Faculty Publications
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Item Synthesis, chemical characterization of novel 1,3-dimethyl acridones as cytotoxic agents, and their DNA-binding studies(2010) Sathish, N.K.; Gopkumar, P.; Rajendra Prasad, V.V.S.; Shanta Kumar, S.M.; Mayur, Y.C.A series of new 1,3-dimethyl acridone derivatives were synthesized with different alkyl side chain (propyl and butyl) substitution at N 10-position and highly basic amine groups at terminal end of alkyl side chain. All the synthesized molecules were screened for their cytotoxic activity against human breast adenocarcinoma (MCF-7) and human promyelocytic leukemia (HL-60) cell lines. DNA binding constants (Ki) of selected compounds were determined with calf-thymus DNA. Results showed that the molecules 7, 8, 10, 11, 12, 13, 14, and 15 exhibited good cytotoxic activity with IC50 value <10 ?M. Compound 14 having (?- hydroxyethyl) piperazine butyl side chain exhibited potent cytotoxic activity against MCF-7 cell line and DNA-intercalating properties. Examination of the relationship between lipophilicity and acridone derivatives showed poor correlation. © Birkhäuser Boston 2009.Item New dihydropyridine derivatives: Anti-inflammatory, analgesic and docking studies(2013) Ulloora, S.; Kumar, S.; Shabaraya, R.; Vasudeva Adhikari, A.V.The present article describes synthesis of new diethyl 2,6-dimethyl-4-(4- (2-substituted amino-2-oxoethoxy) phenyl)-1,4-dihydropyridine-3,5-dicarboxylates (6a-10b) following multistep synthetic route. Structures of newly synthesized intermediates and title compounds were established by spectral and elemental analyses. The final compounds were screened for their in vivo anti-inflammatory and analgesic activities by carrageenan-induced paw oedema and tail immersion methods, respectively. Moreover, molecular docking studies were carried out for active compounds 6c, 6d, 7d, 8 and 10b to study their mode of action, meanwhile in vivo results indicated that these compounds displayed rapid onset of anti-inflammatory action and exhibited prominent activity when compared with the standard drug. Compounds 6d and 7d carrying amide functionality showed the highest anti-inflammatory as well as analgesic activities. The molecular docking results emphasised the in vivo data and all docked molecules were found to display very low binding constant values in nanomolar scale. © 2012 Springer Science+Business Media, LLC.Item Dual colorimetric receptor with logic gate operations: Anion induced solvatochromism(Royal Society of Chemistry, 2014) Kigga, M.; Swathi, N.; Manjunatha, J.R.; Das, U.K.; Nityananda Shetty, A.N.; Trivedi, D.R.A receptor R1 was designed and synthesised for colorimetric detection of F- ions as well as Cu2+ ions via intramolecular charge transfer mechanism. Upon addition of F- ions in dry DMSO, the color of the receptor R1 changed from pale yellow to blue. The receptor showed a unique property of solvatochromism by displaying different coloration with different solvents only in the presence of F- ions, which were applied to determine the percentage composition of binary solvent mixtures. The receptor R1 was able to detect Cu2+ ions colorimetrically where it exhibited a color change from pale yellow to orange-red. In addition, the receptor was subjected to molecular logic gate applications, wherein it showed 'ON-OFF' switching operations. © 2014 The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.Item A new colorimetric chemosensors for Cu2+ and Cd2+ ions detection: Application in environmental water samples and analytical method validation(Elsevier B.V., 2017) Tekuri, V.; Trivedi, D.R.A new heterocyclic thiophene-2-caboxylic acid hydrazide based chemosensor R1 to R4 were designed, synthesized and characterized by various spectroscopic techniques like FT-IR, UV-Vis, 1H NMR, 13C NMR, Mass and SC-XRD. The chemosensor R3 showed a significant color change from colorless to yellow in the presence of Cu2+ ions and chemosensor R4 showed a significant color change from colorless to yellow in the presence of Cd2+ ions over the other tested cations such as Cr3+, Mn2+, Fe2+, Fe3+, Co2+, Ni2+, Zn2+, Ag2+, Al3+, Pb2+, Hg2+, K+, Ca2+ and Mg2+. The high selective and sensitivity of R3 towards Cu2+ and R4 towards Cd2+ ions was confirmed by UV-Vis spectroscopic study. The R3 showed a red shift in the presence of Cu2+ ions by ??max 67 nm and R4 showed a red shift in the presence of Cd2+ ions by ??max 105 nm in the absorption spectrum. The binding stoichiometric ratio of the complex between R3 - Cu2+ and R4 - Cd2+ ions have been found to be 1:1 using the B-H plot. Under optimized experimental conditions, the R3 and R4 exhibits a dynamic linear absorption response range, from 0 to 50 ?M for Cu2+ ions and 0 to 30 ?M for Cd2+ ions, with the detection limit of 2.8 × 10?6 M for Cu2+ and 2.0 × 10?7 M for Cd2+ ions. The proposed analytical method for the quantitative determination of Cu2+ and Cd2+ ions was validated and successfully applied for the environmental samples with good precision and accuracy. © 2017 Elsevier B.V.Item Colorimetric and fluorometric turn-on sensor for selective detection of fluoride ions: Sol-gel transition studies and theoretical insights(Royal Society of Chemistry, 2018) Pangannaya, S.; Mohan, M.; Trivedi, D.R.A new organic receptor R1 based on a naphthyl unit covalently linked to a long alkyl chain has been designed, synthesized and characterized by standard spectroscopic techniques. The colorimetric response of receptor R1 from colorless to a pale yellow color and blue fluorescence emission in the presence of F- ions revealed its selective sensing ability in the solution phase. UV-Vis titration, fluorescence titration and 1H NMR titration studies confirmed the formation of the R1-F- complex. Receptor R1 formed a stable gel in DMSO and was confirmed through the standard heating-and-cooling method. Addition of F- ions resulted in disruption of the gel forming a solution that exhibited blue fluorescence emission. The binding constant of the R1-F- complex was found to be of the order of 5.9 × 105 M-1. DFT studies revealed the formation of the receptor-anion complex agreeing well with the experimental results. The detection limit was calculated and found to be 0.8 ppm, implying the potential for application of receptor R1 in environmental applications. © 2018 The Royal Society of Chemistry and the Centre National de la Recherche Scientifique.Item Screening of chitin deacetylase producing microbes from marine source using a novel receptor on agar plate(Elsevier B.V., 2019) Pawaskar, G.-M.; Pangannaya, S.; Raval, K.; Trivedi, D.; Raval, R.Chitosan is a deacetylated form of naturally occurring polymer; chitin. On an industrial scale, the deacetylation of chitin to chitosan is performed using harsh chemicals like sodium hydroxide. This not only adds to the environmental pollution but the product is also random in terms of its deacetylation. This shortcoming can be addressed by using enzymes like chitin deacetylase (CDA). The screening of these organisms would require a reliable, fast and sensitive screening method. The deacetylation of chitin into chitosan, releases acetate as the byproduct of the reaction. A receptor which specifically binds to the acetate ion was synthesized chemically. The receptor upon binding with the acetate ion emitted a fluorescence which could be viewed using the gel documentation unit. The receptor was optimized for the screening of CDA producing microbes with the positive fungal control as Penicillium sp. and bacterial control as Bacillus megaterium. A parallel study with the 4-Nitroacetanilide, the reported screening indicator for CDA was performed. The results obtained with the receptor in the present study were concordant with the 4-Nitroacetanilide. Upon standardization, the protocol was extended for the screening of CDA producing microbes from the marine crustacean dumped soil and water samples. The CDA activity of these microbes was further confirmed using spectrophotometric MBTH assay. This is the first report using this receptor for the screening of CDA producers. The method is not only sensitive but also reproducible and can be extended for a high throughput screening of CDA producers. © 2019 Elsevier B.V.Item Theoretical insights into molecular mechanism and energy criteria of PARP-2 enzyme inhibition by benzimidazole analogues(John Wiley and Sons Inc, 2021) Venugopal, P.P.; Shilpa, M.; Chakraborty, D.The emergence of poly (ADP-ribose) polymerase (PARP) inhibitors targeting a class of PARP enzymes has gained a great interest in cancer therapy. Majority of the PARP inhibitors are not isoform-selective which may cause unwanted off-target effects. In the present study, we explore the molecular mechanism and energy requirements for PARP-2 inhibition. This involves docking studies, frontier molecular orbital analysis, 500 ns molecular dynamics simulation (MD), binding free energy analysis and principal component analysis. The results clearly suggest the importance of hydrogen bonding (Gly429, Gln332, Ser470, Tyr455) and ?-? stacking interactions (His428, Tyr455, Tyr462, Phe463, Tyr473) between residues and the inhibitor. Presence of lowest unoccupied molecular orbitals favors ?-? stacking interactions and highest occupied molecular orbital orbital favors hydrogen-bonding interactions in the ligands. The stability of most active/PARP-2 complex is confirmed by hydrogen bonding and ?-? stacking interaction parameters. Molecular-mechanics Poisson-Boltzmann surface area energy calculations showed that van der Waals and nonpolar solvation energy terms are crucial components for the stable binding of the ligands. Per residue analysis showed that tyrosine, histidine, and phenyl alanine residues are responsible for hydrophobic interactions with the ligands. Four new inhibitors are designed based on this study and the stability of PARP-2/inhibitor complex is validated by MD, density functional theory studies, and ADME/toxicity properties. Information from the present study can serve as a basis for designing new isoform-selective PARP-2 inhibitors. © 2021 Wiley Periodicals LLC.Item Molecular mechanism of inhibition of COVID-19 main protease by ?-adrenoceptor agonists and adenosine deaminase inhibitors using in silico methods(Taylor and Francis Ltd., 2022) Venugopal, P.P.; Chakraborty, D.Novel coronavirus (COVID-19) responsible for viral pneumonia which emerged in late 2019 has badly affected the world. No clinically proven drugs are available yet as the targeted therapeutic agents for the treatment of this disease. The viral main protease which helps in replication and transcription inside the host can be an effective drug target. In the present study, we aimed to discover the potential of ?-adrenoceptor agonists and adenosine deaminase inhibitors which are used in asthma and cancer/inflammatory disorders, respectively, as repurposing drugs against protease inhibitor by ligand-based and structure-based virtual screening using COVID-19 protease-N3 complex. The AARRR pharmacophore model was used to screen a set of 22,621 molecules to obtain hits, which were subjected to high-throughput virtual screening. Extra precision docking identified four top-scored molecules such as +/?-fenoterol, FR236913 and FR230513 with lower binding energy from both categories. Docking identified three major hydrogen bonds with Gly143, Glu166 and Gln189 residues. 100 ns MD simulation was performed for four top-scored molecules to analyze the stability, molecular mechanism and energy requirements. MM/PBSA energy calculation suggested that van der Waals and electrostatic energy components are the main reasons for the stability of complexes. Water-mediated hydrogen bonds between protein-ligand and flexibility of the ligand are found to be responsible for providing extra stability to the complexes. The insights gained from this combinatorial approach can be used to design more potent and bio-available protease inhibitors against novel coronavirus. Communicated by Ramaswamy H. Sarma. © 2020 Informa UK Limited, trading as Taylor & Francis Group.Item Deciphering the competitive inhibition of dihydropteroate synthase by 8 marcaptoguanine analogs: enhanced potency in phenylsulfonyl fragments(Taylor and Francis Ltd., 2022) Das, B.K.; Chakraborty, D.The emergence of sulfa-drug resistance and reduced efficacy of pterin-based analogs towards Dihydropteroate synthase (DHPS) inhibition dictate a pressing need of developing novel antimicrobial agents for immune-compromised patients. Recently, a series of 8-Marcaptoguanin (8-MG) derivatives synthesized for 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (experimental KD ∼ 100–.0.36) showed remarkable homology with the pteroic-acid and serve as a template for product antagonism in DHPS. The present work integrates ligand-based drug discovery techniques with structure-based docking, enhanced MD simulation, and MM/PBSA techniques to demonstrate the essential features of 8-MG analogs which make it a potent inhibitor for DHPS. The delicate balance in hydrophilic, hydrophobic substitutions on the 8-MG core is the crucial signature for DHPS inhibition. It is found that the dynamic interactions of active compounds are mainly dominated by consistent hydrogen bonding network with Asp 96, Asn 115, Asp 185, Ser 222, Arg 255 and π-π stacking, π-cation interactions with Phe 190, Lys 221. Further, two new 8-MG compounds containing N-phenylacetamide (compound S1, ΔGbind-eff = –62.03 kJ/mol) and phenylsulfonyl (compound S3, ΔGbind-eff = −71.29 kJ/mol) fragments were found to be the most potent inhibitor of DHPS, which stabilize the flexible pABA binding loop, thereby increasing their binding affinity. MM/PBSA calculation shows electrostatic energy contribution to be the principal component in stabilizing the inhibitors in the binding pocket. This fact is further confirmed by the higher energy barrier obtained in umbrella sampling for this class of inhibitors. © 2021 Informa UK Limited, trading as Taylor & Francis Group.Item N-Acyl phenothiazines as mycobacterial ATP synthase inhibitors: Rational design, synthesis and in vitro evaluation against drug sensitive, RR and MDR-TB(Academic Press Inc., 2024) Reddyrajula, R.; Perveen, S.; Negi, A.; Etikyala, U.; Vijjulatha, V.; Sharma, R.; Udayakumar, D.The mycobacterial F-ATP synthase is responsible for the optimal growth, metabolism and viability of Mycobacteria, establishing it as a validated target for the development of anti-TB therapeutics. Herein, we report the discovery of an N-acyl phenothiazine derivative, termed PT6, targeting the mycobacterial F-ATP synthase. PT6 is bactericidal and active against the drug sensitive, Rifampicin-resistant as well as Multidrug-resistant tuberculosis strains. Compound PT6 showed noteworthy inhibition of F-ATP synthesis, exhibiting an IC50 of 0.788 µM in M. smegmatis IMVs and was observed that it could deplete intracellular ATP levels, exhibiting an IC50 of 30 µM. PT6 displayed a high selectivity towards mycobacterial ATP synthase compared to mitochondrial ATP synthase. Compound PT6 showed a minor synergistic effect in combination with Rifampicin and Isoniazid. PT6 demonstrated null cytotoxicity as confirmed by assessing its toxicity against VERO cell lines. Further, the binding mechanism and the activity profile of PT6 were validated by employing in silico techniques such as molecular docking, Prime MM/GBSA, DFT and ADMET analysis. These results suggest that PT6 presents an attractive lead for the discovery of a novel class of mycobacterial F-ATP synthase inhibitors. © 2024 Elsevier Inc.