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Meng JR, Liu J, Fu L, Shu T, Yang L, Zhang X, Jiang ZH, Bai LP. Anti-Entry Activity of Natural Flavonoids against SARS-CoV-2 by Targeting Spike RBD. Viruses 2023; 15:160. [PMID: 36680200 PMCID: PMC9862759 DOI: 10.3390/v15010160] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
COVID-19 is still a global public health concern, and the SARS-CoV-2 mutations require more effective antiviral agents. In this study, the antiviral entry activity of thirty-one flavonoids was systematically evaluated by a SARS-CoV-2 pseudovirus model. Twenty-four flavonoids exhibited antiviral entry activity with IC50 values ranging from 10.27 to 172.63 µM and SI values ranging from 2.33 to 48.69. The structure-activity relationship of these flavonoids as SARS-CoV-2 entry inhibitors was comprehensively summarized. A subsequent biolayer interferometry assay indicated that flavonoids bind to viral spike RBD to block viral interaction with ACE2 receptor, and a molecular docking study also revealed that flavonols could bind to Pocket 3, the non-mutant regions of SARS-CoV-2 variants, suggesting that flavonols might be also active against virus variants. These natural flavonoids showed very low cytotoxic effects on human normal cell lines. Our findings suggested that natural flavonoids might be potential antiviral entry agents against SARS-CoV-2 via inactivating the viral spike. It is hoped that our study will provide some encouraging evidence for the use of natural flavonoids as disinfectants to prevent viral infections.
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Affiliation(s)
- Jie-Ru Meng
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau University of Science and Technology, Taipa 999078, China
| | - Jiazheng Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau University of Science and Technology, Taipa 999078, China
| | - Lu Fu
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau University of Science and Technology, Taipa 999078, China
| | - Tong Shu
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Lingzhi Yang
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Xueji Zhang
- School of Biomedical Engineering, Health Science Center, Shenzhen University, Shenzhen 518060, China
| | - Zhi-Hong Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau University of Science and Technology, Taipa 999078, China
| | - Li-Ping Bai
- State Key Laboratory of Quality Research in Chinese Medicine, Macau Institute for Applied Research in Medicine and Health, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau University of Science and Technology, Taipa 999078, China
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2
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Wang L, Li Z. Smart Nanostructured Materials for SARS-CoV-2 and Variants Prevention, Biosensing and Vaccination. Biosensors (Basel) 2022; 12:1129. [PMID: 36551096 PMCID: PMC9775677 DOI: 10.3390/bios12121129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/29/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has raised great concerns about human health globally. At the current stage, prevention and vaccination are still the most efficient ways to slow down the pandemic and to treat SARS-CoV-2 in various aspects. In this review, we summarize current progress and research activities in developing smart nanostructured materials for COVID-19 prevention, sensing, and vaccination. A few established concepts to prevent the spreading of SARS-CoV-2 and the variants of concerns (VOCs) are firstly reviewed, which emphasizes the importance of smart nanostructures in cutting the virus spreading chains. In the second part, we focus our discussion on the development of stimuli-responsive nanostructures for high-performance biosensing and detection of SARS-CoV-2 and VOCs. The use of nanostructures in developing effective and reliable vaccines for SARS-CoV-2 and VOCs will be introduced in the following section. In the conclusion, we summarize the current research focus on smart nanostructured materials for SARS-CoV-2 treatment. Some existing challenges are also provided, which need continuous efforts in creating smart nanostructured materials for coronavirus biosensing, treatment, and vaccination.
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Affiliation(s)
- Lifeng Wang
- Suzhou Ninth People’s Hospital, Suzhou Ninth Hospital Affiliated to Soochow University, Suzhou 215000, China
| | - Zhiwei Li
- Department of Chemistry, International Institute of Nanotechnology, Northwestern University, Evanston, IL 60208-3113, USA
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3
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Liu XH, Cheng T, Liu BY, Chi J, Shu T, Wang T. Structures of the SARS-CoV-2 spike glycoprotein and applications for novel drug development. Front Pharmacol 2022; 13:955648. [PMID: 36016554 PMCID: PMC9395726 DOI: 10.3389/fphar.2022.955648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022] Open
Abstract
COVID-19 caused by SARS-CoV-2 has raised a health crisis worldwide. The high morbidity and mortality associated with COVID-19 and the lack of effective drugs or vaccines for SARS-CoV-2 emphasize the urgent need for standard treatment and prophylaxis of COVID-19. The receptor-binding domain (RBD) of the glycosylated spike protein (S protein) is capable of binding to human angiotensin-converting enzyme 2 (hACE2) and initiating membrane fusion and virus entry. Hence, it is rational to inhibit the RBD activity of the S protein by blocking the RBD interaction with hACE2, which makes the glycosylated S protein a potential target for designing and developing antiviral agents. In this study, the molecular features of the S protein of SARS-CoV-2 are highlighted, such as the structures, functions, and interactions of the S protein and ACE2. Additionally, computational tools developed for the treatment of COVID-19 are provided, for example, algorithms, databases, and relevant programs. Finally, recent advances in the novel development of antivirals against the S protein are summarized, including screening of natural products, drug repurposing and rational design. This study is expected to provide novel insights for the efficient discovery of promising drug candidates against the S protein and contribute to the development of broad-spectrum anti-coronavirus drugs to fight against SARS-CoV-2.
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4
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Trezza A, Mugnaini C, Corelli F, Santucci A, Spiga O. In Silico Multi-Target Approach Revealed Potential Lead Compounds as Scaffold for the Synthesis of Chemical Analogues Targeting SARS-CoV-2. Biology 2022; 11:465. [PMID: 35336838 PMCID: PMC8945274 DOI: 10.3390/biology11030465] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/04/2022] [Accepted: 03/10/2022] [Indexed: 01/08/2023]
Abstract
Severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2) causes coronavirus disease 2019 (COVID-19), an infectious disease that spreads rapidly in humans. In March 2020, the World Health Organization (WHO) declared a COVID-19 pandemic. Identifying a multi-target-directed ligand approach would open up new opportunities for drug discovery to combat COVID-19. The aim of this work was to perform a virtual screening of an exclusive chemical library of about 1700 molecules containing both pharmacologically active compounds and synthetic intermediates to propose potential protein inhibitors for use against SARS-CoV-2. In silico analysis showed that our compounds triggered an interaction network with key residues of the SARS-CoV-2 spike protein (S-protein), blocking trimer formation and interaction with the human receptor hACE2, as well as with the main 3C-like protease (3CLpro), inhibiting their biological function. Our data may represent a step forward in the search for potential new chemotherapeutic agents for the treatment of COVID-19.
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5
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Malviya S, Parihar A, Parihar DS, Khan R. Natural products as a therapy to combat against SARS-CoV-2 virus infection. Computational Approaches for Novel Therapeutic and Diagnostic Designing to Mitigate SARS-CoV-2 Infection 2022. [PMCID: PMC9300459 DOI: 10.1016/b978-0-323-91172-6.00017-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
The novel coronavirus infection (COVID-19) first reported in December 2019, has become serious global life-threatening disease that has created huge health care crises. Despite huge number of clinical trials for drug and vaccine, only few successful candidates are in market, which led to problem of demand and supply. The low- and middle-income countries faces major health crisis due to financial issues. Studies to search plant originated natural bioactive molecules for prophylactic and therapeutic of COVID-19 infection has gained considerable attention, due to their low-cost, easy availability and lesser side effects. Natural products and herbal medicine have long been known for their role in treating respiratory infections and many of them have been approved/under trial as drugs or over-the-counter food additives to lessen the symptoms. It is undisputable fact that herbal/natural molecules’ medicine is still a promising resource and used as precursor for drug discovery to search prospective prophylactic candidate against COVID-19. These bioactive compounds bind with potential therapeutic target of SARS-COV-2 such as ACE II, Spike protein, TMPRESS, RdRp, Main proteases and endoribonuclease and may prevent or at least slow down the SARS-CoV-2 infection. Therefore, several numbers of clinical trials have registered to investigate the potentials of natural product to halt disease progression. The main aim of present chapter is to discuss the potential role of natural molecules which can be used as therapeutic drugs for treatment of COVID-19 and thus helpful to curb down the mortality rate.
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Chang CK, Lin SM, Satange R, Lin SC, Sun SC, Wu HY, Kehn-Hall K, Hou MH. Targeting protein-protein interaction interfaces in COVID-19 drug discovery. Comput Struct Biotechnol J 2021; 19:2246-2255. [PMID: 33936565 PMCID: PMC8064971 DOI: 10.1016/j.csbj.2021.04.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/30/2021] [Accepted: 04/01/2021] [Indexed: 02/06/2023] Open
Abstract
To date, the COVID-19 pandemic has claimed over 1 million human lives, infected another 50 million individuals and wreaked havoc on the global economy. The crisis has spurred the ongoing development of drugs targeting its etiological agent, the SARS-CoV-2. Targeting relevant protein-protein interaction interfaces (PPIIs) is a viable paradigm for the design of antiviral drugs and enriches the targetable chemical space by providing alternative targets for drug discovery. In this review, we will provide a comprehensive overview of the theory, methods and applications of PPII-targeted drug development towards COVID-19 based on recent literature. We will also highlight novel developments, such as the successful use of non-native protein-protein interactions as targets for antiviral drug screening. We hope that this review may serve as an entry point for those interested in applying PPIIs towards COVID-19 drug discovery and speed up drug development against the pandemic.
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Affiliation(s)
- Chung-Ke Chang
- Taiwan Biobank, Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan
| | - Shan-Meng Lin
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Roshan Satange
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | - Shih-Chao Lin
- Bachelor Degree Program in Marine Biotechnology, National Taiwan Ocean University, Keelung 20224, Taiwan
| | - Sin-Cih Sun
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Hung-Yi Wu
- Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung 40227, Taiwan
| | - Kylene Kehn-Hall
- Department of Biomedical Sciences & Pathobiology, Virginia-Maryland College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Virginia 24061, United States
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan.,Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
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7
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Freidel MR, Armen RS. Mapping major SARS-CoV-2 drug targets and assessment of druggability using computational fragment screening: Identification of an allosteric small-molecule binding site on the Nsp13 helicase. PLoS One 2021; 16:e0246181. [PMID: 33596235 DOI: 10.1371/journal.pone.0246181] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 01/14/2021] [Indexed: 01/18/2023] Open
Abstract
The 2019 emergence of, SARS-CoV-2 has tragically taken an immense toll on human life and far reaching impacts on society. There is a need to identify effective antivirals with diverse mechanisms of action in order to accelerate preclinical development. This study focused on five of the most established drug target proteins for direct acting small molecule antivirals: Nsp5 Main Protease, Nsp12 RNA-dependent RNA polymerase, Nsp13 Helicase, Nsp16 2'-O methyltransferase and the S2 subunit of the Spike protein. A workflow of solvent mapping and free energy calculations was used to identify and characterize favorable small-molecule binding sites for an aromatic pharmacophore (benzene). After identifying the most favorable sites, calculated ligand efficiencies were compared utilizing computational fragment screening. The most favorable sites overall were located on Nsp12 and Nsp16, whereas the most favorable sites for Nsp13 and S2 Spike had comparatively lower ligand efficiencies relative to Nsp12 and Nsp16. Utilizing fragment screening on numerous possible sites on Nsp13 helicase, we identified a favorable allosteric site on the N-terminal zinc binding domain (ZBD) that may be amenable to virtual or biophysical fragment screening efforts. Recent structural studies of the Nsp12:Nsp13 replication-transcription complex experimentally corroborates ligand binding at this site, which is revealed to be a functional Nsp8:Nsp13 protein-protein interaction site in the complex. Detailed structural analysis of Nsp13 ZBD conformations show the role of induced-fit flexibility in this ligand binding site and identify which conformational states are associated with efficient ligand binding. We hope that this map of over 200 possible small-molecule binding sites for these drug targets may be of use for ongoing discovery, design, and drug repurposing efforts. This information may be used to prioritize screening efforts or aid in the process of deciphering how a screening hit may bind to a specific target protein.
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8
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Hong J, Jhun H, Choi YO, Taitt AS, Bae S, Lee Y, Song CS, Yeom SC, Kim S. Structure of SARS-CoV-2 Spike Glycoprotein for Therapeutic and Preventive Target. Immune Netw 2021; 21:e8. [PMID: 33728101 PMCID: PMC7937506 DOI: 10.4110/in.2021.21.e8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/08/2021] [Accepted: 02/14/2021] [Indexed: 12/14/2022] Open
Abstract
The global crisis caused by the coronavirus disease 2019 (COVID-19) led to the most significant economic loss and human deaths after World War II. The pathogen causing this disease is a novel virus called the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). As of December 2020, there have been 80.2 million confirmed patients, and the mortality rate is known as 2.16% globally. A strategy to protect a host from SARS-CoV-2 is by suppressing intracellular viral replication or preventing viral entry. We focused on the spike glycoprotein that is responsible for the entry of SARS-CoV-2 into the host cell. Recently, the US Food and Drug Administration/EU Medicines Agency authorized a vaccine and antibody to treat COVID-19 patients by emergency use approval in the absence of long-term clinical trials. Both commercial and academic efforts to develop preventive and therapeutic agents continue all over the world. In this review, we present a perspective on current reports about the spike glycoprotein of SARS-CoV-2 as a therapeutic target.
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Affiliation(s)
- Jaewoo Hong
- Department of Physiology, Daegu Catholic University School of Medicine, Daegu 42472, Korea
- Laboratory of Cancer Immunometabolism, National Cancer Institute, Frederick, MD 21702, USA
| | - Hyunjhung Jhun
- Technical Assistance Center, Korea Food Research Institute, Wanju 55365, Korea
| | - Yeo-Ok Choi
- Laboratory of Cytokine Immunology, Department of Biomedical Science and Technology, Konkuk University, Seoul 05029, Korea
| | - Afeisha S. Taitt
- Laboratory of Cytokine Immunology, Department of Biomedical Science and Technology, Konkuk University, Seoul 05029, Korea
| | - Suyoung Bae
- Department of Bioequivalence Division for Drug Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Korea
| | - Youngmin Lee
- Department of Medicine, Pusan Paik Hospital, College of Medicine, Inje University, Busan 47392, Korea
| | - Chang-seon Song
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea
| | - Su Cheong Yeom
- Graduate School of International Agricultural Technology, Seoul National University, Pyeongchang 25354, Korea
| | - Soohyun Kim
- Laboratory of Cytokine Immunology, Department of Biomedical Science and Technology, Konkuk University, Seoul 05029, Korea
- College of Veterinary Medicine, Konkuk University, Seoul 05029, Korea
- Veterinary Science Research Institute, Konkuk University, Seoul 05029, Korea
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9
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Mouffouk C, Mouffouk S, Mouffouk S, Hambaba L, Haba H. Flavonols as potential antiviral drugs targeting SARS-CoV-2 proteases (3CL pro and PL pro), spike protein, RNA-dependent RNA polymerase (RdRp) and angiotensin-converting enzyme II receptor (ACE2). Eur J Pharmacol 2021; 891:173759. [PMID: 33249077 PMCID: PMC7691142 DOI: 10.1016/j.ejphar.2020.173759] [Citation(s) in RCA: 65] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 11/01/2020] [Accepted: 11/23/2020] [Indexed: 12/12/2022]
Abstract
The novel coronavirus outbreak (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) represents the actual greatest global public health crisis. The lack of efficacious drugs and vaccines against this viral infection created a challenge for scientific researchers in order to find effective solutions. One of the promising therapeutic approaches is the search for bioactive molecules with few side effects that display antiviral properties in natural sources like medicinal plants and vegetables. Several computational and experimental studies indicated that flavonoids especially flavonols and their derivatives constitute effective viral enzyme inhibitors and possess interesting antiviral activities. In this context, the present study reviews the efficacy of many dietary flavonols as potential antiviral drugs targeting the SARS-CoV-2 enzymes and proteins including Chymotrypsin-Like Protease (3CLpro), Papain Like protease (PLpro), Spike protein (S protein) and RNA-dependent RNA polymerase (RdRp), and also their ability to interact with the angiotensin-converting enzyme II (ACE2) receptor. The relationship between flavonol structures and their SARS-CoV-2 antiviral effects were discussed. On the other hand, the immunomodulatory, the anti-inflammatory and the antiviral effects of secondary metabolites from this class of flavonoids were reported. Also, their bioavailability limitations and toxicity were predicted.
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Affiliation(s)
- Chaima Mouffouk
- Faculty of Nature and Life Sciences, Department of Organisms, University of Batna 2, Algeria.
| | - Soumia Mouffouk
- Laboratory of Chemistry and Environmental Chemistry (L.C.C.E), Department of Chemistry, Faculty of Sciences of the Matter, University of Batna 1, 05000, Batna, Algeria
| | - Sara Mouffouk
- Faculty of Nature and Life Sciences, Department of Organisms, University of Batna 2, Algeria
| | - Leila Hambaba
- Faculty of Nature and Life Sciences, Department of Organisms, University of Batna 2, Algeria
| | - Hamada Haba
- Laboratory of Chemistry and Environmental Chemistry (L.C.C.E), Department of Chemistry, Faculty of Sciences of the Matter, University of Batna 1, 05000, Batna, Algeria
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de Almeida SMV, Santos Soares JC, Dos Santos KL, Alves JEF, Ribeiro AG, Jacob ÍTT, da Silva Ferreira CJ, Dos Santos JC, de Oliveira JF, de Carvalho Junior LB, de Lima MDCA. COVID-19 therapy: What weapons do we bring into battle? Bioorg Med Chem 2020; 28:115757. [PMID: 32992245 PMCID: PMC7481143 DOI: 10.1016/j.bmc.2020.115757] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 07/29/2020] [Accepted: 09/03/2020] [Indexed: 01/18/2023]
Abstract
Urgent treatments, in any modality, to fight SARS-CoV-2 infections are desired by society in general, by health professionals, by Estate-leaders and, mainly, by the scientific community, because one thing is certain amidst the numerous uncertainties regarding COVID-19: knowledge is the means to discover or to produce an effective treatment against this global disease. Scientists from several areas in the world are still committed to this mission, as shown by the accelerated scientific production in the first half of 2020 with over 25,000 published articles related to the new coronavirus. Three great lines of publications related to COVID-19 were identified for building this article: The first refers to knowledge production concerning the virus and pathophysiology of COVID-19; the second regards efforts to produce vaccines against SARS-CoV-2 at a speed without precedent in the history of science; the third comprehends the attempts to find a marketed drug that can be used to treat COVID-19 by drug repurposing. In this review, the drugs that have been repurposed so far are grouped according to their chemical class. Their structures will be presented to provide better understanding of their structural similarities and possible correlations with mechanisms of actions. This can help identifying anti-SARS-CoV-2 promising therapeutic agents.
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Affiliation(s)
- Sinara Mônica Vitalino de Almeida
- Laboratório de Biologia Molecular, Universidade de Pernambuco, Garanhuns, PE, Brazil; Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, PE, Brazil; Laboratório de Imunopatologia Keizo Asami (LIKA), Universidade Federal de Pernambuco, Recife, PE, Brazil.
| | - José Cleberson Santos Soares
- Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Keriolaine Lima Dos Santos
- Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | - Amélia Galdino Ribeiro
- Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | - Íris Trindade Tenório Jacob
- Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | | | - Jamerson Ferreira de Oliveira
- Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, PE, Brazil
| | | | - Maria do Carmo Alves de Lima
- Laboratório de Química e Inovação Terapêutica (LQIT) - Departamento de Antibióticos, Universidade Federal de Pernambuco, Recife, PE, Brazil
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11
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Rosell M, Fernández-Recio J. Docking-based identification of small-molecule binding sites at protein-protein interfaces. Comput Struct Biotechnol J 2020; 18:3750-3761. [PMID: 33250973 PMCID: PMC7679229 DOI: 10.1016/j.csbj.2020.11.029] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 12/19/2022] Open
Abstract
Protein-protein interactions play an essential role in many biological processes, and their perturbation is a major cause of disease. The use of small molecules to modulate them is attracting increased attention, but protein interfaces generally do not have clear cavities for binding small compounds. A proposed strategy is to target interface hot-spot residues, but their identification through computational approaches usually require the complex structure, which is not often available. In this context, pyDock energy-based docking and scoring can predict hot-spots on the unbound proteins, thus not requiring the complex structure. Here, we have devised a new strategy to detect protein–protein inhibitor binding sites, based on the integration of molecular dynamics for the generation of transient cavities, and docking-based interface hot-spot prediction for the selection of the suitable cavities. This integrative approach has been validated on a test set formed by protein–protein complexes with known inhibitors for which complete structural data of unbound molecules and complexes is available. The results show that local conformational sampling with short molecular dynamics can generate transient cavities similar to the known inhibitor binding sites, and that docking simulations can identify the best cavities with similar predictive accuracy as when knowing the real interface. In a few cases, these predicted pockets are shown to be suitable for protein–ligand docking. The proposed strategy will be useful for many protein–protein complexes for which there is no available structure, as long as the the unbound proteins do not deviate dramatically from the bound conformations.
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Affiliation(s)
- Mireia Rosell
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de La Rioja, Gobierno de La Rioja, Logroño, Spain
| | - Juan Fernández-Recio
- Barcelona Supercomputing Center (BSC), Barcelona, Spain.,Instituto de Ciencias de la Vid y del Vino (ICVV), CSIC - Universidad de La Rioja, Gobierno de La Rioja, Logroño, Spain
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12
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Abstract
The coronavirus disease of 2019 (COVID-19) has caused an unprecedented global crisis. The etiological agent is a new virus called the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2). As of October, 2020 there have been 45.4 million confirmed cases with a mortality rate of 2.6% globally. With the lack of a vaccine and effective treatments, the race is on to find a cure for the virus infection using specific antivirals. The viral RNA-dependent RNA polymerase, proteases, spike protein-host angiotensin-converting enzyme 2 binding and fusion have presented as attractive targets for pan-coronavirus and broad spectrum direct-acting antivirals (DAAs). This review presents a perspective on current re-purposing treatments and future DAAs.
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13
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Abstract
The current outbreak of SARS-CoV-2 virus has caused a large increase in mortality and morbidity associated with respiratory diseases. Huge efforts are currently ongoing to develop a vaccine against this virus. However, alternative approaches could be considered in the fight against this disease. Among other strategies, structural-based drug design could be an effective approach to generate specific molecules against SARS-CoV-2, thus reducing viral burden in infected patients. Here, in addition to this structural approach, we also revise several therapeutic strategies to fight against this viral threat. Furthermore, we report ACE-2 genetic polymorphic variants affecting residues involved in close contacts with SARS-CoV-2 that might be associated to different infection risks. These analyses could provide valuable information to predict the course of the disease.
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Affiliation(s)
- Elena Cabezón
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
| | - Ignacio Arechaga
- Instituto de Biomedicina y Biotecnología de Cantabria (IBBTEC), Universidad de Cantabria-CSIC, Santander, Spain
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Trezza A, Iovinelli D, Santucci A, Prischi F, Spiga O. An integrated drug repurposing strategy for the rapid identification of potential SARS-CoV-2 viral inhibitors. Sci Rep 2020; 10:13866. [PMID: 32807895 PMCID: PMC7431416 DOI: 10.1038/s41598-020-70863-9] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Accepted: 07/31/2020] [Indexed: 12/23/2022] Open
Abstract
The Coronavirus disease 2019 (COVID-19) is an infectious disease caused by the severe acute respiratory syndrome-coronavirus 2 (SARS-CoV-2). The virus has rapidly spread in humans, causing the ongoing Coronavirus pandemic. Recent studies have shown that, similarly to SARS-CoV, SARS-CoV-2 utilises the Spike glycoprotein on the envelope to recognise and bind the human receptor ACE2. This event initiates the fusion of viral and host cell membranes and then the viral entry into the host cell. Despite several ongoing clinical studies, there are currently no approved vaccines or drugs that specifically target SARS-CoV-2. Until an effective vaccine is available, repurposing FDA approved drugs could significantly shorten the time and reduce the cost compared to de novo drug discovery. In this study we attempted to overcome the limitation of in silico virtual screening by applying a robust in silico drug repurposing strategy. We combined and integrated docking simulations, with molecular dynamics (MD), Supervised MD (SuMD) and Steered MD (SMD) simulations to identify a Spike protein - ACE2 interaction inhibitor. Our data showed that Simeprevir and Lumacaftor bind the receptor-binding domain of the Spike protein with high affinity and prevent ACE2 interaction.
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Affiliation(s)
- Alfonso Trezza
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100, Siena, Italy
| | - Daniele Iovinelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100, Siena, Italy
| | - Annalisa Santucci
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100, Siena, Italy
| | - Filippo Prischi
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK.
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, 53100, Siena, Italy.
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Trigueiro-Louro J, Correia V, Figueiredo-Nunes I, Gíria M, Rebelo-de-Andrade H. Unlocking COVID therapeutic targets: A structure-based rationale against SARS-CoV-2, SARS-CoV and MERS-CoV Spike. Comput Struct Biotechnol J 2020; 18:2117-2131. [PMID: 32913581 PMCID: PMC7452956 DOI: 10.1016/j.csbj.2020.07.017] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/20/2020] [Accepted: 07/22/2020] [Indexed: 12/11/2022] Open
Abstract
There are no approved target therapeutics against SARS-CoV-2 or other beta-CoVs. The beta-CoV Spike protein is a promising target considering the critical role in viral infection and pathogenesis and its surface exposed features. We performed a structure-based strategy targeting highly conserved druggable regions resulting from a comprehensive large-scale sequence analysis and structural characterization of Spike domains across SARSr- and MERSr-CoVs. We have disclosed 28 main consensus druggable pockets within the Spike. The RBD and SD1 (S1 subunit); and the CR, HR1 and CH (S2 subunit) represent the most promising conserved druggable regions. Additionally, we have identified 181 new potential hot spot residues for the hSARSr-CoVs and 72 new hot spot residues for the SARSr- and MERSr-CoVs, which have not been described before in the literature. These sites/residues exhibit advantageous structural features for targeted molecular and pharmacological modulation. This study establishes the Spike as a promising anti-CoV target using an approach with a potential higher resilience to resistance development and directed to a broad spectrum of Beta-CoVs, including the new SARS-CoV-2 responsible for COVID-19. This research also provides a structure-based rationale for the design and discovery of chemical inhibitors, antibodies or other therapeutic modalities successfully targeting the Beta-CoV Spike protein.
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Key Words
- ACE2, angiotensin-converting enzyme2
- Bat-SL-CoVs, bat SARS-like coronavirus
- Beta-CoVs, betacoronavirus
- Betacoronavirus
- CC, conserved cluster
- CD, connector domain
- CDP, consensus druggable pocket
- CDR, consensus druggable residue
- CH, central helix
- CP, cytoplasmic domain
- CR, connecting region
- CS, conservation score
- CoVs, coronavirus
- Coronavirus disease
- DGSS, DoGSiteScorer
- DPP4, dipeptidyl peptidase-4
- Druggability prediction
- FP, fusion peptide
- HR1, heptad repeat 1
- HR2, heptad repeat 2
- MERS-CoVs, middle east respiratory syndrome coronavirus
- MERSr-CoVs, middle east respiratory syndrome-related coronavirus
- MSA, multiple sequence alignment
- NTD, N-terminal domain
- Novel antiviral targets
- PDB, Protein Data Bank
- PDS, PockDrug-Server
- RBD, Receptor-Binding Domain
- S, Spike
- SARS-CoV-2
- SARS-CoV-2, severe acute respiratory syndrome coronavirus 2
- SARS-CoVs, severe acute respiratory syndrome coronavirus
- SARSr-CoVs, severe acute respiratory syndrome-related coronavirus
- SD1, subdomain 1
- SD2, subdomain 2
- SF, SiteFinder from MOE
- SP, small pocket
- Sequence conservation
- Spike protein
- Sv, shorter variant
- T-RHS, top-ranked hot spots
- TMPRSS2, transmembrane protease serine 2
- aa, amino acid
- hSARSr-CoVs, human Severe acute respiratory syndrome-related coronavirus
- nts, nucleotides
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Affiliation(s)
- João Trigueiro-Louro
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016 Lisbon, Portugal
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
| | - Vanessa Correia
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016 Lisbon, Portugal
| | - Inês Figueiredo-Nunes
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
| | - Marta Gíria
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
| | - Helena Rebelo-de-Andrade
- Antiviral Resistance Lab, Research & Development Unit, Infectious Diseases Department, Instituto Nacional de Saúde Doutor Ricardo Jorge, IP, Av. Padre Cruz, 1649-016 Lisbon, Portugal
- Host-Pathogen Interaction Unit, Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Av. Professor Gama Pinto, 1649-003 Lisbon, Portugal
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