Biology subjects

Hasan, M. F.

Publications and source records attributed to Hasan, M. F..

4 recordsLinked to original sources

bioRxiv2026

Recombinant SIRT1 expression and SIRT1 METTL3 interaction analysis with computational identification of phytochemical SIRT1 activators and inhibitors

Sirtuin 1 (SIRT1), a NAD{+/-}dependent histone deacetylase, regulates diverse biological processes including aging, stress response, and cancer progression. Owing to its dual roles in tumor suppression and promotion, selective modulators of SIRT1 have attracted considerable therapeutic interest. This study explored the interaction of SIRT1 with METTL3 and screened phytochemicals from Indian medicinal plants for potential SIRT1 activation or inhibition. Human SIRT1 (residues 183-665) was cloned, expressed in E. coli, purified, and validated by isothermal titration calorimetry (ITC) to confirm binding with METTL3. Computational approaches, including molecular docking, ADMET profiling, molecular dynamics (MD) simulations, MM-PBSA free energy estimation, and frontier molecular orbital (FMO) analysis, were employed to characterize ligand interactions. Docking revealed Catechin, Epicatechin, Kaempferol, and Bisdemethoxycurcumin as potent inhibitors, showing stronger binding than the reference inhibitor Selisistat by stabilizing the catalytic pocket via key hydrogen bonds and {pi}-{pi} stacking interactions. Among activators, Ginsenosides and Carnosol demonstrated higher affinities than resveratrol, binding the allosteric site through hydrophobic and electrostatic interactions. MD simulations highlighted Catechin and Ginsenosides as the most stable modulators, supported by reduced RMSD, compact Rg values, and favorable hydrogen bond occupancy. MM-PBSA confirmed their strong binding free energies, while ADMET analysis predicted favorable pharmacokinetic properties and low toxicity, particularly for Catechin and Ginsenosides. Overall, this study integrates expression and purification of the protein and computational modeling to identify phytochemicals as potential SIRT1 modulators and provides novel insights into the SIRT1-METTL3 regulatory axis. These findings highlight Catechin and Ginsenosides as promising scaffolds for therapeutic strategies targeting cancer and metabolic disorders.

molecular biology↗

bioRxiv2026

Computational Structure Modeling, Functional Characterization, and Identification of Potential Inhibitors for the cyclic-di-GMP Mediated Biofilm Forming Membrane Protein in Vibrio cholerae

Cholera, caused by Vibrio cholerae, continues to pose a serious global public health challenge, with its impact worsened by rising antibiotic resistance associated with bacterial biofilm formation. This study reveals the role of the hypothetical protein (HP) TYC33605.1 in cyclic-di-GMP (c-di-GMP)-mediated biofilm regulation and identifies natural inhibitors that disrupt this mechanism. Functional annotation revealed TYC33605.1 as a membrane-associated diguanylate cyclase (DGC) with GGDEF and sensory domains, critical for c-di-GMP synthesis and biofilm persistence. Homology modelling and molecular dynamics (MD) simulations validated its stable 3D structure (C-score: -1.22, Ramachandran favoured regions: 91.1%) and dynamic behaviour (average RMSD: 8.55 [A]). Virtual molecular docking screening of 1,092 natural compounds identified Luteolin (CID 5280445) and Sativanone (CID 13886678) as top candidates, exhibiting strong binding affinities (-9.1 and -9.0 kcal/mol, respectively) and forming hydrogen bonds, {pi}-cation, and hydrophobic interactions with key residues (Glu293, Arg364, Ala176). MD simulations (100 ns) confirmed complex stability, with Luteolin and Sativanone showing lower RMSD fluctuations (7.78 [A] and 8.13 [A]) compared to the control and apoprotein. The ADME/Tox profiles highlighted favourable pharmacodynamics (PD), pharmacokinetics (PK), high gastrointestinal absorption, no hepatotoxicity, and drug-likeness (Lipinski compliance). Principal component, probability density function, and binding free energy analyses underscore ligand-induced conformational stability. This study proposes the molecular characterisation of the HP and the bioactive compounds Luteolin and Sativanone as promising inhibitors targeting TYC33605.1, offering a novel strategy to combat biofilm-mediated antibiotic resistance and a framework for analogous antimicrobial discovery in Vibrio cholerae.

bioinformatics↗

bioRxiv2022

Localized network hyperconnectivity leads to hyperexcitability after injury

Brain injury increases the risk of the development of epilepsy. Axonal sprouting and synaptogenesis are homeostatically mediated responses by neurons to injury-induced de-afferentation and de-efferentation. Rewiring which occurs due to axonal sprouting and synaptogenesis may alter network excitability and lead to epilepsy. Excitatory and inhibitory connectivity are both subject to homeostatic rewiring. Thus, post-sprouting hyperexcitability cannot be simply explained as result of altered inhibitory/excitatory balance. In this work, we show computationally and experimentally that hyperconnected local networks are created by homeostatic rewiring near the injury site. These local networks are characterized by altered system dynamics despite preservation of excitatory/inhibitory balance. Hyperconnected local networks have a lower threshold for burst initiation, and generate spontaneous bursts, which in turn ignite seizure-like activity in the larger network. Our findings demonstrate a novel network mechanism of hyperexcitability and seizure generation due to maladaptive recovery after injury.

neuroscience↗

bioRxiv2020

LncRNA PAINT is Associated with Aggressive Prostate Cancer and Dysregulation of Slug and Related Genes

Long non-coding RNAs (lncRNAs) play regulatory roles in cellular processes and their aberrant expression may drive cancer progression. Here we report the function of a lncRNA PAINT (Prostate Cancer Associated Intergenic Non-Coding Transcript) in promoting prostate cancer (PCa) progression. Upregulation of PAINT was noted in advanced stage and metastatic PCa. Inhibition of PAINT decreased cell proliferation, S-phase progression, increased expression of apoptotic markers, and improved sensitivity to docetaxel and Aurora kinase inhibitor VX-680. Inhibition of PAINT decreased cell migration and reduced expression of Slug and Vimentin. Ectopic expression of PAINT suppressed E-cadherin, increased S-phase progression and cell migration. PAINT expression in PCa cells induced larger colony formation and higher expression of mesenchymal markers. Transcriptome analysis followed by qRT-PCR validation showed differentially expressed genes involved in epithelial mesenchymal transition (EMT), apoptosis and drug resistance in PAINT-expressing cells. Our study establishes an oncogenic function of PAINT in PCa.

cancer biology↗