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Shaik B, Gupta SP, Sharma S. Quantitative Structure-Activity Relationship and Docking Studies on a series of H+/K+-ATPase inhibitors. LETT DRUG DES DISCOV 2019. [DOI: 10.2174/1570178616666190222153819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Background:
The Gastric H+/K+-ATPase is also known as proton pump is the enzyme
responsible for the acidification of gastric juice. H+/K+ GastroEsophageal Reflux Disease (GERD)
and other acid related diseases mainly depend on the inhibition of the gastric H+/K+- ATPase which
will finally result in acid secretion in stomach. GERD is one of the diseases that have significant
effect on the quality of human life and are the major burden on health care systems is that leads to
heart burn, acid regurgitation, chest pain, epigastric pain, and respiratory conditions such as chronic
cough. Hence the study of the inhibitors of Gastric H+/K+-ATPase is desired.
Methods:
Research and online content related to imidazo [1, 2-a]pyrazine and heterocyclic ring analogues
(I) that were synthesized and evaluated for their Gastric H+/K+-ATPase inhibitory activity is
reviewed, and in order to design and develop still better and more effective H+/K+-ATPase inhibitors,
we have made Quantitative Structure Activity Relationship (QSAR), docking and ADMET studies
on these compounds.
Results:
The best MLR equation based on four descriptors along with statistical parameters is obtained
using Statistica dataminer software. Using the model expressed by this study we predicted
some new compounds of high H+/K+-ATPase inhibition potency. Each predicted compound has very
high potency with which only a few compounds of existing series can match.
Conclusion:
The QSAR and molecular modelling studies suggested that still better compounds can
be designed if the flexibility of the molecules can be increased for which attempts can be made to
have more saturated atoms in the molecules. Such a compound predicted by us was found to have
interactions with the enzyme H+/K+-ATPase almost in the same manner as the FDA approved compounds,
lansoprazole, pantaprazole.
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Affiliation(s)
- Basheerulla Shaik
- Department of Applied Sciences, National Institute of Technical Teachers' Training and Research, Bhopal-462002, India
| | - Satya Prakash Gupta
- Department of Applied Sciences, Meerut Institute of Engineering and Technology, Meerut-250005, India
| | - Shweta Sharma
- Department of Chemistry, Career College, Career group of Institutions, Bhopal, Madhya Pradesh, India
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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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O'Boyle NM, Sayle RA. Comparing structural fingerprints using a literature-based similarity benchmark. J Cheminform 2016; 8:36. [PMID: 27382417 PMCID: PMC4932683 DOI: 10.1186/s13321-016-0148-0] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Accepted: 06/26/2016] [Indexed: 01/17/2023] Open
Abstract
Background The concept of molecular similarity is one of the central ideas in cheminformatics, despite the fact that it is ill-defined and rather difficult to assess objectively. Here we propose a practical definition of molecular similarity in the context of drug discovery: molecules A and B are similar if a medicinal chemist would be likely to synthesise and test them around the same time as part of the same medicinal chemistry program. The attraction of such a definition is that it matches one of the key uses of similarity measures in early-stage drug discovery. If we make the assumption that molecules in the same compound activity table in a medicinal chemistry paper were considered similar by the authors of the paper, we can create a dataset of similar molecules from the medicinal chemistry literature. Furthermore, molecules with decreasing levels of similarity to a reference can be found by either ordering molecules in an activity table by their activity, or by considering activity tables in different papers which have at least one molecule in common. Results Using this procedure with activity data from ChEMBL, we have created two benchmark datasets for structural similarity that can be used to guide the development of improved measures. Compared to similar results from a virtual screen, these benchmarks are an order of magnitude more sensitive to differences between fingerprints both because of their size and because they avoid loss of statistical power due to the use of mean scores or ranks. We measure the performance of 28 different fingerprints on the benchmark sets and compare the results to those from the Riniker and Landrum (J Cheminf 5:26, 2013. doi:10.1186/1758-2946-5-26) ligand-based virtual screening benchmark. Conclusions Extended-connectivity fingerprints of diameter 4 and 6 are among the best performing fingerprints when ranking diverse structures by similarity, as is the topological torsion fingerprint. However, when ranking very close analogues, the atom pair fingerprint outperforms the others tested. When ranking diverse structures or carrying out a virtual screen, we find that the performance of the ECFP fingerprints significantly improves if the bit-vector length is increased from 1024 to 16,384.An example series from one of the benchmark datasets. Each fingerprint is assessed on its ability to reproduce a specific series order. ![]() Electronic supplementary material The online version of this article (doi:10.1186/s13321-016-0148-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Noel M O'Boyle
- NextMove Software, Innovation Centre, Cambridge Science Park, Milton Road, Cambridge, CB4 0EY UK
| | - Roger A Sayle
- NextMove Software, Innovation Centre, Cambridge Science Park, Milton Road, Cambridge, CB4 0EY UK
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Abstract
In 1989, the reaction of vinyl magnesium halides with ortho-substituted nitroarenes leading to indoles was discovered. This reaction is now frequently reported as the "Bartoli reaction" or the "Bartoli indole synthesis" (BIS). It has rapidly become the shortest and most flexible route to 7-substituted indoles, because the classical indole syntheses generally fail in their preparation. The flexibility of the Bartoli reaction is great as it can be extended to heteroaromatic nitro derivatives and can be run on solid support. This review will focus on the use of the Bartoli indole synthesis as the key step in preparations of complex indoles, which appeared in the literature in the last few years.
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Affiliation(s)
- Giuseppe Bartoli
- Dipartimento Chimica Industriale 'Toso Montanari', Università di Bologna, Viale Risorgimento 4, I-40136 Bologna, Italy.
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Arikawa Y, Hasuoka A, Nishida H, Hirase K, Inatomi N, Takagi T, Tarui N, Kawamoto M, Imanishi A, Itoh F, Kajino M. Synthetic studies of five-membered heteroaromatic derivatives as potassium-competitive acid blockers (P-CABs). Bioorg Med Chem Lett 2015; 25:2037-40. [PMID: 25891103 DOI: 10.1016/j.bmcl.2015.03.094] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 03/26/2015] [Accepted: 03/31/2015] [Indexed: 11/25/2022]
Abstract
On the basis of a series of novel and potent potassium-competitive acid blockers represented by 1-sulfonylpyrrole derivative 7, we prepared several five-membered heterocyclic analogues (8) and evaluated their H(+),K(+)-ATPase activities in vitro. We also assessed the role of the methylaminomethyl side chain by comparison with methylamino and ethylamino derivatives. We observed that the five-membered core ring and its orientation affect inhibitory activity and that the methylaminomethyl moiety is the best side chain. On the basis of potency and ligand-lipophilicity efficiency, compound 7 remains the most drug-like of the compounds studied to date. This study revealed the factors necessary for potent H(+),K(+)-ATPase inhibition, such as differences in electron density, the properties of the lone pair at each apical position of the heteroaromatic ring, and the geometry of the substituents.
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Affiliation(s)
- Yasuyoshi Arikawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi-2-chome, Fujisawa, Kanagawa 251-8555, Japan.
| | - Atsushi Hasuoka
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi-2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Haruyuki Nishida
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi-2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Keizo Hirase
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi-2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Nobuhiro Inatomi
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi-2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Terufumi Takagi
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi-2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Naoki Tarui
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi-2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Makiko Kawamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi-2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Akio Imanishi
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi-2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Fumio Itoh
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi-2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masahiro Kajino
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd, 26-1, Muraokahigashi-2-chome, Fujisawa, Kanagawa 251-8555, Japan
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Rogoza LN, Salakhutdinov NF. Anti-ulcer agents: chemical aspect of solving the problem. RUSSIAN CHEMICAL REVIEWS 2015. [DOI: 10.1070/rcr4430] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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A Quantitative Structure-Activity Relationship and Molecular Modeling Study on a Series of Heteroaryl- and Heterocyclyl-Substituted Imidazo[1,2-a]Pyridine Derivatives Acting as Acid Pump Antagonists. Res Lett Biochem 2013; 2013:141469. [PMID: 24089639 PMCID: PMC3780519 DOI: 10.1155/2013/141469] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 07/29/2013] [Indexed: 11/24/2022] Open
Abstract
A quantitative structure-activity relationship (QSAR) and molecular docking study has been performed on a series of heteroaryl- and heterocyclyl-substituted imidazo[1,2-a]pyridine derivatives acting as acid pump antagonists in order to have a better understanding of the mechanism of H+/K+-ATPase inhibition. The QSAR study shows a significant correlation of activity with Global Topological Charge Indices (GTCI) of the compounds and the hydrophobic constant π of some substituents, indicating that the charge transfer within the molecule and the hydrophobic property of some substituents will be the controlling factor of the activity of these compounds and that there can be dispersion interaction between the molecules and the receptor, where some substituents may have hydrophobic interaction, too. Based on this correlation some new compounds with higher potency have been predicted and their docking study has been performed to see if they can have better interaction with the receptor. The ADME properties of these predicted compounds have also been reported that follow Lipinski's rule of five.
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Arikawa Y, Nishida H, Kurasawa O, Hasuoka A, Hirase K, Inatomi N, Hori Y, Matsukawa J, Imanishi A, Kondo M, Tarui N, Hamada T, Takagi T, Takeuchi T, Kajino M. Discovery of a novel pyrrole derivative 1-[5-(2-fluorophenyl)-1-(pyridin-3-ylsulfonyl)-1H-pyrrol-3-yl]-N-methylmethanamine fumarate (TAK-438) as a potassium-competitive acid blocker (P-CAB). J Med Chem 2012; 55:4446-56. [PMID: 22512618 DOI: 10.1021/jm300318t] [Citation(s) in RCA: 102] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In our pursuit of developing a novel and potent potassium-competitive acid blocker (P-CAB), we synthesized pyrrole derivatives focusing on compounds with low log D and high ligand-lipophilicity efficiency (LLE) values. Among the compounds synthesized, the compound 13e exhibited potent H(+),K(+)-ATPase inhibitory activity and potent gastric acid secretion inhibitory action in vivo. Its maximum efficacy was more potent and its duration of action was much longer than those of proton pump inhibitors (PPIs). Therefore, compound 13e (1-[5-(2-fluorophenyl)-1-(pyridin-3-ylsulfonyl)-1H-pyrrol-3-yl]-N-methylmethanamine fumarate, TAK-438) was selected as a drug candidate for the treatment of gastroesophageal reflux disease (GERD), peptic ulcer, and other acid-related diseases.
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Affiliation(s)
- Yasuyoshi Arikawa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., 26-1, Muraokahigashi-2-chome, Fujisawa, Kanagawa 251-8555, Japan.
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Garton N, Bailey N, Bamford M, Demont E, Farre-Gutierrez I, Hutley G, Bravi G, Pickering P. Discovery of biaryl inhibitors of H+/K+ ATPase. Bioorg Med Chem Lett 2010; 20:1049-54. [DOI: 10.1016/j.bmcl.2009.12.040] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Revised: 12/07/2009] [Accepted: 12/09/2009] [Indexed: 01/24/2023]
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