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Ullah A, Ullah S, Halim SA, Waqas M, Ali B, Ataya FS, El-Sabbagh NM, Batiha GES, Avula SK, Csuk R, Khan A, Al-Harrasi A. Identification of new pharmacophore against SARS-CoV-2 spike protein by multi-fold computational and biochemical techniques. Sci Rep 2024; 14:3590. [PMID: 38351259 PMCID: PMC10864406 DOI: 10.1038/s41598-024-53911-6] [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: 08/06/2023] [Accepted: 02/06/2024] [Indexed: 02/16/2024] Open
Abstract
COVID-19 appeared as a highly contagious disease after its outbreak in December 2019 by the virus, named SARS-CoV-2. The threat, which originated in Wuhan, China, swiftly became an international emergency. Among different genomic products, spike protein of virus plays a crucial role in the initiation of the infection by binding to the human lung cells, therefore, SARS-CoV-2's spike protein is a promising therapeutic target. Using a combination of a structure-based virtual screening and biochemical assay, this study seeks possible therapeutic candidates that specifically target the viral spike protein. A database of ~ 850 naturally derived compounds was screened against SARS-CoV-2 spike protein to find natural inhibitors. Using virtual screening and inhibitory experiments, we identified acetyl 11-keto-boswellic acid (AKBA) as a promising molecule for spike protein, which encouraged us to scan the rest of AKBA derivatives in our in-house database via 2D-similarity searching. Later 19 compounds with > 85% similarity with AKBA were selected and docked with receptor binding domain (RBD) of spike protein. Those hits declared significant interactions at the RBD interface, best possess and excellent drug-likeness and pharmacokinetics properties with high gastrointestinal absorption (GIA) without toxicity and allergenicity. Our in-silico observations were eventually validated by in vitro bioassay, interestingly, 10 compounds (A3, A4, C3, C6A, C6B, C6C, C6E, C6H, C6I, and C6J) displayed significant inhibitory ability with good percent inhibition (range: > 72-90). The compounds C3 (90.00%), C6E (91.00%), C6C (87.20%), and C6D (86.23%) demonstrated excellent anti-SARS CoV-2 spike protein activities. The docking interaction of high percent inhibition of inhibitor compounds C3 and C6E was confirmed by MD Simulation. In the molecular dynamics simulation, we observed the stable dynamics of spike protein inhibitor complexes and the influence of inhibitor binding on the protein's conformational arrangements. The binding free energy ΔGTOTAL of C3 (-38.0 ± 0.08 kcal/mol) and C6E (-41.98 ± 0.08 kcal/mol) respectively indicate a strong binding affinity to Spike protein active pocket. These findings demonstrate that these molecules particularly inhibit the function of spike protein and, therefore have the potential to be evaluated as drug candidates against SARS-CoV-2.
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Affiliation(s)
- Atta Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Saeed Ullah
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Sobia Ahsan Halim
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Muhammad Waqas
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Basharat Ali
- Sulaiman Bin Abdullah Aba Al-Khail-Centre for Interdisciplinary Research in Basic Sciences (SA-CIRBS), International Islamic University, Islamabad, Pakistan
| | - Farid S Ataya
- Department of Biochemistry, College of Science, King Saud University, PO Box 2455, 11451, Riyadh, Saudi Arabia
| | - Nasser M El-Sabbagh
- Department of Veterinary Pharmacology, Faculty of Veterinary Medicine, Alexandria University, Edfina, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, AlBeheira, Egypt
| | - Satya Kumar Avula
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman
| | - Rene Csuk
- Organic Chemistry, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 2, 06120, Halle (Saale), Germany
| | - Ajmal Khan
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman.
| | - Ahmed Al-Harrasi
- Natural and Medical Sciences Research Center, University of Nizwa, Birkat-Ul-Mouz, P.O Box 33, Postal Code 616, Nizwa, Sultanate of Oman.
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2
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Amin FG, Elfiky AA, Nassar AM. In silico targeting of SARS-CoV-2 spike receptor-binding domain from different variants with chaga mushroom terpenoids. J Biomol Struct Dyn 2024; 42:1079-1087. [PMID: 37042960 DOI: 10.1080/07391102.2023.2199084] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/30/2023] [Indexed: 04/13/2023]
Abstract
Terpenoids from the chaga mushroom have been identified as potential antiviral agents against SARS-CoV-2. This is because it can firmly bind to the viral spike receptor binding domain (RBD) and the auxiliary host cell receptor glucose-regulated protein 78 (GRP78). The current work examines the association of the chaga mushroom terpenoids with the RBD of various SARS-CoV-2 variants, including alpha, beta, gamma, delta, and omicron. This association was compared to the SARS-CoV-2 wild-type (WT) RBD using molecular docking analysis and molecular dynamics modeling. The outcomes demonstrated that the mutant RBDs, which had marginally greater average binding affinities (better binding) than the WT, were successfully inhibited by the chaga mushroom terpenoids. The results suggest that the chaga mushroom can be effective against various SARS-CoV-2 variants by targeting both the host-cell surface receptor GRP78 and the viral spike RBD.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fatma G Amin
- Physics Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Abdo A Elfiky
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
| | - Aaya M Nassar
- Biophysics Department, Faculty of Science, Cairo University, Giza, Egypt
- Department of Clinical Research and Leadership, School of Medicine and Health Sciences, George Washington University, Washington, DC, USA
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3
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He P, Xia K, Song Y, Tandon R, Channappanavar R, Zhang F, Linhardt RJ. Synthesis of multivalent sialyllactose-conjugated PAMAM dendrimers: Binding to SARS-CoV-2 spike protein and influenza hemagglutinin. Int J Biol Macromol 2023; 246:125714. [PMID: 37423440 PMCID: PMC10528195 DOI: 10.1016/j.ijbiomac.2023.125714] [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: 03/06/2023] [Revised: 06/05/2023] [Accepted: 07/04/2023] [Indexed: 07/11/2023]
Abstract
Severe acute respiratory syndrome-related coronavirus-2 (SARS-CoV-2) and influenza viruses have spread around the world at an unprecedented rate. Despite multiple vaccines, new variants of SARS-CoV-2 and influenza have caused a remarkable level of pathogenesis. The development of effective antiviral drugs to treat SARS-CoV-2 and influenza remains a high priority. Inhibiting viral cell surface attachment represents an early and efficient means to block virus infection. Sialyl glycoconjugates, on the surface of human cell membranes, play an important role as host cell receptors for influenza A virus and 9-O-acetyl-sialylated glycoconjugates are receptors for MERS, HKU1 and bovine coronaviruses. We designed and synthesized multivalent 6'-sialyllactose-counjugated polyamidoamine dendrimers through click chemistry at room temperature concisely. These dendrimer derivatives have good solubility and stability in aqueous solutions. SPR, a real-time analysis quantitative method for of biomolecular interactions, was used to study the binding affinities of our dendrimer derivatives by utilizing only 200 micrograms of each dendrimer. Three SARS-CoV-2 S-protein receptor binding domain (wild type and two Omicron mutants) bound to multivalent 9-O-acetyl-6'-sialyllactose-counjugated and 6'-sialyllactose-counjugated dendrimers bound to a single H3N2 influenza A virus's HA protein (A/Hong Kong/1/1968), the SPR study results suggest their potential anti-viral activities.
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Affiliation(s)
- Peng He
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Ke Xia
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Yuefan Song
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA
| | - Ritesh Tandon
- Center for Immunology and Microbial Research, Department of Cell Biology, Medicine and BioMolecular Sciences, University of Mississippi Medical Center, Jackson, MS, USA
| | - Rudra Channappanavar
- Department of Veterinary Pathobiology, Oklahoma Center for Respiratory and Infectious Diseases (OCRID), Oklahoma State University, Stillwater, OK, USA
| | - Fuming Zhang
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
| | - Robert J Linhardt
- Department of Chemistry and Chemical Biology, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY 12180, USA; Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY 12180, USA.
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Ganesh S, Dhinakaran AK, Premnath P, Venkatakrishnan K, Tan B. Label-Free Saliva Test for Rapid Detection of Coronavirus Using Nanosensor-Enabled SERS. Bioengineering (Basel) 2023; 10:bioengineering10030391. [PMID: 36978782 PMCID: PMC10045265 DOI: 10.3390/bioengineering10030391] [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: 02/07/2023] [Revised: 03/14/2023] [Accepted: 03/19/2023] [Indexed: 03/30/2023] Open
Abstract
The recent COVID-19 pandemic has highlighted the inadequacies of existing diagnostic techniques and the need for rapid and accurate diagnostic systems. Although molecular tests such as RT-PCR are the gold standard, they cannot be employed as point-of-care testing systems. Hence, a rapid, noninvasive diagnostic technique such as Surface-enhanced Raman scattering (SERS) is a promising analytical technique for rapid molecular or viral diagnosis. Here, we have designed a SERS- based test to rapidly diagnose SARS-CoV-2 from saliva. Physical methods synthesized the nanostructured sensor. It significantly increased the detection specificity and sensitivity by ~ten copies/mL of viral RNA (~femtomolar concentration of nucleic acids). Our technique combines the multiplexing capability of SERS with the sensitivity of novel nanostructures to detect whole virus particles and infection-associated antibodies. We have demonstrated the feasibility of the test with saliva samples from individuals who tested positive for SARS-CoV-2 with a specificity of 95%. The SERS-based test provides a promising breakthrough in detecting potential mutations that may come up with time while also preparing the world to deal with other pandemics in the future with rapid response and very accurate results.
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Affiliation(s)
- Swarna Ganesh
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Department of Mechanical and Industrial Engineering, Toronto Metropolitan University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
| | - Ashok Kumar Dhinakaran
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Department of Mechanical and Industrial Engineering, Toronto Metropolitan University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
| | - Priyatha Premnath
- Department of biomedical engineering, College of Engineering and Applied Sciences, University of Wisconsin, Milwaukee, WI 53211, USA
| | - Krishnan Venkatakrishnan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
- Ultrashort Laser Nanomanufacturing Research Facility, Department of Mechanical and Industrial Engineering, Toronto Metropolitan University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
| | - Bo Tan
- Keenan Research Center for Biomedical Science, Unity Health Toronto, Toronto, ON M5B 1W8, Canada
- Institute for Biomedical Engineering, Science and Technology (I BEST), Partnership between Toronto Metropolitan University and St. Michael's Hospital, Toronto, ON M5B 1W8, Canada
- Nanocharacterization Laboratory, Department of Aerospace Engineering, Toronto Metropolitan University, 350 Victoria Street, Toronto, ON M5B 2K3, Canada
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Santaniello A, Perruolo G, Cristiano S, Agognon AL, Cabaro S, Amato A, Dipineto L, Borrelli L, Formisano P, Fioretti A, Oriente F. SARS-CoV-2 Affects Both Humans and Animals: What Is the Potential Transmission Risk? A Literature Review. Microorganisms 2023; 11:microorganisms11020514. [PMID: 36838479 PMCID: PMC9959838 DOI: 10.3390/microorganisms11020514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 02/14/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
In March 2020, the World Health Organization Department declared the coronavirus (COVID-19) outbreak a global pandemic, as a consequence of its rapid spread on all continents. The COVID-19 pandemic has been not only a health emergency but also a serious general problem as fear of contagion and severe restrictions put economic and social activity on hold in many countries. Considering the close link between human and animal health, COVID-19 might infect wild and companion animals, and spawn dangerous viral mutants that could jump back and pose an ulterior threat to us. The purpose of this review is to provide an overview of the pandemic, with a particular focus on the clinical manifestations in humans and animals, the different diagnosis methods, the potential transmission risks, and their potential direct impact on the human-animal relationship.
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Affiliation(s)
- Antonio Santaniello
- Department of Veterinary Medicine and Animal Production, Federico II University of Naples, 80134 Naples, Italy
- Correspondence: (A.S.); (S.C.); Tel.: +39-081-253-6134 (A.S.)
| | - Giuseppe Perruolo
- Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy
| | - Serena Cristiano
- Department of Veterinary Medicine and Animal Production, Federico II University of Naples, 80134 Naples, Italy
- Correspondence: (A.S.); (S.C.); Tel.: +39-081-253-6134 (A.S.)
| | - Ayewa Lawoe Agognon
- Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy
| | - Serena Cabaro
- Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy
| | - Alessia Amato
- Department of Veterinary Medicine and Animal Production, Federico II University of Naples, 80134 Naples, Italy
| | - Ludovico Dipineto
- Department of Veterinary Medicine and Animal Production, Federico II University of Naples, 80134 Naples, Italy
| | - Luca Borrelli
- Department of Veterinary Medicine and Animal Production, Federico II University of Naples, 80134 Naples, Italy
| | - Pietro Formisano
- Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy
| | - Alessandro Fioretti
- Department of Veterinary Medicine and Animal Production, Federico II University of Naples, 80134 Naples, Italy
| | - Francesco Oriente
- Department of Translational Medical Sciences, Federico II University of Naples, 80131 Naples, Italy
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Sharma P, Kumar M, Tripathi MK, Gupta D, Vishwakarma P, Das U, Kaur P. Genomic and structural mechanistic insight to reveal the differential infectivity of omicron and other variants of concern. Comput Biol Med 2022; 150:106129. [PMID: 36195045 PMCID: PMC9493144 DOI: 10.1016/j.compbiomed.2022.106129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 09/04/2022] [Accepted: 09/18/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND The genome of SARS-CoV-2, is mutating rapidly and continuously challenging the management and preventive measures adopted and recommended by healthcare agencies. The spike protein is the main antigenic site that binds to the host receptor hACE-2 and is recognised by antibodies. Hence, the mutations in this site were analysed to assess their role in differential infectivity of lineages having these mutations, rendering the characterisation of these lineages as variants of concern (VOC) and variants of interest (VOI). METHODS In this work, we examined the genome sequence of SARS-CoV-2 VOCs and their phylogenetic relationships with the other PANGOLIN lineages. The mutational landscape of WHO characterized variants was determined and mutational diversity was compared amongst the different severity groups. We then computationally studied the structural impact of the mutations in receptor binding domain of the VOCs. The binding affinity was quantitatively determined by molecular dynamics simulations and free energy calculations. RESULTS The mutational frequency, as well as phylogenetic distance, was maximum in the case of omicron followed by the delta variant. The maximum binding affinity was for delta variant followed by the Omicron variant. The increased binding affinity of delta strain followed by omicron as compared to other variants and wild type advocates high transmissibility and quick spread of these two variants and high severity of delta variant. CONCLUSION This study delivers a foundation for discovering the improved binding knacks and structural features of SARS-CoV-2 variants to plan novel therapeutics and vaccine candidates against the virus.
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Affiliation(s)
- Priyanka Sharma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Manish Kumar Tripathi
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Deepali Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Poorvi Vishwakarma
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Uddipan Das
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, India.
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Amman BR, Cossaboom CM, Wendling NM, Harvey RR, Rettler H, Taylor D, Kainulainen MH, Ahmad A, Bunkley P, Godino C, Tong S, Li Y, Uehara A, Kelleher A, Zhang J, Lynch B, Behravesh CB, Towner JS. GPS Tracking of Free-Roaming Cats ( Felis catus) on SARS-CoV-2-Infected Mink Farms in Utah. Viruses 2022; 14:2131. [PMID: 36298686 PMCID: PMC9611678 DOI: 10.3390/v14102131] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/19/2022] [Accepted: 09/23/2022] [Indexed: 11/20/2022] Open
Abstract
Zoonotic transmission of SARS-CoV-2 from infected humans to other animals has been documented around the world, most notably in mink farming operations in Europe and the United States. Outbreaks of SARS-CoV-2 on Utah mink farms began in late July 2020 and resulted in high mink mortality. An investigation of these outbreaks revealed active and past SARS-CoV-2 infections in free-roaming and in feral cats living on or near several mink farms. Cats were captured using live traps, were sampled, fitted with GPS collars, and released on the farms. GPS tracking of these cats show they made frequent visits to mink sheds, moved freely around the affected farms, and visited surrounding residential properties and neighborhoods on multiple occasions, making them potential low risk vectors of additional SARS-CoV-2 spread in local communities.
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Affiliation(s)
- Brian R. Amman
- Centers for Disease Control and Prevention, 1600 Clifton Road Ne, Atlanta, GA 30329, USA
| | - Caitlin M. Cossaboom
- Centers for Disease Control and Prevention, 1600 Clifton Road Ne, Atlanta, GA 30329, USA
| | - Natalie M. Wendling
- Centers for Disease Control and Prevention, 1600 Clifton Road Ne, Atlanta, GA 30329, USA
| | - R. Reid Harvey
- National Institute for Occupational Safety and Health, 1095 Willowdale Road, Morgantown, WV 26505, USA
| | - Hannah Rettler
- Utah Department of Health, 288 North 1460 West, Salt Lake City, UT 84114, USA
| | - Dean Taylor
- Utah Department of Agriculture and Food, 4315 South 2700 West #4, Taylorsville, UT 84129, USA
| | - Markus H. Kainulainen
- Centers for Disease Control and Prevention, 1600 Clifton Road Ne, Atlanta, GA 30329, USA
| | - Ausaf Ahmad
- Centers for Disease Control and Prevention, 1600 Clifton Road Ne, Atlanta, GA 30329, USA
| | - Paige Bunkley
- Centers for Disease Control and Prevention, 1600 Clifton Road Ne, Atlanta, GA 30329, USA
| | - Claire Godino
- Centers for Disease Control and Prevention, 1600 Clifton Road Ne, Atlanta, GA 30329, USA
| | - Suxiang Tong
- Centers for Disease Control and Prevention, 1600 Clifton Road Ne, Atlanta, GA 30329, USA
| | - Yan Li
- Centers for Disease Control and Prevention, 1600 Clifton Road Ne, Atlanta, GA 30329, USA
| | - Anna Uehara
- Centers for Disease Control and Prevention, 1600 Clifton Road Ne, Atlanta, GA 30329, USA
| | - Anna Kelleher
- Centers for Disease Control and Prevention, 1600 Clifton Road Ne, Atlanta, GA 30329, USA
| | - Jing Zhang
- Centers for Disease Control and Prevention, 1600 Clifton Road Ne, Atlanta, GA 30329, USA
| | - Brian Lynch
- Centers for Disease Control and Prevention, 1600 Clifton Road Ne, Atlanta, GA 30329, USA
| | - Casey Barton Behravesh
- Centers for Disease Control and Prevention, 1600 Clifton Road Ne, Atlanta, GA 30329, USA
| | - Jonathan S. Towner
- Centers for Disease Control and Prevention, 1600 Clifton Road Ne, Atlanta, GA 30329, USA
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8
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Koley T, Goswami A, Kumar M, Upadhyay N, Hariprasad G. Comparative Structural Analysis of Human ACE2 Receptor with Spike Protein of SARS-CoV-2 Variants: Implications to Understand Infectivity of the Virus. Adv Appl Bioinform Chem 2022; 15:21-27. [PMID: 35734581 PMCID: PMC9208465 DOI: 10.2147/aabc.s360787] [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: 02/02/2022] [Accepted: 06/01/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose Spike protein on SARS-CoV-2 virus plays an integral part during infection as cell entry depends on binding of this protein to human ACE2 receptor. Understanding of infectivity by these variants necessitates a comparative structural analysis of complexes of spike protein-receptor binding domain (RBD) of these variants to receptor. Methodology Wild type SARS-CoV-2 spike protein sequence was retrieved from the UniProt database, and mutations of five variants at receptor binding domain were manually incorporated and aligned using Clustal Omega. Crystal structure complexes of human ACE2 receptor with spike protein RBD domain of SARS-CoV-2 variants of wild type, α, β, and δ were extracted from the RCSB database. Wild type SARS-CoV-2 complex with receptor was used as template to generate model complexes of receptor with spike protein RBD of γ and omicron variants through WinCoot program. These were energy minimized and validated and molecular dynamic simulation was performed using Desmond simulation program. Results Mutations are distributed across the entire length of RBD, but the maximum number of mutations are seen at 11 positions within binding interface motifs of six variant sequences. Interface of spike protein RBDs with human ACE2-receptor shows different mix of hydrogen bonded and ionic interactions. Alpha and β variants have few interactions, while γ and δ variants have higher number of interactions compared to wild type variant. Omicron variant, with 10 polar interactions including two ionic bonds, has the highest binding energy. Conclusion Different mutations on RBD of spike protein results in varying quantity and quality of interactions, thereby affecting potency of each variant. Variations in binding are due to interactions of mutant residues and induced conformational changes on loops of RBDs. Variants α and β have a low potency, while, γ, δ, and omicron have a higher potency. These results correlate with viral infectivity and place clinical observations in the right perspective.
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Affiliation(s)
- Tirthankar Koley
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Arunima Goswami
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Neelam Upadhyay
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
| | - Gururao Hariprasad
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi, 110029, India
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9
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Celik I, Khan A, Dwivany FM, Fatimawali, Wei DQ, Tallei TE. Computational prediction of the effect of mutations in the receptor-binding domain on the interaction between SARS-CoV-2 and human ACE2. Mol Divers 2022; 26:3309-3324. [PMID: 35138508 DOI: 10.1007/s11030-022-10392-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Accepted: 01/20/2022] [Indexed: 01/10/2023]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) causing COVID-19 continues to mutate. Numerous studies have indicated that this viral mutation, particularly in the receptor-binding domain area, may increase the viral affinity for human angiotensin-converting enzyme 2 (hACE2), the receptor for viral entry into host cells, thereby increasing viral virulence and transmission. In this study, we investigated the binding affinity of SARS-CoV-2 variants (Delta plus, Iota, Kappa, Mu, Lambda, and C.1.2) on hACE2 using computational modeling with a protein-protein docking approach. The simulation results indicated that there were differences in the interactions between the RBD and hACE2, including hydrogen bonding, salt bridge interactions, non-bonded interactions, and binding free energy differences among these variants. Molecular dynamics simulations revealed that mutations in the RBD increase the stability of the hACE2-spike protein complex relative to the wild type, following the global stability trend and increasing the binding affinity. The value of binding-free energy calculated using molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) indicated that all mutations in the spike protein increased the contagiousness of SARS-CoV-2 variants. The findings of this study provide a foundation for developing effective interventions against these variants. Computational modeling elucidates that the spike protein of SARS-CoV-2 variants binds considerably stronger than the wild-type to hACE2.
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Affiliation(s)
- Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, 38039, Turkey.
| | - Abbas Khan
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Fenny Martha Dwivany
- School of Life Sciences and Technology, Institut Teknologi Bandung, Bandung, West Java, 40132, Indonesia
| | - Fatimawali
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, North Sulawesi, 95115, Indonesia
| | - Dong-Qing Wei
- Department of Bioinformatics and Biological Statistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China.,State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center On Antibacterial Resistances, Joint Laboratory of International Cooperation in Metabolic and Developmental Sciences, Shanghai Jiao Tong University, Ministry of Education and School of Life Sciences and Biotechnology, Shanghai, 200030, People's Republic of China.,Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen, Guangdong, 518055, People's Republic of China
| | - Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, North Sulawesi, 95115, Indonesia.
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10
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Head RJ, Lumbers ER, Jarrott B, Tretter F, Smith G, Pringle KG, Islam S, Martin JH. Systems analysis shows that thermodynamic physiological and pharmacological fundamentals drive COVID-19 and response to treatment. Pharmacol Res Perspect 2022; 10:e00922. [PMID: 35106955 PMCID: PMC8929328 DOI: 10.1002/prp2.922] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/05/2022] [Indexed: 12/12/2022] Open
Abstract
Why a systems analysis view of this pandemic? The current pandemic has inflicted almost unimaginable grief, sorrow, loss, and terror at a global scale. One of the great ironies with the COVID‐19 pandemic, particularly early on, is counter intuitive. The speed at which specialized basic and clinical sciences described the details of the damage to humans in COVID‐19 disease has been impressive. Equally, the development of vaccines in an amazingly short time interval has been extraordinary. However, what has been less well understood has been the fundamental elements that underpin the progression of COVID‐19 in an individual and in populations. We have used systems analysis approaches with human physiology and pharmacology to explore the fundamental underpinnings of COVID‐19 disease. Pharmacology powerfully captures the thermodynamic characteristics of molecular binding with an exogenous entity such as a virus and its consequences on the living processes well described by human physiology. Thus, we have documented the passage of SARS‐CoV‐2 from infection of a single cell to species jump, to tropism, variant emergence and widespread population infection. During the course of this review, the recurrent observation was the efficiency and simplicity of one critical function of this virus. The lethality of SARS‐CoV‐2 is due primarily to its ability to possess and use a variable surface for binding to a specific human target with high affinity. This binding liberates Gibbs free energy (GFE) such that it satisfies the criteria for thermodynamic spontaneity. Its binding is the prelude to human host cellular entry and replication by the appropriation of host cell constituent molecules that have been produced with a prior energy investment by the host cell. It is also a binding that permits viral tropism to lead to high levels of distribution across populations with newly formed virions. This thermodynamic spontaneity is repeated endlessly as infection of a single host cell spreads to bystander cells, to tissues, to humans in close proximity and then to global populations. The principal antagonism of this process comes from SARS‐CoV‐2 itself, with its relentless changing of its viral surface configuration, associated with the inevitable emergence of variants better configured to resist immune sequestration and importantly with a greater affinity for the host target and higher infectivity. The great value of this physiological and pharmacological perspective is that it reveals the fundamental thermodynamic underpinnings of SARS‐CoV‐2 infection.
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Affiliation(s)
- Richard J Head
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Eugenie R Lumbers
- School of Biomedical Sciences & Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Bevyn Jarrott
- Florey Institute of Neuroscience & Mental Health, University of Melbourne, Parkville, Victoria, Australia
| | - Felix Tretter
- Bertalanffy Center for the Study of Systems Science, Vienna, Austria
| | - Gary Smith
- VP System Practice - International Society for System Sciences, Pontypool, UK
| | - Kirsty G Pringle
- School of Biomedical Sciences & Pharmacy, University of Newcastle, Newcastle, New South Wales, Australia.,Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia
| | - Saiful Islam
- Drug Discovery and Development, Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Jennifer H Martin
- Hunter Medical Research Institute, New Lambton Heights, New South Wales, Australia.,Centre for Drug Repurposing and Medicines Research, Clinical Pharmacology, University of Newcastle, Newcastle, New South Wales, Australia
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11
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Smyth DS, Trujillo M, Gregory DA, Cheung K, Gao A, Graham M, Guan Y, Guldenpfennig C, Hoxie I, Kannoly S, Kubota N, Lyddon TD, Markman M, Rushford C, San KM, Sompanya G, Spagnolo F, Suarez R, Teixeiro E, Daniels M, Johnson MC, Dennehy JJ. Tracking cryptic SARS-CoV-2 lineages detected in NYC wastewater. Nat Commun 2022; 13:635. [PMID: 35115523 PMCID: PMC8813986 DOI: 10.1038/s41467-022-28246-3] [Citation(s) in RCA: 99] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/10/2022] [Indexed: 11/21/2022] Open
Abstract
Tracking SARS-CoV-2 genetic diversity is strongly indicated because diversifying selection may lead to the emergence of novel variants resistant to naturally acquired or vaccine-induced immunity. To monitor New York City (NYC) for the presence of novel variants, we deep sequence most of the receptor binding domain coding sequence of the S protein of SARS-CoV-2 isolated from the New York City wastewater. Here we report detecting increasing frequencies of novel cryptic SARS-CoV-2 lineages not recognized in GISAID's EpiCoV database. These lineages contain mutations that had been rarely observed in clinical samples, including Q493K, Q498Y, E484A, and T572N and share many mutations with the Omicron variant of concern. Some of these mutations expand the tropism of SARS-CoV-2 pseudoviruses by allowing infection of cells expressing the human, mouse, or rat ACE2 receptor. Finally, pseudoviruses containing the spike amino acid sequence of these lineages were resistant to different classes of receptor binding domain neutralizing monoclonal antibodies. We offer several hypotheses for the anomalous presence of these lineages, including the possibility that these lineages are derived from unsampled human COVID-19 infections or that they indicate the presence of a non-human animal reservoir.
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Affiliation(s)
- Davida S Smyth
- Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, TX, 78224, USA
| | - Monica Trujillo
- Department of Biological Sciences and Geology, Queensborough Community College of The City University of New York, Queens, NY, 11364, USA
| | - Devon A Gregory
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Kristen Cheung
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Anna Gao
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Maddie Graham
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Yue Guan
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Caitlyn Guldenpfennig
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Irene Hoxie
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Sherin Kannoly
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Nanami Kubota
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Terri D Lyddon
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Michelle Markman
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Clayton Rushford
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Kaung Myat San
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA
| | - Geena Sompanya
- Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, TX, 78224, USA
| | - Fabrizio Spagnolo
- Department of Biological & Environmental Sciences, Long Island University-Post, Greenvale, New York, 11548, USA
| | - Reinier Suarez
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Emma Teixeiro
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Mark Daniels
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, 65212, USA.
| | - John J Dennehy
- Biology Department, Queens College and The Graduate Center of The City University of New York, Queens, NY, 11367, USA.
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12
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Koley T, Kumar M, Goswami A, Ethayathulla AS, Hariprasad G. Structural modeling of Omicron spike protein and its complex with human ACE-2 receptor: Molecular basis for high transmissibility of the virus. Biochem Biophys Res Commun 2022; 592:51-53. [PMID: 35026605 PMCID: PMC8739823 DOI: 10.1016/j.bbrc.2021.12.082] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/21/2021] [Accepted: 12/22/2021] [Indexed: 01/08/2023]
Abstract
Omicron is a new variant of SARS-CoV-2, which is currently infecting people around the world. Spike glycoprotein, an important molecule in pathogenesis of infection has been modeled and the interaction of its Receptor Binding Domain with human ACE-receptor has been analysed by simulation studies. Structural analysis of Omicron spike glycoprotein shows the 30 mutations to be distributed over all domains of the trimeric protein, wherein the mutant residues are seen to be participating in higher number of intra-molecular interactions including two salt bridges emanating from mutant residues thereby stabilizing their conformation, as compared to wild type. Complex of Receptor Binding Domain (RBD) with human ACE-2 receptor shows seven mutations at interacting interface comprising of two ionic interactions, eight hydrogen bonds and seven Van der Waals interactions. The number and quality of these interactions along with other binding biophysical parameters suggests more potency of RBD domain to the receptor as compared to the wild type counterpart. Results of this study explains the high transmissibility of Omicron variant of SARS-CoV-2 that is currently observed across the world.
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Affiliation(s)
- Tirthankar Koley
- Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India
| | - Manoj Kumar
- Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India
| | - Arunima Goswami
- Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India
| | - Abdul S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India
| | - Gururao Hariprasad
- Department of Biophysics, All India Institute of Medical Sciences, Ansari nagar, New Delhi, 110029, India.
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13
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Tallei TE, Fatimawali, Adam AA, Elseehy MM, El-Shehawi AM, Mahmoud EA, Tania AD, Niode NJ, Kusumawaty D, Rahimah S, Effendi Y, Idroes R, Celik I, Hossain MJ, Emran TB. Fruit Bromelain-Derived Peptide Potentially Restrains the Attachment of SARS-CoV-2 Variants to hACE2: A Pharmacoinformatics Approach. Molecules 2022; 27:260. [PMID: 35011492 PMCID: PMC8746556 DOI: 10.3390/molecules27010260] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Revised: 12/09/2021] [Accepted: 12/10/2021] [Indexed: 12/14/2022] Open
Abstract
Before entering the cell, the SARS-CoV-2 spike glycoprotein receptor-binding domain (RBD) binds to the human angiotensin-converting enzyme 2 (hACE2) receptor. Hence, this RBD is a critical target for the development of antiviral agents. Recent studies have discovered that SARS-CoV-2 variants with mutations in the RBD have spread globally. The purpose of this in silico study was to determine the potential of a fruit bromelain-derived peptide. DYGAVNEVK. to inhibit the entry of various SARS-CoV-2 variants into human cells by targeting the hACE binding site within the RBD. Molecular docking analysis revealed that DYGAVNEVK interacts with several critical RBD binding residues responsible for the adhesion of the RBD to hACE2. Moreover, 100 ns MD simulations revealed stable interactions between DYGAVNEVK and RBD variants derived from the trajectory of root-mean-square deviation (RMSD), radius of gyration (Rg), and root-mean-square fluctuation (RMSF) analysis, as well as free binding energy calculations. Overall, our computational results indicate that DYGAVNEVK warrants further investigation as a candidate for preventing SARS-CoV-2 due to its interaction with the RBD of SARS-CoV-2 variants.
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Affiliation(s)
- Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia
- The University Centre of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado 95115, Indonesia; (F.); (N.J.N.)
| | - Fatimawali
- The University Centre of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado 95115, Indonesia; (F.); (N.J.N.)
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Ahmad Akroman Adam
- Dentistry Study Program, Faculty of Medicine, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Mona M. Elseehy
- Department of Genetics, Faculty of Agriculture, University of Alexandria, Alexandria 21545, Egypt;
| | - Ahmed M. El-Shehawi
- Department of Biotechnology, College of Science, Taif University, P.O. Box 11099, Taif 21944, Saudi Arabia;
| | - Eman A. Mahmoud
- Department of Food Industries, Faculty of Agriculture, Damietta University, Damietta 34511, Egypt;
| | - Adinda Dwi Tania
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado 95115, Indonesia;
| | - Nurdjannah Jane Niode
- The University Centre of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado 95115, Indonesia; (F.); (N.J.N.)
- Department of Dermatology and Venereology, Faculty of Medicine, University of Sam Ratulangi, RD Kandou Hospital, Manado 95163, Indonesia
| | - Diah Kusumawaty
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung 40154, Indonesia;
| | - Souvia Rahimah
- Food Technology Study Program, Department of Food Industrial Technology, Faculty of Agroindustrial Technology, Universitas Padjadjaran, Jatinangor 45363, Indonesia;
| | - Yunus Effendi
- Department of Biology, Faculty of Science and Technology, Al-Azhar Indonesia University, Jakarta 12110, Indonesia;
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Kopelma Darussalam, Banda Aceh 23111, Indonesia;
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri 38039, Turkey;
| | - Md. Jamal Hossain
- Department of Pharmacy, State University of Bangladesh, 77 Satmasjid Road, Dhanmondi, Dhaka 1205, Bangladesh;
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong 4381, Bangladesh
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14
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Korath ADJ, Janda J, Untersmayr E, Sokolowska M, Feleszko W, Agache I, Adel Seida A, Hartmann K, Jensen‐Jarolim E, Pali‐Schöll I. One Health: EAACI Position Paper on coronaviruses at the human-animal interface, with a specific focus on comparative and zoonotic aspects of SARS-CoV-2. Allergy 2022; 77:55-71. [PMID: 34180546 PMCID: PMC8441637 DOI: 10.1111/all.14991] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Accepted: 06/24/2021] [Indexed: 12/15/2022]
Abstract
The latest outbreak of a coronavirus disease in 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), evolved into a worldwide pandemic with massive effects on health, quality of life, and economy. Given the short period of time since the outbreak, there are several knowledge gaps on the comparative and zoonotic aspects of this new virus. Within the One Health concept, the current EAACI position paper dwells into the current knowledge on SARS-CoV-2's receptors, symptoms, transmission routes for human and animals living in close vicinity to each other, usefulness of animal models to study this disease and management options to avoid intra- and interspecies transmission. Similar pandemics might appear unexpectedly and more frequently in the near future due to climate change, consumption of exotic foods and drinks, globe-trotter travel possibilities, the growing world population, the decreasing production space, declining room for wildlife and free-ranging animals, and the changed lifestyle including living very close to animals. Therefore, both the society and the health authorities need to be aware and well prepared for similar future situations, and research needs to focus on prevention and fast development of treatment options (medications, vaccines).
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Affiliation(s)
- Anna D. J. Korath
- Comparative MedicineInteruniversity Messerli Research InstituteUniversity of Veterinary Medicine and Medical University ViennaViennaAustria
| | - Jozef Janda
- Faculty of ScienceCharles UniversityPragueCzech Republic
| | - Eva Untersmayr
- Institute of Pathophysiology and Allergy ResearchCenter of Pathophysiology, Infectiology and ImmunologyMedical University of ViennaViennaAustria
| | - Milena Sokolowska
- Swiss Institute of Allergy and Asthma Research (SIAF),University of ZurichZurichSwitzerland
| | - Wojciech Feleszko
- Department of Paediatric Allergy and PulmonologyThe Medical University of WarsawWarsawPoland
| | | | - Ahmed Adel Seida
- Department of Microbiology and ImmunologyFaculty of Veterinary MedicineCairo UniversityCairoEgypt
| | - Katrin Hartmann
- Medizinische KleintierklinikZentrum für Klinische TiermedizinLMUMunichGermany
| | - Erika Jensen‐Jarolim
- Comparative MedicineInteruniversity Messerli Research InstituteUniversity of Veterinary Medicine and Medical University ViennaViennaAustria
- Institute of Pathophysiology and Allergy ResearchCenter of Pathophysiology, Infectiology and ImmunologyMedical University of ViennaViennaAustria
| | - Isabella Pali‐Schöll
- Comparative MedicineInteruniversity Messerli Research InstituteUniversity of Veterinary Medicine and Medical University ViennaViennaAustria
- Institute of Pathophysiology and Allergy ResearchCenter of Pathophysiology, Infectiology and ImmunologyMedical University of ViennaViennaAustria
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15
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Interactions of the Receptor Binding Domain of SARS-CoV-2 Variants with hACE2: Insights from Molecular Docking Analysis and Molecular Dynamic Simulation. BIOLOGY 2021; 10:biology10090880. [PMID: 34571756 PMCID: PMC8470537 DOI: 10.3390/biology10090880] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/28/2021] [Accepted: 09/02/2021] [Indexed: 12/23/2022]
Abstract
Since the beginning of the coronavirus 19 (COVID-19) pandemic in late 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been evolving through the acquisition of genomic mutations, leading to the emergence of multiple variants of concern (VOCs) and variants of interest (VOIs). Currently, four VOCs (Alpha, Beta, Delta, and Gamma) and seven VOIs (Epsilon, Zeta, Eta, Theta, Iota, Kappa, and Lambda) of SARS-CoV-2 have been identified in worldwide circulation. Here, we investigated the interactions of the receptor-binding domain (RBD) of five SARS-CoV-2 variants with the human angiotensin-converting enzyme 2 (hACE2) receptor in host cells, to determine the extent of molecular divergence and the impact of mutation, using protein-protein docking and dynamics simulation approaches. Along with the wild-type (WT) SARS-CoV-2, this study included the Brazilian (BR/lineage P.1/Gamma), Indian (IN/lineage B.1.617/Delta), South African (SA/lineage B.1.351/Beta), United Kingdom (UK/lineage B.1.1.7/Alpha), and United States (US/lineage B.1.429/Epsilon) variants. The protein-protein docking and dynamics simulation studies revealed that these point mutations considerably affected the structural behavior of the spike (S) protein compared to the WT, which also affected the binding of RBD with hACE2 at the respective sites. Additional experimental studies are required to determine whether these effects have an influence on drug-S protein binding and its potential therapeutic effect.
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16
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Tallei TE, Fatimawali, Yelnetty A, Idroes R, Kusumawaty D, Emran TB, Yesiloglu TZ, Sippl W, Mahmud S, Alqahtani T, Alqahtani AM, Asiri S, Rahmatullah M, Jahan R, Khan MA, Celik I. An Analysis Based on Molecular Docking and Molecular Dynamics Simulation Study of Bromelain as Anti-SARS-CoV-2 Variants. Front Pharmacol 2021; 12:717757. [PMID: 34489706 PMCID: PMC8417730 DOI: 10.3389/fphar.2021.717757] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 08/09/2021] [Indexed: 12/12/2022] Open
Abstract
The rapid spread of a novel coronavirus known as SARS-CoV-2 has compelled the entire world to seek ways to weaken this virus, prevent its spread and also eliminate it. However, no drug has been approved to treat COVID-19. Furthermore, the receptor-binding domain (RBD) on this viral spike protein, as well as several other important parts of this virus, have recently undergone mutations, resulting in new virus variants. While no treatment is currently available, a naturally derived molecule with known antiviral properties could be used as a potential treatment. Bromelain is an enzyme found in the fruit and stem of pineapples. This substance has been shown to have a broad antiviral activity. In this article, we analyse the ability of bromelain to counteract various variants of the SARS-CoV-2 by targeting bromelain binding on the side of this viral interaction with human angiotensin-converting enzyme 2 (hACE2) using molecular docking and molecular dynamics simulation approaches. We have succeeded in making three-dimensional configurations of various RBD variants using protein modelling. Bromelain exhibited good binding affinity toward various variants of RBDs and binds right at the binding site between RBDs and hACE2. This result is also presented in the modelling between Bromelain, RBD, and hACE2. The molecular dynamics (MD) simulations study revealed significant stability of the bromelain and RBD proteins separately up to 100 ns with an RMSD value of 2 Å. Furthermore, despite increases in RMSD and changes in Rog values of complexes, which are likely due to some destabilized interactions between bromelain and RBD proteins, two proteins in each complex remained bonded, and the site where the two proteins bind remained unchanged. This finding indicated that bromelain could have an inhibitory effect on different SARS-CoV-2 variants, paving the way for a new SARS-CoV-2 inhibitor drug. However, more in vitro and in vivo research on this potential mechanism of action is required.
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Affiliation(s)
- Trina Ekawati Tallei
- Department of Biology, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, Indonesia
- The University Centre of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado, Indonesia
| | - Fatimawali
- The University Centre of Excellence for Biotechnology and Conservation of Wallacea, Institute for Research and Community Services, Sam Ratulangi University, Manado, Indonesia
- Pharmacy Study Program, Faculty of Mathematics and Natural Sciences, Sam Ratulangi University, Manado, Indonesia
| | - Afriza Yelnetty
- Department of Animal Production, Faculty of Animal Husbandry, Sam Ratulangi University, Manado, Indonesia
| | - Rinaldi Idroes
- Department of Pharmacy, Faculty of Mathematics and Natural Sciences, Universitas Syiah Kuala, Banda Aceh, Indonesia
| | - Diah Kusumawaty
- Department of Biology, Faculty of Mathematics and Natural Sciences Education, Universitas Pendidikan Indonesia, Bandung, Indonesia
| | - Talha Bin Emran
- Department of Pharmacy, BGC Trust University Bangladesh, Chittagong, Bangladesh
| | | | - Wolfgang Sippl
- Institute of Pharmacy, Martin-Luther University of Halle-Wittenberg, Halle, Germany
| | - Shafi Mahmud
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Taha Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Ali M. Alqahtani
- Department of Pharmacology, College of Pharmacy, King Khalid University, Abha, Saudi Arabia
| | - Saeed Asiri
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Najran University, Najran, Saudi Arabia
| | - Mohammed Rahmatullah
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh
| | - Rownak Jahan
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh
| | - Md. Arif Khan
- Department of Biotechnology and Genetic Engineering, University of Development Alternative, Dhaka, Bangladesh
| | - Ismail Celik
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy, Erciyes University, Kayseri, Turkey
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17
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Ekstrand K, Flanagan AJ, Lin IE, Vejseli B, Cole A, Lally AP, Morris RL, Morgan KN. Animal Transmission of SARS-CoV-2 and the Welfare of Animals during the COVID-19 Pandemic. Animals (Basel) 2021; 11:2044. [PMID: 34359172 PMCID: PMC8300090 DOI: 10.3390/ani11072044] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/29/2021] [Accepted: 07/01/2021] [Indexed: 12/20/2022] Open
Abstract
The accelerated pace of research into Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) necessitates periodic summaries of current research. The present paper reviews virus susceptibilities in species with frequent human contact, and factors that are best predictors of virus susceptibility. Species reviewed were those in contact with humans through entertainment, pet, or agricultural trades, and for whom reports (either anecdotal or published) exist regarding the SARS-CoV-2 virus and/or the resulting disease state COVID-19. Available literature was searched using an artificial intelligence (AI)-assisted engine, as well as via common databases, such as Web of Science and Medline. The present review focuses on susceptibility and transmissibility of SARS-CoV-2, and polymorphisms in transmembrane protease serine 2 (TMPRSS2) and angiotensin-converting enzyme 2 (ACE2) that contribute to species differences. Dogs and pigs appear to have low susceptibility, while ferrets, mink, some hamster species, cats, and nonhuman primates (particularly Old World species) have high susceptibility. Precautions may therefore be warranted in interactions with such species, and more selectivity practiced when choosing appropriate species to serve as models for research.
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Affiliation(s)
| | - Amanda J. Flanagan
- College of Veterinary Medicine, Cornell University, Ithaca, NY 14850, USA;
| | - Ilyan E. Lin
- Department of Biology, Wheaton College, Norton, MA 02766, USA; (I.E.L.); (B.V.); (R.L.M.)
| | - Brendon Vejseli
- Department of Biology, Wheaton College, Norton, MA 02766, USA; (I.E.L.); (B.V.); (R.L.M.)
| | - Allicyn Cole
- Program in Neuroscience, Wheaton College, Norton, MA 02766, USA; (A.C.); (A.P.L.)
| | - Anna P. Lally
- Program in Neuroscience, Wheaton College, Norton, MA 02766, USA; (A.C.); (A.P.L.)
| | - Robert L. Morris
- Department of Biology, Wheaton College, Norton, MA 02766, USA; (I.E.L.); (B.V.); (R.L.M.)
| | - Kathleen N. Morgan
- Program in Neuroscience, Wheaton College, Norton, MA 02766, USA; (A.C.); (A.P.L.)
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