Changdev G Gadhe

Gachon University, Sŏngnam, Gyeonggi-do, South Korea

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Publications (37)67.98 Total impact

  • Changdev G Gadhe · Eunhee Lee · Mi-Hyun Kim
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    ABSTRACT: The STAT/JAK3 pathway is a well-known therapeutic target in various diseases (ex. rheumatoid arthritis and psoriasis). The therapeutic advantage of JAK3 inhibition motivated to find new scaffolds with desired DMPK. For the purpose, in silico high-throughput sieves method is developed consisting of a receptor-guided three-dimensional quantitative structure-activity relationship study and shape-based virtual screening. We developed robust and predictive comparative molecular field analysis (q (2) = 0.760, r (2) = 0.915) and comparative molecular similarity index analysis (q (2) = 0.817, r (2) = 0.981) models and validated these using a test set, which produced satisfactory predictions of 0.925 and 0.838, respectively.
    Archives of Pharmacal Research 05/2015; DOI:10.1007/s12272-015-0607-6 · 1.75 Impact Factor
  • Changdev G Gadhe · Anand Balupuri · Seung Joo Cho
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    ABSTRACT: Human CC-chemokine receptor 8 (CCR8) is a crucial drug target in asthma that belongs to G-protein-coupled receptor superfamily, which is characterized by seven transmembrane helices. To date, there is no X-ray crystal structure available for CCR8; this hampers active research on the target. Molecular basis of interaction mechanism of antagonist with CCR8 remains unclear. In order to provide binding site information and stable binding mode, we performed modeling, docking and molecular dynamics (MD) simulation of CCR8. Docking study of biaryl-ether-piperidine derivative (13C) was performed inside predefined CCR8 binding site to get the representative conformation of 13C. Further, MD simulations of receptor and complex (13C-CCR8) inside dipalmitoylphosphatidylcholine lipid bilayers were performed to explore the effect of lipids. Results analyses showed that the Gln91, Tyr94, Cys106, Val109, Tyr113, Cys183, Tyr184, Ser185, Lys195, Thr198, Asn199, Met202, Phe254, and Glu286 were conserved in both docking and MD simulations. This indicated possible role of these residues in CCR8 antagonism. However, experimental mutational studies on these identified residues could be effective to confirm their importance in CCR8 antagonism. Furthermore, calculated Coulombic interactions represented the crucial roles of Glu286, Lys195, and Tyr113 in CCR8 antagonism. Important residues identified in this study overlap with the previous non-peptide agonist (LMD-009) binding site. Though, the non-peptide agonist and currently studied inhibitor (13C) share common substructure, but they differ in their effects on CCR8. So, to get more insight into their agonist and antagonist effects, further side-by-side experimental studies on both agonist (LMD-009) and antagonist (13C) are suggested.
    Journal of biomolecular Structure & Dynamics 01/2015; DOI:10.1080/07391102.2014.1002006 · 2.98 Impact Factor
  • Changdev G. Gadhe · Mi-hyun Kim
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    ABSTRACT: 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 inhibitor-CCR4 is not well known. In this study, we used the 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-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.
    Molecular BioSystems 11/2014; 11(2). DOI:10.1039/C4MB00568F · 3.18 Impact Factor
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    ABSTRACT: TAK1 is a member of the MAPKKK family, and it is one of the key molecules in inflammatory signaling pathways. It is an interesting drug target recently because of its role in many signaling pathways and various cellular processes. In the present study, a series of recently published 7-aminofuro [2,3-c] pyridine derivatives were taken as TAK1 antagonists, and 3D QSAR study was performed. A reasonable CoMFA (q 2 = 0.690 NOC = 6, r 2 = 0.946) and COMSIA (q 2 = 0.676, NOC = 5, r 2 = 0.904) models were developed. All the developed models were validated using external validation test set, leave five out, bootstrapping, progressive samplings, and rm 2 metrics. Both the models exhibited acceptable values on all validation techniques and, hence, was considered to be robust and predictive. Furthermore, the contour map analysis of CoMFA and COMSIA models exposed important understandings in the substituents to increase the potency of the compounds. Small negative substitutions at R1 position of five-membered ring found to increase the activity. Similarly, hydrophobic substitution and hydrogen bond acceptor group at the R1 position of the five-membered ring could increase the activity. Avoiding bulky substitution and hydrogen bond acceptor group near the phenyl ring at R1 position and R8 would help in increasing the potency of the compounds. Our finding could be used to design a more potent derivative of TAK1 inhibitors. Graphical abstract
    Medicinal Chemistry Research 11/2014; 24(6). DOI:10.1007/s00044-014-1221-8 · 1.61 Impact Factor
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    ABSTRACT: Nociceptin receptor (NOPR) is an orphan G protein-coupled receptor that contains seven transmembrane helices. NOPR has a distinct mechanism of activation, though it shares a significant homology with other opioid receptors. Previously there were reports on homology modeling of NOPR and further molecular dynamics simulation studies for a short period. Recently the crystal structure of NOPR has been reported. In this study, we analyzed the time dependent behavior of NOPR docked with clinically important agonist molecules such as NOP (natural agonist) peptide and compound 10 (SCH-221510 derivative) using molecular dynamics simulations (MDS) for 100 ns. Molecular dynamics simulation of NOPR-agonist complexes allowed us to refine the system and also to identify stable structures with better binding modes. Structure activity relationships (SAR) for SCH221510 derivatives were investigated and reasons for the activities of these derivatives were determined. Our molecular dynamics trajectory analysis of NOPR-peptide and NOPR-compound 10 complexes found residues crucial for binding. Mutagenesis studies on the residues identified from our analysis could be effective. Our results could also provide useful information for structure-based drug design of novel and potent agonists targeting NOPR.
    Molecular BioSystems 09/2014; 10(12). DOI:10.1039/C4MB00323C · 3.18 Impact Factor
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    ABSTRACT: Multidrug resistance (MDR) is a phenomenon whereby cancer cells experience intrinsic or acquired resistance to a broad spectrum of structurally and functionally distinct chemotherapeutic agents. Permeability glycoprotein (P-gp) is the key protein responsible for the development of MDR in cancer cells, as it exports chemotherapeutic agents from cells. In the present study, comparative molecular field analysis (CoMFA), comparative molecular similarity indices analysis (CoMSIA), and hologram quantitative structure activity relationship (HQSAR) techniques were used to derive predictive models for phenylsulfonylfuroxan derivatives as P-gp inhibitors. Cross-validated correlation coefficients (q2) of 0.811, 0.855, and 0.907 and non-cross-validated correlation coefficients (r2) of 0.87, 0.985, and 0.973 were obtained for CoMFA, CoMSIA, and HQSAR derived models, respectively. The predictive power of the models were assessed using an external test set of five compounds and showed reasonable external predictabilities (r2pred) of 0.704, 0.517, and 0.713, respectively. Contour and atomic contribution maps were generated to investigate physicochemical requirements of ligands for better receptor binding affinity. 3D Contour maps suggested molecular interactions such as steric and electrostatic effects and hydrogen bond formation. However, atomic contribution maps indicated that ortho and para positions of the R1 phenylsulfonyl ring are the most desirable regions to modulate P-gp antagonism. The 3rd and 4th positions of the central five-membered ring were also found to be important. Our results are in line with previous reports. Information obtained from the contour and atomic contribution maps were utilized to design more potent compounds containing different R1 fragments. In addition, the activities of these more potent compounds were predicted using derived models.
    Anti-Cancer Agents in Medicinal Chemistry (Formerly Current Medicinal Chemistry - Anti-Cancer Agents) 09/2014; 14(7):1019-1030. DOI:10.2174/18715206113136660335 · 2.94 Impact Factor
  • Changdev G Gadhe · Anand Balupuri · Gugan Kothandan · Seung Joo Cho
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    ABSTRACT: P38 mitogen activated protein (MAP) kinase is an important anti-inflammatory drug target, which can be activated by responding to various stimuli such as stress and immune response. Based on the conformation of the conserved DFG loop (in or out), binding inhibitors are termed as type-I and II. Type-I inhibitors are ATP competitive, whereas type-II inhibitors bind in DFG-out conformation of allosteric pocket. It remains unclear that how these allosteric inhibitors stabilize the DFG-out conformation and interact. Organosilicon compounds provide unusual opportunity to enhance potency and diversity of drug molecules due to their low toxicity. However, very few examples have been reported to utilize this property. In this regard, we performed docking of an inhibitor (BIRB) and its silicon analog (Si-BIRB) in an allosteric binding pocket of p38. Further, molecular dynamics (MD) simulations were performed to study the dynamic behavior of the simulated complexes. The difference in the biological activity and mechanism of action of the simulated inhibitors could be explained based on the molecular mechanics/generalized Born surface area (MM/GBSA) binding free energy per residue decomposition. MM/GBSA showed that biological activities were related with calculated binding free energy of inhibitors. Analyses of the per-residue decomposed energy indicated that van der Waals and non-polar interactions were predominant in the ligand-protein interactions. Further, crucial residues identified for hydrogen bond, salt bridge and hydrophobic interactions were Tyr35, Lys53, Glu71, Leu74, Leu75, Ile84, Met109, Leu167, Asp168 and Phe169. Our results indicate that stronger hydrophobic interaction of Si-BIRB with the binding site residues could be responsible for its greater binding affinity compared with BIRB.
    Bulletin- Korean Chemical Society 08/2014; 35(8):2494 - 2504. DOI:10.5012/bkcs.2014.35.8.2494 · 0.84 Impact Factor
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    ABSTRACT: Checkpoint kinase 1 (Chk1) is a promising target for the design of novel anticancer agents. In the present work, molecular docking simulations and three-dimensional quantitative structure-activity relationship (3D-QSAR) studies were performed on pyridyl aminothiazole derivatives as Chk1 inhibitors. AutoDock was used to determine the probable binding conformations of all the compounds inside the active site of Chk1. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were developed based on the docking conformations and alignments. The CoMFA model produced statistically significant results with a cross-validated correlation coefficient (q(2)) of 0.608 and a coefficient of determination (r(2)) of 0.972. The reliable CoMSIA model with q(2) of 0.662 and r(2) of 0.970 was obtained from the combination of steric, electrostatic and hydrogen bond acceptor fields. The predictive power of the models were assessed using an external test set of 14 compounds and showed reasonable external predictabilities (r(2)pred) of 0.668 and 0.641 for CoMFA and CoMSIA models, respectively. The models were further evaluated by leave-ten-out cross-validation, bootstrapping and progressive scrambling analyses. The study provides valuable information about the key structural elements that are required in the rational design of potential drug candidates of this class of Chk1 inhibitors.
    SAR and QSAR in Environmental Research 06/2014; DOI:10.1080/1062936X.2014.923040 · 1.92 Impact Factor
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    ABSTRACT: A protoberberine derivative library was used to search for selective inhibitors against kinases of the mitogen-activated protein kinase (MAPK) cascades in mammalian cells. Among kinases in mammalian MAPK pathways, we identified a compound (HWY336) that selectively inhibits kinase activity of mitogen-activated protein kinase kinase 4 and 7 (MKK4 and MKK7). The IC50 of HWY336 was 6 µM for MKK4 and 10 µM for MKK7 in vitro. HWY336 bound to both kinases reversibly via noncovalent interactions, and inhibited their activity by interfering with access of a protein substrate to its binding site. The binding affinity of HWY336 to MKK4 was measured by surface plasmon resonance to determine a dissociation constant (Kd) of 3.2 µM. When mammalian cells were treated with HWY336, MKK4 and MKK7 were selectively inhibited, resulting in inhibition of c-Jun NH2-terminal protein kinases in vivo. The structural model of HWY336 bound to either MKK4 or MKK7 predicted that HWY336 was docked to the activation loop, which is adjacent to the substrate binding site. This model suggested the importance of the activation loop of MKKs in HWY336 selectivity. We verified this model by mutating three critical residues within this loop of MKK4 to the corresponding residues in MKK3. The mutant MKK4 displayed similar kinase activity as wild-type kinase, but its activity was not inhibited by HWY336 compared to wild-type MKK4. We propose that the specific association of HWY336 to the activation loop of MKK4/MKK7 is responsible for its selective inhibition.
    PLoS ONE 04/2014; 9(4):e91037. DOI:10.1371/journal.pone.0091037 · 3.23 Impact Factor
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    ABSTRACT: A series of novel coronands having a 2n-crown-n topology based on trioxane (6-crown-3) derivatives are designed and characterized. These neutral hosts can sense anions through pure aliphatic C-H hydrogen bonding (HB) in condensed phases due to the unusual topology of 2n-crown-n. C-H bonds are strongly polarized by two adjacent oxygen atoms in this scaffold. These hosts provide a rare opportunity to modulate anion binding strength by changing the electronic nature of aliphatic C-H bonds and offer ease of synthesis.
    Organic Letters 12/2013; 16(2). DOI:10.1021/ol402819m · 6.32 Impact Factor
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    Changdev G. Gadhe · Seung Joo Cho
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    ABSTRACT: 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.
    12/2013; 6(4). DOI:10.13160/ricns.2013.6.4.205
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    ABSTRACT: The HIV-1 envelope glycoprotein gp120 plays a vital role in the entry of virus into the host cells and is a potential antiviral drug target. Recently, indole derivatives have been reported to inhibit HIV-1 through binding to gp120, and this prevents gp120 and CD4 interaction to inhibit the infectivity of HIV-1. In this work, molecular docking, molecular dynamics (MD) and three-dimensional quantitative structure-activity relationship studies were carried out. Molecular docking studies of the most active and the least active compounds were performed to identify important residues in the binding pocket. We refined the docked poses by MD simulations which resulted in conformational changes. After equilibration, the structure of the ligand and receptor complex was stable. Therefore, we just took the last snapshot as the representative binding pose for this study. This pose for the most active inhibitor was used as a template for receptor-based alignment which was subsequently used for comparative molecular field analysis. Resultant 3D contour maps suggested smaller substituents are desirable at the 7-position of indole ring to avoid steric interactions with Ser375, Phe382 and Tyr384 residues in the active site. These results can be exploited to develop potential leads and for structure-based drug design of novel HIV-1 inhibitors.
    Archives of Pharmacal Research 12/2013; 37(8). DOI:10.1007/s12272-013-0313-1 · 1.75 Impact Factor
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    Gugan Kothandan · Changdev G. Gadhe · Seung Joo Cho
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    ABSTRACT: Chemokine receptor (CCR2) is a G protein-coupled receptor that contains seven transmembrane helices. Recent pharmaceutical research has focused on the antagonism of CCR2 and candidate drugs are currently undergoing clinical studies for the treatment of diseases like arthritis, multiple sclerosis, and type 2 diabetes. In this study, we analyzed the time dependent behavior of CCR2 docked with a potent 4-azetidinyl-1-aryl-cyclohexane (4AAC) derivative using molecular dynamics simulations (MDS) for 20 nanoseconds (ns). Homology modeling of CCR2 was performed and the 4AAC derivative was docked into this binding site. The docked model of selected conformations was then utilized to study the dynamic behavior of the 4AAC enzyme complexes inside lipid membrane. MDS of CCR2-16b of 4AAC complexes allowed us to refine the system since binding of an inhibitor to a receptor is a dynamic process and identify stable structures and better binding modes. Structure activity relationships (SAR) for 4AAC derivatives were investigated and reasons for the activities were determined. Probable binding pose for some CCR2 antagonists were determined from the perspectives of binding site. Initial modeling showed that Tyr49, Trp98, Ser101, Glu291, and additional residues are crucial for 4AAC binding, but MDS analysis showed that Ser101 may not be vital. 4AAC moved away from Ser101 and the hydrogen bonding between 4AAC and Ser101 vanished. The results of this study provide useful information regarding the structure-based drug design of CCR2 antagonists and additionally suggest key residues for further study by mutagenesis.
    Bulletin- Korean Chemical Society 11/2013; 34(11). DOI:10.5012/bkcs.2013.34.11.3429 · 0.84 Impact Factor
  • Changdev G Gadhe · Gugan Kothandan · Seung Joo Cho
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    ABSTRACT: Chemokine receptor 5 (CCR5) is an integral membrane protein that is utilized during human immunodeficiency virus type-1 entry into host cells. CCR5 is a G-protein coupled receptor that contains seven transmembrane (TM) helices. However, the crystal structure of CCR5 has not been reported. A homology model of CCR5 was developed based on the recently reported CXCR4 structure as template. Automated docking of the most potent (14), medium potent (37), and least potent (25) CCR5 antagonists was performed using the CCR5 model. To characterize the mechanism responsible for the interactions between ligands (14, 25, and 37) and CCR5, membrane molecular dynamic (MD) simulations were performed. The position and orientation of ligands (14, 25, and 37) were found to be changed after MD simulations, which demonstrated the ability of this technique to identify binding modes. Furthermore, at the end of simulation, it was found that residues identified by docking were changed and some new residues were introduced in the proximity of ligands. Our results are in line with the majority of previous mutational reports. These results show that hydrophobicity is the determining factor of CCR5 antagonism. In addition, salt bridging and hydrogen bond contacts between ligands (14, 25, and 37) and CCR5 are also crucial for inhibitory activity. The residues newly identified by MD simulation are Ser160, Phe166, Ser180, His181, and Trp190, and so far no site-directed mutagenesis studies have been reported. To determine the contributions made by these residues, additional mutational studies are suggested. We propose a general binding mode for these derivatives based on the MD simulation results of higher (14), medium (37), and lower (25) potent inhibitors. Interestingly, we found some trend for these inhibitors such as, salt bridge interaction between basic nitrogen of ligand and acidic Glu283 seemed necessary for inhibitory activity. Also, two aromatic pockets (pocket I - TM1-3 and pocket II - TM3-6) were linked by the central polar region in TM7, and the simulated inhibitors show important interactions with the Trp86, Tyr89, Tyr108, Phe112, Ile198, Tyr251, Leu255, and Gln280 and Glu283 residues. These results shed light on the usage of MD simulation to identify more stable, optimal binding modes of the inhibitors.
    Journal of biomolecular Structure & Dynamics 11/2013; 31(11):1251-1276. DOI:10.1080/07391102.2012.732342 · 2.98 Impact Factor
  • Changdev Gorakshnath Gadhe · Gugan Kothandan · Seung Joo Cho
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    ABSTRACT: Human immunodeficiency virus type-1 (HIV-1) is a causative agent of Acquired immunodeficiency syndrome (AIDS), which has affected a large population of the world. Viral envelope glycoprotein (gp120) is an intrinsic protein for HIV-1 to enter into human host cells. Molecular docking guided molecular dynamics (MD) simulation was performed to explore the interaction mechanism of heterobiaryl derivative with gp120. MD simulation result of inhibitor-gp120 complex demonstrated stability. Our MD simulation results are consistent with most of the previous mutational and modeling studies. Inhibitor has an interaction with the CD4 binding region. Van der Waals interaction between inhibitor and Val255, Thr257, Asn425, Met426 and Trp427 were important. This preliminary MD model could be useful in exploiting heterobiaryl-gp120 interaction in greater detail, and will likely to shed lights for further utilization in the development of more potent inhibitors.
    Bulletin- Korean Chemical Society 08/2013; 34(8):2466-2472. DOI:10.5012/bkcs.2013.34.8.2466 · 0.84 Impact Factor
  • Changdev G. Gadhe · Gugan Kothandan · Seung Joo Cho
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    ABSTRACT: P-glycoprotein (P-gp) is responsible for the multidrug resistance (MDR) and involved in the expulsion of xenobiotics out of cell. In this paper, homology modeling, docking and molecular dynamics simulation (MDS) was performed for the human P-gp desmosdumotin inhibitor. Docking study was carried out in the P-gp nucleotide binding domain 2 (NBD2). The desmosdumotin binding region occupied the ATP binding region (flavonoid binding region) with hydrophobic and hydrophilic interactions. Analysis of root mean square deviations (RMSDs) of active site residues indicated the binding site residues were stable throughout the simulation period. As shown in previous results with structurally similar flavonoid compounds, van der Waals and electrostatic interactions were found to be important factors for the desmosdumotin-NBD2 inhibition. Docking results suggest that desmosdumotin interacts with the NBD2 through both hydrogen bonds (Lys1076, Ser1077 and Thr1078) and hydrophobic interactions (Tyr1044, Val1052, Gly1073 and Cys1074). In addition, the involvement of other amino-acids was identified via MDS (Lys1076 and Ser1077 for hydrogen bonds and Tyr1044, Val1052, Gly1073, Cys1074 and Gly1075 for hydrophobic interactions). Thus, current preliminary model of interactions between desmosdumotin-NBD2 could be helpful to understand the in-depth inhibition mechanism of P-gp at NBD2 level and to design more potent inhibitors which could effectively overcome MDR of anticancer agents.
    Anti-Cancer Agents in Medicinal Chemistry (Formerly Current Medicinal Chemistry - Anti-Cancer Agents) 06/2013; DOI:10.2174/18715206113139990302 · 2.94 Impact Factor
  • Changdev G Gadhe · Gugan Kothandan · Seung Joo Cho
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    ABSTRACT: P-glycoprotein (P-gp) is responsible for the multidrug resistance (MDR) and involved in the expulsion of xenobiotics out of cell. In this paper, homology modeling, docking and molecular dynamics simulation (MDS) was performed for the human P-gp desmosdumotin inhibitor. Docking study was carried out in the P-gp nucleotide binding domain 2 (NBD2). The desmosdumotin binding region occupied the ATP binding region (flavonoid binding region) with hydrophobic and hydrophilic interactions. Analysis of root mean square deviations (RMSDs) of active site residues indicated the binding site residues were stable throughout the simulation period. As shown in previous results with structurally similar flavonoid compounds, van der Waals and electrostatic interactions were found to be important factors for the desmosdumotin-NBD2 inhibition. Docking results suggest that desmosdumotin interacts with the NBD2 through both hydrogen bonds (Lys1076, Ser1077 and Thr1078) and hydrophobic interactions (Tyr1044, Val1052, Gly1073 and Cys1074). In addition, the involvement of other amino-acids was identified via MDS (Lys1076 and Ser1077 for hydrogen bonds and Tyr1044, Val1052, Gly1073, Cys1074 and Gly1075 for hydrophobic interactions). Thus, current preliminary model of interactions between desmosdumotin-NBD2 could be helpful to understand the in-depth inhibition mechanism of P-gp at NBD2 level and to design more potent inhibitors which could effectively overcome MDR of anticancer agents.
    Anti-cancer agents in medicinal chemistry 06/2013; · 2.94 Impact Factor
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    Changdev G. Gadhe · Seung Joo Cho
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    ABSTRACT: 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 level minimization. It was observed that upto certain increment in temperature the number of unique conformations were increased, but afterword it decreased.
    03/2013; 6(1). DOI:10.13160/ricns.2013.6.1.008
  • Gugan Kothandan · Changdev G Gadhe · Seung Joo Cho
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    ABSTRACT: In this study, we report on modeling of Galanin receptor type 3 (Gal3 ) and its interaction with agonist and antagonists using in silico methodologies. Comparative structural modeling of Gal3 were based on multiple templates. With the availability of reported selective Gal3 antagonists, docking was done into the predicted binding site. Similarly, galanin, a reported agonist, was also modeled and then docked into the receptor's active site. CoMFA models were developed using ligand based (q2 = 0.537, r2 = 0.961, noc = 5,) and receptor guided (docked mode 1: q2 = 0.574, r2 = 0.946, noc = 5) and docked pose based (q2 = 0.499, r2 = 0.954, noc = 5) alignment schemes. CoMFA contour analysis revealed that, bulky substitution around the meta position of the phenyl ring, as well as optimal substitution (para) of the phenyl ring could produce molecules with improved activity. We also found that Gln79, Ile82, Asp86, Trp88, His99, Ile102, Tyr103, Glu170, Pro174, Ala175, Asp185, Arg273, His277 and Tyr281 are crucial and mutational studies on these residues could be helpful. The results obtained from this study can further be exploited for structure based drug design and also help the researchers to identify novel antagonists targeting Gal3 . © 2013 John Wiley & Sons A/S.
    Chemical Biology &amp Drug Design 03/2013; 81(6). DOI:10.1111/cbdd.12128 · 2.51 Impact Factor
  • Changdev G Gadhe · Gugan Kothandan · Seung Joo Cho
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    ABSTRACT: Chemokine receptor 5 (CCR5) is an important receptor used by human immunodeficiency virus type 1 (HIV-1) to gain viral entry into host cell. In this study, we used a combined approach of comparative modeling, molecular docking, and three dimensional quantitative structure activity relationship (3D-QSAR) analyses to elucidate detailed interaction of CCR5 with their inhibitors. Docking study of the most potent inhibitor from a series of compounds was done to derive the bioactive conformation. Parameters such as random selection, rational selection, different charges and grid spacing were utilized in the model development to check their performance on the model predictivity. Final comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) models were chosen based on the rational selection method, Gasteiger-Hückel charges and a grid spacing of 0.5 Å. Rational model for CoMFA (q (2) = 0.722, r (2) = 0.884, Q (2) = 0.669) and CoMSIA (q (2) = 0.712, r (2) = 0.825, Q (2) = 0.522) was obtained with good statistics. Mapping of contour maps onto CCR5 interface led us to better understand of the ligand-protein interaction. Docking analysis revealed that the Glu283 is crucial for interaction. Two new amino acid residues, Tyr89 and Thr167 were identified as important in ligand-protein interaction. No site directed mutagenesis studies on these residues have been reported.
    Archives of Pharmacal Research 01/2013; 36(1). DOI:10.1007/s12272-013-0001-1 · 1.75 Impact Factor