Shravan Kumar Gunda

Inhibition of aldose reductase by dietary antioxidant curcumin: mechanism of inhibition, specificity and significance.

Accumulation of intracellular sorbitol due to increased aldose reductase (ALR2) activity has been implicated in the development of various secondary complications of diabetes. In this study we show that curcumin inhibits ALR2 with an IC50 of 10 μM in a non‐competitive manner, but is a poor inhibitor of closely‐related members of the aldo‐keto reductase superfamily, particularly aldehyde reductase. Results from molecular docking studies are consistent with the pattern of inhibition of ALR2 by curcumin and its specificity. Moreover, curcumin is able to suppress sorbitol accumulation in human erythrocytes under high glucose conditions, demonstrating an in vivo potential of curcumin to prevent sorbitol accumulation. These results suggest that curcumin holds promise as an agent to prevent or treat diabetic complications.

Structural investigations of CXCR2 receptor antagonists by CoMFA, CoMSIA and flexible docking studies.

= Three-dimensional quantitative structure activity relationship (3D QSAR) analysis was carried out on a et of 56 N,N’-diarylsquaramides, N,N’-diarylureas and diaminocyclobutenediones in order to understand their antagonistic activities against CXCR2. The studies included comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). Models with good predictive abilities were generated with CoMFA q2 0.709, r2 (non-cross-validated square of correlation coefficient) = 0.951, F value = 139.903, r2 bs = 0.978 with five components, standard error of estimate = 0.144 and the CoMSIA q2 = 0.592, r2 = 0.955, F value = 122.399, r2 bs = 0.973 with six components, standard error of estimate = 0.141. In addition, a homology model of CXCR2 was used for docking based alignment of the compounds. The most active compound then served as a template for alignment of the remaining structures. Further, mapping of contours onto the active site validated each other in terms of residues involved with reference to the respective contours. This integrated molecular docking based alignment followed by 3D QSAR studies provided a further insight to support the structure-based design of CXCR2 antagonistic agents with improved activity profiles. Furthermore, in silico screening was adapted to the QSAR model in order to predict the structures of new, potentially active compounds. U radu je opisano trodimenzijsko ispitivanje kvantitativnog odnosa strukture i antagonisti~ kog djelovanja na CXCR2 receptore (3D QSAR) u seriji od 56 N,N’-diarilskvaramida, N,N’-diarilurea i diaminociklobutendiona. Provedene studije uklju~uju komparativnu analizu molekulskih polja (CoMFA) i komparativnu analizu indeksa molekulske sli~nosti (CoMSIA). Modeli s dobrom predvidljivo{}u izvedeni su pomo}u CoMFA q2 =0,709, r2 (neunakrsno-validirani kvadrat koeficijenta korelacije) = 0,951, F = 139,903, r2 bs = 0,978 s pet komponenata, standardnom pogre{kom procjene 0,144 i CoMSIA q2 = 0,592, r2 = 0,955, F = 122,399, r2 bs = 0,973 sa {est komponenata, standardnom pogre{kom procjene 0,141. Osim toga, model homologije CXCR2 receptora upotrijebljen je za svrstavanje spojeva doking metodom. Najaktivniji spoj poslu`io je kao predlo`ak za svrstavanje preostalih struktura. Nadalje, mapiranjem kontura na aktivno mjesto spojevi su se uzajamno vrednovali kroz ostatke s obzirom na svoje konture. Ovo integrirano svrstavanje na temelju molekulskog dokinga i naknadnih 3D QSAR studija pomoglo je dizajniranju CXCR2 antagonista s pobolj{anom aktivnosti. In silico pretra`ivanje prilagoðeno je QSAR modelu sa svrhom predviðanja strukture novih, potencijalno aktivnih spojeva.

3D-QSAR AND CONTOUR MAP ANALYSIS OF TARIQUIDAR ANALOGUES AS MULTIDRUG RESISTANCE PROTEIN-1 (MRP1) INHIBITORS

One of the major obstacles to the successful chemotherapy towards several cancers is multidrug resistance of human cancer cells to anti-cancer drugs. An important contributor to multidrug resistance is the human multidrug resistance protein-1 transporter (MRP1), which is an efflux pump of the ABC (ATP binding cassette) superfamily. Thus, highly efficacious, third generation MRP1 inhibitors, like tariquidar analogues, are promising inhibitors of multidrug resistance and are under clinical trials. To maximize the efficacy of MRP1 inhibitors and to reduce systemic toxicity, it is important to limit the exposure of MRP1 inhibitors and anticancer drugs to normal tissues and to increase their co-localization with tumor cells. Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) associated with 3D-Quantitiative structure-activity relationship (3D-QSAR) studies were performed on a series of tariquidar analogues, as selective MDR modulators. Best predictability was obtained with CoMFA model r2 (non-cross-validated square of correlation coefficient) = 0.968, F value = 151.768 with five components, standard error of estimate = 0.107 while the CoMSIA yielded r2 = 0.982, F value = 60.628 with six components, and standard error of estimate = 0.154. These results indicate that steric, electrostatic, hydrophobic (lipophilic), and hydrogen bond donor substituents play significant roles in multidrug resistance modulation of tariquidar analogues upon MRP1. The tariquidar analogue and MRP1 binding and stability data generated from CoMFA and CoMSIA based 3D-contour maps may further aid in study and design of tariquidar analogues as novel, potent and selective MDR modulator drug candidates.

Natural flavonoid derivatives as oral human epidermoid carcinoma cell inhibitors

Natural flavonoid derivatives against cancer for selective KB cell lines (oral human epidermoid carcinoma) are analysed to determine the relationship between biological activities and structural properties of these molecules. Molecular alignment was performed for 88 natural flavonoid derivatives; out of these 88 molecules, 69 molecules were taken into training set and rest of the 19 molecules were used in test set prediction. We describe our elucidation of their structure activity relation (SAR) using three-dimensional quantitative structure activity relationship (3D-QSAR) models. A predictive comparative molecular field analysis (CoMFA) model of q² = 0.888 and r² = 0.940 was obtained and a comparative molecular similarity indices analysis (CoMSIA) model q² = 0.778 and r² = 0.971 was used to describe the non-linearly combined affinity of each functional group in the inhibitors. The contour maps obtained from 3D-QSAR studies were evaluated for the activity trends of the molecules analysed.

P56(lck) kinase inhibitor studies: a 3D QSAR approach towards designing new drugs from flavonoid derivatives.

Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) based on 3D-QSAR (3D-quantitative structure activity relationship) studies were carried out on 97 flavonoid derivatives as potent P56(lck) protein tyrosine kinase inhibitors. The best prediction was obtained with CoMFA standard model (q² = 0.838, r² = 0.948) using steric, electrostatic along with CoMSIA standard model (q² = 0.714, r² = 0.921) using steric, electrostatic, hydrophobic, hydrogen bond donor and acceptor fields. Of the 97 molecules a training set of 76 compounds and the predictive ability of the QSAR model were assessed employing a test set of 21 compounds. The resulting CoMFA and CoMSIA contour maps were used to identify the structural features relevant to the biological activity in this series of flavonoid derivatives, based upon which we identified and designed 10 novel molecules that showed superior inhibitory activity against P56(lck) protein which shed new light on effective therapeutic agents against these classes of enzymes.

Comparative modeling of Rab6 proteins: identification of key residues and their interactions with guanine nucleotides

The cytoplasm of a eukaryotic cell consists of a wide variety of membrane bound cell organelles and continuous flow of proteins amongst these organelles is a major challenge and must be stringently maintained in order to continue the correct biochemical functioning inside a cell. The transportation of various proteins amongst these organelles is facilitated by a vast Tubulo-vesicular network mediated by carrier proteins. The Rabs belong to small G proteins super family involved in the regulation and vesicle transport in between the organelles by shuttling between the active GTP and inactive GDP bound states. In this paper we put forth the homology modeling and docking studies of Rab6A proteins (Mus musculus, Gallus gallus and Caenorhabditis elegans) with GTP, GMP-PNP and GDP molecules and a comparative study between these proteins is done to identify key residues out of which serine of the phosphate binding loop (P – loop) and aspartic acid showed prominent interactions with the GTP, GDP and GMP-PNP nucleotides and cogitate that aspartic acid might also help in the stabilization of the switch I region of the Rab proteins besides serine.

Potential antimicrobial agents from triazole-functionalized 2H-benzo[b][1,4]oxazin-3(4H)-ones

A series of substituted triazole functionalized 2H-benzo[b][1,4]oxazin-3(4H)-ones were synthesized by employing click chemistry and further characterized based on 1H NMR, 13C NMR, IR and mass spectral studies. All the synthesized derivatives were screened for their in vitro antimicrobial activities. Further, molecular docking studies were accomplished to explore the binding interactions between 1,2,3-triazol-4-yl-2H-benzo[b][1,4]oxazin-3(4H)-one and the active site of Staphylococcus aureus (CrtM) dehydrosqualene synthase (PDB ID: 2ZCS). These docking studies revealed that the synthesized derivatives showed high binding energies and strong H-bond interactions with the dehydrosqualene synthase validating the observed antimicrobial activity data. Based on antimicrobial activity and docking studies, the compounds 9c, 9d and 9e were identified as promising antimicrobial leads.

Design, Synthesis, and in vitro antitubercular activity of 1,2,3-triazolyl-dihydroquinoline derivatives

In the quest for new active molecules against Mycobacterium tuberculosis, a series of dihydroquinoline derivatives possessing triazolo substituents were efficiently synthesized using click chemistry. The structure of 6l was evidenced by X‐ray crystallographic study. The newly synthesized compounds were evaluated for their in vitro antitubercular activity against Mycobacterium tuberculosis H37Rv (ATCC27294). The compounds 6a, 6g, and 6j (MIC: 3.13 μg/ml) showed promising activity when compared to the first‐line drug such as ethambutol. In addition, the structure and antitubercular activity relationship were further supported by in silico molecular docking studies of the active compounds against 3IVX.PDB (crystal structure of pantothenate synthetase in complex with 2‐(2‐(benzofuran‐2‐ylsulfonylcarbamoyl)‐5‐methoxy‐1H‐indol‐1‐yl)acetic acid).

3D-QSAR (CoMFA, CoMSIA) and molecular docking studies of natural flavonoid derivatives to explore structural requirements for MCF-7 cell line inhibition

In the present study, molecular modelling studies have been reported on a series of natural flavonoid derivatives to analyse structure activity relationship studies of MCF-7 inhibitors using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA)-based QSAR methods. Eighty-four compounds were used as training set to establish the model and 20 compounds were used as external test set to validate these models. The generated models exhibited good statistical results such as q2, r2. CoMFA analysis yielded the q2 of 0.765 and r2 of 0.968 with five components. CoMSIA model generated using steric, electrostatic, hydrophobic, donor and acceptor fields with q2 value of 0.592 and r2 value of 0.932 with six components was found to be the optimal model among the various models generated. According to contour map results, we have recommended the critical sites for modification in structure which will be useful in designing potent compounds with improved activity.

3D QSAR CoMFA/CoMSIA and docking studies on azole dione derivatives, as anti-cancer inhibitors

Comparative Molecular Field Analysis (CoMFA) and Comparative Molecular Similarity Indices Analysis (CoMSIA) were performed on a series of 103 azole dione derivatives, as selective anti-cancer inhibitors. The atom and shape based root mean square alignment yielded the best predictive CoMFA model q² = 0.923, r² = 0.980, when compared with the CoMSIA model. Docking studies were employed to position the inhibitors into active site of Crystal Structure of Delta (4)-3-ketosteroid 5-beta-reductase (PDB id: 3BUR). Results that indicate steric, electrostatic, hydrophobic, hydrogen bond donor and acceptor substituents play a significant role in design novel, potent and selective anti-cancer activity of the compounds.