@article { ISI:000313165500067, title = {Functional characterization, homology modeling and docking studies of beta-glucosidase responsible for bioactivation of cyanogenic hydroxynitrile glucosides from Leucaena leucocephala (subabul)}, journal = {Molecular Biology Reports}, volume = {40}, number = {2}, year = {2013}, month = {FEB}, pages = {1351-1363}, publisher = {SPRINGER}, address = {VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS}, abstract = {

Glycosyl hydrolase family 1 beta-glucosidases are important enzymes that serve many diverse functions in plants including defense, whereby hydrolyzing the defensive compounds such as hydroxynitrile glucosides. A hydroxynitrile glucoside cleaving beta-glucosidase gene (Llbglu1) was isolated from Leucaena leucocephala, cloned into pET-28a (+) and expressed in E. coli BL21 (DE3) cells. The recombinant enzyme was purified by Ni-NTA affinity chromatography. The optimal temperature and pH for this beta-glucosidase were found to be 45 A degrees C and 4.8, respectively. The purified Llbglu1 enzyme hydrolyzed the synthetic glycosides, pNPGlucoside (pNPGlc) and pNPGalactoside (pNPGal). Also, the enzyme hydrolyzed amygdalin, a hydroxynitrile glycoside and a few of the tested flavonoid and isoflavonoid glucosides. The kinetic parameters K (m) and V (max) were found to be 38.59 mu M and 0.8237 mu M/mg/min for pNPGlc, whereas for pNPGal the values were observed as 1845 mu M and 0.1037 mu M/mg/min. In the present study, a three dimensional (3D) model of the Llbglu1 was built by MODELLER software to find out the substrate binding sites and the quality of the model was examined using the program PROCHEK. Docking studies indicated that conserved active site residues are Glu 199, Glu 413, His 153, Asn 198, Val 270, Asn 340, and Trp 462. Docking of rhodiocyanoside A with the modeled Llbglu1 resulted in a binding with free energy change (Delta G) of -5.52 kcal/mol on which basis rhodiocyanoside A could be considered as a potential substrate.

}, keywords = {Glycosyl hydrolase family 1, homology modeling, Leucaena leucocephala, Molecular docking}, issn = {0301-4851}, doi = {10.1007/s11033-012-2179-6}, author = {Shaik, Noor M. and Misra, Anurag and Singh, Somesh and Fatangare, Amol B. and Ramakumar, Suryanarayanarao and Rawal, Shuban K. and Khan, Bashir Mohammad} } @article { ISI:000347596700001, title = {Molecular recognition pattern of cytotoxic alkaloid vinblastine with multiple targets}, journal = {Journal of Molecular Graphics \& Modelling}, volume = {54}, year = {2014}, month = {NOV}, pages = {1-9}, publisher = {ELSEVIER SCIENCE INC}, address = {360 PARK AVE SOUTH, NEW YORK, NY 10010-1710 USA}, abstract = {

Vinblastine (VLB), a cytotoxic alkaloid is used extensively against various cancer types and the crystal structure of its tubulin complex is already known. Multitarget affinity of vinblastine has been investigated and the nature of binding with biological receptors namely, duplex DNA and Human serum albumin (HSA) has been compared to the binding characteristics of its known complex with natural high affinity receptor tubulin using molecular docking and QM-MM calculations. VLB is found to interact with DNA as well as HSA protein, though, with weaker affinity as compared to tubulin. Analysis of various docked complexes revealed that the H-bonds and cation-pi bonds do not have significant contribution to the binding interactions and despite its large size, VLB remains in relaxed conformation and fits in the hydrophobic regions on the receptors. (C) 2014 Elsevier Inc. All rights reserved.

}, keywords = {Drug-DNA interactions, Drug-protein binding, Human serum albumin, Molecular docking, Multitarget affinity, QM-MM calculation, Vinblastine}, issn = {1093-3263}, doi = {10.1016/j.jmgm.2014.09.001}, author = {Pandya, Prateek and Agarwal, Lokesh Kr and Gupta, Neelima and Pal, Sourav} } @article { ISI:000360934400007, title = {Design and development of cheminfocloud: an integrated cloud enabled platform for virtual screening}, journal = {Combinatorial Chemistry \& High Throughput Screening}, volume = {18}, number = {6}, year = {2015}, month = {JAN}, pages = {604-619}, publisher = {BENTHAM SCIENCE PUBL LTD}, address = {EXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATES}, abstract = {

The power of cloud computing and distributed computing has been harnessed to handle vast and heterogeneous data required to be processed in any virtual screening protocol. A cloud computing platorm ChemInfoCloud was built and integrated with several chemoinformatics and bioinformatics tools. The robust engine performs the core chemoinformatics tasks of lead generation, lead optimisation and property prediction in a fast and efficient manner. It has also been provided with some of the bioinformatics functionalities including sequence alignment, active site pose prediction and protein ligand docking. Text mining, NMR chemical shift (1H, 13C) prediction and reaction fingerprint generation modules for efficient lead discovery are also implemented in this platform. We have developed an integrated problem solving cloud environment for virtual screening studies that also provides workflow management, better usability and interaction with end users using container based virtualization, OpenVz.

}, keywords = {Chemoinformatics, cloud computing, machine learning, Molecular docking, OpenVz, sequence alignment, spectra prediction, text mining, virtual screening}, issn = {1386-2073}, doi = {10.2174/1386207318666150703113656}, author = {Karthikeyan, Muthukumarasamy and Pandit, Deepak and Bhavasar, Arvind and Vyas, Renu} } @article { ISI:000353720700004, title = {Distinct molecular features facilitating ice-binding mechanisms in hyperactive antifreeze proteins closely related to an Antarctic sea ice bacterium}, journal = {Journal of Biomolecular Structure \& Dynamics}, volume = {33}, number = {7}, year = {2015}, month = {JUL}, pages = {1424-1441}, publisher = {TAYLOR \& FRANCIS INC}, address = {530 WALNUT STREET, STE 850, PHILADELPHIA, PA 19106 USA}, abstract = {

Antifreeze proteins or ice-binding proteins (IBPs) facilitate the survival of certain cellular organisms in freezing environment by inhibiting the growth of ice crystals in solution. Present study identifies orthologs of the IBP of Colwellia sp. SLW05, which were obtained from a wide range of taxa. Phylogenetic analysis on the basis of conserved regions (predicted as the {\textquoteleft}ice-binding domain{\textquoteright} [IBD]) present in all the orthologs, separates the bacterial and archaeal orthologs from that of the eukaryotes{\textquoteright}. Correspondence analysis pointed out that the bacterial and archaeal IBDs have relatively higher average hydrophobicity than the eukaryotic members. IBDs belonging to bacterial as well as archaeal AFPs contain comparatively more strands, and therefore are revealed to be under higher evolutionary selection pressure. Molecular docking studies prove that the ice crystals form more stable complex with the bacterial as well as archaeal proteins than the eukaryotic orthologs. Analysis of the docked structures have traced out the ice-binding sites (IBSs) in all the orthologs which continue to facilitate ice-binding activity even after getting mutated with respect to the well-studied IBSs of Typhula ishikariensis and notably, all these mutations performing ice-binding using {\textquoteleft}anchored clathrate mechanism{\textquoteright} have been found to prefer polar and hydrophilic amino acids. Horizontal gene transfer studies point toward a strong selection pressure favoring independent evolution of the IBPs in some polar organisms including prokaryotes as well as eukaryotes because these proteins facilitate the polar organisms to acclimatize to the adversities in their niche, thus safeguarding their existence.

}, keywords = {antifreeze proteins, horizontal gene transfer, ice-recrystallization inhibition, Molecular docking, Phylogenetic analysis}, issn = {0739-1102}, doi = {10.1080/07391102.2014.952665}, author = {Banerjee, Rachana and Chakraborti, Pratim and Bhowmick, Rupa and Mukhopadhyay, Subhasish} } @article { ISI:000348265400007, title = {Genome-wide identification and structure-function studies of proteases and protease inhibitors in cicer arietinum (chickpea)}, journal = {Computers in Biology and Medicine}, volume = {56}, year = {2015}, month = {JAN}, pages = {67-81}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

Background: Proteases are a family of enzymes present in almost all living organisms. In plants they are involved in many biological processes requiring stress response in situations such as water deficiency, pathogen attack, maintaining protein content of the cell, programmed cell death, senescence, reproduction and many more. Similarly, protease inhibitors (PIs) are involved in various important functions like suppression of invasion by pathogenic nematodes, inhibition of spores-germination and mycelium growth of Alternaria alternata and response to wounding and fungal attack. As much as we know, no genome-wide study of proteases together with proteinaceous PIs is reported in any of the sequenced genomes till now. Methods: Phylogenetic studies and domain analysis of proteases were carried out to understand the molecular evolution as well as gene and protein features. Structural analysis was carried out to explore the binding mode and affinity of PIs for cognate proteases and prolyl oligopeptidase protease with inhibitor ligand. Results: In the study reported here, a significant number of proteases and PIs were identified in chickpea genome. The gene expression profiles of proteases and Pis in five different plant tissues revealed a differential expression pattern in more than one plant tissue. Molecular dynamics studies revealed the formation of stable complex owing to increased number of protein-ligand and inter and intramolecular protein-protein hydrogen bonds. Discussion: The genome-wide identification, characterization, evolutionary understanding, gene expression, and structural analysis of proteases and Pis provide a framework for future analysis when defining their roles in stress response and developing a more stress tolerant variety of chickpea. (C) 2014 Elsevier Ltd. All rights reserved.

}, keywords = {Domain, Gene expression, Genome analysis, Homology modelling, Molecular docking, molecular dynamics simulation, Motif, Orthologs, Phylogeny}, issn = {0010-4825}, doi = {10.1016/j.compbiomed.2014.10.019}, author = {Sharma, Ranu and Suresh, C. G.} } @article { ISI:000357458400018, title = {In silico ligand binding studies of cyanogenic beta-glucosidase, dhurrinase-2 from Sorghum bicolor}, journal = {Journal of Molecular Modeling}, volume = {21}, number = {7}, year = {2015}, month = {JUL}, pages = {184}, publisher = {SPRINGER}, address = {233 SPRING ST, NEW YORK, NY 10013 USA}, abstract = {

Dhurrinase, a cyanogenic beta-glucosidase from Sorghum bicolor is the key enzyme responsible for the hydrolysis of dhurrin to produce toxic hydrogen cyanide, as a part of plant defence mechanism. Dhurrinase 1 (SbDhr1) and dhurrinase 2 (SbDhr2), two isozymes have been isolated and characterized from S. bicolor. However, there is no information in the literature about the three dimensional (3D) structure of SbDhr2 and molecular interactions involved between the protein and ligand. In this study, the three dimensional structure of SbDhr2 was built based on homology modeling by using the X-ray crystallographic structure of its close homologue SbDhr1 as the template. The generated 3D model was energy minimized and the quality was validated by Ramachndran plot, various bioinformatic tools and their relevant parameters. Stability, folding-unfolding and flexibility of the modeled SbDhr2 was evaluated on the basis of RMSD, radius of gyration (R-g) and RMSF values respectively, obtained through molecular dynamic (MD) simulation. Further, molecular docking was performed with its natural substrate dhurrin, one substrate analogue, three un-natural substrates, and one inhibitor. Analysis of molecular interactions in the SbDhr2-ligand complexes revealed the key amino acid residues responsible to stabilize the ligands within the binding pocket through non-bonded interactions and some of them were found to be conserved (Glu239, Tyr381, Trp426, Glu454, Trp511). Reasonably broader substrate specificity of SbDhr2 was explained through the wider entrance passage observed in comparison to SbDhr1.

}, keywords = {beta-Glucosidase, Dhurrinase, Molecular docking, Molecular dynamic simulation, Sorghum bicolor}, issn = {1610-2940}, doi = {10.1007/s00894-015-2730-1}, author = {Mahajan, Chavi and Patel, Krunal and Khan, Bashir Mohammad and Rawal, Shuban S.} } @article { ISI:000380574100052, title = {Synthesis and antitubercular activity of new 1,3,4-oxadiazoles bearing pyridyl and thiazolyl scaffolds}, journal = {Bioorganic \& Medicinal Chemistry Letters}, volume = {26}, number = {15}, year = {2016}, month = {AUG}, pages = {3646-3651}, publisher = {PERGAMON-ELSEVIER SCIENCE LTD}, address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND}, abstract = {

In search of more potent and safe new antitubercular agents, here new 2-pyridinyl substituted thiazolyl-5-aryl-1,3,4-oxadiazoles (6a-o), have been designed and synthesized using thionicotinamide as a starting, following novel multistep synthetic route. An intermediate, pyridinyl substituted thiazolyl acid hydrazide (4) when condensed with benzoic acids/nicotinic acids (5a-o) in the presence of silica supported POCl3 yielded better to excellent yields of the title compounds. All the synthesized compounds (6a-o) and intermediate acid hydrazide (4) have been screened for their in vitro antitubercular activity against Mycobacterium tuberculosis H37Ra (MTB) and Mycobacterium bovis BCG. Amongst them, 6f, 6j, 6l and 6o have revealed promising activity against M. bovis BCG at concentrations less than 3 mu g/mL. These compounds have shown low cytotoxicity (CC50: \> 100 mu g/mL) towards four human cancer cell lines. Molecular docking study has also been performed against mycobacterial enoyl reductase (InhA) enzyme to gain an insight into the binding modes of these molecules and recorded good binding affinity. The ADME properties the title products have also been analyzed. (C) 2016 Elsevier Ltd. All rights reserved.

}, keywords = {1, 3, 4-Oxadiazole, Antitubercular activity, Cytotoxicity, Molecular docking, Pyridine, Thiazole}, issn = {0960-894X}, doi = {10.1016/j.bmcl.2016.05.093}, author = {Dhumal, Sambhaji T. and Deshmukh, Amarsinh R. and Bhosle, Manisha R. and Khedkar, Vijay M. and Nawale, Laxman U. and Sarkar, Dhiman and Mane, Ramrao A.} } @article { ISI:000381452800005, title = {Synthesis and antitubercular activity of new benzo[b]thiophenes}, journal = {ACS Medicinal Chemistry Letters}, volume = {7}, number = {8}, year = {2016}, month = {AUG}, pages = {751-756}, publisher = {AMER CHEMICAL SOC}, address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA}, abstract = {

In vitro and ex vivo efficacies of four series of benzo[b]thiophene-2-carboxylic acid derivatives were studied against Mycobacterium tuberculosis H37Ra (MTB). Benzo[b]thiophenes were also tested in vitro against multidrug resistant Mycobacterium tuberculosis H37Ra (MDR-MTB), and 7b was found to be highly active against A- and DMDR-MTB/MTB (MIC ranges 2.73-22.86 mu g/mL). The activity of all benzo[b]-thiophenes against M. bovis BCG (BCG) was also assessed grown under aerobic and under conditions of oxygen depletion. Compounds 8c and 8g showed significant activity with MICs of 0.60 and 0.61 mu g/mL against dormant BCG. The low cytotoxicity and high selectivity index data against human cancer cell lines, HeLa, Panc-1, and THP-1 indicate the potential importance of the development of benzo[b]thiophene-based 1,3-diketones and flavones as lead candidates to treat mycobacterial infections. Molecular docking studies into the active site of DprE1 (Decaprenylphosphoryl-beta-n-ribose-2{\textquoteright}-epimerase) enzyme revealed a similar binding mode to native ligand in the crystal structure thereby helping to understand the ligand protein interactions and establish a structural basis for inhibition of MTB. In summary, its good activity in in vitro and ex vivo model, as well as its activity against multidrug-resistant M. tuberculosis H37Ra in a potentially latent state, makes 7b an attractive drug candidate for the therapy of tuberculosis.

}, keywords = {Benzo[b]thiophene, Cytotoxicity, M. Bovis BCG, MDR-MTB, Molecular docking}, issn = {1948-5875}, doi = {10.1021/acsmedchemlett.6b00077}, author = {Mahajan, Pravin S. and Nikam, Mukesh D. and Nawale, Laxman U. and Khedkar, Vijay M. 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:000380241600003, title = {Ultrasound- and molecular sieves-assisted synthesis, molecular docking and antifungal evaluation of 5-(4-(benzyloxy)-substituted phenyl)-3-((phenylamino)methyl)-1,3,4-oxadiazole-2(3H)-thiones}, journal = {Molecules}, volume = {21}, number = {5}, year = {2016}, month = {MAY}, pages = {484}, publisher = {MDPI AG}, address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND}, abstract = {

A novel series of 5-(4-(benzyloxy) substituted phenyl)-3-((phenyl amino) methyl)-1,3,4-oxadiazole-2(3H)-thione Mannich bases 6a-o were synthesized in good yield from the key compound 5-(4-(benzyloxy) phenyl)-1,3,4-oxadiazole-2(3H)-thione by aminomethylation with paraformaldehyde and substituted amines using molecular sieves and sonication as green chemistry tools. The antifungal activity of the new products was evaluated against seven human pathogenic fungal strains, namely, Candida albicans ATCC 24433, Candida albicans ATCC 10231, Candida glabrata NCYC 388, Cryptococcus neoformans ATCC 34664, Cryptococcus neoformans PRL 518, Aspergillus fumigatus NCIM 902 and Aspergillus niger ATCC 10578. The synthesized compounds 6d, 6f, 6g, 6h and 6j exhibited promising antifungal activity against the tested fungal pathogens. In molecular docking studies, derivatives 6c, 6f and 6i showed good binding at the active site of C. albicans cytochrome P450 enzyme lanosterol 14 alpha-demethylase. The in vitro antifungal activity results and docking studies indicated that the synthesized compounds have potential antifungal activity and can be further optimized as privileged scaffolds to design and develop potent antifungal drugs.

}, keywords = {1, 3, 4-oxadiazoles, Antifungal activity, Mannich reaction, Molecular docking, Molecular sieves, Ultrasound}, issn = {1420-3049}, doi = {10.3390/molecules21050484}, author = {Nimbalkar, Urja D. and Tupe, Santosh G. and Seijas Vazquez, Julio A. and Khan, Firoz A. Kalam and Sangshetti, Jaiprakash N. and Nikalje, Anna Pratima G.} } @article { ISI:000380565100006, title = {Virtual screening techniques to probe the antimalarial activity of some traditionally used phytochemicals}, journal = {Combinatorial Chemistry \& High Throughput Screening}, volume = {19}, number = {7}, year = {2016}, month = {JUL}, pages = {572-591}, publisher = {BENTHAM SCIENCE PUBL LTD}, address = {EXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB EMIRATES}, abstract = {

Malaria parasites show resistance to most of the antimalarial drugs and hence developing antimalarials which can act on multitargets rather than a single target will be a promising strategy of drug design. Here we report a new approach by which virtual screening of 292 unique phytochemicals present in 72 traditionally important herbs is used for finding out inhibitors of plasmepsin-2 and falcipain-2 for antimalarial activity against P. falciparum. Initial screenings of the selected molecules by Random Forest algorithm model of Weka using the bioassay datasets AID 504850 and AID 2302 screened 120 out of the total 292 phytochemicals to be active against the targets. Toxtree scan cautioned 21 compounds to be either carcinogenic or mutagenic and were thus removed for further analysis. Out of the remaining 99 compounds, only 46 compounds offered drug-likeness as per the {\textquoteleft}rule of five{\textquoteright} criteria. Out of ten antimalarial drug targets, only two target proteins such as 3BPF and 3PNR of falcipain-2 and 1PFZ and 2BJU of plasmepsin-2 are selected as targets. The potential binding of the selected 46 compounds to the active sites of these four targets was analyzed using MOE software. The docked conformations and the interactions with the binding pocket residues of the target proteins were understood by {\textquoteleft}Ligplot{\textquoteright} analysis. It has been found that 8 compounds are dual inhibitors of falcipain-2 and plasmepsin-2, with the best binding energies. Compound 117 (6aR, 12aS)-12a-Hydroxy-9-methoxy-2,3-dimethylenedioxy-8-prenylrotenone (Usaratenoid C) present in the plant Millettia usaramensis showed maximum molecular docking score.

}, keywords = {ADME, malaria, Molecular docking, molecular operating environment, Plasmodium falciparum, virtual screening, weka}, issn = {1386-2073}, doi = {10.2174/1386207319666160420141200}, author = {Shibi, Indira G. and Aswathy, Lilly and Jisha, Radhakrishnan S. and Masand, Vijay H. and Gajbhiye, Jayant M.} } @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 {44195, title = {Design, synthesis, and pharmacological evaluation of fluorinated azoles as anti-tubercular agents}, journal = {Archiv Der Pharmazie}, volume = {351}, year = {2018}, month = {FEB}, pages = {e1700294}, type = {Article}, abstract = {

Design, synthesis, and biological screening of 2,2-dimethyl-2,3-dihydrobenzofuran tethered 1,3,4-oxadiazole derivatives as anti-tubercular agents were described. The synthesis of the target compounds was conducted by a series of reaction schemes. All the synthesized compounds were characterized by IR, H-1 NMR, C-13 NMR, and mass spectrometry. The therapeutic potential of the synthesized compounds was confirmed by molecular docking studies. Among the synthesized compounds, 12a, 12c, 12d, 12e, 12g, and 12j were found to be more active against non-replicating than against replicating cultures of Mycobacterium tuberculosis H37Ra ex vivo and in vitro. These compounds exhibit minimum inhibitory concentration (MIC) values in the range of 2.31-23.91g/mL. The cytotoxicity study was conducted against the cell lines THP-1, A549 and PANC-1, and the compounds were observed to be non-toxic to host cells. Molecular docking was conducted with InhA (FabI/ENR) and suggested the antimycobacterial potential of the synthesized compounds. The investigation presented here was found to be adventitious for the development of new therapeutic agents against Mycobacterium infection.

}, keywords = {1, 2, 2-dimethyl-2, 3, 3-dihydrobenzofuran, 4-Oxadiazole, anti-tubercular agents, Cytotoxicity, Molecular docking}, issn = {0365-6233}, doi = {10.1002/ardp.201700294}, author = {Gholap, Somnath and Tambe, Macchindra and Nawale, Laxman and Sarkar, Dhiman and Sangshetti, Jaiprakash and Damale, Manoj} } @article {44512, title = {Synthesis and biological evaluation of novel triazole-biscoumarin conjugates as potential antitubercular and anti-oxidant agents}, journal = {Research on Chemical Intermediates}, volume = {44}, year = {2018}, month = {MAY}, pages = {1-28}, type = {Journal Article}, abstract = {

The synthesis of a new series of triazole-biscoumarin conjugates by using a molecular hybridization approach is described. The newly synthesized compounds 6a{\textendash}k were evaluated for their in vitro antitubercular activity against active and dormant Mtb H37Ra and anti-oxidant activity against DPPH radical scavenging. Molecular docking simulations for the antitubercular activity showed that the conjugates 6a{\textendash}k bind in the pocket of the DprE1 enzyme. Most of the conjugates displayed good antitubercular activity against both the active and dormant Mtb H37Ra strain. The compound 6h displayed very good antitubercular activity against dormant Mtb H37Ra with an IC50 value of 1.44 μg/mL. Most of the synthesized conjugates exhibit excellent anti-oxidant activity with an IC50 of less than the standard BHT. Compound 6b is the most active among all the conjugates with an IC50 value of 08.17 {\textpm} 0.11 μg/mL. The molecular docking study shows good agreement between the observed antitubercular activity and the binding affinity.

}, keywords = {1, 2, 3-triazoles, Anti-oxidant activity, Antitubercular activity, Biscoumarins, Molecular docking}, issn = {9226168}, doi = {10.1007/s11164-018-3490-1}, author = {Danne, Ashruba B.}, editor = {Choudhari, Amit S.} } @article {44650, title = {Synthesis and biological evaluation of some new tricyclic pyrrolo[3,2-e]tetrazolo[1,5-c]pyrimidine derivatives as potential antitubercular agents}, journal = {Archiv Der Pharmazie}, volume = {351}, year = {2018}, month = {AUG}, pages = {e1800040}, abstract = {

A series of new tricyclic pyrrolo[3,2-e]tetrazolo[1,5-c]pyrimidines 8a-l were synthesized and characterized by IR, NMR (H-1 and C-13), and mass spectral analysis. The newly synthesized compounds 8a-l were inspected for their in vitro antitubercular activity against Mycobacterium tuberculosis (MTB) H37Ra using an established XTT reduction menadione assay (XRMA). The title compounds exhibited minimum inhibitory concentrations (MIC90) ranging from 0.09 to \>30g/mL. Five compounds (8c, 8i-l) were further confirmed for their dose-dependent effect against MTB. These compounds were evaluated in the THP-1 infection model, where 8i (MIC90=0.35g/mL), 8j (MIC90=1.17g/mL), 8k (MIC90=2.38g/mL), and 8l (MIC90=1.17g/mL) demonstrated significant antitubercular activity. All the ex vivo active compounds showed insignificant cytotoxicity against the human cancer cell lines, HeLa, MCF-7, and THP-1. Inactivity of all these compounds against Gram positive and Gram negative bacteria indicates their specificity. Molecular docking studies in the active site of the sterol 14alpha-demethylase (CYP51) enzyme revealed a similar binding mode to the native ligand in the crystal structure, thereby helping to understand the ligand-protein interactions and to establish a structural basis for inhibition of MTB. The results suggest novel pharmacophores as selective and specific inhibitors against MTB that can be explored further to synthesize lead compounds against tuberculosis. In summary, the results clearly indicate the identification of some novel, selective, and specific inhibitors against MTB that can be explored further for potential antitubercular drugs.

}, keywords = {2-e]tetrazolo[1, 5-c]pyrimidine, Antituberculosis, Cytotoxicity, Molecular docking, tricyclic pyrrolo[3}, issn = {0365-6233}, doi = {10.1002/ardp.201800040}, author = {Patil, Yogesh and Shingare, Ramesh and Choudhari, Amit and Borkute, Rachana and Sarkar, Dhiman and Madje, Balaji R.} } @article {45456, title = {Ultrasound assisted synthesis of 4-(Benzyloxy)-N-(3-chloro-2-(substitutedphenyl)-4-oxoazetidin-1-yl) benzamide as challenging anti-tubercular scaffold}, journal = { Molecules}, volume = {23}, year = {2018}, month = {AUG}, pages = {Article No: 1945}, type = {Article}, abstract = {

A series of ten novel derivatives of 4-(benzyloxy)-N-(3-chloro-2-(substituted phenyl)-4-oxoazetidin-1-yl) benzamide 6a-j were synthesized in good yield from the key compound 4-(benzyloxy)-N-(substituted benzylidene) benzo hydrazide, called Schiff {\textquoteleft}s bases 5a-j, by Staudinger reaction ([2 + 2] ketene-imine cycloaddition reaction) with chloro acetyl chloride in the presence of catalyst tri ethylamine and solvent dimethyl formamide (DMF), by using ultra-sonication as one of the green chemistry tools. All the synthesised compounds were evaluated for in vitro anti-tubercular activity against Mycobacterium tuberculosis (MTB) and most of them showed promising activity with an IC50 value of less than 1 mu g/mL. To establish the safety, all the synthesized compounds were further tested for cytotoxicity against the human cancer cell line HeLa and all 6a-j compounds were found to be non-cytotoxic in nature. The molecular docking study was carried out with essential enzyme InhA (FabI/ENR) of Mycobacterium responsible for cell wall synthesis which suggests that 6a and 6e are the most active derivatives of the series. The theoretical evaluation of cell permeability based on Lipinski{\textquoteright}s rule of five has helped to rationalize the biological results and hence the synthesized azetidinone derivatives 6a-j were also analyzed for physicochemical evaluation that is, absorption, distribution, metabolism, excretion, and toxicity (ADMET) properties and the results showed that all the derivatives could comply with essential features required for a potential lead in the anti-tubercular drug discovery process.

}, keywords = {ADMET study, anti-tubercular screening, azetidinone, cytotoxicity study, green chemistry, Molecular docking, ultra-sonication}, issn = {1420-3049}, doi = {10.3390/molecules23081945}, author = {Nimbalkar, Urja D. and Seijas, Julio A. and Borkute, Rachna and Damale, Manoj G. and Sangshetti, Jaiprakash N. and Sarkar, Dhiman and Nikalje, Anna Pratima G.} } @article {46125, title = {Design, synthesis and biological evaluation of (E)-5-styryl-1,2,4-oxadiazoles as anti-tubercular agents}, journal = {Bioorganic Chemistry}, volume = {86}, year = {2019}, month = {MAY}, pages = {507-512}, type = {Article}, abstract = {

Cinnamic acid and its derivatives are known for anti-tubercular activity. The present study reports the synthesis of cinnamic acid derivatives via bioisosteric replacement of terminal carboxylic acid with {\textquoteleft}{\textquoteleft}oxadiazole{\textquoteright}{\textquoteright}. A series of cinnamic acid derivatives (styryl oxadiazoles) were designed and synthesized in good yields by reaction of substituted cinnamic acids (2, 15a-15s) with amidoximes. The synthesized styryl oxadiazoles were evaluated in vitro for anti-tubercular activity against Mycobacterium tuberculosis (Mtb) H37Ra strain. The structure-activity relationship (SAR) study has identified several compounds with mixed anti-tubercular profiles. The compound 32 displayed potent anti-tubercular activity (IC50= 0.045 mu g/mL). Molecular docking studies on mycobacterial enoyl-ACP reductase enzyme corroborated well with the experimental findings providing a platform for structure based hit-to-lead development.

}, keywords = {1, 2, 4-Oxadiazole, Anti-tubercular, Bioisosteres, Cinnamic acid, Molecular docking}, issn = {0045-2068}, doi = {10.1016/j.bioorg.2019.01.054}, author = {Upare, Abhay Atmaram and Gadekar, Pradip K. and Sivaramakrishnan, H. and Naik, Nishigandha and Khedkar, Vijay M. and Sarkar, Dhiman and Choudhari, Amit and Roopan, S. Mohana} } @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} } @article {46012, title = {Synthesis and antimycobacterial evaluation of new 5-(1-benzyl-1H-1,2,3-triazol-4-yl)-4-methyl-2-arylthiazole derivatives}, journal = {Medicinal Chemistry Research}, volume = {28}, year = {2019}, month = {JUN}, pages = {805-819}, type = {Article}, abstract = {

A new series of 5-(1-benzyl-1H-1,2,3-triazol-4-yl)-4-methyl-2-arylthiazole derivatives, 6a-w have been synthesized by click reaction of substituted benzylazide, 5a-d with 5-ethynyl-4-methyl-2-substituted phenylthiazole, 4a-f. The starting compounds 4-ethynyl-2-substituted phenylthiazole (4a-f) were synthesized from the corresponding thiazole aldehyde by using the Ohira-Bestmann reagent. The structure of the synthesized compounds was determined by spectral analysis. All the synthesized compounds were screened for their preliminary antitubercular activity against Mycobacterium tuberculosis H37Ra (MTB, ATCC 25177). Most of the synthesized compounds reported good activity against M. tuberculosis H37Ra strain with IC50 range of 0.58-8.23 mu g/mL. Compounds 6g and 6k reported good antitubercular activity with MIC90 values of 4.71 and 2.22 mu g/mL, respectively. Potential antimycobacterial activity suggested that these compounds could serve as good lead compounds for further optimization and development of a newer antitubercular candidate. [GRAPHICS] .

}, keywords = {1, 2, 3-Triazole, Antitubercular activity, Molecular docking, Ohira-Bestmann reagent, Thiazole}, issn = {1054-2523}, doi = {10.1007/s00044-019-02310-y}, author = {Shinde, Vikas and Mahulikar, Pramod and Mhaske, Pravin C. and Chakraborty, Shakti and Choudhari, Amit and Phalle, Siddharth and Choudhari, Prafulla and Sarkar, Dhiman} } @article {47125, title = {In silico studies, synthesis and antitubercular activity of some novel quinoline - azitidinone derivatives}, journal = {Current Computer-Aided Drug Design}, volume = {17}, year = {2021}, month = {JAN}, pages = {134-143}, type = {Article}, abstract = {

Background: Diarylquinolines like Bedaquiline have shown promising antitubercular activity by their action of Mycobacterial ATPase. Objective: The structural features necessary for a good antitubercular activity for a series of quinoline derivatives were explored through computational chemistry tools like QSAR and combinatorial library generation. In the current study, 3-Chloro-4-(2-mercaptoquinoline-3-yl)-1-substitutedphenylazitidin-2-one derivatives have been designed and synthesized based on molecular modeling studies as anti-tubercular agents. Methods: 2D and 3D QSAR analyses were used to designed compounds having a quinoline scaffold. The synthesized compounds were evaluated against active and dormant strains of Mycobacterium tuberculosis (MTB) H37 Ra and Mycobacterium bovis BCG. The compounds were also tested for cytotoxicity against MCF-7, A549 and Panc-1 cell lines using MTT assay. The binding affinity of designed compounds was gauged by molecular docking studies. Results: Statistically significant QSAR models generated by the SA-MLR method for 2D QSAR exhibited r(2) = 0.852, q(2) = 0.811, whereas 3D QSAR with SA-kNN showed q(2) = 0.77. The synthesized compounds exhibited MIC in the range of 1.38-14.59(mu g/ml). These compounds showed some crucial interaction with MTB ATPase. Conclusion: The present study has shown some promising results which can be further explored for lead generation.

}, keywords = {combilib, Molecular docking, mycobacterial ATPase, QSAR, Quinoline}, issn = {1573-4099}, doi = {10.2174/1573409916666200129095952}, author = {Chitre, Trupti S. and Asgaonkar, Kalyani D. and Vikhe, Amrut B. and Patil, Shital M. and Garud, Dinesh R. and Khedkar, Vijay M. and Sarkar, Dhiman and Nawale, Laxman U. and Yeware, Amar} } @article {48370, title = {BESFA: bioinformatics based evolutionary, structural \& functional analysis of prostate, Placenta, Ovary, Testis, and Embryo (POTE) paralogs}, journal = {Heliyon}, volume = {8}, year = {2022}, month = {SEP}, pages = {e10476}, type = {Article}, abstract = {

The POTE family comprises 14 paralogues and is primarily expressed in Prostate, Placenta, Ovary, Testis, Embryo (POTE), and cancerous cells. The prospective function of the POTE protein family under physiological conditions is less understood. We systematically analyzed their cellular localization and molecular docking analysis to elucidate POTE proteins{\textquoteright} structure, function, and Adaptive Divergence. Our results suggest that group three POTE paralogs (POTEE, POTEF, POTEI, POTEJ, and POTEKP (a pseudogene)) exhibits significant variation among other members could be because of their Adaptive Divergence. Furthermore, our molecular docking studies on POTE protein revealed the highest binding affinity with NCI-approved anticancer compounds. Additionally, POTEE, POTEF, POTEI, and POTEJ were subject to an explicit molecular dynamic simulation for 50ns. MM-GBSA and other essential electrostatics were calculated that showcased that only POTEE and POTEF have absolute binding affinities with minimum energy exploitation. Thus, this study{\textquoteright}s outcomes are expected to drive cancer research to successful utilization of POTE genes family as a new biomarker, which could pave the way for the discovery of new therapies.

}, keywords = {(MMGBSA), Adaptive divergence, Evolution, generalized born surface area, Homology, Mechanics, Molecular docking, Molecular dynamic simulation molecular, POTE paralogs}, doi = {10.1016/j.heliyon.2022.e10476}, author = {Qazi, Sahar and Jit, Bimal Prasad and Das, Abhishek and Karthikeyan, Muthukumarasamy and Saxena, Amit and Ray, M. D. and Singh, Angel Rajan and Raza, Khalid and Jayaram, B. and Sharma, Ashok} } @article {48372, title = {Conventional and microwave-assisted organic synthesis of novel antimycobacterial agents bearing furan and pyridine hybrids}, journal = {Drug Development Research}, volume = {83}, year = {2022}, month = {APR}, pages = {416-431}, type = {Article}, abstract = {

Drug resistance in tuberculosis poses a serious threat to humanity because currently available antitubercular drugs are ineffective against Mycobacterium tuberculosis (M. tuberculosis). As a result, the approval of Bedaquiline and Delamanid for the treatment of drug-resistant tuberculosis was accelerated. Still, there is an urgent need to search for new antitubercular drugs with novel mechanisms of action (MoA). Due to this, we have designed a synthetic strategy by utilizing microwave-assisted organic synthesis. We have compared our method with the conventional procedure, and the data show that our procedure is more effective in the preparation of title compounds. A unique series of 1-(2-(furan-2-yl)-5-(pyridin-4-yl)-1,3,4-oxadiazol-3(2H)-yl)-3-(aryl)-pr op-2-en-1-ones (5a-o) was synthesized utilizing conventional and microwave-assisted techniques. Synthetic compounds were investigated for antitubercular activity against Mycobacterium TB H37Ra and Mycobacterium bovis (M. bovis). Compound 5b was reported to be the most effective against M. tuberculosis H37Ra (97.69 percent inhibition at 30 mu g/ml) and M. bovis (97.09 percent inhibition at 30 mu g/ml). An in silico binding affinity study of mycobacterial enoyl-acyl carrier protein reductase (InhA) reveals the binding mechanism and thermodynamic interactions that determine these molecule{\textquoteright}s binding affinity. Compound 5b had a high glide score of -8.991 and low glide energy of -49.893 kcal/mol.

}, keywords = {Antitubercular activity, microwave-assisted organic synthesis, Molecular docking}, issn = {0272-4391}, doi = {10.1002/ddr.21872}, author = {Desai, Nisheeth C. and Bhatt, Kandarp and Jadeja, Dharmpalsinh J. and Mehta, Harsh K. and Khedkar, Vijay M. and Sarkar, Dhiman} } @article {47391, title = {Molecular phylogeny, structure modeling and in silico screening of putative inhibitors of aerolysin of Aeromonas hydrophila EUS112}, journal = {Journal of Biomolecular Structure \& Dynamics}, volume = {40}, year = {2022}, month = {JUN}, type = {Article}, abstract = {

Aeromonas hydrophila, a Gram-negative bacterium, causes diseases in fish, resulting in excessive loss to the aquaculture industry. Aeromonas is a highly heterogeneous group of bacteria, and the heterogeneity of the genus is attributed to variation and diversity in the virulence factors and toxins among various Aeromonas strains. One of the major toxins aerolysin, secreted by the bacterium, causes hemorrhagic-septicemia and diarrhea and can serve as a drug target. Here, we describe characterization, molecular phylogeny, and homology modeling of the aerolysin of A. hydrophila strain EUS112 (Ah(EUS112)) cloned in our lab. The encoded aerolysin is 485 amino acids long with an N-terminal signal sequence of 23 amino acids. Phylogenetic analysis of the aerolysin of Ah(EUS112) revealed that it belongs to a diverse group of toxins, showing maximum similarity with aerolysins of other Aeromonas strains followed by Vibrio toxin. The homology model of the mature aerolysin of Ah(EUS112) was generated using the crystal structure of a mutant aerolysin (PDB\#3g4n) as the template, which showed that the encoded aerolysin exists as a channel protein. Validation of the generated model using bioinformatics tool confirmed it to be a good quality model that can be used for drug design. Molecular dock analysis revealed that drugs, aralia-saponin I, cyclamin, ardisiacrispin B, and aralia-saponin II bind to aerolysin with a higher affinity as compared to other drugs and at functionally important amino acids of aerolysin. Hence, these molecules can act as an effective therapeutics for inhibiting the aerolysin pore formation and curtail the severity of Aeromonas infection. Communicated by Ramaswamy H. Sarma

}, keywords = {Aerolysin, homology modeling, Molecular docking, Molecular dynamic simulation, phylogenetic tree}, issn = {0739-1102}, doi = {10.1080/07391102.2021.1918254, Early Access Date = APR 2021}, author = {Yadav, Sunita Kumari and Panwar, Deepak and Singh, Ankita and Tellis, Meenakshi B. and Joshi, Rakesh Shamsunder and Dixit, Aparna} } @article {47040, title = {Two antibacterial spiro compounds from the roots of Artemisia pallens wall: evidence from molecular docking}, journal = {Natural Product Research}, volume = {36}, year = {2022}, month = {MAY}, pages = {2465-2472}, type = {Article}, abstract = {

Bioassay-guided isolation from acetone extract of the roots of Artemisia pallens Wall yielded two spiro compounds (1 and 2). The structures of these compounds were determined on the basis of spectroscopic techniques such as IR, MS, 1 D and 2 D- NMR. The acetone extract, fractions and the isolated two compounds were investigated for their antibacterial activity against two gram negative (E. coli, P. aeruginosa) and two gram positive (S. aureus, B. subtilis) bacterial strains. Compound (2) showed the best spectra of activity with IC50 and MIC values between 2.48-3.08 and 12.78 - 21.77 mu M and Compound (1) with 2.57-3.69 and 38.17 - 80.57 mu M, respectively, for the four bacterial strains, whereas inactive against Mycobacterium tuberculosis. Molecular docking study could further help in understanding the various interactions between these compounds and DNA gyrase active site in detail and thereby could provide valuable insight into the mechanism of action.

}, keywords = {antibacterial activity, antimycobacterial activity, Artemisia pallens, Asteraceae, Molecular docking, spiro compound}, issn = {1478-6419}, doi = {10.1080/14786419.2021.1902325}, author = {Honmore, Varsha S. and Natu, Arun D. and Khedkar, Vijay M. and Arkile, Manisha A. and Sarkar, Dhiman and Rojatkar, Supada R.} } @article {48474, title = {Design and synthesis of piano-stool ruthenium(II) complexes and their studies on the inhibition of amyloid ? (1-42) peptide aggregation}, journal = {International Journal of Biological Macromolecules}, volume = {239}, year = {2023}, month = {JUN }, pages = {124197}, type = {Article}, abstract = {

Misfolding , protein aggregation have been linked to numerous human neurodegenerative disorders such as Alzheimer{\textquoteright}s, prion , Parkinson{\textquoteright}s diseases. Ruthenium (Ru) complexes have received considerable attention in studying protein aggregation due to their interesting photophysical and photo properties. In this study, we have synthesized the novel Ru complexes ([Ru(p-cymene)Cl(L-1)][PF6](Ru-1), and [Ru(p-cymene)Cl(L-2)][PF6](Ru-2)) and investigated their inhibitory activity against the bovine serum albumin (BSA) aggregation and the A beta 1-42 peptides amyloid formation. Several spectroscopic methods were used to characterize these complexes, and the molecular structure of the complex was determined by X-ray crystallography. Amyloid aggregation and inhi-bition activities were examined using the Thioflavin-T (ThT) assay, and the secondary structures of the protein were analyzed by circular dichroism (CD) spectroscopy and transmission electron microscopy (TEM). The cell viability assay was carried out on the neuroblastoma cell line, revealing that the complex Ru-2 showed better protective effects against A beta 1-42 peptide toxicity on neuro-2a cells than the complex Ru-1. Molecular docking studies elucidate the binding sites and interactions between the Ru-complexes and A beta 1-42 peptides. The exper-imental studies revealed that these complexes significantly inhibited the BSA aggregation and A beta 1-42 amyloid fibril formation at 1:3 and 1:1 molar concentrations, respectively. Antioxidant assays demonstrated that these complexes act as antioxidants, protecting from amyloid-induced oxidative stress. Molecular docking studies with the monomeric A beta 1-42 (PDB: 1IYT) show hydrophobic interaction, and both complexes bind preferably in the central region of the peptide and coordinate with two binding sites of the peptide. Hence, we suggest that the Ru-based complexes could be applied as a potential agent in metallopharmaceutical research against Alzheimer{\textquoteright}s disease.

}, keywords = {Aggregation, Amyloid ?(1-42) peptide, DFT computation, Fibrillization, Molecular docking, Ruthenium complexes}, issn = {0141-8130}, doi = {10.1016/j.ijbiomac.2023.124197}, author = {Singh, Sain and Navale, Govinda R. and Agrawal, Sonia and Singh, Haobam Kisan and Singla, Labhini and Sarkar, Dhiman and Sarma, Manabendra and Choudhury, Anghuman Roy and Ghosh, Kaushik} } @article {48805, title = {Polymerized stimuli-responsive microgels for the removal of organic dye from water}, journal = {Journal of Molecular Liquids}, volume = {375}, year = {2023}, month = {APR }, pages = {121267}, type = {Article}, abstract = {

Polymerized hydrogel materials (PGM) containing uniform-sized stimuli-responsive microgel particles could be promising alternatives for solution-based microgels to remove organic dyes from water. In the current work, PGM is prepared using Poly(N-isopropylacrylamide-co-acrylic acid) based anionic microgels and their ability for uptake and release studies with an oppositely charged dye, methylene blue (MB) is carried out using UV-vis spectroscopy. The mechanism of dye adsorption is understood at a single particle level using light scattering, and zeta potential and the contributions from different molecular interactions among dye molecules and constituting entities of microgels are obtained from molecular docking studies. The maximum dye uptake by PGM is around 80 \% in the swollen state (at pH 7 and 20 degrees C). In contrast, the dye release studies in the deswollen state (at pH 3 and 50 degrees C) show a decrease in the release efficiency from 87 \% to 63 \% of the total dye adsorbed in 4-repeated cycles. The adsorption isotherm follows a sigmoidal (S) model that has been majorly used in different multi-layer adsorption systems. Extensive dynamic and static light scattering studies demonstrate a deswelling of hydrody-namic radius and core-shell radius of microgels at low temperatures (20 degrees C) induced by dye adsorption. At higher temperatures, the dye-adsorbed microgels have a higher hydrodynamic radius than the pure microgels due to the remaining dye molecules within the microgel that do not release even in the deswollen state. Molecular docking studies show that electrostatic interaction dominates between COO- and MB and van der Waals/hydrophobic dominates for MB-NIPAM and MB-COOH docking complex respectively. Our work covering adsorption/desorption properties of the material to the single-particle level can provide a better understanding in formulating reusable smart materials for the remediation of different water pollutants.(c) 2023 Elsevier B.V. All rights reserved.

}, keywords = {dynamic light scattering, Molecular docking, PNIPAM microgels, Removal of organic pollutants, Stimuli -responsive microgels}, issn = {0167-7322}, doi = {10.1016/j.molliq.2023.121267}, author = {Pany, Biswajit and Majundar, Amrito Ghosh and Mohanty, Madhuchhanda and Fyis, K. P. and Dey, Tanima and Tripathy, Gautam and Bhat, Suresh and Yamanaka, Junpei and Mohanty, Priti S.} }