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Liu S, Guo P, Wang K, Zhang S, Li Y, Shen J, Mei L, Ye Y, Zhang Q, Yang H. General Pharmacological Activation Mechanism of K + Channels Bypassing Channel Gates. J Med Chem 2022; 65:10285-10299. [PMID: 35878013 DOI: 10.1021/acs.jmedchem.1c02115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Under the known pharmacological activation mechanisms, activators allosterically or directly open potassium channel gates. However, herein, molecular dynamics simulations on TREK-1, a member of the channel class gated at the filter, suggested that negatively charged activators act with a gate-independent mechanism where compounds increase currents by promoting ions passing through the central cavity. Then, based on studies of KCNQ2, we uncovered that this noncanonical activation mechanism is shared by the other channel class gated at the helix-bundle crossing. Rational drug design found a novel KCNQ2 agonist, CLE030, which stably binds to the central cavity. Functional analysis, molecular dynamics simulations, and calculations of the potential of mean force revealed that the carbonyl oxygen of CLE030 influences permeant ions in the central cavity to contribute to its activation effects. Together, this study discovered a ligand-to-ion activation mechanism for channels that bypasses their gates and thus is conserved across subfamilies with different gates.
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Affiliation(s)
- Shijie Liu
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Peipei Guo
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Kun Wang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Shaoying Zhang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Ya Li
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Juwen Shen
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Lianghe Mei
- Suzhou Institute of Drug Innovation, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Suzhou, Jiangsu 215123, China
| | - Yangliang Ye
- Suzhou AlphaMa Biotechnology Co., Ltd., Suzhou, Jiangsu 215123, China
| | - Qiansen Zhang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
| | - Huaiyu Yang
- Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai 200241, China
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2
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Natale AM, Deal PE, Minor DL. Structural Insights into the Mechanisms and Pharmacology of K 2P Potassium Channels. J Mol Biol 2021; 433:166995. [PMID: 33887333 PMCID: PMC8436263 DOI: 10.1016/j.jmb.2021.166995] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/08/2021] [Accepted: 04/09/2021] [Indexed: 01/10/2023]
Abstract
Leak currents, defined as voltage and time independent flows of ions across cell membranes, are central to cellular electrical excitability control. The K2P (KCNK) potassium channel class comprises an ion channel family that produces potassium leak currents that oppose excitation and stabilize the resting membrane potential in cells in the brain, cardiovascular system, immune system, and sensory organs. Due to their widespread tissue distribution, K2Ps contribute to many physiological and pathophysiological processes including anesthesia, pain, arrythmias, ischemia, hypertension, migraine, intraocular pressure regulation, and lung injury responses. Structural studies of six homomeric K2Ps have established the basic architecture of this channel family, revealed key moving parts involved in K2P function, uncovered the importance of asymmetric pinching and dilation motions in the K2P selectivity filter (SF) C-type gate, and defined two K2P structural classes based on the absence or presence of an intracellular gate. Further, a series of structures characterizing K2P:modulator interactions have revealed a striking polysite pharmacology housed within a relatively modestly sized (~70 kDa) channel. Binding sites for small molecules or lipids that control channel function are found at every layer of the channel structure, starting from its extracellular side through the portion that interacts with the membrane bilayer inner leaflet. This framework provides the basis for understanding how gating cues sensed by different channel parts control function and how small molecules and lipids modulate K2P activity. Such knowledge should catalyze development of new K2P modulators to probe function and treat a wide range of disorders.
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Affiliation(s)
- Andrew M Natale
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Parker E Deal
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA
| | - Daniel L Minor
- Cardiovascular Research Institute, University of California, San Francisco, CA 94158, USA; Departments of Biochemistry and Biophysics, and Cellular and Molecular Pharmacology, University of California, San Francisco, CA 94158, USA; California Institute for Quantitative Biomedical Research, University of California, San Francisco, CA 94158, USA; Kavli Institute for Fundamental Neuroscience University of California, San Francisco, CA 94158, USA; Molecular Biophysics and Integrated Bio-imaging Division Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
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3
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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.
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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.
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Vitali V, Jozefkowicz C, Canessa Fortuna A, Soto G, González Flecha FL, Alleva K. Cooperativity in proton sensing by PIP aquaporins. FEBS J 2018; 286:991-1002. [PMID: 30430736 DOI: 10.1111/febs.14701] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 11/05/2018] [Accepted: 11/13/2018] [Indexed: 11/28/2022]
Abstract
One of the most intriguing properties of plasma membrane intrinsic protein (PIP) aquaporins (AQPs) is their ability to modulate water transport by sensing different levels of intracellular pH through the assembly of homo- and heterotetrameric molecular species in the plasma membrane. In this work, using a phenomenological modeling approach, we demonstrate that cooperativity in PIP biological response cannot be directly attributed to a cooperative proton binding, as it is usually considered, since it could also be the consequence of a cooperative conformation transition between open and closed states of the channel. Moreover, our results show that, when mixed populations of homo- and heterotetrameric PIP channels are coexpressed in the plasma membrane of the same cell, the observed decrease in the degree of positive cooperativity would result from the simultaneous presence of molecular species with different levels of proton sensing. Indeed, the random mixing between different PIP paralogues as subunits in a single tetramer, plus the possibility of mixed populations of homo- and heterotetrameric PIP channels widen the spectrum of cooperative responses of a cell membrane. Our approach offers a deep understanding of cooperative transport of AQP channels, as members of a multiprotein family where the relevant proton binding sites of each member have not been clearly elucidated yet.
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Affiliation(s)
- Victoria Vitali
- Universidad de Buenos Aires, CONICET, Facultad de Farmacia y Bioquímica, Instituto de Química y Fisicoquímica Biológica (IQUIFIB), Argentina.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Fisicomatemática, Argentina
| | - Cintia Jozefkowicz
- Instituto Nacional de Tecnología Agropecuaria, INTA, Castelar, Argentina.,CONICET, Buenos Aires, Argentina
| | - Agustina Canessa Fortuna
- Universidad de Buenos Aires, CONICET, Facultad de Farmacia y Bioquímica, Instituto de Química y Fisicoquímica Biológica (IQUIFIB), Argentina.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Fisicomatemática, Argentina
| | - Gabriela Soto
- Instituto Nacional de Tecnología Agropecuaria, INTA, Castelar, Argentina.,CONICET, Buenos Aires, Argentina
| | - F Luis González Flecha
- Universidad de Buenos Aires, CONICET, Facultad de Farmacia y Bioquímica, Instituto de Química y Fisicoquímica Biológica (IQUIFIB), Argentina
| | - Karina Alleva
- Universidad de Buenos Aires, CONICET, Facultad de Farmacia y Bioquímica, Instituto de Química y Fisicoquímica Biológica (IQUIFIB), Argentina.,Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Departamento de Fisicomatemática, Argentina
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5
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Probing the gating mechanism of the mechanosensitive channel Piezo1 with the small molecule Yoda1. Nat Commun 2018; 9:2029. [PMID: 29795280 PMCID: PMC5966384 DOI: 10.1038/s41467-018-04405-3] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Accepted: 04/16/2018] [Indexed: 01/04/2023] Open
Abstract
Piezo proteins are transmembrane ion channels which transduce many forms of mechanical stimuli into electrochemical signals. Their pore, formed by the assembly of three identical subunits, opens by an unknown mechanism. Here, to probe this mechanism, we investigate the interaction of Piezo1 with the small molecule agonist Yoda1. By engineering chimeras between mouse Piezo1 and its Yoda1-insensitive paralog Piezo2, we first identify a minimal protein region required for Yoda1 sensitivity. We next study the effect of Yoda1 on heterotrimeric Piezo1 channels harboring wild type subunits and Yoda1-insensitive mutant subunits. Using calcium imaging and patch-clamp electrophysiology, we show that hybrid channels harboring as few as one Yoda1-sensitive subunit exhibit Yoda1 sensitivity undistinguishable from homotrimeric wild type channels. Our results show that the Piezo1 pore remains fully open if only one subunit remains activated. This study sheds light on the gating and pharmacological mechanisms of a member of the Piezo channel family. Piezo ion channels transduce mechanical stimuli into biological signals but the underlying mechanism has remained elusive. Here, the authors use the selective agonist Yoda1 to identify molecular determinants of Piezo activation, providing mechanistic insights into Piezo-mediated mechanotransduction.
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6
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The glycine hinge of transmembrane segment 2 modulates the subcellular localization and gating properties in TREK channels. Biochem Biophys Res Commun 2017; 490:1125-1131. [DOI: 10.1016/j.bbrc.2017.06.200] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Accepted: 06/30/2017] [Indexed: 01/09/2023]
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