Biophysical chemistry, protein dynamics, higher order DNA structures, coacervates, emulsions, dissipative assembly
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Scopus Publications
Scopus Publications
Adaptive catalytic compartments emerge from synergistic integration of DNA nanostructures and transient coacervates Abhay Srivastava, Parth Kumar, Mathesh Punugusamy, Sourav Das, Subinoy Rana Nanoscale Horizons, 2025 A catalytic coacervate is introduced using salt–bridge interactions between a biguanide polymer (PHMB) and adenosine triphosphate (ATP). Augmented catalysis is exhibited by the G-rich DNAzyme inside the coacervates, with ATP-fueled activity cycling.
An Unusual Activity of Conformationally Restricted Naphthalene Peri-Dichalcogenides in the Reduction of Nitro and Azide Groups Debasish Giri, Ekta Chauhan, Sourav Das, Govindasamy Mugesh Chemistry A European Journal, 2025 Rigid and conformationally restricted dichalcogenides based on 1,8‐naphthyl system have attracted significant interest as electron donors in charge transfer complexes and organic electrode materials. Recently, naphthalene‐1,8‐peri‐diselenides have been shown to mimic the function of two major selenoenzymes − iodothyronine deiodinase (Dio) and glutathione peroxidase (GPx) − mainly through two‐electron redox processes involving deiodination of thyroid hormones and thiol‐mediated reduction of hydrogen peroxide, respectively. Herein, we report that naphthalene‐1,8‐peri‐dichalcogenides can mediate a six‐electron reduction of organic nitro compounds to produce the corresponding primary amines at physiologically relevant temperature (37 °C) using water as the solvent. The stepwise reduction process is highly dependent on the nature of the chalcogen atom present at the peri‐positions of the naphthyl ring. While no reduction was observed with the disulfide, the selenenyl sulfide mediated a four‐electron reduction of the nitro group to the corresponding hydroxylamine. The diselenide and ditelluride reduced the nitro groups all the way to amines through six‐electron transfer. The diselenides also mediated the reduction of various aromatic azides to the corresponding primary amines.
Common Nefafu (Clerodendrum colebrookianum L.)-Mediated Silver Nanoparticles for Physicochemical Insights into the Protein Corona Formation and Inhibition of Fibrillation of Human Serum Albumin Kakali Baruah, Ajit Kumar Singh, Sourav Das, Sweta Sucharita Sahoo, Kalpana Kumari, Anupam Nath Jha, Atanu Singha Roy Langmuir, 2025 Engineering nanomaterials with products isolated from natural resources is attractive for targeted therapeutic applications. Prior to the biomedicinal applications, one significant facet of nanoparticles is the understanding of protein corona formation and its relative binding aspects. In this perspective, we have synthesized two different silver nanoparticles, one with the extract of the leaves of a traditional herb Clerodendrum colebrookianum, commonly known as “Nefafu”, and the other with one of its major polyphenolic compounds, apigenin, and their complexations were studied with the model protein human serum albumin (HSA). The formation of the protein corona of HSA on the surface of AgNPs was revealed from the observed changes in terms of hydrodynamic size, ξ-potential, and LSPR band positions, and the gray colored layer of diameter ∼3 nm on the surface of AgNPs as visualized in the TEM micrographs. The combined multispectroscopic approaches and molecular dynamics simulation studies on the interaction process revealed the moderate binding affinities (Kb in the order of 104 M–1) of both the AgNPs toward HSA, where their complexations were found to be entropy driven with the involvement of hydrophobic association as the major driving force of interactions. Interestingly, both Nefafu-AgNPs and Apigenin-AgNPs could retain the secondary structural conformation of HSA. These polyphenol-capped NPs were able to significantly inhibit the fibrillation of HSA, where Nefafu-AgNPs with a higher number of polyhydroxy groups showed better inhibition than Apigenin-AgNPs, as revealed from the kinetic study with ThT assay, CR assay, ANS assay, circular dichroism, as well as from the morphological changes from amyloid-sheet structure to small globular units as visualized in fluorescence microscopic imaging.
Multivalent Amine Functionalized Carbon Dots Catalyze Efficient Denitrosylation Manju Solra, Sourav Das, Suman Nayak, Abhay Srivastava, Rohit Kapila, Smarak I. Chaudhury, Subinoy Rana Chemcatchem, 2025 Nitric oxide (NO) is an essential signaling molecule with several biological functions and holds great promise in biomedical applications. However, NO delivery strategies have been challenged with its inherent short half‐life and limited transport distance in human tissues. Strategies focused on the catalytic production of NO at the target site would afford an effective biomaterial. Herein, we introduce a carbon dot (CD) platform featuring multivalent amine groups that catalyze the denitrosylation from S‐nitrosothiols. In the present study, we have developed a novel multivalent amine functionalized carbon dots to catalytically transform endogenous prodrugs S‐nitrosothiols to generate NO at physiological conditions. The mechanism of NO generation follows a nucleophilic attack of the surface primary amine groups on the electrophilic thiol group of S‐nitrosothiols, which is supported by various control studies and electron paramagnetic resonance (EPR). Notably, the release of NO is easily tuned by the prodrug concentration and surface density of amines on the CDs. Significantly, the NO‐releasing feature of CDs is integrated with the prototissue module to evaluate the NO release profile in the biological environment. This study will deepen our understanding of designing useful multivalent systems to generate NO from endogenous prodrugs to realize their therapeutic potential.
Isoflavones and lysozyme interplay: Molecular insights into binding mechanisms and inhibitory efficacies of isoflavones against protein modification Sourav Das, Sadia Nudrat, Sankar Maity, Madhurima Jana, Vinay Kumar Belwal, Atanu Singha Roy Chemical Physics Impact, 2024 In this study, we investigated the complexation of bioactive isoflavones, specifically biochanin A (BCA) and genistein (GEN), with hen egg white lysozyme (HEWL) and explored their inhibitory effects on HEWL modification using a combination of multi-spectroscopic and computational methods. The observed binding affinity was of a moderate nature (on the order of 104 M−1), and a static quenching mechanism was identified in the fluorescence quenching process. Notably, the binding constant (Kb) for GEN (4.449±0.262 × 104 M−1) was found to be higher than that for BCA (3.707±0.108 × 104 M−1) towards HEWL. Our spectroscopic measurements, complemented by molecular docking calculations, suggested the involvement of Trp62 in the binding site of the isoflavones within the geometry of HEWL. The micro-environment surrounding the Trp residues exhibited an increase in hydrophilicity, as indicated by Synchronous fluorescence (SFS) and three-dimensional fluorescence (3D) studies. Interestingly, circular dichroism (CD) studies revealed no marked alteration in the secondary structure of HEWL upon binding with the isoflavones. Furthermore, our investigation into the interaction patterns, employing FTIR and molecular docking studies, revealed a predominance of hydrogen bonding and hydrophobic interactions. Beyond the binding study, the isoflavones demonstrated a promising inhibitory effect on the D-ribose-mediated glycation of HEWL, as well as on HEWL fibrillation, as evidenced by fluorescence emission studies. Our findings not only exhibited an excellent correlation with experimental observations but also provided precise insights into the location and dynamics of isoflavones within the binding site through detailed analyses of molecular docking and molecular dynamics simulation data.
Transient Metallo-Lipidoid Assemblies Amplify Covalent Catalysis of Aqueous and Non-Aqueous Reactions Manju Solra, Rohit Kapila, Sourav Das, Preeti Bhatt, Subinoy Rana Angewandte Chemie International Edition, 2024 Dissipative supramolecular assemblies are hallmarks of living systems, contributing to their complex, dynamic structures and emerging functions. Living cells can spatiotemporally control diverse biochemical reactions in membrane compartments and condensates, regulating metabolite levels, signal transduction or remodeling of the cytoskeleton. Herein, we constructed membranous compartments using self‐assembly of lipid‐like amphiphiles (lipidoid) in aqueous medium. The new double‐tailed lipidoid features Cu(II) coordinated with a tetravalent chelator that dictates the binding of two amphiphilic ligands in cis‐orientation. Hydrophobic interactions between the lipidoids coupled with intermolecular hydrogen bonding led to a well‐defined bilayer vesicle structure. Oil‐soluble SNAr reaction is efficiently upregulated in the hydrophobic cavity, acting as a catalytic crucible. The modular system allows easy incorporation of exposed primary amine groups, which augments the catalysis of retro aldol and C−N bond formation reactions. Moreover, a higher‐affinity chelator enables consumption of the Cu(II) template leveraging the differential thermodynamic stability, which allows a controllable lifetime of the vesicular assemblies. Concomitant temporal upregulation of the catalytic reactions could be tuned by the metal ion concentration. This work offers new possibilities for metal ion‐mediated dynamic supramolecular systems, opening up a massive repertoire of functionally active dynamic “life‐like” materials.
Robust and Multifunctional Wetting Resistance of de novo Engineered Nonfluorinated Metal–Organic Nanocrystals for Environmental Sustainability Manju Solra, Sherafudeen Fathima, Sourav Das, Rohit Kapila, Smarak I. Chaudhury, Subinoy Rana Advanced Engineering Materials, 2024 Direct synthesis of zeolitic imidazole framework crystals using bulky alkyl ligands is challenging. Herein, a bottom‐up approach to de novo synthesis of a superhydrophobic zeolitic metal–organic framework called mZIF, using mixed ligands, is developed. The mZIF nanocrystals contain a newly designed alkyl chain‐substituted 4‐imidazolate ligand, achieving tailorable hydrophobicity by varying the alkyl tail length. The molecular structure presenting appropriate ligands coupled with the porosity and roughness of the coated surfaces imparts superhydrophobic properties to various coated surfaces such as glass, steel, aluminum, and plastic. The resulting surfaces exhibit a high contact angle of ≥157° and a minimal rolling‐off angle (<5°), enabling efficient oil–water separation in a filtration setup. Furthermore, dip coating the mZIF nanocrystals onto a melamine sponge modifies its water wettability, allowing for facile and efficient removal and recovery of oil from diverse oil–water mixtures with exceptional reusability. Additionally, the mZIF‐modified surfaces showcase notable self‐cleaning and anti‐icing properties. The mZIF‐coated surface shows remarkable storage stability (>1 year), durability against harsh environmental conditions, and notable resistance to mechanical abrasion. This research represents a significant advancement in the facile engineering of multifunctional metal–organic framework‐based systems tailored for diverse practical applications.
G-Quadruplex Hydrogel-Based Stimuli-Responsive High-Internal-Phase Emulsion Scaffold for Biocatalytic Cascades and Synergistic Antimicrobial Activity Sourav Das, Manju Solra, Jagabandhu Sahoo, Abhay Srivastava, Sherafudeen Fathima, Mrinmoy De, Subinoy Rana Chemistry of Materials, 2024 High-internal-phase emulsions (HIPEs) are nonequilibrium systems with distorted liquid droplet shapes consisting of a high volume of the internal phase (>74% v/v), enabling a high loading of pharmaceutics and useful viscoelastic properties. However, HIPEs are inherently unstable and require a substantial amount of surfactants in the continuous phase for long-term stability, making it environmentally unfriendly. Utilization of hydrogel as the continuous phase to stabilize HIPEs would offer a robust method to produce stable HIPE gels displaying reconfigurable and biocompatible properties, as well as access the huge repertoire of different biocompatible hydrogels. Herein, we introduce a new gel-immobilized HIPE (HIPEG) using chiral G-quadruplex (GQ)-based hydrogel with external stimuli-responsive dual-drug release behavior, which is scarce for HIPEs. The hydrophilic and hydrophobic compartments of the biocompatible HIPEG allow encapsulation of different drugs in both the compartments, with stimuli-responsive diffusion-mediated release. Encapsulation of natural oils and antibiotics produces synergistic antimicrobial effects on both Gram-positive (MRSA) and Gram-negative (Pseudomonas aeruginosa) bacterial strains through increased oxidative stress and membrane depolarization. Moreover, we demonstrate biocatalytic reaction networks utilizing compartmentalized enzyme dyads. Notably, the ideal viscoelastic property of HIPEGs enables 3D printing of different shapes, making the scaffold suitable for the creation of soft medical devices. Altogether, our approach provides a one-step route to creating stimuli-responsive HIPE microcompartments immobilized in GQ hydrogels with endogenous reactivity and high viscoelasticity, offering a viable step toward the development of biocompatible soft materials with tailorable functionality.
Noncovalent interactions and electrical conductance study of copper(II) coordination complex derived from 2,6-pyridinedicarboxylic acid and aminopyrimidine ligands Journal of the Indian Chemical Society, 2018
