ACE2 receptor, and thus, inhibiting RBD is a promising therapeutic for blocking viral entry. In this study, the structure of lead antiviral candidate binder (LCB1), which has three alpha-helices (H1, H2, and H3), is used as a template to design and simulate several miniprotein RBD inhibitors. LCB1 undergoes two modifications: structural modification by truncation of the H3 to reduce its size, followed by single and double amino acid substitutions to enhance its binding with RBD. We use molecular dynamics (MD) simulations supported by ab initio density functional theory (DFT) calculations. Complete binding profiles of all miniproteins with RBD have been determined. The MD investigations reveal that the H3 truncation results in a small inhibitor with a -1.5 kcal/mol tighter binding to RBD than original LCB1, while the best miniprotein with higher binding affinity involves D17R or E11V + D17R mutation. DFT calculations provide atomic-scale details on the role of hydrogen bonding and partial charge distribution in stabilizing the minibinder:RBD complex. This study provides insights into general principles for designing potential therapeutics for SARS-CoV-2.
Collapse
Affiliation(s)
- Bahaa Jawad
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (B.J.); (P.A.)
- Department of Applied Sciences, University of Technology, Baghdad 10066, Iraq
| | - Puja Adhikari
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (B.J.); (P.A.)
| | - Kun Cheng
- Division of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Missouri-Kansas City, Kansas City, MO 64108, USA;
| | - Rudolf Podgornik
- Wenzhou Institute of the University of Chinese Academy of Sciences, Wenzhou 325000, China;
- School of Physical Sciences and Kavli Institute of Theoretical Science, University of Chinese Academy of Sciences, Beijing 100049, China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100090, China
| | - Wai-Yim Ching
- Department of Physics and Astronomy, University of Missouri-Kansas City, Kansas City, MO 64110, USA; (B.J.); (P.A.)
| |
Collapse
|
17
|
Murugan C, Ramamoorthy S, Kuppuswamy G, Murugan RK, Sivalingam Y, Sundaramurthy A. COVID-19: A review of newly formed viral clades, pathophysiology, therapeutic strategies and current vaccination tasks. Int J Biol Macromol 2021; 193:1165-1200. [PMID: 34710479 PMCID: PMC8545698 DOI: 10.1016/j.ijbiomac.2021.10.144] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/17/2021] [Accepted: 10/19/2021] [Indexed: 02/07/2023]
Abstract
Today, the world population is facing an existential threat by an invisible enemy known as severe acute respiratory syndrome coronavirus 2 (SARS-COV-2) or COVID-19. It is highly contagious and has infected a larger fraction of human population across the globe on various routes of transmission. The detailed knowledge of the SARS-CoV-2 structure and clinical aspects offers an important insight into the evolution of infection, disease progression and helps in executing the different therapies effectively. Herein, we have discussed in detail about the genome structure of SARS-CoV-2 and its role in the proteomic rational spread of different muted species and pathogenesis in infecting the host cells. The mechanisms behind the viral outbreak and its immune response, the availability of existing diagnostics techniques, the treatment efficacy of repurposed drugs and the emerging vaccine trials for the SARS-CoV-2 outbreak also have been highlighted. Furthermore, the possible antiviral effects of various herbal products and their extracted molecules in inhibiting SARS-CoV-2 replication and cellular entry are also reported. Finally, we conclude our opinion on current challenges involved in the drug development, bulk production of drug/vaccines and their storage requirements, logistical procedures and limitations related to dosage trials for larger population.
Collapse
Affiliation(s)
- Chandran Murugan
- SRM Research Institute, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India
| | - Sharmiladevi Ramamoorthy
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India
| | - Guruprasad Kuppuswamy
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India
| | - Rajesh Kumar Murugan
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India
| | - Yuvaraj Sivalingam
- Department of Physics and Nanotechnology, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India
| | - Anandhakumar Sundaramurthy
- SRM Research Institute, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India; Department of Chemical Engineering, SRM Institute of Science and Technology, Chengalpattu 603203, Tamil Nadu, India.
| |
Collapse
|
18
|
Zheng M, Cong W, Peng H, Qing J, Shen H, Tang Y, Geng C, Chen S, Zou Y, Zhang WD, Hu HG, Li X. Stapled Peptides Targeting SARS-CoV-2 Spike Protein HR1 Inhibit the Fusion of Virus to Its Cell Receptor. J Med Chem 2021; 64:17486-17495. [PMID: 34818014 DOI: 10.1021/acs.jmedchem.1c01681] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The pandemic of acute respiratory disease in 2019 caused by highly pathogenic and infectious SARS-CoV-2 has seriously endangered human public safety. The 6-HB (HR1-HR2 complex) formation occurring in the process of spike protein-mediated membrane fusion could serve as a conserved and potential target for the design of fusion inhibitors. Based on the HR2 domain of 6-HB, we designed and synthesized 32 stapled peptides using an all-hydrocarbon peptide stapling strategy. Owing to the improved proteolytic stability and higher helical contents, the optimized stapled peptides termed SCH2-1-20 and SCH2-1-27 showed better inhibitory activities against pseudo and authentic SARS-CoV-2 compared to the linear counterpart. Of note, SCH2-1-20 and SCH2-1-27 were proved to interfere with S protein-mediated membrane fusion. Structural modeling indicated similar binding modes between SCH2-1-20 and the linear peptide. These optimized stapled peptides could serve as potent fusion inhibitors in treating and preventing SARS-CoV-2, and the corresponding SAR could facilitate further optimization.
Collapse
Affiliation(s)
- Mengjun Zheng
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Wei Cong
- Shanghai Engineering Research Center of Organ Repair, Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
| | - Haoran Peng
- Department of Microbiology, Second Military Medical University, Shanghai 200433, China
| | - Jie Qing
- Research Center of Integrated Traditional Chinese and Western Medicine, Affiliated Traditional Medicine Hospital, Southwest Medical University, Luzhou 646000, China
| | - Huaxing Shen
- Shanghai Engineering Research Center of Organ Repair, Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
| | - Yaxin Tang
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Chenchen Geng
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Si Chen
- School of Medicine, Shanghai University, Shanghai 200444, China
| | - Yan Zou
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Wei-Dong Zhang
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| | - Hong-Gang Hu
- Shanghai Engineering Research Center of Organ Repair, Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
| | - Xiang Li
- School of Pharmacy, Second Military Medical University, Shanghai 200433, China
| |
Collapse
|
19
|
Acharya A, Pandey K, Thurman M, Klug E, Trivedi J, Sharma K, Lorson CL, Singh K, Byrareddy SN. Discovery and Evaluation of Entry Inhibitors for SARS-CoV-2 and Its Emerging Variants. J Virol 2021; 95:e0143721. [PMID: 34550770 PMCID: PMC8610590 DOI: 10.1128/jvi.01437-21] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 09/18/2021] [Indexed: 11/20/2022] Open
Abstract
The outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the coronavirus disease 19 (COVID-19) pandemic. Despite unprecedented research and developmental efforts, SARS-CoV-2-specific antivirals are still unavailable for the treatment of COVID-19. In most instances, SARS-CoV-2 infection initiates with the binding of Spike glycoprotein to the host cell ACE2 receptor. Utilizing the crystal structure of the ACE2/Spike receptor-binding domain (S-RBD) complex (PDB file 6M0J) in a computer-aided drug design approach, we identified and validated five potential inhibitors of S-RBD and ACE-2 interaction. Two of the five compounds, MU-UNMC-1 and MU-UNMC-2, blocked the entry of pseudovirus particles expressing SARS-CoV-2 Spike glycoprotein. In live SARS-CoV-2 infection assays, both compounds showed antiviral activity with IC50 values in the micromolar range (MU-UNMC-1: IC50 = 0.67 μM and MU-UNMC-2: IC50 = 1.72 μM) in human bronchial epithelial cells. Furthermore, MU-UNMC-1 and MU-UNMC-2 effectively blocked the replication of rapidly transmitting variants of concern: South African variant B.1.351 (IC50 = 9.27 and 3.00 μM) and Scotland variant B.1.222 (IC50 = 2.64 and 1.39 μM), respectively. Following these assays, we conducted "induced-fit (flexible) docking" to understand the binding mode of MU-UNMC-1/MU-UNMC-2 at the S-RBD/ACE2 interface. Our data showed that mutation N501Y (present in B.1.351 variant) alters the binding mode of MU-UNMC-2 such that it is partially exposed to the solvent and has reduced polar contacts. Finally, MU-UNMC-2 displayed high synergy with remdesivir, the only approved drug for treating hospitalized COVID-19 patients. IMPORTANCE The ongoing coronavirus infectious disease 2019 (COVID-19) pandemic is caused by a novel coronavirus named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). More than 207 million people have been infected globally, and 4.3 million have died due to this viral outbreak. While a few vaccines have been deployed, a SARS-CoV-2-specific antiviral for the treatment of COVID-19 is yet to be approved. As the interaction of SARS-CoV-2 Spike protein with ACE2 is critical for cellular entry, using a combination of a computer-aided drug design (CADD) approach and cell-based in vitro assays, we report the identification of five potential SARS-CoV-2 entry inhibitors. Out of the five, two compounds (MU-UNMC-1 and MU-UNMC-2) have antiviral activity against ancestral SARS-CoV-2 and emerging variants from South Africa and Scotland. Furthermore, MU-UNMC-2 acts synergistically with remdesivir (RDV), suggesting that RDV and MU-UNMC-2 can be developed as a combination therapy to treat COVID-19 patients.
Collapse
Affiliation(s)
- Arpan Acharya
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Kabita Pandey
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Michellie Thurman
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Elizabeth Klug
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Jay Trivedi
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
| | - Kalicharan Sharma
- Delhi Pharmaceutical Sciences and Research University, New Delhi, India
| | - Christian L. Lorson
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, USA
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
| | - Kamal Singh
- Department of Veterinary Pathobiology, University of Missouri, Columbia, Missouri, USA
- Bond Life Sciences Center, University of Missouri, Columbia, Missouri, USA
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
| | - Siddappa N. Byrareddy
- Department of Pharmacology and Experimental Neuroscience, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institute, Stockholm, Sweden
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, Nebraska, USA
- Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, Nebraska, USA
| |
Collapse
|
20
|
Enzyme inhibition as a potential therapeutic strategy to treat COVID-19 infection. Bioorg Med Chem 2021; 48:116389. [PMID: 34543844 PMCID: PMC8448535 DOI: 10.1016/j.bmc.2021.116389] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 08/10/2021] [Accepted: 08/24/2021] [Indexed: 01/04/2023]
Abstract
With the emergence of the third infectious and virulent coronavirus within the past two decades, it has become increasingly important to understand how the virus causes infection. This will inform therapeutic strategies that target vulnerabilities in the vital processes through which the virus enters cells. This review identifies enzymes responsible for SARS-CoV-2 viral entry into cells (ACE2, Furin, TMPRSS2) and discuss compounds proposed to inhibit viral entry with the end goal of treating COVID-19 infection. We argue that TMPRSS2 inhibitors show the most promise in potentially treating COVID-19, in addition to being a pre-existing medication with fewer predicted side-effects.
Collapse
|
21
|
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.
Collapse
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.
| |
Collapse
|
22
|
Li C, Revote J, Ramarathinam SH, Chung SZ, Croft NP, Scull KE, Huang Z, Ayala R, Braun A, Mifsud NA, Illing PT, Faridi P, Purcell AW. Resourcing, annotating, and analysing synthetic peptides of SARS-CoV-2 for immunopeptidomics and other immunological studies. Proteomics 2021; 21:e2100036. [PMID: 33811468 PMCID: PMC8250278 DOI: 10.1002/pmic.202100036] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 03/15/2021] [Accepted: 03/15/2021] [Indexed: 12/27/2022]
Abstract
SARS-CoV-2 has caused a significant ongoing pandemic worldwide. A number of studies have examined the T cell mediated immune responses against SARS-CoV-2, identifying potential T cell epitopes derived from the SARS-CoV-2 proteome. Such studies will aid in identifying targets for vaccination and immune monitoring. In this study, we applied tandem mass spectrometry and proteomic techniques to a library of ∼40,000 synthetic peptides, in order to generate a large dataset of SARS-CoV-2 derived peptide MS/MS spectra. On this basis, we built an online knowledgebase, termed virusMS (https://virusms.erc.monash.edu/), to document, annotate and analyse these synthetic peptides and their spectral information. VirusMS incorporates a user-friendly interface to facilitate searching, browsing and downloading the database content. Detailed annotations of the peptides, including experimental information, peptide modifications, predicted peptide-HLA (human leukocyte antigen) binding affinities, and peptide MS/MS spectral data, are provided in virusMS.
Collapse
Affiliation(s)
- Chen Li
- Department of Biochemistry and Molecular Biology and Infection and Immunity ProgramMonash Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Jerico Revote
- Monash Bioinformatics PlatformMonash UniversityMelbourneVictoriaAustralia
| | - Sri H. Ramarathinam
- Department of Biochemistry and Molecular Biology and Infection and Immunity ProgramMonash Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Shan Zou Chung
- Department of Biochemistry and Molecular Biology and Infection and Immunity ProgramMonash Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Nathan P. Croft
- Department of Biochemistry and Molecular Biology and Infection and Immunity ProgramMonash Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Katherine E. Scull
- Department of Biochemistry and Molecular Biology and Infection and Immunity ProgramMonash Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Ziyi Huang
- Department of Biochemistry and Molecular Biology and Infection and Immunity ProgramMonash Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Rochelle Ayala
- Department of Biochemistry and Molecular Biology and Infection and Immunity ProgramMonash Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Asolina Braun
- Department of Biochemistry and Molecular Biology and Infection and Immunity ProgramMonash Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Nicole A. Mifsud
- Department of Biochemistry and Molecular Biology and Infection and Immunity ProgramMonash Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Patricia T. Illing
- Department of Biochemistry and Molecular Biology and Infection and Immunity ProgramMonash Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Pouya Faridi
- Department of Biochemistry and Molecular Biology and Infection and Immunity ProgramMonash Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| | - Anthony W. Purcell
- Department of Biochemistry and Molecular Biology and Infection and Immunity ProgramMonash Biomedicine Discovery InstituteMonash UniversityClaytonVictoriaAustralia
| |
Collapse
|
23
|
Naidoo D, Kar P, Roy A, Mutanda T, Bwapwa J, Sen A, Anandraj A. Structural Insight into the Binding of Cyanovirin-N with the Spike Glycoprotein, M pro and PL pro of SARS-CoV-2: Protein-Protein Interactions, Dynamics Simulations and Free Energy Calculations. Molecules 2021; 26:molecules26175114. [PMID: 34500548 PMCID: PMC8434238 DOI: 10.3390/molecules26175114] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 07/15/2021] [Accepted: 07/26/2021] [Indexed: 02/06/2023] Open
Abstract
The emergence of COVID-19 continues to pose severe threats to global public health. The pandemic has infected over 171 million people and claimed more than 3.5 million lives to date. We investigated the binding potential of antiviral cyanobacterial proteins including cyanovirin-N, scytovirin and phycocyanin with fundamental proteins involved in attachment and replication of SARS-CoV-2. Cyanovirin-N displayed the highest binding energy scores (−16.8 ± 0.02 kcal/mol, −12.3 ± 0.03 kcal/mol and −13.4 ± 0.02 kcal/mol, respectively) with the spike protein, the main protease (Mpro) and the papainlike protease (PLpro) of SARS-CoV-2. Cyanovirin-N was observed to interact with the crucial residues involved in the attachment of the human ACE2 receptor. Analysis of the binding affinities calculated employing the molecular mechanics-Poisson–Boltzmann surface area (MM-PBSA) approach revealed that all forms of energy, except the polar solvation energy, favourably contributed to the interactions of cyanovirin-N with the viral proteins. With particular emphasis on cyanovirin-N, the current work presents evidence for the potential inhibition of SARS-CoV-2 by cyanobacterial proteins, and offers the opportunity for in vitro and in vivo experiments to deploy the cyanobacterial proteins as valuable therapeutics against COVID-19.
Collapse
Affiliation(s)
- Devashan Naidoo
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
- Correspondence: (D.N.); (A.R.)
| | - Pallab Kar
- Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri 734013, India; (P.K.); (A.S.)
| | - Ayan Roy
- Department of Biotechnology, Lovely Professional University, Phagwara 144411, India
- Correspondence: (D.N.); (A.R.)
| | - Taurai Mutanda
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
| | - Joseph Bwapwa
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
| | - Arnab Sen
- Bioinformatics Facility, Department of Botany, University of North Bengal, Siliguri 734013, India; (P.K.); (A.S.)
| | - Akash Anandraj
- Centre for Algal Biotechnology, Mangosuthu University of Technology, P.O. Box 12363, Durban 4026, South Africa; (T.M.); (J.B.); (A.A.)
| |
Collapse
|
24
|
Zhu Y, Yu D, Hu Y, Wu T, Chong H, He Y. SARS-CoV-2-derived fusion inhibitor lipopeptides exhibit highly potent and broad-spectrum activity against divergent human coronaviruses. Signal Transduct Target Ther 2021; 6:294. [PMID: 34344868 PMCID: PMC8330190 DOI: 10.1038/s41392-021-00698-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Revised: 12/30/2020] [Accepted: 02/02/2021] [Indexed: 12/03/2022] Open
Affiliation(s)
- Yuanmei Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Danwei Yu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yue Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Tong Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Huihui Chong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yuxian He
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| |
Collapse
|
25
|
Sadremomtaz A, Al-Dahmani ZM, Ruiz-Moreno AJ, Monti A, Wang C, Azad T, Bell JC, Doti N, Velasco-Velázquez MA, de Jong D, de Jonge J, Smit J, Dömling A, van Goor H, Groves MR. Synthetic Peptides That Antagonize the Angiotensin-Converting Enzyme-2 (ACE-2) Interaction with SARS-CoV-2 Receptor Binding Spike Protein. J Med Chem 2021; 65:2836-2847. [PMID: 34328726 PMCID: PMC8353989 DOI: 10.1021/acs.jmedchem.1c00477] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
![]()
The SARS-CoV-2 viral
spike protein S receptor-binding domain (S-RBD)
binds ACE2 on host cells to initiate molecular events, resulting in
intracellular release of the viral genome. Therefore, antagonists
of this interaction could allow a modality for therapeutic intervention.
Peptides can inhibit the S-RBD:ACE2 interaction by interacting with
the protein–protein interface. In this study, protein contact
atlas data and molecular dynamics simulations were used to locate
interaction hotspots on the secondary structure elements α1,
α2, α3, β3, and β4 of ACE2. We designed a
library of discontinuous peptides based upon a combination of the
hotspot interactions, which were synthesized and screened in a bioluminescence-based
assay. The peptides demonstrated high efficacy in antagonizing the
SARS-CoV-2 S-RBD:ACE2 interaction and were validated by microscale
thermophoresis which demonstrated strong binding affinity (∼10
nM) of these peptides to S-RBD. We anticipate that such discontinuous
peptides may hold the potential for an efficient therapeutic treatment
for COVID-19.
Collapse
Affiliation(s)
- Afsaneh Sadremomtaz
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Zayana M Al-Dahmani
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands.,Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Angel J Ruiz-Moreno
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands.,Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de Mexico (UNAM), Ciudad de Mexico 04510, Mexico.,Unidad Periférica de Investigación en Biomedicina Translacional, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Félix Cuevas 540, Ciudad de Mexico 03229, Mexico.,Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de Mexico 04510, Mexico
| | - Alessandra Monti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Chao Wang
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Taha Azad
- Center for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, K1H 8L6 ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, K1H 8M5 ON, Canada
| | - John C Bell
- Center for Innovative Cancer Therapeutics, Ottawa Hospital Research Institute, Ottawa, K1H 8L6 ON, Canada.,Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, K1H 8M5 ON, Canada
| | - Nunzianna Doti
- Institute of Biostructures and Bioimaging (IBB)-CNR, Via Mezzocannone, 16, 80134 Napoli, Italy
| | - Marco A Velasco-Velázquez
- Departamento de Farmacología, Facultad de Medicina, Universidad Nacional Autónoma de Mexico (UNAM), Ciudad de Mexico 04510, Mexico.,Unidad Periférica de Investigación en Biomedicina Translacional, Facultad de Medicina, Universidad Nacional Autónoma de México (UNAM), Félix Cuevas 540, Ciudad de Mexico 03229, Mexico.,Doctorado en Ciencias Biomédicas, Universidad Nacional Autónoma de México (UNAM), Ciudad de Mexico 04510, Mexico
| | - Debora de Jong
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Jørgen de Jonge
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), 3720BA Bilthoven, The Netherlands
| | - Jolanda Smit
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Alexander Dömling
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| | - Harry van Goor
- Department of Medical Microbiology and Infection Prevention, University of Groningen, University Medical Center Groningen, 9700RB Groningen, The Netherlands
| | - Matthew R Groves
- XB20 Drug Design, Groningen Research Institute of Pharmacy, University of Groningen, 9700 AD Groningen, The Netherlands
| |
Collapse
|
26
|
Ramesh M, Anand K, Shahbaaz M, Abdellattif MH. Current Perspectives in the Discovery of Newer Medications Against the Outbreak of COVID-19. Front Mol Biosci 2021; 8:648232. [PMID: 34322517 PMCID: PMC8310954 DOI: 10.3389/fmolb.2021.648232] [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: 12/31/2020] [Accepted: 06/08/2021] [Indexed: 12/23/2022] Open
Abstract
A rapid and increasing spread of COVID-19 pandemic disease has been perceived worldwide in 2020. The current COVID-19 disease outbreak is due to the spread of SARS-CoV-2. SARS-CoV-2 is a new strain of coronavirus that has spike protein on the envelope. The spike protein of the virus binds with the ACE-2 receptor of the human lungs surface for entering into the host. Therefore, the blocking of viral entry into the host by targeting the spike protein has been suggested to be a valid strategy to treat COVID-19. The patients of COVID-19 were found to be asymptomatic, cold, mild to severe respiratory illness, and leading to death. The severe illness has been noted mainly in old age people, cardiovascular disease patients, and respiratory disease patients. However, the long-term health effects due to COVID-19 are not yet known. Recently, the vaccines were authorized to protect from COVID-19. However, the researchers have put an effort to discover suitable targets and newer medications in the form of small molecules or peptides, based on in-silico methods and synthetic approaches. This manuscript describes the current perspectives of the causative agent, diagnostic procedure, therapeutic targets, treatment, clinical trials, and development of potential clinical candidates of COVID-19. The study will be useful to identify the potential newer medications for the treatment of COVID-19.
Collapse
Affiliation(s)
- M. Ramesh
- Department of Pharmaceutical Analysis, Omega College of Pharmacy, Hyderabad, India
| | - Krishnan Anand
- Department of Chemical Pathology, School of Pathology, Faculty of Health Sciences and National Health Laboratory Service, University of the Free State, Bloemfontein, South Africa
| | - Mohd Shahbaaz
- South African Medical Research Council Bioinformatics Unit, South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa
| | - Magda H. Abdellattif
- Department of Chemistry, College of Science, Deanship of Scientific Research, Taif University, Taif, Saudi Arabia
| |
Collapse
|
27
|
In Silico Design of Peptide-Based SARS-CoV-2 Fusion Inhibitors That Target WT and Mutant Versions of SARS-CoV-2 HR1 Domains. BIOPHYSICA 2021. [DOI: 10.3390/biophysica1030023] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
In 2019, novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) began infecting humans, resulting in the COVID-19 pandemic. While the push for development of vaccines has yielded some positive results, the emergence of additional variants has led to concerns surrounding sustained vaccine effectiveness as the variants become the dominant strains. This work was undertaken to develop peptide-based antivirals capable of targeting both the wildtype (WT) heptad repeat 1 (HR1) domain of SARS-CoV-2 and the new HR1 variants which have developed. In silico protein mutagenesis, structural characterization, and protein–protein molecular docking were utilized to determine molecular interactions which facilitated binding of peptide-based antivirals targeting the HR1 domains. Molecular dynamics simulations were utilized to predict the final binding affinities of the top five peptide inhibitors designed. This work demonstrated the importance of hydrophobic interactions in the hydrophobic gorge and in the rim of the HR1 domain. Additionally, the placement of charged residues was shown to be essential in maximizing electrostatic interactions. The top five designed peptide inhibitors were all demonstrated to maintain good binding affinity to the WT and the variant HR1 SARS-CoV-2 domains. Therefore, the peptide inhibitors designed in this work could serve as potent antivirals which are effective in targeting both the original SARS-CoV-2 and the HR1 variants that have developed.
Collapse
|
28
|
Zhao M, Su PY, Castro DA, Tripler TN, Hu Y, Cook M, Ko AI, Farhadian SF, Israelow B, Dela Cruz CS, Xiong Y, Sutton RE. Rapid, reliable, and reproducible cell fusion assay to quantify SARS-Cov-2 spike interaction with hACE2. PLoS Pathog 2021; 17:e1009683. [PMID: 34166473 PMCID: PMC8263067 DOI: 10.1371/journal.ppat.1009683] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 07/07/2021] [Accepted: 06/02/2021] [Indexed: 12/13/2022] Open
Abstract
COVID-19 is a global crisis of unimagined dimensions. Currently, Remedesivir is only fully licensed FDA therapeutic. A major target of the vaccine effort is the SARS-CoV-2 spike-hACE2 interaction, and assessment of efficacy relies on time consuming neutralization assay. Here, we developed a cell fusion assay based upon spike-hACE2 interaction. The system was tested by transient co-transfection of 293T cells, which demonstrated good correlation with standard spike pseudotyping for inhibition by sera and biologics. Then established stable cell lines were very well behaved and gave even better correlation with pseudotyping results, after a short, overnight co-incubation. Results with the stable cell fusion assay also correlated well with those of a live virus assay. In summary we have established a rapid, reliable, and reproducible cell fusion assay that will serve to complement the other neutralization assays currently in use, is easy to implement in most laboratories, and may serve as the basis for high throughput screens to identify inhibitors of SARS-CoV-2 virus-cell binding and entry.
Collapse
Affiliation(s)
- Min Zhao
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Pei-Yi Su
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Danielle A. Castro
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Therese N. Tripler
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Yingxia Hu
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Matthew Cook
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Albert I. Ko
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, Connecticut, United States of America
| | - Shelli F. Farhadian
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Benjamin Israelow
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Charles S. Dela Cruz
- Department of Internal Medicine, Section of Pulmonary and Critical Care Medicine, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Yong Xiong
- Department of Molecular Biophysics and Biochemistry, Yale School of Medicine, New Haven, Connecticut, United States of America
| | - Richard E. Sutton
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, Connecticut, United States of America
| | | |
Collapse
|
29
|
Amaral JL, Oliveira JTA, Lopes FES, Freitas CDT, Freire VN, Abreu LV, Souza PFN. Quantum biochemistry, molecular docking, and dynamics simulation revealed synthetic peptides induced conformational changes affecting the topology of the catalytic site of SARS-CoV-2 main protease. J Biomol Struct Dyn 2021; 40:8925-8937. [PMID: 33949286 PMCID: PMC8108194 DOI: 10.1080/07391102.2021.1920464] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/16/2021] [Indexed: 02/07/2023]
Abstract
The recent outbreak caused by SARS-CoV-2 continues to threat and take many lives all over the world. The lack of an efficient pharmacological treatments are serious problems to be faced by scientists and medical staffs worldwide. In this work, an in silico approach based on the combination of molecular docking, dynamics simulations, and quantum biochemistry revealed that the synthetic peptides RcAlb-PepI, PepGAT, and PepKAA, strongly interact with the main protease (Mpro) a pivotal protein for SARS-CoV-2 replication. Although not binding to the proteolytic site of SARS-CoV-2 Mpro, RcAlb-PepI, PepGAT, and PepKAA interact with other protein domain and allosterically altered the protease topology. Indeed, such peptide-SARS-CoV-2 Mpro complexes provoked dramatic alterations in the three-dimensional structure of Mpro leading to area and volume shrinkage of the proteolytic site, which could affect the protease activity and thus the virus replication. Based on these findings, it is suggested that RcAlb-PepI, PepGAT, and PepKAA could interfere with SARS-CoV-2 Mpro role in vivo. Also, unlike other antiviral drugs, these peptides have no toxicity to human cells. This pioneering in silico investigation opens up opportunity for further in vivo research on these peptides, towards discovering new drugs and entirely new perspectives to treat COVID-19.Communicated by Ramaswamy H. Sarma.
Collapse
Affiliation(s)
- Jackson L. Amaral
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Jose T. A. Oliveira
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Francisco E. S. Lopes
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
- Center for Permanent Education in Health Care, CEATS/School of Public Health of Ceará-ESP-CE, Fortaleza, Brazil
| | - Cleverson D. T. Freitas
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Valder N. Freire
- Department of Physics, Federal University of Ceará, Fortaleza, Brazil
| | - Leonardo V. Abreu
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| | - Pedro F. N. Souza
- Department of Biochemistry and Molecular Biology, Federal University of Ceará, Fortaleza, Brazil
| |
Collapse
|
30
|
Citarella A, Scala A, Piperno A, Micale N. SARS-CoV-2 M pro: A Potential Target for Peptidomimetics and Small-Molecule Inhibitors. Biomolecules 2021; 11:607. [PMID: 33921886 PMCID: PMC8073203 DOI: 10.3390/biom11040607] [Citation(s) in RCA: 86] [Impact Index Per Article: 28.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/13/2021] [Accepted: 04/16/2021] [Indexed: 12/17/2022] Open
Abstract
The uncontrolled spread of the COVID-19 pandemic caused by the new coronavirus SARS-CoV-2 during 2020-2021 is one of the most devastating events in the history, with remarkable impacts on the health, economic systems, and habits of the entire world population. While some effective vaccines are nowadays approved and extensively administered, the long-term efficacy and safety of this line of intervention is constantly under debate as coronaviruses rapidly mutate and several SARS-CoV-2 variants have been already identified worldwide. Then, the WHO's main recommendations to prevent severe clinical complications by COVID-19 are still essentially based on social distancing and limitation of human interactions, therefore the identification of new target-based drugs became a priority. Several strategies have been proposed to counteract such viral infection, including the repurposing of FDA already approved for the treatment of HIV, HCV, and EBOLA, inter alia. Among the evaluated compounds, inhibitors of the main protease of the coronavirus (Mpro) are becoming more and more promising candidates. Mpro holds a pivotal role during the onset of the infection and its function is intimately related with the beginning of viral replication. The interruption of its catalytic activity could represent a relevant strategy for the development of anti-coronavirus drugs. SARS-CoV-2 Mpro is a peculiar cysteine protease of the coronavirus family, responsible for the replication and infectivity of the parasite. This review offers a detailed analysis of the repurposed drugs and the newly synthesized molecules developed to date for the treatment of COVID-19 which share the common feature of targeting SARS-CoV-2 Mpro, as well as a brief overview of the main enzymatic and cell-based assays to efficaciously screen such compounds.
Collapse
Affiliation(s)
| | | | | | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical, and Environmental Sciences, University of Messina, 98166 Messina, Italy; (A.C.); (A.S.); (A.P.)
| |
Collapse
|
31
|
Mousavi Maleki MS, Rostamian M, Madanchi H. Antimicrobial peptides and other peptide-like therapeutics as promising candidates to combat SARS-CoV-2. Expert Rev Anti Infect Ther 2021; 19:1205-1217. [PMID: 33844613 PMCID: PMC8054488 DOI: 10.1080/14787210.2021.1912593] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Introduction: There are currently no specific drugs and universal vaccines for Coronavirus disease 2019 (COVID-19), hence urgent effective measures are needed to discover and develop therapeutic agents. Applying peptide therapeutics and their related compounds is a promising strategy to achieve this goal. This review is written based on the literature search using several databases, previous studies, scientific reports, our current knowledge about the antimicrobial peptides (AMPs), and our personal analyses on the potential of the antiviral peptides for the treatment of COVID-19. Areas covered: In this review, we begin with a brief description of SARS-CoV2 followed by a comprehensive description of antiviral peptides (AVPs) including natural and synthetic AMPs or AVPs and peptidomimetics. Subsequently, the structural features, mechanisms of action, limitations, and therapeutic applications of these peptides are explained. Expert opinion: Regarding the lack and the limitations of drugs against COVID-19, AMPs, AVPs, and other peptide-like compounds such as peptidomimetics have captured the attention of researchers due to their potential antiviral activities. Some of these compounds comprise unique properties and have demonstrated the potential to fight SARS-CoV2, particularly melittin, lactoferrin, enfuvirtide, and rupintrivir that have the potential to enter animal and clinical trials for the treatment of COVID-19.
Collapse
Affiliation(s)
- Masoumeh Sadat Mousavi Maleki
- Department of Biotechnology and Biotechnology Research Center, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Mosayeb Rostamian
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Hamid Madanchi
- Department of Biotechnology and Biotechnology Research Center, School of Medicine, Semnan University of Medical Sciences, Semnan, Iran.,Drug Design and Bioinformatics Unit, Department of Medical Biotechnology, Biotechnology Research Center, Pasteur Institute of Iran, Tehran, Iran
| |
Collapse
|
32
|
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.
Collapse
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
| |
Collapse
|
33
|
Acharya A, Pandey K, Thurman M, Klug E, Trivedi J, Lorson CL, Singh K, Byrareddy SN. Discovery and in-vitro evaluation of potent SARS-CoV-2 entry inhibitors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 33821265 DOI: 10.1101/2021.04.02.438204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
SARS-CoV-2 infection initiates with the attachment of spike protein to the ACE2 receptor. While vaccines have been developed, no SARS-CoV-2 specific small molecule inhibitors have been approved. Herein, utilizing the crystal structure of the ACE2/Spike receptor binding domain (S-RBD) complex in computer-aided drug design (CADD) approach, we docked ∼8 million compounds within the pockets residing at S-RBD/ACE2 interface. Five best hits depending on the docking score, were selected and tested for their in vitro efficacy to block SARS-CoV-2 replication. Of these, two compounds (MU-UNMC-1 and MU-UNMC-2) blocked SARS-CoV-2 replication at sub-micromolar IC 50 in human bronchial epithelial cells (UNCN1T) and Vero cells. Furthermore, MU-UNMC-2 was highly potent in blocking the virus entry by using pseudoviral particles expressing SARS-CoV-2 spike. Finally, we found that MU-UNMC-2 is highly synergistic with remdesivir (RDV), suggesting that minimal amounts are needed when used in combination with RDV, and has the potential to develop as a potential entry inhibitor for COVID-19.
Collapse
|
34
|
Maas MN, Hintzen JCJ, Löffler PMG, Mecinović J. Targeting SARS-CoV-2 spike protein by stapled hACE2 peptides. Chem Commun (Camb) 2021; 57:3283-3286. [PMID: 33651072 DOI: 10.1039/d0cc08387a] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
SARS-CoV-2 Spike protein RBD interacts with the hACE2 receptor to initiate cell entry and infection. We set out to develop lactam-based i,i + 4 stapled hACE2 peptides targeting SARS-CoV-2. In vitro screening demonstrates the inhibition of the Spike protein RBD-hACE2 complex formation by the hACE221-55A36K-F40E stapled peptide (IC50: 3.6 μM, Kd: 2.1 μM), suggesting that hACE2 peptidomimetics could form the basis for the development of anti-COVID-19 therapeutics.
Collapse
Affiliation(s)
- Marijn N Maas
- University of Southern Denmark, Department of Physics, Chemistry and Pharmacy, Campusvej 55, 5230 Odense, Denmark.
| | | | | | | |
Collapse
|
35
|
Saadi S, Ghazali HM, Saari N, Abdulkarim SM. The structural reconformation of peptides in enhancing functional and therapeutic properties: Insights into their solid state crystallizations. Biophys Chem 2021; 273:106565. [PMID: 33780688 DOI: 10.1016/j.bpc.2021.106565] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 02/09/2021] [Accepted: 02/19/2021] [Indexed: 01/05/2023]
Abstract
Therapeutic peptides derived proteins with alpha-reconformation states like antibody shape have shown potential effects in combating terrible diseases linked with earlier signs of angiogensis, mutagenesis and transgenesis. Alpha reconformation in material design refers to the folding of the peptide chains and their transitions under reversible chemical bonds of disulfide chemical bridges and further non-covalence lesions. Thus, the rational design of signal peptides into alpha-helix is intended in increasing the defending effects of peptides into cores like adjuvant antibiotic and/or vaccines. Thereby, the signal peptides are able in displaying multiple eradicating regions by changing crystal-depositions and deviation angles. These types of molecular structures could have multiple advantages in tracing disease syndromes and impurities by increasing the host defense against the fates of pathogens and viruses, eventually leading to the loss in signaling by increasing peptide susceptibility levels to folding and unfolding and therefore, formation of transgenic peptide models. Alpha reconformation peptides is aimed in triggering as well as other regulatory functions such as remodulating metabolic chain disorders of lipolysis and glucolysis by increasing the insulin and leptin resistance for best lipid storages and lipoprotein density distributions.
Collapse
Affiliation(s)
- Sami Saadi
- Institut de la Nutrition, de l'Alimentation et des Technologies Agro-alimentaires INATAA 25017, Université Frères Mentouri, Constantine 1, Algeria; Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia.
| | - Hasanah Mohd Ghazali
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Nazamid Saari
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| | - Sabo Mohammed Abdulkarim
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, 43400 Serdang, Selangor, Malaysia
| |
Collapse
|
36
|
Ng KT, Mohd-Ismail NK, Tan YJ. Spike S2 Subunit: The Dark Horse in the Race for Prophylactic and Therapeutic Interventions against SARS-CoV-2. Vaccines (Basel) 2021; 9:178. [PMID: 33672450 PMCID: PMC7923282 DOI: 10.3390/vaccines9020178] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/15/2021] [Accepted: 02/18/2021] [Indexed: 11/16/2022] Open
Abstract
In the midst of the unceasing COVID-19 pandemic, the identification of immunogenic epitopes in the SARS-CoV-2 spike (S) glycoprotein plays a vital role in the advancement and development of intervention strategies. S is expressed on the exterior of the SARS-CoV-2 virion and contains two subunits, namely the N-terminal S1 and C-terminal S2. It is the key element for mediating viral entry as well as a crucial antigenic determinant capable of stimulating protective immune response through elicitation of anti-SARS-CoV-2 antibodies and activation of CD4+ and CD8+ cells in COVID-19 patients. Given that S2 is highly conserved in comparison to the S1, here, we provide a review of the latest findings on the SARS-CoV-2 S2 subunit and further discuss its potential as an attractive and promising target for the development of prophylactic vaccines and therapeutic agents against COVID-19.
Collapse
Affiliation(s)
- Kim Tien Ng
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; (K.T.N.); (N.K.M.-I.)
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Nur Khairiah Mohd-Ismail
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; (K.T.N.); (N.K.M.-I.)
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Yee-Joo Tan
- Infectious Diseases Translational Research Program, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore; (K.T.N.); (N.K.M.-I.)
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Institute of Molecular and Cell Biology (IMCB), A*STAR, Singapore 138673, Singapore
| |
Collapse
|
37
|
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.
Collapse
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.)
| |
Collapse
|
38
|
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.
Collapse
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
| | | |
Collapse
|
39
|
Wall H. Welcome to volume 13 of Future Medicinal Chemistry. Future Med Chem 2021; 13:1-3. [PMID: 33319591 DOI: 10.4155/fmc-2020-0338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- Harriet Wall
- Future Science Group, Unitec House, 2 Albert Place, London, N3 1QB, UK
| |
Collapse
|
40
|
Robson B. Techniques assisting peptide vaccine and peptidomimetic design. Sidechain exposure in the SARS-CoV-2 spike glycoprotein. Comput Biol Med 2020; 128:104124. [PMID: 33276271 PMCID: PMC7679524 DOI: 10.1016/j.compbiomed.2020.104124] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 11/06/2020] [Accepted: 11/11/2020] [Indexed: 01/15/2023]
Abstract
The aim of the present study is to discuss the design of peptide vaccines and peptidomimetics against SARS-COV-2, to develop and apply a method of protein structure analysis that is particularly appropriate to applying and discussing such design, and also to use that method to summarize some important features of the SARS-COV-2 spike protein sequence. A tool for assessing sidechain exposure in the SARS-CoV-2 spike glycoprotein is described. It extends to assessing accessibility of sidechains by considering several different three-dimensional structure determinations of SARS-CoV-2 and SARS-CoV-1 spike protein. The method is designed to be insensitive to a distance limit for counting neighboring atoms and the results are in good agreement with the physical chemical properties and exposure trends of the 20 naturally occurring sidechains. The spike protein sequence is analyzed with comment regarding exposable character. It includes studies of complexes with antibody elements and ACE2. These indicate changes in exposure at sites remote to those at which the antibody binds. They are of interest concerning design of synthetic peptide vaccines, and for peptidomimetics as a basis of drug discovery. The method was also developed in order to provide linear (one-dimensional) information that can be used along with other bioinformatics data of this kind in data mining and machine learning, potentially as genomic data regarding protein polymorphisms to be combined with more traditional clinical data. Bioinformatics studies are carried out on SARS-CoV-2 spike, studying solvent exposure. The methods are particularly suited for synthetic vaccines and d-amino acid peptidomimetics. Methods of generating d-amino acid peptidomimetics are described and reviewed. The effect of antibody binding in stabilizing loop conformation and exposing remote sites is noted.
Collapse
Affiliation(s)
- B Robson
- Ingine Inc. Cleveland Ohio USA and the Dirac Foundation, Oxfordshire, UK.
| |
Collapse
|
41
|
Diamond B, Volpe BT, VanPatten S, Al Abed Y. SARS-CoV-2 and interferon blockade. Mol Med 2020; 26:103. [PMID: 33167852 PMCID: PMC7652589 DOI: 10.1186/s10020-020-00231-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 10/22/2020] [Indexed: 01/08/2023] Open
Abstract
The response to viral infection generally includes an activation of the adaptive immune response to produce cytotoxic T cells and neutralizing antibodies. We propose that SARS-CoV-2 activates the innate immune system through the renin-angiotensin and kallikrein-bradykinin pathways, blocks interferon production and reduces an effective adaptive immune response. This model has therapeutic implications.
Collapse
Affiliation(s)
- Betty Diamond
- Center for Molecular Medicine, The Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY, 11030, USA
| | - Bruce T Volpe
- Center for Molecular Medicine, The Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY, 11030, USA.
| | - Sonya VanPatten
- Center for Bioelectronic Medicine, The Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY, 11030, USA
| | - Yousef Al Abed
- Center for Bioelectronic Medicine, The Feinstein Institute for Medical Research, 350 Community Drive, Manhasset, NY, 11030, USA
| |
Collapse
|
42
|
Wong FC, Ong JH, Chai TT. Identification of Putative Cell-entry-inhibitory Peptides against SARS-CoV-2 from Edible Insects: An in silico Study. EFOOD 2020. [DOI: 10.2991/efood.k.200918.002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
|