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Cao C, Mehmood A, Li D. Molecular dynamic simulation reveals spider antimicrobial peptide Latarcin-1 and human eosinophil cationic protein as peptide inhibitors of SARS-CoV-2 variants. J Biomol Struct Dyn 2024; 42:5858-5868. [PMID: 37938133 DOI: 10.1080/07391102.2023.2274514] [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: 12/06/2022] [Accepted: 06/17/2023] [Indexed: 11/09/2023]
Abstract
COVID-19 has rapidly proliferated around 180 countries, and new cases are reported frequently. No peptide medication has been developed that can reliably block SARS-CoV-2 infection. The investigation focuses on the crucial host receptors angiotensin-converting enzyme 2 (ACE2) , which can bind receptor-binding domain (RBD) on the SARS-CoV-2 spike protein (S). To investigate the inhibitory effects of human Eosinophil Cationic Protein (hECP) and Latarcin-1 (L1)on SARS-CoV-2 infection, we have selected them as research subjects. Further, we ran extensive molecular dynamics simulations to bring the docked peptide-ACE2 complex into its equilibrium state. The outcomes were then evaluated with g_MMPBSA and interaction analysis. We have also considered the Delta and Omicron variants to examine these peptides' inhibitory effects. The experimental findings revealed an enhanced capability of L1 and hECP as SARS-CoV-2 inhibitors, occupying hot spots and numerous key residues in ACE2. These include ASP30, ASP38, GLU35 and GLU75, which significantly inhibit the binding of RBD and ACE2 and are effective against two common variants in a similar manner. In addition, this study can serve as a springboard for future research on SARS-CoV-2 inhibitors.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Cheng Cao
- Institute of Biothermal Science and Technology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, P.R. China
- AI Research Center, Peng Cheng Laboratory, Shenzhen, Guangdong, P.R. China
| | - Aamir Mehmood
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, P.R. China
| | - Daixi Li
- Institute of Biothermal Science and Technology, School of Health Science and Engineering, University of Shanghai for Science and Technology, Shanghai, P.R. China
- AI Research Center, Peng Cheng Laboratory, Shenzhen, Guangdong, P.R. China
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Yang ZS, Li TS, Huang YS, Chang CC, Chien CM. Targeting the receptor binding domain and heparan sulfate binding for antiviral drug development against SARS-CoV-2 variants. Sci Rep 2024; 14:2753. [PMID: 38307890 PMCID: PMC10837157 DOI: 10.1038/s41598-024-53111-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 01/27/2024] [Indexed: 02/04/2024] Open
Abstract
The emergence of SARS-CoV-2 variants diminished the efficacy of current antiviral drugs and vaccines. Hence, identifying highly conserved sequences and potentially druggable pockets for drug development was a promising strategy against SARS-CoV-2 variants. In viral infection, the receptor-binding domain (RBD) proteins are essential in binding to the host receptor. Others, Heparan sulfate (HS), widely distributed on the surface of host cells, is thought to play a central role in the viral infection cycle of SARS-CoV-2. Therefore, it might be a reasonable strategy for antiviral drug design to interfere with the RBD in the HS binding site. In this study, we used computational approaches to analyze multiple sequences of coronaviruses and reveal important information about the binding of HS to RBD in the SARS-CoV-2 spike protein. Our results showed that the potential hot-spots, including R454 and E471, in RBD, exhibited strong interactions in the HS-RBD binding region. Therefore, we screened different compounds in the natural product database towards these hot-spots to find potential antiviral candidates using LibDock, Autodock vina and furthermore applying the MD simulation in AMBER20. The results showed three potential natural compounds, including Acetoside (ACE), Hyperoside (HYP), and Isoquercitrin (ISO), had a strong affinity to the RBD. Our results demonstrate a feasible approach to identify potential antiviral agents by evaluating the binding interaction between viral glycoproteins and host receptors. The present study provided the applications of the structure-based computational approach for designing and developing of new antiviral drugs against SARS-CoV-2 variants.
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Affiliation(s)
- Zi-Sin Yang
- Department of Medical Sciences Industry, College of Health Sciences, Chang Jung Christian University, Tainan, 711, Taiwan
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Tzong-Shiun Li
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Taichung, 402, Taiwan
- Department of Plastic Surgery, Chang Bing Show Chwan Memorial Hospital, Changhua, 500, Taiwan
| | - Yu-Sung Huang
- Institute of Bioinformatics and Structural Biology, National Tsing Hua University, Hsinchu, 300, Taiwan
| | - Cheng-Chung Chang
- Graduate Institute of Biomedical Engineering, National Chung Hsing University, Taichung, 402, Taiwan
| | - Ching-Ming Chien
- Department of Medical Sciences Industry, College of Health Sciences, Chang Jung Christian University, Tainan, 711, Taiwan.
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Pathak RK, Kim JM. Identification of histidine kinase inhibitors through screening of natural compounds to combat mastitis caused by Streptococcus agalactiae in dairy cattle. J Biol Eng 2023; 17:59. [PMID: 37752501 PMCID: PMC10523694 DOI: 10.1186/s13036-023-00378-0] [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: 06/14/2023] [Accepted: 09/18/2023] [Indexed: 09/28/2023] Open
Abstract
BACKGROUND Mastitis poses a major threat to dairy farms globally; it results in reduced milk production, increased treatment costs, untimely compromised genetic potential, animal deaths, and economic losses. Streptococcus agalactiae is a highly virulent bacteria that cause mastitis. The administration of antibiotics for the treatment of this infection is not advised due to concerns about the emergence of antibiotic resistance and potential adverse effects on human health. Thus, there is a critical need to identify new therapeutic approaches to combat mastitis. One promising target for the development of antibacterial therapies is the transmembrane histidine kinase of bacteria, which plays a key role in signal transduction pathways, secretion systems, virulence, and antibiotic resistance. RESULTS In this study, we aimed to identify novel natural compounds that can inhibit transmembrane histidine kinase. To achieve this goal, we conducted a virtual screening of 224,205 natural compounds, selecting the top ten based on their lowest binding energy and favorable protein-ligand interactions. Furthermore, molecular docking of eight selected antibiotics and five histidine kinase inhibitors with transmembrane histidine kinase was performed to evaluate the binding energy with respect to top-screened natural compounds. We also analyzed the ADMET properties of these compounds to assess their drug-likeness. The top two compounds (ZINC000085569031 and ZINC000257435291) and top-screened antibiotics (Tetracycline) that demonstrated a strong binding affinity were subjected to molecular dynamics simulations (100 ns), free energy landscape, and binding free energy calculations using the MM-PBSA method. CONCLUSION Our results suggest that the selected natural compounds have the potential to serve as effective inhibitors of transmembrane histidine kinase and can be utilized for the development of novel antibacterial veterinary medicine for mastitis after further validation through clinical studies.
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Affiliation(s)
- Rajesh Kumar Pathak
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong-si, Gyeonggi-do, 17546, Republic of Korea.
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Singh U, Gandhi HA, Bhattacharya J, Tandon R, Tiwari GL, Tandon R. Cyanometabolites: molecules with immense antiviral potential. Arch Microbiol 2023; 205:164. [PMID: 37012452 PMCID: PMC10069739 DOI: 10.1007/s00203-023-03514-y] [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: 01/26/2023] [Revised: 03/22/2023] [Accepted: 03/23/2023] [Indexed: 04/05/2023]
Abstract
Cyanometabolites are active compounds derived from cyanobacteria that include small low molecular weight peptides, oligosaccharides, lectins, phenols, fatty acids, and alkaloids. Some of these compounds may pose a threat to human and environment. However, majority of them are known to have various health benefits with antiviral properties against pathogenic viruses including Human immunodeficiency virus (HIV), Ebola virus (EBOV), Herpes simplex virus (HSV), Influenza A virus (IAV) etc. Cyanometabolites classified as lectins include scytovirin (SVN), Oscillatoria agardhii agglutinin (OAAH), cyanovirin-N (CV-N), Microcystis viridis lectin (MVL), and microvirin (MVN) also possess a potent antiviral activity against viral diseases with unique properties to recognize different viral epitopes. Studies showed that a small linear peptide, microginin FR1, isolated from a water bloom of Microcystis species, inhibits angiotensin-converting enzyme (ACE), making it useful for the treatment of coronavirus disease 2019 (COVID-19). Our review provides an overview of the antiviral properties of cyanobacteria from the late 90s till now and emphasizes the significance of their metabolites in combating viral diseases, particularly severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has received limited attention in previous publications. The enormous medicinal potential of cyanobacteria is also emphasized in this review, which justifies their use as a dietary supplement to fend off pandemics in future.
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Affiliation(s)
- Uma Singh
- Department of Botany, University of Allahabad, Prayagraj, 211002, India
| | - Harsh A Gandhi
- Nanobiotechnology Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Jaydeep Bhattacharya
- Nanobiotechnology Laboratory, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - Ravi Tandon
- Laboratory of AIDS Research and Immunology, School of Biotechnology, Jawaharlal Nehru University, New Delhi, 110067, India
| | - G L Tiwari
- Department of Botany, University of Allahabad, Prayagraj, 211002, India
| | - Richa Tandon
- Department of Botany, S. S. Khanna Girls Degree College, University of Allahabad, Prayagraj, 211003, India.
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Muñoz-Basagoiti J, Monteiro FLL, Krumpe LRH, Armario-Najera V, Shenoy SR, Perez-Zsolt D, Westgarth HJ, Villorbina G, Bomfim LM, Raïch-Regué D, Nogueras L, Henrich CJ, Gallemí M, Moreira FRR, Torres P, Wilson J, D’arc M, Marfil S, Herlinger AL, Pradenas E, Higa LM, Portero-Otin M, Trinité B, Twyman RM, Capell T, Tanuri A, Blanco J, Izquierdo-Useros N, Rech EL, Christou P, O’Keefe BR. Cyanovirin-N binds to select SARS-CoV-2 spike oligosaccharides outside of the receptor binding domain and blocks infection by SARS-CoV-2. Proc Natl Acad Sci U S A 2023; 120:e2214561120. [PMID: 36853940 PMCID: PMC10013841 DOI: 10.1073/pnas.2214561120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 01/12/2023] [Indexed: 03/01/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped positive stranded RNA virus which has caused the recent deadly pandemic called COVID-19. The SARS-CoV-2 virion is coated with a heavily glycosylated Spike glycoprotein which is responsible for attachment and entry into target cells. One, as yet unexploited strategy for preventing SARS-CoV-2 infections, is the targeting of the glycans on Spike. Lectins are carbohydrate-binding proteins produced by plants, algae, and cyanobacteria. Some lectins can neutralize enveloped viruses displaying external glycoproteins, offering an alternative therapeutic approach for the prevention of infection with virulent β-coronaviruses, such as SARS-CoV-2. Here we show that the cyanobacterial lectin cyanovirin-N (CV-N) can selectively target SARS-CoV-2 Spike oligosaccharides and inhibit SARS-CoV-2 infection in vitro and in vivo. CV-N neutralizes Delta and Omicron variants in vitro better than earlier circulating viral variants. CV-N binds selectively to Spike with a Kd as low as 15 nM and a stoichiometry of 2 CV-N: 1 Spike but does not bind to the receptor binding domain (RBD). Further mapping of CV-N binding sites on Spike shows that select high-mannose oligosaccharides in the S1 domain of Spike are targeted by CV-N. CV-N also reduced viral loads in the nares and lungs in vivo to protect hamsters against a lethal viral challenge. In summary, we present an anti-coronavirus agent that works by an unexploited mechanism and prevents infection by a broad range of SARS-CoV-2 strains.
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Affiliation(s)
| | - Fábio Luís Lima Monteiro
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Lauren R. H. Krumpe
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute-Frederick, NIH, Frederick, MD21702
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD21702
| | - Victoria Armario-Najera
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio Center, Lleida25198, Spain
| | - Shilpa R. Shenoy
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute-Frederick, NIH, Frederick, MD21702
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD21702
| | - Daniel Perez-Zsolt
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
| | - Harrison James Westgarth
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Gemma Villorbina
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio Center, Lleida25198, Spain
| | - Larissa Maciel Bomfim
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Dàlia Raïch-Regué
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
| | - Lara Nogueras
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio Center, Lleida25198, Spain
| | - Curtis J. Henrich
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute-Frederick, NIH, Frederick, MD21702
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD21702
| | - Marçal Gallemí
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
| | - Filipe Romero Rebello Moreira
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Pascual Torres
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio Center, Lleida25198, Spain
| | - Jennifer Wilson
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute-Frederick, NIH, Frederick, MD21702
- Basic Science Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD21702
| | - Mirela D’arc
- Laboratory of Diversity and Viral Diseases, Institute of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Silvia Marfil
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
| | - Alice Laschuk Herlinger
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Edwards Pradenas
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
| | - Luiza Mendonça Higa
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Manuel Portero-Otin
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio Center, Lleida25198, Spain
| | - Benjamin Trinité
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
| | | | - Teresa Capell
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio Center, Lleida25198, Spain
| | - Amilcar Tanuri
- Laboratory of Molecular Virology, Institute of Biology, Department of Genetics, Federal University of Rio de Janeiro, Rio de Janeiro21941-90, Brazil
| | - Julià Blanco
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
- Germans Trias i Pujol Research Institute, Badalona08916, Spain
- Centro de Investigación Biomédica en Red Enfermedades Infecciosas, Madrid28029, Spain
- Universitat de Vic - Universitat Central de Catalunya, Vic08500, Spain
| | - Nuria Izquierdo-Useros
- IrsiCaixa Acquired Immune Deficiency Syndrome Research Institute, Badalona08916, Spain
- Germans Trias i Pujol Research Institute, Badalona08916, Spain
- Centro de Investigación Biomédica en Red Enfermedades Infecciosas, Madrid28029, Spain
| | - Elibio L. Rech
- Embrapa Genetic Resources and Biotechnology National Institute of Science and Technology in Synthetic Biology, Brasília70770-917, Brazil
| | - Paul Christou
- Department of Crop and Forest Sciences, University of Lleida-Agrotecnio Center, Lleida25198, Spain
- ICREA, Catalan Institute for Research and Advanced Studies, Barcelona08010, Spain
| | - Barry R. O’Keefe
- Molecular Targets Program, Center for Cancer Research, National Cancer Institute-Frederick, NIH, Frederick, MD21702
- Natural Products Branch, Developmental Therapeutics Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Frederick, MD21702
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