1
|
Hsieh CY, Tsai CY, Chou YF, Hsu CJ, Wu HP, Wu CC. Otoprotection against aminoglycoside- and cisplatin-induced ototoxicity focusing on the upstream drug uptake pathway. J Chin Med Assoc 2024; 87:17-24. [PMID: 37962398 DOI: 10.1097/jcma.0000000000001023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/15/2023] Open
Abstract
Aminoglycoside- and cisplatin-induced ototoxicity, which is a significant issue owing to the widespread use of these drugs in clinical practice, involves the entry of aminoglycosides and cisplatin into the endolymph and hair cells via specific channels or transporters, followed by reactive oxygen species (ROS) generation and hair cells apoptosis. Current strategies focalize primarily on interference with downstream ROS effects; however, recent evidence has demonstrated that inhibiting the uptake of aminoglycosides and cisplatin by hair cells is another promising strategy for tackling the upstream drug uptake pathway. With advances in structural biology, the conformations of certain aminoglycoside and cisplatin channels and transporters, such as the mechanoelectrical transduction channel and organic cation transporter-2, have been largely elucidated. These channels and transporters may become potential targets for the introduction of new otoprotective strategies. This review focuses on the strategies for inhibiting ototoxic drugs uptake by auditory hair cells and provides potential targets for recent developments in the field of otoprotection. Molecular dynamics (MD) simulations of these proteins could help identify the molecules that inhibit the uptake of aminoglycosides and cisplatin by hair cells. Integrating upstream drug uptake pathway targets and MD simulations may help dissect molecular mechanisms and develop novel otoprotective strategies for aminoglycoside- and cisplatin-induced ototoxicity.
Collapse
Affiliation(s)
- Cheng-Yu Hsieh
- Department of Otolaryngology Head and Neck Surgery, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan, ROC
- Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
| | - Cheng-Yu Tsai
- Graduate Institute of Medical Genomics and Proteomics, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan, ROC
| | - Yi-Fan Chou
- Department of Otolaryngology Head and Neck Surgery, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan, ROC
- School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Chuan-Jen Hsu
- Department of Otolaryngology Head and Neck Surgery, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan, ROC
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan, ROC
| | - Hung-Pin Wu
- Department of Otolaryngology Head and Neck Surgery, Taichung Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Taichung, Taiwan, ROC
- School of Medicine, Tzu Chi University, Hualien, Taiwan, ROC
| | - Chen-Chi Wu
- Department of Otolaryngology, National Taiwan University Hospital, Taipei, Taiwan, ROC
- Graduate Institute of Clinical Medicine, National Taiwan University College of Medicine, Taipei, Taiwan, ROC
- Department of Medical Research, National Taiwan University Hospital Hsin-Chu Branch, Hsinchu, Taiwan, ROC
| |
Collapse
|
2
|
Haddad S, Oktay L, Erol I, Şahin K, Durdagi S. Utilizing Heteroatom Types and Numbers from Extensive Ligand Libraries to Develop Novel hERG Blocker QSAR Models Using Machine Learning-Based Classifiers. ACS OMEGA 2023; 8:40864-40877. [PMID: 37929100 PMCID: PMC10620895 DOI: 10.1021/acsomega.3c06074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 09/13/2023] [Indexed: 11/07/2023]
Abstract
The human ether-à-go-go-related gene (hERG) channel plays a crucial role in membrane repolarization. Any disruptions in its function can lead to severe cardiovascular disorders such as long QT syndrome (LQTS), which increases the risk of serious cardiovascular problems such as tachyarrhythmia and sudden cardiac death. Drug-induced LQTS is a significant concern and has resulted in drug withdrawals from the market in the past. The main objective of this study is to pinpoint crucial heteroatoms present in ligands that initiate interactions leading to the effective blocking of the hERG channel. To achieve this aim, ligand-based quantitative structure-activity relationships (QSAR) models were constructed using extensive ligand libraries, considering the heteroatom types and numbers, and their associated hERG channel blockage pIC50 values. Machine learning-assisted QSAR models were developed to analyze the key structural components influencing compound activity. Among the various methods, the KPLS method proved to be the most efficient, allowing the construction of models based on eight distinct fingerprints. The study delved into investigating the influence of heteroatoms on the activity of hERG blockers, revealing their significant role. Furthermore, by quantifying the effect of heteroatom types and numbers on ligand activity at the hERG channel, six compound pairs were selected for molecular docking. Subsequent molecular dynamics simulations and per residue MM/GBSA calculations were performed to comprehensively analyze the interactions of the selected pair compounds.
Collapse
Affiliation(s)
- Safa Haddad
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahçeşehir
University, Istanbul 34353, Turkey
- Computational
Drug Design Center (HITMER), Bahçeşehir
University, Istanbul 34353, Turkey
| | - Lalehan Oktay
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahçeşehir
University, Istanbul 34353, Turkey
- Computational
Drug Design Center (HITMER), Bahçeşehir
University, Istanbul 34353, Turkey
| | - Ismail Erol
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahçeşehir
University, Istanbul 34353, Turkey
- Computational
Drug Design Center (HITMER), Bahçeşehir
University, Istanbul 34353, Turkey
| | - Kader Şahin
- Department
of Analytical Chemistry, School of Pharmacy, Bahçeşehir University, Istanbul 34734, Turkey
| | - Serdar Durdagi
- Computational
Biology and Molecular Simulations Laboratory, Department of Biophysics,
School of Medicine, Bahçeşehir
University, Istanbul 34353, Turkey
- Computational
Drug Design Center (HITMER), Bahçeşehir
University, Istanbul 34353, Turkey
- Molecular
Therapy Lab, Department of Pharmaceutical Chemistry, School of Pharmacy, Bahçeşehir University, Istanbul 34353, Turkey
| |
Collapse
|
3
|
El Harchi A, Hancox JC. hERG agonists pose challenges to web-based machine learning methods for prediction of drug-hERG channel interaction. J Pharmacol Toxicol Methods 2023; 123:107293. [PMID: 37468081 DOI: 10.1016/j.vascn.2023.107293] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 05/23/2023] [Accepted: 07/12/2023] [Indexed: 07/21/2023]
Abstract
Pharmacological blockade of the IKr channel (hERG) by diverse drugs in clinical use is associated with the Long QT Syndrome that can lead to life threatening arrhythmia. Various computational tools including machine learning models (MLM) for the prediction of hERG inhibition have been developed to facilitate the throughput screening of drugs in development and optimise thus the prediction of hERG liabilities. The use of MLM relies on large libraries of training compounds for the quantitative structure-activity relationship (QSAR) modelling of hERG inhibition. The focus on inhibition omits potential effects of hERG channel agonist molecules and their associated QT shortening risk. It is instructive, therefore, to consider how known hERG agonists are handled by MLM. Here, two highly developed online computational tools for the prediction of hERG liability, Pred-hERG and HergSPred were probed for their ability to detect hERG activator drug molecules as hERG interactors. In total, 73 hERG blockers were tested with both computational tools giving overall good predictions for hERG blockers with reported IC50s below Pred-hERG and HergSPred cut-off threshold for hERG inhibition. However, for compounds with reported IC50s above this threshold such as disopyramide or sotalol discrepancies were observed. HergSPred identified all 20 hERG agonists selected as interacting with the hERG channel. Further studies are warranted to improve online MLM prediction of hERG related cardiotoxicity, by explicitly taking into account channel agonism as well as inhibition.
Collapse
Affiliation(s)
- Aziza El Harchi
- School of Physiology and Pharmacology and Neuroscience, Biomedical Sciences Building, The University of Bristol, University Walk, Bristol BS8 1TD, UK.
| | - Jules C Hancox
- School of Physiology and Pharmacology and Neuroscience, Biomedical Sciences Building, The University of Bristol, University Walk, Bristol BS8 1TD, UK
| |
Collapse
|
4
|
Huang HJ, Lee YH, Chou CL, Zheng CM, Chiu HW. Investigation of potential descriptors of chemical compounds on prevention of nephrotoxicity via QSAR approach. Comput Struct Biotechnol J 2022; 20:1876-1884. [PMID: 35521549 PMCID: PMC9052077 DOI: 10.1016/j.csbj.2022.04.013] [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: 01/28/2022] [Revised: 04/02/2022] [Accepted: 04/11/2022] [Indexed: 11/15/2022] Open
Abstract
Drug-induced nephrotoxicity remains a common problem after exposure to medications and diagnostic agents, which may be heightened in the kidney microenvironment and deteriorate kidney function. In this study, the toxic effects of fourteen marked drugs with the individual chemical structure were evaluated in kidney cells. The quantitative structure-activity relationship (QSAR) approach was employed to investigate the potential structural descriptors of each drug-related to their toxic effects. The most reasonable equation of the QSAR model displayed that the estimated regression coefficients such as the number of ring assemblies, three-membered rings, and six-membered rings were strongly related to toxic effects on renal cells. Meanwhile, the chemical properties of the tested compounds including carbon atoms, bridge bonds, H-bond donors, negative atoms, and rotatable bonds were favored properties and promote the toxic effects on renal cells. Particularly, more numbers of rotatable bonds were positively correlated with strong toxic effects that displayed on the most toxic compound. The useful information discovered from our regression QSAR models may help to identify potential hazardous moiety to avoid nephrotoxicity in renal preventive medicine.
Collapse
Key Words
- AKI, acute kidney injury
- CKD, chronic kidney disease
- DIKD, drug-induced kidney disease
- ESRD, end‐stage renal disease
- GFA, genetic function approximation
- GFR, glomerular filtration rate
- Genetic algorithm
- KCSF, keratinocyte serum-free
- Nephrotoxicity
- PBS, phosphate buffered saline
- QSAR
- QSAR, quantitative structure-activity relationship
- SRB, sulforhodamine B
Collapse
Affiliation(s)
- Hung-Jin Huang
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Hsuan Lee
- Department of Cosmeceutics, China Medical University, Taichung, Taiwan
| | - Chu-Lin Chou
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, Taiwan
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei, Taiwan
- Division of Nephrology, Department of Internal Medicine, Hsin Kuo Min Hospital, Taipei Medical University, Taoyuan City, Taiwan
| | - Cai-Mei Zheng
- Division of Nephrology, Department of Internal Medicine, School of Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Division of Nephrology, Department of Internal Medicine, Shuang Ho Hospital, Taipei Medical University, Taiwan
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei, Taiwan
| | - Hui-Wen Chiu
- TMU Research Center of Urology and Kidney, Taipei Medical University, Taipei, Taiwan
- Graduate Institute of Clinical Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
- Department of Medical Research, Shuang Ho Hospital, Taipei Medical University, New Taipei City, Taiwan
| |
Collapse
|
5
|
Lagoutte-Renosi J, Allemand F, Ramseyer C, Yesylevskyy S, Davani S. Molecular modeling in cardiovascular pharmacology: Current state of the art and perspectives. Drug Discov Today 2021; 27:985-1007. [PMID: 34863931 DOI: 10.1016/j.drudis.2021.11.026] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/02/2021] [Accepted: 11/25/2021] [Indexed: 01/10/2023]
Abstract
Molecular modeling in pharmacology is a promising emerging tool for exploring drug interactions with cellular components. Recent advances in molecular simulations, big data analysis, and artificial intelligence (AI) have opened new opportunities for rationalizing drug interactions with their pharmacological targets. Despite the obvious utility and increasing impact of computational approaches, their development is not progressing at the same speed in different fields of pharmacology. Here, we review current in silico techniques used in cardiovascular diseases (CVDs), cardiological drug discovery, and assessment of cardiotoxicity. In silico techniques are paving the way to a new era in cardiovascular medicine, but their use somewhat lags behind that in other fields.
Collapse
Affiliation(s)
- Jennifer Lagoutte-Renosi
- EA 3920 Université Bourgogne Franche-Comté, 25000 Besançon, France; Laboratoire de Pharmacologie Clinique et Toxicologie-CHU de Besançon, 25000 Besançon, France
| | - Florentin Allemand
- EA 3920 Université Bourgogne Franche-Comté, 25000 Besançon, France; Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France
| | - Christophe Ramseyer
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France
| | - Semen Yesylevskyy
- Laboratoire Chrono Environnement UMR CNRS 6249, Université de Bourgogne Franche-Comté, 16 route de Gray, 25000 Besançon, France; Department of Physics of Biological Systems, Institute of Physics of The National Academy of Sciences of Ukraine, Nauky Sve. 46, Kyiv, Ukraine; Receptor.ai inc, 16192 Coastal Highway, Lewes, DE, USA
| | - Siamak Davani
- EA 3920 Université Bourgogne Franche-Comté, 25000 Besançon, France; Laboratoire de Pharmacologie Clinique et Toxicologie-CHU de Besançon, 25000 Besançon, France.
| |
Collapse
|
6
|
Ramírez D, Bedoya M, Kiper AK, Rinné S, Morales-Navarro S, Hernández-Rodríguez EW, Sepúlveda FV, Decher N, González W. Structure/Activity Analysis of TASK-3 Channel Antagonists Based on a 5,6,7,8 tetrahydropyrido[4,3-d]pyrimidine. Int J Mol Sci 2019; 20:ijms20092252. [PMID: 31067753 PMCID: PMC6539479 DOI: 10.3390/ijms20092252] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/18/2019] [Accepted: 04/20/2019] [Indexed: 11/16/2022] Open
Abstract
TASK-3 potassium (K+) channels are highly expressed in the central nervous system, regulating the membrane potential of excitable cells. TASK-3 is involved in neurotransmitter action and has been identified as an oncogenic K+ channel. For this reason, the understanding of the action mechanism of pharmacological modulators of these channels is essential to obtain new therapeutic strategies. In this study we describe the binding mode of the potent antagonist PK-THPP into the TASK-3 channel. PK-THPP blocks TASK-1, the closest relative channel of TASK-3, with almost nine-times less potency. Our results confirm that the binding is influenced by the fenestrations state of TASK-3 channels and occurs when they are open. The binding is mainly governed by hydrophobic contacts between the blocker and the residues of the binding site. These interactions occur not only for PK-THPP, but also for the antagonist series based on 5,6,7,8 tetrahydropyrido[4,3-d]pyrimidine scaffold (THPP series). However, the marked difference in the potency of THPP series compounds such as 20b, 21, 22 and 23 (PK-THPP) respect to compounds such as 17b, inhibiting TASK-3 channels in the micromolar range is due to the presence of a hydrogen bond acceptor group that can establish interactions with the threonines of the selectivity filter.
Collapse
Affiliation(s)
- David Ramírez
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile. El Llano Subercaseaux 2801-Piso 6, 7500912 Santiago, Chile.
| | - Mauricio Bedoya
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca. 1 Poniente No. 1141, 3460000 Talca, Chile.
| | - Aytug K Kiper
- Institute for Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, Deutschhausstraße 2, 35037 Marburg, Germany.
| | - Susanne Rinné
- Institute for Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, Deutschhausstraße 2, 35037 Marburg, Germany.
| | - Samuel Morales-Navarro
- Bachillerato en Ciencias, Facultad de Ciencias, Universidad Santo Tomás, Av. Circunvalación Poniente #1855, 3460000 Talca, Chile.
| | - Erix W Hernández-Rodríguez
- Centro de Bioinformática y Simulación Molecular (CBSM), Universidad de Talca. 1 Poniente No. 1141, 3460000 Talca, Chile.
- Escuela de Química y Farmacia. Facultad de Medicina. Universidad Católica del Maule, 3460000 Talca, Chile.
| | | | - Niels Decher
- Institute for Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, Deutschhausstraße 2, 35037 Marburg, 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, 3460000 Talca, Chile.
| |
Collapse
|
7
|
Schewe M, Sun H, Mert Ü, Mackenzie A, Pike ACW, Schulz F, Constantin C, Vowinkel KS, Conrad LJ, Kiper AK, Gonzalez W, Musinszki M, Tegtmeier M, Pryde DC, Belabed H, Nazare M, de Groot BL, Decher N, Fakler B, Carpenter EP, Tucker SJ, Baukrowitz T. A pharmacological master key mechanism that unlocks the selectivity filter gate in K + channels. Science 2019; 363:875-880. [PMID: 30792303 PMCID: PMC6982535 DOI: 10.1126/science.aav0569] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 01/28/2019] [Indexed: 12/13/2022]
Abstract
Potassium (K+) channels have been evolutionarily tuned for activation by diverse biological stimuli, and pharmacological activation is thought to target these specific gating mechanisms. Here we report a class of negatively charged activators (NCAs) that bypass the specific mechanisms but act as master keys to open K+ channels gated at their selectivity filter (SF), including many two-pore domain K+ (K2P) channels, voltage-gated hERG (human ether-à-go-go-related gene) channels and calcium (Ca2+)-activated big-conductance potassium (BK)-type channels. Functional analysis, x-ray crystallography, and molecular dynamics simulations revealed that the NCAs bind to similar sites below the SF, increase pore and SF K+ occupancy, and open the filter gate. These results uncover an unrecognized polypharmacology among K+ channel activators and highlight a filter gating machinery that is conserved across different families of K+ channels with implications for rational drug design.
Collapse
Affiliation(s)
- Marcus Schewe
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany.
| | - Han Sun
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Structural Biology, 13125 Berlin, Germany
| | - Ümit Mert
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Alexandra Mackenzie
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Ashley C W Pike
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
| | - Friederike Schulz
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Cristina Constantin
- Institute of Physiology II, Albert-Ludwigs University of Freiburg, 79104 Freiburg, Germany
- Centers for Biological Signaling Studies CIBSS and BIOSS, 79104 Freiburg, Germany
| | - Kirsty S Vowinkel
- Institute of Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, 35037 Marburg, Germany
| | - Linus J Conrad
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Aytug K Kiper
- Institute of Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, 35037 Marburg, Germany
| | - Wendy Gonzalez
- Centro de Bioinformatica y Simulacion Molecular, Universidad de Talca, 3465548 Talca, Chile
- Millennium Nucleus of Ion Channels-Associated Diseases (MiNICAD), Universidad de Talca, 3465548 Talca, Chile
| | - Marianne Musinszki
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - Marie Tegtmeier
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany
| | - David C Pryde
- Pfizer Worldwide Medicinal Chemistry, Neuroscience and Pain Research Unit, Portway Building, Granta Park, Great Abington, Cambridgeshire CB21 6GS, UK
| | - Hassane Belabed
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Medicinal Chemistry, 13125 Berlin, Germany
| | - Marc Nazare
- Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Department of Medicinal Chemistry, 13125 Berlin, Germany
| | - Bert L de Groot
- Computational Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Niels Decher
- Institute of Physiology and Pathophysiology, Vegetative Physiology, Philipps-University of Marburg, 35037 Marburg, Germany
| | - Bernd Fakler
- Institute of Physiology II, Albert-Ludwigs University of Freiburg, 79104 Freiburg, Germany
- Centers for Biological Signaling Studies CIBSS and BIOSS, 79104 Freiburg, Germany
| | - Elisabeth P Carpenter
- Structural Genomics Consortium, University of Oxford, Oxford OX3 7DQ, UK
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK
| | - Stephen J Tucker
- OXION Initiative in Ion Channels and Disease, University of Oxford, Oxford OX1 3PN, UK
- Clarendon Laboratory, Department of Physics, University of Oxford, Oxford OX1 3PU, UK
| | - Thomas Baukrowitz
- Institute of Physiology, Christian-Albrechts University of Kiel, 24118 Kiel, Germany.
| |
Collapse
|
8
|
Mayr F, Vieider C, Temml V, Stuppner H, Schuster D. Open-Access Activity Prediction Tools for Natural Products. Case Study: hERG Blockers. PROGRESS IN THE CHEMISTRY OF ORGANIC NATURAL PRODUCTS 2019; 110:177-238. [PMID: 31621014 DOI: 10.1007/978-3-030-14632-0_6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Interference with the hERG potassium ion channel may cause cardiac arrhythmia and can even lead to death. Over the last few decades, several drugs, already on the market, and many more investigational drugs in various development stages, have had to be discontinued because of their hERG-associated toxicity. To recognize potential hERG activity in the early stages of drug development, a wide array of computational tools, based on different principles, such as 3D QSAR, 2D and 3D similarity, and machine learning, have been developed and are reviewed in this chapter. The various available prediction tools Similarity Ensemble Approach, SuperPred, SwissTargetPrediction, HitPick, admetSAR, PASSonline, Pred-hERG, and VirtualToxLab™ were used to screen a dataset of known hERG synthetic and natural product actives and inactives to quantify and compare their predictive power. This contribution will allow the reader to evaluate the suitability of these computational methods for their own related projects. There is an unmet need for natural product-specific prediction tools in this field.
Collapse
Affiliation(s)
- Fabian Mayr
- Institute of Pharmacy/Pharmacognosy, University of Innsbruck, Innsbruck, Austria
- Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Christian Vieider
- Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, Austria
| | - Veronika Temml
- Institute of Pharmacy/Pharmacognosy, University of Innsbruck, Innsbruck, Austria
| | - Hermann Stuppner
- Institute of Pharmacy/Pharmacognosy, University of Innsbruck, Innsbruck, Austria
| | - Daniela Schuster
- Institute of Pharmacy/Pharmaceutical Chemistry, University of Innsbruck, Innsbruck, Austria.
- Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Paracelsus Medical University Salzburg, Salzburg, Austria.
| |
Collapse
|