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Ayubov MS, Mirzakhmedov MK, Yusupov AN, Asrorov AM, Nosirov BV, Usmanov DE, Shermatov SE, Ubaydullaeva KA, Abdukarimov A, Buriev ZT, Abdurakhmonov IY. Most accurate mutations in SARS-CoV-2 genomes identified in Uzbek patients show novel amino acid changes. Front Med (Lausanne) 2024; 11:1401655. [PMID: 38882660 PMCID: PMC11176497 DOI: 10.3389/fmed.2024.1401655] [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: 03/15/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024] Open
Abstract
Purpose The rapid changes in the coronavirus genomes created new strains after the first variation was found in Wuhan in 2019. SARS-CoV-2 genotypes should periodically undergo whole genome sequencing to control it because it has been extremely helpful in combating the virus. Many diagnoses, treatments, and vaccinations have been developed against it based on genome sequencing. With its practical implications, this study aimed to determine changes in the delta variant of SARS-CoV-2 widespread in Uzbekistan during the pandemic by genome sequencing, thereby providing crucial insights for developing effective control strategies that can be directly applied in the field. Design We meticulously generated 17 high-quality whole-genome sequence data from 48 SARS-CoV-2 genotypes of COVID-19 patients who tested positive by PCR in Tashkent, Uzbekistan. Our rigorous approach, which includes stringent quality control measures and multiple rounds of verification, ensures the accuracy and reliability of our findings. Methods Our study employed a unique combination of genome sequencing and bioinformatics web tools to analyze amino acid (AA) changes in the virus genomes. This approach allowed us to understand the genetic changes in the delta variant of SARS-CoV-2 widespread in Uzbekistan during the pandemic. Results Our study revealed significant nucleotide polymorphisms, including non-synonymous (missense) and synonymous mutations in the coding regions of the sequenced sample genomes. These findings, categorized by phylogenetic analysis into the G clade (or GK sub-clade), contribute to our understanding of the delta variant of SARS-CoV-2 widespread in Uzbekistan during the pandemic. A total of 134 mutations were identified, consisting of 65 shared and 69 unique mutations. These nucleotide changes, including one frameshift mutation, one conservative and disruptive insertion-deletion, four upstream region mutations, four downstream region mutations, 39 synonymous mutations, and 84 missense mutations, are crucial in the ongoing battle against the virus. Conclusion The comprehensive whole-genome sequencing data presented in this study aids in tracing the origins and sources of circulating SARS-CoV-2 variants and analyzing emerging variations within Uzbekistan and globally. The genome sequencing of SARS-CoV-2 from samples collected in Uzbekistan in late 2021, during the peak of the pandemic's second wave nationwide, is detailed here. Following acquiring these sequences, research efforts have focused on developing DNA and plant-based edible vaccines utilizing prevalent SARS-CoV-2 strains in Uzbekistan, which are currently undergoing clinical trials.
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Affiliation(s)
- Mirzakamol S Ayubov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
| | | | - Abdurakhmon N Yusupov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
| | - Akmal M Asrorov
- Department of Chemistry for Natural Substances, National University of Uzbekistan, Tashkent, Uzbekistan
| | | | - Dilshod E Usmanov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
| | - Shukhrat E Shermatov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
| | - Khurshida A Ubaydullaeva
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
| | - Abdusattor Abdukarimov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
| | - Zabardast T Buriev
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
| | - Ibrokhim Y Abdurakhmonov
- Center of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Tashkent, Republic of Uzbekistan
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Eni DB, Cassel J, Namba-Nzanguim CT, Simoben CV, Tietjen I, Akunuri R, Salvino JM, Ntie-Kang F. Design, synthesis, and biochemical and computational screening of novel oxindole derivatives as inhibitors of Aurora A kinase and SARS-CoV-2 spike/host ACE2 interaction. Med Chem Res 2024; 33:620-634. [PMID: 38646411 PMCID: PMC11024012 DOI: 10.1007/s00044-024-03201-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Accepted: 02/09/2024] [Indexed: 04/23/2024]
Abstract
Isatin (indol-2,3-dione), a secondary metabolite of tryptophan, has been used as the core structure to design several compounds that have been tested and identified as potent inhibitors of apoptosis, potential antitumor agents, anticonvulsants, and antiviral agents. In this work, several analogs of isatin hybrids have been synthesized and characterized, and their activities were established as inhibitors of both Aurora A kinase and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike/host angiotensin-converting enzyme II (ACE2) interactions. Amongst the synthesized isatin hybrids, compounds 6a, 6f, 6g, and 6m exhibited Aurora A kinase inhibitory activities (with IC50 values < 5 μ M), with GScore values of -7.9, -7.6, -8.2 and -7.7 kcal/mol, respectively. Compounds 6g and 6i showed activities in blocking SARS-CoV-2 spike/ACE2 binding (with IC50 values in the range < 30 μ M), with GScore values of -6.4 and -6.6 kcal/mol, respectively. Compounds 6f, 6g, and 6i were both capable of inhibiting spike/ACE2 binding and blocking Aurora A kinase. Pharmacophore profiling indicated that compound 6g tightly fits Aurora A kinase and SARS-CoV-2 pharmacophores, while 6d fits SARS-CoV-2 and 6l fits Aurora A kinase pharmacophore. This work is a proof of concept that some existing cancer drugs may possess antiviral properties. Molecular modeling showed that the active compound for each protein adopted different binding modes, hence interacting with a different set of amino acid residues in the binding site. The weaker activities against spike/ACE2 could be explained by the small sizes of the ligands that fail to address the important interactions for binding to the ACE2 receptor site.
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Affiliation(s)
- Donatus B. Eni
- Center for Drug Discovery, Faculty of Science, University of Buea, Buea, Cameroon
- Department of Chemistry, Faculty of Science, University of Buea, Buea, Cameroon
| | | | - Cyril T. Namba-Nzanguim
- Center for Drug Discovery, Faculty of Science, University of Buea, Buea, Cameroon
- Department of Chemistry, Faculty of Science, University of Buea, Buea, Cameroon
| | - Conrad V. Simoben
- Center for Drug Discovery, Faculty of Science, University of Buea, Buea, Cameroon
| | | | | | | | - Fidele Ntie-Kang
- Center for Drug Discovery, Faculty of Science, University of Buea, Buea, Cameroon
- Department of Chemistry, Faculty of Science, University of Buea, Buea, Cameroon
- Institute of Pharmacy, Martin-Luther University Halle-Wittenberg, Halle (Saale), Germany
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3
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Lin CH, Chang HJ, Lin MW, Yang XR, Lee CH, Lin CS. Inhibitory Efficacy of Main Components of Scutellaria baicalensis on the Interaction between Spike Protein of SARS-CoV-2 and Human Angiotensin-Converting Enzyme II. Int J Mol Sci 2024; 25:2935. [PMID: 38474182 DOI: 10.3390/ijms25052935] [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: 01/27/2024] [Revised: 02/22/2024] [Accepted: 02/29/2024] [Indexed: 03/14/2024] Open
Abstract
Blocking the interaction between the SARS-CoV-2 spike protein and the human angiotensin-converting enzyme II (hACE2) protein serves as a therapeutic strategy for treating COVID-19. Traditional Chinese medicine (TCM) treatments containing bioactive products could alleviate the symptoms of severe COVID-19. However, the emergence of SARS-CoV-2 variants has complicated the process of developing broad-spectrum drugs. As such, the aim of this study was to explore the efficacy of TCM treatments against SARS-CoV-2 variants through targeting the interaction of the viral spike protein with the hACE2 receptor. Antiviral activity was systematically evaluated using a pseudovirus system. Scutellaria baicalensis (S. baicalensis) was found to be effective against SARS-CoV-2 infection, as it mediated the interaction between the viral spike protein and the hACE2 protein. Moreover, the active molecules of S. baicalensis were identified and analyzed. Baicalein and baicalin, a flavone and a flavone glycoside found in S. baicalensis, respectively, exhibited strong inhibitory activities targeting the viral spike protein and the hACE2 protein, respectively. Under optimized conditions, virus infection was inhibited by 98% via baicalein-treated pseudovirus and baicalin-treated hACE2. In summary, we identified the potential SARS-CoV-2 inhibitors from S. baicalensis that mediate the interaction between the Omicron spike protein and the hACE2 receptor. Future studies on the therapeutic application of baicalein and baicalin against SARS-CoV-2 variants are needed.
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Affiliation(s)
- Cheng-Han Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Ho-Ju Chang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Meng-Wei Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Xin-Rui Yang
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
| | - Che-Hsiung Lee
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Department of Plastic and Reconstructive Surgery, Chang Gung Memorial Hospital, Linkou, Taoyuan 333423, Taiwan
| | - Chih-Sheng Lin
- Department of Biological Science and Technology, National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-Devices (IDS2B), National Yang Ming Chiao Tung University, Hsinchu 30068, Taiwan
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Ábrahám E, Bajusz C, Marton A, Borics A, Mdluli T, Pardi N, Lipinszki Z. Expression and purification of the receptor-binding domain of SARS-CoV-2 spike protein in mammalian cells for immunological assays. FEBS Open Bio 2024; 14:380-389. [PMID: 38129177 PMCID: PMC10909970 DOI: 10.1002/2211-5463.13754] [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: 10/19/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 12/23/2023] Open
Abstract
The receptor-binding domain (RBD) of the spike glycoprotein of SARS-CoV-2 virus mediates the interaction with the host cell and is required for virus internalization. It is, therefore, the primary target of neutralizing antibodies. The receptor-binding domain soon became the major target for COVID-19 research and the development of diagnostic tools and new-generation vaccines. Here, we provide a detailed protocol for high-yield expression and one-step affinity purification of recombinant RBD from transiently transfected Expi293F cells. Expi293F mammalian cells can be grown to extremely high densities in a specially formulated serum-free medium in suspension cultures, which makes them an excellent tool for secreted protein production. The highly purified RBD is glycosylated, structurally intact, and forms homomeric complexes. With this quick and easy method, we are able to produce large quantities of RBD (80 mg·L-1 culture) that we have successfully used in immunological assays to examine antibody titers and seroconversion after mRNA-based vaccination of mice.
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Affiliation(s)
- Edit Ábrahám
- MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Institute of BiochemistryHUN‐REN Biological Research CentreSzegedHungary
- National Laboratory for Biotechnology, Institute of GeneticsHUN‐REN Biological Research CentreSzegedHungary
| | - Csaba Bajusz
- National Laboratory for Biotechnology, Institute of GeneticsHUN‐REN Biological Research CentreSzegedHungary
| | - Annamária Marton
- National Laboratory for Biotechnology, Institute of GeneticsHUN‐REN Biological Research CentreSzegedHungary
| | - Attila Borics
- Laboratory of Chemical Biology, Institute of BiochemistryHUN‐REN Biological Research CentreSzegedHungary
| | - Thandiswa Mdluli
- Department of MicrobiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Norbert Pardi
- Department of MicrobiologyUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Zoltán Lipinszki
- MTA SZBK Lendület Laboratory of Cell Cycle Regulation, Institute of BiochemistryHUN‐REN Biological Research CentreSzegedHungary
- National Laboratory for Biotechnology, Institute of GeneticsHUN‐REN Biological Research CentreSzegedHungary
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Son L, Kost V, Maiorov V, Sukhov D, Arkhangelskaya P, Ivanov I, Kudryavtsev D, Siniavin A, Utkin Y, Kasheverov I. Efficient Expression in Leishmania tarentolae (LEXSY) of the Receptor-Binding Domain of the SARS-CoV-2 S-Protein and the Acetylcholine-Binding Protein from Lymnaea stagnalis. Molecules 2024; 29:943. [PMID: 38474455 DOI: 10.3390/molecules29050943] [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: 11/22/2023] [Revised: 01/31/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Leishmania tarentolae (LEXSY) system is an inexpensive and effective expression approach for various research and medical purposes. The stated advantages of this system are the possibility of obtaining the soluble product in the cytoplasm, a high probability of correct protein folding with a full range of post-translational modifications (including uniform glycosylation), and the possibility of expressing multi-subunit proteins. In this paper, a LEXSY expression system has been employed for obtaining the receptor binding domain (RBD) of the spike-protein of the SARS-CoV-2 virus and the homopentameric acetylcholine-binding protein (AChBP) from Lymnaea stagnalis. RBD is actively used to obtain antibodies against the virus and in various scientific studies on the molecular mechanisms of the interaction of the virus with host cell targets. AChBP represents an excellent structural model of the ligand-binding extracellular domain of all subtypes of nicotinic acetylcholine receptors (nAChRs). Both products were obtained in a soluble glycosylated form, and their structural and functional characteristics were compared with those previously described.
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Affiliation(s)
- Lina Son
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Vladimir Kost
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Valery Maiorov
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Dmitry Sukhov
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Polina Arkhangelskaya
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Igor Ivanov
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Denis Kudryavtsev
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Andrei Siniavin
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Ivanovsky Institute of Virology, N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Yuri Utkin
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Igor Kasheverov
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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Valdez-Cruz NA, Rosiles-Becerril D, Martínez-Olivares CE, García-Hernández E, Cobos-Marín L, Garzón D, López-Salas FE, Zavala G, Luviano A, Olvera A, Alagón A, Ramírez OT, Trujillo-Roldán MA. Oral administration of a recombinant modified RBD antigen of SARS-CoV-2 as a possible immunostimulant for the care of COVID-19. Microb Cell Fact 2024; 23:41. [PMID: 38321489 PMCID: PMC10848483 DOI: 10.1186/s12934-024-02320-5] [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: 10/20/2023] [Accepted: 01/27/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Developing effective vaccines against SARS-CoV-2 that consider manufacturing limitations, equitable access, and acceptance is necessary for developing platforms to produce antigens that can be efficiently presented for generating neutralizing antibodies and as a model for new vaccines. RESULTS This work presents the development of an applicable technology through the oral administration of the SARS-CoV-2 RBD antigen fused with a peptide to improve its antigenic presentation. We focused on the development and production of the recombinant receptor binding domain (RBD) produced in E. coli modified with the addition of amino acids extension designed to improve antigen presentation. The production was carried out in shake flask and bioreactor cultures, obtaining around 200 mg/L of the antigen. The peptide-fused RBD and peptide-free RBD proteins were characterized and compared using SDS-PAGE gel, high-performance chromatography, and circular dichroism. The peptide-fused RBD was formulated in an oil-in-water emulsion for oral mice immunization. The peptide-fused RBD, compared to RBD, induced robust IgG production in mice, capable of recognizing the recombinant RBD in Enzyme-linked immunosorbent assays. In addition, the peptide-fused RBD generated neutralizing antibodies in the sera of the dosed mice. The formulation showed no reactive episodes and no changes in temperature or vomiting. CONCLUSIONS Our study demonstrated the effectiveness of the designed peptide added to the RBD to improve antigen immunostimulation by oral administration.
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Affiliation(s)
- Norma A Valdez-Cruz
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de Mexico, México. AP. 70228, CP. 04510, México, D.F, Mexico.
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 Carretera, 22860, Tijuana-Ensenada, Baja California, Mexico.
| | - Diego Rosiles-Becerril
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de Mexico, México. AP. 70228, CP. 04510, México, D.F, Mexico
| | - Constanza E Martínez-Olivares
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de Mexico, México. AP. 70228, CP. 04510, México, D.F, Mexico
| | - Enrique García-Hernández
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Laura Cobos-Marín
- Departamento de Microbiología e Inmunología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Ciudad Universitaria, 04510, Ciudad de México, Mexico
| | - Daniel Garzón
- Unidad de Modelos Biológicos, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de Mexico, Mexico. AP. 70228, CP. 04510, México, D.F, Mexico
| | - Francisco E López-Salas
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de Mexico, México. AP. 70228, CP. 04510, México, D.F, Mexico
| | - Guadalupe Zavala
- Unidad de Microscopia Electrónica, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Axel Luviano
- Departamento de Genética del Desarrollo y Fisiologia Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Mor, Mexico
| | - Alejandro Olvera
- Departamento de Biología Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Mor, Mexico
| | - Alejandro Alagón
- Departamento de Biología Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Mor, Mexico
| | - Octavio T Ramírez
- Departamento de Biología Molecular y Bioprocesos, Instituto de Biotecnología, Universidad Nacional Autónoma de México, 62210, Cuernavaca, Mor, Mexico
| | - Mauricio A Trujillo-Roldán
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Cd. Universitaria, Coyoacán, Ciudad de Mexico, México. AP. 70228, CP. 04510, México, D.F, Mexico.
- Centro de Nanociencias y Nanotecnología, Universidad Nacional Autónoma de México, Km 107 Carretera, 22860, Tijuana-Ensenada, Baja California, Mexico.
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Pashameah RA, Soltane R, Sayed AM. A novel inhibitor of SARS-CoV infection: Lactulose octasulfate interferes with ACE2-Spike protein binding. Heliyon 2024; 10:e23222. [PMID: 38163229 PMCID: PMC10754899 DOI: 10.1016/j.heliyon.2023.e23222] [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: 10/14/2023] [Revised: 11/28/2023] [Accepted: 11/29/2023] [Indexed: 01/03/2024] Open
Abstract
The ongoing challenge of managing coronaviruses, particularly SARS-CoV-2, necessitates the development of effective antiviral agents. This study introduces Lactulose octasulfate (LOS), a sulfated disaccharide, demonstrating significant antiviral activity against key coronaviruses including SARS-CoV-2, SARS-CoV, and MERS-CoV. We hypothesize LOS operates extracellularly, targeting the ACE2-S-protein axis, due to its low cellular permeability. Our investigation combines biolayer interferometry (BLI), isothermal titration calorimetry (ITC)-based experiments with in silico studies, revealing LOS's ability to reduce SARS-CoV-2's RBD's affinity for ACE2 in a dose-dependent manner, and bind tightly to ACE2 without inhibiting its enzymatic activity. Gaussian accelerated molecular dynamics simulations (GaMD) further supported these findings, illustrating LOS's potential as a broad-spectrum antiviral agent against current and future coronavirus strains, meriting in vivo and clinical exploration.
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Affiliation(s)
- Rami Adel Pashameah
- Department of Chemistry, Faculty of Applied Science, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Raya Soltane
- Department of Biology, Adham University College, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Ahmed M. Sayed
- Department of Pharmacognosy, Faculty of Pharmacy, Nahda University, 62513 Beni-Suef, Egypt
- Department of Pharmacognosy, collage of Pharmacy, Almaaqal University, 61014 Basra, Iraq
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Esquivel Gomez LR, Weber A, Kocher A, Kühnert D. Recombination-aware phylogenetic analysis sheds light on the evolutionary origin of SARS-CoV-2. Sci Rep 2024; 14:541. [PMID: 38177346 PMCID: PMC10766966 DOI: 10.1038/s41598-023-50952-1] [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: 10/21/2022] [Accepted: 12/28/2023] [Indexed: 01/06/2024] Open
Abstract
SARS-CoV-2 can infect human cells through the recognition of the human angiotensin-converting enzyme 2 receptor. This affinity is given by six amino acid residues located in the variable loop of the receptor binding domain (RBD) within the Spike protein. Genetic recombination involving bat and pangolin Sarbecoviruses, and natural selection have been proposed as possible explanations for the acquisition of the variable loop and these amino acid residues. In this study we employed Bayesian phylogenetics to jointly reconstruct the phylogeny of the RBD among human, bat and pangolin Sarbecoviruses and detect recombination events affecting this region of the genome. A recombination event involving RaTG13, the closest relative of SARS-CoV-2 that lacks five of the six residues, and an unsampled Sarbecovirus lineage was detected. This result suggests that the variable loop of the RBD didn't have a recombinant origin and the key amino acid residues were likely present in the common ancestor of SARS-CoV-2 and RaTG13, with the latter losing five of them probably as the result of recombination.
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Affiliation(s)
- Luis Roger Esquivel Gomez
- Transmission, Infection, Diversification and Evolution Group (tide), Max Planck Institute of Geoanthropology (Formerly MPI for the Science of Human History), Jena, Germany.
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Phylogenomics Unit, Center for Artificial Intelligence in Public Health Research, Robert Koch Institute, Wildau, Germany.
| | - Ariane Weber
- Transmission, Infection, Diversification and Evolution Group (tide), Max Planck Institute of Geoanthropology (Formerly MPI for the Science of Human History), Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Arthur Kocher
- Transmission, Infection, Diversification and Evolution Group (tide), Max Planck Institute of Geoanthropology (Formerly MPI for the Science of Human History), Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group (tide), Max Planck Institute of Geoanthropology (Formerly MPI for the Science of Human History), Jena, Germany.
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Phylogenomics Unit, Center for Artificial Intelligence in Public Health Research, Robert Koch Institute, Wildau, Germany.
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9
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de Oliveira DF. In silico identification of five binding sites on the SARS-CoV-2 spike protein and selection of seven ligands for such sites. J Biomol Struct Dyn 2023:1-19. [PMID: 37921757 DOI: 10.1080/07391102.2023.2278077] [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: 01/27/2023] [Accepted: 10/26/2023] [Indexed: 11/04/2023]
Abstract
To contribute to the development of products capable of complexing with the SARS-CoV-2 spike protein, and thus preventing the virus from entering the host cell, this work aimed at discovering binding sites in the whole protein structure, as well as selecting substances capable of binding efficiently to such sites. Initially, the three-dimensional structure of the protein, with all receptor binding domains in the closed state, underwent blind docking with 38 substances potentially capable of binding to this protein according to the literature. This allowed the identification of five binding sites. Then, those substances with more affinities for these sites underwent pharmacophoric search in the ZINC15 database. The 14,329 substances selected from ZINC15 were subjected to docking to the five selected sites of the spike protein. The ligands with more affinities for the protein sites, as well as the selected sites themselves, were used in the de novo design of new ligands that were also docked to the binding sites of the protein. The best ligands, regardless of their origins, were used to form complexes with the spike protein, which were subsequently used in molecular dynamics simulations and calculations of ligands affinities to the protein through the molecular mechanics/Poisson-Boltzmann surface area method (MMPBSA). Seven substances with good affinities to the spike protein (-12.9 to -20.6 kcal/mol), satisfactory druggability (Bioavailability score: 0.17 to 0.55), and low acute toxicity to mice (LD50: 751 to 1421 mg/kg) were selected as potentially useful for the future development of new products to manage COVID-19 infections.Communicated by Ramaswamy H. Sarma.
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Peka M, Balatsky V. Analysis of RBD-ACE2 interactions in livestock species as a factor in the spread of SARS-CoV-2 among animals. Vet Anim Sci 2023; 21:100303. [PMID: 37521409 PMCID: PMC10372456 DOI: 10.1016/j.vas.2023.100303] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/01/2023] Open
Abstract
The high mutation rate of SARS-CoV-2, which has led to the emergence of a number of virus variants, creates risks of transmission from humans to animal species and the emergence of new animal reservoirs of COVID-19. This study aimed to identify animal species among livestock susceptible to infection and develop an approach that would be possible to use for assessing the hazards caused by new SARS-CoV-2 variants for animals. Bioinformatic analysis was used to evaluate the ability of receptor-binding domains (RBDs) of different SARS-CoV-2 variants to interact with ACE2 receptors of livestock species. The results indicated that the stability of RBD-ACE2 complexes depends on both amino acid residues in the ACE2 sequences of animal species and on mutations in the RBDs of SARS-CoV-2 variants, with the residues in the interface of the RBD-ACE2 complex being the most important. All studied SARS-CoV-2 variants had high affinity for ferret and American mink receptors, while the affinity for horse, donkey, and bird species' receptors significantly increased in the highly mutated Omicron variant. Hazards that future SARS-CoV-2 variants may acquire specificity to new animal species remain high given the mutability of the virus. The continued use and expansion of the bioinformatic approach presented in this study may be relevant for monitoring transmission risks and preventing the emergence of new reservoirs of COVID-19 among animals.
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Affiliation(s)
- Mykyta Peka
- V. N. Karazin Kharkiv National University, 4 Svobody Sq, Kharkiv, 61022, Ukraine
- Institute of Pig Breeding and Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, 1 Shvedska Mohyla St, Poltava, 36013, Ukraine
| | - Viktor Balatsky
- V. N. Karazin Kharkiv National University, 4 Svobody Sq, Kharkiv, 61022, Ukraine
- Institute of Pig Breeding and Agroindustrial Production, National Academy of Agrarian Sciences of Ukraine, 1 Shvedska Mohyla St, Poltava, 36013, Ukraine
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Hameed NS, Arif IS, Al-Sudani BT. Preventive treatment of coronavirus disease-2019 virus using coronavirus disease-2019-receptor-binding domain 1C aptamer by suppress the expression of angiotensin-converting enzyme 2 receptor. J Adv Pharm Technol Res 2023; 14:185-190. [PMID: 37692001 PMCID: PMC10483903 DOI: 10.4103/japtr.japtr_117_23] [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: 02/26/2023] [Revised: 04/19/2023] [Accepted: 05/13/2023] [Indexed: 09/12/2023] Open
Abstract
The cause of the worldwide coronavirus disease-2019 (COVID-19) pandemic is the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). It is known to employ the same entry portal as SARS-CoV, which is the type 1 transmembrane angiotensin-converting enzyme 2 (ACE2) receptor. The receptor-binding domain (RBD) is located on the spike S-protein's S1 subunit of the spike glycoprotein. The most important and effective therapy method is inhibiting the interaction between the ACE2 receptor and the S-spike RBD. An aptamer is a small, single-chain oligonucleotide that binds strongly to the target molecule. Recently, a CoV-2-RBD-1C aptamer-based system with a 51-base hairpin structure was discovered to have substantial binding affinity against the SARS-CoV-2RBD with similar binding sites at ACE. In the current study, we will study the aptamer's effect as a SARS-CoV-2 spike blocker and inhibit its ACE2 receptors' binding by studying the toxicity of aptamer for this cell line by calcein assay and the inhibition test of CoV-2-RBD-1C aptamers on spike RBD-ACE2 binding. The results show the half-maximum inhibitory concentration of CoV-2-RBD-1C aptamer is 0.08188 μM. The inhibition effect of CoV-2-RBD-1C aptamer on spike RBD-ACE2 binding was determined at half-maximal effective concentration of 0.5 μM concentration. The percentage of spike-ACE2 binding inhibition in A549-hACE2 cells in the D614G variant after 30 s was 77%. This percentage is higher than D614 and N501Y and equals 55% and 65%, respectively, at 0.15 μM of CoV-2-RBD-1C aptamer. The CoV-2-RBD-1C aptamer prevents virus entrance through spike inhibition, which results in a 90% reduction in spike D614 virus transduction at 1.28 μM. In conclusion, the CoV-2-RBD-1C aptamer might be an effective treatment against COVID-19 infection because it directly affects the virus by blocking the S-spike of SARS-CoV-2 and preventing ACE2 receptor binding.
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Affiliation(s)
- Noor S. Hameed
- Department of Toxicology, College of Pharmacy, Mustansiriyah University, Baghdad, Iraq
| | - Inam Sameh Arif
- Department of Toxicology, College of Pharmacy, Mustansiriyah University, Baghdad, Iraq
| | - Basma Talib Al-Sudani
- Department of Clinical Laboratory Sciences, College of Pharmacy, Mustansiriyah University, Baghdad, Iraq
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Astrakhantseva IV, Ershova AE, Chuvpilo SA, Kruglova NA, Ishmukhametov AA, Drutskaya MS, Kozlovskaya LI, Nedospasov SA. SARS-CoV-2 Binding and Neutralization Properties of Peptides Derived from N-Terminus of Human ACE2. Int J Mol Sci 2023; 24:ijms24098269. [PMID: 37175976 PMCID: PMC10179272 DOI: 10.3390/ijms24098269] [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: 04/15/2023] [Revised: 04/27/2023] [Accepted: 05/03/2023] [Indexed: 05/15/2023] Open
Abstract
The binding properties of synthetic and recombinant peptides derived from N-terminal part of ACE2, the main receptor for SARS-CoV-2, were evaluated. Additionally, the ability of these peptides to prevent virus entry in vitro was addressed using both pseudovirus particles decorated with the S protein, as well as through infection of Vero cells with live SARS-CoV-2 virus. Surprisingly, in spite of effective binding to S protein, all linear peptides of various lengths failed to neutralize the viral infection in vitro. However, the P1st peptide that was chemically "stapled" in order to stabilize its alpha-helical structure was able to interfere with virus entry into ACE2-expressing cells. Interestingly, this peptide also neutralized pseudovirus particles decorated with S protein derived from the Omicron BA.1 virus, in spite of variations in key amino acid residues contacting ACE2.
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Affiliation(s)
- Irina V Astrakhantseva
- Division of Immunobiology and Biomedicine, Sirius University of Science and Technology, Sirius, Krasnodarsky Krai, 354349 Sochi, Russia
| | - Alina E Ershova
- Division of Immunobiology and Biomedicine, Sirius University of Science and Technology, Sirius, Krasnodarsky Krai, 354349 Sochi, Russia
| | - Sergei A Chuvpilo
- Division of Immunobiology and Biomedicine, Sirius University of Science and Technology, Sirius, Krasnodarsky Krai, 354349 Sochi, Russia
| | - Natalia A Kruglova
- Laboratory of Gene Therapy of Socially Significant Diseases, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, 119334 Moscow, Russia
| | - Aydar A Ishmukhametov
- Department of Emerging and Reemerging Infections, Chumakov Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences (Institute of Poliomyelitis), 108819 Moscow, Russia
- Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Marina S Drutskaya
- Laboratory of Molecular Mechanisms of Immunity, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Liubov I Kozlovskaya
- Department of Emerging and Reemerging Infections, Chumakov Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences (Institute of Poliomyelitis), 108819 Moscow, Russia
- Institute for Translational Medicine and Biotechnology, Sechenov First Moscow State Medical University (Sechenov University), 119435 Moscow, Russia
| | - Sergei A Nedospasov
- Division of Immunobiology and Biomedicine, Sirius University of Science and Technology, Sirius, Krasnodarsky Krai, 354349 Sochi, Russia
- Laboratory of Molecular Mechanisms of Immunity, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991 Moscow, Russia
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