Temperature Dependency on Conformational Sampling of 12-Crown-4 by Simulated Annealing

Gadhe, Changdev G.,Cho, Seung Joo The Basic Science Institute Chosun University 2013 조선자연과학논문집 Vol.6 No.1

In this manuscript, we report a protocol to determine most of the lowest energy conformations from the ensemble of conformations. 12-crown-4 was taken as study compound to get the most of energy minima conformations. Molecular dynamic (MD) simulation for 1 nanosecond (ns) was performed at 300, 500, 700, 900 and 1100 K temperature. At particular interval conformations were sampled. Then Gaussian program was used to minimize compounds using PM6 energy levels. Duplicates were removed by checking energy as well as mirror image conformations, and only unique conformations were retained for the next $6-31+G^*$ level minimization. It was observed that upto certain increment in temperature the number of unique conformations were increased, but afterword it decreased.

Holographic Quantitative Structure-Activity Relationship (HQSAR) Study of 3,4-Dihydroxychalcone Derivatives as 5-Lipoxygenase Inhibitors

Gadhe, Changdev G. The Basic Science Institute Chosun University 2011 조선자연과학논문집 Vol.4 No.3

Holographic quantitative structure-activity relationships (HQSAR) is a useful tool to correlates structures with their biological activities. HQSAR is a two dimensional (2D) QSAR methodology, which generates QSAR equations through 2D fingerprint and correlates it with biological activity. Here, we report a 2D-QSAR model for a series of fifty-one 3,4-dihydroxychalcones derivatives utilizing HQSAR methodology. We developed HQSAR model with 6 optimum numbers of components (ONC), which resulted in cross-validated correlation coefficient ($q^2$) of 0.855 with 0.283 standard error of estimate (SEE). The non-cross-validated correlation coefficient (r2) with 0.966 indicates the model is predictive enough for analysis. Developed HQSAR model was binned in to a hologram length of 257. Atomic contribution map revealed the importance of dihydroxy substitution on phenyl ring.

Insights into the binding modes of CC chemokine receptor 4 (CCR4) inhibitors: a combined approach involving homology modelling, docking, and molecular dynamics simulation studies

Gadhe, Changdev G.,Kim, Mi-hyun The Royal Society of Chemistry 2015 Molecular bioSystems Vol.11 No.2

<P>CC chemokine receptor 4 (CCR4), a G protein-coupled receptor (GPCR), plays a vital role in the progression of asthma, T-cell lymphoma, inflammation, and Alzheimer's disease. To date, the structure of CCR4 has not been determined. Therefore, the nature of the interactions between inhibitors and CCR4 is not well known. In this study, we used CCR5 as a template to model the structure of CCR4. Docking studies were performed for four naphthalene-sulphonamide derivatives and crucial ligand–protein interactions were analysed. Molecular dynamics (MD) simulations of these complexes (100 ns each) were carried out to gain insights into the interactions between ligands and CCR4. MD simulations revealed that the residues identified by the docking were displaced and new residues were inserted near the ligands. Results of a principal component analysis (PCA) suggested that CCR4 unfolds at the extracellular site surrounding the ligands. Our simulations identified crucial residues involved in CCR4 antagonism, which were supported by previous mutational studies. Additionally, we identified Ser3.29, Leu3.33, Ser5.39, Phe6.47, Ile7.35, Thr7.38, Thr7.40, and Ala7.42 as residues that play crucial roles in CCR4 antagonism. Mutational studies will help elucidate the significance of these residues in CCR4 antagonism. An understanding of ligand–CCR4 interactions might aid in the design of novel CCR4 inhibitors.</P> <P>Graphic Abstract</P><P>CC chemokine receptor 4 (CCR4), a G protein-coupled receptor (GPCR), plays a vital role in the progression of asthma, T-cell lymphoma, inflammation, and Alzheimer's disease. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c4mb00568f'> </P>

Comparative Modeling of Human P-gp NBD2 and Docking and Binding Mode Analysis of 8-Geranyl Chrysin as a P-gp Modulator

Gadhe, Changdev G. The Basic Science Institute Chosun University 2012 조선자연과학논문집 Vol.5 No.1

The resistance of tumour cells against cytotoxic drug is significant limitation in successful chemotherapeutic treatment of cancer. To date, no crystal structure is available for human P-gp. We developed homology model for human P-gp NBD2 by using coordinates of transporter associated protein (TAP1). Docking study was performed for 8-geranyl-chrysin (Flavonoids) inhibitor in the NBD2 model. Ligand-protein interactions were determined which indicates that the 8-geranyl chrysin shares two overlapping sites in the cytosolic domains of P-gp, the ATP site and a hydrophobic steroid-binding site.

Modulation of Multidrug Resistance in Cancer by P-Glycoprotein

Gadhe, Changdev G.,Cho, Seung Joo The Basic Science Institute Chosun University 2011 조선자연과학논문집 Vol.4 No.1

Multidrug resistance (MDR) is one of the main obstacles in the chemotherapy of cancer. MDR is associated with the over expression of P-glycoprotein (P-gp), resulting in increased efflux of chemotherapy from cancer cells. Inhibiting P-gp as a method to reverse MDR in cancer patients has been studied extensively, but the results have generally been disappointing. First-generation agents were limited by unacceptable toxicity, whereas second-generation agents had better tolerability but were confounded by unpredictable pharmacokinetic interactions and interactions with other transporter proteins. Third-generation inhibitors have high potency and specificity for P-gp. Furthermore, pharmacokinetic studies to date have shown no appreciable impact on drug metabolism and no clinically significant drug interactions with common chemotherapy agents. Third-generation P-gp inhibitors have shown promise in clinical trials. The continued development of these agents may establish the true therapeutic potential of P-gp-mediated MDR reversal.

Flavonoids: An Emerging Lead in the P-glycoprotein Inhibition

Gadhe, Changdev G.,Cho, Seung Joo The Basic Science Institute Chosun University 2012 조선자연과학논문집 Vol.5 No.2

Multidrug resistance is a major obstacle in cancer chemotherapy. Cancer cells efflux chemotherapeutic drug out of cell by means of transporter and reduce the active concentration of it inside cell. Such transporters are member of the ATP binding cassettes (ABC) protein. It includes P-gp, multiple resistant protein (MRP), and breast cancer resistant protein (BCRP). These proteins are widely distributed in the human cells such as kidney, lung, endothelial cells of blood brain barrier etc. However, there are number of drugs developed for it, but most of them are getting transported by it. So, still there is necessity of a good modulator, which could effectively combat the transport of chemotherapeutic agents. Natural products origin modulators were found to be effective against transporter such as flavonoids, which belongs to third generation modulators. They have advantage over synthetic inhibitor in the sense that they have simple structure and abundant in nature. This review focuses on the P-gp structure its architecture, efflux mechanism, herbal inhibitors and their mechanism of action.

Importance of Silicon Atom in the Drug Design Process

Gadhe, Changdev G.,Cho, Seung Joo The Basic Science Institute Chosun University 2012 조선자연과학논문집 Vol.5 No.4

The pharmaceutical industry has an ongoing need for new, safe medicines with genuine biomedical effects. Most of the candidate molecules are far from becomes a drug, because of their pharmacokinetic and pharmacodynamic properties. The introduction of bioisostere to improve properties of molecules and to obtain new class of compound is currently increased. Silicon substitution of carbon of existing drugs is an attractive strategy to search a new candidate with improved biological and physicochemical properties. The fundamental differences between carbon and silicon can lead to improved profile of the silicon containing candidate, and could be exploited to get further benefit in drug design process.

Investigation of Binding Modes of the Verapamil and Curcumin into Human P-glycoprotein (P-gp)

Gadhe, Changdev G.,Cho, Seung Joo The Basic Science Institute Chosun University 2013 조선자연과학논문집 Vol.6 No.4

Human P-gp is a protein responsible for the multidrug resistance (MDR) and causes failure of cancer chemotherapy. Till date no X-ray crystal structure is reported for this membrane protein, which hampers active research in the field. We performed homology modeling to develop three dimensional (3D) model of P-gp, and docking studies of the verapamil and curcumin have been performed to gain insight into the interaction mechanism between inhibitors and P-gp. It was identified that the inhibitors docked into the upper part of P-gp and interacted through the hydrophobic interactions.

CoMFA vs. Topomer CoMFA, which One is better a Case Study with 5-Lipoxygenase Inhibitors

Gadhe, Changdev G. The Basic Science Institute Chosun University 2011 조선자연과학논문집 Vol.4 No.2

Quantitative structure-activity relationships (QSAR) have been applied for two decades in the development of relationships between physicochemical properties of chemical substances and their biological activities to obtain a reliable statistical model for prediction of the activities of new chemical entities. The fundamental principle underlying the QSAR is that the structural difference is responsible for the variations in biological activities of the compounds. In this work, we developed 3D-QSAR model for a series of 5-Lipoxygenase inhibitors, utilizing comparative molecular field analysis (CoMFA) and Topomer CoMFA methodologies. Our developed models addressed superiority of Topomer CoMFA over CoMFA. The CoMFA model was obtained with $q^2$=0.593, $r^2$=0.939, $Q^2$=0.334 with 6 optimum number of components (ONC). Higher statistical results were obtained with the Topomer CoMFA model ($q^2$=0.819, $r^2$=0.947, ONC=5). Further robustness of developed models was checked with the ANOVA test and it shows F=113 for CoMFA and F=162.4 for Topomer CoMFA model. Contour map analysis indicated that the more requirement of electrostatic parameter for improved potency.

3D Computational Modeling of Human P-gp NBD2 with Papyriferic Acid Derivatives

Gadhe, Changdev G. The Basic Science Institute Chosun University 2012 조선자연과학논문집 Vol.5 No.3

Human P-gp is one of the protein responsible for the multidrug resistance (MDR) develpment. MDR is a major cause of the cancer chemotherapy. In this paper, we performed homology modeling, docking study of papayriferic acid into the P-gp nucleotide binding domain (NBD2). For human P-gp, X-ray crystal structure is not known yet. We developed homology model for human NBD2 using HlyB ABC transporter structure (PDB code: 1XEF, resolution 2.5 ${\AA}$). Docking study was performed using Autodock. Docking result was analyzed, which shows that ligand docks into steroid binding site and interacts through hydrophobic and hydrophilic interactions.