1
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Uenishi S, Kakigi R, Hideshima K, Miyawaki A, Matsuoka J, Ogata T, Tomioka K, Yamamoto Y. Asymmetric total synthesis of (−)-javaberine A and (−)-epi-javaberine A based on catalytic intramolecular hydroamination of N-methyl-2-(2-styrylaryl)ethylamine. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132165] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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2
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Zhou XQ, Carbo-Bague I, Siegler MA, Hilgendorf J, Basu U, Ott I, Liu R, Zhang L, Ramu V, IJzerman AP, Bonnet S. Rollover Cyclometalation vs Nitrogen Coordination in Tetrapyridyl Anticancer Gold(III) Complexes: Effect on Protein Interaction and Toxicity. JACS AU 2021; 1:380-395. [PMID: 34056633 PMCID: PMC8154207 DOI: 10.1021/jacsau.0c00104] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Indexed: 05/05/2023]
Abstract
In this work, a pair of gold(III) complexes derived from the analogous tetrapyridyl ligands H2biqbpy1 and H2biqbpy2 was prepared: the rollover, bis-cyclometalated [Au(biqbpy1)Cl ([1]Cl) and its isomer [Au(biqbpy2)Cl ([2]Cl). In [1]+, two pyridyl rings coordinate to the metal via a Au-C bond (C∧N∧N∧C coordination) and the two noncoordinated amine bridges of the ligand remain protonated, while in [2]+ all four pyridyl rings of the ligand coordinate to the metal via a Au-N bond (N∧N∧N∧N coordination), but both amine bridges are deprotonated. As a result, both complexes are monocationic, which allowed comparison of the sole effect of cyclometalation on the chemistry, protein interaction, and anticancer properties of the gold(III) compounds. Due to their identical monocationic charge and similar molecular shape, both complexes [1]Cl and [2]Cl displaced reference radioligand [3H]dofetilide equally well from cell membranes expressing the Kv11.1 (hERG) potassium channel, and more so than the tetrapyridyl ligands H2biqbpy1 and H2biqbpy2. By contrast, cyclometalation rendered [1]Cl coordinatively stable in the presence of biological thiols, while [2]Cl was reduced by a millimolar concentration of glutathione into metastable Au(I) species releasing the free ligand H2biqbpy2 and TrxR-inhibiting Au+ ions. The redox stability of [1]Cl dramatically decreased its thioredoxin reductase (TrxR) inhibition properties, compared to [2]Cl. On the other hand, unlike [2]Cl, [1]Cl aggregated into nanoparticles in FCS-containing medium, which resulted in much more efficient gold cellular uptake. [1]Cl had much more selective anticancer properties than [2]Cl and cisplatin, as it was almost 10 times more cytotoxic to human cancer cells (A549, A431, A375, and MCF7) than to noncancerous cells (MRC5). Mechanistic studies highlight the strikingly different mode of action of the two compounds: while for [1]Cl high gold cellular uptake, nuclear DNA damage, and interaction with hERG may contribute to cell killing, for [2]Cl extracellular reduction released TrxR-inhibiting Au+ ions that were taken up in minute amounts in the cytosol, and a toxic tetrapyridyl ligand also capable of binding to hERG. These results demonstrate that bis-cyclometalation is an appealing method to improve the redox stability of Au(III) compounds and to develop gold-based cytotoxic compounds that do not rely on TrxR inhibition to kill cancer cells.
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Affiliation(s)
- Xue-Quan Zhou
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Imma Carbo-Bague
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
- Department
of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Maxime A. Siegler
- Department
of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Jonathan Hilgendorf
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Uttara Basu
- Institute
of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstrasse 55, 38106 Braunschweig, Germany
| | - Ingo Ott
- Institute
of Medicinal and Pharmaceutical Chemistry, Technische Universität Braunschweig, Beethovenstrasse 55, 38106 Braunschweig, Germany
| | - Rongfang Liu
- Division
of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Liyan Zhang
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Vadde Ramu
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
| | - Adriaan P. IJzerman
- Division
of Drug Discovery & Safety, Leiden Academic Centre for Drug Research, Leiden University, 2333 CC Leiden, The Netherlands
| | - Sylvestre Bonnet
- Leiden
Institute of Chemistry, Leiden University, Einsteinweg 55, 2333 CC Leiden, The Netherlands
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3
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Yamamoto Y, Kirii M, Matsuoka J, Miyawaki A, Tomioka K. Stereoselective Synthesis of Diastereomeric Berberine Alkaloids, O-Methylcorytenchirine and Coralydine. HETEROCYCLES 2021. [DOI: 10.3987/com-20-s(k)49] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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4
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Liu Z, Jiang T, Wang B, Ke B, Zhou Y, Du L, Li M. Environment-Sensitive Fluorescent Probe for the Human Ether-a-go-go-Related Gene Potassium Channel. Anal Chem 2016; 88:1511-5. [PMID: 26730746 PMCID: PMC4741275 DOI: 10.1021/acs.analchem.5b04220] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
![]()
A novel
environment-sensitive probe S2 with turn-on switch for
Human Ether-a-go-go-Related Gene (hERG) potassium channel was developed
herein. After careful evaluation, this fluorescent probe showed high
binding affinity with hERG potassium channel with an IC50 value of 41.65 nM and can be well applied to hERG channel imaging
or cellular distribution study for hERG channel blockers. Compared
with other imaging techniques, such as immunofluorescence and fluorescent
protein-based approaches, this method is convenient and affordable,
especially since a washing procedure is not needed. Meanwhile, this
environment-sensitive turn-on design strategy may provide a good example
for the probe development for these targets that have no reactive
or catalytic activity.
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Affiliation(s)
- Zhenzhen Liu
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Shandong University , Jinan, Shandong 250012, China
| | - Tianyu Jiang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Shandong University , Jinan, Shandong 250012, China
| | - Beilei Wang
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Shandong University , Jinan, Shandong 250012, China
| | - Bowen Ke
- Laboratory of Anaesthesiology and Critical Care Medicine, West China Hospital, Sichuan University , Chengdu, Sichuan 610041, China
| | - Yubin Zhou
- Institute of Biosciences and Technology, Texas A&M University Health Science Center , Houston, Texas 77030, United States
| | - Lupei Du
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Shandong University , Jinan, Shandong 250012, China
| | - Minyong Li
- Department of Medicinal Chemistry, Key Laboratory of Chemical Biology (MOE), School of Pharmacy, Shandong University , Jinan, Shandong 250012, China
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5
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Tseng TS, Lee YC, Hsiao NW, Liu YR, Tsai KC. Comparative study between 3D-QSAR and Docking-Based Pharmacophore models for potent Plasomodium falciparum dihydroorotate dehydrogenase inhibitors. Bioorg Med Chem Lett 2016; 26:265-271. [DOI: 10.1016/j.bmcl.2015.12.043] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 11/03/2015] [Accepted: 12/12/2015] [Indexed: 12/17/2022]
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6
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Abstract
The voltage-gated potassium channel encoded by hERG carries a delayed rectifying potassium current (IKr) underlying repolarization of the cardiac action potential. Pharmacological blockade of the hERG channel results in slowed repolarization and therefore prolongation of action potential duration and an increase in the QT interval as measured on an electrocardiogram. Those are possible to cause sudden death, leading to the withdrawals of many drugs, which is the reason for hERG screening. Computational in silico prediction models provide a rapid, economic way to screen compounds during early drug discovery. In this review, hERG prediction models are classified as 2D and 3D quantitative structure–activity relationship models, pharmacophore models, classification models, and structure based models (using homology models of hERG).
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7
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Du F, Babcock JJ, Yu H, Zou B, Li M. Global analysis reveals families of chemical motifs enriched for HERG inhibitors. PLoS One 2015; 10:e0118324. [PMID: 25700001 PMCID: PMC4336329 DOI: 10.1371/journal.pone.0118324] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2014] [Accepted: 12/01/2014] [Indexed: 11/18/2022] Open
Abstract
Promiscuous inhibition of the human ether-à-go-go-related gene (hERG) potassium channel by drugs poses a major risk for life threatening arrhythmia and costly drug withdrawals. Current knowledge of this phenomenon is derived from a limited number of known drugs and tool compounds. However, in a diverse, naïve chemical library, it remains unclear which and to what degree chemical motifs or scaffolds might be enriched for hERG inhibition. Here we report electrophysiology measurements of hERG inhibition and computational analyses of >300,000 diverse small molecules. We identify chemical ‘communities’ with high hERG liability, containing both canonical scaffolds and structurally distinctive molecules. These data enable the development of more effective classifiers to computationally assess hERG risk. The resultant predictive models now accurately classify naïve compound libraries for tendency of hERG inhibition. Together these results provide a more complete reference map of characteristic chemical motifs for hERG liability and advance a systematic approach to rank chemical collections for cardiotoxicity risk.
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Affiliation(s)
- Fang Du
- The Solomon H. Snyder Department of Neuroscience, High Throughput Biology Center and Johns Hopkins Ion Channel Center (JHICC), Johns Hopkins University, 733 North Broadway, Baltimore, MD 21205, United States of America
| | - Joseph J. Babcock
- The Solomon H. Snyder Department of Neuroscience, High Throughput Biology Center and Johns Hopkins Ion Channel Center (JHICC), Johns Hopkins University, 733 North Broadway, Baltimore, MD 21205, United States of America
| | - Haibo Yu
- The Solomon H. Snyder Department of Neuroscience, High Throughput Biology Center and Johns Hopkins Ion Channel Center (JHICC), Johns Hopkins University, 733 North Broadway, Baltimore, MD 21205, United States of America
| | - Beiyan Zou
- The Solomon H. Snyder Department of Neuroscience, High Throughput Biology Center and Johns Hopkins Ion Channel Center (JHICC), Johns Hopkins University, 733 North Broadway, Baltimore, MD 21205, United States of America
| | - Min Li
- The Solomon H. Snyder Department of Neuroscience, High Throughput Biology Center and Johns Hopkins Ion Channel Center (JHICC), Johns Hopkins University, 733 North Broadway, Baltimore, MD 21205, United States of America
- * E-mail:
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8
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Wang R, Liu Z, Du L, Li M. Design, synthesis and biological evaluation of 4-chromanone derivatives as IKr inhibitors. Drug Discov Ther 2014; 8:76-83. [DOI: 10.5582/ddt.8.76] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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9
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Carvalho JFS, Louvel J, Doornbos MLJ, Klaasse E, Yu Z, Brussee J, IJzerman AP. Strategies to reduce HERG K+ channel blockade. Exploring heteroaromaticity and rigidity in novel pyridine analogues of dofetilide. J Med Chem 2013; 56:2828-40. [PMID: 23473309 DOI: 10.1021/jm301564f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Drug-induced blockade of the human ether-a-go-go-related gene K(+) channel (hERG) represents one of the major antitarget concerns in pharmaceutical industry. SAR studies of this ion channel have shed light on the structural requirements for hERG interaction but most importantly may reveal drug design principles to reduce hERG affinity. In the present study, a novel library of neutral and positively charged heteroaromatic derivatives of the class III antiarrhythmic agent dofetilide was synthesized and assessed for hERG affinity in radioligand binding and manual patch clamp assays. Structural modifications of the pyridine moiety, side chain, and peripheral aromatic moieties were evaluated, thereby revealing approaches for reducing hERG binding affinity. In particular, we found that the extra rigidity imposed close to the positively charged pyridine moiety can be very efficient in decreasing hERG affinity.
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Affiliation(s)
- João F S Carvalho
- Leiden Academic Center for Drug Research, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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10
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Moorthy NSHN, Ramos MJ, Fernandes PA. Analysis of van der Waals surface area properties for human ether-a-go-go-related gene blocking activity: computational study on structurally diverse compounds. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2012; 23:521-536. [PMID: 22452318 DOI: 10.1080/1062936x.2012.666264] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In the present investigation, a computational analysis was performed on a data set comprised of human ether-a-go-go-related gene (hERG) blockers (triethanolamine, 1,3-thiazol-2-yl and tetrasubstituted imidazoline derivatives) in order to investigate the structural features required to reduce the hERG-induced cardiotoxicity problems in an early stage of drug discovery. The results derived from the quantitative structure-activity relationship (QSAR) analysis showed that the volume, surface area and shape descriptors (vsurf_) contributed significantly in all the models. This reveals that the hydrogen-bonding and hydrophilicity properties (vsurf_HB1, vsurf_CW4 and a_acc) on the van der Waals (vdW) surface of the molecule is negatively contributed for the hERG blocking activity and the hydrophobic property (vsurf_D6) and the total polar volume (vsurf_Wp2) on the vdW surface of the molecule are favourable for the activity. Further, the pharmacophore analysis also shows that the Aro/Hyd/Acc contour is one of the important biophore sites for the hERG blocking activity. This suggests that the presence of aromatic, hydrophobic and hydrogen-bonding groups in the molecules is favourable for interaction. In comparison with our earlier works (explaining the role of topological and hydrophobicity properties for the hERG blocking activity), these studies provided additional information on the importance of vdW surface area properties for the hERG blocking activity. These results can be used with other molecular modelling studies for the design of novel molecules that are free of cardiotoxicity.
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Affiliation(s)
- N S H N Moorthy
- Requimte, Department of Chemistry and Biochemistry, Faculty of Sciences, University of Porto, Porto, Portugal.
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11
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Sakkiah S, Thangapandian S, Lee KW. Ligand-Based Virtual Screening and Molecular Docking Studies to Identify the Critical Chemical Features of Potent Cathepsin D Inhibitors. Chem Biol Drug Des 2012; 80:64-79. [DOI: 10.1111/j.1747-0285.2012.01339.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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12
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Moorthy NHN, Ramos MJ, Fernandes PA. hERG binding feature analysis of structurally diverse compounds by QSAR and fragmental analysis. RSC Adv 2011. [DOI: 10.1039/c1ra00131k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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13
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Ladduwahetty T, Gilligan M, Humphries A, Merchant KJ, Fish R, McAlister G, Ivarsson M, Dominguez M, O'Connor D, MacLeod AM. Non-basic ligands for aminergic GPCRs: the discovery and development diaryl sulfones as selective, orally bioavailable 5-HT2A receptor antagonists for the treatment of sleep disorders. Bioorg Med Chem Lett 2010; 20:3708-12. [PMID: 20493697 DOI: 10.1016/j.bmcl.2010.04.090] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2010] [Revised: 04/19/2010] [Accepted: 04/19/2010] [Indexed: 11/29/2022]
Abstract
Scaffold hopping from a non-basic series of 5-HT(2A) receptor antagonists developed in-house that possessed reduced activity in vivo enabled the discovery of a novel series of diaryl sulfones that gave excellent occupancy on oral dosing. Not only does this work further demonstrate that oral bioavailability of a given series can be enhanced by improving physicochemical parameters such as log P, but it corroborates the growing evidence that a protonated amine is not essential for affinity at aminergic GPCRs.
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14
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Harris RN, Stabler RS, Repke DB, Kress JM, Walker KA, Martin RS, Brothers JM, Ilnicka M, Lee SW, Mirzadegan T. Highly potent, non-basic 5-HT6 ligands. Site mutagenesis evidence for a second binding mode at 5-HT6 for antagonism. Bioorg Med Chem Lett 2010; 20:3436-40. [PMID: 20434910 DOI: 10.1016/j.bmcl.2010.03.110] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 03/26/2010] [Accepted: 03/26/2010] [Indexed: 11/29/2022]
Abstract
A series of 5-HT(6) ligands derived from (R)-1-(amino)methyl-6-(phenyl)sulfonyltetralin was prepared that yielded several non-basic analogs having sub-nanomolar affinity. Ligand structure-activity relationships, receptor point mutation studies, and molecular modeling of these novel ligands all combined to reveal a new alternative binding mode to 5-HT(6) for antagonism.
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Affiliation(s)
- Ralph N Harris
- Roche Palo Alto LLC, 3431 Hillview Ave., Palo Alto, CA 94304, USA
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15
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Roy K, Ghosh G. QSTR with extended topochemical atom (ETA) indices. 13. Modelling of hERG K+channel blocking activity of diverse functional drugs using different chemometric tools. MOLECULAR SIMULATION 2009. [DOI: 10.1080/08927020903015379] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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16
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Tsai KC, Teng LW, Shao YM, Chen YC, Lee YC, Li M, Hsiao NW. The first pharmacophore model for potent NF-κB inhibitors. Bioorg Med Chem Lett 2009; 19:5665-9. [DOI: 10.1016/j.bmcl.2009.08.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2009] [Revised: 08/04/2009] [Accepted: 08/05/2009] [Indexed: 11/28/2022]
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17
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Polak S, Wiśniowska B, Brandys J. Collation, assessment and analysis of literature in vitro data on hERG receptor blocking potency for subsequent modeling of drugs' cardiotoxic properties. J Appl Toxicol 2009; 29:183-206. [PMID: 18988205 DOI: 10.1002/jat.1395] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The assessment of the torsadogenic potency of a new chemical entity is a crucial issue during lead optimization and the drug development process. It is required by the regulatory agencies during the registration process. In recent years, there has been a considerable interest in developing in silico models, which allow prediction of drug-hERG channel interaction at the early stage of a drug development process. The main mechanism underlying an acquired QT syndrome and a potentially fatal arrhythmia called torsades de pointes is the inhibition of potassium channel encoded by hERG (the human ether-a-go-go-related gene). The concentration producing half-maximal block of the hERG potassium current (IC(50)) is a surrogate marker for proarrhythmic properties of compounds and is considered a test for cardiac safety of drugs or drug candidates. The IC(50) values, obtained from data collected during electrophysiological studies, are highly dependent on experimental conditions (i.e. model, temperature, voltage protocol). For the in silico models' quality and performance, the data quality and consistency is a crucial issue. Therefore the main objective of our work was to collect and assess the hERG IC(50) data available in accessible scientific literature to provide a high-quality data set for further studies.
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Affiliation(s)
- Sebastian Polak
- Toxicology Department, Faculty of Pharmacy, Medical Collage, Jagiellonian University, Poland.
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18
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Lee PJ, Bhonsle JB, Gaona HW, Huddler DP, Heady TN, Kreishman-Deitrick M, Bhattacharjee A, McCalmont WF, Gerena L, Lopez-Sanchez M, Roncal NE, Hudson TH, Johnson JD, Prigge ST, Waters NC. Targeting the fatty acid biosynthesis enzyme, beta-ketoacyl-acyl carrier protein synthase III (PfKASIII), in the identification of novel antimalarial agents. J Med Chem 2009; 52:952-63. [PMID: 19191586 DOI: 10.1021/jm8008103] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The importance of fatty acids to the human malaria parasite, Plasmodium falciparum, and differences due to a type I fatty acid synthesis (FAS) pathway in the parasite, make it an attractive drug target. In the present study, we developed and a utilized a pharmacophore to select compounds for testing against PfKASIII, the initiating enzyme of FAS. This effort identified several PfKASIII inhibitors that grouped into various chemical classes of sulfides, sulfonamides, and sulfonyls. Approximately 60% of the submicromolar inhibitors of PfKASIII inhibited in vitro growth of the malaria parasite. These compounds inhibited both drug sensitive and resistant parasites and testing against a mammalian cell line revealed an encouraging in vitro therapeutic index for the most active compounds. Docking studies into the active site of PfKASIII suggest a potential binding mode that exploits amino acid residues at the mouth of the substrate tunnel.
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Affiliation(s)
- Patricia J Lee
- Division of Experimental Therapeutics, Walter Reed Army Institute of Research, Silver Spring, Maryland 20910, USA
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19
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Chen CYC. Pharmacoinformatics approach for mPGES-1 in anti-inflammation by 3D-QSAR pharmacophore mapping. J Taiwan Inst Chem Eng 2009. [DOI: 10.1016/j.jtice.2008.07.010] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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20
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Molecular hybridization, synthesis, and biological evaluation of novel chroman IKr and IKs dual blockers. Bioorg Med Chem Lett 2009; 19:1477-80. [DOI: 10.1016/j.bmcl.2009.01.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2008] [Revised: 12/11/2008] [Accepted: 01/09/2009] [Indexed: 01/27/2023]
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21
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Yang Q, Du L, Tsai KC, Wang X, Li M, You Q. Pharmacophore Mapping for Kv1.5 Potassium Channel Blockers. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200810050] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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22
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WANG XJ, YANG Q, YIN DL, CHEN YD, YOU QD. A Pharmacophore Modeling Study of Drugs Inducing Cardiotoxic Side Effects. CHINESE J CHEM 2008. [DOI: 10.1002/cjoc.200890380] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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23
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Prediction of hERG Potassium Channel Blockade Using kNN-QSAR and Local Lazy Regression Methods. ACTA ACUST UNITED AC 2008. [DOI: 10.1002/qsar.200810072] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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24
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Yang Q, Du L, Wang X, Li M, You Q. Modeling the binding modes of Kv1.5 potassium channel and blockers. J Mol Graph Model 2008; 27:178-87. [DOI: 10.1016/j.jmgm.2008.04.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2008] [Accepted: 04/03/2008] [Indexed: 11/25/2022]
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25
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Abstract
hERG blockade is one of the major toxicological problems in lead structure optimization. Reliable ligand-based in silico models for predicting hERG blockade therefore have considerable potential for saving time and money, as patch-clamp measurements are very expensive and no crystal structures of the hERG-encoded channel are available. Herein we present a predictive QSAR model for hERG blockade that differentiates between specific and nonspecific binding. Specific binders are identified by preliminary pharmacophore scanning. In addition to descriptor-based models for the compounds selected as hitting one of two different pharmacophores, we also use a model for nonspecific binding that reproduces blocking properties of molecules that do not fit either of the two pharmacophores. PLS and SVR models based on interpretable quantum mechanically derived descriptors on a literature dataset of 113 molecules reach overall R(2) values between 0.60 and 0.70 for independent validation sets and R(2) values between 0.39 and 0.76 after partitioning according to the pharmacophore search for the test sets. Our findings suggest that hERG blockade may occur through different types of binding, so that several different models may be necessary to assess hERG toxicity.
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Affiliation(s)
- Christian Kramer
- Department of Lead Discovery, Boehringer-Ingelheim Pharma GmbH & Co. KG, 88397 Biberach, Germany
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26
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Shamovsky I, Connolly S, David L, Ivanova S, Nordén B, Springthorpe B, Urbahns K. Overcoming Undesirable hERG Potency of Chemokine Receptor Antagonists Using Baseline Lipophilicity Relationships. J Med Chem 2008; 51:1162-78. [DOI: 10.1021/jm070543k] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Igor Shamovsky
- Department of Medicinal Chemistry, AstraZeneca R&D Lund, S-22187 Lund, Sweden, and Department of Medicinal Chemistry, AstraZeneca R&D Charnwood, Loughborough, Leicestershire LE11 5RH, United Kingdom
| | - Stephen Connolly
- Department of Medicinal Chemistry, AstraZeneca R&D Lund, S-22187 Lund, Sweden, and Department of Medicinal Chemistry, AstraZeneca R&D Charnwood, Loughborough, Leicestershire LE11 5RH, United Kingdom
| | - Laurent David
- Department of Medicinal Chemistry, AstraZeneca R&D Lund, S-22187 Lund, Sweden, and Department of Medicinal Chemistry, AstraZeneca R&D Charnwood, Loughborough, Leicestershire LE11 5RH, United Kingdom
| | - Svetlana Ivanova
- Department of Medicinal Chemistry, AstraZeneca R&D Lund, S-22187 Lund, Sweden, and Department of Medicinal Chemistry, AstraZeneca R&D Charnwood, Loughborough, Leicestershire LE11 5RH, United Kingdom
| | - Bo Nordén
- Department of Medicinal Chemistry, AstraZeneca R&D Lund, S-22187 Lund, Sweden, and Department of Medicinal Chemistry, AstraZeneca R&D Charnwood, Loughborough, Leicestershire LE11 5RH, United Kingdom
| | - Brian Springthorpe
- Department of Medicinal Chemistry, AstraZeneca R&D Lund, S-22187 Lund, Sweden, and Department of Medicinal Chemistry, AstraZeneca R&D Charnwood, Loughborough, Leicestershire LE11 5RH, United Kingdom
| | - Klaus Urbahns
- Department of Medicinal Chemistry, AstraZeneca R&D Lund, S-22187 Lund, Sweden, and Department of Medicinal Chemistry, AstraZeneca R&D Charnwood, Loughborough, Leicestershire LE11 5RH, United Kingdom
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27
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Kawai M, Nakamura H, Sakurada I, Shimokawa H, Tanaka H, Matsumizu M, Ando K, Hattori K, Ohta A, Nukui S, Omura A, Kawamura M. Discovery of novel and orally active NR2B-selective N-methyl-D-aspartate (NMDA) antagonists, pyridinol derivatives with reduced HERG binding affinity. Bioorg Med Chem Lett 2007; 17:5533-6. [PMID: 17768047 DOI: 10.1016/j.bmcl.2007.08.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2007] [Revised: 07/30/2007] [Accepted: 08/02/2007] [Indexed: 10/22/2022]
Abstract
Novel NR2B antagonists with an amide tether were found by an approach to avoid pharmacophoric similarity to dofetilide. Structure-activity relationship investigation led to N-[cis-4-hydroxy-4-(5-hydroxypyridin-2-yl)cyclohexyl]-3-henylpropanamide as an orally active NR2B-subtype selective N-methyl-D-aspartate (NMDA) receptor antagonist with very weak HERG (human ether-a-go-go related gene) binding (IC(50)> 30 microM). This compound exhibited potent in vivo anti-allodynic activity in the mouse partial sciatic nerve ligation (PSL) model (minimum effective dose=10 mg/kg, po).
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Affiliation(s)
- Makoto Kawai
- Discovery Chemistry, Pfizer Global Research & Development, Nagoya Laboratories, 5-2 Taketoyo, Aichi 470-2393, Japan.
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28
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Exploring QSTR and toxicophore of hERG K+ channel blockers using GFA and HypoGen techniques. J Mol Graph Model 2007; 26:966-76. [PMID: 17928249 DOI: 10.1016/j.jmgm.2007.08.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2007] [Revised: 08/10/2007] [Accepted: 08/10/2007] [Indexed: 01/12/2023]
Abstract
Predictive quantitative structure-toxicity and toxicophore models were developed for a diverse series of hERG K+ channel blockers, acting as anti-arrhythmic agents using QSAR+ module in Cerius2 and HypoGen module in Catalyst software, respectively. The 2D-QSTR analysis has been performed on a dataset of 68 molecules carefully selected from literature for which IC50 values measured on hERG K+ channels expressed in mammalian cells lines using the voltage patch clamp assay technique were reported. Their biological data, expressed as IC50, spanned from 7.0nM to 1.4mM, with 7 orders difference. Several types of descriptors including electrotopological, thermodynamic, ADMET, graph theoretical (topological and information content) were used to derive a quantitative relationship between the channel blockers and its physico-chemical properties. Statistically significant QSTR model was obtained using genetic function approximation methodology, having seven descriptors, with a correlation coefficient (r2) of 0.837, cross-validated correlation coefficient (q2) of 0.776 and predictive correlation coefficient (r2 pred) of 0.701, indicating the robustness of the model. Toxicophore model generated using HypoGen module in Catalyst, on these datasets, showed three important features for hERG K+ channel blockers, (i) hydrophobic group (HP), (ii) ring aromatic group (RA) and (iii) hydrogen bond acceptor lipid group (HBAl). The most predictive hypothesis (Hypo 1), consisting of these three features had a best correlation coefficient of 0.820, a low rms deviation of 1.740, and a high cost difference of 113.50, which represents a true correlation and a good predictivity. The hypothesis, Hypo 1 was validated by a test set consisting of 12 molecules and by a cross-validation of 95% confidence level. Accordingly, our 2D-QSTR and toxicophore model has strong predictivity to identify structurally diverse hERG K+ channel blockers with desired biological activity. These models provide a useful framework for understanding binding, and gave structural insight into the specific protein-ligand interactions responsible for affinity, and how one might modify any given structure to mitigate binding.
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29
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Diller DJ, Hobbs DW. Understanding hERG inhibition with QSAR models based on a one-dimensional molecular representation. J Comput Aided Mol Des 2007; 21:379-93. [PMID: 17549583 DOI: 10.1007/s10822-007-9122-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2007] [Accepted: 04/29/2007] [Indexed: 10/23/2022]
Abstract
Blockage of the potassium channel encoded by the human ether-a-go-go related gene (hERG) is well understood to be the root cause of the cardio-toxicity of numerous approved and investigational drugs. As such, a cascade of in vitro and in vivo assays have been developed to filter compounds with hERG inhibitory activity. Quantitative structure activity relationship (QSAR) models are used at the very earliest part of this cascade to eliminate compounds that are likely to have this undesirable activity prior to synthesis. Here a new QSAR technique based on the one-dimensional representation is described in the context of the development of a model to predict hERG inhibition. The model is shown to perform close to the limits of the quality of the data used for model building. In order to make optimal use of the available data, a general robust mathematical scheme was developed and is described to simultaneously incorporate quantitative data, such as IC50 = 50 nM, and qualitative data, such as inactive or IC50 > 30 microM into QSAR models without discarding any experimental information.
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Affiliation(s)
- David J Diller
- Department of Molecular Modeling, Pharmacopeia Inc, CN5350, Princeton, NJ 08543-5350, USA.
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30
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Du L, Li M, You Q, Xia L. A novel structure-based virtual screening model for the hERG channel blockers. Biochem Biophys Res Commun 2007; 355:889-94. [PMID: 17331468 DOI: 10.1016/j.bbrc.2007.02.068] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2007] [Accepted: 02/09/2007] [Indexed: 11/15/2022]
Abstract
The hERG potassium channel is a key effector of cardiac repolarization and the blockade of this channel could cause arrhythmia. Thus, hERG channel blockade plays an important role for the potential pro-arrhythmic liability. In this report, binding of blockers to the hERG potassium channel is investigated using a combination of homology modeling, molecular docking, and molecular simulations, where blockade activities are evaluated using the linear regression model of GoldScore fitness. This structure-based virtual screening model is able to estimate the pIC(50) value of a wide range of ligands for the hERG potassium channel. The docked poses for ligands are also consistent with published mutation. Therefore, this model for the prediction of hERG channel blockade has the potential to provide cost-effective virtual screening tools for the evaluation of the cardiac liability of new chemical entities.
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Affiliation(s)
- Lupei Du
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
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31
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Gepp MM, Hutter MC. Determination of hERG channel blockers using a decision tree. Bioorg Med Chem 2006; 14:5325-32. [PMID: 16616507 DOI: 10.1016/j.bmc.2006.03.043] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2005] [Revised: 03/20/2006] [Accepted: 03/24/2006] [Indexed: 11/23/2022]
Abstract
A decision tree approach for the in silico prediction of Torsade de Pointes (TdP)-causing drugs is presented. As TdP is frequently associated with QT-interval prolongation due to inhibition of the rapid activating delayed rectifier potassium channel in the heart (hERG channel), the properties of such blockers were investigated by molecular modeling and semi-empirical AM1 molecular orbital calculations. In addition, we derived a pharmacophoric SMARTS string using structural information from high affinity compounds. A corresponding search in the PubChem database identified several compounds that exhibit QT-interval prolonging activity that were not among our data set. This SMARTS string furthermore showed to be the most significant descriptor in the decision tree approach from which guidelines for the design of safe compounds are suggested.
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Affiliation(s)
- Michael M Gepp
- Center for Bioinformatics, Saarland University, Building C7 1, P.O. Box 15 11 50, D-66041 Saarbruecken, Germany
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32
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Ladduwahetty T, Boase AL, Mitchinson A, Quin C, Patel S, Chapman K, MacLeod AM. A new class of selective, non-basic 5-HT2A receptor antagonists. Bioorg Med Chem Lett 2006; 16:3201-4. [PMID: 16632354 DOI: 10.1016/j.bmcl.2006.03.050] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2006] [Revised: 03/13/2006] [Accepted: 03/16/2006] [Indexed: 11/23/2022]
Abstract
Based on an existing series of 5-HT2A receptor ligands containing a basic nitrogen, we designed a non-basic lead that had reduced affinity for both the 5-HT2A receptor and the IKr potassium channel. The present paper describes the development of this lead to a novel series of non-basic piperidine sulfonamides and amides that have high affinity for the 5-HT2A receptor, whilst maintaining excellent selectivity over off target activities such as the IKr channel. This work has shown that the proposed pharmacophore model for the 5-HT2A receptor which suggests that a basic nitrogen is required for the binding of ligands is questionable.
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Affiliation(s)
- Tammy Ladduwahetty
- The Neuroscience Centre, Merck Sharp & Dohme, Eastwick Road, Harlow, Essex CM20 2QR, UK.
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33
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Li MY, Tsai KC, Xia L. Pharmacophore identification of α1A-adrenoceptor antagonists. Bioorg Med Chem Lett 2005; 15:657-64. [PMID: 15664832 DOI: 10.1016/j.bmcl.2004.11.032] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2004] [Revised: 11/11/2004] [Accepted: 11/15/2004] [Indexed: 11/19/2022]
Abstract
A chemical feature based pharmacophore model was developed for alpha(1A)-adrenoceptor antagonists by HypoGen module implemented in catalyst software package. The best scoring pharmacophore hypothesis, Hypo1, consisted of four important chemical features (one positive ion, one hydrogen-bond donor, one aromatic ring, and one hydrophobic group). The results of our study provide a valuable tool in designing new leads with desired biological activity by virtual screening.
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Affiliation(s)
- Min-Yong Li
- Department of Medicinal Chemistry, China Pharmaceutical University, Nanjing 210009, China
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