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Ku T, Cao J, Won SJ, Guo J, Camacho-Hernandez GA, Okorom AV, Salomon KW, Lee KH, Loland CJ, Duff HJ, Shi L, Newman AH. Series of (([1,1'-Biphenyl]-2-yl)methyl)sulfinylalkyl Alicyclic Amines as Novel and High Affinity Atypical Dopamine Transporter Inhibitors with Reduced hERG Activity. ACS Pharmacol Transl Sci 2024; 7:515-532. [PMID: 38357284 PMCID: PMC10863442 DOI: 10.1021/acsptsci.3c00322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 02/16/2024]
Abstract
Currently, there are no FDA-approved medications for the treatment of psychostimulant use disorders (PSUD). We have previously discovered "atypical" dopamine transporter (DAT) inhibitors that do not display psychostimulant-like behaviors and may be useful as medications to treat PSUD. Lead candidates (e.g., JJC8-091, 1) have shown promising in vivo profiles in rodents; however, reducing hERG (human ether-à-go-go-related gene) activity, a predictor of cardiotoxicity, has remained a challenge. Herein, a series of 30 (([1,1'-biphenyl]-2-yl)methyl)sulfinylalkyl alicyclic amines was synthesized and evaluated for DAT and serotonin transporter (SERT) binding affinities. A subset of analogues was tested for hERG activity, and the IC50 values were compared to those predicted by our hERG QSAR models, which showed robust predictive power. Multiparameter optimization scores (MPO > 3) indicated central nervous system (CNS) penetrability. Finally, comparison of affinities in human DAT and its Y156F and Y335A mutants suggested that several compounds prefer an inward facing conformation indicating an atypical DAT inhibitor profile.
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Affiliation(s)
- Therese
C. Ku
- Molecular
Targets and Medications Discovery Branch, National Institute on Drug
Abuse–Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Jianjing Cao
- Molecular
Targets and Medications Discovery Branch, National Institute on Drug
Abuse–Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Sung Joon Won
- Molecular
Targets and Medications Discovery Branch, National Institute on Drug
Abuse–Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Jiqing Guo
- Faculty
of Medicine, Libin Institute, Calgary T2N 4N1, Canada
| | - Gisela A. Camacho-Hernandez
- Molecular
Targets and Medications Discovery Branch, National Institute on Drug
Abuse–Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Amarachi V. Okorom
- Molecular
Targets and Medications Discovery Branch, National Institute on Drug
Abuse–Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Kristine Walloe Salomon
- Laboratory
for Membrane Protein Dynamics, Department of Neuroscience, Faculty
of Health and Medical Sciences, University
of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Kuo Hao Lee
- Molecular
Targets and Medications Discovery Branch, National Institute on Drug
Abuse–Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Claus J. Loland
- Laboratory
for Membrane Protein Dynamics, Department of Neuroscience, Faculty
of Health and Medical Sciences, University
of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Henry J. Duff
- Laboratory
for Membrane Protein Dynamics, Department of Neuroscience, Faculty
of Health and Medical Sciences, University
of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen, Denmark
| | - Lei Shi
- Molecular
Targets and Medications Discovery Branch, National Institute on Drug
Abuse–Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
| | - Amy Hauck Newman
- Molecular
Targets and Medications Discovery Branch, National Institute on Drug
Abuse–Intramural Research Program, National Institutes of Health, 333 Cassell Drive, Baltimore, Maryland 21224, United States
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El Harchi A, Brincourt O. Pharmacological activation of the hERG K + channel for the management of the long QT syndrome: A review. J Arrhythm 2022; 38:554-569. [PMID: 35936037 PMCID: PMC9347208 DOI: 10.1002/joa3.12741] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/28/2022] [Accepted: 05/16/2022] [Indexed: 11/10/2022] Open
Abstract
In the human heart, the rapid delayed rectifier K+ current (I Kr) contributes significantly to ventricular action potential (AP) repolarization and to set the duration of the QT interval of the surface electrocardiogram (ECG). The pore-forming (α) subunit of the I Kr channel is encoded by KCNH2 or human ether-à-go-go-related gene 1 (hERG1). Impairment of hERG function through either gene mutation (congenital) or pharmacological blockade by diverse drugs in clinical use (acquired) can cause a prolongation of the AP duration (APD) reflected onto the surface ECG as a prolonged QT interval or Long QT Syndrome (LQTS). LQTS can increase the risk of triggered activity of ventricular cardiomyocytes and associated life-threatening arrhythmia. Current treatments all focus on reducing the incidence of arrhythmia or terminating it after its onset but there is to date no prophylactic treatment for the pharmacological management of LQTS. A new class of hERG modulators (agonists) have been suggested through direct interaction with the hERG channel to shorten the action potential duration (APD) and/or increase the postrepolarisation refractoriness period (PRRP) of ventricular cardiomyocytes protecting thereby against triggered activity and associated arrhythmia. Although promising drug candidates, there remain major obstacles to their clinical development. The aim of this review is to summarize the latest advances as well as the limitations of this proposed pharmacotherapy.
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Affiliation(s)
- Aziza El Harchi
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences BuildingUniversity of Bristol, University WalkBristolUK
| | - Oriane Brincourt
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences BuildingUniversity of Bristol, University WalkBristolUK
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Zangerl-Plessl EM, Berger M, Drescher M, Chen Y, Wu W, Maulide N, Sanguinetti M, Stary-Weinzinger A. Toward a Structural View of hERG Activation by the Small-Molecule Activator ICA-105574. J Chem Inf Model 2020; 60:360-371. [PMID: 31877041 DOI: 10.1021/acs.jcim.9b00737] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Outward current conducted by human ether-à-go-go-related gene type 1 (hERG1) K+ channels is important for action potential repolarization in the human ventricle. Rapid, voltage-dependent inactivation greatly reduces outward currents conducted by hERG1 channels and involves conformational changes in the ion selectivity filter (SF). Recently, compounds have been found that activate hERG1 channel function by modulating gating mechanisms such as reducing inactivation. Such activating compounds could represent a novel approach to prevent arrhythmias associated with prolonged ventricular repolarization associated with inherited or acquired long QT syndrome. ICA-105574 (ICA), a 3-nitro-n-(4-phenoxyphenyl) benzamide derivative activates hERG1 by strongly attenuating pore-type inactivation. We previously mapped the putative binding site for ICA to a hydrophobic pocket located between two adjacent subunits. Here, we used the recently reported cryoelectron microscopy structures of hERG1 to elucidate the structural mechanisms by which ICA influences the stability of the SF. By combining molecular dynamics simulations, voltage-clamp electrophysiology, and the synthesis of novel ICA derivatives, we provide atomistic insights into SF dynamics and propose a structural link between the SF and S6 segments. Further, our study highlights the importance of the nitro moiety, at the meta position of the benzamide ring, for the activity of ICA and reveals that the (bio)isosteric substitution of this side chain can switch the activity to weak inhibitors. Our findings indicate that ICA increases the stability of the SF to attenuate channel inactivation, and this action requires a fine-tuned compound geometry.
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Affiliation(s)
- Eva-Maria Zangerl-Plessl
- Department of Pharmacology and Toxicology , University of Vienna , Althanstrasse 14 , Wien , Vienna 1090 , Austria
| | - Martin Berger
- Institute of Organic Chemistry , University of Vienna , Währinger Strasse 38 , Wien , Vienna 1090 , Austria
| | - Martina Drescher
- Institute of Organic Chemistry , University of Vienna , Währinger Strasse 38 , Wien , Vienna 1090 , Austria
| | - Yong Chen
- Institute of Organic Chemistry , University of Vienna , Währinger Strasse 38 , Wien , Vienna 1090 , Austria
| | - Wei Wu
- Nora Eccles Harrison Cardiovascular Research and Training Institute and Division of Cardiovascular Medicine, Department of Internal Medicine , University of Utah , Salt Lake City , Utah 84132-340 , United States
| | - Nuno Maulide
- Institute of Organic Chemistry , University of Vienna , Währinger Strasse 38 , Wien , Vienna 1090 , Austria
| | - Michael Sanguinetti
- Nora Eccles Harrison Cardiovascular Research and Training Institute and Division of Cardiovascular Medicine, Department of Internal Medicine , University of Utah , Salt Lake City , Utah 84132-340 , United States
| | - Anna Stary-Weinzinger
- Department of Pharmacology and Toxicology , University of Vienna , Althanstrasse 14 , Wien , Vienna 1090 , Austria
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Kudaibergenova M, Perissinotti LL, Noskov SY. Lipid roles in hERG function and interactions with drugs. Neurosci Lett 2019; 700:70-77. [DOI: 10.1016/j.neulet.2018.05.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/08/2018] [Accepted: 05/11/2018] [Indexed: 01/29/2023]
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Perissinotti LL, De Biase PM, Guo J, Yang PC, Lee MC, Clancy CE, Duff HJ, Noskov SY. Determinants of Isoform-Specific Gating Kinetics of hERG1 Channel: Combined Experimental and Simulation Study. Front Physiol 2018; 9:207. [PMID: 29706893 PMCID: PMC5907531 DOI: 10.3389/fphys.2018.00207] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/23/2018] [Indexed: 12/22/2022] Open
Abstract
IKr is the rapidly activating component of the delayed rectifier potassium current, the ion current largely responsible for the repolarization of the cardiac action potential. Inherited forms of long QT syndrome (LQTS) (Lees-Miller et al., 1997) in humans are linked to functional modifications in the Kv11.1 (hERG) ion channel and potentially life threatening arrhythmias. There is little doubt now that hERG-related component of IKr in the heart depends on the tetrameric (homo- or hetero-) channels formed by two alternatively processed isoforms of hERG, termed hERG1a and hERG1b. Isoform composition (hERG1a- vs. the b-isoform) has recently been reported to alter pharmacologic responses to some hERG blockers and was proposed to be an essential factor pre-disposing patients for drug-induced QT prolongation. Very little is known about the gating and pharmacological properties of two isoforms in heart membranes. For example, how gating mechanisms of the hERG1a channels differ from that of hERG1b is still unknown. The mechanisms by which hERG 1a/1b hetero-tetramers contribute to function in the heart, or what role hERG1b might play in disease are all questions to be answered. Structurally, the two isoforms differ only in the N-terminal region located in the cytoplasm: hERG1b is 340 residues shorter than hERG1a and the initial 36 residues of hERG1b are unique to this isoform. In this study, we combined electrophysiological measurements for HEK cells, kinetics and structural modeling to tease out the individual contributions of each isoform to Action Potential formation and then make predictions about the effects of having various mixture ratios of the two isoforms. By coupling electrophysiological data with computational kinetic modeling, two proposed mechanisms of hERG gating in two homo-tetramers were examined. Sets of data from various experimental stimulation protocols (HEK cells) were analyzed simultaneously and fitted to Markov-chain models (M-models). The minimization procedure presented here, allowed assessment of suitability of different Markov model topologies and the corresponding parameters that describe the channel kinetics. The kinetics modeling pointed to key differences in the gating kinetics that were linked to the full channel structure. Interactions between soluble domains and the transmembrane part of the channel appeared to be critical determinants of the gating kinetics. The structures of the full channel in the open and closed states were compared for the first time using the recent Cryo-EM resolved structure for full open hERG channel and an homology model for the closed state, based on the highly homolog EAG1 channel. Key potential interactions which emphasize the importance of electrostatic interactions between N-PAS cap, S4-S5, and C-linker are suggested based on the structural analysis. The derived kinetic parameters were later used in higher order models of cells and tissue to track down the effect of varying the ratios of hERG1a and hERG1b on cardiac action potentials and computed electrocardiograms. Simulations suggest that the recovery from inactivation of hERG1b may contribute to its physiologic role of this isoform in the action potential. Finally, the results presented here contribute to the growing body of evidence that hERG1b significantly affects the generation of the cardiac Ikr and plays an important role in cardiac electrophysiology. We highlight the importance of carefully revisiting the Markov models previously proposed in order to properly account for the relative abundance of the hERG1 a- and b- isoforms.
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Affiliation(s)
- Laura L Perissinotti
- Centre for Molecular Simulations, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Pablo M De Biase
- Centre for Molecular Simulations, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Jiqing Guo
- Libin Cardiovascular Institute of Alberta, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
| | - Pei-Chi Yang
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Miranda C Lee
- Centre for Molecular Simulations, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
| | - Colleen E Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Henry J Duff
- Libin Cardiovascular Institute of Alberta, Faculty of Medicine, University of Calgary, Calgary, AB, Canada
| | - Sergei Y Noskov
- Centre for Molecular Simulations, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, AB, Canada
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Durdagi S, Aksoydan B, Erol I, Kantarcioglu I, Ergun Y, Bulut G, Acar M, Avsar T, Liapakis G, Karageorgos V, Salmas RE, Sergi B, Alkhatib S, Turan G, Yigit BN, Cantasir K, Kurt B, Kilic T. Integration of multi-scale molecular modeling approaches with experiments for the in silico guided design and discovery of novel hERG-Neutral antihypertensive oxazalone and imidazolone derivatives and analysis of their potential restrictive effects on cell proliferation. Eur J Med Chem 2017; 145:273-290. [PMID: 29329002 DOI: 10.1016/j.ejmech.2017.12.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 12/05/2017] [Accepted: 12/06/2017] [Indexed: 12/13/2022]
Abstract
AT1 antagonists is the most recent drug class of molecules against hypertension and they mediate their actions through blocking detrimental effects of angiotensin II (A-II) when acts on type I (AT1) A-II receptor. The effects of AT1 antagonists are not limited to cardiovascular diseases. AT1 receptor blockers may be used as potential anti-cancer agents - due to the inhibition of cell proliferation stimulated by A-II. Therefore, AT1 receptors and the A-II biosynthesis mechanisms are targets for the development of new synthetic drugs and therapeutic treatment of various cardiovascular and other diseases. In this work, multi-scale molecular modeling approaches were performed and it is found that oxazolone and imidazolone derivatives reveal similar/better interaction energy profiles compared to the FDA approved sartan molecules at the binding site of the AT1 receptor. In silico-guided designed hit molecules were then synthesized and tested for their binding affinities to human AT1 receptor in radioligand binding studies, using [125I-Sar1-Ile8] AngII. Among the compounds tested, 19d and 9j molecules bound to receptor in a dose response manner and with relatively high affinities. Next, cytotoxicity and wound healing assays were performed for these hit molecules. Since hit molecule 19d led to deceleration of cell motility in all three cell lines (NIH3T3, A549, and H358) tested in this study, this molecule is investigated in further tests. In two cell lines (HUVEC and MCF-7) tested, 19d induced G2/M cell cycle arrest in a concentration dependent manner. Adherent cells detached from the plates and underwent cell death possibly due to apoptosis at 19d concentrations that induced cell cycle arrest.
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Affiliation(s)
- Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey.
| | - Busecan Aksoydan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey
| | - Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | - Isik Kantarcioglu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Bioengineering Program, Graduate School of Natural and Applied Sciences, Bahcesehir University, Istanbul, Turkey
| | - Yavuz Ergun
- Department of Chemistry, Dokuz Eylul University, Izmir, Turkey
| | - Gulay Bulut
- Department of Molecular Biology and Genetics, Bahcesehir University, Istanbul, Turkey
| | - Melih Acar
- Department of Medical Biology, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Timucin Avsar
- Department of Medical Biology, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey
| | - George Liapakis
- Department of Pharmacology, Faculty of Medicine, University of Crete, Greece
| | - Vlasios Karageorgos
- Department of Pharmacology, Faculty of Medicine, University of Crete, Greece
| | - Ramin E Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Barış Sergi
- Department of Molecular Biology and Genetics, Bahcesehir University, Istanbul, Turkey
| | - Sara Alkhatib
- Bioengineering Program, Graduate School of Natural and Applied Sciences, Bahcesehir University, Istanbul, Turkey
| | - Gizem Turan
- Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey
| | - Berfu Nur Yigit
- Neuroscience Program, Graduate School of Health Sciences, Bahcesehir University, Istanbul, Turkey
| | - Kutay Cantasir
- School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Bahar Kurt
- School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Turker Kilic
- Department of Neurosurgery, School of Medicine, Bahcesehir University, Istanbul, Turkey
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Aksoydan B, Kantarcioglu I, Erol I, Salmas RE, Durdagi S. Structure-based design of hERG-neutral antihypertensive oxazalone and imidazolone derivatives. J Mol Graph Model 2017; 79:103-117. [PMID: 29156380 DOI: 10.1016/j.jmgm.2017.10.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Angiotensin II receptor type 1 (AT1) antagonists are the most recent drug class against hypertension. Recently first crystal structure of AT1 receptor is deposited to the protein data bank (PDB ID: 4YAY). In this work, several molecular screening methods such as molecular docking and de novo design studies were performed and it is found that oxazolone and imidazolone derivatives reveal similar/better interaction energy profiles compared to the FDA approved sartan molecules at the binding site of the AT1 receptor. A database consisting of 3500-fragments were used to enumerate de novo designed imidazolone and oxazolone derivatives and hereby more than 50000 novel small molecules were generated. These derivatives were then used in high throughput virtual screening simulations (Glide/HTVS) to find potent hit molecules. In addition, virtual screening of around 18 million small drug-like compounds from ZINC database were screened at the binding pocket of the AT1 receptor via Glide/HTVS method. Filtered structures were then used in more sophisticated molecular docking simulations protocols (i.e., Glide/SP; Glide/XP; Glide/IFD; Glide/QPLD, and GOLD). However, the K+ ion channel/drug interactions should also be considered in studies implemented in molecular level against their cardiovascular risks. Thus, selected compounds with high docking scores via all diverse docking algorithms are also screened at the pore domain regions of human ether-a-go-go-related gene (hERG1) K+ channel to remove the high affinity hERG1 blocking compounds. High docking scored compounds at the AT1 with low hERG1 affinity is considered for long molecular dynamics (MD) simulations. Post-processing analysis of MD simulations assisted for better understanding of molecular mechanism of studied compounds at the binding cavity of AT1 receptor. Results of this study can be useful for designing of novel and safe AT1 inhibitors.
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Affiliation(s)
- Busecan Aksoydan
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Isik Kantarcioglu
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey; Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey
| | - Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University (BAU), Istanbul, Turkey.
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Kayık G, Tüzün NŞ, Durdagi S. Structural investigation of vesnarinone at the pore domains of open and open-inactivated states of hERG1 K + channel. J Mol Graph Model 2017; 77:399-412. [DOI: 10.1016/j.jmgm.2017.08.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/22/2022]
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9
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Publisher's note. J Mol Graph Model 2017; 77:240-249. [DOI: 10.1016/j.jmgm.2017.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2017] [Revised: 08/02/2017] [Accepted: 08/03/2017] [Indexed: 11/17/2022]
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Huo J, Guo X, Lu Q, Qiang H, Liu P, Bai L, Huang CLH, Zhang Y, Ma A. NS1643 enhances ionic currents in a G604S-WT hERG co-expression system associated with long QT syndrome 2. Clin Exp Pharmacol Physiol 2017; 44:1125-1133. [PMID: 28741726 DOI: 10.1111/1440-1681.12820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 06/27/2017] [Accepted: 07/17/2017] [Indexed: 12/19/2022]
Affiliation(s)
- JianHua Huo
- Department of Cardiovascular Medicine; First Affiliated Hospital of Xi'an Jiaotong University; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University); Ministry of Education; Xi'an Shaanxi China
| | - Xueyan Guo
- Shaanxi Provincial People's Hospital; Xi'an Shaanxi China
| | - Qun Lu
- Department of Cardiovascular Medicine; First Affiliated Hospital of Xi'an Jiaotong University; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University); Ministry of Education; Xi'an Shaanxi China
| | - Hua Qiang
- Department of Cardiovascular Medicine; First Affiliated Hospital of Xi'an Jiaotong University; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University); Ministry of Education; Xi'an Shaanxi China
| | - Ping Liu
- Department of Cardiovascular Medicine; First Affiliated Hospital of Xi'an Jiaotong University; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University); Ministry of Education; Xi'an Shaanxi China
| | - Ling Bai
- Department of Cardiovascular Medicine; First Affiliated Hospital of Xi'an Jiaotong University; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University); Ministry of Education; Xi'an Shaanxi China
| | | | - Yanmin Zhang
- Department of Pediatric Cardiology; Childrens Research Institute; affiliate children's hospital of Xi'an Jiaotong University; Xi'an Shaanxi China
| | - Aiqun Ma
- Department of Cardiovascular Medicine; First Affiliated Hospital of Xi'an Jiaotong University; Key Laboratory of Environment and Genes Related to Diseases (Xi'an Jiaotong University); Ministry of Education; Xi'an Shaanxi China
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11
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Durdagi S, Erol I, Salmas RE, Patterson M, Noskov SY. First universal pharmacophore model for hERG1 K + channel activators: acthER. J Mol Graph Model 2017; 74:153-170. [PMID: 28499268 DOI: 10.1016/j.jmgm.2017.03.020] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 03/28/2017] [Accepted: 03/29/2017] [Indexed: 01/31/2023]
Abstract
The intra-cavitary drug blockade of hERG1 channel has been extensively studied, both experimentally and theoretically. Structurally diverse ligands inadvertently block the hERG1 K+ channel currents lead to drug induced Long QT Syndrome (LQTS). Accordingly, designing either hERG1 channel openers or current activators, with the potential to target other binding pockets of the channel, has been introduced as a viable approach in modern anti-arrhythmia drug development. However, reports and investigations on the molecular mechanisms underlying activators binding to the hERG1 channel remain sparse and the overall molecular design principles are largely unknown. Most of the hERG1 activators were discovered during mandatory screening for hERG1 blockade. To fill this apparent deficit, the first universal pharmacophore model for hERG1 K+ channel activators was developed using PHASE. 3D structures of 18 hERG1 K+ channel activators and their corresponding measured binding affinity values were used in the development of pharmacophore models. These compounds spanned a range of structurally different chemotypes with moderate variation in binding affinity. A five sites AAHRR (A, hydrogen-bond accepting, H, hydrophobic, R, aromatic) pharmacophore model has shown reasonable high statistical results compared to the other developed more than 1000 hypotheses. This model was used to construct steric and electrostatic contour maps. The predictive power of the model was tested with 3 external test set compounds as true unknowns. Finally, the pharmacophore model was combined with the previously developed receptor-based model of hERG1 K+ channel to develop and screen novel activators. The results are quite striking and it suggests a greater future role for pharmacophore modeling and virtual drug screening simulations in deciphering complex patterns of molecular mechanisms of hERG1 channel openers at the target sites. The developed model is available upon request and it may serve as basis for the synthesis of novel therapeutic hERG1 activators.
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Affiliation(s)
- Serdar Durdagi
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey.
| | - Ismail Erol
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey; Department of Chemistry, Gebze Technical University, Kocaeli, Turkey
| | - Ramin Ekhteiari Salmas
- Computational Biology and Molecular Simulations Laboratory, Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Matthew Patterson
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Sergei Y Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
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12
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Kayık G, Tüzün NŞ, Durdagi S. Investigation of PDE5/PDE6 and PDE5/PDE11 selective potent tadalafil-like PDE5 inhibitors using combination of molecular modeling approaches, molecular fingerprint-based virtual screening protocols and structure-based pharmacophore development. J Enzyme Inhib Med Chem 2017; 32:311-330. [PMID: 28150511 PMCID: PMC6009860 DOI: 10.1080/14756366.2016.1250756] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
The essential biological function of phosphodiesterase (PDE) type enzymes is to regulate the cytoplasmic levels of intracellular second messengers, 3′,5′-cyclic guanosine monophosphate (cGMP) and/or 3′,5′-cyclic adenosine monophosphate (cAMP). PDE targets have 11 isoenzymes. Of these enzymes, PDE5 has attracted a special attention over the years after its recognition as being the target enzyme in treating erectile dysfunction. Due to the amino acid sequence and the secondary structural similarity of PDE6 and PDE11 with the catalytic domain of PDE5, first-generation PDE5 inhibitors (i.e. sildenafil and vardenafil) are also competitive inhibitors of PDE6 and PDE11. Since the major challenge of designing novel PDE5 inhibitors is to decrease their cross-reactivity with PDE6 and PDE11, in this study, we attempt to identify potent tadalafil-like PDE5 inhibitors that have PDE5/PDE6 and PDE5/PDE11 selectivity. For this aim, the similarity-based virtual screening protocol is applied for the “clean drug-like subset of ZINC database” that contains more than 20 million small compounds. Moreover, molecular dynamics (MD) simulations of selected hits complexed with PDE5 and off-targets were performed in order to get insights for structural and dynamical behaviors of the selected molecules as selective PDE5 inhibitors. Since tadalafil blocks hERG1 K channels in concentration dependent manner, the cardiotoxicity prediction of the hit molecules was also tested. Results of this study can be useful for designing of novel, safe and selective PDE5 inhibitors.
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Affiliation(s)
- Gülru Kayık
- a Department of Chemistry , Istanbul Technical University , Istanbul , Turkey.,b Department of Pharmacy , University of Pisa , Pisa , Italy
| | - Nurcan Ş Tüzün
- a Department of Chemistry , Istanbul Technical University , Istanbul , Turkey
| | - Serdar Durdagi
- c Department of Biophysics , School of Medicine, Bahcesehir University , Istanbul , Turkey
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13
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Guo J, Cheng YM, Lees-Miller JP, Perissinotti LL, Claydon TW, Hull CM, Thouta S, Roach DE, Durdagi S, Noskov SY, Duff HJ. NS1643 interacts around L529 of hERG to alter voltage sensor movement on the path to activation. Biophys J 2016; 108:1400-1413. [PMID: 25809253 DOI: 10.1016/j.bpj.2014.12.055] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Revised: 11/25/2014] [Accepted: 12/08/2014] [Indexed: 12/17/2022] Open
Abstract
Activators of hERG1 such as NS1643 are being developed for congenital/acquired long QT syndrome. Previous studies identify the neighborhood of L529 around the voltage-sensor as a putative interacting site for NS1643. With NS1643, the V1/2 of activation of L529I (-34 ± 4 mV) is similar to wild-type (WT) (-37 ± 3 mV; P > 0.05). WT and L529I showed no difference in the slope factor in the absence of NS1643 (8 ± 0 vs. 9 ± 0) but showed a difference in the presence of NS1643 (9 ± 0.3 vs. 22 ± 1; P < 0.01). Voltage-clamp-fluorimetry studies also indicated that in L529I, NS1643 reduces the voltage-sensitivity of S4 movement. To further assess mechanism of NS1643 action, mutations were made in this neighborhood. NS1643 shifts the V1/2 of activation of both K525C and K525C/L529I to hyperpolarized potentials (-131 ± 4 mV for K525C and -120 ± 21 mV for K525C/L529I). Both K525C and K525C/K529I had similar slope factors in the absence of NS1643 (18 ± 2 vs. 34 ± 5, respectively) but with NS1643, the slope factor of K525C/L529I increased from 34 ± 5 to 71 ± 10 (P < 0.01) whereas for K525C the slope factor did not change (18 ± 2 at baseline and 16 ± 2 for NS1643). At baseline, K525R had a slope factor similar to WT (9 vs. 8) but in the presence of NS1643, the slope factor of K525R was increased to 24 ± 4 vs. 9 ± 0 mV for WT (P < 0.01). Molecular modeling indicates that L529I induces a kink in the S4 voltage-sensor helix, altering a salt-bridge involving K525. Moreover, docking studies indicate that NS1643 binds to the kinked structure induced by the mutation with a higher affinity. Combining biophysical, computational, and electrophysiological evidence, a mechanistic principle governing the action of some activators of hERG1 channels is proposed.
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Affiliation(s)
- Jiqing Guo
- Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada
| | - Yen May Cheng
- Department of Biomedical Physiology and Kinesiology, Molecular Cardiac Physiology Group, Simon Fraser University, Burnaby, British Columbia, Canada
| | - James P Lees-Miller
- Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada
| | - Laura L Perissinotti
- Centre for Molecular Simulations, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Tom W Claydon
- Department of Biomedical Physiology and Kinesiology, Molecular Cardiac Physiology Group, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Christina M Hull
- Department of Biomedical Physiology and Kinesiology, Molecular Cardiac Physiology Group, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Samrat Thouta
- Department of Biomedical Physiology and Kinesiology, Molecular Cardiac Physiology Group, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Daniel E Roach
- Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada
| | - Serdar Durdagi
- Centre for Molecular Simulations, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | - Sergei Y Noskov
- Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada; Centre for Molecular Simulations, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada.
| | - Henry J Duff
- Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada.
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14
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Şahin A, Şentürk M, Salmas RE, Durdagi S, Ayan A, Karagölge A, Mestanoğlu M. Investigation of inhibition of human glucose 6-phosphate dehydrogenase by some 99mTc chelators by in silico and in vitro methods. J Enzyme Inhib Med Chem 2016; 31:141-147. [PMID: 27143114 DOI: 10.1080/14756366.2016.1178735] [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] [Indexed: 10/21/2022] Open
Abstract
The inhibitory effects of methoxyisobutylisonitrile (MIBI), diethylene triamine pentaacetic acid (DTPA), dimercaptosuccinic acid (DMSA) and metilendifosfonat (MDP) on human erythrocyte glucose 6-phosphate dehydrogenase (hG6PD) activity were investigated. For this purpose, hG6PD was initially purified 557-fold at a yield of 51.43% using 2',5'-adenosine diphosphate (ADP) sepharose 4B affinity gel chromatography. The in vitro effects of these chelators on hG6PD enzyme were studied. IC50 values of MIBI, DTPA, DMSA and MDP were 0.056, 0.172, 0.274 and 0.175 mM, of hG6PD, respectively. It was detected in in vitro studies that the hG6PD enzyme is inhibited due to these radiopharmaceutical chelators. In addition to in vitro studies, in order to better understand the molecular mechanism of studied compounds, combined in silico approaches, including molecular docking and molecular dynamics (MD), simulations were successfully performed. MD simulations shed light on inhibition mechanisms of the individual inhibitors into the ligand-binding pocket of hG6PD. Essential amino acids for binding are also investigated using per-residue interaction analysis studies.
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Affiliation(s)
- Ali Şahin
- a Faculty of Medicine , Department of Nuclear Medicine, Ataturk University , Erzurum , Turkey
| | - Murat Şentürk
- b Science and Arts Faculty, Department of Chemistry, Agri Ibrahim Cecen University , Agri , Turkey
| | - Ramin E Salmas
- c School of Medicine, Department of Biophysics, Bahcesehir University , Istanbul , Turkey , and
| | - Serdar Durdagi
- c School of Medicine, Department of Biophysics, Bahcesehir University , Istanbul , Turkey , and
| | - Arif Ayan
- a Faculty of Medicine , Department of Nuclear Medicine, Ataturk University , Erzurum , Turkey
| | - Ali Karagölge
- a Faculty of Medicine , Department of Nuclear Medicine, Ataturk University , Erzurum , Turkey
| | - Mert Mestanoğlu
- d School of Medicine, Bahcesehir University , Istanbul , Turkey
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15
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Yu Z, van Veldhoven JPD, 't Hart IME, Kopf AH, Heitman LH, IJzerman AP. Synthesis and biological evaluation of negative allosteric modulators of the Kv11.1(hERG) channel. Eur J Med Chem 2015; 106:50-9. [PMID: 26519929 DOI: 10.1016/j.ejmech.2015.10.032] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 10/14/2015] [Accepted: 10/16/2015] [Indexed: 01/13/2023]
Abstract
We synthesized and evaluated a series of compounds for their allosteric modulation at the Kv11.1 (hERG) channel. Most compounds were negative allosteric modulators of [(3)H]dofetilide binding to the channel, in particular 7f, 7h-j and 7p. Compounds 7f and 7p were the most potent negative allosteric modulators amongst all ligands, significantly increasing the dissociation rate of dofetilide in the radioligand kinetic binding assay, while remarkably reducing the affinities of dofetilide and astemizole in a competitive displacement assay. Additionally, both 7f and 7p displayed peculiar displacement characteristics with Hill coefficients significantly distinct from unity as shown by e.g., dofetilide, further indicative of their allosteric effects on dofetilide binding. Our findings in this investigation yielded several promising negative allosteric modulators for future functional and clinical research with respect to their antiarrhythmic propensities, either alone or in combination with known Kv11.1 blockers.
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Affiliation(s)
- Zhiyi Yu
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Jacobus P D van Veldhoven
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Ingrid M E 't Hart
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Adrian H Kopf
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Laura H Heitman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands
| | - Adriaan P IJzerman
- Division of Medicinal Chemistry, Leiden Academic Centre for Drug Research, Leiden University, 2300 RA Leiden, The Netherlands.
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16
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Alsop JD, Mitchell JC. Interolog interfaces in protein-protein docking. Proteins 2015; 83:1940-6. [PMID: 25740680 PMCID: PMC5054918 DOI: 10.1002/prot.24788] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 02/17/2015] [Accepted: 02/24/2015] [Indexed: 12/26/2022]
Abstract
Proteins are essential elements of biological systems, and their function typically relies on their ability to successfully bind to specific partners. Recently, an emphasis of study into protein interactions has been on hot spots, or residues in the binding interface that make a significant contribution to the binding energetics. In this study, we investigate how conservation of hot spots can be used to guide docking prediction. We show that the use of evolutionary data combined with hot spot prediction highlights near‐native structures across a range of benchmark examples. Our approach explores various strategies for using hot spots and evolutionary data to score protein complexes, using both absolute and chemical definitions of conservation along with refinements to these strategies that look at windowed conservation and filtering to ensure a minimum number of hot spots in each binding partner. Finally, structure‐based models of orthologs were generated for comparison with sequence‐based scoring. Using two data sets of 22 and 85 examples, a high rate of top 10 and top 1 predictions are observed, with up to 82% of examples returning a top 10 hit and 35% returning top 1 hit depending on the data set and strategy applied; upon inclusion of the native structure among the decoys, up to 55% of examples yielded a top 1 hit. The 20 common examples between data sets show that more carefully curated interolog data yields better predictions, particularly in achieving top 1 hits. Proteins 2015; 83:1940–1946. © 2015 The Authors. Proteins: Structure, Function, and Bioinformatics Published by Wiley Periodicals, Inc.
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Affiliation(s)
- James D Alsop
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin
| | - Julie C Mitchell
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin.,Department of Mathematics, University of Wisconsin, Madison, Wisconsin
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17
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Salmas RE, Unlu A, Yurtsever M, Noskov SY, Durdagi S. In silicoinvestigation of PARP-1 catalytic domains inholoandapostates for the design of high-affinity PARP-1 inhibitors. J Enzyme Inhib Med Chem 2015; 31:112-20. [DOI: 10.3109/14756366.2015.1005011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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18
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Perissinotti LL, Guo J, De Biase PM, Clancy CE, Duff HJ, Noskov SY. Kinetic model for NS1643 drug activation of WT and L529I variants of Kv11.1 (hERG1) potassium channel. Biophys J 2015; 108:1414-1424. [PMID: 25809254 PMCID: PMC4375712 DOI: 10.1016/j.bpj.2014.12.056] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2014] [Revised: 11/24/2014] [Accepted: 12/08/2014] [Indexed: 11/28/2022] Open
Abstract
Congenital and acquired (drug-induced) forms of the human long-QT syndrome are associated with alterations in Kv11.1 (hERG) channel-controlled repolarizing IKr currents of cardiac action potentials. A mandatory drug screen implemented by many countries led to a discovery of a large group of small molecules that can activate hERG currents and thus may act as potent antiarrhythmic agents. Despite significant progress in identification of channel activators, little is known about their mechanism of action. A combination of electrophysiological studies with molecular and kinetic modeling was used to examine the mechanism of a model activator (NS1643) action on the hERG channel and its L529I mutant. The L529I mutant has gating dynamics similar to that of wild-type while its response to application of NS1643 is markedly different. We propose a mechanism compatible with experiments in which the model activator binds to the closed (C3) and open states (O). We suggest that NS1643 is affecting early gating transitions, probably during movements of the voltage sensor that precede the opening of the activation gate.
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Affiliation(s)
- Laura L Perissinotti
- Centre for Molecular Modeling, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Jiqing Guo
- Libin Cardiovascular Institute of Alberta, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Pablo M De Biase
- Centre for Molecular Modeling, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada
| | - Colleen E Clancy
- Department of Pharmacology, University of California at Davis, Davis, California.
| | - Henry J Duff
- Libin Cardiovascular Institute of Alberta, Faculty of Medicine, University of Calgary, Calgary, Alberta, Canada.
| | - Sergei Y Noskov
- Centre for Molecular Modeling, Department of Biological Sciences, Faculty of Science, University of Calgary, Calgary, Alberta, Canada.
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19
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Rasmusson RL, Anumonwo JM. Activation of HERG channels: opening new applications for the biophysics of antiarrhythmic therapy. Biophys J 2015; 108:1309-1311. [PMID: 25809242 DOI: 10.1016/j.bpj.2015.01.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2015] [Revised: 01/14/2015] [Accepted: 01/16/2015] [Indexed: 11/26/2022] Open
Affiliation(s)
- Randall L Rasmusson
- Department of Physiology and Biophysics, State University of New York, University at Buffalo, Buffalo, New York
| | - Justus M Anumonwo
- Department of Internal Medicine-Cardiovascular Medicine, University of Michigan Medical School, Ann Arbor, Michigan; Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, Michigan.
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20
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Proline scan of the HERG channel S6 helix reveals the location of the intracellular pore gate. Biophys J 2014; 106:1057-69. [PMID: 24606930 DOI: 10.1016/j.bpj.2014.01.035] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2013] [Revised: 01/14/2014] [Accepted: 01/23/2014] [Indexed: 11/23/2022] Open
Abstract
In Shaker-like channels, the activation gate is formed at the bundle crossing by the convergence of the inner S6 helices near a conserved proline-valine-proline motif, which introduces a kink that allows for electromechanical coupling with voltage sensor motions via the S4-S5 linker. Human ether-a-go-go-related gene (hERG) channels lack the proline-valine-proline motif and the location of the intracellular pore gate and how it is coupled to S4 movement is less clear. Here, we show that proline substitutions within the S6 of hERG perturbed pore gate closure, trapping channels in the open state. Performing a proline scan of the inner S6 helix, from Ile(655) to Tyr(667) revealed that gate perturbation occurred with proximal (I655P-Q664P), but not distal (R665P-Y667P) substitutions, suggesting that Gln(664) marks the position of the intracellular gate in hERG channels. Using voltage-clamp fluorimetry and gating current analysis, we demonstrate that proline substitutions trap the activation gate open by disrupting the coupling between the voltage-sensing unit and the pore of the channel. We characterize voltage sensor movement in one such trapped-open mutant channel and demonstrate the kinetics of what we interpret to be intrinsic hERG voltage sensor movement.
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21
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Li P, Chen X, Zhang Q, Zheng Y, Jiang H, Yang H, Gao Z. The human ether-a-go-go-related gene activator NS1643 enhances epilepsy-associated KCNQ channels. J Pharmacol Exp Ther 2014; 351:596-604. [PMID: 25232191 DOI: 10.1124/jpet.114.217703] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Human ether-a-go-go-related gene (hERG) and KCNQ channels are two classes of voltage-gated potassium channels. Specific mutations have been identified that are causal for type II long QT (LQT2) syndrome, neonatal epilepsy, and benign familial neonatal convulsions. Increasing evidence from clinical studies suggests that LQT2 and epilepsy coexist in some patients. Therefore, an integral approach to investigating and treating the two diseases is likely more effective. In the current study, we found that NS1643 [1,3-bis-(2-hydroxy-5-trifluoromethyl-phenyl)-urea], a previously reported hERG activator, is also an activator of KCNQ channels. It potentiates the neuronal KCNQ2, KCNQ4, and KCNQ2/Q3 channels, but not the cardiac KCNQ1. The effects of NS1643 on the KCNQ2 channel include left shifting of voltage for reaching 50% of the maximum conductance and slowing of deactivation. Analysis of the dose-response curve of NS1643 revealed an EC50 value of 2.44 ± 0.25 μM. A hydrophobic phenylalanine (F137) located at the middle region of the voltage-sensing domain was identified as critical for NS1643 activity on KCNQ2. When testing NS1643 effects in rescuing LQT2 hERG mutants and the KCNQ2 BFNC mutants, we found it is particularly efficacious in some cases. Considering the substantial relationship between LQT2 and epilepsy, these findings reveal that NS1643 is a useful compound to elucidate the causal connection of LQT2 and epilepsy. More generally, this may provide a strategy in the development of therapeutics for LQT2 and epilepsy.
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Affiliation(s)
- Ping Li
- CAS Key Laboratory of Receptor Research (P.L., X.C., Y.Z., Z.G.), and State Key Laboratory of Drug Research (Q.Z., H.J., H.Y.), Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Xueqin Chen
- CAS Key Laboratory of Receptor Research (P.L., X.C., Y.Z., Z.G.), and State Key Laboratory of Drug Research (Q.Z., H.J., H.Y.), Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Qiansen Zhang
- CAS Key Laboratory of Receptor Research (P.L., X.C., Y.Z., Z.G.), and State Key Laboratory of Drug Research (Q.Z., H.J., H.Y.), Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Yueming Zheng
- CAS Key Laboratory of Receptor Research (P.L., X.C., Y.Z., Z.G.), and State Key Laboratory of Drug Research (Q.Z., H.J., H.Y.), Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Hualiang Jiang
- CAS Key Laboratory of Receptor Research (P.L., X.C., Y.Z., Z.G.), and State Key Laboratory of Drug Research (Q.Z., H.J., H.Y.), Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Huaiyu Yang
- CAS Key Laboratory of Receptor Research (P.L., X.C., Y.Z., Z.G.), and State Key Laboratory of Drug Research (Q.Z., H.J., H.Y.), Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
| | - Zhaobing Gao
- CAS Key Laboratory of Receptor Research (P.L., X.C., Y.Z., Z.G.), and State Key Laboratory of Drug Research (Q.Z., H.J., H.Y.), Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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22
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Guo J, Durdagi S, Changalov M, Perissinotti LL, Hargreaves JM, Back TG, Noskov SY, Duff HJ. Structure driven design of novel human ether-a-go-go-related-gene channel (hERG1) activators. PLoS One 2014; 9:e105553. [PMID: 25191697 PMCID: PMC4156305 DOI: 10.1371/journal.pone.0105553] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/22/2014] [Indexed: 01/01/2023] Open
Abstract
One of the main culprits in modern drug discovery is apparent cardiotoxicity of many lead-candidates via inadvertent pharmacologic blockade of K+, Ca2+ and Na+ currents. Many drugs inadvertently block hERG1 leading to an acquired form of the Long QT syndrome and potentially lethal polymorphic ventricular tachycardia. An emerging strategy is to rely on interventions with a drug that may proactively activate hERG1 channels reducing cardiovascular risks. Small molecules-activators have a great potential for co-therapies where the risk of hERG-related QT prolongation is significant and rehabilitation of the drug is impractical. Although a number of hERG1 activators have been identified in the last decade, their binding sites, functional moieties responsible for channel activation and thus mechanism of action, have yet to be established. Here, we present a proof-of-principle study that combines de-novo drug design, molecular modeling, chemical synthesis with whole cell electrophysiology and Action Potential (AP) recordings in fetal mouse ventricular myocytes to establish basic chemical principles required for efficient activator of hERG1 channel. In order to minimize the likelihood that these molecules would also block the hERG1 channel they were computationally engineered to minimize interactions with known intra-cavitary drug binding sites. The combination of experimental and theoretical studies led to identification of functional elements (functional groups, flexibility) underlying efficiency of hERG1 activators targeting binding pocket located in the S4–S5 linker, as well as identified potential side-effects in this promising line of drugs, which was associated with multi-channel targeting of the developed drugs.
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Affiliation(s)
- Jiqing Guo
- Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada
| | - Serdar Durdagi
- Centre for Molecular Simulation, Biochemistry Research Cluster, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Mohamed Changalov
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
| | - Laura L. Perissinotti
- Centre for Molecular Simulation, Biochemistry Research Cluster, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | | | - Thomas G. Back
- Department of Chemistry, University of Calgary, Calgary, Alberta, Canada
- * E-mail: (TGB); (SYN); (HJD)
| | - Sergei Y. Noskov
- Centre for Molecular Simulation, Biochemistry Research Cluster, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
- * E-mail: (TGB); (SYN); (HJD)
| | - Henry J. Duff
- Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada
- * E-mail: (TGB); (SYN); (HJD)
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23
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Buturak B, Durdagi S, Noskov SY, Ildeniz ATO. Designing of multi-targeted molecules using combination of molecular screening and in silico drug cardiotoxicity prediction approaches. J Mol Graph Model 2014; 50:16-34. [PMID: 24699019 DOI: 10.1016/j.jmgm.2014.02.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2013] [Revised: 02/03/2014] [Accepted: 02/11/2014] [Indexed: 01/25/2023]
Abstract
We have previously investigated and reported a set of phenol- and indole-based derivatives at the binding pockets of carbonic anhydrase isoenzymes using in silico and in vitro analyses. In this study, we extended our analysis to explore multi-targeted molecules from this set of compounds. Thus, 26 ligands are screened at the binding sites of 229 proteins from 5 main enzyme family classes using molecular docking algorithms. Derived docking scores are compared with reported results of ligands at carbonic anhydrase I and II isoenzymes. Results showed potency of multi-targeted drugs of a few compounds from investigated ligand set. These promising ligands are then tested in silico for their cardiotoxicity risks. Results of this work can be used to improve the desired effects of these compounds by molecular engineering studies. In addition these results may lead to further investigation of studied molecules by medicinal chemists to explore different therapeutic aims.
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Affiliation(s)
- Birce Buturak
- Computational Biology and Bioinformatics, Graduate School of Science and Engineering, Kadir Has University, Istanbul, Turkey
| | - Serdar Durdagi
- Department of Biophysics, School of Medicine, Bahcesehir University, Istanbul, Turkey
| | - Sergei Y Noskov
- Institute for Biocomplexity and Informatics, University of Calgary, Calgary, AB, Canada.
| | - A Tugba Ozal Ildeniz
- Computational Biology and Bioinformatics, Graduate School of Science and Engineering, Kadir Has University, Istanbul, Turkey; Department of Bioinformatics and Genetics, Kadir Has University, Istanbul, Turkey.
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24
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Moorthy NSHN, Ramos MJ, Fernandes PA. Predictive QSAR models development and validation for human ether-a-go-go related gene (hERG) blockers using newer tools. J Enzyme Inhib Med Chem 2013; 29:317-24. [DOI: 10.3109/14756366.2013.779264] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
| | - Maria J. Ramos
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto
PortoPortugal
| | - Pedro A. Fernandes
- REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto
PortoPortugal
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Bilet A, Bauer CK. Effects of the small molecule HERG activator NS1643 on Kv11.3 channels. PLoS One 2012; 7:e50886. [PMID: 23226420 PMCID: PMC3511382 DOI: 10.1371/journal.pone.0050886] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2012] [Accepted: 10/26/2012] [Indexed: 01/15/2023] Open
Abstract
NS1643 is one of the small molecule HERG (Kv11.1) channel activators and has also been found to increase erg2 (Kv11.2) currents. We now investigated whether NS1643 is also able to act as an activator of Kv11.3 (erg3) channels expressed in CHO cells. Activation of rat Kv11.3 current occurred in a dose-dependent manner and maximal current increasing effects were obtained with 10 µM NS1643. At this concentration, steady-state outward current increased by about 80% and the current increase was associated with a significant shift in the voltage dependence of activation to more negative potentials by about 15 mV. In addition, activation kinetics were accelerated, whereas deactivation was slowed. There was no significant effect on the kinetics of inactivation and recovery from inactivation. The strong current-activating agonistic effect of NS1643 did not result from a shift in the voltage dependence of Kv11.3 channel inactivation and was independent from external Na+ or Ca2+. At the higher concentration of 20 µM, NS1643 induced clearly less current increase. The left shift in the voltage dependence of activation reversed and the voltage sensitivity of activation dramatically decreased along with a slowing of Kv11.3 channel activation. These data show that, in comparison to other Kv11 family members, NS1643 exerts distinct effects on Kv11.3 channels with especially pronounced partial antagonistic effects at higher concentration.
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Affiliation(s)
- Arne Bilet
- Institute of Cellular and Integrative Physiology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
| | - Christiane K. Bauer
- Institute of Cellular and Integrative Physiology, University Medical Center Hamburg-Eppendorf (UKE), Hamburg, Germany
- * E-mail:
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