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Singh V, Gohil N, Ramírez-García R. New insight into the control of peptic ulcer by targeting the histamine H 2 receptor. J Cell Biochem 2017; 119:2003-2011. [PMID: 28817204 DOI: 10.1002/jcb.26361] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Accepted: 08/15/2017] [Indexed: 11/09/2022]
Abstract
Peptic ulcer disease is one of the major challenges in public health globally and new evidence shows that it can be controlled by targeting the histamine H2 receptor (H2 R). Recently, a number of H2 R antagonists have been synthesized and used to block the action of histamine on the parietal cells in the stomach and decrease the acid production. In this study, we modeled the H2 R by homology modeling using the 3-D crystal structure and this model was validated based on free energy and amino acid residues present in the allowed regions of a Ramachandran plot. We used this 3-D model for screening of highly potent drugs using molecular docking. We found cimetidine, cimetex, and famotidine as the most potent drugs based on the binding affinity of drug-protein interactions. We also generated a cellular network for H2 R that could be useful for better understanding of cellular mechanism and drug targets. These findings provide a new insight into the development of suitable, specific, and effective anti-ulcer drugs for a most effective treatment of ulcerous diseases.
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Affiliation(s)
- Vijai Singh
- Department of Microbiology, Synthetic Biology Laboratory, School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area, Gandhinagar, India
| | - Nisarg Gohil
- Department of Microbiology, Synthetic Biology Laboratory, School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area, Gandhinagar, India
| | - Robert Ramírez-García
- Department of Microbiology, Synthetic Biology Laboratory, School of Biological Sciences and Biotechnology, Institute of Advanced Research, Koba Institutional Area, Gandhinagar, India
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Lokeshwari DM, Rekha ND, Srinivasan B, Vivek HK, Kariyappa AK. Design, synthesis of novel furan appended benzothiazepine derivatives and in vitro biological evaluation as potent VRV-PL-8a and H+/K+ ATPase inhibitors. Bioorg Med Chem Lett 2017; 27:3048-3054. [DOI: 10.1016/j.bmcl.2017.05.059] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 04/18/2017] [Accepted: 05/19/2017] [Indexed: 01/13/2023]
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Jana K, Chandar NB, Bandyopadhyay T, Ganguly B. Role of Noncovalent Interactions in Designing Inhibitors for H+,K+-ATPase: Combined QM and MD Based Investigations. ChemistrySelect 2016. [DOI: 10.1002/slct.201601458] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Kalyanashis Jana
- Computation and Simulation Unit, Analytical Discipline & Centralized Instrument Facility, and Academy of Scientific and Innovative Research; CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar; Gujarat 364002 India
| | - Nellore Bhanu Chandar
- Computation and Simulation Unit, Analytical Discipline & Centralized Instrument Facility, and Academy of Scientific and Innovative Research; CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar; Gujarat 364002 India
| | - Tusar Bandyopadhyay
- Theorectical Chemistry Section, Chemistry Group MOD LAB; Bhabha Atomic Research Centre, Trombay; Mumbai 400 085 India
| | - Bishwajit Ganguly
- Computation and Simulation Unit, Analytical Discipline & Centralized Instrument Facility, and Academy of Scientific and Innovative Research; CSIR-Central Salt and Marine Chemicals Research Institute, Bhavnagar; Gujarat 364002 India
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Luo HJ, Wang JZ, Huang NY, Deng WQ, Zou K. Computational insights into the interaction mechanism of triazolyl substituted tetrahydrobenzofuran derivatives with H(+),K(+)-ATPase at different pH. J Comput Aided Mol Des 2015; 30:27-37. [PMID: 26667240 DOI: 10.1007/s10822-015-9886-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 12/07/2015] [Indexed: 11/29/2022]
Abstract
The interaction mechanism of triazolyl substituted tetrahydrobenzofuran derivatives (compound 1 (N, N-Dipropyl-1-(2-phenyl-4,5,6,7-tetrahydrobenzofuran-4-yl)-1H-1,2,3-triazole-4-methanamine) and 2 (1-(2-Phenyl-4,5,6,7-tetrahydrobenzofuran-4-yl)-4-(morpholin-4-ylmethyl)-1H-1,2,3-triazole)) with H(+),K(+)-ATPase at different pH were studied by induced-fit docking, QM/MM optimization and MM/GBSA binding free energy calculations of two forms (neutral and protonated form) of compounds. The inhibition activity of compound 1 is measured and almost unchanged at different pH, while the activity of compound 2 increases significantly with pH value decreased. This phenomenon could be explained by their protonated form percentages and the calculated binding free energies of protonated and neutral mixture of compounds at different pH. The binding free energy of protonated form is higher than that of neutral form of compound, and the protonated form could be a powerful inhibitor of H(+),K(+)-ATPase. By the decomposed energy comparisons of residues in binding sites, Asp137 should be the key binding site to protonated form of compound because of the hydrogen bond and electrostatic interactions. These calculation results could help for further rational design of novel H(+),K(+)-ATPase inhibitors.
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Affiliation(s)
- Hua-Jun Luo
- Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Science, China Three Gorges University, Yichang, China.
| | - Jun-Zhi Wang
- Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Science, China Three Gorges University, Yichang, China
| | - Nian-Yu Huang
- Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Science, China Three Gorges University, Yichang, China
| | - Wei-Qiao Deng
- Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Science, China Three Gorges University, Yichang, China.,State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Kun Zou
- Hubei Key Laboratory of Natural Products Research and Development, College of Biological and Pharmaceutical Science, China Three Gorges University, Yichang, China
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ATP4A gene regulatory network for fine-tuning of proton pump and ion channels. SYSTEMS AND SYNTHETIC BIOLOGY 2013; 7:23-32. [PMID: 24432139 DOI: 10.1007/s11693-012-9103-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 12/31/2012] [Accepted: 12/31/2012] [Indexed: 12/11/2022]
Abstract
The ATP4A encodes α subunit of H(+), K(+)-ATPase that contains catalytic sites of the enzyme forming pores through cell membrane which allows the ion transport. H(+), K(+)-ATPase is a membrane bound P-type ATPase enzyme which is found on the surface of parietal cells and uses the energy derived from each cycle of ATP hydrolysis that can help in exchanging ions (H(+), K(+) and Cl(-)) across the cell membrane secreting acid into the gastric lumen. The 3-D model of α-subunit of H(+), K(+)-ATPase was generated by homology modeling. It was evaluated and validated on the basis of free energies and amino acid residues. The inhibitor binding amino acid active pockets were identified in the 3-D model by molecular docking. The two drugs Omeprazole and Rabeprazole were found more potent interactions with generated model of α-subunit of H(+), K(+)-ATPase on the basis of their affinity between drug-protein interactions. We have generated ATP4A gene regulatory networks for interactions with other proteins which involved in regulation that can help in fine-tuning of proton pump and ion channels. These findings provide a new dimension for discovery and development of proton pump inhibitors and gene regulation of the ATPase. It can be helpful in better understanding of human physiology and also using synthetic biology strategy for reprogramming of parietal cells for control of gastric ulcers.
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Vyas VK, Ukawala RD, Ghate M, Chintha C. Homology modeling a fast tool for drug discovery: current perspectives. Indian J Pharm Sci 2012. [PMID: 23204616 PMCID: PMC3507339 DOI: 10.4103/0250-474x.102537] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Major goal of structural biology involve formation of protein-ligand complexes; in which the protein molecules act energetically in the course of binding. Therefore, perceptive of protein-ligand interaction will be very important for structure based drug design. Lack of knowledge of 3D structures has hindered efforts to understand the binding specificities of ligands with protein. With increasing in modeling software and the growing number of known protein structures, homology modeling is rapidly becoming the method of choice for obtaining 3D coordinates of proteins. Homology modeling is a representation of the similarity of environmental residues at topologically corresponding positions in the reference proteins. In the absence of experimental data, model building on the basis of a known 3D structure of a homologous protein is at present the only reliable method to obtain the structural information. Knowledge of the 3D structures of proteins provides invaluable insights into the molecular basis of their functions. The recent advances in homology modeling, particularly in detecting and aligning sequences with template structures, distant homologues, modeling of loops and side chains as well as detecting errors in a model contributed to consistent prediction of protein structure, which was not possible even several years ago. This review focused on the features and a role of homology modeling in predicting protein structure and described current developments in this field with victorious applications at the different stages of the drug design and discovery.
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Affiliation(s)
- V K Vyas
- Department of Pharmaceutical Chemistry, Institute of Pharmacy, Nirma University, Ahmedabad-382 481, India
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Yang GX, Li X, Snyder M. Investigating metabolite-protein interactions: an overview of available techniques. Methods 2012; 57:459-66. [PMID: 22750303 PMCID: PMC3448827 DOI: 10.1016/j.ymeth.2012.06.013] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2012] [Revised: 06/18/2012] [Accepted: 06/21/2012] [Indexed: 12/18/2022] Open
Abstract
Metabolites comprise the molar majority of chemical substances in living cells, and metabolite-protein interactions are expected to be quite common. Many interactions have already been identified and have been shown to be involved in the regulation of different types of cellular processes including signaling events, enzyme activities, protein localizations and interactions. Recent technological advances have greatly facilitated the detection of metabolite-protein interactions at high sensitivity and some of these have been applied on a large scale. In this manuscript, we review the available in vitro, in silico and in vivo technologies for mapping small-molecule-protein interactions. Although some of these were developed for drug-protein interactions they can be applied for mapping metabolite-protein interactions. Information gained from the use of these approaches can be applied to the manipulation of cellular processes and therapeutic applications.
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Affiliation(s)
- Grace Xiaolu Yang
- Department of Genetics, Stanford University, Stanford, CA
- Department of Chemistry, Stanford University, Stanford CA
| | - Xiyan Li
- Department of Genetics, Stanford University, Stanford, CA
| | - Michael Snyder
- Department of Genetics, Stanford University, Stanford, CA
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Chourasia M, Sastry GN. The nucleotide, inhibitor, and cation binding sites of P-type II ATPases. Chem Biol Drug Des 2012; 79:617-27. [PMID: 22260628 DOI: 10.1111/j.1747-0285.2012.01334.x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
P-type ATPases constitute a ubiquitous superfamily of cation transport enzymes, responsible for carrying out actions of paramount importance in biology such as ion transport and expulsion of toxic ions from cells. The harmonized toggling of gates in the extra- and intracellular domains explain the phenomenon of specific cation binding in selective physiological states. A quantitative understanding of the fundamental aspects of ion transport mechanism and regulation of P-type ATPases requires detailed knowledge of thermodynamical, structural, and functional properties. Computational studies have made significant contributions to our understanding of biological ion pumps. Various 3D structures of Ca(2+) -ATPase between E1 and E2 transition states have given a impetus to the theorists to work on the Na(+) K(+) - and H(+) K(+) -ATPase to address important questions about their function. The current review delineates the importance of cation, nucleotide, and inhibitor binding domains, with a focus on the therapeutic potential and biological relevance of the three P-type II ATPases. This will give an insight into the ion selectivity and their conduction across the transmembrane helices of P-type II ATPases, which may pave the way to a range of fundamental questions about the mechanism and aid in the efforts of structure- and analog-based drug design.
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Affiliation(s)
- Mukesh Chourasia
- Molecular Modeling Group, Indian Institute of Chemical Technology, Hyderabad, India
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Vangheluwe P, Sepúlveda MR, Missiaen L, Raeymaekers L, Wuytack F, Vanoevelen J. Intracellular Ca2+- and Mn2+-Transport ATPases. Chem Rev 2009; 109:4733-59. [DOI: 10.1021/cr900013m] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Peter Vangheluwe
- Laboratory of Ca2+-transport ATPases and Laboratory of Molecular and Cellular Signaling, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - M. Rosario Sepúlveda
- Laboratory of Ca2+-transport ATPases and Laboratory of Molecular and Cellular Signaling, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Ludwig Missiaen
- Laboratory of Ca2+-transport ATPases and Laboratory of Molecular and Cellular Signaling, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Luc Raeymaekers
- Laboratory of Ca2+-transport ATPases and Laboratory of Molecular and Cellular Signaling, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Frank Wuytack
- Laboratory of Ca2+-transport ATPases and Laboratory of Molecular and Cellular Signaling, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jo Vanoevelen
- Laboratory of Ca2+-transport ATPases and Laboratory of Molecular and Cellular Signaling, Department of Molecular Cell Biology, Katholieke Universiteit Leuven, Leuven, Belgium
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P-type ATPases as drug targets: tools for medicine and science. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2009; 1787:207-20. [PMID: 19388138 DOI: 10.1016/j.bbabio.2008.12.019] [Citation(s) in RCA: 117] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
P-type ATPases catalyze the selective active transport of ions like H+, Na+, K+, Ca2+, Zn2+, and Cu2+ across diverse biological membrane systems. Many members of the P-type ATPase protein family, such as the Na+,K+-, H+,K+-, Ca2+-, and H+-ATPases, are involved in the development of pathophysiological conditions or provide critical function to pathogens. Therefore, they seem to be promising targets for future drugs and novel antifungal agents and herbicides. Here, we review the current knowledge about P-type ATPase inhibitors and their present use as tools in science, medicine, and biotechnology. Recent structural information on a variety of P-type ATPase family members signifies that all P-type ATPases can be expected to share a similar basic structure and a similar basic machinery of ion transport. The ion transport pathway crossing the membrane lipid bilayer is constructed of two access channels leading from either side of the membrane to the ion binding sites at a central cavity. The selective opening and closure of the access channels allows vectorial access/release of ions from the binding sites. Recent structural information along with new homology modeling of diverse P-type ATPases in complex with known ligands demonstrate that the most proficient way for the development of efficient and selective drugs is to target their ion transport pathway.
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Levin D, DiPaolo RJ, Brinster C, Revilleza MJR, Boyd LF, Teyton L, Natarajan K, Mage MG, Shevach EM, Margulies DH. Availability of autoantigenic epitopes controls phenotype, severity, and penetrance in TCR Tg autoimmune gastritis. Eur J Immunol 2009; 38:3339-53. [PMID: 19039784 DOI: 10.1002/eji.200838584] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We examined TCR:MHC/peptide interactions and in vivo epitope availability to explore the Th1- or Th2-like phenotype of autoimmune disease in two TCR Tg mouse models of autoimmune gastritis (AIG). The TCR of strains A23 and A51 recognize distinct IA(d)-restricted peptides from the gastric parietal cell H/K-ATPase. Both peptides form extremely stable MHC/peptide (MHC/p) complexes. All A23 animals develop a Th1-like aggressive, inflammatory AIG early in life, while A51 mice develop indolent Th2-like AIG at 6-8 wk with incomplete penetrance. A51 T cells were more sensitive than A23 to low doses of soluble antigen and to MHC/p complexes. Staining with IA(d)/peptide tetramers was only detectable on previously activated T cells from A51. Thus, despite inducing a milder AIG, the A51 TCR displays a higher avidity for its cognate IA(d)/peptide. Nonetheless, in vivo proliferation of adoptively transferred A51 CFSE-labeled T cells in the gastric lymph node was relatively poor compared with A23 T cells. Also, DC from WT gastric lymph node, presenting processed antigen available in vivo, stimulated proliferation of A23 T cells better than A51. Thus, the autoimmune potential of these TCR in their respective Tg lines is strongly influenced by the availability of the peptide epitope, rather than by differential avidity for their respective MHC/p complexes.
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Affiliation(s)
- Ditza Levin
- Department of Biotechnology Engineering, Ort Braude College, Karmiel, Israel
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Bamford M. 3 H+/K+ ATPase Inhibitors in the Treatment of Acid-Related Disorders. PROGRESS IN MEDICINAL CHEMISTRY 2009; 47:75-162. [DOI: 10.1016/s0079-6468(08)00203-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Betz M, Saxena K, Schwalbe H. Biomolecular NMR: a chaperone to drug discovery. Curr Opin Chem Biol 2006; 10:219-25. [PMID: 16679046 PMCID: PMC7185745 DOI: 10.1016/j.cbpa.2006.04.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Accepted: 04/24/2006] [Indexed: 11/16/2022]
Abstract
Biomolecular NMR now contributes routinely to every step in the development of new chemical entities ahead of clinical trials. The versatility of NMR--from detection of ligand binding over a wide range of affinities and a wide range of drug targets with its wealth of molecular information, to metabolomic profiling, both ex vivo and in vivo--has paved the way for broadly distributed applications in academia and the pharmaceutical industry. Proteomics and initial target selection both benefit from NMR: screenings by NMR identify lead compounds capable of inhibiting protein-protein interactions, still one of the most difficult development tasks in drug discovery. NMR hardware improvements have given access to the microgram domain of phytochemistry, which should lead to the discovery of novel bioactive natural compounds. Steering medicinal chemists through the lead optimisation process by providing detailed information about protein-ligand interactions has led to impressive success in the development of novel drugs. The study of biofluid composition--metabonomics--provides information about pharmacokinetics and helps toxicological safety assessment in animal model systems. In vivo, magnetic resonance spectroscopy interrogates metabolite distributions in living cells and tissues with increasing precision, which significantly impacts the development of anticancer or neurological disorder therapeutics. An overview of different steps in recent drug discovery is presented to illuminate the links with the most recent advances in NMR methodology.
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