Browsing by Author "Ekta Pathak"

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A novel mutation in FRMD7 causes X-linked idiopathic congenital nystagmus in a North Indian family
(Elsevier Ireland Ltd, 2015) Shashank Gupta; Ekta Pathak; Vidya Nair Chaudhry; Prashaant Chaudhry; Rajeev Mishra; Abhishek Chandra; Ashim Mukherjee; Mousumi Mutsuddi
Idiopathic congenital nystagmus (ICN) is the most common form of oculomotor disorder characterized by involuntary bilateral ocular oscillations. Primarily the disease is an ocular anomaly but the pathophysiology is associated with neuronal cytoskeletal dynamics in the brain. In the current study, a three generation North Indian family affected with X-linked idiopathic congenital nystagmus (XLICN) was recruited. Our aim was to identify the causal mutation for ICN in the family by screening the candidate gene, FERM domain containing-7 (. FRMD7). This gene has been implicated in XLICN as it regulates neuronal cytoskeletal proteins and neurite outgrowth in the developing brain. Therefore, the entire protein coding region, including splice junctions, 5' UTR and 3' UTR of FRMD7 was screened by PCR-Sanger sequencing. Targeted sequencing revealed a novel A to G transition in the exon seven (c.556A.>. G), resulting in a conservative substitution of methionine by valine at codon 186 (p.M186V). A cohort of healthy individuals was also checked for presence of the putative causal variant by allele specific PCR. All the affected males and carriers in the family shared this variant; however, this was absent in the unaffected males as well as 100 unrelated healthy individuals. Further, protein homology modeling revealed that the change p.M186V might destabilize the interaction between the FERM-M and FERM-C domains. The in silico prediction supports pathogenicity of the mutation; nevertheless it needs in vivo validation in the future. This is the first genetic investigation of XLICN in a North Indian family where we report a novel causal mutation c.556A. >. G (p.M186V) in the gene FRMD7. © 2015 Elsevier Ireland Ltd.
Computational exploration of the dual role of the phytochemical fortunellin: Antiviral activities against SARS-CoV-2 and immunomodulatory abilities against the host
(Elsevier Ltd, 2022) Shivangi Agrawal; Ekta Pathak; Rajeev Mishra; Vibha Mishra; Afifa Parveen; Sunil Kumar Mishra; Parameswarappa S. Byadgi; Sushil Kumar Dubey; Ashvanee Kumar Chaudhary; Vishwambhar Singh; Rameshwar Nath Chaurasia; Neelam Atri
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infections generate approximately one million virions per day, and the majority of available antivirals are ineffective against it due to the virus's inherent genetic mutability. This necessitates the investigation of concurrent inhibition of multiple SARS-CoV-2 targets. We show that fortunellin (acacetin 7-O-neohesperidoside), a phytochemical, is a promising candidate for preventing and treating coronavirus disease (COVID-19) by targeting multiple key viral target proteins. Fortunellin supports protective immunity while inhibiting pro-inflammatory cytokines and apoptosis pathways and protecting against tissue damage. Fortunellin is a phytochemical found in Gojihwadi kwath, an Indian traditional Ayurvedic formulation with an antiviral activity that is effective in COVID-19 patients. The mechanistic action of its antiviral activity, however, is unknown. The current study comprehensively evaluates the potential therapeutic mechanisms of fortunellin in preventing and treating COVID-19. We have used molecular docking, molecular dynamics simulations, free-energy calculations, host target mining of fortunellin, gene ontology enrichment, pathway analyses, and protein-protein interaction analysis. We discovered that fortunellin reliably binds to key targets that are necessary for viral replication, growth, invasion, and infectivity including Nucleocapsid (N-CTD) (−54.62 kcal/mol), Replicase-monomer at NSP-8 binding site (−34.48 kcal/mol), Replicase-dimer interface (−31.29 kcal/mol), Helicase (−30.02 kcal/mol), Papain-like-protease (−28.12 kcal/mol), 2′-O-methyltransferase (−23.17 kcal/mol), Main-protease (−21.63 kcal/mol), Replicase-monomer at dimer interface (−22.04 kcal/mol), RNA-dependent-RNA-polymerase (−19.98 kcal/mol), Nucleocapsid-NTD (−16.92 kcal/mol), and Endoribonuclease (−16.81 kcal/mol). Furthermore, we identify and evaluate the potential human targets of fortunellin and its effect on the SARS-CoV-2 infected tissues, including normal-human-bronchial-epithelium (NHBE) and lung cells and organoids such as pancreatic, colon, liver, and cornea using a network pharmacology approach. Thus, our findings indicate that fortunellin has a dual role; multi-target antiviral activities against SARS-CoV-2 and immunomodulatory capabilities against the host. © 2022 Elsevier Ltd
Deciphering the role of the two conserved motifs of the ECF41 family σ factor in the autoregulation of its own promoter in Azospirillum brasilense Sp245
(John Wiley and Sons Inc, 2022) Ekta Pathak; Ashutosh Prakash Dubey; Vijay Shankar Singh; Rajeev Mishra; Anil Kumar Tripathi
In Azospirillum brasilense, an extra-cytoplasmic function σ factor (RpoE10) shows the characteristic 119 amino acid long C-terminal extension found in ECF41-type σ factors, which possesses three conserved motifs (WLPEP, DGGGR, and NPDKV), one in the linker region between the σ2 and σ4, and the other two in the SnoaL_2 domain of the C-terminal extension. Here, we have described the role of the two conserved motifs in the SnoaL_2 domain of RpoE10 in the inhibition and activation of its activity, respectively. Truncation of the distal part of the C-terminal sequence of the RpoE10 (including NPDKV but excluding the DGGGR motif) results in its promoter's activation suggesting autoregulation. Further truncation of the C-terminal sequence up to its proximal part, including NPDKV and DGGGR motif, abolished promoter activation. Replacement of NPDKV motif with NAAAV in RpoE10 increased its ability to activate its promoter, whereas replacement of DGGGR motif led to reduced promoter activation. We have explored the dynamic modulation of σ2 -σ4 domains and the relevant molecular interactions mediated by the two conserved motifs of the SnoaL2 domain using molecular dynamics simulation. The analysis enabled us to explain that the NPDKV motif located distally in the C-terminus negatively impacts transcriptional activation. In contrast, the DGGGR motif found proximally of the C-terminal extension is required to activate RpoE10. © 2022 Wiley Periodicals LLC.
Evaluation of binding of potential ADMET/tox screened saquinavir analogues for inhibition of HIV-protease via molecular dynamics and binding free energy calculations
(Taylor and Francis Ltd., 2022) Amit Jayaswal; Ekta Pathak; Hirdyesh Mishra; Kavita Shah
Developing novel drug molecules against HIV is a scientific quest necessitated by development of drug resistance against used drugs. We report comparative results of molecular dynamics simulation studies on 11 structural analogues of Saquinavir (SQV)–against HIV-protease that were earlier examined for pharmacodynamic and pharmacokinetic properties. We reported analogues S1, S5 and S8 to qualify the ADMET criterion and may be considered as potential lead molecules. In this study the designed molecules were successively docked with native HIV-protease at AutoDock. Docking scores established relative goodness of the 11 analogues against the benchmark for Saquinavir. The docked complexes were subjected to molecular dynamics simulation studies using GROMACS 4.6.2. Four parameters viz. H-bonding, RMSD, Binding energy and Protein–Ligand Distance were used for comparative analyses of the analogues relative to Saquinavir. The comparison and analysis of the results are indicative that analogues S8, S9 and S1 are promising candidates among all the analogues studied. From our earlier work and present study it is evident that among the three S8 and S1 qualify the ADMET criterion and between S1 and S8, the analogue S8 shows more target efficacy and specificity over S1 and have better molecular dynamics simulation results. Thus, of the 11 de novo Saquinavir analogues, the S8 appears to be the most promising candidate as lead molecule for HIV-protease inhibitor and is best suited for testing under biological system. Further validation of the proposed lead molecules through wet lab studies involving antiviral assays however is required. Communicated by Ramaswamy H. Sarma. © 2021 Informa UK Limited, trading as Taylor & Francis Group.
Single-Cell Transcriptome Analysis Reveals the Role of Pancreatic Secretome in COVID-19 Associated Multi-organ Dysfunctions
(Springer Science and Business Media Deutschland GmbH, 2022) Ekta Pathak; Neelam Atri; Rajeev Mishra
The SARS-CoV-2 infection affects the lungs, heart, kidney, intestine, olfactory epithelia, liver, and pancreas and brings forward multi-organ dysfunctions (MODs). However, mechanistic details of SARS-CoV-2-induced MODs are unclear. Here, we have investigated the role of pancreatic secretory proteins to mechanistically link COVID-19 with MODs using single-cell transcriptome analysis. Secretory proteins were identified using the Human Protein Atlas. Gene ontology, pathway, and disease enrichment analyses were used to highlight the role of upregulated pancreatic secretory proteins (secretome). We show that SARS-CoV-2 infection shifts the expression profile of pancreatic endocrine cells to acinar and ductal cell-specific profiles, resulting in increased expression of acinar and ductal cell-specific genes. Among all the secretory proteins, the upregulated expression of IL1B, AGT, ALB, SPP1, CRP, SERPINA1, C3, TFRC, TNFSF10, and MIF was mainly associated with disease of diverse organs. Extensive literature and experimental evidence are used to validate the association of the upregulated pancreatic secretome with the coagulation cascade, complement activation, renin-angiotensinogen system dysregulation, endothelial cell injury and thrombosis, immune system dysregulation, and fibrosis. Our finding suggests the influence of an upregulated secretome on multi-organ systems such as nervous, cardiovascular, immune, digestive, and urogenital systems. Our study provides evidence that an upregulated pancreatic secretome is a possible cause of SARS-CoV-2-induced MODs. This finding may have a significant impact on the clinical setting regarding the prevention of SARS-CoV-2-induced MODs. Graphical abstract: [Figure not available: see fulltext.] © 2022, International Association of Scientists in the Interdisciplinary Areas.
Targeting Matrix Metalloproteinase-1, Matrix Metalloproteinase-7, and Serine Protease Inhibitor E1: Implications in preserving lung vascular endothelial integrity and immune modulation in COVID-19
(Elsevier B.V., 2025) Vibha Mishra; Shivangi Agrawal; Divya Malik; Divya Mishra; Bhavya Bhavya; Ekta Pathak; Rajeev Kumar Mishra
Background: SARS-CoV-2 disrupts lung vascular endothelial integrity, contributing to severe COVID-19 complications. However, the molecular mechanisms driving endothelial dysfunction remain underexplored, and targeted therapeutic strategies are lacking. Objective: This study investigates Naringenin-7-O-glucoside (N7G) as a multi-target therapeutic candidate for modulating vascular integrity and immune response by inhibiting MMP1, MMP7, and SERPINE1—key regulators of extracellular matrix (ECM) remodeling and inflammation. Methods & results: RNA-seq analysis of COVID-19 lung tissues identified 17 upregulated N7G targets, including MMP1, MMP7, and SERPINE1, with the latter exhibiting the highest expression. PPI network analysis linked these targets to ECM degradation, IL-17, HIF-1, and AGE-RAGE signaling pathways, and endothelial dysfunction. Disease enrichment associated these genes with idiopathic pulmonary fibrosis and asthma. Molecular docking, 200 ns MD simulations (triplicate), and MMGBSA calculations confirmed N7G's stable binding affinity to MMP1, MMP7, and SERPINE1. Immune profiling revealed increased neutrophils and activated CD4+ T cells, alongside reduced mast cells, NK cells, and naïve B cells, indicating immune dysregulation. Correlation analysis linked MMP1, MMP7, and SERPINE1 to distinct immune cell populations, supporting N7G's immunomodulatory role. Conclusion: These findings suggest that N7G exhibits multi-target therapeutic potential by modulating vascular integrity, ECM remodeling, and immune dysregulation, positioning it as a promising candidate for mitigating COVID-19-associated endothelial dysfunction. © 2025 Elsevier B.V.
Unveiling the molecular mechanisms of hemorrhagic shock and acute lung injury: An integrative RNA-Seq and network analysis
(Elsevier Inc., 2025) Manjaree Mishra; Shivangi Agrawal; Shashi Prakash Mishra; Rajiv Kumar; Katyayani Mishra; Ekta Pathak; Rajeev Kumar Mishra
Acute lung injury (ALI), especially when resulting from trauma-associated hemorrhagic shock (THS), is a life-threatening condition with limited treatment options and high mortality. Understanding the molecular mechanisms driving ALI in this context is essential to identify reliable biomarkers and therapeutic targets. This study aimed to explore the transcriptomic alterations and protein interaction networks in a rat model of THS-induced ALI using RNA sequencing and bioinformatics tools. RNA-seq analysis was performed on lung tissues from five THS-induced and five normal rats. Analysis revealed 1003 differentially expressed genes, including 365 upregulated and 638 downregulated. Functional enrichment pointed to significant involvement of pathways related to oxidative stress, hypoxia response, neutrophil degranulation, ferroptosis, and immune activation. Protein-protein interaction network analysis identified four key gene modules, with Module 3 notably associated with iron metabolism and neutrophilic inflammation. Hub genes such as Cd163, Nqo1, Gclc, Lcn2, and Mmp8 were identified as central regulators and validated in independent samples (three THS-induced and three controls). Lcn2 and cathepsins (CTSS, CTSK, CTSL) emerged as particularly relevant for their multifaceted roles in inflammation, iron homeostasis, and matrix remodeling. These findings provide novel insights into the immunometabolic dysregulation underlying THS-induced ALI and suggest promising molecular targets for future therapeutic interventions aimed at mitigating lung injury in critically injured trauma patients. © 2025
Whole exome sequencing unveils a frameshift mutation in CNGB3 for cone dystrophy
(Lippincott Williams and Wilkins, 2017) Shashank Gupta; Amit Chaurasia; Ekta Pathak; Rajeev Mishra; Vidya Nair Chaudhry; Prashaant Chaudhry; Ashim Mukherjee; Mousumi Mutsuddi
Rationale:Genetic elucidation of cone-dominated retinal dystrophies in Indian subcontinent is much needed to identify and catalog underlying genetic defects. In this context, the present study recruited a consanguineous Indian family affected with autosomal recessive cone dystrophy (CD). Considering the huge genetic heterogeneity and recessive inheritance of the disease, we chose to dissect out causal variant in this family by whole exome sequencing (WES). Patient concerns:In the recruited family, three of the six siblings had complaints of poor visual acuity, photophobia, and disturbed colour vision since early childhood. Fundus examination disclosed vascular attenuation and macular retinal pigment epithelium (RPE) changes in all the affected siblings, signifying degeneration of photoreceptor cells. Diagnosis:Complete clinical investigation and electroretinography studies led to the diagnosis of cone dystrophy in three siblings of the family. Interventions:Detailed ophthalmic examination, including family history, visual function testing, and retinal imaging, was performed. We captured and sequenced exomes of 2 affected siblings and their mother using SureSelect Human All Exon V5 Kit on Illumina HiSeq 2000/2500 platform with 100 bp paired-end sequencing method. Candidates after data analysis were screened by segregation analysis and Sanger sequencing. Considering recessive inheritance and consanguinity in the pedigree, we attempted to map large loci homozygous by descent in the genome of patients using exome sequencing variants. Extensive protein modeling was carried out to assess possible consequences of the identified variant on the 3-dimensional structure of the protein. Outcomes:WES generated more than 65,000 variants for each individual. Assuming recessive inheritance, 13,026 variants were selected. Further filtering on the basis of their position in gene, class, and minor allele frequency constricted the huge list to 12 rare variants. Finally, we ascertained a single base deletion c.1148delC (p.Thr383fs) in the gene CNGB3 as the causal variant. This is a recurrent frameshift mutation resulting in truncated CNGB3 protein. We mapped a large 15-Mb stretch of homozygous markers spanning the causal variant in the proband. The gene CNGB3 encodes modulatory subunit of cyclic nucleotide-gated channels in cone photoreceptors. Protein modeling reveals loss of 2 transmembrane helices and conserved CAP-ED domain in truncated CNGB3, which eventually is predicted to form nonfunctional channels and hamper phototransduction. Lessons:We have identified a recurrent mutation c.1148delC (p.Thr383fs) in CNGB3 for autosomal recessive CD. The present report provides the first description of CNGB3 mutation from India. It is also the foremost investigation of familial CD in Indian patients; therefore, it presents the primary genetic etiology of CD in India. © 2017 the Author(s). Published by Wolters Kluwer Health, Inc.