1
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Reddyrajula R, Perveen S, Negi A, Etikyala U, Manga V, Sharma R, Dalimba UK. N-Acyl phenothiazines as mycobacterial ATP synthase inhibitors: Rational design, synthesis and in vitro evaluation against drug sensitive, RR and MDR-TB. Bioorg Chem 2024; 151:107702. [PMID: 39142196 DOI: 10.1016/j.bioorg.2024.107702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/31/2024] [Accepted: 08/05/2024] [Indexed: 08/16/2024]
Abstract
The mycobacterial F-ATP synthase is responsible for the optimal growth, metabolism and viability of Mycobacteria, establishing it as a validated target for the development of anti-TB therapeutics. Herein, we report the discovery of an N-acyl phenothiazine derivative, termed PT6, targeting the mycobacterial F-ATP synthase. PT6 is bactericidal and active against the drug sensitive, Rifampicin-resistant as well as Multidrug-resistant tuberculosis strains. Compound PT6 showed noteworthy inhibition of F-ATP synthesis, exhibiting an IC50 of 0.788 µM in M. smegmatis IMVs and was observed that it could deplete intracellular ATP levels, exhibiting an IC50 of 30 µM. PT6 displayed a high selectivity towards mycobacterial ATP synthase compared to mitochondrial ATP synthase. Compound PT6 showed a minor synergistic effect in combination with Rifampicin and Isoniazid. PT6 demonstrated null cytotoxicity as confirmed by assessing its toxicity against VERO cell lines. Further, the binding mechanism and the activity profile of PT6 were validated by employing in silico techniques such as molecular docking, Prime MM/GBSA, DFT and ADMET analysis. These results suggest that PT6 presents an attractive lead for the discovery of a novel class of mycobacterial F-ATP synthase inhibitors.
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Affiliation(s)
- Rajkumar Reddyrajula
- Central Research Facility, National Institute of Technology Karnataka, Surathkal, Mangalore 575 025, India; Department of Chemical Sciences, National Institute of Pharmaceutical Education and Research (NIPER), Hyderabad 500 037, India
| | - Summaya Perveen
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180 001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Anjali Negi
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180 001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India
| | - Umadevi Etikyala
- Medicinal Chemistry Laboratory, Department of Chemistry, Osmania University, Hyderabad 500 076, India
| | - Vijjulatha Manga
- Medicinal Chemistry Laboratory, Department of Chemistry, Osmania University, Hyderabad 500 076, India
| | - Rashmi Sharma
- Infectious Diseases Division, CSIR- Indian Institute of Integrative Medicine, Jammu 180 001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India.
| | - Udaya Kumar Dalimba
- Organic and Materials Chemistry Laboratory, Department of Chemistry, National Institute of Technology Karnataka, Surathkal, Mangalore 575 025, India.
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2
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Hong D, Lee K. Polymorphic structures of 3-phenyl-1 H-1,3-benzo-diazol-2(3 H)-one. Acta Crystallogr E Crystallogr Commun 2023; 79:534-537. [PMID: 37288468 PMCID: PMC10242737 DOI: 10.1107/s2056989023003961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 05/03/2023] [Indexed: 06/09/2023]
Abstract
The polymorphic structures (I and II) of 3-phenyl-1H-1,3-benzo-diazol-2(3H)-one, C13H10N2O, acquired from pentane diffusion into the solution in THF, are reported. The structures show negligible differences in bond distances and angles, but the C-N-C-C torsion angles between the backbone and the phenyl substituent, 123.02 (15)° for I and 137.18 (11)° for II, are different. Compound I features a stronger C=O⋯H-N hydrogen bond than that in II, while the structure of II exhibits a stronger π-π inter-action than in I, as confirmed by the shorter inter-centroid distance [3.3257 (8) Å in II in comparison to 3.6862 (7) Å in I]. Overall, the supra-molecular inter-actions of I and II are distinct, presumably originating from the variation in the dihedral angle.
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Affiliation(s)
- Dabeen Hong
- Department of Chemical Education and Research Institute of Natural Sciences, Gyeongsang National University, Gyeongsangnam-do 52828, Republic of Korea
| | - Kyounghoon Lee
- Department of Chemical Education and Research Institute of Natural Sciences, Gyeongsang National University, Gyeongsangnam-do 52828, Republic of Korea
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3
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Wang Y, Guo C, Tao S, Liu J, Zhao J, Liu N, Dai B. Basicity-Tuned Selectivity: Synthesis of Benzimidazolone and Benzodiazepine from N-Alkyl- N-(2-(pyridin-2-ylamino)-phenyl)formamides. CHINESE J ORG CHEM 2022. [DOI: 10.6023/cjoc202107062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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4
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Calculate protein-ligand binding affinities with the extended linear interaction energy method: application on the Cathepsin S set in the D3R Grand Challenge 3. J Comput Aided Mol Des 2018; 33:105-117. [PMID: 30218199 DOI: 10.1007/s10822-018-0162-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 09/10/2018] [Indexed: 10/28/2022]
Abstract
We participated in the Cathepsin S (CatS) sub-challenge of the Drug Design Data Resource (D3R) Grand Challenge 3 (GC3) in 2017 to blindly predict the binding poses of 24 CatS-bound ligands, the binding affinity ranking of 136 ligands, and the binding free energies of a subset of 33 ligands in Stage 1A and Stage 2. Our submitted predictions ranked relatively well compared to the submissions from other participants. Here we present our methodologies used in the challenge. For the binding pose prediction, we employed the Glide module in the Schrodinger Suite 2017 and AutoDock Vina. For the binding affinity/free energy prediction, we carried out molecular dynamics simulations of the complexes in explicit water solvent with counter ions, and then estimated the binding free energies with our newly developed model of extended linear interaction energy (ELIE), which is inspired by two other popular end-point approaches: the linear interaction energy (LIE) method, and the molecular mechanics with Poisson-Boltzmann surface area solvation method (MM/PBSA). Our studies suggest that ELIE is a good trade-off between efficiency and accuracy, and it is appropriate for filling the gap between the high-throughput docking and scoring methods and the rigorous but much more computationally demanding methods like free energy perturbation (FEP) or thermodynamics integration (TI) in computer-aided drug design (CADD) projects.
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5
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Meng Y, Wang B, Ren L, Zhao Q, Yu W, Chang J. I2-Mediated transition-metal-free aromatic C–H amination for the synthesis of benzimidazol-2-ones and related heterocycles. NEW J CHEM 2018. [DOI: 10.1039/c8nj03166e] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A practical I2-mediated aromatic C–H amination reaction was established for benzimidazol-2-one synthesis under transition-metal-free conditions. The present reaction can be performed directly from disubstituted amines and isocyanates without the purification of the urea intermediates in a scalable fashion.
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Affiliation(s)
- Yinggao Meng
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- China
| | - Bingnan Wang
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- China
| | - Linning Ren
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- China
| | - Qiongli Zhao
- Collaborative Innovation Centre of New Drug Research and Safety Evaluation
- China
- School of Pharmaceutical Sciences
- Zhengzhou University
- Zhengzhou
| | - Wenquan Yu
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- China
| | - Junbiao Chang
- College of Chemistry and Molecular Engineering
- Zhengzhou University
- Zhengzhou
- China
- Collaborative Innovation Centre of New Drug Research and Safety Evaluation
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6
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Zhang L, Zhang B, Zhao J, Zhi Y, Wang L, Lu T, Chen Y. Structure-based design, synthesis, and evaluation of 4,5,6,7-tetrahydro-1 H -pyrazolo[4,3-c]pyridine derivatives as novel c-Met inhibitors. Eur J Med Chem 2017; 138:942-951. [DOI: 10.1016/j.ejmech.2017.06.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Revised: 05/11/2017] [Accepted: 06/21/2017] [Indexed: 10/19/2022]
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7
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Shingare R, Kulkarni AS, Sutar RL, Reddy DS. Route to Benzimidazol-2-ones via Decarbonylative Ring Contraction of Quinoxalinediones: Application to the Synthesis of Flibanserin, A Drug for Treating Hypoactive Sexual Desire Disorder in Women and Marine Natural Product Hunanamycin Analogue. ACS OMEGA 2017; 2:5137-5141. [PMID: 30023739 PMCID: PMC6044990 DOI: 10.1021/acsomega.7b00819] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2017] [Accepted: 08/15/2017] [Indexed: 06/08/2023]
Abstract
A simple and practical method to access a variety of benzimidazol-2-ones is reported here. A series of N-alkyl-substituted benzimidazol-2-ones were synthesized by decarbonylative ring contraction starting from corresponding quinoxalinediones for the first time. The utility of the method has been demonstrated by synthesizing recently approved controversial drug flibanserin (Addyi) and a urea analogue of marine antibiotic natural product hunanamycin-A.
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Affiliation(s)
- Rahul
D. Shingare
- Division
of Organic Chemistry, CSIR-National Chemical
Laboratory, Dr. Homi
Bhabha Road, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), New Delhi 110 025, India
| | - Akshay S. Kulkarni
- Division
of Organic Chemistry, CSIR-National Chemical
Laboratory, Dr. Homi
Bhabha Road, Pune 411008, India
| | - Revannath L. Sutar
- Division
of Organic Chemistry, CSIR-National Chemical
Laboratory, Dr. Homi
Bhabha Road, Pune 411008, India
| | - D. Srinivasa Reddy
- Division
of Organic Chemistry, CSIR-National Chemical
Laboratory, Dr. Homi
Bhabha Road, Pune 411008, India
- Academy
of Scientific and Innovative Research (AcSIR), New Delhi 110 025, India
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8
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Yu J, Gao C, Song Z, Yang H, Fu H. Metal-Free Oxidative C-H Amidation ofN,N′-Diarylureas with PhI(OAc)2: Synthesis of Benzimidazol-2-one Derivatives. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500726] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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9
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Andreoli F, Kaid-Slimane R, Coppola F, Farran D, Roussel C, Vanthuyne N. Access to N-Thioalkenyl and N-(o-Thio)aryl-benzimidazol-2-ones by Ring Opening of Thiazolobenzimidazolium and Benzimidazobenzothiazolium Salts and C–O Bond Cleavage of an Alkoxide. J Org Chem 2015; 80:3233-41. [DOI: 10.1021/acs.joc.5b00221] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Federico Andreoli
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397 Marseille, France
| | - Radia Kaid-Slimane
- Laboratoire
de synthèse organique appliquée, Département
de Chimie, Faculté des Sciences, Université d’Oran (Es Sénia), B.P. 1524, El M’naouer
Oran, Algérie
| | - Fabien Coppola
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397 Marseille, France
| | - Daniel Farran
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397 Marseille, France
| | - Christian Roussel
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397 Marseille, France
| | - Nicolas Vanthuyne
- Aix Marseille Université, Centrale Marseille, CNRS, iSm2 UMR 7313, 13397 Marseille, France
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10
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Mamedov VA, Zhukova NA, Zamaletdinova AI, Beschastnova TN, Kadyrova MS, Rizvanov IK, Syakaev VV, Latypov SK. Reaction for the synthesis of benzimidazol-2-ones, imidazo[5,4-b]-, and imidazo[4,5-c]pyridin-2-ones via the rearrangement of quinoxalin-2-ones and their aza analogues when exposed to enamines. J Org Chem 2014; 79:9161-9. [PMID: 25203611 DOI: 10.1021/jo501526a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A synthetically useful protocol has been developed for the preparation of highly functionalized N-pyrrolylbenzimidazol-2-ones. The reaction of variously substituted 3-aroyl- and 3-alkanoylquinoxalin-2(1H)-ones with commercially available enamines in acetic acid results in a rapid rearrangement and formation of N-pyrrolylbenzimidazol-2-ones in modest to excellent yields. The key step of the rearrangement involves the novel ring contraction of 3-aroyl- and 3-alkanoylquinoxalin-2(1H)-ones with enamines. In this case, the atom of carbon which is displaced from the pyrazine ring of quinoxalin-2(1H)-one becomes the fourth carbon atom of the newly formed pyrrole ring. The method is applicable for the aza analogues of quinoxalin-2(1H)-ones.
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Affiliation(s)
- Vakhid A Mamedov
- A.E. Arbuzov Institute of Organic and Physical Chemistry, Kazan Scientific Center of the Russian Academy of Sciences , Arbuzov str. 8, Kazan 420088, Russian Federation
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11
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Ernst JB, Tay NES, Jui NT, Buchwald SL. Regioselective synthesis of benzimidazolones via cascade C-N coupling of monosubstituted ureas. Org Lett 2014; 16:3844-6. [PMID: 24971635 PMCID: PMC4216194 DOI: 10.1021/ol501531q] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
![]()
A direct
method for the regioselective construction of benzimidazolones
is reported wherein a single palladium catalyst is employed to couple
monosubstituted urea substrates with differentially substituted 1,2-dihaloaromatic
systems. In this method, the catalyst is able to promote a cascade
of two discrete chemoselective C–N bond-forming processes that
allows the highly selective and predictable formation of complex heterocycles
from simple, readily available starting materials.
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Affiliation(s)
- Johannes B Ernst
- Department of Chemistry, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
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12
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Yogeeswari P, Sharma M, Samala G, Gangadhar M, Karthick S, Mallipeddi S, Semwal A, Sriram D. Discovery of novel tetrahydro-pyrazolo [4,3-c] pyridines for the treatment of neuropathic pain: synthesis and neuropharmacology. Eur J Med Chem 2013; 66:211-20. [PMID: 23807113 DOI: 10.1016/j.ejmech.2013.05.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2013] [Revised: 05/11/2013] [Accepted: 05/18/2013] [Indexed: 10/26/2022]
Abstract
We disclose the discovery of a novel series of tetrahydropyrido-pyrazoles that are potent inhibitors of tumour necrosis factor-alpha (TNF-α), nitric oxide and cannabinoid receptor subtype 1 (CB₁). We report herein the synthesis and neuropharmacological screening results of the titled compounds in two acute pain and two neuropathic pain models in rodents. Particularly the analogue N-(4-bromophenyl)-3-tert-butyl-5-ethyl-4,5,6,7-tetrahydro-1H-pyrazolo[4,3-c]pyridine-1-carboxamide (8a) exhibited pronounced acute antinociceptive efficacy, also being effective in chronic constriction injury (ED₅₀ = 23.8 mg/kg) and partial sciatic nerve injury (ED₅₀ = 29.0 mg/kg) models with CB₁ receptor activity (IC₅₀ = 49.6 nM) and inhibitory effect on TNF-α (86.4% inhibition at 100 mg/kg). These results suggest the importance of the development of this lead as multi-targeted treatment strategy for neuropathic pain.
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Affiliation(s)
- Perumal Yogeeswari
- Neuropathic Pain Research Laboratory, Department of Pharmacy, Birla Institute of Technology & Science - Pilani, Hyderabad Campus, RR District, 500078 Andhra Pradesh, India.
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13
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Wiener JJ, Wickboldt AT, Nguyen S, Sun S, Rynberg R, Rizzolio M, Karlsson L, Edwards JP, Grice CA. Pyrazole-based arylalkyne Cathepsin S inhibitors. Part III: Modification of P4 region. Bioorg Med Chem Lett 2013; 23:1070-4. [DOI: 10.1016/j.bmcl.2012.12.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2012] [Revised: 11/28/2012] [Accepted: 12/10/2012] [Indexed: 11/25/2022]
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14
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Singh GS, Mollet K, D’hooghe M, De Kimpe N. Epihalohydrins in Organic Synthesis. Chem Rev 2012; 113:1441-98. [DOI: 10.1021/cr3003455] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Girija S. Singh
- Chemistry Department, Faculty
of Science, University of Botswana, Private
Bag 0022, Gaborone, Botswana
| | - Karen Mollet
- Department of Sustainable Organic
Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent,
Belgium
| | - Matthias D’hooghe
- Department of Sustainable Organic
Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent,
Belgium
| | - Norbert De Kimpe
- Department of Sustainable Organic
Chemistry and Technology, Faculty of Bioscience Engineering, Ghent University, Coupure Links 653, B-9000 Ghent,
Belgium
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15
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Sams AG, Larsen K, Mikkelsen GK, Hentzer M, Christoffersen CT, Jensen KG, Frederiksen K, Bang-Andersen B. Hit-to-lead investigation of a series of novel combined dopamine D2 and muscarinic M1 receptor ligands with putative antipsychotic and pro-cognitive potential. Bioorg Med Chem Lett 2012; 22:5134-40. [PMID: 22677319 DOI: 10.1016/j.bmcl.2012.05.048] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2012] [Revised: 05/09/2012] [Accepted: 05/10/2012] [Indexed: 12/22/2022]
Abstract
We describe the discovery of a series of compounds based on 1-{3-[4-(2-oxo-2,3-dihydro-benzoimidazol-1-yl)-piperidin-1-yl]-propyl}-3,4-dihydro-1H-quinolin-2-one (3), showing combined D(2) receptor affinity and M(1) receptor agonism. Based on a strategy of controlling logP, we herein describe a hit-to-lead investigation with the aim of retaining the combined D(2)/M(1) profile, while removing the propensity of the compounds to inhibit the hERG channel, as well as at obtaining acceptable pharmacokinetic properties. Although a SAR was evident for all four parameters in question, it was not possible to separate hERG channel inhibition and D(2) receptor affinity by this effort; whilst it was feasible to obtain compounds with M(1) receptor agonism, acceptable clearance, and weak hERG inhibition.
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Affiliation(s)
- Anette Graven Sams
- Neuroscience Drug Discovery Denmark, H. Lundbeck A/S, Copenhagen-Valby, Denmark.
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16
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Beyer A, Reucher CMM, Bolm C. Potassium hydroxide/dimethyl sulfoxide promoted intramolecular cyclization for the synthesis of benzimidazol-2-ones. Org Lett 2011; 13:2876-9. [PMID: 21534616 DOI: 10.1021/ol2008878] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new protocol for intramolecular N-arylations of ureas to form benzimidazol-2-ones has been developed. The cyclization reaction occurs in the presence of KOH and DMSO at close to ambient temperature. Under these conditions the yields are high and a wide range of functional groups are tolerated.
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Affiliation(s)
- Astrid Beyer
- Institute of Organic Chemistry, RWTH Aachen University, Aachen, Germany
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17
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Ameriks MK, Bembenek SD, Burdett MT, Choong IC, Edwards JP, Gebauer D, Gu Y, Karlsson L, Purkey HE, Staker BL, Sun S, Thurmond RL, Zhu J. Diazinones as P2 replacements for pyrazole-based cathepsin S inhibitors. Bioorg Med Chem Lett 2010; 20:4060-4. [DOI: 10.1016/j.bmcl.2010.05.086] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2010] [Accepted: 05/20/2010] [Indexed: 10/19/2022]
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18
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Discovery and SAR of novel pyrazole-based thioethers as cathepsin S inhibitors: Part 1. Bioorg Med Chem Lett 2010; 20:2370-4. [DOI: 10.1016/j.bmcl.2010.01.108] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 01/15/2010] [Accepted: 01/20/2010] [Indexed: 11/24/2022]
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19
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Wiener DK, Lee-Dutra A, Bembenek S, Nguyen S, Thurmond RL, Sun S, Karlsson L, Grice CA, Jones TK, Edwards JP. Thioether acetamides as P3 binding elements for tetrahydropyrido-pyrazole cathepsin S inhibitors. Bioorg Med Chem Lett 2010; 20:2379-82. [DOI: 10.1016/j.bmcl.2010.01.103] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 01/15/2010] [Accepted: 01/20/2010] [Indexed: 11/29/2022]
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20
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Wiener JJ, Wickboldt AT, Wiener DK, Lee-Dutra A, Edwards JP, Karlsson L, Nguyen S, Sun S, Jones TK, Grice CA. Discovery and SAR of novel pyrazole-based thioethers as cathepsin S inhibitors. Part 2: Modification of P3, P4, and P5 regions. Bioorg Med Chem Lett 2010; 20:2375-8. [DOI: 10.1016/j.bmcl.2010.01.104] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2009] [Revised: 01/15/2010] [Accepted: 01/20/2010] [Indexed: 11/16/2022]
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21
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Deng X, Liang JT, Peterson M, Rynberg R, Cheung E, Mani NS. Practical Synthesis of a Cathepsin S Inhibitor: Route Identification, Purification Strategies, and Serendipitous Discovery of a Crystalline Salt Form. J Org Chem 2010; 75:1940-7. [DOI: 10.1021/jo902650b] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xiaohu Deng
- Johnson & Johnson Pharmaceutical Research & Development LLC, 3210 Merryfield Row, San Diego, California 92121
| | - Jimmy T. Liang
- Johnson & Johnson Pharmaceutical Research & Development LLC, 3210 Merryfield Row, San Diego, California 92121
| | - Matthew Peterson
- Johnson & Johnson Pharmaceutical Research & Development LLC, 3210 Merryfield Row, San Diego, California 92121
| | - Raymond Rynberg
- Johnson & Johnson Pharmaceutical Research & Development LLC, 3210 Merryfield Row, San Diego, California 92121
| | - Eugene Cheung
- Johnson & Johnson Pharmaceutical Research & Development LLC, 3210 Merryfield Row, San Diego, California 92121
| | - Neelakandha S. Mani
- Johnson & Johnson Pharmaceutical Research & Development LLC, 3210 Merryfield Row, San Diego, California 92121
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22
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Stumpfe D, Sisay M, Frizler M, Vogt I, Gütschow M, Bajorath JÃ. Inhibitors of Cathepsins K and S Identified Using the DynaMAD Virtual Screening Algorithm. ChemMedChem 2010; 5:61-4. [DOI: 10.1002/cmdc.200900457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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23
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Ameriks MK, Cai H, Edwards JP, Gebauer D, Gleason E, Gu Y, Karlsson L, Nguyen S, Sun S, Thurmond RL, Zhu J. Pyrazole-based arylalkyne cathepsin S inhibitors. Part II: Optimization of cellular potency. Bioorg Med Chem Lett 2009; 19:6135-9. [DOI: 10.1016/j.bmcl.2009.09.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2009] [Revised: 09/02/2009] [Accepted: 09/04/2009] [Indexed: 11/29/2022]
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Caglic D, Kosec G, Bojic L, Reinheckel T, Turk V, Turk B. Murine and human cathepsin B exhibit similar properties: possible implications for drug discovery. Biol Chem 2009; 390:175-9. [PMID: 19040356 DOI: 10.1515/bc.2009.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Validation of drug targets and subsequent preclinical studies are usually carried out on animal disease models, with mouse being the most commonly used. However, results from mouse models cannot always be directly related to human disease. Major discrepancies between the properties of murine and human variants were observed during the evaluation of compounds targeting cathepsins S and K. It is important, therefore, to know whether similar differences exist between murine and human cathepsin B. Thus, both enzymes were expressed and biochemically characterized. The enzymes exhibited similar biochemical properties, indicating that cathepsin B transgenic mouse models could be useful for studying its role in human pathologies.
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Affiliation(s)
- Dejan Caglic
- Department of Biochemistry and Molecular and Structural Biology, Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia
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25
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Han X, Civiello RL, Mercer SE, Macor JE, Dubowchik GM. Syntheses of aza and fluorine-substituted 3-(piperidin-4-yl)-4,5-dihydro-1H-benzo[d][1,3]diazepin-2(3H)-ones. Tetrahedron Lett 2009. [DOI: 10.1016/j.tetlet.2008.11.012] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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26
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Markt P, McGoohan C, Walker B, Kirchmair J, Feldmann C, De Martino G, Spitzer G, Distinto S, Schuster D, Wolber G, Laggner C, Langer T. Discovery of novel cathepsin S inhibitors by pharmacophore-based virtual high-throughput screening. J Chem Inf Model 2008; 48:1693-705. [PMID: 18637674 DOI: 10.1021/ci800101j] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The cysteine protease cathepsin S (CatS) is involved in the pathogenesis of autoimmune disorders, atherosclerosis, and obesity. Therefore, it represents a promising pharmacological target for drug development. We generated ligand-based and structure-based pharmacophore models for noncovalent and covalent CatS inhibitors to perform virtual high-throughput screening of chemical databases in order to discover novel scaffolds for CatS inhibitors. An in vitro evaluation of the resulting 15 structures revealed seven CatS inhibitors with kinetic constants in the low micromolar range. These compounds can be subjected to further chemical modifications to obtain drugs for the treatment of autoimmune disorders and atherosclerosis.
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Affiliation(s)
- Patrick Markt
- Department of Pharmaceutical Chemistry, Institute of Pharmacy and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 52c, 6020 Innsbruck, Austria
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27
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Rearrangement of spiro-benzimidazolines: preparation of N-alkenyl- and N-alkyl-benzimidazol-2-ones. Tetrahedron 2007. [DOI: 10.1016/j.tet.2007.06.106] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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28
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Wei J, Pio BA, Cai H, Meduna SP, Sun S, Gu Y, Jiang W, Thurmond RL, Karlsson L, Edwards JP. Pyrazole-based cathepsin S inhibitors with improved cellular potency. Bioorg Med Chem Lett 2007; 17:5525-8. [PMID: 17822900 DOI: 10.1016/j.bmcl.2007.08.038] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2007] [Revised: 08/13/2007] [Accepted: 08/15/2007] [Indexed: 11/22/2022]
Abstract
High potency pyrazole-based noncovalent inhibitors of human cathepsin S (CatS) were developed by modification of the benzo-fused 5-membered ring heterocycles found in earlier series of CatS inhibitors. Although substitutions on this heterocyclic framework had a moderate impact on enzymatic potency, dramatic effects on cellular activity were observed. Optimization afforded indole- and benzothiophene-derived analogues that were high affinity CatS inhibitors (IC(50)=20-40 nM) with good cellular potency (IC(50)=30-340 nM).
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Affiliation(s)
- Jianmei Wei
- Johnson & Johnson Pharmaceutical Research & Development, L.L.C., 3210 Merryfield Row, San Diego, CA 92121, USA
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29
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Wheeler RC, Benali O, Deal M, Farrant E, MacDonald SJF, Warrington BH. Mesoscale Flow Chemistry: A Plug-Flow Approach to Reaction Optimisation. Org Process Res Dev 2007. [DOI: 10.1021/op7000707] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rob C. Wheeler
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NI, United Kingdom
| | - Otman Benali
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NI, United Kingdom
| | - Martyn Deal
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NI, United Kingdom
| | - Elizabeth Farrant
- GlaxoSmithKline, Gunnels Wood Road, Stevenage SG1 2NI, United Kingdom
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30
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Le GT, Abbenante G, Madala PK, Hoang HN, Fairlie DP. Organic Azide Inhibitors of Cysteine Proteases. J Am Chem Soc 2006; 128:12396-7. [PMID: 16984172 DOI: 10.1021/ja0637649] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cysteine proteases are crucial regulatory enzymes in human physiology and disease. Inhibitors are usually designed with reactive electrophiles to covalently bond to the catalytic cysteinyl sulfur, and consequently they also indiscriminately interact with biological thiolates and other nucleophiles, leading to toxic side effects in vivo. Here we describe an alternative to using reactive electrophiles, demonstrating the use of a much less reactive azidomethylene substituent (-CH2-N3) that confers potent inhibition of cysteine proteases. This new approach resulted in potent, reversible, competitive inhibitors of caspase-1 (IC50 < 10 nM), with significant advantages over aldehydes such as high stability in vitro to thiols (10 mM dithiothreitol (pH 7.2), 20 mM glutathione (pH 7.2, 9, 11)) and aqueous media, as well as some highly desirable druglike features. It was also demonstrated that azides can be incorporated into inhibitors of other caspases (e.g. 3, 8) and cathepsins (e.g. K, S, B), indicating the versatility of this valuable new approach to cysteine protease inhibition.
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Affiliation(s)
- Giang Thanh Le
- Centre for Drug Design and Development, Institute for Molecular Bioscience, University of Queensland, Brisbane, Qld 4072, Australia
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31
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Black WC, Percival MD. The Consequences of Lysosomotropism on the Design of Selective Cathepsin K Inhibitors. Chembiochem 2006; 7:1525-35. [PMID: 16921579 DOI: 10.1002/cbic.200600149] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Many drug candidates contain a basic functional group that results in lysosomotropism--the accumulation of drug in the acidic lysosomes of a cell. When evaluating inhibitors of lysosomal enzymes, such as the cathepsins, this physical property can have a dramatic impact on the functional selectivity of the test compounds. A basic P3 substituent in cathepsin K inhibitors provides a means of achieving potent and selective enzyme inhibition. To evaluate the whole-cell selectivity of the basic cathepsin K inhibitor L-006235, we identified the irreversible pan-selective cathepsin probe BIL-DMK and used it to design whole-cell enzyme-occupancy assays. These cell-based assays showed a dramatic reduction in selectivity against cathepsins B, L, and S relative to the selectivities observed in enzyme assays. Two-photon confocal fluorescence microscopy showed punctated subcellular localization of L-006235, which colocalized with BODIPY-labelled Lysotracker, consistent with compound lysosomotropism. To address this potential problem, a series of potent cathepsin K inhibitors was developed by replacing the P2--P3 amide bond with a metabolically stable trifluoroethylamine moiety. X-ray crystallography has identified the binding of this functional group to active-site residues in cathepsin K. This modification resulted in increased potency and selectivity that allowed the removal of the basic P3 substituent. The resulting nonbasic inhibitor L-873724 is a 0.2 nM inhibitor of cathepsin K with cathepsin B, L, and S potencies that were not shifted between purified enzyme and whole-cell assays; thus indicating that this compound is not lysosomotropic. L-873724 exhibits excellent pharmacokinetics and is orally active in a monkey model of osteoporosis at 3 mg kg(-1) q.d.
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Affiliation(s)
- W Cameron Black
- Department of Medicinal Chemistry, Merck Frosst Centre for Therapeutic Research, Pointe-Claire-Dorval, Québec, Canada.
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32
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Grice CA, Tays K, Khatuya H, Gustin DJ, Butler CR, Wei J, Sehon CA, Sun S, Gu Y, Jiang W, Thurmond RL, Karlsson L, Edwards JP. The SAR of 4-substituted (6,6-bicyclic) piperidine cathepsin S inhibitors. Bioorg Med Chem Lett 2006; 16:2209-12. [PMID: 16458510 DOI: 10.1016/j.bmcl.2006.01.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2005] [Revised: 01/09/2006] [Accepted: 01/10/2006] [Indexed: 11/19/2022]
Abstract
A series of competitive, reversible cathepsin S (CatS) inhibitors was investigated. An earlier disclosure detailed the discovery of the 4-(2-keto-1-benzimidazolinyl)-piperidin-1-yl moiety as an effective replacement for the 4-arylpiperazin-1-yl group found in our screening hit. Continued investigation into replacements for the 4-aryl piperazine resulted in the identification of potentially useful CatS inhibitors with enzymatic and cellular activity similar to that of JNJ 10329670 as disclosed in a previous publication.
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Affiliation(s)
- Cheryl A Grice
- Johnson and Johnson Pharmaceutical Research and Development, L.L.C., 3210 Merryfield Row, San Diego, CA 92121, USA.
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