Faculty Publications
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Item Understanding the role of water on temperature-dependent structural modifications of SARS CoV-2 main protease binding sites(Elsevier B.V., 2022) Venugopal, P.P.; Singh, O.; Chakraborty, D.Thermally stable and labile proteases are found in microorganisms. Protease mediates the cleavage of polyproteins in the virus replication and transcription process. 6 µs MD simulations were performed for monomer/dimer SARS CoV-2 main protease system in both SPC/E and mTIP3P water model to analyse the temperature-dependent behaviour of the protein. It is found that maximum conformational changes are observed at 348 K which is near the melting temperature. Network distribution of evolved conformations shows an increase in the number of communities with the rise in the temperature. The global conformation of the protein was found to be intact whereas a local conformational space evolved due to thermal fluctuations. The global conformational change in the free energy ΔΔG value for the monomer and the dimer between 278 K and 383 K is found to be 2.51 and 2.10 kJ/mol respectively. A detailed analysis was carried out on the effect of water on the temperature-dependent structural modifications of four binding pockets of SARS CoV-2 main protease namely, catalytic dyad, substrate-binding site, dimerization site and allosteric site. It is found that the water structure around the binding sites is altered with temperature. The water around the dimer sites is more ordered than the monomer sites regardless of the rise in temperature due to structural rigidity. The energy expense of binding the small molecules at substrate binding is less compared to the allosteric site. The water-water hydrogen bond lifetime is found to be more near the cavity of His41. Also, it is observed that mTIP3P water molecules have a similar effect to that of SPC/E water molecules on the main protease. © 2022 Elsevier B.V.Item Colorimetric differentiation of arsenite and arsenate anions using a bithiophene sensor with two binding sites: DFT studies and application in food and water samples(Royal Society of Chemistry, 2024) K, K.; Nityananda Shetty, A.N.; Trivedi, D.R.Chemosensor N7R1 with two acidic binding sites was synthesized, and the ability of the sensor to differentiate arsenite and arsenate in the organo-aqueous medium was evaluated using colorimetric sensing methods. N7R1 distinguished arsenite with a peacock blue color and arsenate with a pale green color in a DMSO/H2O (9 : 1, v/v) solvent mixture. The specific selectivity for arsenite was achieved in DMSO/H2O (7 : 3, v/v). The sensor demonstrated stability over a pH range of 5 to 12. The computed high binding constant of 9.3176 × 1011 M−2 and a lower detection limit of 11.48 ppb for arsenite exposed the chemosensor's higher potential for arsenite detection. The binding mechanism with a 1 : 2 binding process is confirmed using UV-Vis and 1H NMR titrations, electrochemical studies, mass spectral analysis and DFT calculations. Practical applications were demonstrated by utilizing test strips and molecular logic gates. Chemosensor N7R1 successfully detected arsenite in real water samples, as well as honey and milk samples. © 2024 The Royal Society of Chemistry.Item Design, synthesis and molecular docking of 5-fluoro indole derivatives as inhibitors of PI3K/Akt signalling pathway in cervical cancer(Elsevier B.V., 2024) Etikyala, U.; Reddyrajula, R.; Pasha, A.; Udayakumar, U.; Pawar, S.C.; Vijjulatha, V.The PI3K/Akt signalling pathway promotes variety of cellular processes and the inhibition of PI3K/Akt signalling pathway could lead to decrease in tumour growth effectively in cancer cells. AD412, an indole derivative, is a potent immunosuppressive agent which also reported as an anticancer agent through significant inhibition of PI3K/Akt signalling pathway. In this current work, we designed and synthesized the two diverse lead series of 5-fluoro indole derivatives (6a-l and 11a-l) by specific structural modifications of AD412. In total, 24 new derivatives were evaluated for their antiproliferative activity against two cervical cancer cell lines (HeLa and SiHa) and a normal cell line (HEK 293). Among them, 6e exhibited excellent antiproliferative activity against HeLa and SiHa cells with IC50 values of 9.366 and 8.475 µM respectively, as well displayed a low toxicity profile. Further, 6e inhibited the migration and invasion of HeLa cells in a dose-dependent manner by affecting the synthesis of DNA. Moreover, the Western blot analysis revealed that 6e could inhibit cervical cancer progression by downregulating the PI3K-p85 and phosphorylation of Akt in Hela cells. In vitro mechanism studies demonstrated that 6e could significantly increase apoptosis in HeLa cells by upregulating the expression of proapoptosis related protein Bax. The binding mechanism and the activity profile of 5-fluoro indole derivatives were validated by employing molecular docking studies against the active sites of Akt and PI3K enzymes. In addition, in silico ADME and pharmacokinetic parameters prediction of compound 6e resulted in good oral bioavailability. Therefore, compound 6e could be a lead compound for further development of PI3K/Akt inhibitors and anticancer agents. © 2024Item Selective chromogenic nanomolar level sensing of arsenite anions in food samples using dual binding site probes(Elsevier Ltd, 2025) K, K.; Nityananda Shetty, A.N.; Trivedi, D.R.In the present study, two chromogenic probes, N7R2 and N7R3, each containing two binding sites, were designed and synthesized for the selective detection of arsenite in DMSO/H2O (1:1, v/v). The probes exhibited stability across a pH range spanning from 5 to 12. The lower detection limits of 2.01 ppb (18.86 nM) for N7R2 and 1.79 ppb (16.75 nM) for N7R3, which are much lower than the WHO recommended permissible limit of arsenite, confirmed the superior efficiency of the probes in detecting arsenite. The detection mechanism for arsenite was proposed through UV and 1H NMR titrations, electrochemical studies, and DFT calculations. Practical applications were demonstrated through the fabrication of test strips and molecular logic gates. The probes efficiently recognized arsenite in real water, honey, milk samples, and fruit/vegetable juices. Both N7R2 and N7R3 exhibited excellent recovery rates in the analysis of food samples, demonstrating the probes' usefulness in real sample analysis. © 2024Item Efficient multi-pollutant removal: The role of Keggin polyoxometalates in polysulfone-chitosan blend membranes(Elsevier B.V., 2025) Fashapoyeh, M.A.; Shokrollahzadeh, S.; Isloor, A.M.; Streb, C.Membrane filtration is a vital area in separation science, providing an effective method for water purification due to the unique properties of membranes. This study presents the development of blend membranes composed of polysulfone (PS), chitosan (CS), and polyvinyl alcohol (PVA), incorporating two types of Keggin polyoxometalates: K?[?-SiW??O??] ({SiW11}) and K?[?-SiW??O??] ({SiW12}) at a concentration of 0.05 to 1.0 wt% each. Our findings reveal that the incorporation of 0.1 wt% {SiW11} results in an optimum membrane exhibiting high porosity, a finger-like pore structure, and enhanced hydrophilicity. This membrane achieves a water flux of 34.8 L/m2h and significantly enhances the simultaneous removal of multiple pollutants. Specifically, this membrane achieved rejection rates of >88 % for heavy metal ions (Ni2+, Cu2+, and Pb2+) and > 98 % for organic dyes (Congo Red and Methylene Blue). The improved rejection rates and water fluxes observed with the optimal amounts of polyoxometalates (POMs) can be attributed to the combined effects of surface charge (Donnan effect), size exclusion, and adsorption at the binding sites of the POMs. Notably, the nanofiltration membrane containing {SiW11} outperformed the one with {SiW12} in filtering multi-contaminant solutions, underscoring its superior effectiveness. © 2025 Elsevier B.V.Item Croconic acid-based zwitterionic conjugated porous polymer featuring nitrogen-rich triazine cores for enhanced iodine capture(Elsevier B.V., 2025) Ravikumar, M.V.; Lakshmi, V.Increased nuclear energy consumption leads to the enormous release of hazardous gases such as iodine into the environment. To address this concern, two zwitterionic Conjugated Porous Polymers (CPPs) CTTz and STTz have been synthesized by incorporating nitrogen-rich TTz with zwitterionic CA/SA under catalyst-free solvothermal conditions to achieve efficient multi-state iodine adsorption. The multiple active binding sites serve their dominance in trapping iodine species effectively. The polymers demonstrated exceptional iodine adsorption capabilities in both vapour phase and solution phases, with ?6.4 g/g and ?1.1 g/g iodine adsorption for CTTz and ?4.6 g/g and ?1.6 g/g for STTz, respectively. The zwitterionic backbones (CA/SA) in the polymer framework facilitated the formation of charge transfer complexes with iodine species, and the presence of triazine moieties enhances adsorption. The exceptional iodine capturing by CTTz and STTz lasted over a period of five cycles (?80 %). The iodine-loaded and recovered CPPs were analyzed using FTIR, FESEM, BET, XRD, and Raman spectroscopic studies, revealing the capture and release of different iodine species (I2, I3-, and I5-) by adsorbents. These findings offer valuable insights for designing and developing advanced zwitterionic adsorbent materials for effective dual-phase iodine capture and removal. Environmental implication: Uncontrolled release of radioactive iodine from nuclear energy sources poses a significant environmental and public health risk due to its volatility, mobility, and potential for bioaccumulation. Thus, it is essential to develop highly efficient, regenerable, and chemically stable adsorbents for removing iodine contamination in both vapour and solution phases. This study presents CTTz and STTz synthesised using Tris(4-aminophenyl)triazine and croconic/squaric acid building blocks, demonstrating exceptional iodine capture in both phases. Their robust structures, rich in nitrogen, oxygen and ionic binding sites, enable efficient charge-transfer complex formation with iodine species under ambient conditions. These results promote next-generation adsorbent development for nuclear waste management and provide a viable solution for preventing iodine radionuclide environmental contamination. © 2025 Elsevier B.V.Item ortho-Halogen functionalized N-squaraines: structure–property relationship and dual-mode colorimetric and fluorometric sulfide ion detection(Royal Society of Chemistry, 2025) Fernandes, P.P.; Shenoy, A.M.; Grover, V.; Veeranagaiah, N.S.; Lakshmi, V.Symmetric ortho-halogen derivatives of anilinium N-squaraines were synthesized and characterized using 1H-NMR, mass, FT-IR, and single-crystal X-ray diffraction techniques. The effect of halogen substituents (–F, –Cl, –Br, –I) on the optoelectronic and electrochemical properties of N-squaraines has been thoroughly investigated. Additionally, the theoretical calculations demonstrated that the ortho functionalization slightly lowers the HOMO–LUMO energy band gap, which aligns with the optical band gap. Moreover, the solid-state photophysical characterization revealed that the photo-excited state remains a singlet, even in the presence of heavy atoms like bromine and iodine. The solid-state fluorescence emission was also significantly higher than in the solution state, with the quantum yields soaring up to 24%. Further, the two acidic binding sites in the synthesized compounds 2–5 were evaluated for anion sensing. The o-halo-derivatives act as selective dual-mode colorimetric and “Turn-On” fluorometric chemosensors for sulfide anions, with the solution changing from colorless to yellow and a four-fold enhanced emission intensity. Furthermore, adding acid makes the solution turn colorless again, as investigated in detail using the o-chloro-derivative. The chemosensor displayed good reversibility for up to seven cycles and demonstrated applications in molecular logic gates. This journal is © The Royal Society of Chemistry, 2025