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Ahuja R, Vishwakarma P, Raj S, Kumar V, Khatri R, Lohiya B, Saxena S, Kaur G, Singh G, Asthana S, Ahmed S, Samal S. Characterization and immunogenicity assessment of MERS-CoV pre-fusion spike trimeric oligomers as vaccine immunogen. Hum Vaccin Immunother 2024; 20:2351664. [PMID: 38757508 PMCID: PMC11110700 DOI: 10.1080/21645515.2024.2351664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 05/01/2024] [Indexed: 05/18/2024] Open
Abstract
Middle East respiratory syndrome coronavirus (MERS-CoV) is a lethal beta-coronavirus that emerged in 2012. The virus is part of the WHO blueprint priority list with a concerning fatality rate of 35%. Scientific efforts are ongoing for the development of vaccines, anti-viral and biotherapeutics, which are majorly directed toward the structural spike protein. However, the ongoing effort is challenging due to conformational instability of the spike protein and the evasion strategy posed by the MERS-CoV. In this study, we have expressed and purified the MERS-CoV pre-fusion spike protein in the Expi293F mammalian expression system. The purified protein was extensively characterized for its biochemical and biophysical properties. Thermal stability analysis showed a melting temperature of 58°C and the protein resisted major structural changes at elevated temperature as revealed by fluorescence spectroscopy and circular dichroism. Immunological assessment of the MERS-CoV spike immunogen in BALB/c mice with AddaVaxTM and Imject alum adjuvants showed elicitation of high titer antibody responses but a more balanced Th1/Th2 response with AddaVaxTM squalene like adjuvant. Together, our results suggest the formation of higher-order trimeric pre-fusion MERS-CoV spike proteins, which were able to induce robust immune responses. The comprehensive characterization of MERS-CoV spike protein warrants a better understanding of MERS spike protein and future vaccine development efforts.
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MESH Headings
- Middle East Respiratory Syndrome Coronavirus/immunology
- Animals
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/genetics
- Mice, Inbred BALB C
- Antibodies, Viral/immunology
- Antibodies, Viral/blood
- Viral Vaccines/immunology
- Mice
- Female
- Coronavirus Infections/prevention & control
- Coronavirus Infections/immunology
- Immunogenicity, Vaccine
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/blood
- Adjuvants, Immunologic/administration & dosage
- Adjuvants, Vaccine
- Humans
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Affiliation(s)
- Rahul Ahuja
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Preeti Vishwakarma
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Sneha Raj
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Varun Kumar
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Ritika Khatri
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Bharat Lohiya
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Shikha Saxena
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Gurleen Kaur
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Gagandeep Singh
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
- Computational Biophysics and CADD Group, Computational and Mathematical Biology Center (CMBC), Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Shailendra Asthana
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
- Computational Biophysics and CADD Group, Computational and Mathematical Biology Center (CMBC), Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
| | - Shubbir Ahmed
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
- Centralized Core Research Facility (CCRF), All India Institute of Medical Sciences (AIIMS), New Delhi, India
| | - Sweety Samal
- Influenza and Respiratory Virus Laboratory, Translational Health Science and Technology Institute (THSTI), NCR-Biotech Science Cluster, Faridabad, Haryana, India
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Sharma S, Singh M, Chiranjivi AK, Dadwal A, Ahmed S, Asthana S, Das S. Structural insights into trypanosomatid Mnk kinase orthologues (kMnks) suggest altered mechanism in the kinase domain. Int J Biol Macromol 2024; 277:134428. [PMID: 39097052 DOI: 10.1016/j.ijbiomac.2024.134428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/31/2024] [Accepted: 07/31/2024] [Indexed: 08/05/2024]
Abstract
Mitogen-activated protein kinase (MAPK) interacting protein kinases (Mnk1 and Mnk2) mediated phosphorylation of the eukaryotic initiation factor eIF4E is an important translation initiation control, in Mnk-mediated oncogenic activity and other disease conditions. Thus, Mnk kinases are an important target for therapy. Trypanosomatids are a class of kinetoplastids, some of which are protozoan parasites and cause diseases in humans. While protein translation initiation is well understood in eukaryotes and prokaryotes, there is a lack of sufficient structural information of this process in trypanosomatids. Here, we report that trypanosomatids have one orthologue of Mnk kinase with low overall sequence homology but high homology in the kinase domain and an additional C-terminal domain containing putative calmodulin binding site(s). We show that while many of the domains and motifs are conserved, homology modeling/structure prediction, docking analysis and molecular dynamics simulation studies suggest that trypanosomatid kMnk kinases, kinase domains are present in DFG-in conformation as opposed to the auto-inhibited DFD-out conformation of un-phosphorylated human Mnk1. Furthermore, we observed that several regulatory features are different in trypanosomatid kMnk kinases. Our study indicates that mechanism and regulation in the kinase domain of trypanosomatid kMnks are likely to be altered, and that they can be important drug targets.
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Affiliation(s)
- Shilpa Sharma
- Computational Biophysics and CADD Group, Computational and Mathematical Biology Center (CMBC), Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India
| | - Mrityunjay Singh
- Computational Biophysics and CADD Group, Computational and Mathematical Biology Center (CMBC), Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India
| | | | - Anica Dadwal
- Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India
| | - Shubbir Ahmed
- Centralized Core Research Facility (CCRF), All India Institute of Medical Science (AIIMS), New Delhi 110029, India
| | - Shailendra Asthana
- Computational Biophysics and CADD Group, Computational and Mathematical Biology Center (CMBC), Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India.
| | - Supratik Das
- Translational Health Science and Technology Institute, Faridabad 121001, Haryana, India.
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Yu T, Sudhakar N, Okafor CD. Illuminating ligand-induced dynamics in nuclear receptors through MD simulations. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2024; 1867:195025. [PMID: 38614450 DOI: 10.1016/j.bbagrm.2024.195025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Revised: 03/27/2024] [Accepted: 04/06/2024] [Indexed: 04/15/2024]
Abstract
Nuclear receptors (NRs) regulate gene expression in critical physiological processes, with their functionality finely tuned by ligand-induced conformational changes. While NRs may sometimes undergo significant conformational motions in response to ligand-binding, these effects are more commonly subtle and challenging to study by traditional structural or biophysical methods. Molecular dynamics (MD) simulations are a powerful tool to bridge the gap between static protein-ligand structures and dynamical changes that govern NR function. Here, we summarize a handful of recent studies that apply MD simulations to study NRs. We present diverse methodologies for analyzing simulation data with a detailed examination of the information each method can yield. By delving into the strengths, limitations and unique contributions of these tools, this review provides guidance for extracting meaningful data from MD simulations to advance the goal of understanding the intricate mechanisms by which ligands orchestrate a range of functional outcomes in NRs.
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Affiliation(s)
- Tracy Yu
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Nishanti Sudhakar
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - C Denise Okafor
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA 16802, USA; Department of Chemistry, Pennsylvania State University, University Park, PA 16802, USA.
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Agarwal S, Saha S, Ghosh R, Sarmadhikari D, Asthana S, Maiti TK, Khadgawat R, Guchhait P. Elevated glycosylation of CD36 in platelets is a risk factor for oxLDL-mediated platelet activation in type 2 diabetes. FEBS J 2024; 291:376-391. [PMID: 37845743 DOI: 10.1111/febs.16976] [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: 06/27/2023] [Revised: 08/19/2023] [Accepted: 10/12/2023] [Indexed: 10/18/2023]
Abstract
Platelet activation and related cardiovascular complications are the hallmarks of type 2 diabetes (T2D). We investigated the mechanism of platelet activation in T2D using MS-based identification of differentially expressed platelet proteins with a focus on glycosylated forms. Glycosylation is considered one of the common post-translational modifications in T2D, and N/O-linked glycosylation of glycoproteins (GPs)/integrins is known to play crucial roles in platelet activation. Our platelet proteome data revealed elevated levels of GPs GPIbα, GPIIbIIIa, GPIV (CD36), GPV and integrins in T2D patients. T2D platelets had elevated N-linked glycosylation of CD36 at asparagine (Asn)408,417 . Enrichment analysis revealed a close association of glycosylated CD36 with thrombospondin-1, fibrinogen and SERPINA1 in T2D platelets. The glycosylation of CD36 has previously been reported to increase cellular uptake of long-chain fatty acids. Our in silico molecular docking data also showed a favorable binding of cholesterol with glycosylated Asn417 CD36 compared to the non-glycosylated form. We further investigated the CD36:LDL cholesterol axis in T2D. Elevated levels of oxidized-low density lipoprotein (oxLDL) were found to cause significant platelet activation via CD36-mediated stimulation of Lyn-JNK signaling. Sulfo-N-succinimidyl oleate, an inhibitor of CD36, effectively inhibited oxLDL-mediated platelet activation and adhesion in vitro. Our study suggests increased glycosylation of CD36 in T2D platelets as a potential route for oxLDL-mediated platelet activation. The oxLDL:CD36 axis may thus be exploited as a prospective target to develop therapeutics against thrombosis in T2D.
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Affiliation(s)
- Sakshi Agarwal
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India
| | - Sandhini Saha
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India
| | - Riya Ghosh
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India
| | - Debapriyo Sarmadhikari
- Translational Health Science Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, India
| | - Shailendra Asthana
- Translational Health Science Technology Institute, National Capital Region Biotech Science Cluster, Faridabad, India
| | - Tushar K Maiti
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India
| | | | - Prasenjit Guchhait
- Regional Centre for Biotechnology, National Capital Region Biotech Science Cluster, Faridabad, India
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Mir YR, Agrahari AK, Hassan A, Choudhary A, Asthana S, Taneja AK, Nawaz S, Ilyas M, Scotti C, Kuchay RAH. Identification and structural characterization of a pathogenic ARSA missense variant in two consanguineous families from Jammu and Kashmir (India) with late infantile metachromatic leukodystrophy. Mol Biol Rep 2023; 51:30. [PMID: 38153581 DOI: 10.1007/s11033-023-09072-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2023] [Accepted: 11/01/2023] [Indexed: 12/29/2023]
Abstract
BACKGROUND Metachromatic leukodystrophy (MLD) is a rare lysosomal storage disorder caused by a deficiency of Arylsulfatase A (ARSA) enzyme activity. Its clinical manifestations include progressive motor and cognitive decline. ARSA gene mutations are frequent in MLD. METHODS AND RESULTS In the present study, whole exome sequencing (WES) was employed to decipher the genetic cause of motor and cognitive decline in proband's of two consanguineous families from J&K (India). Clinical investigations using radiological and biochemical analysis revealed MLD-like features. WES confirmed a pathogenic variant in the ARSA gene. Molecular simulation dynamics was applied for structural characterization of the variant. CONCLUSION We report the identification of a pathogenic missense variant (c.1174 C > T; p.Arg390Trp) in the ARSA gene in two cases of late infantile MLD from consanguineous families in Jammu and Kashmir, India. Our study utilized genetic analysis and molecular dynamics simulations to identify and investigate the structural consequences of this mutation. The molecular dynamics simulations revealed significant alterations in the structural dynamics, residue interactions, and stability of the ARSA protein harbouring the p.Arg390Trp mutation. These findings provide valuable insights into the molecular mechanisms underlying the pathogenicity of this variant in MLD.
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Affiliation(s)
- Yaser Rafiq Mir
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, J&K, 185234, India
| | - Ashish Kumar Agrahari
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Asima Hassan
- Department of Ophthalmology GMC Srinagar, Srinagar, J&K, India
| | | | - Shailendra Asthana
- Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana, India
| | - Atul Kumar Taneja
- Department of Radiology, UT Southwestern Medical Center, Dallas, TX, USA
| | - Shah Nawaz
- Department of Pediatrics, GMC Jammu, Jammu, J&K, India
| | | | - Claudia Scotti
- Department of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, Italy
| | - Raja A H Kuchay
- Department of Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, J&K, 185234, India.
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Khatri R, Lohiya B, Kaur G, Maithil V, Goswami A, Sarmadhikari D, Asthana S, Samal S. Understanding the role of conserved proline and serine residues in the SARS-CoV-2 spike cleavage sites in the virus entry, fusion, and infectivity. 3 Biotech 2023; 13:323. [PMID: 37663753 PMCID: PMC10469153 DOI: 10.1007/s13205-023-03749-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 07/27/2023] [Indexed: 09/05/2023] Open
Abstract
The spike (S) glycoprotein of the SARS-CoV-2 virus binds to the host cell receptor and promotes the virus's entry into the target host cell. This interaction is primed by host cell proteases like furin and TMPRSS2, which act at the S1/S2 and S2´ cleavage sites, respectively. Both cleavage sites have serine or proline residues flanking either the single or polybasic region and were found to be conserved in coronaviruses. Unravelling the effects of these conserved residues on the virus entry and infectivity might facilitate the development of novel therapeutics. Here, we have investigated the role of the conserved serine and proline residues in the SARS-CoV-2 spike mediated entry, fusogenicity, and viral infectivity by using the HIV-1/spike-based pseudovirus system. A conserved serine residue mutation to alanine (S2´S-A) at the S2´ cleavage site resulted in the complete loss of spike cleavage. Exogenous treatment with trypsin or overexpression of TMPRSS2 protease could not rescue the loss of spike cleavage and biological activity. The S2´S-A mutant showed no significant responses against E-64d, TMPRSS2 or other relevant inhibitors. Taken together, serine at the S2´ site in the spike protein was indispensable for spike protein cleavage and virus infectivity. Thus, novel interventions targeting the conserved serine at the S2´ cleavage site should be explored to reduce severe disease caused by SARS-CoV-2-and novel emerging variants. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03749-y.
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Affiliation(s)
- Ritika Khatri
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Bharat Lohiya
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Gurleen Kaur
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Vikas Maithil
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Abhishek Goswami
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Debapriyo Sarmadhikari
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Shailendra Asthana
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
| | - Sweety Samal
- Translational Health Science & Technology Institute, NCR Biotech Science Cluster, Faridabad, Haryana 121001 India
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