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Liu F, Li T, Gong H, Tian F, Bai Y, Wang H, Yang C, Li Y, Guo F, Liu S, Chen Q. Structural insights into the molecular effects of the anthelmintics monepantel and betaine on the Caenorhabditis elegans acetylcholine receptor ACR-23. EMBO J 2024; 43:3787-3806. [PMID: 39009676 PMCID: PMC11377560 DOI: 10.1038/s44318-024-00165-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 06/27/2024] [Accepted: 06/28/2024] [Indexed: 07/17/2024] Open
Abstract
Anthelmintics are drugs used for controlling pathogenic helminths in animals and plants. The natural compound betaine and the recently developed synthetic compound monepantel are both anthelmintics that target the acetylcholine receptor ACR-23 and its homologs in nematodes. Here, we present cryo-electron microscopy structures of ACR-23 in apo, betaine-bound, and betaine- and monepantel-bound states. We show that ACR-23 forms a homo-pentameric channel, similar to some other pentameric ligand-gated ion channels (pLGICs). While betaine molecules are bound to the classical neurotransmitter sites in the inter-subunit interfaces in the extracellular domain, monepantel molecules are bound to allosteric sites formed in the inter-subunit interfaces in the transmembrane domain of the receptor. Although the pore remains closed in betaine-bound state, monepantel binding results in an open channel by wedging into the cleft between the transmembrane domains of two neighboring subunits, which causes dilation of the ion conduction pore. By combining structural analyses with site-directed mutagenesis, electrophysiology and in vivo locomotion assays, we provide insights into the mechanism of action of the anthelmintics monepantel and betaine.
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Affiliation(s)
- Fenglian Liu
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Tianyu Li
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Department of Anesthesiology, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 201204, China
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
| | - Huihui Gong
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Fei Tian
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yan Bai
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Haowei Wang
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Chonglin Yang
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China
| | - Yang Li
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China
| | - Fei Guo
- State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, 201203, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, 200040, China.
| | - Sheng Liu
- Institute of Pediatrics, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, 518026, China.
- Department of Infectious Diseases, Shenzhen Children's Hospital, Shenzhen, Guangdong Province, 518038, China.
| | - Qingfeng Chen
- Center for Life Sciences, Yunnan Key Laboratory of Cell Metabolism and Diseases, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, 650091, China.
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Mazzaferro S, Kang G, Natarajan K, Hibbs RE, Sine SM. Structural bases for stoichiometry-selective calcium potentiation of a neuronal nicotinic receptor. Br J Pharmacol 2024; 181:1973-1992. [PMID: 38454578 DOI: 10.1111/bph.16321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 01/05/2024] [Accepted: 01/08/2024] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND AND PURPOSE α4β2 nicotinic acetylcholine (nACh) receptors assemble in two stoichiometric forms, one of which is potentiated by calcium. The sites of calcium binding that underpin potentiation are not known. EXPERIMENTAL APPROACH To identify calcium binding sites, we applied cryo-electron microscopy (cryo-EM) and molecular dynamics (MD) simulations to each stoichiometric form of the α4β2 nACh receptor in the presence of calcium ions. To test whether the identified calcium sites are linked to potentiation, we generated mutants of anionic residues at the sites, expressed wild type and mutant receptors in clonal mammalian fibroblasts, and recorded ACh-elicited single-channel currents with or without calcium. KEY RESULTS Both cryo-EM and MD simulations show calcium bound to a site between the extracellular and transmembrane domains of each α4 subunit (ECD-TMD site). Substituting alanine for anionic residues at the ECD-TMD site abolishes stoichiometry-selective calcium potentiation, as monitored by single-channel patch clamp electrophysiology. Additionally, MD simulation reveals calcium association at subunit interfaces within the extracellular domain. Substituting alanine for anionic residues at the ECD sites reduces or abolishes stoichiometry-selective calcium potentiation. CONCLUSIONS AND IMPLICATIONS Stoichiometry-selective calcium potentiation of the α4β2 nACh receptor is achieved by calcium association with topographically distinct sites framed by anionic residues within the α4 subunit and between the α4 and β2 subunits. Stoichiometry-selective calcium potentiation could result from the greater number of calcium sites in the stoichiometric form with three rather than two α4 subunits. The results are relevant to modulation of signalling via α4β2 nACh receptors in physiological and pathophysiological conditions.
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Affiliation(s)
- Simone Mazzaferro
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
- Wellcome Trust - Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Wellcome Trust - Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - Guipeun Kang
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Kathiresan Natarajan
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
| | - Ryan E Hibbs
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, Texas, USA
- Department of Neurobiology, University of California San Diego, La Jolla, California, USA
| | - Steven M Sine
- Department of Physiology and Biomedical Engineering, Mayo Clinic, Rochester, Minnesota, USA
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, Minnesota, USA
- Department of Neurology, Mayo Clinic College of Medicine and Science, Rochester, Minnesota, USA
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3
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Söllner J, Derler I. Genetic code expansion, an emerging tool in the Ca 2+ ion channel field. J Physiol 2024; 602:3297-3313. [PMID: 38695316 DOI: 10.1113/jp285840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/15/2024] [Indexed: 07/17/2024] Open
Abstract
Various methods for characterizing binding forces as well as for monitoring and remote control of ion channels are still emerging. A recent innovation is the direct incorporation of unnatural amino acids (UAAs) with corresponding biophysical or biochemical properties, which are integrated using genetic code expansion technology. Minimal changes to natural amino acids, which are achieved by chemical synthesis of corresponding UAAs, are valuable tools to provide insight into the contributions of physicochemical properties of side chains in binding events. To gain unique control over the conformational changes or function of ion channels, a series of light-sensitive, chemically reactive and posttranslationally modified UAAs have been developed and utilized. Here, we present the existing UAA tools, their mode of action, their potential and limitations as well as their previous applications to Ca2+-permeable ion channels.
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Affiliation(s)
- Julia Söllner
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz, Austria
| | - Isabella Derler
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz, Austria
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Tae HS, Ortells MO, Yousuf A, Xu SQ, Akk G, Adams DJ, Arias HR. Tabernanthalog and ibogainalog inhibit the α7 and α9α10 nicotinic acetylcholine receptors via different mechanisms and with higher potency than the GABA A receptor and Ca V2.2 channel. Biochem Pharmacol 2024; 223:116183. [PMID: 38580167 PMCID: PMC11151864 DOI: 10.1016/j.bcp.2024.116183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/19/2024] [Accepted: 03/29/2024] [Indexed: 04/07/2024]
Abstract
In this study, we have investigated the pharmacological activity and structural interaction of two novel psychoplastogens, tabernanthalog (TBG) and ibogainalog (IBG) at heterologously-expressed rat (r) and human (h) nicotinic acetylcholine receptors (nAChRs), the rα1β2γ2L γ-aminobutyric acid type A receptor (GABAAR), and the human voltage-gated N-type calcium channel (CaV2.2 channel). Both compounds inhibited the nAChRs with the following receptor selectivity: α9α10 > α7 > α3β2 ≅ α3β4, indicating that β2/β4 subunits are relatively less important for their activity. The potencies of TBG and IBG were comparable at hα7 and hα9α10 subtypes, and comparable to their rat counterparts. TBG- and IBG-induced inhibition of rα7 was ACh concentration-independent and voltage-dependent, whereas rα9α10 inhibition was ACh concentration-dependent and voltage-independent, suggesting that they interact with the α7 ion channel pore and α9α10 orthosteric ligand binding site, respectively. These results were supported by molecular docking studies showing that at the α7 model TBG forms stable interactions with luminal rings at 9', 13', and 16', whereas IBG mostly interacts with the extracellular-transmembrane junction. In the α9α10 model, however, these compounds interacted with several residues from the principal (+) and complementary (-) sides in the transmitter binding site. Ibogaminalog (DM506) also interacted with a non-luminal site at α7, and one α9α10 orthosteric site. TBG and IBG inhibited the GABAAR and CaV2.2 channels with 10 to 30-fold lower potencies. In sum, we show that TBG and IBG inhibit the α7 and α9α10 nAChRs by noncompetitive and competitive mechanisms, respectively, and with higher potency than the GABAAR and CaV2.2 channel.
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Affiliation(s)
- Han-Shen Tae
- Molecular Horizons/Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia.
| | - Marcelo O Ortells
- Facultad de Medicina, Universidad de Morón, and CONICET, Morón, Argentina
| | - Arsalan Yousuf
- Molecular Horizons/Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Sophia Q Xu
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Gustav Akk
- Department of Anesthesiology, Washington University School of Medicine, St. Louis, MO, USA; The Taylor Family Institute for Innovative Psychiatric Research, Washington University School of Medicine, St. Louis, MO, USA
| | - David J Adams
- Molecular Horizons/Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522, Australia
| | - Hugo R Arias
- Department of Pharmacology and Physiology, Oklahoma State University College of Osteopathic Medicine, Tahlequah, OK, USA
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Bourne Y, Sulzenbacher G, Chabaud L, Aráoz R, Radić Z, Conrod S, Taylor P, Guillou C, Molgó J, Marchot P. The Cyclic Imine Core Common to the Marine Macrocyclic Toxins Is Sufficient to Dictate Nicotinic Acetylcholine Receptor Antagonism. Mar Drugs 2024; 22:149. [PMID: 38667766 PMCID: PMC11050823 DOI: 10.3390/md22040149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/22/2024] [Accepted: 03/25/2024] [Indexed: 04/28/2024] Open
Abstract
Macrocyclic imine phycotoxins are an emerging class of chemical compounds associated with harmful algal blooms and shellfish toxicity. Earlier binding and electrophysiology experiments on nAChR subtypes and their soluble AChBP surrogates evidenced common trends for substantial antagonism, binding affinities, and receptor-subtype selectivity. Earlier, complementary crystal structures of AChBP complexes showed that common determinants within the binding nest at each subunit interface confer high-affinity toxin binding, while distinctive determinants from the flexible loop C, and either capping the nest or extending toward peripheral subsites, dictate broad versus narrow receptor subtype selectivity. From these data, small spiroimine enantiomers mimicking the functional core motif of phycotoxins were chemically synthesized and characterized. Voltage-clamp analyses involving three nAChR subtypes revealed preserved antagonism for both enantiomers, despite lower subtype specificity and binding affinities associated with faster reversibility compared with their macrocyclic relatives. Binding and structural analyses involving two AChBPs pointed to modest affinities and positional variability of the spiroimines, along with a range of AChBP loop-C conformations denoting a prevalence of antagonistic properties. These data highlight the major contribution of the spiroimine core to binding within the nAChR nest and confirm the need for an extended interaction network as established by the macrocyclic toxins to define high affinities and marked subtype specificity. This study identifies a minimal set of functional pharmacophores and binding determinants as templates for designing new antagonists targeting disease-associated nAChR subtypes.
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Affiliation(s)
- Yves Bourne
- Lab “Architecture et Fonction des Macromolécules Biologiques” (AFMB), Aix-Marseille Univ, CNRS, Faculté des Sciences Campus Luminy, 13288 Marseille cedex 09, France; (Y.B.); (G.S.)
| | - Gerlind Sulzenbacher
- Lab “Architecture et Fonction des Macromolécules Biologiques” (AFMB), Aix-Marseille Univ, CNRS, Faculté des Sciences Campus Luminy, 13288 Marseille cedex 09, France; (Y.B.); (G.S.)
| | - Laurent Chabaud
- Institut de Chimie des Substances Naturelles (ICSN), Univ Paris-Saclay, CNRS, 91198 Gif-sur-Yvette, France; (L.C.); (C.G.)
| | - Rómulo Aráoz
- Service d’Ingénierie Moléculaire pour la Santé (SIMoS) EMR CNRS 9004, Département Médicaments et Technologies pour la Santé, Institut des Sciences du Vivant Frédéric Joliot, CEA, INRAE, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (R.A.); (J.M.)
| | - Zoran Radić
- Skaggs School of Pharmacy and Pharmaceutical Sciences (SSPPS), University of California San Diego, La Jolla, CA 92093-0751, USA; (Z.R.); (P.T.)
| | - Sandrine Conrod
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille (CRN2M), Aix Marseille Univ, CNRS, 13344 Marseille, France;
| | - Palmer Taylor
- Skaggs School of Pharmacy and Pharmaceutical Sciences (SSPPS), University of California San Diego, La Jolla, CA 92093-0751, USA; (Z.R.); (P.T.)
| | - Catherine Guillou
- Institut de Chimie des Substances Naturelles (ICSN), Univ Paris-Saclay, CNRS, 91198 Gif-sur-Yvette, France; (L.C.); (C.G.)
| | - Jordi Molgó
- Service d’Ingénierie Moléculaire pour la Santé (SIMoS) EMR CNRS 9004, Département Médicaments et Technologies pour la Santé, Institut des Sciences du Vivant Frédéric Joliot, CEA, INRAE, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (R.A.); (J.M.)
| | - Pascale Marchot
- Lab “Architecture et Fonction des Macromolécules Biologiques” (AFMB), Aix-Marseille Univ, CNRS, Faculté des Sciences Campus Luminy, 13288 Marseille cedex 09, France; (Y.B.); (G.S.)
- Centre de Recherche en Neurobiologie et Neurophysiologie de Marseille (CRN2M), Aix Marseille Univ, CNRS, 13344 Marseille, France;
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6
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Son L, Kost V, Maiorov V, Sukhov D, Arkhangelskaya P, Ivanov I, Kudryavtsev D, Siniavin A, Utkin Y, Kasheverov I. Efficient Expression in Leishmania tarentolae (LEXSY) of the Receptor-Binding Domain of the SARS-CoV-2 S-Protein and the Acetylcholine-Binding Protein from Lymnaea stagnalis. Molecules 2024; 29:943. [PMID: 38474455 DOI: 10.3390/molecules29050943] [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: 11/22/2023] [Revised: 01/31/2024] [Accepted: 02/15/2024] [Indexed: 03/14/2024] Open
Abstract
Leishmania tarentolae (LEXSY) system is an inexpensive and effective expression approach for various research and medical purposes. The stated advantages of this system are the possibility of obtaining the soluble product in the cytoplasm, a high probability of correct protein folding with a full range of post-translational modifications (including uniform glycosylation), and the possibility of expressing multi-subunit proteins. In this paper, a LEXSY expression system has been employed for obtaining the receptor binding domain (RBD) of the spike-protein of the SARS-CoV-2 virus and the homopentameric acetylcholine-binding protein (AChBP) from Lymnaea stagnalis. RBD is actively used to obtain antibodies against the virus and in various scientific studies on the molecular mechanisms of the interaction of the virus with host cell targets. AChBP represents an excellent structural model of the ligand-binding extracellular domain of all subtypes of nicotinic acetylcholine receptors (nAChRs). Both products were obtained in a soluble glycosylated form, and their structural and functional characteristics were compared with those previously described.
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Affiliation(s)
- Lina Son
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Vladimir Kost
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Valery Maiorov
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Dmitry Sukhov
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Polina Arkhangelskaya
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Igor Ivanov
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Denis Kudryavtsev
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Andrei Siniavin
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
- Ivanovsky Institute of Virology, N.F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia
| | - Yuri Utkin
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
| | - Igor Kasheverov
- Department of Molecular Bases of Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 117997 Moscow, Russia
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Nguyen QA, Klein PM, Xie C, Benthall KN, Iafrati J, Homidan J, Bendor JT, Dudok B, Farrell JS, Gschwind T, Porter CL, Keravala A, Dodson GS, Soltesz I. Acetylcholine receptor based chemogenetics engineered for neuronal inhibition and seizure control assessed in mice. Nat Commun 2024; 15:601. [PMID: 38238329 PMCID: PMC10796428 DOI: 10.1038/s41467-024-44853-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 01/09/2024] [Indexed: 01/22/2024] Open
Abstract
Epilepsy is a prevalent disorder involving neuronal network hyperexcitability, yet existing therapeutic strategies often fail to provide optimal patient outcomes. Chemogenetic approaches, where exogenous receptors are expressed in defined brain areas and specifically activated by selective agonists, are appealing methods to constrain overactive neuronal activity. We developed BARNI (Bradanicline- and Acetylcholine-activated Receptor for Neuronal Inhibition), an engineered channel comprised of the α7 nicotinic acetylcholine receptor ligand-binding domain coupled to an α1 glycine receptor anion pore domain. Here we demonstrate that BARNI activation by the clinical stage α7 nicotinic acetylcholine receptor-selective agonist bradanicline effectively suppressed targeted neuronal activity, and controlled both acute and chronic seizures in male mice. Our results provide evidence for the use of an inhibitory acetylcholine-based engineered channel activatable by both exogenous and endogenous agonists as a potential therapeutic approach to treating epilepsy.
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Affiliation(s)
- Quynh-Anh Nguyen
- Department of Neurosurgery, Stanford University, Stanford, CA, 94305, USA.
| | - Peter M Klein
- Department of Neurosurgery, Stanford University, Stanford, CA, 94305, USA.
| | - Cheng Xie
- CODA Biotherapeutics, 240 East Grand Ave., South San Francisco, CA, 94080, USA
| | - Katelyn N Benthall
- CODA Biotherapeutics, 240 East Grand Ave., South San Francisco, CA, 94080, USA
| | - Jillian Iafrati
- CODA Biotherapeutics, 240 East Grand Ave., South San Francisco, CA, 94080, USA
| | - Jesslyn Homidan
- Department of Neurosurgery, Stanford University, Stanford, CA, 94305, USA
| | - Jacob T Bendor
- CODA Biotherapeutics, 240 East Grand Ave., South San Francisco, CA, 94080, USA
| | - Barna Dudok
- Department of Neurosurgery, Stanford University, Stanford, CA, 94305, USA
- Department of Neurology, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Jordan S Farrell
- Department of Neurosurgery, Stanford University, Stanford, CA, 94305, USA
| | - Tilo Gschwind
- Department of Neurosurgery, Stanford University, Stanford, CA, 94305, USA
| | - Charlotte L Porter
- Department of Neurosurgery, Stanford University, Stanford, CA, 94305, USA
| | - Annahita Keravala
- CODA Biotherapeutics, 240 East Grand Ave., South San Francisco, CA, 94080, USA
| | - G Steven Dodson
- CODA Biotherapeutics, 240 East Grand Ave., South San Francisco, CA, 94080, USA
| | - Ivan Soltesz
- Department of Neurosurgery, Stanford University, Stanford, CA, 94305, USA
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8
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FitzGerald EA, Vagrys D, Opassi G, Klein HF, Hamilton DJ, Talibov VO, Abramsson M, Moberg A, Lindgren MT, Holmgren C, Davis B, O'Brien P, Wijtmans M, Hubbard RE, de Esch IJP, Danielson UH. Multiplexed experimental strategies for fragment library screening against challenging drug targets using SPR biosensors. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2024; 29:40-51. [PMID: 37714432 DOI: 10.1016/j.slasd.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 09/01/2023] [Accepted: 09/05/2023] [Indexed: 09/17/2023]
Abstract
Surface plasmon resonance (SPR) biosensor methods are ideally suited for fragment-based lead discovery. However, generally applicable experimental procedures and detailed protocols are lacking, especially for structurally or physico-chemically challenging targets or when tool compounds are not available. Success depends on accounting for the features of both the target and the chemical library, purposely designing screening experiments for identification and validation of hits with desired specificity and mode-of-action, and availability of orthogonal methods capable of confirming fragment hits. The range of targets and libraries amenable to an SPR biosensor-based approach for identifying hits is considerably expanded by adopting multiplexed strategies, using multiple complementary surfaces or experimental conditions. Here we illustrate principles and multiplexed approaches for using flow-based SPR biosensor systems for screening fragment libraries of different sizes (90 and 1056 compounds) against a selection of challenging targets. It shows strategies for the identification of fragments interacting with 1) large and structurally dynamic targets, represented by acetyl choline binding protein (AChBP), a Cys-loop receptor ligand gated ion channel homologue, 2) targets in multi protein complexes, represented by lysine demethylase 1 and a corepressor (LSD1/CoREST), 3) structurally variable or unstable targets, represented by farnesyl pyrophosphate synthase (FPPS), 4) targets containing intrinsically disordered regions, represented by protein tyrosine phosphatase 1B (PTP1B), and 5) aggregation-prone proteins, represented by an engineered form of human tau (tau K18M). Practical considerations and procedures accounting for the characteristics of the proteins and libraries, and that increase robustness, sensitivity, throughput and versatility are highlighted. The study shows that the challenges for addressing these types of targets is not identification of potentially useful fragments per se, but establishing methods for their validation and evolution into leads.
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Affiliation(s)
- Edward A FitzGerald
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Beactica Therapeutics AB, Virdings allé 2, Uppsala, Sweden
| | - Darius Vagrys
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom; YSBL, Department of Chemistry, University of York, York, United Kingdom
| | - Giulia Opassi
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | - Hanna F Klein
- Department of Chemistry, University of York, York, United Kingdom
| | - David J Hamilton
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | | | - Mia Abramsson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden
| | | | | | | | - Ben Davis
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom
| | - Peter O'Brien
- Department of Chemistry, University of York, York, United Kingdom
| | - Maikel Wijtmans
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - Roderick E Hubbard
- Vernalis (R&D) Ltd., Granta Park, Great Abington, Cambridge, United Kingdom; YSBL, Department of Chemistry, University of York, York, United Kingdom
| | - Iwan J P de Esch
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Sciences, Vrije Universiteit Amsterdam, De Boelelaan 1108, 1081 HZ, Amsterdam, The Netherlands
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University, Uppsala, Sweden; Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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Lu X, Xu H, Zhang X, Sun T, Lin Y, Li H, Li X, Zhang L, Duan H, Yang X, Ling Y. Target-Based Design, Synthesis, and Biological Evaluation of Novel 1,2,4-Triazolone Derivatives as Potential nAChR Modulators. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2023; 71:19333-19342. [PMID: 38050804 DOI: 10.1021/acs.jafc.3c04998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Novel agrochemicals have been successfully developed using target-based drug design (TBDD). To discover a novel, efficient, and highly selective nicotinic insecticide candidate, we developed a unified pharmacological model using TBDD by studying the binding modes of 11 nicotinic acetylcholine receptor (nAChR) modulators with acetylcholine binding protein (AChBP) targets for the first time. This model was used to design and develop a series of 1,2,4-triazolone derivatives. Bioassays demonstrated excellent insecticidal activities against Aphis glycines of compounds 4k (LC50 = 4.95 mg/L) and 4q (LC50 = 3.17 mg/L), and low toxicities to Apis mellifera. Additionally, compound 4q was stably bound to Aplysia californica AChBP, which was consistent with the pharmacological model obtained via molecular docking and molecular dynamics simulations. Therefore, compound 4q could be a potential lead candidate targeting nAChR. The explicit pharmacological model of nAChR modulators with Ac-AChBP in this study may facilitate the future rational design of eco-friendly nicotinic insecticides.
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Affiliation(s)
- Xingxing Lu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Huan Xu
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Xiaoming Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Tengda Sun
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Yufan Lin
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Honghong Li
- Guangxi Key Laboratory of Agro-Environment and Agro-Product Safety, Agricultural College, Guangxi University, Nanning, Guangxi Province 530004, China
| | - Xuesheng Li
- Guangxi Key Laboratory of Agro-Environment and Agro-Product Safety, Agricultural College, Guangxi University, Nanning, Guangxi Province 530004, China
| | - Li Zhang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Hongxia Duan
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Xinling Yang
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
| | - Yun Ling
- Innovation Center of Pesticide Research, Department of Applied Chemistry, College of Science, China Agricultural University, Beijing 100193, China
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10
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Pirayesh E, Do HQ, Ferreira G, Pandhare A, Gallardo ZR, Jansen M. Identification of a binding site for bupropion in Gloeobacter violaceus ligand-gated ion channel. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.09.561596. [PMID: 37873398 PMCID: PMC10592773 DOI: 10.1101/2023.10.09.561596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Bupropion is an atypical antidepressant and smoking cessation drug which causes adverse effects such as insomnia, irritability, and anxiety. Bupropion inhibits dopamine and norepinephrine reuptake transporters and eukaryotic cation-conducting pentameric ligand-gated ion channels (pLGICs), such as nicotinic acetylcholine (nACh) and serotonin type 3A (5-HT3A) receptors, at clinically relevant concentrations. However, the binding sites and binding mechanisms of bupropion are still elusive. To further understand the inhibition of pLGICs by bupropion, in this work, using a prokaryotic homologue of pLGICs as a model, we examined the inhibitory potency of bupropion in Gloeobacter violaceus ligand-gated ion channel (GLIC), a proton-gated ion channel. Bupropion inhibited proton-induced currents in GLIC with an inhibitory potency of 14.9 ± 2.0 μM, comparable to clinically attainable concentrations previously shown to also modulate eukaryotic pLGICs. Using single amino acid substitutions in GLIC and two-electrode voltage-clamp recordings, we further determined a binding site for bupropion in the lower third of the first transmembrane segment M1 at residue T214. The sidechain of M1 T214 together with additional residues of M1 and also of M3 of the adjacent subunit have previously been shown to contribute to binding of other lipophilic molecules like allopregnanolone and pregnanolone.
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Affiliation(s)
- Elham Pirayesh
- Medical Student Summer Research Program, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430 USA
| | - Hoa Quynh Do
- Medical Student Summer Research Program, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430 USA
| | - Garren Ferreira
- Medical Student Summer Research Program, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430 USA
| | - Akash Pandhare
- Medical Student Summer Research Program, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430 USA
| | - Zackary Ryan Gallardo
- Medical Student Summer Research Program, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430 USA
| | - Michaela Jansen
- Medical Student Summer Research Program, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430 USA
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11
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Raisch T, Raunser S. The modes of action of ion-channel-targeting neurotoxic insecticides: lessons from structural biology. Nat Struct Mol Biol 2023; 30:1411-1427. [PMID: 37845413 DOI: 10.1038/s41594-023-01113-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 08/31/2023] [Indexed: 10/18/2023]
Abstract
Insecticides are indispensable tools for plant protection in modern agriculture. Despite having highly heterogeneous structures, many neurotoxic insecticides use similar principles to inhibit or deregulate neuronal ion channels. Insecticides targeting pentameric ligand-gated channels are structural mimetics of neurotransmitters or manipulate and deregulate the proteins. Those binding to (pseudo-)tetrameric voltage-gated(-like) channels, on the other hand, are natural or synthetic compounds that directly block the ion-conducting pore or prevent conformational changes in the transmembrane domain necessary for opening and closing the pore. The use of a limited number of inhibition mechanisms can be problematic when resistances arise and become more widespread. Therefore, there is a rising interest in the development of insecticides with novel mechanisms that evade resistance and are pest-insect-specific. During the last decade, most known insecticide targets, many with bound compounds, have been structurally characterized, bringing the rational design of novel classes of agrochemicals within closer reach than ever before.
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Affiliation(s)
- Tobias Raisch
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
| | - Stefan Raunser
- Department of Structural Biochemistry, Max Planck Institute of Molecular Physiology, Dortmund, Germany.
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12
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Viscarra F, Chrestia JF, Sanchez Y, Pérez EG, Biggin PC, Bouzat C, Bermudez I, López JJ. Side Groups Convert the α7 Nicotinic Receptor Agonist Ether Quinuclidine into a Type I Positive Allosteric Modulator. ACS Chem Neurosci 2023; 14:2876-2887. [PMID: 37535446 DOI: 10.1021/acschemneuro.3c00225] [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] [Indexed: 08/05/2023] Open
Abstract
The quinuclidine scaffold has been extensively used for the development of nicotinic acetylcholine receptor (nAChR) agonists, with hydrophobic substituents at position 3 of the quinuclidine framework providing selectivity for α7 nAChRs. In this study, six new ligands (4-9) containing a 3-(pyridin-3-yloxy)quinuclidine moiety (ether quinuclidine) were synthesized to gain a better understanding of the structural-functional properties of ether quinuclidines. To evaluate the pharmacological activity of these ligands, two-electrode voltage-clamp and single-channel recordings were performed. Only ligand 4 activated α7 nAChR. Ligands 5 and 7 had no effects on α7 nAChR, but ligands 6, 8, and 9 potentiated the currents evoked by ACh. Ligand 6 was the most potent and efficacious of the potentiating ligands, with an estimated EC50 for potentiation of 12.6 ± 3.32 μM and a maximal potentiation of EC20 ACh responses of 850 ± 120%. Ligand 6 increased the maximal ACh responses without changing the kinetics of the current responses. At the single-channel level, the potentiation exerted by ligand 6 was evidenced in the low micromolar concentration range by the appearance of prolonged bursts of channel openings. Furthermore, computational studies revealed the preference of ligand 6 for an intersubunit site in the transmembrane domain and highlighted some putative key interactions that explain the different profiles of the synthesized ligands. Notably, Met276 in the 15' position of the transmembrane domain 2 almost abolished the effects of ligand 6 when mutated to Leu. We conclude that ligand 6 is a novel type I positive allosteric modulator (PAM-I) of α7 nAChR.
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Affiliation(s)
- Franco Viscarra
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford OX3 0BP, U.K
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, U.K
| | - Juan Facundo Chrestia
- Departamento de Biología, Bioquímica y Farmacia, Instituto de Investigaciones Bioquímicas de Bahía Blanca, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Camino La Carrindanga Km 7, Bahía Blanca 8000, Argentina
| | - Yaima Sanchez
- Department of Organic Chemistry, Faculty of Chemistry, Universidad de Concepción, Edmundo Larenas 129, Concepción 4070371, Chile
| | - Edwin G Pérez
- Department of Organic Chemistry, Faculty of Chemistry and Pharmacy, Pontificia Universidad Católica de Chile, Av. Vicuña Mackenna 4860, Santiago 7820436, Chile
| | - Philip C Biggin
- Structural Bioinformatics and Computational Biochemistry, Department of Biochemistry, Oxford University, South Parks Road, Oxford OX1 3QU, U.K
| | - Cecilia Bouzat
- Departamento de Biología, Bioquímica y Farmacia, Instituto de Investigaciones Bioquímicas de Bahía Blanca, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Camino La Carrindanga Km 7, Bahía Blanca 8000, Argentina
| | - Isabel Bermudez
- Department of Biological and Medical Sciences, Oxford Brookes University, Gipsy Lane, Oxford OX3 0BP, U.K
| | - Jhon J López
- Department of Organic Chemistry, Faculty of Chemistry, Universidad de Concepción, Edmundo Larenas 129, Concepción 4070371, Chile
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13
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Taguchi S, Fujimoto D, Shiga M, Obata N, Mizobuchi S. Rocuronium action can be affected by hyperventilation: a case report and computational simulation. J Clin Monit Comput 2023:10.1007/s10877-023-01022-4. [PMID: 37138040 DOI: 10.1007/s10877-023-01022-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 04/19/2023] [Indexed: 05/05/2023]
Abstract
The neuromuscular blocking potency of rocuronium varies with respiratory pH changes, increasing at lower pH and decreasing at higher pH; thus, hyperventilation-induced respiratory alkalosis is expected to decrease the potency of rocuronium. We report a case of anesthetic management of modified electroconvulsive therapy (m-ECT) for a patient monitored with electromyography-based neuromuscular monitoring during two patterns of ventilation to elucidate their relationship and propose the possible mechanisms underlying the effects by computational simulations. Case presentation: The patient was a 25-year-old man with schizophrenia. In m-ECT, hyperventilation may be used to produce longer seizures. We compared the neuromuscular monitoring data recorded during hyperventilation and during normal ventilation while receiving the same dose of rocuronium. Despite receiving the same dose of rocuronium, the time required for the first twitch to decrease to 80% of the control value was delayed in hyperventilation compared to normal ventilation. Conclusions: This case report and computational simulation suggest that respiratory alkalosis might delay the action of rocuronium. It is necessary to consider the delayed action of rocuronium when hyperventilation is performed.
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Affiliation(s)
- Shinya Taguchi
- Department of Anesthesiology, Kobe University Hospital, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe city, 650-0017, Hyogo, Japan.
| | - Daichi Fujimoto
- Department of Anesthesiology, Kobe University Hospital, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe city, 650-0017, Hyogo, Japan
| | - Moe Shiga
- Department of Anesthesiology, Kobe University Hospital, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe city, 650-0017, Hyogo, Japan
| | - Norihiko Obata
- Department of Anesthesiology, Kobe University Hospital, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe city, 650-0017, Hyogo, Japan
| | - Satoshi Mizobuchi
- Department of Anesthesiology, Kobe University Hospital, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe city, 650-0017, Hyogo, Japan
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14
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Elgoyhen AB. The α9α10 acetylcholine receptor: a non-neuronal nicotinic receptor. Pharmacol Res 2023; 190:106735. [PMID: 36931539 DOI: 10.1016/j.phrs.2023.106735] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023]
Abstract
Within the superfamily of pentameric ligand-gated ion channels, cholinergic nicotinic receptors (nAChRs) were classically identified to mediate synaptic transmission in the nervous system and the neuromuscular junction. The α9 and α10 nAChR subunits were the last ones to be identified. Surprisingly, they do not fall into the dichotomic neuronal/muscle classification of nAChRs. They assemble into heteropentamers with a well-established function as canonical ion channels in inner ear hair cells, where they mediate central nervous system control of auditory and vestibular sensory processing. The present review includes expression, pharmacological, structure-function, molecular evolution and pathophysiological studies, that define receptors composed from α9 and α10 subunits as distant and distinct members within the nAChR family. Thus, although α9 and α10 were initially included within the neuronal subdivision of nAChR subunits, they form a distinct clade within the phylogeny of nAChRs. Following the classification of nAChR subunits based on their main synaptic site of action, α9 and α10 should receive a name in their own right.
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Affiliation(s)
- Ana Belén Elgoyhen
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres" (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Vuelta de Obligado 2490, Buenos Aires 1428, Argentina.
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15
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Selvam B, Landagaray E, Cartereau A, Laurent AD, Graton J, Lebreton J, Thany SH, Mathé-Allainmat M, Le Questel JY. Identification of sulfonamide compounds active on the insect nervous system: Molecular modeling, synthesis and biological evaluation. Bioorg Med Chem Lett 2023; 80:129124. [PMID: 36610552 DOI: 10.1016/j.bmcl.2023.129124] [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: 09/02/2022] [Revised: 12/01/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023]
Abstract
Insect nicotinic acetylcholine receptors (nAChRs) are a recognized target for insecticide design. In this work, we have identified, from a structure-based approach using molecular modeling tools, ligands with potential selective activity for pests versus pollinators. A high-throughput virtual screening with the Openeye software was performed using a library from the ZINC database, thiacloprid being used as the target structure. The top sixteen molecules were then docked in α6 cockroach and honeybee homomeric nAChRs to check from a theoretical point of view relevant descriptors in favor of pest selectivity. Among the selected molecules, one original sulfonamide compound has afterward been synthesized, together with various analogs. Two compounds of this family have been shown to behave as activators of the cockroach cholinergic synaptic transmission.
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Affiliation(s)
- Balaji Selvam
- Nantes Université, CNRS, CEISAM, UMR 6230, F-44000 Nantes, France; Gossamer Bio, 3013 Science Park Road, Suite 200, San Diego, CA 92121, France
| | | | - Alison Cartereau
- Université d'Orléans, Laboratoire Biologie des Ligneux et des Grandes Cultures, USC INRAE 1328, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
| | - Adèle D Laurent
- Nantes Université, CNRS, CEISAM, UMR 6230, F-44000 Nantes, France
| | - Jérôme Graton
- Nantes Université, CNRS, CEISAM, UMR 6230, F-44000 Nantes, France
| | - Jacques Lebreton
- Nantes Université, CNRS, CEISAM, UMR 6230, F-44000 Nantes, France
| | - Steeve H Thany
- Université d'Orléans, Laboratoire Biologie des Ligneux et des Grandes Cultures, USC INRAE 1328, Rue de Chartres, BP 6759, 45067 Orléans Cedex 2, France
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16
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Ho TNT, Abraham N, Lewis RJ. Unravelling the allosteric binding mode of αD-VxXXB at nicotinic acetylcholine receptors. Front Pharmacol 2023; 14:1170514. [PMID: 37124228 PMCID: PMC10133702 DOI: 10.3389/fphar.2023.1170514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 03/30/2023] [Indexed: 05/02/2023] Open
Abstract
αD-conotoxins are 11 kDa homodimers that potently inhibit nicotinic acetylcholine receptors (nAChRs) through a non-competitive (allosteric) mechanism. In this study, we describe the allosteric binding mode of the granulin-like C-terminal (CTD) of VxXXB bound to Lymnea stagnalis acetylcholine binding protein (Ls-AChBP), a soluble homologue of the extracellular ligand-binding domain of nAChRs. This co-crystal complex revealed a novel allosteric binding site for nAChR antagonists outside the C-loop that caps the orthosteric site defined by the nAChR agonist nicotine and the antagonist epibatidine. Mutational and docking studies on Ls-AChBP supported a two-site binding mode for full-length VxXXB, with the first CTD binding site located outside the C-loop as seen in the co-crystal complex, with a second CTD binding site located near the N-terminal end of the adjacent subunit of AChBP. These results provide new structural insight into a novel allosteric mechanism of nAChR inhibition and define the cooperative binding mode of the N-terminal domain linked granulin core domains of αD-conotoxins.
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17
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Wei ZC, Wang Q, Min LJ, Bajsa-Hirschel J, Cantrell CL, Han L, Tan CX, Weng JQ, Li YX, Sun NB, Duke SO, Liu XH. Synthesis and Pesticidal Activity of New Niacinamide Derivatives Containing a Flexible, Chiral Chain. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010047. [PMID: 36615249 PMCID: PMC9822348 DOI: 10.3390/molecules28010047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
Natural products are a source for pesticide or drug discovery. In order to discover lead compounds with high fungicidal or herbicidal activity, new niacinamide derivatives derived from the natural product niacinamide, containing chiral flexible chains, were designed and synthesized. Their structures were confirmed by 1H NMR, 13C NMR and HRMS analysis. The fungicidal and herbicidal activities of these compounds were tested. The fungicidal activity results demonstrated that the compound (S)-2-(2-chloronicotinamido)propyl-2-methylbenzoate (3i) exhibited good fungicidal activity (92.3% inhibition) against the plant pathogen Botryosphaeria berengriana at 50 μg/mL and with an EC50 of 6.68 ± 0.72 μg/mL, which is the same as the positive control (fluxapyroxad). Compound 3i was not phytotoxic and could therefore be used as a fungicide on crops. Structure-activity relationships (SAR) were studied by molecular docking simulations with the succinate dehydrogenase of the fungal mitochondrial respiratory chain.
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Affiliation(s)
- Zhe-Cheng Wei
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Qiao Wang
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Li-Jing Min
- Key Laboratory of Vector Biology and Pathogen Control of Zhejiang Province, College of Life Science, Huzhou University, Huzhou 313000, China
| | - Joanna Bajsa-Hirschel
- Natural Products Utilization Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Oxford, MS 38677, USA
| | - Charles L. Cantrell
- Natural Products Utilization Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Oxford, MS 38677, USA
| | - Liang Han
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Cheng-Xia Tan
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Jian-Quan Weng
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China
| | - Yu-Xin Li
- State Key Laboratory of Elemento-Organic Chemistry, Department of Chemistry, Nankai University, Tianjin 300071, China
- Key Laboratory of Study and Discovery of Small Targeted Molecules of Hunan Province, Hunan Normal University, Changsha 430081, China
| | - Na-Bo Sun
- College of Biology and Environmental Engineering, Zhejiang Shuren University, Hangzhou 310015, China
- Correspondence: (N.-B.S.); (S.O.D.); (X.-H.L.)
| | - Stephen O. Duke
- National Center for Natural Product Research, School of Pharmacy, University of Mississippi, Oxford, MS 38677, USA
- Correspondence: (N.-B.S.); (S.O.D.); (X.-H.L.)
| | - Xing-Hai Liu
- College of Chemical Engineering, Zhejiang University of Technology, Hangzhou 310014, China
- Correspondence: (N.-B.S.); (S.O.D.); (X.-H.L.)
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18
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Batista VS, Gonçalves AM, Nascimento-Júnior NM. Pharmacophore Mapping Combined with dbCICA Reveal New Structural Features for the Development of Novel Ligands Targeting α4β2 and α7 Nicotinic Acetylcholine Receptors. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238236. [PMID: 36500328 PMCID: PMC9735964 DOI: 10.3390/molecules27238236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/29/2022]
Abstract
The neuronal nicotinic acetylcholine receptors (nAChRs) belong to the ligand-gated ion channel (GLIC) group, presenting a crucial role in several biological processes and neuronal disorders. The α4β2 and α7 nAChRs are the most abundant in the central nervous system (CNS), being involved in challenging diseases such as epilepsy, Alzheimer's disease, schizophrenia, and anxiety disorder, as well as alcohol and nicotine dependencies. In addition, in silico-based strategies may contribute to revealing new insights into drug design and virtual screening to find new drug candidates to treat CNS disorders. In this context, the pharmacophore maps were constructed and validated for the orthosteric sites of α4β2 and α7 nAChRs, through a docking-based Comparative Intermolecular Contacts Analysis (dbCICA). In this sense, bioactive ligands were retrieved from the literature for each receptor. A molecular docking protocol was developed for all ligands in both receptors by using GOLD software, considering GoldScore, ChemScore, ASP, and ChemPLP scoring functions. Output GOLD results were post-processed through dbCICA to identify critical contacts involved in protein-ligand interactions. Moreover, Crossminer software was used to construct a pharmacophoric map based on the most well-behaved ligands and negative contacts from the dbCICA model for each receptor. Both pharmacophore maps were validated by using a ROC curve. The results revealed important features for the ligands, such as the presence of hydrophobic regions, a planar ring, and hydrogen bond donor and acceptor atoms for α4β2. Parallelly, a non-planar ring region was identified for α7. These results can enable fragment-based drug design (FBDD) strategies, such as fragment growing, linking, and merging, allowing an increase in the activity of known fragments. Thus, our results can contribute to a further understanding of structural subunits presenting the potential for key ligand-receptor interactions, favoring the search in molecular databases and the design of novel ligands.
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Affiliation(s)
- Victor S. Batista
- Laboratory of Medicinal Chemistry, Organic Synthesis and Molecular Modeling (LaQMedSOMM), Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University (Unesp), Rua Professor Francisco Degni, 55, Jardim Quitandinha, Araraquara 14800-060, SP, Brazil
| | - Adriano Marques Gonçalves
- Laboratory of Medicinal Chemistry, Organic Synthesis and Molecular Modeling (LaQMedSOMM), Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University (Unesp), Rua Professor Francisco Degni, 55, Jardim Quitandinha, Araraquara 14800-060, SP, Brazil
- Department of Biological and Health Sciences, University of Araraquara (Uniara), Rua Carlos Gomes, 1217, Centro, Araraquara 14801-340, SP, Brazil
| | - Nailton M. Nascimento-Júnior
- Laboratory of Medicinal Chemistry, Organic Synthesis and Molecular Modeling (LaQMedSOMM), Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University (Unesp), Rua Professor Francisco Degni, 55, Jardim Quitandinha, Araraquara 14800-060, SP, Brazil
- Correspondence:
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19
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Slobodyanyuk M, Banda-Vázquez JA, Thompson MJ, Dean RA, Baenziger JE, Chica RA, daCosta CJB. Origin of acetylcholine antagonism in ELIC, a bacterial pentameric ligand-gated ion channel. Commun Biol 2022; 5:1264. [PMID: 36400839 PMCID: PMC9674596 DOI: 10.1038/s42003-022-04227-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 11/04/2022] [Indexed: 11/20/2022] Open
Abstract
ELIC is a prokaryotic homopentameric ligand-gated ion channel that is homologous to vertebrate nicotinic acetylcholine receptors. Acetylcholine binds to ELIC but fails to activate it, despite bringing about conformational changes indicative of activation. Instead, acetylcholine competitively inhibits agonist-activated ELIC currents. What makes acetylcholine an agonist in an acetylcholine receptor context, and an antagonist in an ELIC context, is not known. Here we use available structures and statistical coupling analysis to identify residues in the ELIC agonist-binding site that contribute to agonism. Substitution of these ELIC residues for their acetylcholine receptor counterparts does not convert acetylcholine into an ELIC agonist, but in some cases reduces the sensitivity of ELIC to acetylcholine antagonism. Acetylcholine antagonism can be abolished by combining two substitutions that together appear to knock out acetylcholine binding. Thus, making the ELIC agonist-binding site more acetylcholine receptor-like, paradoxically reduces the apparent affinity for acetylcholine, demonstrating that residues important for agonist binding in one context can be deleterious in another. These findings reinforce the notion that although agonism originates from local interactions within the agonist-binding site, it is a global property with cryptic contributions from distant residues. Finally, our results highlight an underappreciated mechanism of antagonism, where agonists with appreciable affinity, but negligible efficacy, present as competitive antagonists. A structural and functional study of the prokaryotic ligand-gated ion channel, ELIC, provides insight into the origin of agonism and antagonism at nicotinic acetylcholine receptors.
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20
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Li Z, Chan KC, Nickels JD, Cheng X. Electrostatic Contributions to the Binding Free Energy of Nicotine to the Acetylcholine Binding Protein. J Phys Chem B 2022; 126:8669-8679. [PMID: 36260486 PMCID: PMC10056799 DOI: 10.1021/acs.jpcb.2c04641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Biomolecular binding relies on specific attractive interactions between two partner molecules, including electrostatics, dispersion, hydrophobicity, and solvation. Assessing the contributions of electrostatic interactions to binding is key to the understanding of ligand binding mechanisms and the design of improved biomolecular binders. For example, nicotine is a well-known agonist of nicotinic acetylcholine receptors (nAChRs), but the molecular mechanisms for the differential action of nicotine on brain and muscle nAChRs remain elusive. In this work, we have chosen the acetylcholine binding protein (AChBP) in complex with nicotine as a model system to interrogate the electrostatic contributions to nicotine binding. Our absolute binding free energy simulations confirm that nicotine binds AChBP predominantly in its protonated (charged) form. By comparing energetic contributions from decomposed interactions for either neutral or charged nicotine, our calculations shed light on the nature of the binding of nicotine to the AChBP. The preferred binding of charged nicotine over neutral nicotine originates from its stronger electrostatic interactions with AChBP, a cation-π interaction to a tryptophan residue and a hydrogen bond between nicotine and the backbone carbonyl of the tryptophan, whereas the major force driving the binding process appears to be van der Waals interactions. The various nonelectrostatic terms can also indirectly modulate the electrostatic interactions through fine-tuning the binding pose of the ligand in the binding site, providing an explanation of why the binding specificity of nicotine to the brain versus muscle nAChRs is driven by electrostatic interaction, given that the immediate binding site residues, including the key tryptophan residue, are identical in the two receptors.
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Affiliation(s)
- Zoe Li
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio43210, United States
| | - Kevin C Chan
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio43210, United States
| | - Jonathan D Nickels
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, Ohio45221, United States
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio43210, United States
- Translational Data Analytics Institute (TDAI) at The Ohio State University, Columbus, Ohio43210, United States
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21
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Kaiser J, Gertzen CG, Bernauer T, Höfner G, Niessen KV, Seeger T, Paintner FF, Wanner KT, Worek F, Thiermann H, Gohlke H. A novel binding site in the nicotinic acetylcholine receptor for MB327 can explain its allosteric modulation relevant for organophosphorus-poisoning treatment. Toxicol Lett 2022; 373:160-171. [DOI: 10.1016/j.toxlet.2022.11.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Accepted: 11/25/2022] [Indexed: 11/27/2022]
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22
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Aguado R, Mata S, Sanz-Novo M, Alonso ER, León I, Alonso JL. The Nicotinic Agonist Cytisine: The Role of the NH···N Interaction. J Phys Chem Lett 2022; 13:9991-9996. [PMID: 36264108 PMCID: PMC9619914 DOI: 10.1021/acs.jpclett.2c02021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
We report a detailed structural study of cytisine, an alkaloid used to help with smoking cessation, looking forward to unveiling its role as a nicotinic agonist. High-resolution rotational spectroscopy has allowed us to characterize two different conformers exhibiting axial and equatorial arrangements of the piperidinic NH group. Unexpectedly, the axial form has been found as the predominant configuration, in contrast to that observed for related molecules, such as piperidine. This anomalous behavior has been justified in terms of an intramolecular NH···N hydrogen bond. Moreover, this interaction justifies the overstabilization of the axial conformer over the equatorial one and is crucial for the mechanism of action of cytisine over the nicotinic receptor, further rationalizing its behavior as a nicotinic agonist.
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Affiliation(s)
- Raúl Aguado
- Grupo
de Espectroscopía Molecular (GEM), Edificio Quifima, Área
de Química-Física, Laboratorios de Espectroscopía
y Bioespectroscopía, Parque Científico UVa, Unidad Asociada
CSIC, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Santiago Mata
- Grupo
de Espectroscopía Molecular (GEM), Edificio Quifima, Área
de Química-Física, Laboratorios de Espectroscopía
y Bioespectroscopía, Parque Científico UVa, Unidad Asociada
CSIC, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Miguel Sanz-Novo
- Grupo
de Espectroscopía Molecular (GEM), Edificio Quifima, Área
de Química-Física, Laboratorios de Espectroscopía
y Bioespectroscopía, Parque Científico UVa, Unidad Asociada
CSIC, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Elena R. Alonso
- Grupo
de Espectroscopía Molecular (GEM), Edificio Quifima, Área
de Química-Física, Laboratorios de Espectroscopía
y Bioespectroscopía, Parque Científico UVa, Unidad Asociada
CSIC, Universidad de Valladolid, 47011 Valladolid, Spain
| | - Iker León
- Grupo
de Espectroscopía Molecular (GEM), Edificio Quifima, Área
de Química-Física, Laboratorios de Espectroscopía
y Bioespectroscopía, Parque Científico UVa, Unidad Asociada
CSIC, Universidad de Valladolid, 47011 Valladolid, Spain
| | - José L. Alonso
- Grupo
de Espectroscopía Molecular (GEM), Edificio Quifima, Área
de Química-Física, Laboratorios de Espectroscopía
y Bioespectroscopía, Parque Científico UVa, Unidad Asociada
CSIC, Universidad de Valladolid, 47011 Valladolid, Spain
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23
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Design, Synthesis and Bioactivity of Novel Low Bee-Toxicity Compounds Based on Flupyrimin. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27186133. [PMID: 36144866 PMCID: PMC9505580 DOI: 10.3390/molecules27186133] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/13/2022] [Accepted: 09/15/2022] [Indexed: 11/17/2022]
Abstract
Neonicotinoids are important insecticides for controlling aphids in agriculture. Growing research suggested that neonicotinoid insecticides are a key factor causing the decline of global pollinator insects, such as bees. Flupyrimin (FLP) is a novel nicotinic insecticide with unique biological properties and no cross-resistance, and is safe for pollinators. Using FLP as the lead compound, a series of novel compounds were designed and synthesized by replacing the amide fragment with a sulfonamideone. Their structures were confirmed by 1H NMR, 13C NMR and HRMS spectra. Bioassay results showed that compound 2j had good insecticidal activity against Aphis glycines with an LC50 value of 20.93 mg/L. Meanwhile, compound 2j showed significantly lower acute oral and contact toxicity to Apis mellifera. In addition, compound 2j interacted well with the protein in insect acetylcholine binding protein (AChBP). The molecular docking on honeybee nicotinic acetylcholine receptor (nAChR) indicated that the sulfonamide group of compound 2j did not form a hydrogen bond with Arg173 of the β subunit, which conforms to the reported low bee-toxicity conformation. In general, target compound 2j can be regarded as a bee-friendly insecticide candidate.
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24
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Parker HP, Dawson A, Jones MJ, Yan R, Ouyang J, Hong R, Hunter WN. Delineating the activity of the potent nicotinic acetylcholine receptor agonists (+)-anatoxin-a and (−)-hosieine-A. Acta Crystallogr F Struct Biol Commun 2022; 78:313-323. [PMID: 36048081 PMCID: PMC9435674 DOI: 10.1107/s2053230x22007762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 08/01/2022] [Indexed: 11/10/2022] Open
Abstract
The affinity and thermodynamic parameters for the interactions of two naturally occurring neurotoxins, (+)-anatoxin-a and (−)-hosieine-A, with acetylcholine-binding protein were investigated using a fluorescence-quenching assay and isothermal titration calorimetry. The crystal structures of their complexes with acetylcholine-binding protein from Aplysia californica (AcAChBP) were determined and reveal details of molecular recognition in the orthosteric binding site. Comparisons treating AcAChBP as a surrogate for human α4β2 and α7 nicotinic acetylcholine receptors (nAChRs) suggest that the molecular features involved in ligand recognition and affinity for the protein targets are conserved. The ligands exploit interactions with similar residues as the archetypal nAChR agonist nicotine, but with greater affinity. (−)-Hosieine-A in particular has a high affinity for AcAChBP driven by a favorable entropic contribution to binding. The ligand affinities help to rationalize the potent biological activity of these alkaloids. The structural data, together with comparisons with related molecules, suggest that there may be opportunities to extend the hosieine-A scaffold to incorporate new interactions with the complementary side of the orthosteric binding site. Such a strategy may guide the design of new entities to target human α4β2 nAChR that may have therapeutic benefit.
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25
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Maity AN, Chen JR, Li QY, Ke SC. The Nitrogen Atom of Vitamin B 6 Is Essential for the Catalysis of Radical Aminomutases. Int J Mol Sci 2022; 23:ijms23095210. [PMID: 35563602 PMCID: PMC9105233 DOI: 10.3390/ijms23095210] [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: 03/28/2022] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022] Open
Abstract
Radical aminomutases are pyridoxal 5'-phosphate (PLP, a B6 vitamer)-dependent enzymes that require the generation of a 5'-deoxyadenosyl radical to initiate the catalytic cycle, to perform a 1,2 amino group shift reaction. The role of the nitrogen atom of PLP in radical aminomutases has not been investigated extensively yet. We report an alternative synthetic procedure to provide easy access to 1-deazaPLP (dAPLP), an isosteric analog of PLP which acts as a probe for studying the role of the nitrogen atom. Our results revealed that lysine 5,6-aminomutase (5,6-LAM), a radical aminomutase, reconstituted with dAPLP cannot turn over a substrate, demonstrating that the nitrogen atom is essential for radical aminomutases. In contrast, biochemical and spectroscopic studies on the S238A variant reconstituted with PLP revealed a minuscule loss of activity. This apparent anomaly can be explained by a water-mediated rescue of activity in S238A, as if mimicking the active site of lysine 2,3-aminomutase. This study leads to a better comprehension of how enzymes harness the optimum capability of PLP to realize catalysis.
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26
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Zlotos DP, Mandour YM, Jensen AA. Strychnine and its mono- and dimeric analogues: a pharmaco-chemical perspective. Nat Prod Rep 2022; 39:1910-1937. [PMID: 35380133 DOI: 10.1039/d1np00079a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Covering: up to November 2021Since its isolation in 1818, strychnine has attracted the attention of a plethora of chemists and pharmacologists who have established its structure, developed total syntheses, and examined its complex pharmacology. While numerous reviews on structure elucidation and total synthesis of strychnine are available, reports on structure-activity relationships (SARs) of this fascinating alkaloid are rare. In this review, we present and discuss structures, synthetic approaches, metabolic transformations, and the diverse pharmacological actions of strychnine and its mono- and dimeric analogues. Particular attention is given to its SARs at glycine receptors (GlyRs) in light of recently published high-resolution structures of strychnine-GlyR complexes. Other pharmacological actions of strychnine and its derivatives, such as their antagonistic properties at nicotinic acetylcholine receptors (nAChRs), allosteric modulation of muscarinic acetylcholine receptors as well as anti-cancer and anti-plasmodial effects are also critically reviewed, and possible future developments in the field are discussed.
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Affiliation(s)
- Darius P Zlotos
- Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, The German University in Cairo, New Cairo City, 11835 Cairo, Egypt.
| | - Yasmine M Mandour
- School of Life and Medical Sciences, University of Hertfordshire hosted by Global Academic Foundation, New Administrative Capital, Cairo, Egypt
| | - Anders A Jensen
- Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, DK-2100 Copenhagen, Denmark
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27
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Rahman MM, Basta T, Teng J, Lee M, Worrell BT, Stowell MHB, Hibbs RE. Structural mechanism of muscle nicotinic receptor desensitization and block by curare. Nat Struct Mol Biol 2022; 29:386-394. [PMID: 35301478 DOI: 10.1038/s41594-022-00737-3] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/04/2022] [Indexed: 11/09/2022]
Abstract
Binding of the neurotransmitter acetylcholine to its receptors on muscle fibers depolarizes the membrane and thereby triggers muscle contraction. We sought to understand at the level of three-dimensional structure how agonists and antagonists alter nicotinic acetylcholine receptor conformation. We used the muscle-type receptor from the Torpedo ray to first define the structure of the receptor in a resting, activatable state. We then determined the receptor structure bound to the agonist carbachol, which stabilizes an asymmetric, closed channel desensitized state. We find conformational changes in a peripheral membrane helix are tied to recovery from desensitization. To probe mechanisms of antagonism, we obtained receptor structures with the active component of curare, a poison arrow toxin and precursor to modern muscle relaxants. d-Tubocurarine stabilizes the receptor in a desensitized-like state in the presence and absence of agonist. These findings define the transitions between resting and desensitized states and reveal divergent means by which antagonists block channel activity of the muscle-type nicotinic receptor.
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Affiliation(s)
- Md Mahfuzur Rahman
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Tamara Basta
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Jinfeng Teng
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Myeongseon Lee
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Brady T Worrell
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA
| | - Michael H B Stowell
- Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO, USA.
| | - Ryan E Hibbs
- Department of Neuroscience, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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28
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Bueno RV, Davis S, Dawson A, Ondachi PW, Carroll FI, Hunter WN. Interactions between 2′-fluoro-(carbamoylpyridinyl)deschloroepibatidine analogues and acetylcholine-binding protein inform on potent antagonist activity against nicotinic receptors. Acta Crystallogr D Struct Biol 2022; 78:353-362. [PMID: 35234149 PMCID: PMC8900824 DOI: 10.1107/s2059798322000754] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 01/21/2022] [Indexed: 11/29/2022] Open
Abstract
The binding of a series of epibatidine derivatives to acetylcholine-binding protein was investigated using biolayer interferometry. The structures of three complexes inform discussion on the biological implications for interactions with nicotinic acetylcholine receptor subtypes, which are important targets for control of pain. Low-nanomolar binding constants were recorded for a series of six 2′-fluoro-(carbamoylpyridinyl)deschloroepibatidine analogues with acetylcholine-binding protein (AChBP). The crystal structures of three complexes with AChBP reveal details of molecular recognition in the orthosteric binding site and imply how the other three ligands bind. Comparisons exploiting AChBP as a surrogate for α4β2 and α7 nicotinic acetylcholine receptors (nAChRs) suggest that the key interactions are conserved. The ligands interact with the same residues as the archetypal nAChR agonist nicotine yet display greater affinity, thereby rationalizing their in vivo activity as potent antagonists of nicotine-induced antinociception. An oxyanion-binding site is formed on the periphery of the AChBP orthosteric site by Lys42, Asp94, Glu170 and Glu210. These residues are highly conserved in the human α4, β2 and α7 nAChR sequences. However, specific sequence differences are discussed that could contribute to nAChR subtype selectivity and in addition may represent a point of allosteric modulation. The ability to engage with this peripheral site may explain, in part, the function of a subset of ligands to act as agonists of α7 nAChR.
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29
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Moutoussamy EE, Waheed Q, Binford GJ, Khan HM, Moran SM, Eitel AR, Cordes MHJ, Reuter N. Specificity of Loxosceles α clade phospholipase D enzymes for choline-containing lipids: Role of a conserved aromatic cage. PLoS Comput Biol 2022; 18:e1009871. [PMID: 35180220 PMCID: PMC8893692 DOI: 10.1371/journal.pcbi.1009871] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Revised: 03/03/2022] [Accepted: 01/27/2022] [Indexed: 11/18/2022] Open
Abstract
Spider venom GDPD-like phospholipases D (SicTox) have been identified to be one of the major toxins in recluse spider venom. They are divided into two major clades: the α clade and the β clade. Most α clade toxins present high activity against lipids with choline head groups such as sphingomyelin, while activities in β clade toxins vary and include preference for substrates containing ethanolamine headgroups (Sicarius terrosus, St_βIB1). A structural comparison of available structures of phospholipases D (PLDs) reveals a conserved aromatic cage in the α clade. To test the potential influence of the aromatic cage on membrane-lipid specificity we performed molecular dynamics (MD) simulations of the binding of several PLDs onto lipid bilayers containing choline headgroups; two SicTox from the α clade, Loxosceles intermedia αIA1 (Li_αIA) and Loxosceles laeta αIII1 (Ll_αIII1), and one from the β clade, St_βIB1. The simulation results reveal that the aromatic cage captures a choline-headgroup and suggest that the cage plays a major role in lipid specificity. We also simulated an engineered St_βIB1, where we introduced the aromatic cage, and this led to binding with choline-containing lipids. Moreover, a multiple sequence alignment revealed the conservation of the aromatic cage among the α clade PLDs. Here, we confirmed that the i-face of α and β clade PLDs is involved in their binding to choline and ethanolamine-containing bilayers, respectively. Furthermore, our results suggest a major role in choline lipid recognition of the aromatic cage of the α clade PLDs. The MD simulation results are supported by in vitro liposome binding assay experiments. Envenomation following bites from recluse spiders (Loxosceles) causes loxoscelism, a necrotic tissue breakdown in mammals, and leads to skin degeneration and systemic reactions in the worst case. Recluse spiders belong to the Sicariidae family which also includes six-eyed sand spiders in the genera Sicarius and Hexopthalma. While sicariid spiders are found natively on all continents except Australia, treatments of loxoscelism are typically antibody based and available in some regions of the Americas. Sphingomyelinase D/phospholipase D enzymes are one of the major toxins in venom of sicariid spiders, and have been divided in two clades called α and β. The activity of α and β clades toxins differs; most α clade toxins present high activity against lipids with choline headgroups (-N (CH3)3+) such as sphingomyelin, while activities in β clade toxins vary and include preference for substrates containing ethanolamine headgroups (-NH3+). When comparing the structures of two α clade toxins and one β clade toxin, we noticed the presence in the α clade toxins only of a cage consisting of three aromatic amino acids. In this work we used numerical molecular simulations to probe the role of this cage in the preference of α clade toxins for choline head groups over ethanolamine head groups.
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Affiliation(s)
- Emmanuel E. Moutoussamy
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Qaiser Waheed
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Greta J. Binford
- Department of Biology, Lewis and Clark College, Portland, Oregon, United States
| | - Hanif M. Khan
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Biological Sciences, University of Bergen, Bergen, Norway
| | - Shane M. Moran
- Department of Chemistry and Biochemistry, University of Arizona, Arizona, United States
| | - Anna R. Eitel
- Department of Chemistry and Biochemistry, University of Arizona, Arizona, United States
| | - Matthew H. J. Cordes
- Department of Chemistry and Biochemistry, University of Arizona, Arizona, United States
| | - Nathalie Reuter
- Computational Biology Unit, Department of Informatics, University of Bergen, Bergen, Norway
- Department of Chemistry, University of Bergen, Bergen, Norway
- * E-mail:
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30
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Montgomery M, Rendine S, Zimmer CT, Elias J, Schaetzer J, Pitterna T, Benfatti F, Skaljac M, Bigot A. Structural Biology-Guided Design, Synthesis, and Biological Evaluation of Novel Insect Nicotinic Acetylcholine Receptor Orthosteric Modulators. J Med Chem 2022; 65:2297-2312. [PMID: 34986308 DOI: 10.1021/acs.jmedchem.1c01767] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The development of novel and safe insecticides remains an important need for a growing world population to protect crops and animal and human health. New chemotypes modulating the insect nicotinic acetylcholine receptors have been recently brought to the agricultural market, yet with limited understanding of their molecular interactions at their target receptor. Herein, we disclose the first crystal structures of these insecticides, namely, sulfoxaflor, flupyradifurone, triflumezopyrim, flupyrimin, and the experimental compound, dicloromezotiaz, in a double-mutated acetylcholine-binding protein which mimics the insect-ion-channel orthosteric site. Enabled by these findings, we discovered novel pharmacophores with a related mode of action, and we describe herein their design, synthesis, and biological evaluation.
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Affiliation(s)
- Mark Montgomery
- Syngenta Crop Protection, Jealott's Hill International Research Centre, RG42 6EY Bracknell, Berkshire, U.K
| | - Stefano Rendine
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Christoph T Zimmer
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Jan Elias
- Syngenta Crop Protection AG, Rosentalstrasse 67, 4002 Basel, Switzerland
| | - Jürgen Schaetzer
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Thomas Pitterna
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Fides Benfatti
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Marisa Skaljac
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
| | - Aurélien Bigot
- Syngenta Crop Protection AG, Schaffhauserstrasse 101, CH-4332 Stein, Switzerland
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31
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Interactions of Nereistoxin and Its Analogs with Vertebrate Nicotinic Acetylcholine Receptors and Molluscan ACh Binding Proteins. Mar Drugs 2022; 20:md20010049. [PMID: 35049904 PMCID: PMC8777805 DOI: 10.3390/md20010049] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/09/2021] [Accepted: 12/14/2021] [Indexed: 02/04/2023] Open
Abstract
Nereistoxin (NTX) is a marine toxin isolated from an annelid worm that lives along the coasts of Japan. Its insecticidal properties were discovered decades ago and this stimulated the development of a variety of insecticides such as Cartap that are readily transformed into NTX. One unusual feature of NTX is that it is a small cyclic molecule that contains a disulfide bond. In spite of its size, it acts as an antagonist at insect and mammalian nicotinic acetylcholine receptors (nAChRs). The functional importance of the disulfide bond was assessed by determining the effects of inserting a methylene group between the two sulfur atoms, creating dimethylaminodithiane (DMA-DT). We also assessed the effect of methylating the NTX and DMA-DT dimethylamino groups on binding to three vertebrate nAChRs. Radioligand receptor binding experiments were carried out using washed membranes from rat brain and fish (Torpedo) electric organ; [3H]-cytisine displacement was used to assess binding to the predominantly high affinity alpha4beta2 nAChRs and [125I]-alpha-bungarotoxin displacement was used to measure binding of NTX and analogs to the alpha7 and skeletal muscle type nAChRs. While the two quaternary nitrogen analogs, relative to their respective tertiary amines, displayed lower α4β2 nAChR binding affinities, both displayed much higher affinities for the Torpedo muscle nAChR and rat alpha7 brain receptors than their respective tertiary amine forms. The binding affinities of DMA-DT for the three nAChRs were lower than those of NTX and MeNTX. An AChBP mutant lacking the C loop disulfide bond that would potentially react with the NTX disulfide bond displayed an NTX affinity very similar to the parent AChBP. Inhibition of [3H]-epibatidine binding to the AChBPs was not affected by exposure to NTX or MeNTX for up to 24 hr prior to addition of the radioligand. Thus, the disulfide bond of NTX is not required to react with the vicinal disulfide in the AChBP C loop for inhibition of [3H]-epibatidine binding. However, a reversible disulfide interchange reaction of NTX with nAChRs might still occur, especially under reducing conditions. Labeled MeNTX, because it can be readily prepared with high specific radioactivity and possesses relatively high affinity for the nAChR-rich Torpedo nAChR, would be a useful probe to detect and identify any nereistoxin adducts.
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32
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Nichols AL, Blumenfeld Z, Fan C, Luebbert L, Blom AEM, Cohen BN, Marvin JS, Borden PM, Kim CH, Muthusamy AK, Shivange AV, Knox HJ, Campello HR, Wang JH, Dougherty DA, Looger LL, Gallagher T, Rees DC, Lester HA. Fluorescence activation mechanism and imaging of drug permeation with new sensors for smoking-cessation ligands. eLife 2022; 11:e74648. [PMID: 34982029 PMCID: PMC8820738 DOI: 10.7554/elife.74648] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/03/2022] [Indexed: 12/16/2022] Open
Abstract
Nicotinic partial agonists provide an accepted aid for smoking cessation and thus contribute to decreasing tobacco-related disease. Improved drugs constitute a continued area of study. However, there remains no reductionist method to examine the cellular and subcellular pharmacokinetic properties of these compounds in living cells. Here, we developed new intensity-based drug-sensing fluorescent reporters (iDrugSnFRs) for the nicotinic partial agonists dianicline, cytisine, and two cytisine derivatives - 10-fluorocytisine and 9-bromo-10-ethylcytisine. We report the first atomic-scale structures of liganded periplasmic binding protein-based biosensors, accelerating development of iDrugSnFRs and also explaining the activation mechanism. The nicotinic iDrugSnFRs detect their drug partners in solution, as well as at the plasma membrane (PM) and in the endoplasmic reticulum (ER) of cell lines and mouse hippocampal neurons. At the PM, the speed of solution changes limits the growth and decay rates of the fluorescence response in almost all cases. In contrast, we found that rates of membrane crossing differ among these nicotinic drugs by >30-fold. The new nicotinic iDrugSnFRs provide insight into the real-time pharmacokinetic properties of nicotinic agonists and provide a methodology whereby iDrugSnFRs can inform both pharmaceutical neuroscience and addiction neuroscience.
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Affiliation(s)
- Aaron L Nichols
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Zack Blumenfeld
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Chengcheng Fan
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Laura Luebbert
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Institute of Biology, Leiden UniversityLeidenNetherlands
| | - Annet EM Blom
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Bruce N Cohen
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Jonathan S Marvin
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Philip M Borden
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Charlene H Kim
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Anand K Muthusamy
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Amol V Shivange
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Hailey J Knox
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | | | - Jonathan H Wang
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | | | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
- Howard Hughes Medical Institute, California Institute of TechnologyPasadenaUnited States
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
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33
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Manturthi S, Bhattacharya D, Sakhare KR, Narayan KP, Patri SV. Nicotinic acid-based cationic vectors for efficient gene delivery to glioblastoma cells. NEW J CHEM 2022. [DOI: 10.1039/d2nj03207d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A tocopherol-conjugated nicotinic acid-based lipid (NGT) was used for liposomal formation with the co-lipid DOPE and exhibited enhanced transfection of glioblastoma cells for eGFP and β-galactosidase protein expression.
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Affiliation(s)
- Shireesha Manturthi
- Department of Chemistry, National Institute of Technology Warangal, Hanamkonda, Telangana-506004, India
| | - Dwaipayan Bhattacharya
- Department of Biological Science, Bits pilani-hyderabad, Hyderabad, Telangana-500078, India
| | - Kalyani Rajesh Sakhare
- Department of Biological Science, Bits pilani-hyderabad, Hyderabad, Telangana-500078, India
| | - Kumar Pranav Narayan
- Department of Biological Science, Bits pilani-hyderabad, Hyderabad, Telangana-500078, India
| | - Srilakshmi V. Patri
- Department of Chemistry, National Institute of Technology Warangal, Hanamkonda, Telangana-506004, India
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34
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Takeda N, Hirata K, Tsuruta K, Santis GD, Xantheas SS, Ishiuchi SI, Fujii M. Gas phase protonated nicotine is a mixture of pyridine- and pyrrolidine-protonated conformers: implications for its native structure in the nicotinic acetylcholine receptor. Phys Chem Chem Phys 2021; 24:5786-5793. [PMID: 34939632 DOI: 10.1039/d1cp05175j] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The infrared (IR) spectra of gas phase protonated nicotine has been measured in the never-before probed N-H "fingerprint region" (3200-3500 cm-1). The protonated molecules generated by an electrospray source are thermalized in the first ion trap with water vapor and He gas at a pre-determined temperature prior to being probed by IR spectroscopy in the second ion trap at 4 K. The IR spectra exhibit two N-H stretching bands which are assigned to the pyridine and pyrrolidine protomers with the aid of high-level electronic structure calculations. This finding is in sharp contrast to previous spectroscopic studies that suggested a single population of the pyridine protomer. The relative populations of the two protomers vary by changing the temperature of the thermalizing trap from 180-300 K. The relative conformer populations at 240 K and 300 K are well reproduced by the theoretical calculations, unequivocally determining that gas phase nicotine is a 3 : 2 mixture of both pyridine and pyrrolidine protomers at room temperature. The thermalizing anhydrous vapor does not result in any population change. It rather demonstrates the catalytic role of water in achieving equilibrium between the two protomers. The combination of IR spectroscopy and electronic structure calculations establish the small energy difference between the pyridine and pyrrolidine protomers in nicotine. One of the gas phase nicotine pyrrolidine protomers has the closest conformational resemblance among all low-lying energy isomers with the X-ray structure of nicotine in the nicotinic acetylcholine receptor (nAChR).
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Affiliation(s)
- Naoya Takeda
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Keisuke Hirata
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 4259 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. .,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
| | - Kazuya Tsuruta
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan
| | - Garrett D Santis
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA
| | - Sotiris S Xantheas
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Department of Chemistry, University of Washington, Seattle, WA 98195, USA.,Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, WA 99352, USA
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,Department of Chemistry, School of Science, Tokyo Institute of Technology, 2-12-1 4259 Ookayama, Meguro-ku, Tokyo, 152-8550, Japan. .,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan. .,School of Life Science and Technology, Tokyo Institute of Technology, 4259 Nagatsuta-cho, Midori-ku, Yokohama, Kanagawa, 226-8503, Japan.,Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research, Tokyo Institute of Technology, 4259, Nagatsuta-cho, Midori-ku, Yokohama, 226-8503, Japan.
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35
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Friesen S, Fedotova MV, Kruchinin SE, Bešter-Rogač M, Podlipnik Č, Buchner R. Hydration and counterion binding of aqueous acetylcholine chloride and carbamoylcholine chloride. Phys Chem Chem Phys 2021; 23:25086-25096. [PMID: 34747952 DOI: 10.1039/d1cp03543f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The hydration and Cl- ion binding of the neurot†ransmitter acetylcholine (ACh+) and its synthetic analogue, carbamoylcholine (CCh+), were studied by combining dilute-solution conductivity measurements with dielectric relaxation spectroscopy and statistical mechanics calculations at 1D-RISM and 3D-RISM level. Chloride ion binding was found to be weak but not negligible. From the ∼30 water molecules coordinating ACh and CCh+ only ∼1/3 is affected in its rotational dynamics by the cation, with the majority - situated close to the hydrophobic moieties - only retarded by a factor of ∼2.5. At vanishing solute concentration cations and the ∼3-4 H2O molecules hydrogen bonding to the CO group of the solute exhibit similar rotational dynamics but increasing concentration and temperature markedly dehydrates ACh+ and CCh+.
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Affiliation(s)
- Sergej Friesen
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany.
| | - Marina V Fedotova
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Kademicheskaya st. 1, 153045 Ivanovo, Russian Federation.
| | - Sergey E Kruchinin
- G. A. Krestov Institute of Solution Chemistry, Russian Academy of Sciences, Kademicheskaya st. 1, 153045 Ivanovo, Russian Federation.
| | - Marija Bešter-Rogač
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.
| | - Črtomir Podlipnik
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.
| | - Richard Buchner
- Institut für Physikalische und Theoretische Chemie, Universität Regensburg, 93040 Regensburg, Germany.
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36
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Nin-Hill A, Mueller NPF, Molteni C, Rovira C, Alfonso-Prieto M. Photopharmacology of Ion Channels through the Light of the Computational Microscope. Int J Mol Sci 2021; 22:12072. [PMID: 34769504 PMCID: PMC8584574 DOI: 10.3390/ijms222112072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022] Open
Abstract
The optical control and investigation of neuronal activity can be achieved and carried out with photoswitchable ligands. Such compounds are designed in a modular fashion, combining a known ligand of the target protein and a photochromic group, as well as an additional electrophilic group for tethered ligands. Such a design strategy can be optimized by including structural data. In addition to experimental structures, computational methods (such as homology modeling, molecular docking, molecular dynamics and enhanced sampling techniques) can provide structural insights to guide photoswitch design and to understand the observed light-regulated effects. This review discusses the application of such structure-based computational methods to photoswitchable ligands targeting voltage- and ligand-gated ion channels. Structural mapping may help identify residues near the ligand binding pocket amenable for mutagenesis and covalent attachment. Modeling of the target protein in a complex with the photoswitchable ligand can shed light on the different activities of the two photoswitch isomers and the effect of site-directed mutations on photoswitch binding, as well as ion channel subtype selectivity. The examples presented here show how the integration of computational modeling with experimental data can greatly facilitate photoswitchable ligand design and optimization. Recent advances in structural biology, both experimental and computational, are expected to further strengthen this rational photopharmacology approach.
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Affiliation(s)
- Alba Nin-Hill
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain; (A.N.-H.); (C.R.)
| | - Nicolas Pierre Friedrich Mueller
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany;
- Faculty of Mathematics and Natural Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Carla Molteni
- Physics Department, King’s College London, London WC2R 2LS, UK;
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain; (A.N.-H.); (C.R.)
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany;
- Cécile and Oskar Vogt Institute for Brain Research, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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37
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Mashmoushi N, Juhász DR, Coughlan NJA, Schneider BB, Le Blanc JCY, Guna M, Ziegler BE, Campbell JL, Hopkins WS. UVPD Spectroscopy of Differential Mobility-Selected Prototropic Isomers of Rivaroxaban. J Phys Chem A 2021; 125:8187-8195. [PMID: 34432451 DOI: 10.1021/acs.jpca.1c05564] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two ion populations of protonated Rivaroxaban, [C19H18ClN3O5S + H]+, are separated under pure N2 conditions using differential mobility spectrometry prior to characterization in a hybrid triple quadrupole linear ion trap mass spectrometer. These populations are attributed to bare protonated Rivaroxaban and to a proton-bound Rivaroxaban-ammonia complex, which dissociates prior to mass-selecting the parent ion. Ultraviolet photodissociation (UVPD) and collision-induced dissociation (CID) studies indicate that both protonated Rivaroxaban ion populations are comprised of the computed global minimum prototropic isomer. Two ion populations are also observed when the collision environment is modified with 1.5% (v/v) acetonitrile. In this case, the protonated Rivaroxaban ion populations are produced by the dissociation of the ammonium complex and by the dissociation of a proton-bound Rivaroxaban-acetonitrile complex prior to mass selection. Again, both populations exhibit a similar CID behavior; however, UVPD spectra indicate that the two ion populations are associated with different prototropic isomers. The experimentally acquired spectra are compared with computed spectra and are assigned to two prototropic isomers that exhibit proton sharing between distal oxygen centers.
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Affiliation(s)
- Nour Mashmoushi
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | - Daniel R Juhász
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
| | - Neville J A Coughlan
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada
| | | | | | - Mircea Guna
- SCIEX, 71 Four Valley Drive, Concord, Ontario L4K 4V8, Canada
| | - Blake E Ziegler
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada
| | - J Larry Campbell
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada.,Bedrock Scientific, Milton, Ontario L6T 6J9, Canada
| | - W Scott Hopkins
- Department of Chemistry, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada.,Waterloo Institute for Nanotechnology, University of 200 University Avenue West, Waterloo, Ontario N2L 3G1, Canada.,Watermine Innovation, Waterloo, Ontario N0B 2T0, Canada.,Centre for Eye and Vision Research, New Territories 999077, Hong Kong
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38
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Cartereau A, Taillebois E, Le Questel JY, Thany SH. Mode of Action of Neonicotinoid Insecticides Imidacloprid and Thiacloprid to the Cockroach Pameα7 Nicotinic Acetylcholine Receptor. Int J Mol Sci 2021; 22:9880. [PMID: 34576043 PMCID: PMC8471617 DOI: 10.3390/ijms22189880] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/01/2021] [Accepted: 09/08/2021] [Indexed: 12/28/2022] Open
Abstract
The functional expression of the cockroach Pameα7 nicotinic acetylcholine receptor subunit has been previously studied, and was found to be able to form a homomeric receptor when expressed in Xenopus laevis oocytes. In this study, we found that the neonicotinoid insecticide imidacloprid is unable to activate the cockroach Pameα7 receptor, although thiacloprid induces low inward currents, suggesting that it is a partial agonist. In addition, the co-application or 5 min pretreatment with 10 µM imidacloprid increased nicotine current amplitudes, while the co-application or 5 min pretreatment with 10 µM thiacloprid decreased nicotine-evoked current amplitudes by 54% and 28%, respectively. This suggesting that these two representatives of neonicotinoid insecticides bind differently to the cockroach Pameα7 receptor. Interestingly, the docking models demonstrate that the orientation and interactions of the two insecticides in the cockroach Pameα7 nAChR binding pocket are very similar. Electrophysiological results have provided evidence to suggest that imidacloprid and thiacloprid could act as modulators of the cockroach Pameα7 receptors.
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Affiliation(s)
- Alison Cartereau
- Université d’Orléans, LBLGC USC INRAE 1328, 45067 Orléans, France; (A.C.); (E.T.)
| | - Emiliane Taillebois
- Université d’Orléans, LBLGC USC INRAE 1328, 45067 Orléans, France; (A.C.); (E.T.)
| | | | - Steeve H. Thany
- Université d’Orléans, LBLGC USC INRAE 1328, 45067 Orléans, France; (A.C.); (E.T.)
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39
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Natarajan K, Mukhtasimova N, Corradi J, Lasala M, Bouzat C, Sine SM. Mechanism of calcium potentiation of the α7 nicotinic acetylcholine receptor. J Gen Physiol 2021; 152:151971. [PMID: 32702089 PMCID: PMC7478872 DOI: 10.1085/jgp.202012606] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/19/2020] [Accepted: 06/22/2020] [Indexed: 12/14/2022] Open
Abstract
The α7 nicotinic acetylcholine receptor (nAChR) is among the most abundant types of nAChR in the brain, yet the ability of nerve-released ACh to activate α7 remains enigmatic. In particular, a major population of α7 resides in extra-synaptic regions where the ACh concentration is reduced, owing to dilution and enzymatic hydrolysis, yet ACh shows low potency in activating α7. Using high-resolution single-channel recording techniques, we show that extracellular calcium is a powerful potentiator of α7 activated by low concentrations of ACh. Potentiation manifests as robust increases in the frequency of channel opening and the average duration of the openings. Molecular dynamics simulations reveal that calcium binds to the periphery of the five ligand binding sites and is framed by a pair of anionic residues from the principal and complementary faces of each site. Mutation of residues identified by simulation prevents calcium from potentiating ACh-elicited channel opening. An anionic residue is conserved at each of the identified positions in all vertebrate species of α7. Thus, calcium associates with a novel structural motif on α7 and is an obligate cofactor in regions of limited ACh concentration.
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Affiliation(s)
- Kathiresan Natarajan
- Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, MN
| | - Nuriya Mukhtasimova
- Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, MN
| | - Jeremías Corradi
- Instituto de Investigaciones Bioquímicas, Departamento de Biologia, Bioquimica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca, Argentina
| | - Matías Lasala
- Instituto de Investigaciones Bioquímicas, Departamento de Biologia, Bioquimica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca, Argentina
| | - Cecilia Bouzat
- Instituto de Investigaciones Bioquímicas, Departamento de Biologia, Bioquimica y Farmacia, Universidad Nacional del Sur-Consejo Nacional de Investigaciones Científicas y Técnicas, Bahía Blanca, Argentina
| | - Steven M Sine
- Receptor Biology Laboratory, Department of Physiology and Biomedical Engineering, Mayo Clinic College of Medicine, Rochester, MN.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic College of Medicine, Rochester, MN.,Department of Neurology, Mayo Clinic College of Medicine, Rochester, MN
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40
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Du S, Hu X, Li M, Jiang X, Xu X, Cheng J, Qian X. Discovery of novel iminosydnone compounds with insecticidal activities based on the binding mode of triflumezopyrim. Bioorg Med Chem Lett 2021; 46:128120. [PMID: 34015502 DOI: 10.1016/j.bmcl.2021.128120] [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] [Received: 04/14/2021] [Revised: 05/07/2021] [Accepted: 05/13/2021] [Indexed: 11/16/2022]
Abstract
Triflumezopyrim (TFM) is a new mesoionic insecticide developed by DuPont. Like other neonicotinoid insecticides, it binds to the orthosteric site of the nicotinic acetylcholine receptor (nAChR), but the binding mode has not been reported. Nicotinic acetylcholine binding proteins (nAChBPs) are ideal alternative structure for nAChRs. In this study, molecular docking, molecular dynamics (MD) simulations, binding free energy calculation, and per-residue binding free energy decomposition were used to study the binding modes of TFM and other 12 mesoionic insecticides. By comparing the binding free energy and the insecticidal activity, it was found that the sub-pocket around the benzyl group of the mesoionic insecticide is the key area for maintaining its activity, which is composed of A: Val116, A: Met124, A: Ile126, B: Trp155 and B: Val156. In order to verify the druggability of the sub-pocket, a series of iminosydnone compounds were designed and synthesized based on the structure of the sub-pocket. The lethality rate of compound 1 against Mythimna separata were 100% at 500 mg/L. Our research provides a basis for designing new mesoionic insecticides based on structure.
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Affiliation(s)
- Shaoqing Du
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xueping Hu
- Hangzhou Institute of Innovative Medicine, College of Pharmaceutical Sciences, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Mengnan Li
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xiaoqun Jiang
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Xiaoyong Xu
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China
| | - Jiagao Cheng
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China.
| | - Xuhong Qian
- Shanghai Key Laboratory of Chemical Biology, School of Pharmacy, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, China; School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200241, China.
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41
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Structures of ABCB4 provide insight into phosphatidylcholine translocation. Proc Natl Acad Sci U S A 2021; 118:2106702118. [PMID: 34385322 DOI: 10.1073/pnas.2106702118] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
ABCB4 is expressed in hepatocytes and translocates phosphatidylcholine into bile canaliculi. The mechanism of specific lipid recruitment from the canalicular membrane, which is essential to mitigate the cytotoxicity of bile salts, is poorly understood. We present cryogenic electron microscopy structures of human ABCB4 in three distinct functional conformations. An apo-inward structure reveals how phospholipid can be recruited from the inner leaflet of the membrane without flipping its orientation. An occluded structure reveals a single phospholipid molecule in a central cavity. Its choline moiety is stabilized by cation-π interactions with an essential tryptophan residue, rationalizing the specificity of ABCB4 for phosphatidylcholine. In an inhibitor-bound structure, a posaconazole molecule blocks phospholipids from reaching the central cavity. Using a proteoliposome-based translocation assay with fluorescently labeled phosphatidylcholine analogs, we recapitulated the substrate specificity of ABCB4 in vitro and confirmed the role of the key tryptophan residue. Our results provide a structural basis for understanding an essential translocation step in the generation of bile and its sensitivity to azole drugs.
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42
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Bavo F, Pallavicini M, Appiani R, Bolchi C. Determinants for α4β2 vs. α3β4 Subtype Selectivity of Pyrrolidine-Based nAChRs Ligands: A Computational Perspective with Focus on Recent cryo-EM Receptor Structures. Molecules 2021; 26:molecules26123603. [PMID: 34204637 PMCID: PMC8231201 DOI: 10.3390/molecules26123603] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/08/2021] [Accepted: 06/10/2021] [Indexed: 12/26/2022] Open
Abstract
The selectivity of α4β2 nAChR agonists over the α3β4 nicotinic receptor subtype, predominant in ganglia, primarily conditions their therapeutic range and it is still a complex and challenging issue for medicinal chemists and pharmacologists. Here, we investigate the determinants for such subtype selectivity in a series of more than forty α4β2 ligands we have previously reported, docking them into the structures of the two human subtypes, recently determined by cryo-electron microscopy. They are all pyrrolidine based analogues of the well-known α4β2 agonist N-methylprolinol pyridyl ether A-84543 and differ in the flexibility and pattern substitution of their aromatic portion. Indeed, the direct or water mediated interaction with hydrophilic residues of the relatively narrower β2 minus side through the elements decorating the aromatic ring and the stabilization of the latter by facing to the not conserved β2-Phe119 result as key distinctive features for the α4β2 affinity. Consistently, these compounds show, despite the structural similarity, very different α4β2 vs. α3β4 selectivities, from modest to very high, which relate to rigidity/extensibility degree of the portion containing the aromatic ring and to substitutions at the latter. Furthermore, the structural rationalization of the rat vs. human differences of α4β2 vs. α3β4 selectivity ratios is here proposed.
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Affiliation(s)
- Francesco Bavo
- Dipartimento di Scienze Farmaceutiche, Universita’degli Studi di Milano, I-20133 Milano, Italy; (F.B.); (M.P.); (R.A.)
- Department of Drug Design and Pharmacology, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Marco Pallavicini
- Dipartimento di Scienze Farmaceutiche, Universita’degli Studi di Milano, I-20133 Milano, Italy; (F.B.); (M.P.); (R.A.)
| | - Rebecca Appiani
- Dipartimento di Scienze Farmaceutiche, Universita’degli Studi di Milano, I-20133 Milano, Italy; (F.B.); (M.P.); (R.A.)
| | - Cristiano Bolchi
- Dipartimento di Scienze Farmaceutiche, Universita’degli Studi di Milano, I-20133 Milano, Italy; (F.B.); (M.P.); (R.A.)
- Correspondence:
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43
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Bregestovski PD, Ponomareva DN. Photochromic Modulation of Cys-loop
Ligand-gated Ion Channels. J EVOL BIOCHEM PHYS+ 2021. [DOI: 10.1134/s0022093021020162] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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44
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Yu J, Zhu H, Lape R, Greiner T, Du J, Lü W, Sivilotti L, Gouaux E. Mechanism of gating and partial agonist action in the glycine receptor. Cell 2021; 184:957-968.e21. [PMID: 33567265 PMCID: PMC8115384 DOI: 10.1016/j.cell.2021.01.026] [Citation(s) in RCA: 68] [Impact Index Per Article: 22.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 10/16/2020] [Accepted: 01/15/2021] [Indexed: 12/14/2022]
Abstract
Ligand-gated ion channels mediate signal transduction at chemical synapses and transition between resting, open, and desensitized states in response to neurotransmitter binding. Neurotransmitters that produce maximum open channel probabilities (Po) are full agonists, whereas those that yield lower than maximum Po are partial agonists. Cys-loop receptors are an important class of neurotransmitter receptors, yet a structure-based understanding of the mechanism of partial agonist action has proven elusive. Here, we study the glycine receptor with the full agonist glycine and the partial agonists taurine and γ-amino butyric acid (GABA). We use electrophysiology to show how partial agonists populate agonist-bound, closed channel states and cryo-EM reconstructions to illuminate the structures of intermediate, pre-open states, providing insights into previously unseen conformational states along the receptor reaction pathway. We further correlate agonist-induced conformational changes to Po across members of the receptor family, providing a hypothetical mechanism for partial and full agonist action at Cys-loop receptors.
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Affiliation(s)
- Jie Yu
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Hongtao Zhu
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Remigijus Lape
- Department of Neuroscience, Physiology and Pharmacology, University College London, Medical Sciences Building, Gower Street, London WC1E 6BT, UK
| | - Timo Greiner
- Department of Neuroscience, Physiology and Pharmacology, University College London, Medical Sciences Building, Gower Street, London WC1E 6BT, UK
| | - Juan Du
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Wei Lü
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA
| | - Lucia Sivilotti
- Department of Neuroscience, Physiology and Pharmacology, University College London, Medical Sciences Building, Gower Street, London WC1E 6BT, UK.
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science University, Portland, OR 97239, USA; Howard Hughes Medical Institute, Oregon Health & Science University, Portland, OR 97239, USA.
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45
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Beck ME, Riplinger C, Neese F, Bistoni G. Unraveling individual host-guest interactions in molecular recognition from first principles quantum mechanics: Insights into the nature of nicotinic acetylcholine receptor agonist binding. J Comput Chem 2021; 42:293-302. [PMID: 33232540 DOI: 10.1002/jcc.26454] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 10/30/2020] [Accepted: 11/02/2020] [Indexed: 11/08/2022]
Abstract
Drug binding to a protein target is governed by a complex pattern of noncovalent interactions between the ligand and the residues in the protein's binding pocket. Here we introduce a generally applicable, parameter-free, computational method that allows for the identification, quantification, and analysis of the key ligand-residue interactions responsible for molecular recognition. Our strategy relies on Local Energy Decomposition analysis at the "gold-standard" coupled cluster DLPNO-CCSD(T) level. In the study case shown in this paper, nicotine and imidacloprid binding to the nicotinic acetylcholine receptor, our approach provides new insights into how individual amino acids in the active site determine sensitivity and selectivity of the ligands, extending and refining classical pharmacophore hypotheses. By inference, the method is applicable to any kind of host/guest interactions with potential applications in industrial biocatalysis and protein engineering.
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Affiliation(s)
- Michael Edmund Beck
- Department Computational Life Science, Bayer AG, Division Cropscience, Monheim am Rhein, Germany
| | | | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
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46
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FitzGerald EA, Butko MT, Boronat P, Cederfelt D, Abramsson M, Ludviksdottir H, van Muijlwijk-Koezen JE, de Esch IJP, Dobritzsch D, Young T, Danielson UH. Discovery of fragments inducing conformational effects in dynamic proteins using a second-harmonic generation biosensor. RSC Adv 2021; 11:7527-7537. [PMID: 35423271 PMCID: PMC8694943 DOI: 10.1039/d0ra09844b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 01/28/2021] [Indexed: 01/13/2023] Open
Abstract
Biophysical screening of compound libraries for the identification of ligands that interact with a protein is efficient, but does typically not reveal if (or how) ligands may interfere with its functional properties. For this a biochemical/functional assay is required. But for proteins whose function is dependent on a conformational change, such assays are typically complex or have low throughput. Here we have explored a high-throughput second-harmonic generation (SHG) biosensor to detect fragments that induce conformational changes upon binding to a protein in real time and identify dynamic regions. Multiwell plate format SHG assays were developed for wild-type and six engineered single-cysteine mutants of acetyl choline binding protein (AChBP), a homologue to ligand gated ion channels (LGICs). They were conjugated with second harmonic-active labels via amine or maleimide coupling. To validate the assay, it was confirmed that the conformational changes induced in AChBP by nicotinic acetyl choline receptor (nAChR) agonists and antagonists were qualitatively different. A 1056 fragment library was subsequently screened against all variants and conformational modulators of AChBP were successfully identified, with hit rates from 9-22%, depending on the AChBP variant. A subset of four hits was selected for orthogonal validation and structural analysis. A time-resolved grating-coupled interferometry-based biosensor assay confirmed the interaction to be a reversible 1-step 1 : 1 interaction, and provided estimates of affinities and interaction kinetic rate constants (K D = 0.28-63 μM, k a = 0.1-6 μM-1 s-1, k d = 1 s-1). X-ray crystallography of two of the fragments confirmed their binding at a previously described conformationally dynamic site, corresponding to the regulatory site of LGICs. These results reveal that SHG has the sensitivity to identify fragments that induce conformational changes in a protein. A selection of fragment hits with a response profile different to known LGIC regulators was characterized and confirmed to bind to dynamic regions of the protein.
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Affiliation(s)
- Edward A FitzGerald
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
- Beactica Therapeutics Virdings allé 2 Uppsala 754 40 Sweden
| | | | - Pierre Boronat
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Daniela Cederfelt
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
| | - Mia Abramsson
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
| | | | - Jacqueline E van Muijlwijk-Koezen
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Iwan J P de Esch
- Amsterdam Institute of Molecular and Life Sciences (AIMMS), Division of Medicinal Chemistry, Faculty of Science, Vrije Universiteit Amsterdam De Boelelaan 1108 1081 HZ Amsterdam The Netherlands
| | - Doreen Dobritzsch
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
| | - Tracy Young
- Biodesy, Inc. 170 Harbor Way South San Francisco 94080 CA USA
| | - U Helena Danielson
- Department of Chemistry - BMC, Uppsala University Uppsala 751 23 Sweden
- Science for Life Laboratory, Uppsala University Sweden
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Abstract
Herein, I intend to capture highlights shared with my academic and research colleagues over the 60 years I devoted initially to my graduate and postdoctoral training and then to academic endeavors starting as an assistant professor in a new medical school at the University of California, San Diego (UCSD). During this period, the Department of Pharmacology emerged from a division within the Department of Medicine to become the first basic science department, solely within the School of Medicine at UCSD in 1979. As part of the school's plans to reorganize and to retain me at UCSD, I was appointed as founding chair. Some years later in 2002, faculty, led largely within the Department of Pharmacology and by practicing pharmacists within UCSD Healthcare, started the independent Skaggs School of Pharmacy and Pharmaceutical Sciences with a doctor of pharmacy (PharmD) program, where I served as the founding dean. My career pathway, from working at my family-owned pharmacy to chairing a department in a school of medicine and then becoming the dean of a school of pharmacy at a research-intensive, student-centered institution, involved some risky decisions. But the academic, curricular, and accreditation challenges posed were met by a cadre of creative faculty colleagues. I offer my experiences to individuals confronted with a multiplicity of real or imagined opportunities in academic health sciences, the related pharmaceutical industry, and government oversight agencies.
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Affiliation(s)
- Palmer Taylor
- Department of Pharmacology, Skaggs School of Pharmacy and Pharmaceutical Sciences, and School of Medicine, University of California, San Diego, La Jolla, California 92093, USA
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Bavo F, Pallavicini M, Gotti C, Appiani R, Moretti M, Colombo SF, Pucci S, Viani P, Budriesi R, Renzi M, Fucile S, Bolchi C. Modifications at C(5) of 2-(2-Pyrrolidinyl)-Substituted 1,4-Benzodioxane Elicit Potent α4β2 Nicotinic Acetylcholine Receptor Partial Agonism with High Selectivity over the α3β4 Subtype. J Med Chem 2020; 63:15668-15692. [PMID: 33325696 DOI: 10.1021/acs.jmedchem.0c01150] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of diastereomeric 2-(2-pyrrolidinyl)-1,4-benzodioxanes bearing a small, hydrogen-bonding substituent at the 7-, 6-, or 5-position of benzodioxane have been studied for α4β2 and α3β4 nicotinic acetylcholine receptor affinity and activity. Analogous to C(5)H replacement with N and to a much greater extent than decoration at C(7), substitution at benzodioxane C(5) confers very high α4β2/α3β4 selectivity to the α4β2 partial agonism. Docking into the two receptor structures recently determined by cryo-electron microscopy and site-directed mutagenesis at the minus β2 side converge in indicating that the limited accommodation capacity of the β2 pocket, compared to that of the β4 pocket, makes substitution at C(5) rather than at more projecting C(7) position determinant for this pursued subtype selectivity.
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Affiliation(s)
- Francesco Bavo
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, I-20133 Milano, Italy
| | - Marco Pallavicini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, I-20133 Milano, Italy
| | - Cecilia Gotti
- Institute of Neuroscience, CNR, Via Vanvitelli 32, I-20129 Milano, Italy
| | - Rebecca Appiani
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, I-20133 Milano, Italy
| | - Milena Moretti
- Institute of Neuroscience, CNR, Via Vanvitelli 32, I-20129 Milano, Italy.,Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Via Vanvitelli 32, I-20129 Milano, Italy
| | | | - Susanna Pucci
- Institute of Neuroscience, CNR, Via Vanvitelli 32, I-20129 Milano, Italy.,Hunimed University, Via Rita Levi-Montalcini 4, Pieve Emanuele, I-20090 Milan, Italy
| | - Paola Viani
- Department of Medical Biotechnology and Translational Medicine, Università degli Studi di Milano, Via Vanvitelli 32, I-20129 Milano, Italy
| | - Roberta Budriesi
- Dipartimento di Farmacia e Biotecnologie, Università degli Studi di Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
| | - Massimiliano Renzi
- Dipartimento di Fisiologia e Farmacologia, Sapienza Università di Roma, Piazzale Moro 5, 00185 Roma, Italy
| | - Sergio Fucile
- Dipartimento di Fisiologia e Farmacologia, Sapienza Università di Roma, Piazzale Moro 5, 00185 Roma, Italy.,I.R.C.C.S. Neuromed, Via Atinese 18, 86077 Pozzilli, Italy
| | - Cristiano Bolchi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, Via Mangiagalli 25, I-20133 Milano, Italy
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49
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Maldonado-Hernández R, Quesada O, Colón-Sáez JO, Lasalde-Dominicci JA. Sequential purification and characterization of Torpedo californica nAChR-DC supplemented with CHS for high-resolution crystallization studies. Anal Biochem 2020; 610:113887. [PMID: 32763308 DOI: 10.1016/j.ab.2020.113887] [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] [Received: 05/24/2020] [Revised: 07/14/2020] [Accepted: 07/22/2020] [Indexed: 01/26/2023]
Abstract
Over the past 10 years we have been developing a multi-attribute analytical platform that allows for the preparation of milligram amounts of functional, high-pure, and stable Torpedo (muscle-type) nAChR detergent complexes for crystallization purpose. In the present work, we have been able to significantly improve and optimize the purity and yield of nicotinic acetylcholine receptors in detergent complexes (nAChR-DC) without compromising stability and functionality. We implemented new methods in the process, such as analysis and rapid production of samples for future crystallization preparations. Native nAChR was extracted from the electric organ of Torpedo californica using the lipid-like detergent LysoFos Choline 16 (LFC-16), followed by three consecutive steps of chromatography purification. We evaluated the effect of cholesteryl hemisuccinate (CHS) supplementation during the affinity purification steps of nAChR-LFC-16 in terms of receptor secondary structure, stability and functionality. CHS produced significant changes in the degree of β-secondary structure, these changes compromise the diffusion of the nAChR-LFC-16 in lipid cubic phase. The behavior was reversed by Methyl-β-Cyclodextrin treatment. Also, CHS decreased acetylcholine evoked currents of Xenopus leavis oocyte injected with nAChR-LFC-16 in a concentration-dependent manner. Methyl-β-Cyclodextrin treatment do not reverse functionality, however column delipidation produced a functional protein similar to nAChR-LFC-16 without CHS treatment.
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Affiliation(s)
- Rafael Maldonado-Hernández
- Department of the Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico; Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - Orestes Quesada
- Department of Physical Sciences, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico; Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico
| | - José O Colón-Sáez
- Pharmaceutical Sciences, University of Puerto Rico Medical Science Campus, Puerto Rico
| | - José A Lasalde-Dominicci
- Department of the Biology, University of Puerto Rico, Río Piedras Campus, San Juan, Puerto Rico; Molecular Sciences Research Center, University of Puerto Rico, San Juan, Puerto Rico; Institute of Neurobiology, University of Puerto Rico Medical Science Campus, Puerto Rico.
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50
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Kaji MD, Geary TG, Beech RN. A Functional Comparison of Homopentameric Nicotinic Acetylcholine Receptors (ACR-16) Receptors From Necator americanus and Ancylostoma ceylanicum. Front Mol Neurosci 2020; 13:601102. [PMID: 33324163 PMCID: PMC7725692 DOI: 10.3389/fnmol.2020.601102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Accepted: 11/04/2020] [Indexed: 12/24/2022] Open
Abstract
Effective control of hookworm infections in humans and animals relies on using a small group of anthelmintics. Many of these drugs target cholinergic ligand-gated ion channels, yet the direct activity of anthelmintics has only been studied in a subset of these receptors, primarily in the non-parasitic nematode, Caenorhabditis elegans. Here we report the characterization of a homopentameric ionotropic acetylcholine receptor (AChR), ACR-16, from Necator americanus and Ancylostoma ceylanicum, the first known characterization of human hookworm ion channels. We used two-electrode voltage clamp electrophysiology in Xenopus laevis oocytes to determine the pharmacodynamics of cholinergics and anthelmintics on ACR-16 from both species of hookworm. The A. ceylanicum receptor (Ace-ACR-16) was more sensitive to acetylcholine (EC50 = 20.64 ± 0.32 μM) and nicotine (EC50 = 24.37 ± 2.89 μM) than the N. americanus receptor (Nam-ACR-16) (acetylcholine EC50 = 170.1 ± 19.23 μM; nicotine EC50 = 597.9 ± 59.12 μM), at which nicotine was a weak partial agonist (% maximal acetylcholine response = 30.4 ± 7.4%). Both receptors were inhibited by 500 μM levamisole (Ace-ACR-16 = 65.1 ± 14.3% inhibition, Nam-ACR-16 = 79.5 ± 7.7% inhibition), and responded to pyrantel, but only Ace-ACR-16 responded to oxantel. We used in silico homology modeling to investigate potential structural differences that account for the differences in agonist binding and identified a loop E isoleucine 130 of Nam-ACR-16 as possibly playing a role in oxantel insensitivity. These data indicate that key functional differences exist among ACR-16 receptors from closely related species and suggest mechanisms for differential drug sensitivity.
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Affiliation(s)
- Mark D. Kaji
- Institute of Parasitology, McGill University, Montreal, QC, Canada
| | - Timothy G. Geary
- Institute of Parasitology, McGill University, Montreal, QC, Canada
- School of Biological Sciences, Queen’s University-Belfast, Belfast, United Kingdom
| | - Robin N. Beech
- Institute of Parasitology, McGill University, Montreal, QC, Canada
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