Biology subjects

Rajagopal, R.

Publications and source records attributed to Rajagopal, R..

5 recordsLinked to original sources

bioRxiv2026

Deciphering the Molecular Structure of the Type III Secretion System in Chlamydia trachomatis for Structure-Based Therapeutic Targeting

Chlamydia trachomatis is an obligate intracellular pathogen that causes sexually transmitted infections and trachoma. Its persistent forms show reduced antibiotic susceptibility, creating a need for new antivirulence strategies. The C. trachomatis injectisome or type III Secretion System (T3SS) injects effector proteins into host cells, yet the molecular structure of the complete apparatus is unknown. Here, we identify and validate all 13 T3SS constituent proteins using TXSSScan and reverse-BLAST analysis, and model and assemble them into the complete T3SS apparatus using an integrated computational pipeline. Template-based modeling revealed a conserved architecture despite low sequence identity (18-46%), and the assemblies were validated stereochemically and energetically against homolog controls. Targeting the oligomerization interface of the CdsN ATPase through structure-based virtual screening of the e-Drug3D and IMPPAT libraries, followed by ADMET filtering, including predicted membrane permeability for intracellular targeting, identified three repurposable FDA-approved candidates: M Roflumilast, Elacestrant, and Tecovirimat. MM-GBSA calculations and molecular dynamics simulations confirmed stable complexes with two adjacent CdsN monomers. Elacestrant showed the most favorable binding free energy. These results provide the first molecular-level map of the C. trachomatis T3SS and a rational basis for antivirulence drug repurposing. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=93 SRC="FIGDIR/small/723290v2_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@6893c8org.highwire.dtl.DTLVardef@1be5eddorg.highwire.dtl.DTLVardef@1462b25org.highwire.dtl.DTLVardef@1baadab_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2026

PARP16 protects against cardiac hypertrophic response by ADP-ribosylation-dependent inhibition of NFAT transcription factor

Mono-ADP-ribosylation is a post-translational modification that regulates diverse cellular processes. PARP16 is an endoplasmic reticulum-associated mono-ADP-ribosyltransferase implicated in stress-response signalling; however, its role in cardiac remodelling and dysfunction has not been fully defined. Our results suggest that PARP16 expression was reduced in human heart failure samples. Deletion of PARP16 in several mice models promoted ventricular dilatation, fibrosis, fetal gene reactivation, and systolic dysfunction, whereas cardiomyocyte-specific overexpression of PARP16 attenuated isoproterenol-induced remodelling in mice. Transcriptomic profiling and functional studies identified NFAT signalling as a major downstream pathway activated following PARP16 deficiency. Specifically, loss of PARP16 increased nuclear accumulation, promoter occupancy, and transcriptional activity of NFAT1. Mechanistically, PARP16 interacted with NFAT1 and suppressed NFAT-dependent transcription through a catalytic activity-dependent mechanism. Proteomic, structural, and functional analyses identified E398 and T533 residues of NFAT1 associated with PARP16-mediated regulation. Furthermore, pharmacological inhibition of NFAT improved cardiac function and remodelling in PARP16-deficient mice. These findings indicate that PARP16 acts as a negative regulator of NFAT signalling and contributes to protection against adverse cardiac remodelling.

cell biology↗

bioRxiv2026

Structural Characterization of the Type IV Secretion System in Brucella melitensis for Virtual Screening-Based Therapeutic Targeting

Brucellosis is a globally important zoonotic disease caused by Brucella melitensis, the most virulent and clinically significant species affecting both humans and livestock. Unlike many Gram-negative pathogens, B. melitensis, a facultative intracellular pathogen, lacks conventional virulence factors and instead relies on specialized systems such as the Type IV Secretion System (T4SS) for secretion of effector proteins. In this study, an integrated computational pipeline was implemented to identify, model, and assemble the T4SS components, encoded by virB operon, from the complete B. melitensis proteome. Template-based modeling strategies were employed to generate structures of T4SS subcomplexes, referencing crystallographic data from E. coli T4SS. Structural superposition with E. coli homologs revealed highly conserved architecture despite only 30-50% sequence identity. Stereochemical validation confirmed high model quality and favorable interactions among most VirB protein pairs. Membrane insertion analysis of the membrane-embedded assemblies further corroborated the spatial orientation of the modeled T4SS. Potential of T4SS as a drug target was explored by targeting dimeric interface of VirB11 ATPase to disrupt protein-protein interactions that could disarm the pathogen. Virtual screening of compounds from DrugBank database revealed compounds with docking score [≤] -7.0 kcal/mol that were screened based on ADMET properties, yielding three promising candidates - Ezetimibe (Drug Id: DB00973), Chlordiazepoxide (Drug Id: DB00475), and Alloin (Drug Id: DB15477). MM-GBSA analysis estimated favorable binding free energies for these compounds and molecular dynamics simulation for 200 ns further confirmed the protein-ligand interaction stability. Collectively, these findings provide new insights into the architecture of B. melitensis T4SS and identify three potential drug molecules targeting T4SS. This supports FDA - approved drug repurposing as an effective strategy for anti-virulence therapy against Brucellosis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/706537v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@847c4borg.highwire.dtl.DTLVardef@1fc2551org.highwire.dtl.DTLVardef@f62a7corg.highwire.dtl.DTLVardef@15f3468_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2019

Transcription factors NFIA and NFIB induce cellular differentiation high-grade astrocytoma

Astrocytomas are composed of heterogeneous cell populations. Compared to grade IV glioblastoma, low-grade astrocytomas have more differentiated cells and are associated with a better prognosis. Therefore, inducing cellular differentiation may serve as a therapeutic strategy. The nuclear factor one (NFI) transcription factors are essential for normal astrocytic differentiation and therefore could be effectors of cellular differentiation in glioblastoma. We analysed expression of family members NFIA and NFIB using high-grade astrocytoma mRNA expression datasets, and with immunofluorescence co-staining. Their expression is reduced in glioblastomas and is associated with differentiated and mature astrocyte-like cells at a cellular level. Furthermore, induction of NFI expression is sufficient to promote cellular differentiation in patient-derived glioblastoma xenografts. Our findings indicate that NFI proteins may have an endogenous pro-differentiative function in astrocytomas, similar to their role in normal development. Overall, our study establishes a basis for further investigation of targeting NFI-mediated differentiation as a potential differentiation therapy.

cancer biology↗

bioRxiv2019

Integrated Approach On Degaradtion Of Azo Dyes Using Laccase Enzyme And Nanoparticle With Its Interaction By In Silco Analysis

Azo dyes, released by the textile industries causes severe damage to the environment and living organisms. The degradation of azo dyes is widely studied using enzymatic methods. Laccase, is a copper containing enzyme that degrades the azo dyes into less toxic compounds. In this work, Laccase enzyme produced by the alkaliphile Pseudomonas mendocina in the degradation of mixed azo dye showed 0.386 U/Ml activity at pH 8.5. Combination of enzymatic and green synthesised nanoparticle were used in the degradation mixed azo dye. Laccase used in the degradation of mixed azo dyes showed 58.46% in 72 hours while the photocatalytic degradation of mixed azo dyes showed 15.98%. The degradation of azo dyes using copper iodide nanoparticle resulted in 15.835% of mixed azo dye degradation. But it was noticed that combined method removed 62.35% of mixed azo dyes in 60 minutes. Interaction of laccase enzyme with azo dyes using in silico analysis predicted the binding energy of RR (-7.19 kcal/mol), RB (-8.57 kcal/mol) and RBL (-9.17 kcal/mol).

microbiology↗