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Altunayar-Unsalan C, Unsalan O. Molecular Structure, Antioxidant Potential, and Pharmacokinetic Properties of Plant Flavonoid Blumeatin and Investigating Its Inhibition Mechanism on Xanthine Oxidase for Hyperuricemia by Molecular Modeling. ACS OMEGA 2024; 9:13284-13297. [PMID: 38524493 PMCID: PMC10956095 DOI: 10.1021/acsomega.3c10083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Revised: 02/22/2024] [Accepted: 02/27/2024] [Indexed: 03/26/2024]
Abstract
Hyperuricemia, which usually results in metabolic syndrome symptoms, is increasing rapidly all over the world and becoming a global public health issue. Xanthine oxidase (XO) is regarded as a key drug target for the treatment of this disease. Therefore, finding natural, nontoxic, and highly active XO inhibitors is quite important. To get insights into inhibitory potential toward XO and determine antioxidant action mechanism depending on the molecular structure, plant flavonoid blumeatin was investigated for the first time by Fourier transform infrared (FTIR) spectroscopy, density functional theory (DFT), ADME/Tox (absorption, distribution, metabolism, excretion, and toxicity) analysis, and molecular docking study. Theoretical findings indicated that blumeatin has high radical scavenging activity due to its noncoplanarity and over twisted torsion angle (-94.64°) with respect to its flavanone skeleton could explain that there might be a correlation between antioxidant activity and planarity of blumeatin. Based on the ADME/Tox analysis, it is determined that blumeatin has a high absorption profile in the human intestine (81.93%), and this plant flavonoid is not carcinogenic or mutagenic. A molecular docking study showed that Thr1010, Val1011, Phe914, and Ala1078 are the main amino acid residues participating in XO's interaction with blumeatin via hydrogen bonds.
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Affiliation(s)
- Cisem Altunayar-Unsalan
- Graduate
School of Natural and Applied Sciences, Ege University, 35100 Bornova, Izmir, Turkey
- Central
Research Testing and Analysis Laboratory Research and Application
Center, Ege University, 35100 Bornova, Izmir, Turkey
| | - Ozan Unsalan
- Department
of Physics, Faculty of Science, Ege University, 35100 Bornova, Izmir, Turkey
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2
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Ngo K, Yarov-Yarovoy V, Clancy CE, Vorobyov I. Harnessing AlphaFold to reveal state secrets: Prediction of hERG closed and inactivated states. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.27.577468. [PMID: 38352360 PMCID: PMC10862728 DOI: 10.1101/2024.01.27.577468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/20/2024]
Abstract
To design safe, selective, and effective new therapies, there must be a deep understanding of the structure and function of the drug target. One of the most difficult problems to solve has been resolution of discrete conformational states of transmembrane ion channel proteins. An example is KV11.1 (hERG), comprising the primary cardiac repolarizing current, IKr. hERG is a notorious drug anti-target against which all promising drugs are screened to determine potential for arrhythmia. Drug interactions with the hERG inactivated state are linked to elevated arrhythmia risk, and drugs may become trapped during channel closure. However, the structural details of multiple conformational states have remained elusive. Here, we guided AlphaFold2 to predict plausible hERG inactivated and closed conformations, obtaining results consistent with myriad available experimental data. Drug docking simulations demonstrated hERG state-specific drug interactions aligning well with experimental results, revealing that most drugs bind more effectively in the inactivated state and are trapped in the closed state. Molecular dynamics simulations demonstrated ion conduction that aligned with earlier studies. Finally, we identified key molecular determinants of state transitions by analyzing interaction networks across closed, open, and inactivated states in agreement with earlier mutagenesis studies. Here, we demonstrate a readily generalizable application of AlphaFold2 as a novel method to predict discrete protein conformations and novel linkages from structure to function.
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Affiliation(s)
- Khoa Ngo
- Biophysics Graduate Group, University of California, Davis, CA
- Department of Physiology and Membrane Biology, University of California, Davis, CA
- Center for Precision Medicine and Data Science, University of California, Davis, CA
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, CA
- Department of Anesthesiology and Pain Medicine, University of California, Davis, CA
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, CA
- Department of Pharmacology, University of California, Davis, CA
- Center for Precision Medicine and Data Science, University of California, Davis, CA
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, CA
- Department of Pharmacology, University of California, Davis, CA
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3
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Emigh Cortez AM, DeMarco KR, Furutani K, Bekker S, Sack JT, Wulff H, Clancy CE, Vorobyov I, Yarov-Yarovoy V. Structural modeling of hERG channel-drug interactions using Rosetta. Front Pharmacol 2023; 14:1244166. [PMID: 38035013 PMCID: PMC10682396 DOI: 10.3389/fphar.2023.1244166] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 10/23/2023] [Indexed: 12/02/2023] Open
Abstract
The human ether-a-go-go-related gene (hERG) not only encodes a potassium-selective voltage-gated ion channel essential for normal electrical activity in the heart but is also a major drug anti-target. Genetic hERG mutations and blockage of the channel pore by drugs can cause long QT syndrome, which predisposes individuals to potentially deadly arrhythmias. However, not all hERG-blocking drugs are proarrhythmic, and their differential affinities to discrete channel conformational states have been suggested to contribute to arrhythmogenicity. We used Rosetta electron density refinement and homology modeling to build structural models of open-state hERG channel wild-type and mutant variants (Y652A, F656A, and Y652A/F656 A) and a closed-state wild-type channel based on cryo-electron microscopy structures of hERG and EAG1 channels. These models were used as protein targets for molecular docking of charged and neutral forms of amiodarone, nifekalant, dofetilide, d/l-sotalol, flecainide, and moxifloxacin. We selected these drugs based on their different arrhythmogenic potentials and abilities to facilitate hERG current. Our docking studies and clustering provided atomistic structural insights into state-dependent drug-channel interactions that play a key role in differentiating safe and harmful hERG blockers and can explain hERG channel facilitation through drug interactions with its open-state hydrophobic pockets.
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Affiliation(s)
- Aiyana M. Emigh Cortez
- Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Kevin R. DeMarco
- Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Kazuharu Furutani
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Pharmacology, Tokushima Bunri University, Tokushima, Japan
| | - Slava Bekker
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- American River College, Sacramento, CA, United States
| | - Jon T. Sack
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA, United States
| | - Heike Wulff
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
- Center for Precision Medicine and Data Sciences, University of California, Davis, Davis, CA, United States
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Anesthesiology and Pain Medicine, University of California, Davis, Davis, CA, United States
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4
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Chen Y, Yu X, Li W, Tang Y, Liu G. In silico prediction of hERG blockers using machine learning and deep learning approaches. J Appl Toxicol 2023; 43:1462-1475. [PMID: 37093028 DOI: 10.1002/jat.4477] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 04/04/2023] [Accepted: 04/19/2023] [Indexed: 04/25/2023]
Abstract
The human ether-à-go-go-related gene (hERG) is associated with drug cardiotoxicity. If the hERG channel is blocked, it will lead to prolonged QT interval and cause sudden death in severe cases. Therefore, it is important to evaluate the hERG-blocking property of compounds in early drug discovery. In this study, a dataset containing 4556 compounds with IC50 values determined by patch clamp techniques on mammalian lineage cells was collected, and hERG blockers and non-blockers were distinguished according to three single thresholds and two binary thresholds. Four machine learning (ML) algorithms combining four molecular fingerprints and molecular descriptors as well as graph convolutional neural networks (GCNs) were used to construct a series of binary classification models. The results showed that the best models varied for different thresholds. The ML models implemented by support vector machine and random forest performed well based on Morgan fingerprints and molecular descriptors, with AUCs ranging from 0.884 to 0.950. GCN showed superior prediction performance with AUCs above 0.952, which might be related to its direct extraction of molecular features from the original input. Meanwhile, the classification of binary threshold was better than that of single threshold, which could provide us with a more accurate prediction of hERG blockers. At last, the applicability domain for the model was defined, and seven structural alerts that might generate hERG blockage were identified by information gain and substructure frequency analysis. Our work would be beneficial for identifying hERG blockers in chemicals.
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Affiliation(s)
- Yuanting Chen
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Xinxin Yu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Weihua Li
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Yun Tang
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
| | - Guixia Liu
- Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, China
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Helliwell MV, Zhang Y, El Harchi A, Dempsey CE, Hancox JC. Inhibition of the hERG Potassium Channel by a Methanesulphonate-Free E-4031 Analogue. Pharmaceuticals (Basel) 2023; 16:1204. [PMID: 37765012 PMCID: PMC10536391 DOI: 10.3390/ph16091204] [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: 07/28/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 09/29/2023] Open
Abstract
hERG (human Ether-à-go-go Related Gene)-encoded potassium channels underlie the cardiac rapid delayed rectifier (IKr) potassium current, which is a major target for antiarrhythmic agents and diverse non-cardiac drugs linked to the drug-induced form of long QT syndrome. E-4031 is a high potency hERG channel inhibitor from the methanesulphonanilide drug family. This study utilized a methanesulphonate-lacking E-4031 analogue, "E-4031-17", to evaluate the role of the methanesulphonamide group in E-4031 inhibition of hERG. Whole-cell patch-clamp measurements of the hERG current (IhERG) were made at physiological temperature from HEK 293 cells expressing wild-type (WT) and mutant hERG constructs. For E-4031, WT IhERG was inhibited by a half-maximal inhibitory concentration (IC50) of 15.8 nM, whilst the comparable value for E-4031-17 was 40.3 nM. Both compounds exhibited voltage- and time-dependent inhibition, but they differed in their response to successive applications of a long (10 s) depolarisation protocol, consistent with greater dissociation of E-4031-17 than the parent compound between applied commands. Voltage-dependent inactivation was left-ward voltage shifted for E-4031 but not for E-4031-17; however, inhibition by both compounds was strongly reduced by attenuated-inactivation mutations. Mutations of S6 and S5 aromatic residues (F656V, Y652A, F557L) greatly attenuated actions of both drugs. The S624A mutation also reduced IhERG inhibition by both molecules. Overall, these results demonstrate that the lack of a methanesulphonate in E-4031-17 is not an impediment to high potency inhibition of IhERG.
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Affiliation(s)
- Matthew V. Helliwell
- School of Biochemistry, Biomedical Sciences Building, University Walk, University of Bristol, Bristol BS8 1TD, UK; (M.V.H.); (C.E.D.)
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences Building, University Walk, University of Bristol, Bristol BS8 1TD, UK; (Y.Z.); (A.E.H.)
| | - Yihong Zhang
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences Building, University Walk, University of Bristol, Bristol BS8 1TD, UK; (Y.Z.); (A.E.H.)
| | - Aziza El Harchi
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences Building, University Walk, University of Bristol, Bristol BS8 1TD, UK; (Y.Z.); (A.E.H.)
| | - Christopher E. Dempsey
- School of Biochemistry, Biomedical Sciences Building, University Walk, University of Bristol, Bristol BS8 1TD, UK; (M.V.H.); (C.E.D.)
| | - Jules C. Hancox
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences Building, University Walk, University of Bristol, Bristol BS8 1TD, UK; (Y.Z.); (A.E.H.)
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6
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Negami T, Terada T. Calculations of the binding free energies of the Comprehensive in vitro Proarrhythmia Assay (CiPA) reference drugs to cardiac ion channels. Biophys Physicobiol 2023; 20:e200016. [PMID: 38496247 PMCID: PMC10941965 DOI: 10.2142/biophysico.bppb-v20.0016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 03/24/2023] [Indexed: 03/19/2024] Open
Abstract
The evaluation of the inhibitory activities of drugs on multiple cardiac ion channels is required for the accurate assessment of proarrhythmic risks. Moreover, the in silico prediction of such inhibitory activities of drugs on cardiac channels can improve the efficiency of the drug-development process. Here, we performed molecular docking simulations to predict the complex structures of 25 reference drugs that were proposed by the Comprehensive in vitro Proarrhythmia Assay consortium using two cardiac ion channels, the human ether-a-go-go-related gene (hERG) potassium channel and human NaV1.5 (hNaV1.5) sodium channel, with experimentally available structures. The absolute binding free energy (ΔGbind) values of the predicted structures were calculated by a molecular dynamics-based method and compared with the experimental half-maximal inhibitory concentration (IC50) data. Furthermore, the regression analysis between the calculated values and negative of the common logarithm of the experimental IC50 values (pIC50) revealed that the calculated values of four and ten drugs deviated significantly from the regression lines of the hERG and hNaV1.5 channels, respectively. We reconsidered the docking poses and protonation states of the drugs based on the experimental data and recalculated their ΔGbind values. Finally, the calculated ΔGbind values of 24 and 19 drugs correlated with their experimental pIC50 values (coefficients of determination=0.791 and 0.613 for the hERG and hNaV1.5 channels, respectively). Thus, the regression analysis between the calculated ΔGbind and experimental IC50 data ensured the realization of an increased number of reliable complex structures.
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Affiliation(s)
- Tatsuki Negami
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
| | - Tohru Terada
- Department of Biotechnology, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan
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7
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Vittorio S, Lunghini F, Pedretti A, Vistoli G, Beccari AR. Ensemble of structure and ligand-based classification models for hERG liability profiling. Front Pharmacol 2023; 14:1148670. [PMID: 37033661 PMCID: PMC10076575 DOI: 10.3389/fphar.2023.1148670] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 03/13/2023] [Indexed: 04/11/2023] Open
Abstract
Drug-induced cardiotoxicity represents one of the most critical safety concerns in the early stages of drug development. The blockade of the human ether-à-go-go-related potassium channel (hERG) is the most frequent cause of cardiotoxicity, as it is associated to long QT syndrome which can lead to fatal arrhythmias. Therefore, assessing hERG liability of new drugs candidates is crucial to avoid undesired cardiotoxic effects. In this scenario, computational approaches have emerged as useful tools for the development of predictive models able to identify potential hERG blockers. In the last years, several efforts have been addressed to generate ligand-based (LB) models due to the lack of experimental structural information about hERG channel. However, these methods rely on the structural features of the molecules used to generate the model and often fail in correctly predicting new chemical scaffolds. Recently, the 3D structure of hERG channel has been experimentally solved enabling the use of structure-based (SB) strategies which may overcome the limitations of the LB approaches. In this study, we compared the performances achieved by both LB and SB classifiers for hERG-related cardiotoxicity developed by using Random Forest algorithm and employing a training set containing 12789 hERG binders. The SB models were trained on a set of scoring functions computed by docking and rescoring calculations, while the LB classifiers were built on a set of physicochemical descriptors and fingerprints. Furthermore, models combining the LB and SB features were developed as well. All the generated models were internally validated by ten-fold cross-validation on the TS and further verified on an external test set. The former revealed that the best performance was achieved by the LB model, while the model combining the LB and the SB attributes displayed the best results when applied on the external test set highlighting the usefulness of the integration of LB and SB features in correctly predicting unseen molecules. Overall, our predictive models showed satisfactory performances providing new useful tools to filter out potential cardiotoxic drug candidates in the early phase of drug discovery.
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Affiliation(s)
- Serena Vittorio
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Milano, Italy
| | | | - Alessandro Pedretti
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Milano, Italy
| | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università Degli Studi di Milano, Milano, Italy
| | - Andrea R. Beccari
- EXSCALATE, Dompé Farmaceutici SpA, Napoli, Italy
- *Correspondence: Andrea R. Beccari,
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Kudaibergenova M, Guo J, Khan HM, Lees-Miller J, Mousaei M, Miranda W, Ngo VA, Noskov SY, Tieleman DP, Duff HJ. The voltage-sensing domain of a hERG1 mutant is a cation-selective channel. Biophys J 2022; 121:4585-4599. [PMID: 36815709 PMCID: PMC9748372 DOI: 10.1016/j.bpj.2022.10.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 06/29/2022] [Accepted: 10/24/2022] [Indexed: 11/24/2022] Open
Abstract
A cationic leak current known as an "omega current" may arise from mutations of the first charged residue in the S4 of the voltage sensor domains of sodium and potassium voltage-gated channels. The voltage-sensing domains (VSDs) in these mutated channels act as pores allowing nonspecific passage of cations, such as Li+, K+, Cs+, and guanidinium. Interestingly, no omega currents have been previously detected in the nonswapped voltage-gated potassium channels such as the human-ether-a-go-go-related (hERG1), hyperpolarization-activated cyclic nucleotide-gated, and ether-a-go-go channels. In this work, we discovered a novel omega current by mutating the first charged residue of the S4 of the hERG1, K525 to serine. To characterize this omega current, we used various probes, including the hERG1 pore domain blocker, dofetilide, to show that the omega current does not require cation flux via the canonical pore domain. In addition, the omega flux does not cross the conventional selectivity filter. We also show that the mutated channel (K525S hERG1) conducts guanidinium. These data are indicative of the formation of an omega current channel within the VSD. Using molecular dynamics simulations with replica-exchange umbrella sampling simulations of the wild-type hERG1 and the K525S hERG1, we explored the molecular underpinnings governing the cation flow in the VSD of the mutant. We also show that the wild-type hERG1 may form water crevices supported by the biophysical surface accessibility data. Overall, our multidisciplinary study demonstrates that the VSD of hERG1 may act as a cation-selective channel wherein a mutation of the first charged residue in the S4 generates an omega current. Our simulation uncovers the atomistic underpinning of this mechanism.
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Affiliation(s)
- Meruyert Kudaibergenova
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Jiqing Guo
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, AB, Canada
| | - Hanif M Khan
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - James Lees-Miller
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, AB, Canada
| | - Mahdi Mousaei
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Williams Miranda
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Van A Ngo
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Sergei Yu Noskov
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - D Peter Tieleman
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.
| | - Henry J Duff
- Department of Cardiac Sciences, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, AB, Canada.
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9
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Maly J, Emigh AM, DeMarco KR, Furutani K, Sack JT, Clancy CE, Vorobyov I, Yarov-Yarovoy V. Structural modeling of the hERG potassium channel and associated drug interactions. Front Pharmacol 2022; 13:966463. [PMID: 36188564 PMCID: PMC9523588 DOI: 10.3389/fphar.2022.966463] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
The voltage-gated potassium channel, KV11.1, encoded by the human Ether-à-go-go-Related Gene (hERG), is expressed in cardiac myocytes, where it is crucial for the membrane repolarization of the action potential. Gating of the hERG channel is characterized by rapid, voltage-dependent, C-type inactivation, which blocks ion conduction and is suggested to involve constriction of the selectivity filter. Mutations S620T and S641A/T within the selectivity filter region of hERG have been shown to alter the voltage dependence of channel inactivation. Because hERG channel blockade is implicated in drug-induced arrhythmias associated with both the open and inactivated states, we used Rosetta to simulate the effects of hERG S620T and S641A/T mutations to elucidate conformational changes associated with hERG channel inactivation and differences in drug binding between the two states. Rosetta modeling of the S641A fast-inactivating mutation revealed a lateral shift of the F627 side chain in the selectivity filter into the central channel axis along the ion conduction pathway and the formation of four lateral fenestrations in the pore. Rosetta modeling of the non-inactivating mutations S620T and S641T suggested a potential molecular mechanism preventing F627 side chain from shifting into the ion conduction pathway during the proposed inactivation process. Furthermore, we used Rosetta docking to explore the binding mechanism of highly selective and potent hERG blockers - dofetilide, terfenadine, and E4031. Our structural modeling correlates well with much, but not all, existing experimental evidence involving interactions of hERG blockers with key residues in hERG pore and reveals potential molecular mechanisms of ligand interactions with hERG in an inactivated state.
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Affiliation(s)
- Jan Maly
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
| | - Aiyana M. Emigh
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
| | - Kevin R. DeMarco
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Biophysics Graduate Group, University of California, Davis, Davis, CA, United States
| | - Kazuharu Furutani
- Department of Pharmacology, Tokushima Bunri University, Tokushima, Japan
| | - Jon T. Sack
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
| | - Colleen E. Clancy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Igor Vorobyov
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
- Department of Pharmacology, University of California, Davis, Davis, CA, United States
| | - Vladimir Yarov-Yarovoy
- Department of Physiology and Membrane Biology, University of California, Davis, Davis, CA, United States
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10
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Mészáros B, Csoti A, Szanto TG, Telek A, Kovács K, Toth A, Volkó J, Panyi G. The hEag1 K + Channel Inhibitor Astemizole Stimulates Ca 2+ Deposition in SaOS-2 and MG-63 Osteosarcoma Cultures. Int J Mol Sci 2022; 23:ijms231810533. [PMID: 36142445 PMCID: PMC9504018 DOI: 10.3390/ijms231810533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 08/27/2022] [Accepted: 09/06/2022] [Indexed: 11/29/2022] Open
Abstract
The hEag1 (Kv10.1) K+ channel is normally found in the brain, but it is ectopically expressed in tumor cells, including osteosarcoma. Based on the pivotal role of ion channels in osteogenesis, we tested whether pharmacological modulation of hEag1 may affect osteogenic differentiation of osteosarcoma cell lines. Using molecular biology (RT-PCR), electrophysiology (patch-clamp) and pharmacology (astemizole sensitivity, IC50 = 0.135 μM) we demonstrated that SaOS-2 osteosarcoma cells also express hEag1 channels. SaOS-2 cells also express to KCa1.1 K+ channels as shown by mRNA expression and paxilline sensitivity of the current. The inhibition of hEag1 (2 μM astemizole) or KCa1.1 (1 mM TEA) alone did not induce Ca2+ deposition in SaOS-2 cultures, however, these inhibitors, at identical concentrations, increased Ca2+ deposition evoked by the classical or pathological (inorganic phosphate, Pi) induction pathway without causing cytotoxicity, as reported by three completer assays (LDH release, MTT assay and SRB protein assay). We observed a similar effect of astemizole on Ca2+ deposition in MG-63 osteosarcoma cultures as well. We propose that the increase in the osteogenic stimuli-induced mineral matrix formation of osteosarcoma cell lines by inhibiting hEag1 may be a useful tool to drive terminal differentiation of osteosarcoma.
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Affiliation(s)
- Beáta Mészáros
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Life Science Building, Egyetem Ter 1, H-4032 Debrecen, Hungary
- MTA-DE Cell Biology and Signaling Research Group, Life Science Building, Egyetem Ter 1, H-4032 Debrecen, Hungary
| | - Agota Csoti
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Life Science Building, Egyetem Ter 1, H-4032 Debrecen, Hungary
| | - Tibor G. Szanto
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Life Science Building, Egyetem Ter 1, H-4032 Debrecen, Hungary
| | - Andrea Telek
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Life Science Building, Egyetem Ter 1, H-4032 Debrecen, Hungary
| | - Katalin Kovács
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Life Science Building, Egyetem Ter 1, H-4032 Debrecen, Hungary
| | - Agnes Toth
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Life Science Building, Egyetem Ter 1, H-4032 Debrecen, Hungary
| | - Julianna Volkó
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Life Science Building, Egyetem Ter 1, H-4032 Debrecen, Hungary
| | - Gyorgy Panyi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Life Science Building, Egyetem Ter 1, H-4032 Debrecen, Hungary
- Correspondence: ; Tel.: +36-52-258603; Fax: +36-52-532201
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11
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Goel H, Yu W, MacKerell AD. hERG Blockade Prediction by Combining Site Identification by Ligand Competitive Saturation and Physicochemical Properties. CHEMISTRY (BASEL, SWITZERLAND) 2022; 4:630-646. [PMID: 36712295 PMCID: PMC9881610 DOI: 10.3390/chemistry4030045] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Human ether-a-go-go-related gene (hERG) potassium channel is well-known contributor to drug-induced cardiotoxicity and therefore an extremely important target when performing safety assessments of drug candidates. Ligand-based approaches in connection with quantitative structure active relationships (QSAR) analyses have been developed to predict hERG toxicity. Availability of the recent published cryogenic electron microscopy (cryo-EM) structure for the hERG channel opened the prospect for using structure-based simulation and docking approaches for hERG drug liability predictions. In recent time, the idea of combining structure- and ligand-based approaches for modeling hERG drug liability has gained momentum offering improvements in predictability when compared to ligand-based QSAR practices alone. The present article demonstrates uniting the structure-based SILCS (site-identification by ligand competitive saturation) approach in conjunction with physicochemical properties to develop predictive models for hERG blockade. This combination leads to improved model predictability based on Pearson's R and percent correct (represents rank-ordering of ligands) metric for different validation sets of hERG blockers involving diverse chemical scaffold and wide range of pIC50 values. The inclusion of the SILCS structure-based approach allows determination of the hERG region to which compounds bind and the contribution of different chemical moieties in the compounds to blockade, thereby facilitating the rational ligand design to minimize hERG liability.
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Affiliation(s)
- Himanshu Goel
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St. Baltimore, MD 21201, United States
| | - Wenbo Yu
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St. Baltimore, MD 21201, United States
| | - Alexander D. MacKerell
- Computer Aided Drug Design Center, Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn St. Baltimore, MD 21201, United States
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12
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Shan M, Jiang C, Qin L, Cheng G. A Review of Computational Methods in Predicting hERG Channel Blockers. ChemistrySelect 2022. [DOI: 10.1002/slct.202201221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mengyi Shan
- School of Pharmaceutical Sciences Zhejiang Chinese Medical University Hangzhou 310053 People's Republic of China
| | - Chen Jiang
- QuanMin RenZheng (HangZhou) Technology Co. Ltd. China
| | - Lu‐Ping Qin
- School of Pharmaceutical Sciences Zhejiang Chinese Medical University Hangzhou 310053 People's Republic of China
| | - Gang Cheng
- School of Pharmaceutical Sciences Zhejiang Chinese Medical University Hangzhou 310053 People's Republic of China
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13
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Kokot M, Weiss M, Zdovc I, Anderluh M, Hrast M, Minovski N. Diminishing hERG inhibitory activity of aminopiperidine-naphthyridine linked NBTI antibacterials by structural and physicochemical optimizations. Bioorg Chem 2022; 128:106087. [PMID: 35970069 DOI: 10.1016/j.bioorg.2022.106087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/05/2022] [Accepted: 08/05/2022] [Indexed: 11/02/2022]
Abstract
Novel bacterial topoisomerase inhibitors (NBTIs) are an important new class of antibacterials targeting bacterial type II topoisomerases (DNA gyrase and topoisomerase IV). Notwithstanding their potent antibacterial activity, they suffer from a detrimental class-related hERG blockage. In this study, we designed and synthesized an optimized library of NBTIs comprising different linker moieties that exhibit reduced hERG inhibition and retain inhibitory potencies on DNA gyrase and topoisomerase IV of Staphylococcus aureus and Escherichia coli, respectively, as well as potent antibacterial activities. Substitution of the linker's tertiary amine with polar groups outcome in diminished hERG inhibition. Compound 17 expresses nanomolar enzyme inhibitory potency and antibacterial activity against both Gram-positive and Gram-negative bacteria as well as reduced hERG inhibition relative to our previously published NBTI analogs. Here, we point to some important NBTI's structural features that influence their hERG inhibitory activity.
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Affiliation(s)
- Maja Kokot
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia; The Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Matjaž Weiss
- The Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Irena Zdovc
- Institute of Microbiology and Parasitology, Veterinary Faculty, University of Ljubljana, Gerbičeva 60, 1000 Ljubljana, Slovenia
| | - Marko Anderluh
- The Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia
| | - Martina Hrast
- The Department of Pharmaceutical Chemistry, Faculty of Pharmacy, University of Ljubljana, Aškerčeva cesta 7, 1000 Ljubljana, Slovenia.
| | - Nikola Minovski
- Theory Department, Laboratory for Cheminformatics, National Institute of Chemistry, Hajdrihova 19, 1001 Ljubljana, Slovenia.
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14
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Harley BK, Amponsah IK, Ben IO, Mireku-Gyimah NA, Anokwah D, Neglo D, Amengor CDK, Fleischer TC. Hypoglycaemic activity of Oleanonic acid, a 3-oxotriterpenoid isolated from Aidia Genipiflora (DC.) Dandy, involves inhibition of carbohydrate metabolic enzymes and promotion of glucose uptake. Biomed Pharmacother 2022; 149:112833. [PMID: 35316751 DOI: 10.1016/j.biopha.2022.112833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 11/02/2022] Open
Abstract
The present study evaluated the antidiabetic activities of the 70% ethanol stem bark extract of Aidia genipiflora (AGB) and one of its constituents, oleanonic acid in streptozotocin (40 mg/kg)-induced diabetic rats. In vitro assays of glucose uptake and inhibition of carbohydrate metabolizing enzymes were then used to investigate their mechanism(s) of hypoglycaemic action. In silico evaluation of the pharmacokinetic and toxicity properties of the compound was also carried out. Administration of AGB (100-400 mg/kg) and oleanonic acid (15 - 60 mg/kg) resulted in significant reductions (p < 0.001) in the blood glucose and considerable decrease (p < 0.05) in the elevated lipid parameters of the diabetic animals. AGB activity at 200 and 400 mg/kg; and oleanonic acid at 60 mg/kg were comparable to glibenclamide (5 mg/kg). The extract and its isolate strongly inhibited α-glucosidase and α-amylase activity with IC50 values of (10.48 ± 1.39 µg/mL and 14.51 ± 1.26 µg/mL) and (36.52 ± 1.95 µM and 105.84 ± 1.08 µM) respectively. The glucose uptake assays showed that AGB and oleanonic acid exerted both insulin-dependent and independent promotional effect of glucose transport into the periphery by upregulating the expression of PI3K and PPARγ transcripts with a concomitant increase in GLUT-4 transcripts. Although oleanonic acid was predicted to be teratogenic, it was found to be generally non-lethal with favourable pharmacokinetics properties making it suitable for further studies. The study has shown that the stem bark of A. genipiflora is a source of new hypoglycaemic agents and that oleanonic acid possesses hypoglycaemic and anti-hyperlipidaemic activities.
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Affiliation(s)
- Benjamin Kingsley Harley
- Department of Pharmacognosy and Herbal Medicine, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana.
| | - Isaac Kingsley Amponsah
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Inemesit Okon Ben
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Nana Ama Mireku-Gyimah
- Department of Pharmacognosy and Herbal Medicine, School of Pharmacy, University of Ghana, Accra, Ghana
| | - Daniel Anokwah
- Department of Pharmacognosy and Herbal Medicine, School of Pharmacy, University of Cape-Coast, Cape-Coast, Ghana
| | - David Neglo
- Department of Basic Science, School of Basic and Biomedical Sciences, University of Health and Allied Sciences, Ho, Ghana
| | - Cedric Dzidzor K Amengor
- Department of Pharmaceutical Chemistry, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Theophilus Christian Fleischer
- Department of Pharmacognosy and Herbal Medicine, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
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15
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Staszak M, Staszak K, Wieszczycka K, Bajek A, Roszkowski K, Tylkowski B. Machine learning in drug design: Use of artificial intelligence to explore the chemical structure–biological activity relationship. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2022. [DOI: 10.1002/wcms.1568] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Maciej Staszak
- Institute of Technology and Chemical Engineering Poznan University of Technology Poznan Poland
| | - Katarzyna Staszak
- Institute of Technology and Chemical Engineering Poznan University of Technology Poznan Poland
| | - Karolina Wieszczycka
- Institute of Technology and Chemical Engineering Poznan University of Technology Poznan Poland
| | - Anna Bajek
- Department of Tissue Engineering Collegium Medicum, Nicolaus Copernicus University Bydgoszcz Poland
| | - Krzysztof Roszkowski
- Department of Oncology Collegium Medicum Nicolaus Copernicus University Bydgoszcz Poland
| | - Bartosz Tylkowski
- Department of Chemical Engineering University Rovira i Virgili Tarragona Spain
- Eurecat, Centre Tecnològic de Catalunya Chemical Technologies Unit Tarragona Spain
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16
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Bassan A, Alves VM, Amberg A, Anger LT, Beilke L, Bender A, Bernal A, Cronin MT, Hsieh JH, Johnson C, Kemper R, Mumtaz M, Neilson L, Pavan M, Pointon A, Pletz J, Ruiz P, Russo DP, Sabnis Y, Sandhu R, Schaefer M, Stavitskaya L, Szabo DT, Valentin JP, Woolley D, Zwickl C, Myatt GJ. In silico approaches in organ toxicity hazard assessment: Current status and future needs for predicting heart, kidney and lung toxicities. COMPUTATIONAL TOXICOLOGY (AMSTERDAM, NETHERLANDS) 2021; 20:100188. [PMID: 35721273 PMCID: PMC9205464 DOI: 10.1016/j.comtox.2021.100188] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The kidneys, heart and lungs are vital organ systems evaluated as part of acute or chronic toxicity assessments. New methodologies are being developed to predict these adverse effects based on in vitro and in silico approaches. This paper reviews the current state of the art in predicting these organ toxicities. It outlines the biological basis, processes and endpoints for kidney toxicity, pulmonary toxicity, respiratory irritation and sensitization as well as functional and structural cardiac toxicities. The review also covers current experimental approaches, including off-target panels from secondary pharmacology batteries. Current in silico approaches for prediction of these effects and mechanisms are described as well as obstacles to the use of in silico methods. Ultimately, a commonly accepted protocol for performing such assessment would be a valuable resource to expand the use of such approaches across different regulatory and industrial applications. However, a number of factors impede their widespread deployment including a lack of a comprehensive mechanistic understanding, limited in vitro testing approaches and limited in vivo databases suitable for modeling, a limited understanding of how to incorporate absorption, distribution, metabolism, and excretion (ADME) considerations into the overall process, a lack of in silico models designed to predict a safe dose and an accepted framework for organizing the key characteristics of these organ toxicants.
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Affiliation(s)
- Arianna Bassan
- Innovatune srl, Via Giulio Zanon 130/D, 35129 Padova, Italy
| | - Vinicius M. Alves
- The National Institute of Environmental Health Sciences, Division of the National Toxicology Program, Research Triangle Park, NC 27709, United States
| | - Alexander Amberg
- Sanofi, R&D Preclinical Safety Frankfurt, Industriepark Hoechst, D-65926 Frankfurt am Main, Germany
| | - Lennart T. Anger
- Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, United States
| | - Lisa Beilke
- Toxicology Solutions Inc., San Diego, CA, United States
| | - Andreas Bender
- AI and Data Analytics, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
- Centre for Molecular Informatics, Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United States
| | | | - Mark T.D. Cronin
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Jui-Hua Hsieh
- The National Institute of Environmental Health Sciences, Division of the National Toxicology Program, Research Triangle Park, NC 27709, United States
| | | | - Raymond Kemper
- Nuvalent, One Broadway, 14th floor, Cambridge, MA 02142, United States
| | - Moiz Mumtaz
- Agency for Toxic Substances and Disease Registry, US Department of Health and Human Services, Atlanta, GA, United States
| | - Louise Neilson
- Broughton Nicotine Services, Oak Tree House, West Craven Drive, Earby, Lancashire BB18 6JZ UK
| | - Manuela Pavan
- Innovatune srl, Via Giulio Zanon 130/D, 35129 Padova, Italy
| | - Amy Pointon
- Functional and Mechanistic Safety, Clinical Pharmacology and Safety Sciences, R&D, AstraZeneca, Cambridge, UK
| | - Julia Pletz
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, L3 3AF, UK
| | - Patricia Ruiz
- Agency for Toxic Substances and Disease Registry, US Department of Health and Human Services, Atlanta, GA, United States
| | - Daniel P. Russo
- The Rutgers Center for Computational and Integrative Biology, Camden, NJ 08102, United States
- Department of Chemistry, Rutgers University, Camden, NJ 08102, United States
| | - Yogesh Sabnis
- UCB Biopharma SRL, Chemin du Foriest, B-1420 Braine-l’Alleud, Belgium
| | - Reena Sandhu
- SafeDose Ltd., 20 Dundas Street West, Suite 921, Toronto, Ontario M5G2H1, Canada
| | - Markus Schaefer
- Sanofi, R&D Preclinical Safety Frankfurt, Industriepark Hoechst, D-65926 Frankfurt am Main, Germany
| | - Lidiya Stavitskaya
- US Food and Drug Administration, Center for Drug Evaluation and Research, Silver Spring, MD 20993, USA
| | | | | | - David Woolley
- ForthTox Limited, PO Box 13550, Linlithgow, EH49 7YU, UK
| | - Craig Zwickl
- Transendix LLC, 1407 Moores Manor, Indianapolis, IN 46229, United States
| | - Glenn J. Myatt
- Instem, 1393 Dublin Road, Columbus, OH 43215, United States
- Corresponding author: (G.J. Myatt)
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17
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Creanza TM, Delre P, Ancona N, Lentini G, Saviano M, Mangiatordi GF. Structure-Based Prediction of hERG-Related Cardiotoxicity: A Benchmark Study. J Chem Inf Model 2021; 61:4758-4770. [PMID: 34506150 PMCID: PMC9282647 DOI: 10.1021/acs.jcim.1c00744] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Drug-induced blockade of the human
ether-à-go-go-related
gene (hERG) channel is today considered the main
cause of cardiotoxicity in postmarketing surveillance. Hence, several
ligand-based approaches were developed in the last years and are currently
employed in the early stages of a drug discovery process for in silico cardiac safety assessment of drug candidates.
Herein, we present the first structure-based classifiers able to discern hERG binders from nonbinders. LASSO regularized support
vector machines were applied to integrate docking scores and protein–ligand
interaction fingerprints. A total of 396 models were trained and validated
based on: (i) high-quality experimental bioactivity information returned
by 8337 curated compounds extracted from ChEMBL (version 25) and (ii)
structural predictor data. Molecular docking simulations were performed
using GLIDE and GOLD software programs and four different hERG structural models, namely, the recently published structures
obtained by cryoelectron microscopy (PDB codes: 5VA1 and 7CN1) and
two published homology models selected for comparison. Interestingly,
some classifiers return performances comparable to ligand-based models
in terms of area under the ROC curve (AUCMAX = 0.86 ±
0.01) and negative predictive values (NPVMAX = 0.81 ±
0.01), thus putting forward the herein proposed computational workflow
as a valuable tool for predicting hERG-related cardiotoxicity
without the limitations of ligand-based models, typically affected
by low interpretability and a limited applicability domain. From a
methodological point of view, our study represents the first example
of a successful integration of docking scores and protein–ligand
interaction fingerprints (IFs) through a support vector machine (SVM)
LASSO regularized strategy. Finally, the study highlights the importance
of using hERG structural models accounting for ligand-induced
fit effects and allowed us to select the best-performing protein conformation
(made available in the Supporting Information, SI) to be employed
for a reliable structure-based prediction of hERG-related cardiotoxicity.
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Affiliation(s)
- Teresa Maria Creanza
- CNR-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, Via Amendola 122/o, 70126 Bari, Italy
| | - Pietro Delre
- Chemistry Department, University of Bari "Aldo Moro", via E. Orabona, 4, I-70125 Bari, Italy.,CNR-Institute of Crystallography, Via Amendola 122/o, 70126 Bari, Italy
| | - Nicola Ancona
- CNR-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing, Via Amendola 122/o, 70126 Bari, Italy
| | - Giovanni Lentini
- Department of Pharmacy-Pharmaceutical Sciences, University of Bari "Aldo Moro", via E. Orabona, 4, I-70125 Bari, Italy
| | - Michele Saviano
- CNR-Institute of Crystallography, Via Amendola 122/o, 70126 Bari, Italy
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18
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Lee KH, Fant AD, Guo J, Guan A, Jung J, Kudaibergenova M, Miranda WE, Ku T, Cao J, Wacker S, Duff HJ, Newman AH, Noskov SY, Shi L. Toward Reducing hERG Affinities for DAT Inhibitors with a Combined Machine Learning and Molecular Modeling Approach. J Chem Inf Model 2021; 61:4266-4279. [PMID: 34420294 DOI: 10.1021/acs.jcim.1c00856] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Psychostimulant drugs, such as cocaine, inhibit dopamine reuptake via blockading the dopamine transporter (DAT), which is the primary mechanism underpinning their abuse. Atypical DAT inhibitors are dissimilar to cocaine and can block cocaine- or methamphetamine-induced behaviors, supporting their development as part of a treatment regimen for psychostimulant use disorders. When developing these atypical DAT inhibitors as medications, it is necessary to avoid off-target binding that can produce unwanted side effects or toxicities. In particular, the blockade of a potassium channel, human ether-a-go-go (hERG), can lead to potentially lethal ventricular tachycardia. In this study, we established a counter screening platform for DAT and against hERG binding by combining machine learning-based quantitative structure-activity relationship (QSAR) modeling, experimental validation, and molecular modeling and simulations. Our results show that the available data are adequate to establish robust QSAR models, as validated by chemical synthesis and pharmacological evaluation of a validation set of DAT inhibitors. Furthermore, the QSAR models based on subsets of the data according to experimental approaches used have predictive power as well, which opens the door to target specific functional states of a protein. Complementarily, our molecular modeling and simulations identified the structural elements responsible for a pair of DAT inhibitors having opposite binding affinity trends at DAT and hERG, which can be leveraged for rational optimization of lead atypical DAT inhibitors with desired pharmacological properties.
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Affiliation(s)
- Kuo Hao Lee
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Andrew D Fant
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Jiqing Guo
- Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Andy Guan
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Joslyn Jung
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Mary Kudaibergenova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Williams E Miranda
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Therese Ku
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Jianjing Cao
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Soren Wacker
- Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada.,Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada.,Achlys Inc., 7-126 Li Ka Shing Center for Health and Innovation, Edmonton, Alberta T6G 2E1, Canada
| | - Henry J Duff
- Libin Cardiovascular Institute of Alberta, Cumming School of Medicine, University of Calgary, Calgary, Alberta T2N 4N1, Canada
| | - Amy Hauck Newman
- Medicinal Chemistry Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
| | - Sergei Y Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta T2N 1N4, Canada
| | - Lei Shi
- Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse-Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States
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19
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Toplak Ž, Merzel F, Pardo LA, Peterlin Mašič L, Tomašič T. Molecular Dynamics-Derived Pharmacophore Model Explaining the Nonselective Aspect of K V10.1 Pore Blockers. Int J Mol Sci 2021; 22:ijms22168999. [PMID: 34445705 PMCID: PMC8396485 DOI: 10.3390/ijms22168999] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/18/2021] [Accepted: 08/19/2021] [Indexed: 11/21/2022] Open
Abstract
The KV10.1 voltage-gated potassium channel is highly expressed in 70% of tumors, and thus represents a promising target for anticancer drug discovery. However, only a few ligands are known to inhibit KV10.1, and almost all also inhibit the very similar cardiac hERG channel, which can lead to undesirable side-effects. In the absence of the structure of the KV10.1–inhibitor complex, there remains the need for new strategies to identify selective KV10.1 inhibitors and to understand the binding modes of the known KV10.1 inhibitors. To investigate these binding modes in the central cavity of KV10.1, a unique approach was used that allows derivation and analysis of ligand–protein interactions from molecular dynamics trajectories through pharmacophore modeling. The final molecular dynamics-derived structure-based pharmacophore model for the simulated KV10.1–ligand complexes describes the necessary pharmacophore features for KV10.1 inhibition and is highly similar to the previously reported ligand-based hERG pharmacophore model used to explain the nonselectivity of KV10.1 pore blockers. Moreover, analysis of the molecular dynamics trajectories revealed disruption of the π–π network of aromatic residues F359, Y464, and F468 of KV10.1, which has been reported to be important for binding of various ligands for both KV10.1 and hERG channels. These data indicate that targeting the KV10.1 channel pore is also likely to result in undesired hERG inhibition, and other potential binding sites should be explored to develop true KV10.1-selective inhibitors as new anticancer agents.
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Affiliation(s)
- Žan Toplak
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia; (Ž.T.); (L.P.M.)
| | - Franci Merzel
- Theory Department, National Institute of Chemistry, 1000 Ljubljana, Slovenia;
| | - Luis A. Pardo
- AG Oncophysiology, Max-Planck Institute for Experimental Medicine, 37075 Göttingen, Germany;
| | - Lucija Peterlin Mašič
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia; (Ž.T.); (L.P.M.)
| | - Tihomir Tomašič
- Faculty of Pharmacy, University of Ljubljana, 1000 Ljubljana, Slovenia; (Ž.T.); (L.P.M.)
- Correspondence: ; Tel.: +386-14769-556
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20
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Baracaldo-Santamaría D, Llinás-Caballero K, Corso-Ramirez JM, Restrepo CM, Dominguez-Dominguez CA, Fonseca-Mendoza DJ, Calderon-Ospina CA. Genetic and Molecular Aspects of Drug-Induced QT Interval Prolongation. Int J Mol Sci 2021; 22:8090. [PMID: 34360853 PMCID: PMC8347245 DOI: 10.3390/ijms22158090] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 07/04/2021] [Accepted: 07/06/2021] [Indexed: 12/22/2022] Open
Abstract
Long QT syndromes can be either acquired or congenital. Drugs are one of the many etiologies that may induce acquired long QT syndrome. In fact, many drugs frequently used in the clinical setting are a known risk factor for a prolonged QT interval, thus increasing the chances of developing torsade de pointes. The molecular mechanisms involved in the prolongation of the QT interval are common to most medications. However, there is considerable inter-individual variability in drug response, thus making the application of personalized medicine a relevant aspect in long QT syndrome, in order to evaluate the risk of every individual from a pharmacogenetic standpoint.
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Affiliation(s)
- Daniela Baracaldo-Santamaría
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia; (D.B.-S.); (J.M.C.-R.); (C.A.D.-D.)
| | - Kevin Llinás-Caballero
- GENIUROS Research Group, Center for Research in Genetics and Genomics (CIGGUR), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia; (K.L.-C.); (C.M.R.); (D.J.F.-M.)
- Institute for Immunological Research, University of Cartagena, Cartagena 130014, Colombia
| | - Julián Miguel Corso-Ramirez
- School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia; (D.B.-S.); (J.M.C.-R.); (C.A.D.-D.)
| | - Carlos Martín Restrepo
- GENIUROS Research Group, Center for Research in Genetics and Genomics (CIGGUR), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia; (K.L.-C.); (C.M.R.); (D.J.F.-M.)
| | | | - Dora Janeth Fonseca-Mendoza
- GENIUROS Research Group, Center for Research in Genetics and Genomics (CIGGUR), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia; (K.L.-C.); (C.M.R.); (D.J.F.-M.)
| | - Carlos Alberto Calderon-Ospina
- GENIUROS Research Group, Center for Research in Genetics and Genomics (CIGGUR), School of Medicine and Health Sciences, Universidad del Rosario, Bogotá 111221, Colombia; (K.L.-C.); (C.M.R.); (D.J.F.-M.)
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21
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Al-Moubarak E, Sharifi M, Hancox JC. In silico Exploration of Interactions Between Potential COVID-19 Antiviral Treatments and the Pore of the hERG Potassium Channel-A Drug Antitarget. Front Cardiovasc Med 2021; 8:645172. [PMID: 34017865 PMCID: PMC8129016 DOI: 10.3389/fcvm.2021.645172] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 03/30/2021] [Indexed: 12/24/2022] Open
Abstract
Background: In the absence of SARS-CoV-2 specific antiviral treatments, various repurposed pharmaceutical approaches are under investigation for the treatment of COVID-19. Antiviral drugs considered for this condition include atazanavir, remdesivir, lopinavir-ritonavir, and favipiravir. Whilst the combination of lopinavir and ritonavir has been previously linked to prolongation of the QTc interval on the ECG and risk of torsades de pointes arrhythmia, less is known in this regard about atazanavir, remdesivir, and favipiravir. Unwanted abnormalities of drug-induced QTc prolongation by diverse drugs are commonly mediated by a single cardiac anti-target, the hERG potassium channel. This computational modeling study was undertaken in order to explore the ability of these five drugs to interact with known determinants of drug binding to the hERG channel pore. Methods: Atazanavir, remdesivir, ritonavir, lopinavir and favipiravir were docked to in silico models of the pore domain of hERG, derived from cryo-EM structures of hERG and the closely related EAG channel. Results: Atazanavir was readily accommodated in the open hERG channel pore in proximity to the S6 Y652 and F656 residues, consistent with published experimental data implicating these aromatic residues in atazanavir binding to the channel. Lopinavir, ritonavir, and remdesivir were also accommodated in the open channel, making contacts in a model-dependent fashion with S6 aromatic residues and with residues at the base of the selectivity filter/pore helix. The ability of remdesivir (at 30 μM) to inhibit the channel was confirmed using patch-clamp recording. None of these four drugs could be accommodated in the closed channel structure. Favipiravir, a much smaller molecule, was able to fit within the closed channel and could adopt multiple binding poses in the open channel, but with few simultaneous interactions with key binding residues. Only favipiravir and remdesivir showed the potential to interact with lateral pockets below the selectivity filter of the channel. Conclusions: All the antiviral drugs studied here can, in principle, interact with components of the hERG potassium channel canonical binding site, but are likely to differ in their ability to access lateral binding pockets. Favipiravir's small size and relatively paucity of simultaneous interactions may confer reduced hERG liability compared to the other drugs. Experimental structure-function studies are now warranted to validate these observations.
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Affiliation(s)
- Ehab Al-Moubarak
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, United Kingdom
| | | | - Jules C. Hancox
- School of Physiology, Pharmacology and Neuroscience, University of Bristol, Biomedical Sciences Building, University Walk, Bristol, United Kingdom
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22
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Saponara S, Fusi F, Iovinelli D, Ahmed A, Trezza A, Spiga O, Sgaragli G, Valoti M. Flavonoids and hERG channels: Friends or foes? Eur J Pharmacol 2021; 899:174030. [PMID: 33727059 DOI: 10.1016/j.ejphar.2021.174030] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 02/28/2021] [Accepted: 03/11/2021] [Indexed: 01/24/2023]
Abstract
The cardiac action potential is regulated by several ion channels. Drugs capable to block these channels, in particular the human ether-à-go-go-related gene (hERG) channel, also known as KV11.1 channel, may lead to a potentially lethal ventricular tachyarrhythmia called "Torsades de Pointes". Thus, evaluation of the hERG channel off-target activity of novel chemical entities is nowadays required to safeguard patients as well as to avoid attrition in drug development. Flavonoids, a large class of natural compounds abundantly present in food, beverages, herbal medicines, and dietary food supplements, generally escape this assessment, though consumed in consistent amounts. Continuously growing evidence indicates that these compounds may interact with the hERG channel and block it. The present review, by examining numerous studies, summarizes the state-of-the-art in this field, describing the most significant examples of direct and indirect inhibition of the hERG channel current operated by flavonoids. A description of the molecular interactions between a few of these natural molecules and the Rattus norvegicus channel protein, achieved by an in silico approach, is also presented.
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Affiliation(s)
- Simona Saponara
- Dipartimento di Scienze della Vita, Università degli Studi di Siena, via A. Moro 2, 53100, Siena, Italy
| | - Fabio Fusi
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via A. Moro 2, 53100, Siena, Italy.
| | - Daniele Iovinelli
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via A. Moro 2, 53100, Siena, Italy
| | - Amer Ahmed
- Dipartimento di Scienze della Vita, Università degli Studi di Siena, via A. Moro 2, 53100, Siena, Italy
| | - Alfonso Trezza
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via A. Moro 2, 53100, Siena, Italy
| | - Ottavia Spiga
- Dipartimento di Biotecnologie, Chimica e Farmacia, Università degli Studi di Siena, via A. Moro 2, 53100, Siena, Italy
| | - Giampietro Sgaragli
- Dipartimento di Scienze della Vita, Università degli Studi di Siena, via A. Moro 2, 53100, Siena, Italy; Accademia Italiana della Vite e del Vino, via Logge degli Uffizi Corti 1, 50122, Florence, Italy
| | - Massimo Valoti
- Dipartimento di Scienze della Vita, Università degli Studi di Siena, via A. Moro 2, 53100, Siena, Italy
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23
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Koulgi S, Jani V, Nair V, Saini JS, Phukan S, Sonavane U, Joshi R, Kamboj R, Palle V. Molecular dynamics of hERG channel: insights into understanding the binding of small molecules for detuning cardiotoxicity. J Biomol Struct Dyn 2021; 40:5996-6012. [PMID: 33494645 DOI: 10.1080/07391102.2021.1875883] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Evaluation of cardiotoxicity potential of new chemical entities (NCEs) has lately become one of the stringent filters in the drug discovery and development process. Cardiotoxicity is caused mainly by the inhibition of human ether-a-go-go related gene (hERG) channel protein. Inhibition of the hERG channel leads to a life-threatening condition known as cardiac arrhythmia. Knowledge of the structural behaviour of the hERG would aid greatly in the design of new drug molecules that do not interact with the protein and add to the safety index. In this study, a computational model for the active-state of hERG was developed. This model was equilibrated by performing the molecular dynamics simulations for 100 ns followed by clustering and selection of a representative structure based on the largest populated cluster. To study the changes in the protein structure on inhibition, three inhibitory ligands, namely, dofetilide, cisapride and terfenadine were docked, followed by molecular dynamics simulations of 200 ns for the apo and each ligand-bound structure. It was observed that docking and simulation studies of the hERG model exhibited noticeable conformational changes in the protein upon ligand-binding. A significant change in the kink of the S6-transmembrane helix was observed. Inter-chain distances between the crucial residues Y652 and F656 (present below the ion-selectivity filter), their side-chain orientation and hydrogen bonding indicated a probable collapse of the pore. These changes may infer the initiation in transition of hERG from an open to an inactive state. Hence, these findings would help in designing compounds devoid of hERG inhibition with reduced cardiotoxicity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shruti Koulgi
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Panchawati, Pashan, Pune
| | - Vinod Jani
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Panchawati, Pashan, Pune
| | | | - Jagmohan S Saini
- Novel Drug Discovery and Development, Lupin Research Park, Pune, India
| | - Samiron Phukan
- Novel Drug Discovery and Development, Lupin Research Park, Pune, India
| | - Uddhavesh Sonavane
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Panchawati, Pashan, Pune
| | - Rajendra Joshi
- High Performance Computing - Medical and Bioinformatics Applications Group, Centre for Development of Advanced Computing, Panchawati, Pashan, Pune
| | - Raj Kamboj
- Novel Drug Discovery and Development, Lupin Research Park, Pune, India
| | - Venkata Palle
- Novel Drug Discovery and Development, Lupin Research Park, Pune, India
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24
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Asai T, Adachi N, Moriya T, Oki H, Maru T, Kawasaki M, Suzuki K, Chen S, Ishii R, Yonemori K, Igaki S, Yasuda S, Ogasawara S, Senda T, Murata T. Cryo-EM Structure of K +-Bound hERG Channel Complexed with the Blocker Astemizole. Structure 2021; 29:203-212.e4. [PMID: 33450182 DOI: 10.1016/j.str.2020.12.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 11/25/2020] [Accepted: 12/10/2020] [Indexed: 12/11/2022]
Abstract
The hERG channel is a voltage-gated potassium channel involved in cardiac repolarization. Off-target hERG inhibition by drugs has become a critical issue in the pharmaceutical industry. The three-dimensional structure of the hERG channel was recently reported at 3.8-Å resolution using cryogenic electron microscopy (cryo-EM). However, the drug inhibition mechanism remains unclear because of the scarce structural information regarding the drug- and potassium-bound hERG channels. In this study, we obtained the cryo-EM density map of potassium-bound hERG channel complexed with astemizole, a well-known hERG inhibitor that increases risk of potentially fatal arrhythmia, at 3.5-Å resolution. The structure suggested that astemizole inhibits potassium conduction by binding directly below the selectivity filter. Furthermore, we propose a possible binding model of astemizole to the hERG channel and provide insights into the unusual sensitivity of hERG to several drugs.
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Affiliation(s)
- Tatsuki Asai
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Naruhiko Adachi
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1, Oho, Tsukuba 305-0801, Japan
| | - Toshio Moriya
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1, Oho, Tsukuba 305-0801, Japan
| | - Hideyuki Oki
- Axcelead Drug Discovery Partners, Inc., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Takamitsu Maru
- Axcelead Drug Discovery Partners, Inc., 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-0012, Japan
| | - Masato Kawasaki
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1, Oho, Tsukuba 305-0801, Japan
| | - Kano Suzuki
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Sisi Chen
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Ryohei Ishii
- Structure-Based Drug Design Group, Organic Synthesis Department, Daiichi Sankyo RD Novare Co., Ltd, 1-16-13 Kitakasai, Edogawa-ku, Tokyo 134-8630, Japan
| | - Kazuko Yonemori
- Drug Safety Research and Evaluation, Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Shigeru Igaki
- Drug Safety Research and Evaluation, Research, Takeda Pharmaceutical Company Limited, 26-1 Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Satoshi Yasuda
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan; Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Satoshi Ogasawara
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan; Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan
| | - Toshiya Senda
- Structural Biology Research Center, Institute of Materials Structure Science, High Energy Accelerator Research Organization (KEK), 1-1, Oho, Tsukuba 305-0801, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan; Molecular Chirality Research Center, Chiba University, 1-33 Yayoi-cho, Inage, Chiba 263-8522, Japan.
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25
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Inhibition of the hERG potassium channel by phenanthrene: a polycyclic aromatic hydrocarbon pollutant. Cell Mol Life Sci 2021; 78:7899-7914. [PMID: 34727194 PMCID: PMC8629796 DOI: 10.1007/s00018-021-03967-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 09/25/2021] [Accepted: 10/01/2021] [Indexed: 11/07/2022]
Abstract
The lipophilic polycyclic aromatic hydrocarbon (PAH) phenanthrene is relatively abundant in polluted air and water and can access and accumulate in human tissue. Phenanthrene has been reported to interact with cardiac ion channels in several fish species. This study was undertaken to investigate the ability of phenanthrene to interact with hERG (human Ether-à-go-go-Related Gene) encoded Kv11.1 K+ channels, which play a central role in human ventricular repolarization. Pharmacological inhibition of hERG can be proarrhythmic. Whole-cell patch clamp recordings of hERG current (IhERG) were made from HEK293 cells expressing wild-type (WT) and mutant hERG channels. WT IhERG1a was inhibited by phenanthrene with an IC50 of 17.6 ± 1.7 µM, whilst IhERG1a/1b exhibited an IC50 of 1.8 ± 0.3 µM. WT IhERG block showed marked voltage and time dependence, indicative of dependence of inhibition on channel gating. The inhibitory effect of phenanthrene was markedly impaired by the attenuated inactivation N588K mutation. Remarkably, mutations of S6 domain aromatic amino acids (Y652, F656) in the canonical drug binding site did not impair the inhibitory action of phenanthrene; the Y652A mutation augmented IhERG block. In contrast, the F557L (S5) and M651A (S6) mutations impaired the ability of phenanthrene to inhibit IhERG, as did the S624A mutation below the selectivity filter region. Computational docking using a cryo-EM derived hERG structure supported the mutagenesis data. Thus, phenanthrene acts as an inhibitor of the hERG K+ channel by directly interacting with the channel, binding to a distinct site in the channel pore domain.
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26
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Mousaei M, Kudaibergenova M, MacKerell AD, Noskov S. Assessing hERG1 Blockade from Bayesian Machine-Learning-Optimized Site Identification by Ligand Competitive Saturation Simulations. J Chem Inf Model 2020; 60:6489-6501. [PMID: 33196188 PMCID: PMC7839320 DOI: 10.1021/acs.jcim.0c01065] [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: 12/13/2022]
Abstract
Drug-induced cardiotoxicity is a potentially lethal and yet one of the most common side effects with the drugs in clinical use. Most of the drug-induced cardiotoxicity is associated with an off-target pharmacological blockade of K+ currents carried out by the cardiac Human-Ether-a-go-go-Related (hERG1) potassium channel. There is a compulsory preclinical stage safety assessment for the hERG1 blockade for all classes of drugs, which adds substantially to the cost of drug development. The availability of a high-resolution cryogenic electron microscopy (cryo-EM) structure for the channel in its open/depolarized state solved in 2017 enabled the application of molecular modeling for rapid assessment of drug blockade by molecular docking and simulation techniques. More importantly, if successful, in silico methods may allow a path to lead-compound salvaging by mapping out key block determinants. Here, we report the blind application of the site identification by the ligand competitive saturation (SILCS) protocol to map out druggable/regulatory hotspots in the hERG1 channel available for blockers and activators. The SILCS simulations use small solutes representative of common functional groups to sample the chemical space for the entire protein and its environment using all-atom simulations. The resulting chemical maps, FragMaps, explicitly account for receptor flexibility, protein-fragment interactions, and fragment desolvation penalty allowing for rapid ranking of potential ligands as blockers or nonblockers of hERG1. To illustrate the power of the approach, SILCS was applied to a test set of 55 blockers with diverse chemical scaffolds and pIC50 values measured under uniform conditions. The original SILCS model was based on the all-atom modeling of the hERG1 channel in an explicit lipid bilayer and was further augmented with a Bayesian-optimization/machine-learning (BML) stage employing an independent literature-derived training set of 163 molecules. BML approach was used to determine weighting factors for the FragMaps contributions to the scoring function. pIC50 predictions from the combined SILCS/BML approach to the 55 blockers showed a Pearson correlation (PC) coefficient of >0.535 relative to the experimental data. SILCS/BML model was shown to yield substantially improved performance as compared to commonly used rigid and flexible molecular docking methods for a well-established cohort of hERG1 blockers, where no correlation with experimental data was recorded. SILCS/BML results also suggest that a proper weighting of protonation states of common blockers present at physiological pH is essential for accurate predictions of blocker potency. The precalculated and optimized SILCS FragMaps can now be used for the rapid screening of small molecules for their cardiotoxic potential as well as for exploring alternative binding pockets in the hERG1 channel with applications to the rational design of activators.
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Affiliation(s)
- Mahdi Mousaei
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Meruyert Kudaibergenova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - Alexander D. MacKerell
- Computer-Aided Drug Design Center, Department of Pharmaceutical Science, School of Pharmacy, University of Maryland, Baltimore, MD 21201, USA
| | - Sergei Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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27
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Zequn Z, Yujia W, Dingding Q, Jiangfang L. Off-label use of chloroquine, hydroxychloroquine, azithromycin and lopinavir/ritonavir in COVID-19 risks prolonging the QT interval by targeting the hERG channel. Eur J Pharmacol 2020; 893:173813. [PMID: 33345848 PMCID: PMC7746509 DOI: 10.1016/j.ejphar.2020.173813] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 11/29/2020] [Accepted: 12/11/2020] [Indexed: 12/20/2022]
Abstract
Coronavirus disease-2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), poses an enormous challenge to the medical system, especially the lack of safe and effective COVID-19 treatment methods, forcing people to look for drugs that may have therapeutic effects as soon as possible. Some old drugs have shown clinical benefits after a few small clinical trials that attracted great attention. Clinically, however, many drugs, including those currently used in COVID-19, such as chloroquine, hydroxychloroquine, azithromycin, and lopinavir/ritonavir, may cause cardiotoxicity by acting on cardiac potassium channels, especially hERG channel through their off-target effects. The blocking of the hERG channel prolongs QT intervals on electrocardiograms; thus, it might induce severe ventricular arrhythmias and even sudden cardiac death. Therefore, while focusing on the efficacy of COVID-19 drugs, the fact that they block hERG channels to cause arrhythmias cannot be ignored. To develop safer and more effective drugs, it is necessary to understand the interactions between drugs and the hERG channel and the molecular mechanism behind this high affinity. In this review, we focus on the biochemical and molecular mechanistic aspects of drug-related blockade of the hERG channel to provide insights into QT prolongation caused by off-label use of related drugs in COVID-19, and hope to weigh the risks and benefits when using these drugs.
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Affiliation(s)
- Zheng Zequn
- Medical College, Ningbo University, Ningbo, Zhejiang, 315000, China
| | - Wu Yujia
- Medical College, Ningbo University, Ningbo, Zhejiang, 315000, China
| | - Qian Dingding
- Department of Cardiovascular, Lihuili Hospital Affiliated to Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Lian Jiangfang
- Department of Cardiovascular, Lihuili Hospital Affiliated to Ningbo University, Ningbo, Zhejiang, 315211, China.
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28
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Sinha M, Jagadeesan R, Kumar N, Saha S, Kothandan G, Kumar D. In-silico studies on Myo inositol-1-phosphate synthase of Leishmania donovani in search of anti-leishmaniasis. J Biomol Struct Dyn 2020; 40:3371-3384. [PMID: 33200690 DOI: 10.1080/07391102.2020.1847194] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Myo-inositol is one of the vital nutritional requirements for the Leishmania parasites' survival and virulence in the mammalian host. . Myo-inositol-1-phosphate synthase (MIPS) is responsible for the synthesis of myo-inositol in Leishmania, which plays a vital role in Leishmania's virulence to mammalian hosts. Earlier studies suggest MIP synthase as a potential drug target against which valproate was used as a drug. So, MIP synthase can be used as a target for anti-leishmanial drugs, and its inhibition may help in preventing leishmaniasis. The present study aims to identify valproate's potent analogs as drugs against MIP synthase of L. donovani (Ld-MIPS) with minimum side effects and toxicity to host.In this study, the three-dimensional structure of Ld-MIPS was built, followed by active site prediction. Ligand-based virtual screening was done using hybrid similarity recognition methods. The best 123 valproate analogs were filtered based on their quantitative structure activity relationship (QSAR) properties and were docked against Ld-MIPS using FlexX, PyRx and iGEMDOCK software. The topmost five ligands were selected for molecular dynamics simulation and pharmacokinetic analysis based on the docking score. Simulation studies up to 30 ns revealed that all five lead molecules bound with Ld-MIPS throughout MD simulation and there was no variation in their backbone. All the chosen inhibitors exhibited good pharmacokinetics/ADMET predictions with an excellent absorption profile, metabolism, oral bioavailability, solubility, excretion, and minimal toxicity, suggesting that these inhibitors may further be developed as anti-leishmaniasis drugs to prevent the spread of leishmaniasis.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mousumi Sinha
- Department of Microbiology, Assam University, Silchar, Assam, India
| | - Rahul Jagadeesan
- CAS in Crystallography and Biophysics, Guindy Campus, University of Madras, Chennai, Tamil Nadu, India
| | - Neeraj Kumar
- Functional Genomics & Complex System Lab, Biotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, Himachal Pradesh, India
| | - Satabdi Saha
- Department of Microbiology, Assam University, Silchar, Assam, India
| | - Gugan Kothandan
- CAS in Crystallography and Biophysics, Guindy Campus, University of Madras, Chennai, Tamil Nadu, India
| | - Diwakar Kumar
- Department of Microbiology, Assam University, Silchar, Assam, India
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29
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Synthesis, Molecular Docking, Druglikeness Analysis, and ADMET Prediction of the Chlorinated Ethanoanthracene Derivatives as Possible Antidepressant Agents. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10217727] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Ethanoanthracene cycloadducts (5–7) anti, (5–7) syn, and (5–7) dec have been synthesized from the Diels–Alder (DA) reaction of diene 1,8-dichloroanthracene 2, with the dienophiles; acrylonitrile 3, 1-cynavinyl acetate 4, and phenyl vinyl sulfone 5, individually. The steric effect of dienophile substituents were more favorable toward the anti-isomer formation as deduced from 1H-NMR spectrum. The cheminformatics prediction for (5–7) anti and (5–7) syn was investigated. The in silico anticipated anti-depression activity of the (5–7) anti and (5–7) syn compounds were investigated and compared to maprotiline 9 as reference anti-depressant drug. The study showed that steric interactions play a crucial role in the binding affinity of these compounds to the representative models; 4xnx, 2QJU, and 3GWU. The pharmacokinetic and drug-like properties of (5–7) anti and (5–7) syn exhibited that these compounds could be represented as potential candidates for further development into antidepressant-like agents.
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Harley BK, Dickson RA, Amponsah IK, Ben IO, Adongo DW, Fleischer TC, Habtemariam S. Flavanols and triterpenoids from Myrianthus arboreus ameliorate hyperglycaemia in streptozotocin-induced diabetic rats possibly via glucose uptake enhancement and α-amylase inhibition. Biomed Pharmacother 2020; 132:110847. [PMID: 33068933 DOI: 10.1016/j.biopha.2020.110847] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 10/01/2020] [Accepted: 10/04/2020] [Indexed: 01/30/2023] Open
Abstract
Myrianthus arboreus is use traditionally as an antidiabetic agent in Ghana. We reported the in vivo antidiabetic activity of its 70 % ethanol stem bark extract (MAB) which we found to be strongly concentrated in its EtOAc fraction using glucose uptake and enzyme inhibitory assays. The present study sought to investigate the in vivo hypoglycaemic and anti-hyperlipidaemic activity of this ethyl acetate fraction of MAB (MAB-EtOAc, 50 and 100 mg/kg) in streptozotocin (STZ)-induced diabetic rats for 21 days, isolate and evaluate the bioactive constituents responsible for the antidiabetic activity. In silico pharmacokinetic and toxicity properties of the most active compound was also determined. MAB-EtOAc significantly (p < 0.001) reduced the blood glucose levels while normalizing considerably the altered serum lipid parameters of the diabetic rats which was comparable to glibenclamide (5 mg/kg). Chemical investigation of MAB-EtOAc led to the isolation of seven known compounds including three flavanols which are reported for the first time in the plant: epicatechin (1), epigallocatechin (2), dulcisflavan (3), euscaphic acid (4), tormentic acid (5), sitosterol-3-O-β-d-glucopyranoside (6) and arjunolic acid (7). The compounds markedly inhibited the action of α-amylase and, except for 4 and 6, which stimulated considerably glucose uptake in C2C12 cells. Compounds 2, 3, 5, 6 and 7 which were further evaluated in STZ-induced diabetic rats demonstrated hypoglycaemic and anti-hyperlipidaemic activities which, however, were not comparable with MAB-EtOAc. Compound 3, the most active compound was predicted to be non-toxic, non-mutagenic, has reasonable oral bioavailability and a decent substrate for further drug development. The findings of this study show that the isolated compounds may contribute to the antidiabetic activity of M. arboreus and could serve as marker compounds for the quality control of herbal medicines that would be made from the plant.
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Affiliation(s)
- Benjamin Kingsley Harley
- Department of Pharmacognosy and Herbal Medicine, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana.
| | - Rita Akosua Dickson
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Isaac Kingsley Amponsah
- Department of Pharmacognosy, Faculty of Pharmacy and Pharmaceutical Sciences, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Inemesit Okon Ben
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Donatus Wewura Adongo
- Department of Pharmacology and Toxicology, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Theophilus Christian Fleischer
- Department of Pharmacognosy and Herbal Medicine, School of Pharmacy, University of Health and Allied Sciences, Ho, Ghana
| | - Solomon Habtemariam
- Pharmacognosy Research Laboratories Medway School of Science, University of Greenwich, Central Avenue, Chatham-Maritime, Kent, ME4 4TB, UK
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31
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A structure-based computational workflow to predict liability and binding modes of small molecules to hERG. Sci Rep 2020; 10:16262. [PMID: 33004839 PMCID: PMC7530726 DOI: 10.1038/s41598-020-72889-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Accepted: 09/07/2020] [Indexed: 02/06/2023] Open
Abstract
Off-target interactions of drugs with the human ether-à-go-go related gene 1 (hERG1) channel have been associated with severe cardiotoxic conditions leading to the withdrawal of many drugs from the market over the last decades. Consequently, predicting drug-induced hERG-liability is now a prerequisite in any drug discovery campaign. Understanding the atomic level interactions of drug with the channel is essential to guide the efficient development of safe drugs. Here we utilize the recent cryo-EM structure of the hERG channel and describe an integrated computational workflow to characterize different drug-hERG interactions. The workflow employs various structure-based approaches and provides qualitative and quantitative insights into drug binding to hERG. Our protocol accurately differentiated the strong blockers from weak and revealed three potential anchoring sites in hERG. Drugs engaging in all these sites tend to have high affinity towards hERG. Our results were cross-validated using a fluorescence polarization kit binding assay and with electrophysiology measurements on the wild-type (WT-hERG) and on the two hERG mutants (Y652A-hERG and F656A-hERG), using the patch clamp technique on HEK293 cells. Finally, our analyses show that drugs binding to hERG disrupt and hijack certain native—structural networks in the channel, thereby, gaining more affinity towards hERG.
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Kudaibergenova M, Guo J, Khan HM, Zahid F, Lees-Miller J, Noskov SY, Duff HJ. Allosteric Coupling Between Drug Binding and the Aromatic Cassette in the Pore Domain of the hERG1 Channel: Implications for a State-Dependent Blockade. Front Pharmacol 2020; 11:914. [PMID: 32694995 PMCID: PMC7338687 DOI: 10.3389/fphar.2020.00914] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 06/04/2020] [Indexed: 12/18/2022] Open
Abstract
Human-ether-a-go-go-related channel (hERG1) is the pore-forming domain of the delayed rectifier K+ channel in the heart which underlies the IKr current. The channel has been extensively studied due to its propensity to bind chemically diverse group of drugs. The subsequent hERG1 block can lead to a prolongation of the QT interval potentially leading to an abnormal cardiac electrical activity. The recently solved cryo-EM structure featured a striking non-swapped topology of the Voltage-Sensor Domain (VSD) which is packed against the pore-domain as well as a small and hydrophobic intra-cavity space. The small size and hydrophobicity of the cavity was unexpected and challenges the already-established hypothesis of drugs binding to the wide cavity. Recently, we showed that an amphipathic drug, ivabradine, may favorably bind the channel from the lipid-facing surface and we discovered a mutant (M651T) on the lipid facing domain between the VSD and the PD which inhibited the blocking capacity of the drug. Using multi-microseconds Molecular Dynamics (MD) simulations of wild-type and M651T mutant hERG1, we suggested the block of the channel through the lipid mediated pathway, the opening of which is facilitated by the flexible phenylalanine ring (F656). In this study, we characterize the dynamic interaction of the methionine-aromatic cassette in the S5-S6 helices by combining data from electrophysiological experiments with MD simulations and molecular docking to elucidate the complex allosteric coupling between drug binding to lipid-facing and intra-cavity sites and aromatic cassette dynamics. We investigated two well-established hERG1 blockers (ivabradine and dofetilide) for M651 sensitivity through electrophysiology and mutagenesis techniques. Our electrophysiology data reveal insensitivity of dofetilide to the mutations at site M651 on the lipid facing side of the channel, mirroring our results obtained from docking experiments. Moreover, we show that the dofetilide-induced block of hERG1 occurs through the intracellular space, whereas little to no block of ivabradine is observed during the intracellular application of the drug. The dynamic conformational rearrangement of the F656 appears to regulate the translocation of ivabradine into the central cavity. M651T mutation appears to disrupt this entry pathway by altering the molecular conformation of F656.
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Affiliation(s)
- Meruyert Kudaibergenova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada.,Cumming School of Medicine, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, AB, Canada
| | - Jiqing Guo
- Cumming School of Medicine, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, AB, Canada
| | - Hanif M Khan
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Farhan Zahid
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - James Lees-Miller
- Cumming School of Medicine, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, AB, Canada
| | - Sergei Yu Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB, Canada
| | - Henry J Duff
- Cumming School of Medicine, Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, AB, Canada
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Choi KE, Balupuri A, Kang NS. The Study on the hERG Blocker Prediction Using Chemical Fingerprint Analysis. Molecules 2020; 25:E2615. [PMID: 32512802 PMCID: PMC7321128 DOI: 10.3390/molecules25112615] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 06/01/2020] [Accepted: 06/02/2020] [Indexed: 01/31/2023] Open
Abstract
Human ether-a-go-go-related gene (hERG) potassium channel blockage by small molecules may cause severe cardiac side effects. Thus, it is crucial to screen compounds for activity on the hERG channels early in the drug discovery process. In this study, we collected 5299 hERG inhibitors with diverse chemical structures from a number of sources. Based on this dataset, we evaluated different machine learning (ML) and deep learning (DL) algorithms using various integer and binary type fingerprints. A training set of 3991 compounds was used to develop quantitative structure-activity relationship (QSAR) models. The performance of the developed models was evaluated using a test set of 998 compounds. Models were further validated using external set 1 (263 compounds) and external set 2 (47 compounds). Overall, models with integer type fingerprints showed better performance than models with no fingerprints, converted binary type fingerprints or original binary type fingerprints. Comparison of ML and DL algorithms revealed that integer type fingerprints are suitable for ML, whereas binary type fingerprints are suitable for DL. The outcomes of this study indicate that the rational selection of fingerprints is important for hERG blocker prediction.
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Affiliation(s)
| | | | - Nam Sook Kang
- Graduate School of New Drug Discovery and Development, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Korea; (K.-E.C.); (A.B.)
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34
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Van Theemsche KM, Van de Sande DV, Snyders DJ, Labro AJ. Hydrophobic Drug/Toxin Binding Sites in Voltage-Dependent K + and Na + Channels. Front Pharmacol 2020; 11:735. [PMID: 32499709 PMCID: PMC7243439 DOI: 10.3389/fphar.2020.00735] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Accepted: 05/04/2020] [Indexed: 12/26/2022] Open
Abstract
In the Nav channel family the lipophilic drugs/toxins binding sites and the presence of fenestrations in the channel pore wall are well defined and categorized. No such classification exists in the much larger Kv channel family, although certain lipophilic compounds seem to deviate from binding to well-known hydrophilic binding sites. By mapping different compound binding sites onto 3D structures of Kv channels, there appear to be three distinct lipid-exposed binding sites preserved in Kv channels: the front and back side of the pore domain, and S2-S3/S3-S4 clefts. One or a combination of these sites is most likely the orthologous equivalent of neurotoxin site 5 in Nav channels. This review describes the different lipophilic binding sites and location of pore wall fenestrations within the Kv channel family and compares it to the knowledge of Nav channels.
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Affiliation(s)
- Kenny M Van Theemsche
- Laboratory of Molecular, Cellular, and Network Excitability, University of Antwerp, Antwerp, Belgium
| | - Dieter V Van de Sande
- Laboratory of Molecular, Cellular, and Network Excitability, University of Antwerp, Antwerp, Belgium
| | - Dirk J Snyders
- Laboratory of Molecular, Cellular, and Network Excitability, University of Antwerp, Antwerp, Belgium
| | - Alain J Labro
- Laboratory of Molecular, Cellular, and Network Excitability, University of Antwerp, Antwerp, Belgium
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35
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Brewer KR, Kuenze G, Vanoye CG, George AL, Meiler J, Sanders CR. Structures Illuminate Cardiac Ion Channel Functions in Health and in Long QT Syndrome. Front Pharmacol 2020; 11:550. [PMID: 32431610 PMCID: PMC7212895 DOI: 10.3389/fphar.2020.00550] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 04/09/2020] [Indexed: 12/13/2022] Open
Abstract
The cardiac action potential is critical to the production of a synchronized heartbeat. This electrical impulse is governed by the intricate activity of cardiac ion channels, among them the cardiac voltage-gated potassium (Kv) channels KCNQ1 and hERG as well as the voltage-gated sodium (Nav) channel encoded by SCN5A. Each channel performs a highly distinct function, despite sharing a common topology and structural components. These three channels are also the primary proteins mutated in congenital long QT syndrome (LQTS), a genetic condition that predisposes to cardiac arrhythmia and sudden cardiac death due to impaired repolarization of the action potential and has a particular proclivity for reentrant ventricular arrhythmias. Recent cryo-electron microscopy structures of human KCNQ1 and hERG, along with the rat homolog of SCN5A and other mammalian sodium channels, provide atomic-level insight into the structure and function of these proteins that advance our understanding of their distinct functions in the cardiac action potential, as well as the molecular basis of LQTS. In this review, the gating, regulation, LQTS mechanisms, and pharmacological properties of KCNQ1, hERG, and SCN5A are discussed in light of these recent structural findings.
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Affiliation(s)
- Kathryn R. Brewer
- Center for Structural Biology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
| | - Georg Kuenze
- Center for Structural Biology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
| | - Carlos G. Vanoye
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Alfred L. George
- Department of Pharmacology, Feinberg School of Medicine, Northwestern University, Chicago, IL, United States
| | - Jens Meiler
- Center for Structural Biology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, United States
- Department of Chemistry, Vanderbilt University, Nashville, TN, United States
- Department of Pharmacology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, United States
- Institute for Drug Discovery, Leipzig University Medical School, Leipzig, Germany
| | - Charles R. Sanders
- Center for Structural Biology, Vanderbilt University School of Medicine Basic Sciences, Nashville, TN, United States
- Department of Biochemistry, Vanderbilt University, Nashville, TN, United States
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36
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Garrido A, Lepailleur A, Mignani SM, Dallemagne P, Rochais C. hERG toxicity assessment: Useful guidelines for drug design. Eur J Med Chem 2020; 195:112290. [PMID: 32283295 DOI: 10.1016/j.ejmech.2020.112290] [Citation(s) in RCA: 109] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 03/27/2020] [Accepted: 03/27/2020] [Indexed: 02/06/2023]
Abstract
All along the drug development process, one of the most frequent adverse side effects, leading to the failure of drugs, is the cardiac arrhythmias. Such failure is mostly related to the capacity of the drug to inhibit the human ether-à-go-go-related gene (hERG) cardiac potassium channel. The early identification of hERG inhibition properties of biological active compounds has focused most of attention over the years. In order to prevent the cardiac side effects, a great number of in silico, in vitro and in vivo assays have been performed. The main goal of these studies is to understand the reasons of these effects, and then to give information or instructions to scientists involved in drug development to avoid the cardiac side effects. To evaluate anticipated cardiovascular effects, early evaluation of hERG toxicity has been strongly recommended for instance by the regulatory agencies such as U.S. Food and Drug Administration (FDA) and European Medicines Agency (EMA). Thus, following an initial screening of a collection of compounds to find hits, a great number of pharmacomodulation studies on the novel identified chemical series need to be performed including activity evaluation towards hERG. We provide in this concise review clear guidelines, based on described examples, illustrating successful optimization process to avoid hERG interactions as cases studies and to spur scientists to develop safe drugs.
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Affiliation(s)
- Amanda Garrido
- Normandie Univ, UNICAEN, Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), Caen, France
| | - Alban Lepailleur
- Normandie Univ, UNICAEN, Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), Caen, France
| | - Serge M Mignani
- UMR 860, Laboratoire de Chimie et de Biochimie Pharmacologiques et Toxicologique, Université Paris Descartes, PRES Sorbonne Paris Cité, CNRS, 45 rue des Saints Pères, 75006, Paris, France; CQM - Centro de Química da Madeira, MMRG, Universidade da Madeira, Campus da Penteada, 9020-105, Funchal, Portugal
| | - Patrick Dallemagne
- Normandie Univ, UNICAEN, Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), Caen, France
| | - Christophe Rochais
- Normandie Univ, UNICAEN, Centre d'Etudes et de Recherche sur le Médicament de Normandie (CERMN), Caen, France.
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37
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Qile M, Ji Y, Golden TD, Houtman MJ, Romunde F, Fransen D, van Ham WB, IJzerman AP, January CT, Heitman LH, Stary-Weinzinger A, Delisle BP, van der Heyden MA. LUF7244 plus Dofetilide Rescues Aberrant Kv11.1 Trafficking and Produces Functional IKv11.1. Mol Pharmacol 2020; 97:355-364. [DOI: 10.1124/mol.119.118190] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 03/24/2020] [Indexed: 11/22/2022] Open
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38
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Jiao L, Machuki JO, Wu Q, Shi M, Fu L, Adekunle AO, Tao X, Xu C, Hu X, Yin Z, Sun H. Estrogen and calcium handling proteins: new discoveries and mechanisms in cardiovascular diseases. Am J Physiol Heart Circ Physiol 2020; 318:H820-H829. [PMID: 32083972 DOI: 10.1152/ajpheart.00734.2019] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Estrogen deficiency is considered to be an important factor leading to cardiovascular diseases (CVDs). Indeed, the prevalence of CVDs in postmenopausal women exceeds that of premenopausal women and men of the same age. Recent research findings provide evidence that estrogen plays a pivotal role in the regulation of calcium homeostasis and therefore fine-tunes normal cardiomyocyte contraction and relaxation processes. Disruption of calcium homeostasis is closely associated with the pathological mechanism of CVDs. Thus, this paper maps out and summarizes the effects and mechanisms of estrogen on calcium handling proteins in cardiac myocytes, including L-type Ca2+ channel, the sarcoplasmic reticulum Ca2+ release channel named ryanodine receptor, sarco(endo)plasmic reticulum Ca2+-ATPase, and sodium-calcium exchanger. In so doing, we provide theoretical and experimental evidence for the successful design of estrogen-based prevention and treatment therapies for CVDs.
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Affiliation(s)
- Lijuan Jiao
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | | | - Qi Wu
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Mingjin Shi
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Lu Fu
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | | | - Xi Tao
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Chenxi Xu
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Xide Hu
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Zeyuan Yin
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
| | - Hong Sun
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, China
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39
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Butler A, Helliwell MV, Zhang Y, Hancox JC, Dempsey CE. An Update on the Structure of hERG. Front Pharmacol 2020; 10:1572. [PMID: 32038248 PMCID: PMC6992539 DOI: 10.3389/fphar.2019.01572] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 12/04/2019] [Indexed: 01/22/2023] Open
Abstract
The human voltage-sensitive K+ channel hERG plays a fundamental role in cardiac action potential repolarization, effectively controlling the QT interval of the electrocardiogram. Inherited loss- or gain-of-function mutations in hERG can result in dangerous “long” (LQTS) or “short” QT syndromes (SQTS), respectively, and the anomalous susceptibility of hERG to block by a diverse range of drugs underlies an acquired LQTS. A recent open channel cryo-EM structure of hERG should greatly advance understanding of the molecular basis of hERG channelopathies and drug-induced LQTS. Here we describe an update of recent research that addresses the nature of the particular gated state of hERG captured in the new structure, and the insight afforded by the structure into the molecular basis for high affinity drug block of hERG, the binding of hERG activators and the molecular basis of hERG's peculiar gating properties. Interpretation of the pharmacology of natural SQTS mutants in the context of the structure is a promising approach to understanding the molecular basis of hERG inactivation, and the structure suggests how voltage-dependent changes in the membrane domain may be transmitted to an extracellular “turret” to effect inactivation through aromatic side chain motifs that are conserved throughout the KCNH family of channels.
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Affiliation(s)
- Andrew Butler
- School of Physiology, Pharmacology and Neuroscience, Medical Sciences Building, Bristol, United Kingdom
| | - Matthew V Helliwell
- School of Physiology, Pharmacology and Neuroscience, Medical Sciences Building, Bristol, United Kingdom
| | - Yihong Zhang
- School of Physiology, Pharmacology and Neuroscience, Medical Sciences Building, Bristol, United Kingdom
| | - Jules C Hancox
- School of Physiology, Pharmacology and Neuroscience, Medical Sciences Building, Bristol, United Kingdom
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40
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Dickson CJ, Velez-Vega C, Duca JS. Revealing Molecular Determinants of hERG Blocker and Activator Binding. J Chem Inf Model 2020; 60:192-203. [PMID: 31880933 DOI: 10.1021/acs.jcim.9b00773] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Kv11.1 potassium channel, encoded by the human ether-a-go-go-related gene (hERG), plays an essential role in the cardiac action potential. hERG blockade by small molecules can induce "torsade de pointes" arrhythmias and sudden death; as such, it is an important off-target to avoid during drug discovery. Recently, a cryo-EM structure of the open channel state of hERG was reported, opening the door to in silico docking analyses and interpretation of hERG structure-activity relationships, with a view to avoiding blocking activity. Despite this, docking directly to this cryo-EM structure has been reported to yield binding modes that are unable to explain known mutagenesis data. In this work, we use molecular dynamics simulations to sample a range of channel conformations and run ensemble docking campaigns at the known hERG binding site below the selectivity filter, composed of the central cavity and the four deep hydrophobic pockets. We identify a hERG conformational state allowing discrimination of blockers vs nonblockers from docking; furthermore, the binding pocket agrees with mutagenesis data, and blocker binding modes fit the hERG blocker pharmacophore. We then use the same protocol to identify a binding pocket in the hERG channel pore for hERG activators, again agreeing with the reported mutagenesis. Our approach may be useful in drug discovery campaigns to prioritize candidate compounds based on hERG liability via virtual docking screens.
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Affiliation(s)
- Callum J Dickson
- Computer-Aided Drug Discovery, Global Discovery Chemistry , Novartis Institutes for BioMedical Research , 181 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Camilo Velez-Vega
- Computer-Aided Drug Discovery, Global Discovery Chemistry , Novartis Institutes for BioMedical Research , 181 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
| | - Jose S Duca
- Computer-Aided Drug Discovery, Global Discovery Chemistry , Novartis Institutes for BioMedical Research , 181 Massachusetts Avenue , Cambridge , Massachusetts 02139 , United States
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41
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Negami T, Araki M, Okuno Y, Terada T. Calculation of absolute binding free energies between the hERG channel and structurally diverse drugs. Sci Rep 2019; 9:16586. [PMID: 31719645 PMCID: PMC6851376 DOI: 10.1038/s41598-019-53120-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 10/28/2019] [Indexed: 11/11/2022] Open
Abstract
The human ether-a-go-go-related gene (hERG) encodes a voltage-gated potassium channel that plays an essential role in the repolarization of action potentials in cardiac muscle. However, various drugs can block the ion current by binding to the hERG channel, resulting in potentially lethal cardiac arrhythmia. Accordingly, in silico studies are necessary to clarify the mechanisms of how these drugs bind to the hERG channel. Here, we used the experimental structure of the hERG channel, determined by cryo-electron microscopy, to perform docking simulations to predict the complex structures that occur between the hERG channel and structurally diverse drugs. The absolute binding free energies for the models were calculated using the MP-CAFEE method; calculated values were well correlated with experimental ones. By applying the regression equation obtained here, the affinity of a drug for the hERG channel can be accurately predicted from the calculated value of the absolute binding free energy.
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Affiliation(s)
- Tatsuki Negami
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Mitsugu Araki
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Yasushi Okuno
- Graduate School of Medicine, Kyoto University, 53 Shogoin-Kawaharacho, Sakyo-ku, Kyoto, 606-8507, Japan
| | - Tohru Terada
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo, 113-8657, Japan. .,Interfaculty Initiative in Information Studies, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan.
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42
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Cernuda B, Fernandes CT, Allam SM, Orzillo M, Suppa G, Chia Chang Z, Athanasopoulos D, Buraei Z. The molecular determinants of R-roscovitine block of hERG channels. PLoS One 2019; 14:e0217733. [PMID: 31479461 PMCID: PMC6719874 DOI: 10.1371/journal.pone.0217733] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 08/17/2019] [Indexed: 02/06/2023] Open
Abstract
Human ether-à-go-go-related gene (Kv11.1, or hERG) is a potassium channel that conducts the delayed rectifier potassium current (IKr) during the repolarization phase of cardiac action potentials. hERG channels have a larger pore than other K+channels and can trap many unintended drugs, often resulting in acquired LQTS (aLQTS). R-roscovitine is a cyclin-dependent kinase (CDK) inhibitor that induces apoptosis in colorectal, breast, prostate, multiple myeloma, other cancer cell lines, and tumor xenografts, in micromolar concentrations. It is well tolerated in phase II clinical trials. R-roscovitine inhibits open hERG channels but does not become trapped in the pore. Two-electrode voltage clamp recordings from Xenopus oocytes expressing wild-type (WT) or hERG pore mutant channels (T623A, S624A, Y652A, F656A) demonstrated that compared to WT hERG, T623A, Y652A, and F656A inhibition by 200 μM R-roscovitine was ~ 48%, 29%, and 73% weaker, respectively. In contrast, S624A hERG was inhibited more potently than WT hERG, with a ~ 34% stronger inhibition. These findings were further supported by the IC50 values, which were increased for T623A, Y652A and F656A (by ~5.5, 2.75, and 42 fold respectively) and reduced 1.3 fold for the S624A mutant. Our data suggest that while T623, Y652, and F656 are critical for R-roscovitine-mediated inhibition, S624 may not be. Docking studies further support our findings. Thus, R-roscovitine’s relatively unique features, coupled with its tolerance in clinical trials, could guide future drug screens.
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Affiliation(s)
- Bryan Cernuda
- Department of Biology, Pace University, New York, NY, United States of America
| | | | - Salma Mohamed Allam
- Department of Biology, Pace University, New York, NY, United States of America
| | - Matthew Orzillo
- Department of Biology, Pace University, New York, NY, United States of America
| | - Gabrielle Suppa
- Department of Biology, Pace University, New York, NY, United States of America
| | - Zuleen Chia Chang
- Department of Biology, Pace University, New York, NY, United States of America
| | | | - Zafir Buraei
- Department of Biology, Pace University, New York, NY, United States of America
- * E-mail:
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Qile M, Beekman HDM, Sprenkeler DJ, Houtman MJC, van Ham WB, Stary-Weinzinger A, Beyl S, Hering S, van den Berg DJ, de Lange ECM, Heitman LH, IJzerman AP, Vos MA, van der Heyden MAG. LUF7244, an allosteric modulator/activator of K v 11.1 channels, counteracts dofetilide-induced torsades de pointes arrhythmia in the chronic atrioventricular block dog model. Br J Pharmacol 2019; 176:3871-3885. [PMID: 31339551 PMCID: PMC6780032 DOI: 10.1111/bph.14798] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 07/08/2019] [Accepted: 07/11/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND AND PURPOSE Kv 11.1 (hERG) channel blockade is an adverse effect of many drugs and lead compounds, associated with lethal cardiac arrhythmias. LUF7244 is a negative allosteric modulator/activator of Kv 11.1 channels that inhibits early afterdepolarizations in vitro. We tested LUF7244 for antiarrhythmic efficacy and potential proarrhythmia in a dog model. EXPERIMENTAL APPROACH LUF7244 was tested in vitro for (a) increasing human IKv11.1 and canine IKr and (b) decreasing dofetilide-induced action potential lengthening and early afterdepolarizations in cardiomyocytes derived from human induced pluripotent stem cells and canine isolated ventricular cardiomyocytes. In vivo, LUF7244 was given intravenously to anaesthetized dogs in sinus rhythm or with chronic atrioventricular block. KEY RESULTS LUF7244 (0.5-10 μM) concentration dependently increased IKv11.1 by inhibiting inactivation. In vitro, LUF7244 (10 μM) had no effects on IKIR2.1 , INav1.5 , ICa-L , and IKs , doubled IKr , shortened human and canine action potential duration by approximately 50%, and inhibited dofetilide-induced early afterdepolarizations. LUF7244 (2.5 mg·kg-1 ·15 min-1 ) in dogs with sinus rhythm was not proarrhythmic and shortened, non-significantly, repolarization parameters (QTc: -6.8%). In dogs with chronic atrioventricular block, LUF7244 prevented dofetilide-induced torsades de pointes arrhythmias in 5/7 animals without normalization of the QTc. Peak LUF7244 plasma levels were 1.75 ± 0.80 during sinus rhythm and 2.34 ± 1.57 μM after chronic atrioventricular block. CONCLUSIONS AND IMPLICATIONS LUF7244 counteracted dofetilide-induced early afterdepolarizations in vitro and torsades de pointes in vivo. Allosteric modulators/activators of Kv 11.1 channels might neutralize adverse cardiac effects of existing drugs and newly developed compounds that display QTc lengthening.
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Affiliation(s)
- Muge Qile
- Department of Medical Physiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Henriette D M Beekman
- Department of Medical Physiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - David J Sprenkeler
- Department of Medical Physiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Marien J C Houtman
- Department of Medical Physiology, University Medical Centre Utrecht, Utrecht, The Netherlands
| | - Willem B van Ham
- Department of Medical Physiology, University Medical Centre Utrecht, Utrecht, The Netherlands.,Department of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | | | - Stanislav Beyl
- Department of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | - Steffen Hering
- Department of Pharmacology and Toxicology, University of Vienna, Vienna, Austria
| | - Dirk-Jan van den Berg
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Elizabeth C M de Lange
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Laura H Heitman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Ad P IJzerman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Leiden, The Netherlands
| | - Marc A Vos
- Department of Medical Physiology, University Medical Centre Utrecht, Utrecht, The Netherlands
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Dierich M, van Ham WB, Stary‐Weinzinger A, Leitner MG. Histidine at position 462 determines the low quinine sensitivity of ether-à-go-go channel superfamily member K v 12.1. Br J Pharmacol 2019; 176:2708-2723. [PMID: 31032878 PMCID: PMC6609544 DOI: 10.1111/bph.14693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 04/03/2019] [Accepted: 04/15/2019] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND AND PURPOSE The ether-à-go-go (Eag) Kv superfamily comprises closely related Kv 10, Kv 11, and Kv 12 subunits. Kv 11.1 (termed hERG in humans) gained much attention, as drug-induced inhibition of these channels is a frequent cause of sudden death in humans. The exclusive drug sensitivity of Kv 11.1 can be explained by central drug-binding pockets that are absent in most other channels. Currently, it is unknown whether Kv 12 channels are equipped with an analogous drug-binding pocket and whether drug-binding properties are conserved in all Eag superfamily members. EXPERIMENTAL APPROACH We analysed sensitivity of recombinant Kv 12.1 channels to quinine, a substituted quinoline that blocks Kv 10.1 and Kv 11.1 at low micromolar concentrations. KEY RESULTS Quinine inhibited Kv 12.1, but its affinity was 10-fold lower than for Kv 11.1. Contrary to Kv 11.1, quinine inhibited Kv 12.1 in a largely voltage-independent manner and induced channel opening at more depolarised potentials. Low sensitivity of Kv 12.1 and characteristics of quinine-dependent inhibition were determined by histidine 462, as site-directed mutagenesis of this residue into the homologous tyrosine of Kv 11.1 conferred Kv 11.1-like quinine block to Kv 12.1(H462Y). Molecular modelling demonstrated that the low affinity of Kv 12.1 was determined by only weak interactions of residues in the central cavity with quinine. In contrast, more favourable interactions can explain the higher quinine sensitivity of Kv 12.1(H462Y) and Kv 11.1 channels. CONCLUSIONS AND IMPLICATIONS The quinoline-binding "motif" is not conserved within the Eag superfamily, although the overall architecture of these channels is apparently similar. Our findings highlight functional and pharmacological diversity in this group of evolutionary-conserved channels.
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Affiliation(s)
- Marlen Dierich
- Department of Neurophysiology, Institute of Physiology and PathophysiologyPhilipps‐University MarburgMarburgGermany
| | - Willem B. van Ham
- Department of Medical PhysiologyUniversity Medical Center UtrechtUtrechtThe Netherlands
- Department of Pharmacology and ToxicologyUniversity of ViennaViennaAustria
| | | | - Michael G. Leitner
- Department of Neurophysiology, Institute of Physiology and PathophysiologyPhilipps‐University MarburgMarburgGermany
- Division of Physiology, Department of Physiology and Medical PhysicsMedical University of InnsbruckInnsbruckAustria
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Potent hERG channel inhibition by sarizotan, an investigative treatment for Rett Syndrome. J Mol Cell Cardiol 2019; 135:22-30. [PMID: 31362019 PMCID: PMC6856717 DOI: 10.1016/j.yjmcc.2019.07.012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Accepted: 07/26/2019] [Indexed: 12/31/2022]
Abstract
Rett Syndrome (RTT) is an X-linked neurodevelopmental disorder associated with respiratory abnormalities and, in up to ~40% of patients, with prolongation of the cardiac QTc interval. QTc prolongation calls for cautious use of drugs with a propensity to inhibit hERG channels. The STARS trial has been undertaken to investigate the efficacy of sarizotan, a 5-HT1A receptor agonist, at correcting RTT respiratory abnormalities. The present study investigated whether sarizotan inhibits hERG potassium channels and prolongs ventricular repolarization. Whole-cell patch-clamp measurements were made at 37 °C from hERG-expressing HEK293 cells. Docking analysis was conducted using a recent cryo-EM structure of hERG. Sarizotan was a potent inhibitor of hERG current (IhERG; IC50 of 183 nM) and of native ventricular IKr from guinea-pig ventricular myocytes. 100 nM and 1 μM sarizotan prolonged ventricular action potential (AP) duration (APD90) by 14.1 ± 3.3% (n = 6) and 29.8 ± 3.1% (n = 5) respectively and promoted AP triangulation. High affinity IhERG inhibition by sarizotan was contingent upon channel gating and intact inactivation. Mutagenesis experiments and docking analysis implicated F557, S624 and Y652 residues in sarizotan binding, with weaker contribution from F656. In conclusion, sarizotan inhibits IKr/IhERG, accessing key binding residues on channel gating. This action and consequent ventricular AP prolongation occur at concentrations relevant to those proposed to treat breathing dysrhythmia in RTT. Sarizotan should only be used in RTT patients with careful evaluation of risk factors for QTc prolongation.
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Escudero F, Ardenghi JS, Jasen P. Temperature effect on the magnetic oscillations in 2D materials. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2019; 31:285804. [PMID: 30925493 DOI: 10.1088/1361-648x/ab14b6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We study the magnetic oscillations (MO) in 2D materials with a buckled honeycomb lattice, considering a perpendicular electric and magnetic field. At zero temperature the MO consist of the sum of four sawtooth oscillations, with two unique frequencies and phases. The values of these frequencies depend on the Fermi energy and electric field, which in turn determine the condition for a beating phenomenon in the MO. We analyse the temperature effect in the MO by considering its local corrections over each magnetization peak, given by Fermi-Dirac like functions. We show that the width of these functions is related to the minimum temperature necessary to observe the spin and valley properties in the MO. In particular, we find that in order to observe the spin splitting, the width must be lower than the MO phase difference. Likewise, in order to observe valley mixing effects, the width must be lower than the MO period. We also show that at high temperatures, all the maxima and minima in the MO shift to a constant value, in which case we obtain a simple expression for the MO and its envelope. The results obtained show unique features in the MO in 2D materials, given by the interplay between the valley and spin.
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Affiliation(s)
- F Escudero
- Departamento de Física, Universidad Nacional del Sur, Av. Alem 1253, B8000CPB Bahía Blanca, Argentina. Instituto de Física del Sur (IFISUR, UNS-CONICET), Av. Alem 1253, B8000CPB Bahía Blanca, Argentina
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Bedoya M, Rinné S, Kiper AK, Decher N, González W, Ramírez D. TASK Channels Pharmacology: New Challenges in Drug Design. J Med Chem 2019; 62:10044-10058. [PMID: 31260312 DOI: 10.1021/acs.jmedchem.9b00248] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Rational drug design targeting ion channels is an exciting and always evolving research field. New medicinal chemistry strategies are being implemented to explore the wild chemical space and unravel the molecular basis of the ion channels modulators binding mechanisms. TASK channels belong to the two-pore domain potassium channel family and are modulated by extracellular acidosis. They are extensively distributed along the cardiovascular and central nervous systems, and their expression is up- and downregulated in different cancer types, which makes them an attractive therapeutic target. However, TASK channels remain unexplored, and drugs designed to target these channels are poorly selective. Here, we review TASK channels properties and their known blockers and activators, considering the new challenges in ion channels drug design and focusing on the implementation of computational methodologies in the drug discovery process.
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Affiliation(s)
- Mauricio Bedoya
- Centro de Bioinformática y Simulación Molecular (CBSM) , Universidad de Talca , 1 Poniente No. 1141 , 3460000 Talca , Chile
| | - Susanne Rinné
- Institute for Physiology and Pathophysiology, Vegetative Physiology and Marburg Center for Mind, Brain and Behavior, MCMBB , Philipps-University of Marburg , Deutschhausstraße 2 , Marburg 35037 , Germany
| | - Aytug K Kiper
- Institute for Physiology and Pathophysiology, Vegetative Physiology and Marburg Center for Mind, Brain and Behavior, MCMBB , Philipps-University of Marburg , Deutschhausstraße 2 , Marburg 35037 , Germany
| | - Niels Decher
- Institute for Physiology and Pathophysiology, Vegetative Physiology and Marburg Center for Mind, Brain and Behavior, MCMBB , Philipps-University of Marburg , Deutschhausstraße 2 , Marburg 35037 , Germany
| | - Wendy González
- Centro de Bioinformática y Simulación Molecular (CBSM) , Universidad de Talca , 1 Poniente No. 1141 , 3460000 Talca , Chile.,Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD) , Universidad de Talca , 1 Poniente No. 1141 , 3460000 Talca , Chile
| | - David Ramírez
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud , Universidad Autónoma de Chile , El Llano Subercaseaux 2801, Piso 6 , 8900000 Santiago , Chile
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McAleer CW, Pointon A, Long CJ, Brighton RL, Wilkin BD, Bridges LR, Narasimhan Sriram N, Fabre K, McDougall R, Muse VP, Mettetal JT, Srivastava A, Williams D, Schnepper MT, Roles JL, Shuler ML, Hickman JJ, Ewart L. On the potential of in vitro organ-chip models to define temporal pharmacokinetic-pharmacodynamic relationships. Sci Rep 2019; 9:9619. [PMID: 31270362 PMCID: PMC6610665 DOI: 10.1038/s41598-019-45656-4] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 06/07/2019] [Indexed: 12/20/2022] Open
Abstract
Functional human-on-a-chip systems hold great promise to enable quantitative translation to in vivo outcomes. Here, we explored this concept using a pumpless heart only and heart:liver system to evaluate the temporal pharmacokinetic/pharmacodynamic (PKPD) relationship for terfenadine. There was a time dependent drug-induced increase in field potential duration in the cardiac compartment in response to terfenadine and that response was modulated using a metabolically competent liver module that converted terfenadine to fexofenadine. Using this data, a mathematical model was developed to predict the effect of terfenadine in preclinical species. Developing confidence that microphysiological models could have a transformative effect on drug discovery, we also tested a previously discovered proprietary AstraZeneca small molecule and correctly determined the cardiotoxic response to its metabolite in the heart:liver system. Overall our findings serve as a guiding principle to future investigations of temporal concentration response relationships in these innovative in vitro models, especially, if validated across multiple time frames, with additional pharmacological mechanisms and molecules representing a broad chemical diversity.
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Affiliation(s)
| | - Amy Pointon
- Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Christopher J Long
- Hesperos, Inc., 3259 Progress Dr., Room 158, Orlando, FL, 32826-3230, USA
| | - Rocky L Brighton
- Hesperos, Inc., 3259 Progress Dr., Room 158, Orlando, FL, 32826-3230, USA
| | - Benjamin D Wilkin
- Hesperos, Inc., 3259 Progress Dr., Room 158, Orlando, FL, 32826-3230, USA
| | - L Richard Bridges
- Hesperos, Inc., 3259 Progress Dr., Room 158, Orlando, FL, 32826-3230, USA
| | | | - Kristin Fabre
- Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Waltham, USA
| | - Robin McDougall
- Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Waltham, USA
| | - Victorine P Muse
- Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Waltham, USA
| | - Jerome T Mettetal
- Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Waltham, USA
| | | | - Dominic Williams
- Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Mark T Schnepper
- NanoScience Technology Center, 12424 Research Parkway, Suite 400, Orlando, FL, 32826, USA
| | - Jeff L Roles
- Hesperos, Inc., 3259 Progress Dr., Room 158, Orlando, FL, 32826-3230, USA
| | - Michael L Shuler
- Hesperos, Inc., 3259 Progress Dr., Room 158, Orlando, FL, 32826-3230, USA
| | - James J Hickman
- Hesperos, Inc., 3259 Progress Dr., Room 158, Orlando, FL, 32826-3230, USA.
- NanoScience Technology Center, 12424 Research Parkway, Suite 400, Orlando, FL, 32826, USA.
| | - Lorna Ewart
- Drug Safety and Metabolism, IMED Biotech Unit, AstraZeneca, Cambridge, UK.
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Perissinotti L, Guo J, Kudaibergenova M, Lees-Miller J, Ol'khovich M, Sharapova A, Perlovich GL, Muruve DA, Gerull B, Noskov SY, Duff HJ. The Pore-Lipid Interface: Role of Amino-Acid Determinants of Lipophilic Access by Ivabradine to the hERG1 Pore Domain. Mol Pharmacol 2019; 96:259-271. [PMID: 31182542 DOI: 10.1124/mol.118.115642] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 05/28/2019] [Indexed: 12/14/2022] Open
Abstract
Abnormal cardiac electrical activity is a common side effect caused by unintended block of the promiscuous drug target human ether-à-go-go-related gene (hERG1), the pore-forming domain of the delayed rectifier K+ channel in the heart. hERG1 block leads to a prolongation of the QT interval, a phase of the cardiac cycle that underlies myocyte repolarization detectable on the electrocardiogram. Even newly released drugs such as heart-rate lowering agent ivabradine block the rapid delayed rectifier current IKr, prolong action potential duration, and induce potentially lethal arrhythmia known as torsades de pointes. In this study, we describe a critical drug-binding pocket located at the lateral pore surface facing the cellular membrane. Mutations of the conserved M651 residue alter ivabradine-induced block but not by the common hERG1 blocker dofetilide. As revealed by molecular dynamics simulations, binding of ivabradine to a lipophilic pore access site is coupled to a state-dependent reorientation of aromatic residues F557 and F656 in the S5 and S6 helices. We show that the M651 mutation impedes state-dependent dynamics of F557 and F656 aromatic cassettes at the protein-lipid interface, which has a potential to disrupt drug-induced block of the channel. This fundamentally new mechanism coupling the channel dynamics and small-molecule access from the membrane into the hERG1 intracavitary site provides a simple rationale for the well established state-dependence of drug blockade. SIGNIFICANCE STATEMENT: The drug interference with the function of the cardiac hERG channels represents one of the major sources of drug-induced heart disturbances. We found a novel and a critical drug-binding pocket adjacent to a lipid-facing surface of the hERG1 channel, which furthers our molecular understanding of drug-induced QT syndrome.
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Affiliation(s)
- Laura Perissinotti
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Jiqing Guo
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Meruyert Kudaibergenova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - James Lees-Miller
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Marina Ol'khovich
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Angelica Sharapova
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - German L Perlovich
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Daniel A Muruve
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Brenda Gerull
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Sergei Yu Noskov
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
| | - Henry J Duff
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada (L.P., M.K., S.Y.N.); Libin Cardiovascular Institute of Alberta (J.G., J.-L.M., H.J.D.) and Snyder Institute for Chronic Diseases (D.A.M.), Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Institute of Solution Chemistry, Russian Academy of Sciences, Ivanovo, Russian Federation (M.O., A.S., G.L.P.); Department of Cardiac Sciences and Libin Cardiovascular Institute of Alberta, University of Calgary, Calgary, Alberta, Canada (B.G.); and Comprehensive Heart Failure Center and Department of Internal Medicine I, University Hospital Würzburg, Würzburg, Germany (B.G.)
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Palomo-Ligas L, Gutiérrez-Gutiérrez F, Ochoa-Maganda VY, Cortés-Zárate R, Charles-Niño CL, Castillo-Romero A. Identification of a novel potassium channel (GiK) as a potential drug target in Giardia lamblia: Computational descriptions of binding sites. PeerJ 2019; 7:e6430. [PMID: 30834181 PMCID: PMC6397635 DOI: 10.7717/peerj.6430] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 01/10/2019] [Indexed: 12/12/2022] Open
Abstract
Background The protozoan Giardia lamblia is the causal agent of giardiasis, one of the main diarrheal infections worldwide. Drug resistance to common antigiardial agents and incidence of treatment failures have increased in recent years. Therefore, the search for new molecular targets for drugs against Giardia infection is essential. In protozoa, ionic channels have roles in their life cycle, growth, and stress response. Thus, they are promising targets for drug design. The strategy of ligand-protein docking has demonstrated a great potential in the discovery of new targets and structure-based drug design studies. Methods In this work, we identify and characterize a new potassium channel, GiK, in the genome of Giardia lamblia. Characterization was performed in silico. Because its crystallographic structure remains unresolved, homology modeling was used to construct the three-dimensional model for the pore domain of GiK. The docking virtual screening approach was employed to determine whether GiK is a good target for potassium channel blockers. Results The GiK sequence showed 24–50% identity and 50–90% positivity with 21 different types of potassium channels. The quality assessment and validation parameters indicated the reliability of the modeled structure of GiK. We identified 110 potassium channel blockers exhibiting high affinity toward GiK. A total of 39 of these drugs bind in three specific regions. Discussion The GiK pore signature sequence is related to the small conductance calcium-activated potassium channels (SKCa). The predicted binding of 110 potassium blockers to GiK makes this protein an attractive target for biological testing to evaluate its role in the life cycle of Giardia lamblia and potential candidate for the design of novel antigiardial drugs.
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Affiliation(s)
- Lissethe Palomo-Ligas
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Filiberto Gutiérrez-Gutiérrez
- Departamento de Química, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Verónica Yadira Ochoa-Maganda
- Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Rafael Cortés-Zárate
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Claudia Lisette Charles-Niño
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | - Araceli Castillo-Romero
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
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