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Stagno C, Mancuso F, Ciaglia T, Ostacolo C, Piperno A, Iraci N, Micale N. In Silico Methods for the Discovery of Kv7.2/7.3 Channels Modulators: A Comprehensive Review. Molecules 2024; 29:3234. [PMID: 38999185 PMCID: PMC11243076 DOI: 10.3390/molecules29133234] [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: 06/15/2024] [Revised: 07/03/2024] [Accepted: 07/05/2024] [Indexed: 07/14/2024] Open
Abstract
The growing interest in Kv7.2/7.3 agonists originates from the involvement of these channels in several brain hyperexcitability disorders. In particular, Kv7.2/7.3 mutants have been clearly associated with epileptic encephalopathies (DEEs) as well as with a spectrum of focal epilepsy disorders, often associated with developmental plateauing or regression. Nevertheless, there is a lack of available therapeutic options, considering that retigabine, the only molecule used in clinic as a broad-spectrum Kv7 agonist, has been withdrawn from the market in late 2016. This is why several efforts have been made both by both academia and industry in the search for suitable chemotypes acting as Kv7.2/7.3 agonists. In this context, in silico methods have played a major role, since the precise structures of different Kv7 homotetramers have been only recently disclosed. In the present review, the computational methods used for the design of Kv.7.2/7.3 small molecule agonists and the underlying medicinal chemistry are discussed in the context of their biological and structure-function properties.
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Affiliation(s)
- Claudio Stagno
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (CHIBIOFARAM), University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Francesca Mancuso
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (CHIBIOFARAM), University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Tania Ciaglia
- Department of Pharmacy, University of Salerno, Via G. Paolo II, 84084 Fisciano, Italy
| | - Carmine Ostacolo
- Department of Pharmacy, University of Salerno, Via G. Paolo II, 84084 Fisciano, Italy
| | - Anna Piperno
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (CHIBIOFARAM), University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Nunzio Iraci
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (CHIBIOFARAM), University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
| | - Nicola Micale
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences (CHIBIOFARAM), University of Messina, Viale F. Stagno d'Alcontres 31, 98166 Messina, Italy
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Bazard P, Frisina RD, Acosta AA, Dasgupta S, Bauer MA, Zhu X, Ding B. Roles of Key Ion Channels and Transport Proteins in Age-Related Hearing Loss. Int J Mol Sci 2021; 22:6158. [PMID: 34200434 PMCID: PMC8201059 DOI: 10.3390/ijms22116158] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/30/2021] [Accepted: 05/31/2021] [Indexed: 12/25/2022] Open
Abstract
The auditory system is a fascinating sensory organ that overall, converts sound signals to electrical signals of the nervous system. Initially, sound energy is converted to mechanical energy via amplification processes in the middle ear, followed by transduction of mechanical movements of the oval window into electrochemical signals in the cochlear hair cells, and finally, neural signals travel to the central auditory system, via the auditory division of the 8th cranial nerve. The majority of people above 60 years have some form of age-related hearing loss, also known as presbycusis. However, the biological mechanisms of presbycusis are complex and not yet fully delineated. In the present article, we highlight ion channels and transport proteins, which are integral for the proper functioning of the auditory system, facilitating the diffusion of various ions across auditory structures for signal transduction and processing. Like most other physiological systems, hearing abilities decline with age, hence, it is imperative to fully understand inner ear aging changes, so ion channel functions should be further investigated in the aging cochlea. In this review article, we discuss key various ion channels in the auditory system and how their functions change with age. Understanding the roles of ion channels in auditory processing could enhance the development of potential biotherapies for age-related hearing loss.
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Affiliation(s)
- Parveen Bazard
- Department of Medical Engineering, College of Engineering, University of South Florida, Tampa, FL 33620, USA; (P.B.); (A.A.A.); (S.D.); (M.A.B.); (X.Z.); (B.D.)
- Global Center for Hearing and Speech Research, University of South Florida, Tampa, FL 33612, USA
| | - Robert D. Frisina
- Department of Medical Engineering, College of Engineering, University of South Florida, Tampa, FL 33620, USA; (P.B.); (A.A.A.); (S.D.); (M.A.B.); (X.Z.); (B.D.)
- Global Center for Hearing and Speech Research, University of South Florida, Tampa, FL 33612, USA
- Department Communication Sciences and Disorders, College of Behavioral & Communication Sciences, Tampa, FL 33620, USA
| | - Alejandro A. Acosta
- Department of Medical Engineering, College of Engineering, University of South Florida, Tampa, FL 33620, USA; (P.B.); (A.A.A.); (S.D.); (M.A.B.); (X.Z.); (B.D.)
- Global Center for Hearing and Speech Research, University of South Florida, Tampa, FL 33612, USA
| | - Sneha Dasgupta
- Department of Medical Engineering, College of Engineering, University of South Florida, Tampa, FL 33620, USA; (P.B.); (A.A.A.); (S.D.); (M.A.B.); (X.Z.); (B.D.)
- Global Center for Hearing and Speech Research, University of South Florida, Tampa, FL 33612, USA
| | - Mark A. Bauer
- Department of Medical Engineering, College of Engineering, University of South Florida, Tampa, FL 33620, USA; (P.B.); (A.A.A.); (S.D.); (M.A.B.); (X.Z.); (B.D.)
- Global Center for Hearing and Speech Research, University of South Florida, Tampa, FL 33612, USA
| | - Xiaoxia Zhu
- Department of Medical Engineering, College of Engineering, University of South Florida, Tampa, FL 33620, USA; (P.B.); (A.A.A.); (S.D.); (M.A.B.); (X.Z.); (B.D.)
- Global Center for Hearing and Speech Research, University of South Florida, Tampa, FL 33612, USA
| | - Bo Ding
- Department of Medical Engineering, College of Engineering, University of South Florida, Tampa, FL 33620, USA; (P.B.); (A.A.A.); (S.D.); (M.A.B.); (X.Z.); (B.D.)
- Global Center for Hearing and Speech Research, University of South Florida, Tampa, FL 33612, USA
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Noh W, Pak S, Choi G, Yang S, Yang S. Transient Potassium Channels: Therapeutic Targets for Brain Disorders. Front Cell Neurosci 2019; 13:265. [PMID: 31263403 PMCID: PMC6585177 DOI: 10.3389/fncel.2019.00265] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/28/2019] [Indexed: 01/04/2023] Open
Abstract
Transient potassium current channels (IA channels), which are expressed in most brain areas, have a central role in modulating feedforward and feedback inhibition along the dendroaxonic axis. Loss of the modulatory channels is tightly associated with a number of brain diseases such as Alzheimer’s disease, epilepsy, fragile X syndrome (FXS), Parkinson’s disease, chronic pain, tinnitus, and ataxia. However, the functional significance of IA channels in these diseases has so far been underestimated. In this review, we discuss the distribution and function of IA channels. Particularly, we posit that downregulation of IA channels results in neuronal (mostly dendritic) hyperexcitability accompanied by the imbalanced excitation and inhibition ratio in the brain’s networks, eventually causing the brain diseases. Finally, we propose a potential therapeutic target: the enhanced action of IA channels to counteract Ca2+-permeable channels including NMDA receptors could be harnessed to restore dendritic excitability, leading to a balanced neuronal state.
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Affiliation(s)
- Wonjun Noh
- Department of Nano-Bioengineering, Incheon National University, Incheon, South Korea
| | - Sojeong Pak
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Geunho Choi
- Department of Computer Science and Engineering, Incheon National University, Incheon, South Korea
| | - Sungchil Yang
- Department of Biomedical Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Sunggu Yang
- Department of Nano-Bioengineering, Incheon National University, Incheon, South Korea
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Detergent-free solubilization of human Kv channels expressed in mammalian cells. Chem Phys Lipids 2019; 219:50-57. [DOI: 10.1016/j.chemphyslip.2019.01.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/30/2019] [Accepted: 01/30/2019] [Indexed: 12/13/2022]
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Cvetkov TL, Huynh KW, Cohen MR, Moiseenkova-Bell VY. Molecular architecture and subunit organization of TRPA1 ion channel revealed by electron microscopy. J Biol Chem 2011; 286:38168-38176. [PMID: 21908607 DOI: 10.1074/jbc.m111.288993] [Citation(s) in RCA: 97] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Transient receptor potential ankyrin 1 (TRPA1) is a non-selective ion channel, which is expressed in nociceptor sensory neurons and transduces chemical, inflammatory, and neuropathic pain signals. Numerous non-reactive compounds and electrophilic compounds, such as endogenous inflammatory mediators and exogenous pungent chemicals, can activate TRPA1. Here we report a 16-Å resolution structure of purified, functional, amphipol-stabilized TRPA1 analyzed by single-particle EM. Molecular models of the N and C termini of the channel were generated using the I-TASSER protein structure prediction server and docked into the EM density to provide insight into the TRPA1 subunit organization. This structural analysis suggests a location for critical N-terminal cysteine residues involved in electrophilic activation at the interface between neighboring subunits. Our results indicate that covalent modifications within this pocket may alter interactions between subunits and promote conformational changes that lead to channel activation.
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Affiliation(s)
- Teresa L Cvetkov
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Kevin W Huynh
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Matthew R Cohen
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106
| | - Vera Y Moiseenkova-Bell
- Department of Pharmacology, School of Medicine, Case Western Reserve University, Cleveland, Ohio 44106.
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The Domain and Conformational Organization in Potassium Voltage-Gated Ion Channels. J Neuroimmune Pharmacol 2008; 4:71-82. [DOI: 10.1007/s11481-008-9130-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Accepted: 09/10/2008] [Indexed: 11/26/2022]
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Abstract
The transient receptor potential (TRP) family of ion channels participate in many signaling pathways. TRPV1 functions as a molecular integrator of noxious stimuli, including heat, low pH, and chemical ligands. Here, we report the 3D structure of full-length rat TRPV1 channel expressed in the yeast Saccharomyces cerevisiae and purified by immunoaffinity chromatography. We demonstrate that the recombinant purified TRPV1 channel retains its structural and functional integrity and is suitable for structural analysis. The 19-A structure of TRPV1 determined by using single-particle electron cryomicroscopy exhibits fourfold symmetry and comprises two distinct regions: a large open basket-like domain, likely corresponding to the cytoplasmic N- and C-terminal portions, and a more compact domain, corresponding to the transmembrane portion. The assignment of transmembrane and cytoplasmic regions was supported by fitting crystal structures of the structurally homologous Kv1.2 channel and isolated TRPV1 ankyrin repeats into the TRPV1 structure.
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SUGAWARA K, TERAUCHI A, KAMIYA N, HIRABAYASHI G, KURAMITZ H. Voltammetric Behaviors of Wheat-Germ Agglutinin on a Chitin-modified Carbon-Paste Electrode. ANAL SCI 2008; 24:583-7. [DOI: 10.2116/analsci.24.583] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | | | | | | | - Hideki KURAMITZ
- Department of Environmental Biology and Chemistry, Faculty of Science, University of Toyama
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Patel SP, Campbell DL. Transient outward potassium current, 'Ito', phenotypes in the mammalian left ventricle: underlying molecular, cellular and biophysical mechanisms. J Physiol 2005; 569:7-39. [PMID: 15831535 PMCID: PMC1464208 DOI: 10.1113/jphysiol.2005.086223] [Citation(s) in RCA: 147] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 03/07/2005] [Accepted: 04/13/2005] [Indexed: 11/08/2022] Open
Abstract
At least two functionally distinct transient outward K(+) current (I(to)) phenotypes can exist across the free wall of the left ventricle (LV). Based upon their voltage-dependent kinetics of recovery from inactivation, these two phenotypes are designated 'I(to,fast)' (recovery time constants on the order of tens of milliseconds) and 'I(to,slow)' (recovery time constants on the order of thousands of milliseconds). Depending upon species, either I(to,fast), I(to,slow) or both current phenotypes may be expressed in the LV free wall. The expression gradients of these two I(to) phenotypes across the LV free wall are typically heterogeneous and, depending upon species, may consist of functional phenotypic gradients of both I(to,fast) and I(to,slow) and/or density gradients of either phenotype. We review the present evidence (molecular, biophysical, electrophysiological and pharmacological) for Kv4.2/4.3 alpha subunits underlying LV I(to,fast) and Kv1.4 alpha subunits underlying LV I(to,slow) and speculate upon the potential roles of each of these currents in determining frequency-dependent action potential characteristics of LV subepicardial versus subendocardial myocytes in different species. We also review the possible functional implications of (i) ancillary subunits that regulate Kv1.4 and Kv4.2/4.3 (Kvbeta subunits, DPPs), (ii) KChIP2 isoforms, (iii) spider toxin-mediated block of Kv4.2/4.3 (Heteropoda toxins, phrixotoxins), and (iv) potential mechanisms of modulation of I(to,fast) and I(to,slow) by cellular redox state, [Ca(2)(+)](i) and kinase-mediated phosphorylation. I(to) phenotypic activation and state-dependent gating models and molecular structure-function relationships are also discussed.
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Affiliation(s)
- Sangita P Patel
- Department of Physiology and Biophysics, University at Buffalo, State University of New York, NY 14214-3078, USA.
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Huang X, Dong F, Zhou HX. Electrostatic Recognition and Induced Fit in the κ-PVIIA Toxin Binding to Shaker Potassium Channel. J Am Chem Soc 2005; 127:6836-49. [PMID: 15869307 DOI: 10.1021/ja042641q] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Brownian dynamics (BD) and molecular dynamics (MD) simulations and electrostatic calculations were performed to study the binding process of kappa-PVIIA to the Shaker potassium channel and the structure of the resulting complex. BD simulations, guided by electrostatic interactions, led to an initial alignment between the toxin and the channel protein. MD simulations were then carried out to allow for rearrangements from this initial structure. After approximately 4 ns, a critical "induced fit" process was observed to last for approximately 2 ns. In this process, the interface was reorganized, and side chains were moved so that favorable atomic contacts were formed or strengthened, while unfavorable contacts were eliminated. The final complex structure was stabilized through electrostatic interactions with the positively charged side chain of Lys7 of kappa-PVIIA deeply inserted into the channel pore and other hydrogen bonds and by hydrophobic interactions involving Phe9 and Phe23 of the toxin. The validity of the predicted structure for the complex was assessed by calculating the effects of mutating charged and polar residues of both the toxin and the channel protein, with the calculated effects correlating reasonably well with experimental data. The present study suggests a general binding mechanism, whereby proteins are pre-aligned in their diffusional encounter by long-range electrostatic attraction, and nanosecond-scale rearrangements within the initial complex then lead to a specifically bound complex.
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Affiliation(s)
- Xiaoqin Huang
- Institute of Molecular Biophysics and School of Computational Science, Department of Physics, Florida State University, Tallahassee, FL 32306, USA
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