@article { ISI:000350841100024, title = {Biophysical characterization and molecular docking studies of imidazolium based polyelectrolytes-DNA complexes: role of hydrophobicity}, journal = {Biomacromolecules}, volume = {16}, number = {3}, year = {2015}, month = {MAR}, pages = {894-903}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

Nonviral gene delivery vectors are acquiring greater attention in the field of gene therapy by replacing the biological viral vectors. DNA-cationic polymer complexes are one of the most promising systems to find application in gene therapy. Hence, a complete insight of their biophysical characterization and binding energy profile is important in understanding the mechanism involved in nonviral gene therapy. In this investigation, the interaction between calf thymus DNA (ctDNA) and imidazolium-based poly(ionic liquids) (PILs) also known as polyelectrolytes with three different alkyl side chains (ethyl, butyl, and hexyl) in physiological conditions using various spectroscopic experiments with constant DNA concentration and varying polyelectrolyte concentrations is reported. UV-visible absorption, fluorescence quenching studies, gel electrophoresis, circular dichroism (CD), and Fourier transform infrared spectroscopy (FTIR) have confirmed the binding of polyelectrolytes with DNA. UV-vis absorption measurements and fluorescence quenching revealed that the binding between DNA and the polyelectrolyte is dominated by electrostatic interactions. Additionally, CD and FTIR results indicated that the DNA retained its B-form with minor perturbation in the phosphate backbone without significant change in the conformation of its base pairs. Preference for alkyl side chains (KPIL-Ethyl Br \< KPIL-Butyl Br \< KPIL-Hexyl Br) toward efficient binding between the polyelectrolyte and DNA was inferred from the binding and quenching constants calculated from the absorption and emission spectra, respectively. Further, in silico molecular docking studies not only validated the observed binding trend but also provided insight into the binding mode of the polyelectrolyte-DNA complex.

}, issn = {1525-7797}, doi = {10.1021/bm5018029}, author = {Manojkumar, Kasina and Charan, K. T. Prabhu and Sivaramakrishna, Akella and Jha, Prakash C. and Khedkar, Vijay M. and Siva, Ramamoorthy and Jayaraman, Gurunathan and Vijayakrishna, Kari} } @article { ISI:000361120000056, title = {Evaluation of imidazolium-based ionic liquids towards vermicidal activity: in vitro \& in silico studies}, journal = {RSC Advances}, volume = {5}, number = {92}, year = {2015}, month = {AUG}, pages = {75415-75424}, publisher = {ROYAL SOC CHEMISTRY}, address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS, ENGLAND}, abstract = {

A series of six different ionic liquids (ILs) of the kind 1-alkyl-3-methylimidazolium bromide/hydroxide (IL-Br and IL-OH) tailored with different N-alkyl side chains (ethyl, butyl, octyl) were synthesized and evaluated for their vermicidal activity against the Indian earthworm, Pheretima posthuma. The percentage of paralysis and mortality of earthworms against ILs were recorded in a dose dependent (at different concentrations 2, 4, 8 and 16 mM) and time dependent manner. The ILs with hydroxide as the counter anion (IL-OH) showed higher vermicidal activity compared to their bromide counterparts (IL-Br). Moreover, the ILs with the longest alkyl chain (octyl) were observed to have significant vermicidal activity compared to the rest (ethyl and butyl) as well as the standard drug, Albendazole. Furthermore, theoretical modeling was carried out to visualize the preferential docking positions of these ILs into the active site of beta-tubulin. Fascinatingly, it was found that the ILs with longest alkyl side chain showed remarkable vermicidal activity compared to the rest, and the molecular docking studies not only validated the experimental results, but also showed per-residue interaction analysis between the ILs and the different components of beta-tubulin.

}, issn = {2046-2069}, doi = {10.1039/c5ra13469b}, author = {Charan, K. T. Prabhu and Ranjan, Prabodh and Manojkumar, Kasina and Pothanagandhi, Nellepalli and Jha, Prakash C. and Khedkar, Vijay M. and Sivaramakrishna, Akella and Vijayakrishna, Kari} } @article {43443, title = {Design, synthesis, and biological evaluation of novel fluorinated pyrazole encompassing pyridyl 1,3,4-oxadiazole motifs}, journal = {Medicinal Chemistry Research}, volume = {25}, year = {2016}, month = {NOV}, pages = {2698-2717}, abstract = {A rational approach was adopted for the synthesis of 1-(2-(3-(4-fluorophenyl)-1-phenyl-1H-pyrazol-4-yl)-5-(pyridin-4-yl)-1,3,4-oxadiazol-3(2H)-yl)-3-(aryl)prop-2-en-1-ones (5a-n) using conventional heating as well as microwave irradiation techniques. Compounds 5a-n were tested for their in vitro antimicrobial activity and cytotoxicity. Compounds 5g showed most potent antibacterial activity, while compound 5k emerged as the most effective antifungal agent. The most active compounds 5f, 5g, 5l, and 5m were also screened against methicillin-resistant Staphylococcus aureus. Among these compounds, 5g and 5m inhibited the growth against MRSA at low level of cytotoxicity. A binary quantitative structure-activity relationship based recursive partitioning model was developed to probe the physico-chemical properties influencing the structure-activity relationship for this class of molecules, which was used to correctly classify active and inactive compounds.}, doi = {10.1007/s00044-016-1683-y}, author = {Desai, Nisheeth C. and Kotadiya, Ghanshyam M. and Trivedi, Amit R. and Khedkar, Vijay M. and Jha, Prakash C.} } @article { ISI:000368702300006, title = {Molecular interaction of selected phytochemicals under the charged environment of Plasmodium falciparum chloroquine resistance transporter (PfCRT) model}, journal = {Journal of Biomolecular Structure \& Dynamics}, volume = {34}, number = {2}, year = {2016}, month = {FEB}, pages = {290-303}, publisher = {TAYLOR \& FRANCIS INC}, address = {530 WALNUT STREET, STE 850, PHILADELPHIA, PA 19106 USA}, abstract = {

Phytochemicals of Catharanthus roseus Linn. and Tylophora indica have been known for their inhibition of malarial parasite, Plasmodium falciparum in cell culture. Resistance to chloroquine (CQ), a widely used antimalarial drug, is due to the CQ resistance transporter (CRT) system. The present study deals with computational modeling of Plasmodium falciparum chloroquine resistance transporter (PfCRT) protein and development of charged environment to mimic a condition of resistance. The model of PfCRT was developed using Protein homology/analogy engine (PHYRE ver 0.2) and was validated based on the results obtained using PSI-PRED. Subsequently, molecular interactions of selected phytochemicals extracted from C. roseus Linn. and T. indica were studied using multiple-iterated genetic algorithm-based docking protocol in order to investigate the translocation of these legends across the PfCRT protein. Further, molecular dynamics studies exhibiting interaction energy estimates of these compounds within the active site of the protein showed that compounds are more selective toward PfCRT. Clusters of conformations with the free energy of binding were estimated which clearly demonstrated the potential channel and by this means the translocation across the PfCRT is anticipated.

}, keywords = {homology modeling, molecular dynamics, Plasmodium falciparum chloroquine, resistance transporter model}, issn = {0739-1102}, doi = {10.1080/07391102.2015.1028449}, author = {Patel, Saumya K. and Khedkar, Vijay M. and Jha, Prakash C. and Jasrai, Yogesh T. and Pandya, Himanshu A. and George, Linz-Buoy and Highland, Hyacinth N. and Skelton, Adam A.} } @article { ISI:000373739700025, title = {Synthesis and docking studies of pyrazine-thiazolidinone hybrid scaffold targeting dormant tuberculosis}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {26}, number = {9}, year = {2016}, month = {MAY}, pages = {2224-2228}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

The persistence of Mycobacterium tuberculosis (MTB) in dormant stage assists the pathogen to develop resistance against current antimycobactrial drugs. To address this issue, we report herein the synthesis of N-(4-oxo-2 substituted thiazolidin-3yl) pyrazine-2-carbohydrazide derivatives designed by following the molecular hybridization approach using pyrazine and thiazolidenone scaffolds. The compounds were evaluated against MTB H37Ra and Mycobacterium bovis BCG in dormancy model. Most of the compounds had IC50 values in 0.3-1 mu g/ml range. The active compounds were further tested for anti-proliferative activity against THP-1, Panc-1, A549, and MCF-7 cell lines using MTT assay and exhibited no significant cytotoxicity. We also report molecular docking studies using active analogs and MTB Decaprenylphosphoryl-beta-D-ribose-2{\textquoteright}-epimerase (DprE1) to rationalize the biological activity and to provide an insight into the probable mechanism of action and binding mode of hybridized structures. The results obtained validate the use of molecular hybridization approach and also suggest that reported compounds can provide a novel pharmacophore to synthesize lead compounds against dormat MTB. (C) 2016 Elsevier Ltd. All rights reserved.

}, keywords = {docking, Dormant, Hybrid design, Pyrazine, Thiazolidenone, tuberculosis}, issn = {0960-894X}, doi = {10.1016/j.bmcl.2016.03.055}, author = {Chitre, T. S. and Asgaonkar, K. D. and Miniyar, P. B. and Dharme, A. B. and Arkile, Manisha A. and Yeware, A. and Sarkar, Dhiman and Khedkar, Vijay M. and Jha, Prakash C.} } @article { ISI:000372031300074, title = {Synthesis, biological evaluation and molecular docking studies of N-acylheteroaryl hydrazone derivatives as antioxidant and anti-inflammatory agents}, journal = {Research on Chemical Intermediates}, volume = {42}, number = {3}, year = {2016}, month = {MAR}, pages = {2707-2729}, publisher = {SPRINGER}, address = {VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS}, abstract = {

In search of new therapeutics with greater potency, three new series of 3-methyl-1-phenyl-1H-thieno[2,3-c]pyrazole-5-carbohydrazide derivatives have been synthesized and evaluated for their in vitro antioxidant and anti-inflammatory activities. The hydrazones bearing a core pyrazole, chromone and tetrazolo[1,5-a]quinoline scaffold showed promising activities. Interestingly, compounds 3a (EC50 = 06.00 +/- A 2.36) and 5c (EC50 = 07.21 +/- A 0.67) showed the most potent antioxidant activity, while compounds 3a (EC50 = 10.25 +/- A 1.08), 7b (EC50 = 10.50 +/- A 0.99) and 7c (EC50 = 11.18 +/- A 0.15) showed significant anti-inflammatory activity. Furthermore, molecular docking studies also revealed a significant correlation between the binding score and biological activity for these compounds to describe the molecular basis for the structure activity relationship (SAR) results. As these compounds are good cyclooxygenase inhibitors, isoenzyme inhibitory potency studies are warranted.

}, keywords = {Anti-inflammatory, Antioxidant, Docking study, N-Acylhydrazones, Structure-activity relationship}, issn = {0922-6168}, doi = {10.1007/s11164-015-2176-1}, author = {Mahajan, Pravin S. and Nikam, Mukesh D. and Khedkar, Vijay M. and Jha, Prakash C. and Sarkar, Dhiman and Gill, Charansingh H.} } @article { ISI:000371344600027, title = {Synthesis, biological evaluation and molecular docking study of some novel indole and pyridine based 1,3,4-oxadiazole derivatives as potential antitubercular agents}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {26}, number = {7}, year = {2016}, month = {APR }, pages = {1776-1783}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

A series of indole and pyridine based 1,3,4-oxadiazole derivatives 5a-t were synthesized and evaluated for their in vitro antitubercular activity against Mycobacterium tuberculosis H37Ra (MTB) and Mycobacterium bovis BCG both in active and dormant state. Compounds 5b, 5e, 5g and 5q exhibited very good antitubercular activity. All the newly synthesized compounds 5a-t were further evaluated for antiproliferative activity against HeLa, A549 and PANC-1 cell lines using modified MTT assay and found to be noncytotoxic. On the basis of cytotoxicity and MIC values against Mycobacterium bovis BCG, selectivity index (SI) of most active compounds 5b, 5e, 5g and 5q was calculated (SI = GI(50)/MIC) in active and dormant state. Compounds 5b, 5e and 5g demonstrated SI values \>= 10 against all three cell lines and were found to safe for advance screening. Compounds 5a-t were further screened for their antibacterial activity against four bacteria strains to assess their selectivity towards MTB. In addition, the molecular docking studies revealed the binding modes of these compounds in active site of enoyl reductase (InhA), which in turn helped to establish a structural basis of inhibition of mycobacteria. The potency, low cytotoxicity and selectivity of these compounds make them valid lead compounds for further optimization. (C) 2016 Elsevier Ltd. All rights reserved.

}, keywords = {1, 3, 4-Oxadiazole, Antitubercular activity, Cytotoxicity, Indole, Molecular docking, Pyridine}, issn = {0960-894X}, doi = {10.1016/j.bmcl.2016.02.043}, author = {Desai, N. C. and Somani, Hardik and Trivedi, Amit and Bhatt, Kandarp and Nawale, Laxman and Khedkar, Vijay M. and Jha, Prakash C. and Sarkar, Dhiman} } @article { ISI:000371304100013, title = {Synthesis, biological valuation, and QSAR studies of novel pyrazole bearing pyridyl oxadiazole analogues as potential antimicrobial agents}, journal = {Medicinal Chemistry Research}, volume = {25}, number = {4}, year = {2016}, month = {APR}, pages = {712-727}, publisher = {SPRINGER BIRKHAUSER}, address = {233 SPRING STREET, 6TH FLOOR, NEW YORK, NY 10013 USA}, abstract = {

A new series of 1-(2-(3-(4-nitrophenyl)-1-phenyl-1H-pyrazol-4-yl)-5-(pyridin-4-yl)-1,3,4 -oxadiazol-3(2H)-yl)-3-(aryl)prop-2-en-1-ones (5a-l) were synthesized by a simple and efficient synthetic protocol. The newly synthesized compounds were characterized by IR, H-1 NMR, C-13 NMR and Mass spectroscopy. The resulting structural diversity was screened for its antimicrobial activity the following bacterial and fungal strains: two Gram-positive bacteria [Staphylococcus aureus (MTCC-96), Streptococcus pyogenes (MTCC-442)], two Gram-negative bacteria [Escherichia coli (MTCC-443), Pseudomonas aeruginosa (MTCC-1688)] and three fungal species (C. albicans, A. niger and A. clavatus). Following this, in vitro cytotoxicity activity against HeLa cell lines was measured by MTT [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazoliumbromide] assay. The observations derived from the diverse assays were utilized for building classification models based on a binary QSAR approach termed recursive partitioning (RP) analysis to probe the physic-chemical properties influencing the SAR for molecules. The decision tree derived from RP analysis could highlight structural characteristics that discriminate the actives from inactives which can serve as guide to design molecules with improved potency. In silico ADME predictions were performed to gauge their pharmacokinetic, safety and drug likeness profile.

}, keywords = {1, 3, 4-Oxadiazole, Antimicrobial activity, Cytotoxicity, Pyrazole, Pyridine, QSAR}, issn = {1054-2523}, doi = {10.1007/s00044-016-1511-4}, author = {Desai, N. C. and Kotadiya, G. M. and Trivedi, A. R. and Khedkar, Vijay M. and Jha, Prakash C.} } @article {45705, title = {Synthesis, structure and DNA interaction studies of bisphosphoramides: theoretical and experimental insights}, journal = {Inorganica Chimica Acta}, volume = {461}, year = {2017}, month = {MAY }, pages = {84-91}, type = {Article}, abstract = {

New bisphosphoramides (having phenyl (EDAPOPh(2)) and ethoxy (EDADEP) substituents attached to phosphoryl groups bridged with ethylenediamine spacer) are synthesized and structurally characterized by spectroscopic techniques as well as elemental analysis. The molecular structure of EDAPOPh(2) was determined by single crystal X-ray diffraction technique. The interaction of these bisphosphoramides with calf thymus DNA (ct-DNA) is investigated using UV-Visible absorption and fluorescence spectral data as well as the DFT calculations. These studies reveal that EDAPOPh(2) and EDADEP interact with DNA in a partial intercalation mode. The intrinsic binding constants K-b of two different bisphosphoramides with ct-DNA were determined by fluorescence spectroscopy as 2.08 x 10(4) and 3.86 x 10(4) M-1 respectively. The results indicated that the two compounds bind to ct-DNA with different binding affinities, i.e. EDAPOPh(2) \> EDADEP. The binding mechanism of these bisphosphoramides to ct-DNA is also discussed. (C) 2017 Elsevier B.V. All rights reserved.

}, keywords = {Bisphosphoramides, crystal structure, DNA interaction, Molecular docking}, issn = {0020-1693}, doi = {10.1016/j.ica.2017.02.017}, author = {Goud, E. Veerashekhar and Sivaramakrishna, Akella and Vijayakrishna, Kari and Rao, C. V. S. Brahmmananda and Khedkar, Vijay M. and Jha, Prakash C.} } @article {44476, title = {Facile and solvent-free domino synthesis of new quinolidinyl-2,4-thiazolidinones: antifungal activityand molecular docking}, journal = {Mini-Reviews in Medicinal Chemistry}, volume = {18}, year = {2018}, month = {JAN}, pages = {622-630}, abstract = {Objective: We have synthesized new quinolidinyl-thiazolidinones via Knoevenagel condensation-alkylation reaction, catalyzed by [Et3NH][HSO4]. The present approach offers several advantages such as higher yields, eco-friendly reaction condition and economic availability of the catalyst. Method: The newly synthesized compounds were evaluated for their in vitro antifungal activity against six fungal strains. Some of the synthesized conjugates displayed good to moderate antifungal activity. Conclusion: Again, the molecular docking study performed against the fungal sterol 14 alpha-demethylase (CYP51) showed an excellent binding affinity towards the enzyme which could rationalize the promising antifungal activity portrayed by these derivatives and provides a platform for structure based drug design.}, doi = {10.2174/1389557516666161226161152}, author = {Subhedar, Dnyaneshwar D. and Shaikh, Mubarak H. and Tupe, Santosh G. and Deshpande, Mukund V. and Khedkar, Vijay M. and Jha, Prakash C. and Shingate, Bapurao B.} } @article {46359, title = {Non nucleoside reverse transcriptase inhibitors, molecular docking studies and antitubercular activity of thiazolidin-4-one derivatives}, journal = {Current Computer-Aided Drug Design}, volume = {15}, year = {2019}, month = {JAN}, pages = {433-444}, type = {Article}, abstract = {

Background: Management of Co-existence of Acquired immunodeficiency syndrome and Tuberculosis has become a global challenge due to the emergence of resistant strains and pill burden. Objective: Hence the aim of the present work was to design and evaluate compounds for their dual activity on HIV-1 and Tuberculosis (TB). Methods: A series of seven, novel Thiazolidin-4-one derivatives were synthesized and evaluated for their anti-HIV and anti-tubercular activity along with Molecular docking studies. All the seven compounds displayed promising activity against the replication of HIV-1 in cell-based assays. The four most active compounds were further evaluated against X4 tropic HIV-1(UG)(070) and R5 tropic HIV-1(vB59) primary isolates. The binding affinity of all the designed compounds for HIV-RT and Mycobacterium tuberculosis Enol Reductase (MTB InhA) was gauged by molecular docking studies which revealed crucial thermodynamic interactions governing their binding. Results: The CC50 values for the test compounds were in the range of, 15.08-34.9 mu g/ml, while the IC50 values were in the range of 16.1-27.13(UG(070); X4) and 12.03-23.64 (VB59; R5) mu g/ml. The control drug Nevirapine (NVP) exhibited CC50 value of 77.13 mu g/ml and IC50 value of 0.03 mu g/ml. Amongst all these compounds, compound number 3 showed significant activity with a TI value of 2.167 and 2.678 against the HIV-1 X4 and the R5 tropic virus respectively. In anti-mycobacterial screening, the compounds proved effective in inhibiting the growth of both log phase and starved MTB cultures. Conclusion: Compound 3 has been found to be active against HIV-1 as well as MTB.

}, keywords = {anti-HIV-1 activity, Antitubercular activity, human immunodeficiency virus-1, Molecular docking, Non nucleoside reverse transcriptase, thiazolidin-4-ones}, issn = {1573-4099}, doi = {10.2174/1573409915666181221102903}, author = {Chitre, Trupti S. and Patil, Shital M. and Sujalegaonkar, Anagha G. and Asgaonkar, Kalyani D. and Khedkar, Vijay M. and Garud, Dinesh R. and Jha, Prakash C. and Gaikwad, Sharddha Y. and Kulkarni, Smita and Choudhari, Amit and Sarkar, Dhiman} }