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Li H, Sun X, Cui W, Xu M, Dong J, Ekundayo BE, Ni D, Rao Z, Guo L, Stahlberg H, Yuan S, Vogel H. Computational drug development for membrane protein targets. Nat Biotechnol 2024; 42:229-242. [PMID: 38361054 DOI: 10.1038/s41587-023-01987-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 09/13/2023] [Indexed: 02/17/2024]
Abstract
The application of computational biology in drug development for membrane protein targets has experienced a boost from recent developments in deep learning-driven structure prediction, increased speed and resolution of structure elucidation, machine learning structure-based design and the evaluation of big data. Recent protein structure predictions based on machine learning tools have delivered surprisingly reliable results for water-soluble and membrane proteins but have limitations for development of drugs that target membrane proteins. Structural transitions of membrane proteins have a central role during transmembrane signaling and are often influenced by therapeutic compounds. Resolving the structural and functional basis of dynamic transmembrane signaling networks, especially within the native membrane or cellular environment, remains a central challenge for drug development. Tackling this challenge will require an interplay between experimental and computational tools, such as super-resolution optical microscopy for quantification of the molecular interactions of cellular signaling networks and their modulation by potential drugs, cryo-electron microscopy for determination of the structural transitions of proteins in native cell membranes and entire cells, and computational tools for data analysis and prediction of the structure and function of cellular signaling networks, as well as generation of promising drug candidates.
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Affiliation(s)
- Haijian Li
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Xiaolin Sun
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Wenqiang Cui
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Marc Xu
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Junlin Dong
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Babatunde Edukpe Ekundayo
- Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Dongchun Ni
- Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland
| | - Zhili Rao
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Liwei Guo
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China
| | - Henning Stahlberg
- Laboratory of Biological Electron Microscopy, IPHYS, SB, EPFL and Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland.
| | - Shuguang Yuan
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China.
| | - Horst Vogel
- Center for Computer-Aided Drug Discovery, Faculty of Pharmaceutical Sciences, Shenzhen Institute of Advanced Technology/Chinese Academy of Sciences (SIAT/CAS), Shenzhen, China.
- Institut des Sciences et Ingénierie Chimiques (ISIC), Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland.
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Ridley J, Manyweathers S, Tang R, Goetze T, Becker N, Rinke-Weiß I, Kirby R, Obergrussberger A, Rogers M. Development of ASIC1a ligand-gated ion channel drug screening assays across multiple automated patch clamp platforms. Front Mol Neurosci 2022; 15:982689. [PMID: 36340694 PMCID: PMC9629855 DOI: 10.3389/fnmol.2022.982689] [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: 06/30/2022] [Accepted: 09/12/2022] [Indexed: 02/05/2023] Open
Abstract
Human acid-sensing ion channels (ASIC) are ligand-gated ionotropic receptors expressed widely in peripheral tissues as well as sensory and central neurons and implicated in detection of inflammation, tissue injury, and hypoxia-induced acidosis. This makes ASIC channels promising targets for drug discovery in oncology, pain and ischemia, and several modulators have progressed into clinical trials. We describe the use of hASIC1a as a case study for the development and validation of low, medium and high throughput automated patch clamp (APC) assays suitable for the screening and mechanistic profiling of new ligands for this important class of ligand-gated ion channel. Initial efforts to expand on previous manual patch work describing an endogenous hASIC1a response in HEK cells were thwarted by low current expression and unusual pharmacology, so subsequent work utilized stable hASIC1a CHO cell lines. Ligand-gated application protocols and screening assays on the Patchliner, QPatch 48, and SyncroPatch 384 were optimized and validated based on pH activation and nM-μM potency of reference antagonists (e.g., Amiloride, Benzamil, Memantine, Mambalgin-3, A-317567, PcTx1). By optimizing single and stacked pipette tip applications available on each APC platform, stable pH-evoked currents during multiple ligand applications enabled cumulative EC50 and IC50 determinations with minimized receptor desensitization. Finally, we successfully demonstrated for the first time on an APC platform the ability to use current clamp to implement the historical technique of input resistance tracking to measure ligand-gated changes in membrane conductance on the Patchliner platform.
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Affiliation(s)
- John Ridley
- Metrion Biosciences Ltd., Cambridge, United Kingdom
| | | | - Raymond Tang
- Metrion Biosciences Ltd., Cambridge, United Kingdom
| | - Tom Goetze
- Nanion Technologies GmbH, Munich, Germany
| | | | | | - Robert Kirby
- Metrion Biosciences Ltd., Cambridge, United Kingdom
| | | | - Marc Rogers
- Metrion Biosciences Ltd., Cambridge, United Kingdom
- *Correspondence: Marc Rogers,
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Gornati D, Ciccone R, Vinciguerra A, Ippati S, Pannaccione A, Petrozziello T, Pizzi E, Hassan A, Colombo E, Barbini S, Milani M, Caccavone C, Randazzo P, Muzio L, Annunziato L, Menegon A, Secondo A, Mastrangelo E, Pignataro G, Seneci P. Synthesis and Characterization of Novel Mono- and Bis-Guanyl Hydrazones as Potent and Selective ASIC1 Inhibitors Able to Reduce Brain Ischemic Insult. J Med Chem 2021; 64:8333-8353. [PMID: 34097384 DOI: 10.1021/acs.jmedchem.1c00305] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Acid-sensitive ion channels (ASICs) are sodium channels partially permeable to Ca2+ ions, listed among putative targets in central nervous system (CNS) diseases in which a pH modification occurs. We targeted novel compounds able to modulate ASIC1 and to reduce the progression of ischemic brain injury. We rationally designed and synthesized several diminazene-inspired diaryl mono- and bis-guanyl hydrazones. A correlation between their predicted docking affinities for the acidic pocket (AcP site) in chicken ASIC1 and their inhibition of homo- and heteromeric hASIC1 channels in HEK-293 cells was found. Their activity on murine ASIC1a currents and their selectivity vs mASIC2a were assessed in engineered CHO-K1 cells, highlighting a limited isoform selectivity. Neuroprotective effects were confirmed in vitro, on primary rat cortical neurons exposed to oxygen-glucose deprivation followed by reoxygenation, and in vivo, in ischemic mice. Early lead 3b, showing a good selectivity for hASIC1 in human neurons, was neuroprotective against focal ischemia induced in mice.
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Affiliation(s)
- Davide Gornati
- Chemistry Department, University of Milan, Via Golgi 19, 20133 Milan, Italy
| | - Roselia Ciccone
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples Federico II, Via Pansini 5, I-80131 Naples, Italy
| | - Antonio Vinciguerra
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples Federico II, Via Pansini 5, I-80131 Naples, Italy
| | - Stefania Ippati
- Experimental Imaging Center, ALEMBIC-Advanced Light and Electron Microscopy BioImaging Center, San Raffaele Scientific Institute, Via Olgettina 60, I-20132 Milan, Italy
| | - Anna Pannaccione
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples Federico II, Via Pansini 5, I-80131 Naples, Italy
| | - Tiziana Petrozziello
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples Federico II, Via Pansini 5, I-80131 Naples, Italy
| | - Erika Pizzi
- Experimental Imaging Center, ALEMBIC-Advanced Light and Electron Microscopy BioImaging Center, San Raffaele Scientific Institute, Via Olgettina 60, I-20132 Milan, Italy
| | - Amal Hassan
- National Research Council-Biophysics Institute (CNR-IBF), and Biosciences Department University of Milan, Via Celoria, 26, I-20133 Milan, Italy
| | - Eleonora Colombo
- Chemistry Department, University of Milan, Via Golgi 19, 20133 Milan, Italy
| | - Stefano Barbini
- Chemistry Department, University of Milan, Via Golgi 19, 20133 Milan, Italy
| | - Mario Milani
- National Research Council-Biophysics Institute (CNR-IBF), and Biosciences Department University of Milan, Via Celoria, 26, I-20133 Milan, Italy
| | - Cecilia Caccavone
- Experimental Imaging Center, ALEMBIC-Advanced Light and Electron Microscopy BioImaging Center, San Raffaele Scientific Institute, Via Olgettina 60, I-20132 Milan, Italy
| | | | - Luca Muzio
- INSPE-Institute of Experimental Neurology, San Raffaele Scientific Institute, Via Olgettina 60, I-20132 Milan, Italy
| | | | - Andrea Menegon
- Experimental Imaging Center, ALEMBIC-Advanced Light and Electron Microscopy BioImaging Center, San Raffaele Scientific Institute, Via Olgettina 60, I-20132 Milan, Italy
| | - Agnese Secondo
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples Federico II, Via Pansini 5, I-80131 Naples, Italy
| | - Eloise Mastrangelo
- National Research Council-Biophysics Institute (CNR-IBF), and Biosciences Department University of Milan, Via Celoria, 26, I-20133 Milan, Italy
| | - Giuseppe Pignataro
- Division of Pharmacology, Department of Neuroscience, School of Medicine, University of Naples Federico II, Via Pansini 5, I-80131 Naples, Italy
| | - Pierfausto Seneci
- Chemistry Department, University of Milan, Via Golgi 19, 20133 Milan, Italy
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Mele A, Mantuano P, Fonzino A, Rana F, Capogrosso RF, Sanarica F, Rolland JF, Cappellari O, De Luca A. Ultrasonography validation for early alteration of diaphragm echodensity and function in the mdx mouse model of Duchenne muscular dystrophy. PLoS One 2021; 16:e0245397. [PMID: 33434240 PMCID: PMC7802948 DOI: 10.1371/journal.pone.0245397] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 12/29/2020] [Indexed: 12/26/2022] Open
Abstract
The mdx mouse model of Duchenne muscular dystrophy is characterized by functional and structural alterations of the diaphragm since early stages of pathology, closely resembling patients' condition. In recent years, ultrasonography has been proposed as a useful longitudinal non-invasive technique to assess mdx diaphragm dysfunction and evaluate drug efficacy over time. To date, only a few preclinical studies have been conducted. Therefore, an independent validation of this method by different laboratories is needed to increase results reliability and reduce biases. Here, we performed diaphragm ultrasonography in 3- and 6-month-old mdx mice, the preferred age-window for pharmacology studies. The alteration of diaphragm function over time was measured as diaphragm ultrasound movement amplitude. At the same time points, a first-time assessment of diaphragm echodensity was performed, as an experimental index of progressive loss of contractile tissue. A parallel evaluation of other in vivo and ex vivo dystrophy-relevant readouts was carried out. Both 3- and 6-month-old mdx mice showed a significant decrease in diaphragm amplitude compared to wild type (wt) mice. This index was well-correlated either with in vivo running performance or ex vivo isometric tetanic force of isolated diaphragm. In addition, diaphragms from 6-month-old dystrophic mice were also highly susceptible to eccentric contraction ex vivo. Importantly, we disclosed an age-dependent increase in echodensity in mdx mice not observed in wt animals, which was independent from abdominal wall thickness. This was accompanied by a notable increase of pro-fibrotic TGF-β1 levels in the mdx diaphragm and of non-muscle tissue amount in diaphragm sections stained by hematoxylin & eosin. Our findings corroborate the usefulness of diaphragm ultrasonography in preclinical drug studies as a powerful tool to monitor mdx pathology progression since early stages.
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Affiliation(s)
- Antonietta Mele
- Section of Pharmacology, Department of Pharmacy—Drug Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Paola Mantuano
- Section of Pharmacology, Department of Pharmacy—Drug Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Adriano Fonzino
- Section of Pharmacology, Department of Pharmacy—Drug Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Francesco Rana
- Section of Pharmacology, Department of Pharmacy—Drug Sciences, University of Bari "Aldo Moro", Bari, Italy
| | | | - Francesca Sanarica
- Section of Pharmacology, Department of Pharmacy—Drug Sciences, University of Bari "Aldo Moro", Bari, Italy
| | | | - Ornella Cappellari
- Section of Pharmacology, Department of Pharmacy—Drug Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Annamaria De Luca
- Section of Pharmacology, Department of Pharmacy—Drug Sciences, University of Bari "Aldo Moro", Bari, Italy
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Altamura C, Desaphy JF, Conte D, De Luca A, Imbrici P. Skeletal muscle ClC-1 chloride channels in health and diseases. Pflugers Arch 2020; 472:961-975. [PMID: 32361781 DOI: 10.1007/s00424-020-02376-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 03/18/2020] [Accepted: 03/31/2020] [Indexed: 12/14/2022]
Abstract
In 1970, the study of the pathomechanisms underlying myotonia in muscle fibers isolated from myotonic goats highlighted the importance of chloride conductance for skeletal muscle function; 20 years later, the human ClC-1 chloride channel has been cloned; last year, the crystal structure of human protein has been solved. Over the years, the efforts of many researchers led to significant advances in acknowledging the role of ClC-1 in skeletal muscle physiology and the mechanisms through which ClC-1 dysfunctions lead to impaired muscle function. The wide spectrum of pathophysiological conditions associated with modification of ClC-1 activity, either as the primary cause, such as in myotonia congenita, or as a secondary adaptive mechanism in other neuromuscular diseases, supports the idea that ClC-1 is relevant to preserve not only for skeletal muscle excitability, but also for skeletal muscle adaptation to physiological or harmful events. Improving this understanding could open promising avenues toward the development of selective and safe drugs targeting ClC-1, with the aim to restore normal muscle function. This review summarizes the most relevant research on ClC-1 channel physiology, associated diseases, and pharmacology.
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Affiliation(s)
- Concetta Altamura
- Department of Biomedical Sciences and Human Oncology, School of Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Jean-Francois Desaphy
- Department of Biomedical Sciences and Human Oncology, School of Medicine, University of Bari "Aldo Moro", Bari, Italy
| | - Diana Conte
- Department of Pharmacy-Drug Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Annamaria De Luca
- Department of Pharmacy-Drug Sciences, University of Bari "Aldo Moro", Bari, Italy
| | - Paola Imbrici
- Department of Pharmacy-Drug Sciences, University of Bari "Aldo Moro", Bari, Italy.
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Kobayashi M, Nishimura M, Kawamura M, Kamemura N, Nagamune H, Tabata A. Change in membrane potential induced by streptolysin O, a pore‐forming toxin: flow cytometric analysis using a voltage‐sensitive fluorescent probe and rat thymic lymphocytes. Microbiol Immunol 2019; 64:10-22. [DOI: 10.1111/1348-0421.12748] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/23/2019] [Accepted: 09/29/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Miho Kobayashi
- Department of Biological Science and Technology, Graduate School of Advanced Technology and ScienceTokushima UniversityTokushima Tokushima Japan
| | - Madoka Nishimura
- Department of Biological Science and Technology, Faculty of EngineeringTokushima UniversityTokushima Tokushima Japan
| | - Mina Kawamura
- Department of Bioscience and Bioindustry, Faculty of Bioscience and BioindustryTokushima UniversityTokushima Tokushima Japan
| | - Norio Kamemura
- Department of Food‐Nutritional Sciences, Faculty of Life SciencesTokushima Bunri UniversityTokushima Tokushima Japan
| | - Hideaki Nagamune
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social SciencesTokushima UniversityTokushima Tokushima Japan
| | - Atsushi Tabata
- Division of Bioscience and Bioindustry, Graduate School of Technology, Industrial and Social SciencesTokushima UniversityTokushima Tokushima Japan
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Bencheva LI, De Matteo M, Ferrante L, Ferrara M, Prandi A, Randazzo P, Ronzoni S, Sinisi R, Seneci P, Summa V, Gallo M, Veneziano M, Cellucci A, Mazzocchi N, Menegon A, Di Fabio R. Identification of Isoform 2 Acid-Sensing Ion Channel Inhibitors as Tool Compounds for Target Validation Studies in CNS. ACS Med Chem Lett 2019; 10:627-632. [PMID: 30996808 DOI: 10.1021/acsmedchemlett.8b00591] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/07/2019] [Indexed: 01/21/2023] Open
Abstract
Acid-sensing ion channels (ASICs) are a family of ion channels permeable to cations and largely responsible for the onset of acid-evoked ion currents both in neurons and in different types of cancer cells, thus representing a potential target for drug discovery. Owing to the limited attention ASIC2 has received so far, an exploratory program was initiated to identify ASIC2 inhibitors using diminazene, a known pan-ASIC inhibitor, as a chemical starting point for structural elaboration. The performed exploration enabled the identification of a novel series of ASIC2 inhibitors. In particular, compound 2u is a brain penetrant ASIC2 inhibitor endowed with an optimal pharmacokinetic profile. This compound may represent a useful tool to validate in animal models in vivo the role of ASIC2 in different neurodegenerative central nervous system pathologies.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Pierfausto Seneci
- Promidis, Via Olgettina 60, 20132 Milan, Italy
- Chemistry Department, Università degli Studi di Milano, Via Golgi 19, I-20133 Milan, Italy
| | - Vincenzo Summa
- IRBM Science Park, Via Pontina Km 30.600, 00070 Pomezia, Rome, Italy
| | - Mariana Gallo
- IRBM Science Park, Via Pontina Km 30.600, 00070 Pomezia, Rome, Italy
| | - Maria Veneziano
- IRBM Science Park, Via Pontina Km 30.600, 00070 Pomezia, Rome, Italy
| | | | - Nausicaa Mazzocchi
- San Raffaele Scientific Institute, Experimental Imaging Center, ALEMBIC, Advanced Light and Electron Microscopy BioImaging Center, Via Olgettina 60, 20132 Milan, Italy
| | - Andrea Menegon
- San Raffaele Scientific Institute, Experimental Imaging Center, ALEMBIC, Advanced Light and Electron Microscopy BioImaging Center, Via Olgettina 60, 20132 Milan, Italy
| | - Romano Di Fabio
- Promidis, Via Olgettina 60, 20132 Milan, Italy
- IRBM Science Park, Via Pontina Km 30.600, 00070 Pomezia, Rome, Italy
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Membrane potential changes occurring upon acidification influence the binding of small-molecule inhibitors to ASIC1a. Neuropharmacology 2019; 148:366-376. [DOI: 10.1016/j.neuropharm.2019.01.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Revised: 01/10/2019] [Accepted: 01/31/2019] [Indexed: 12/23/2022]
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