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Graur A, Haymond A, Lee KH, Viscarra F, Russo P, Luchini A, Paige M, Bermudez-Diaz I, Kabbani N. Protein Painting Mass Spectrometry in the Discovery of Interaction Sites within the Acetylcholine Binding Protein. ACS Chem Neurosci 2024; 15:2322-2333. [PMID: 38804618 PMCID: PMC11157483 DOI: 10.1021/acschemneuro.4c00149] [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: 03/15/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) are a family of ligand-gated ion channel receptors that contribute to cognition, memory, and motor control in many organisms. The pharmacological targeting of these receptors, using small molecules or peptides, presents an important strategy for the development of drugs that can treat important human diseases, including neurodegenerative disorders. The Aplysia californica acetylcholine binding protein (Ac-AChBP) is a structural surrogate of the nAChR with high homology to the extracellular ligand binding domain of homopentameric nAChRs. In this study, we optimized protein-painting-based mass spectrometry to identify regions of interaction between the Ac-AChBP and several nAChR ligands. Using molecular dyes that adhere to the surface of a solubilized Ac-AChBP complex, we identified amino acid residues that constitute a contact site within the Ac-AChBP for α-bungarotoxin, choline, nicotine, and amyloid-β 1-42. By integrating innovation in protein painting mass spectrometry with computational structural modeling, we present a new experimental tool for analyzing protein interactions of the nAChR.
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Affiliation(s)
- Alexandru Graur
- School
of Systems Biology, George Mason University, Fairfax, Virginia 22030, United States
| | - Amanda Haymond
- Center
for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110, United States
| | - Kyung Hyeon Lee
- Department
of Chemistry and Biochemistry, George Mason
University, Fairfax, Virginia 20110, United States
| | - Franco Viscarra
- Department
of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Headington, Oxford OX3 0BP, United Kingdom
- Structural
Bioinformatics and Computational Biochemistry, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom
| | - Paul Russo
- Center
for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110, United States
| | - Alessandra Luchini
- Center
for Applied Proteomics and Molecular Medicine, George Mason University, Manassas, Virginia 20110, United States
| | - Mikell Paige
- Department
of Chemistry and Biochemistry, George Mason
University, Fairfax, Virginia 20110, United States
| | - Isabel Bermudez-Diaz
- Department
of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Headington, Oxford OX3 0BP, United Kingdom
| | - Nadine Kabbani
- School
of Systems Biology, George Mason University, Fairfax, Virginia 22030, United States
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2
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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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3
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Tsetlin V, Shelukhina I, Kozlov S, Kasheverov I. Fifty Years of Animal Toxin Research at the Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry RAS. Int J Mol Sci 2023; 24:13884. [PMID: 37762187 PMCID: PMC10530976 DOI: 10.3390/ijms241813884] [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: 08/18/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
This review covers briefly the work carried out at our institute (IBCh), in many cases in collaboration with other Russian and foreign laboratories, for the last 50 years. It discusses the discoveries and studies of various animal toxins, including protein and peptide neurotoxins acting on the nicotinic acetylcholine receptors (nAChRs) and on other ion channels. Among the achievements are the determination of the primary structures of the α-bungarotoxin-like three-finger toxins (TFTs), covalently bound dimeric TFTs, glycosylated cytotoxin, inhibitory cystine knot toxins (ICK), modular ICKs, and such giant molecules as latrotoxins and peptide neurotoxins from the snake, as well as from other animal venoms. For a number of toxins, spatial structures were determined, mostly by 1H-NMR spectroscopy. Using this method in combination with molecular modeling, the molecular mechanisms of the interactions of several toxins with lipid membranes were established. In more detail are presented the results of recent years, among which are the discovery of α-bungarotoxin analogs distinguishing the two binding sites in the muscle-type nAChR, long-chain α-neurotoxins interacting with α9α10 nAChRs and with GABA-A receptors, and the strong antiviral effects of dimeric phospholipases A2. A summary of the toxins obtained from arthropod venoms includes only highly cited works describing the molecules' success story, which is associated with IBCh. In marine animals, versatile toxins in terms of structure and molecular targets were discovered, and careful work on α-conotoxins differing in specificity for individual nAChR subtypes gave information about their binding sites.
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Affiliation(s)
- Victor Tsetlin
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklay Str., 117997 Moscow, Russia; (I.S.); (I.K.)
| | - Irina Shelukhina
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklay Str., 117997 Moscow, Russia; (I.S.); (I.K.)
| | - Sergey Kozlov
- Department of Molecular Neurobiology, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklay Str., 117997 Moscow, Russia;
| | - Igor Kasheverov
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, 16/10 Miklukho-Maklay Str., 117997 Moscow, Russia; (I.S.); (I.K.)
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4
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Gao B, Huang Y, Peng C, Lin B, Liao Y, Bian C, Yang J, Shi Q. High-Throughput Prediction and Design of Novel Conopeptides for Biomedical Research and Development. BIODESIGN RESEARCH 2022; 2022:9895270. [PMID: 37850131 PMCID: PMC10521759 DOI: 10.34133/2022/9895270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 07/23/2022] [Indexed: 10/19/2023] Open
Abstract
Cone snail venoms have been considered a valuable treasure for international scientists and businessmen, mainly due to their pharmacological applications in development of marine drugs for treatment of various human diseases. To date, around 800 Conus species are recorded, and each of them produces over 1,000 venom peptides (termed as conopeptides or conotoxins). This reflects the high diversity and complexity of cone snails, although most of their venoms are still uncharacterized. Advanced multiomics (such as genomics, transcriptomics, and proteomics) approaches have been recently developed to mine diverse Conus venom samples, with the main aim to predict and identify potentially interesting conopeptides in an efficient way. Some bioinformatics techniques have been applied to predict and design novel conopeptide sequences, related targets, and their binding modes. This review provides an overview of current knowledge on the high diversity of conopeptides and multiomics advances in high-throughput prediction of novel conopeptide sequences, as well as molecular modeling and design of potential drugs based on the predicted or validated interactions between these toxins and their molecular targets.
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Affiliation(s)
- Bingmiao Gao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, Hainan 570102, China
| | - Yu Huang
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China
| | - Chao Peng
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China
- BGI-Marine Research Institute for Biomedical Technology, Shenzhen Huahong Marine Biomedicine Co. Ltd., Shenzhen, Guangdong 518119, China
| | - Bo Lin
- Hainan Provincial Key Laboratory of Carcinogenesis and Intervention, Hainan Medical University, Haikou, Hainan 570102, China
| | - Yanling Liao
- Key Laboratory of Tropical Translational Medicine of Ministry of Education, School of Pharmacy, Hainan Medical University, Haikou, Hainan 570102, China
| | - Chao Bian
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China
| | - Jiaan Yang
- Research and Development Department, Micro Pharmtech Ltd., Wuhan, Hubei 430075, China
| | - Qiong Shi
- Shenzhen Key Lab of Marine Genomics, Guangdong Provincial Key Lab of Molecular Breeding in Marine Economic Animals, BGI Academy of Marine Sciences, BGI Marine, Shenzhen, Guangdong 518081, China
- BGI-Marine Research Institute for Biomedical Technology, Shenzhen Huahong Marine Biomedicine Co. Ltd., Shenzhen, Guangdong 518119, China
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5
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Marine Origin Ligands of Nicotinic Receptors: Low Molecular Compounds, Peptides and Proteins for Fundamental Research and Practical Applications. Biomolecules 2022; 12:biom12020189. [PMID: 35204690 PMCID: PMC8961598 DOI: 10.3390/biom12020189] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 01/18/2022] [Accepted: 01/19/2022] [Indexed: 02/05/2023] Open
Abstract
The purpose of our review is to briefly show what different compounds of marine origin, from low molecular weight ones to peptides and proteins, offer for understanding the structure and mechanism of action of nicotinic acetylcholine receptors (nAChRs) and for finding novel drugs to combat the diseases where nAChRs may be involved. The importance of the mentioned classes of ligands has changed with time; a protein from the marine snake venom was the first excellent tool to characterize the muscle-type nAChRs from the electric ray, while at present, muscle and α7 receptors are labeled with the radioactive or fluorescent derivatives prepared from α-bungarotoxin isolated from the many-banded krait. The most sophisticated instruments to distinguish muscle from neuronal nAChRs, and especially distinct subtypes within the latter, are α-conotoxins. Such information is crucial for fundamental studies on the nAChR revealing the properties of their orthosteric and allosteric binding sites and mechanisms of the channel opening and closure. Similar data are provided by low-molecular weight compounds of marine origin, but here the main purpose is drug design. In our review we tried to show what has been obtained in the last decade when the listed classes of compounds were used in the nAChR research, applying computer modeling, synthetic analogues and receptor mutants, X-ray and electron-microscopy analyses of complexes with the nAChRs, and their models which are acetylcholine-binding proteins and heterologously-expressed ligand-binding domains.
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Tsetlin V, Haufe Y, Safronova V, Serov D, Shadamarshan P, Son L, Shelukhina I, Kudryavtsev D, Kryukova E, Kasheverov I, Nicke A, Utkin Y. Interaction of α9α10 Nicotinic Receptors With Peptides and Proteins From Animal Venoms. Front Cell Neurosci 2022; 15:765541. [PMID: 35002625 PMCID: PMC8732759 DOI: 10.3389/fncel.2021.765541] [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: 08/27/2021] [Accepted: 11/15/2021] [Indexed: 12/13/2022] Open
Abstract
Unlike most neuronal nicotinic acetylcholine receptor (nAChR) subunits, α7, α9, and α10 subunits are able to form functional homo- or heteromeric receptors without any β subunits. While the α7 subtype is widely distributed in the mammalian brain and several peripheral tissues, α9 and α9α10 nAChRs are mainly found in the cochlea and immune cells. α-Conotoxins that specifically block the α9α10 receptor showed anti-nociceptive and anti-hyperalgesic effects in animal models. Hence, this subtype is considered a drug target for analgesics. In contrast to the α9α10-selective α-conotoxins, the three-finger toxin α-bungarotoxin inhibits muscle-type and α7 nAChRs in addition to α9α10 nAChRs. However, the selectivity of α-neurotoxins at the α9α10 subtype was less intensively investigated. Here, we compared the potencies of α-conotoxins and α-neurotoxins at the human α9α10 nAChR by two-electrode voltage clamp analysis upon expression in Xenopus oocytes. In addition, we analyzed effects of several α9α10-selective α-conotoxins on mouse granulocytes from bone marrow to identify possible physiological functions of the α9α10 nAChR subtype in these cells. The α-conotoxin-induced IL-10 release was measured upon LPS-stimulation. We found that α-conotoxins RgIA, PeIA, and Vc1.1 enhance the IL-10 expression in granulocytes which might explain the known anti-inflammatory and associated analgesic activities of α9α10-selective α-conotoxins. Furthermore, we show that two long-chain α-neurotoxins from the cobra Naja melanoleuca venom that were earlier shown to bind to muscle-type and α7 nAChRs, also inhibit the α9α10 subtype at nanomolar concentrations with one of them showing a significantly slower dissociation from this receptor than α-bungarotoxin.
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Affiliation(s)
- Victor Tsetlin
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Yves Haufe
- Faculty of Medicine, Walther Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Valentina Safronova
- Laboratory of Cellular Neurobiology, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Dmitriy Serov
- Laboratory of Cellular Neurobiology, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - PranavKumar Shadamarshan
- Faculty of Medicine, Walther Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Lina Son
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Irina Shelukhina
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Denis Kudryavtsev
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Elena Kryukova
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Igor Kasheverov
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Annette Nicke
- Faculty of Medicine, Walther Straub Institute of Pharmacology and Toxicology, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Yuri Utkin
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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7
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Ho TNT, Abraham N, Lewis RJ. Unique Pharmacological Properties of α-Conotoxin OmIA at α7 nAChRs. Front Pharmacol 2021; 12:803397. [PMID: 34955864 PMCID: PMC8692984 DOI: 10.3389/fphar.2021.803397] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 11/22/2021] [Indexed: 11/13/2022] Open
Abstract
OmIA, isolated from Conus omaria venom, is a potent antagonist at α7 nAChRs. We determined the co-crystal structure of OmIA with Lymnae stagnalis acetylcholine binding protein (Ls-AChBP) that identified His5, Val10 and Asn11 as key determinants for the high potency of OmIA at α7 nAChRs. Remarkably, despite a competitive binding mode observed in the co-crystal structure, OmIA and analogues displayed functional insurmountable antagonism at α7 and α3β4 nAChRs, except OmIA analogues having long side chain at position 10 ([V10Q]OmIA and [V10L]OmIA), which were partial insurmountable antagonist at α7 nAChRs in the presence of type II positive allosteric modulators (PAMs). A “two-state, two-step” model was used to explain these observations, with [V10Q]OmIA and [V10L]OmIA co-existing in a fast reversible/surmountable as well as a tight binding/insurmountable state. OmIA and analogues also showed biphasic-inhibition at α7 nAChRs in the presence of PNU120596, with a preference for the high-affinity binding site following prolonged exposure. The molecular basis of binding and complex pharmacological profile of OmIA at α7 nAChRs presented in here expands on the potential of α-conotoxins to probe the pharmacological properties of nAChRs and may help guide the development novel α7 modulators.
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Affiliation(s)
- Thao N T Ho
- Centre for Pain Research, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Nikita Abraham
- Centre for Pain Research, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
| | - Richard J Lewis
- Centre for Pain Research, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
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8
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From Crystal Structures of RgIA4 in Complex with Ac-AChBP to Molecular Determinants of Its High Potency of α9α10 nAChR. Mar Drugs 2021; 19:md19120709. [PMID: 34940708 PMCID: PMC8709174 DOI: 10.3390/md19120709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 12/14/2021] [Accepted: 12/14/2021] [Indexed: 12/02/2022] Open
Abstract
α9-containing nicotinic acetylcholine receptors (nAChRs) have been shown to play critical roles in neuropathic pain. The α-conotoxin (α-CTx) RgIA and its analog RgIA4 were identified as the most selective inhibitor of α9α10 nAChR. However, the mechanism of their selectivity toward α9α10 nAChR remains elusive. Here, we reported the co-crystal structure of RgIA and RgIA4 in complex with Aplysia californica acetylcholine binding protein (Ac-AChBP) at resolution of 2.6 Å, respectively. Based on the structure of the complexes, together with molecular dynamic simulation (MD-simulation), we suggested the key residues of α9α10 nAChR in determining its high affinity for RgIA/RgIA4. This is the first time the complex between pain-related conotoxins and Ac-AChBP was reported and the complementary side of α9 subunit in binding of the antagonists shown. These results provide realistic template for the design of new therapeutic in neuropathic pain.
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Wei N, Chu Y, Liu H, Xu Q, Jiang T, Yu R. Antagonistic Mechanism of α-Conotoxin BuIA toward the Human α3β2 Nicotinic Acetylcholine Receptor. ACS Chem Neurosci 2021; 12:4535-4545. [PMID: 34738810 DOI: 10.1021/acschemneuro.1c00568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) are pentameric ligand-gated ion channels that are abundantly expressed in the central and peripheral nervous systems, playing an important role in mediating neurotransmitter release and inter-synaptic signaling. Dysfunctional nAChRs are associated with neurological disorders, and studying the structure and function of nAChRs is essential for development of drugs or strategies for treatment of related diseases. α-Conotoxins are selective antagonists of the nAChR and are an important class of drug leads. So far, the antagonistic mechanism of α-conotoxins toward the nAChRs is still unclear. In this study, we built an α3β2 nAChR homology model and investigated its conformational transition mechanism upon binding with a highly potent inhibitor, α-conotoxin BuIA, through μs molecular dynamic simulations and site-directed mutagenesis studies. The results suggested that the α3β2 nAChR underwent global conformational transitions and was stabilized into a closed state with three hydrophobic gates present in the transmembrane domain by BuIA. Finally, the probable antagonistic mechanism of BuIA was proposed. Overall, the closed-state model of the α3β2 nAChR bound with BuIA is not only essential for understanding the antagonistic mechanism of α-conotoxins but also particularly valuable for development of therapeutic inhibitors in future.
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Affiliation(s)
- Ningning Wei
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao 266021, China
| | - Yanyan Chu
- Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266200, China
- Molecular Synthesis Center & Key Laboratory of Marine Drugs, Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Innovation Platform of Marine Drug Screening & Evaluation, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong 266100, China
| | - Huijie Liu
- Department of Pharmacology, School of Pharmacy, Qingdao University, Qingdao 266021, China
| | - Qingliang Xu
- Molecular Synthesis Center & Key Laboratory of Marine Drugs, Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Tao Jiang
- Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266200, China
- Molecular Synthesis Center & Key Laboratory of Marine Drugs, Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
| | - Rilei Yu
- Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao 266200, China
- Molecular Synthesis Center & Key Laboratory of Marine Drugs, Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, 5 Yushan Road, Qingdao 266003, China
- Innovation Platform of Marine Drug Screening & Evaluation, Pilot National Laboratory for Marine Science and Technology (Qingdao), Qingdao, Shandong 266100, China
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10
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Ho TNT, Abraham N, Lewis RJ. Rigidity of loop 1 contributes to equipotency of globular and ribbon isomers of α-conotoxin AusIA. Sci Rep 2021; 11:21928. [PMID: 34753970 PMCID: PMC8578332 DOI: 10.1038/s41598-021-01277-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/19/2021] [Indexed: 11/09/2022] Open
Abstract
α-Conotoxins are small disulfide-rich peptides targeting nicotinic acetylcholine receptors (nAChRs) characterised by a CICII-Xm-CIII-Xn-CIV framework that invariably adopt the native globular conformations which is typically most potent. α-Conotoxins are divided into several structural subgroups based on the number of residues within the two loops braced by the disulfide bonds (m/n), with the 4/7 and 4/3 subgroups dominating. AusIA is a relatively rare α5/5-conotoxin isolated from the venom of Conus australis. Surprisingly, the ribbon isomer displayed equipotency to the wild-type globular AusIA at human α7-containing nAChR. To understand the molecular basis for equipotency, we determined the co-crystal structures of both isomers at Lymnea stagnalis acetylcholine binding protein. The additional residue in the first loop of AusIA was found to be a critical determinant of equipotency, with 11-fold and 86-fold shifts in potency in favour of globular AusIA over ribbon AusIA observed following deletion of Ala4 or Arg5, respectively. This divergence in the potency between globular AusIA and ribbon AusIA was further enhanced upon truncation of the non-conserved Val at the C-termini. Conversely, equipotency could be replicated in LsIA and TxIA [A10L] following insertion of an Ala in the first loop. These findings provide a new understanding of the role the first loop in ribbon and globular α-conotoxins can play in directing α-conotoxin nAChR pharmacology.
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Affiliation(s)
- Thao N T Ho
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4067, Australia
| | - Nikita Abraham
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4067, Australia
| | - Richard J Lewis
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, 4067, Australia.
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11
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Guo M, Yu J, Zhu X, Zhangsun D, Luo S. Characterization of an α 4/7-Conotoxin LvIF from Conus lividus That Selectively Blocks α3β2 Nicotinic Acetylcholine Receptor. Mar Drugs 2021; 19:md19070398. [PMID: 34356823 PMCID: PMC8306566 DOI: 10.3390/md19070398] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 11/16/2022] Open
Abstract
Nicotinic acetylcholine receptor (nAChR), a member of pentameric ligand-gated ion channel transmembrane protein composed of five subunits, is widely distributed in the central and peripheral nervous system. The nAChRs are associated with various neurological diseases, including schizophrenia, Alzheimer’s disease, Parkinson’s disease, epilepsy and neuralgia. Receptors containing the α3 subunit are associated with analgesia, generating our interest in their role in pharmacological studies. In this study, α-conotoxin (α-CTx) LvIF was identified as a 16 amino acid peptide using a genomic DNA clone of Conus lividus (C. lividus). The mature LvIF with natural structure was synthesized by a two-step oxidation method. The blocking potency of α-CTx lvIF on nAChR was detected by a two-electrode voltage clamp. Our results showed that α-CTx LvIF was highly potent against rα3β2 and rα6/α3β2β3 nAChR subtypes, The half-maximal inhibitory concentration (IC50) values of α-CTx LvIF against rα3β2 and rα6/α3β2β3 nAChRs expressed in Xenopus oocytes were 8.9 nM and 14.4 nM, respectively. Furthermore, α-CTx LvIF exhibited no obvious inhibition on other nAChR subtypes. Meanwhile, we also conducted a competitive binding experiment between α-CTxs MII and LvIF, which showed that α-CTxs LvIF and MII bind with rα3β2 nAChR at the partial overlapping domain. These results indicate that the α-CTx LvIF has high potential as a new candidate tool for the studying of rα3β2 nAChR related neurophysiology and pharmacology.
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Affiliation(s)
- Man Guo
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Laboratory for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China;
| | - Jinpeng Yu
- Medical School, Guangxi University, Nanning 530004, China; (J.Y.); (X.Z.)
| | - Xiaopeng Zhu
- Medical School, Guangxi University, Nanning 530004, China; (J.Y.); (X.Z.)
| | - Dongting Zhangsun
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Laboratory for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China;
- Medical School, Guangxi University, Nanning 530004, China; (J.Y.); (X.Z.)
- Correspondence: (D.Z.); (S.L.)
| | - Sulan Luo
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Laboratory for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China;
- Medical School, Guangxi University, Nanning 530004, China; (J.Y.); (X.Z.)
- Correspondence: (D.Z.); (S.L.)
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12
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Katz D, DiMattia MA, Sindhikara D, Li H, Abraham N, Leffler AE. Potency- and Selectivity-Enhancing Mutations of Conotoxins for Nicotinic Acetylcholine Receptors Can Be Predicted Using Accurate Free-Energy Calculations. Mar Drugs 2021; 19:367. [PMID: 34202022 PMCID: PMC8306581 DOI: 10.3390/md19070367] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 06/18/2021] [Accepted: 06/22/2021] [Indexed: 01/18/2023] Open
Abstract
Nicotinic acetylcholine receptor (nAChR) subtypes are key drug targets, but it is challenging to pharmacologically differentiate between them because of their highly similar sequence identities. Furthermore, α-conotoxins (α-CTXs) are naturally selective and competitive antagonists for nAChRs and hold great potential for treating nAChR disorders. Identifying selectivity-enhancing mutations is the chief aim of most α-CTX mutagenesis studies, although doing so with traditional docking methods is difficult due to the lack of α-CTX/nAChR crystal structures. Here, we use homology modeling to predict the structures of α-CTXs bound to two nearly identical nAChR subtypes, α3β2 and α3β4, and use free-energy perturbation (FEP) to re-predict the relative potency and selectivity of α-CTX mutants at these subtypes. First, we use three available crystal structures of the nAChR homologue, acetylcholine-binding protein (AChBP), and re-predict the relative affinities of twenty point mutations made to the α-CTXs LvIA, LsIA, and GIC, with an overall root mean square error (RMSE) of 1.08 ± 0.15 kcal/mol and an R2 of 0.62, equivalent to experimental uncertainty. We then use AChBP as a template for α3β2 and α3β4 nAChR homology models bound to the α-CTX LvIA and re-predict the potencies of eleven point mutations at both subtypes, with an overall RMSE of 0.85 ± 0.08 kcal/mol and an R2 of 0.49. This is significantly better than the widely used molecular mechanics-generalized born/surface area (MM-GB/SA) method, which gives an RMSE of 1.96 ± 0.24 kcal/mol and an R2 of 0.06 on the same test set. Next, we demonstrate that FEP accurately classifies α3β2 nAChR selective LvIA mutants while MM-GB/SA does not. Finally, we use FEP to perform an exhaustive amino acid mutational scan of LvIA and predict fifty-two mutations of LvIA to have greater than 100X selectivity for the α3β2 nAChR. Our results demonstrate the FEP is well-suited to accurately predict potency- and selectivity-enhancing mutations of α-CTXs for nAChRs and to identify alternative strategies for developing selective α-CTXs.
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Affiliation(s)
- Dana Katz
- Schrödinger, Inc., 120 West 45th St., New York, NY 10036, USA; (D.K.); (M.A.D.); (D.S.); (H.L.)
| | - Michael A. DiMattia
- Schrödinger, Inc., 120 West 45th St., New York, NY 10036, USA; (D.K.); (M.A.D.); (D.S.); (H.L.)
| | - Dan Sindhikara
- Schrödinger, Inc., 120 West 45th St., New York, NY 10036, USA; (D.K.); (M.A.D.); (D.S.); (H.L.)
| | - Hubert Li
- Schrödinger, Inc., 120 West 45th St., New York, NY 10036, USA; (D.K.); (M.A.D.); (D.S.); (H.L.)
| | | | - Abba E. Leffler
- Schrödinger, Inc., 120 West 45th St., New York, NY 10036, USA; (D.K.); (M.A.D.); (D.S.); (H.L.)
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13
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Bekbossynova A, Zharylgap A, Filchakova O. Venom-Derived Neurotoxins Targeting Nicotinic Acetylcholine Receptors. Molecules 2021; 26:molecules26113373. [PMID: 34204855 PMCID: PMC8199771 DOI: 10.3390/molecules26113373] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 01/02/2023] Open
Abstract
Acetylcholine was the first neurotransmitter described. The receptors targeted by acetylcholine are found within organisms spanning different phyla and position themselves as very attractive targets for predation, as well as for defense. Venoms of snakes within the Elapidae family, as well as those of marine snails within the Conus genus, are particularly rich in proteins and peptides that target nicotinic acetylcholine receptors (nAChRs). Such compounds are invaluable tools for research seeking to understand the structure and function of the cholinergic system. Proteins and peptides of venomous origin targeting nAChR demonstrate high affinity and good selectivity. This review aims at providing an overview of the toxins targeting nAChRs found within venoms of different animals, as well as their activities and the structural determinants important for receptor binding.
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14
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Ho TNT, Abraham N, Lewis RJ. Structure-Function of Neuronal Nicotinic Acetylcholine Receptor Inhibitors Derived From Natural Toxins. Front Neurosci 2020; 14:609005. [PMID: 33324158 PMCID: PMC7723979 DOI: 10.3389/fnins.2020.609005] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2020] [Accepted: 10/30/2020] [Indexed: 12/19/2022] Open
Abstract
Neuronal nicotinic acetylcholine receptors (nAChRs) are prototypical cation-selective, ligand-gated ion channels that mediate fast neurotransmission in the central and peripheral nervous systems. nAChRs are involved in a range of physiological and pathological functions and hence are important therapeutic targets. Their subunit homology and diverse pentameric assembly contribute to their challenging pharmacology and limit their drug development potential. Toxins produced by an extensive range of algae, plants and animals target nAChRs, with many proving pivotal in elucidating receptor pharmacology and biochemistry, as well as providing templates for structure-based drug design. The crystal structures of these toxins with diverse chemical profiles in complex with acetylcholine binding protein (AChBP), a soluble homolog of the extracellular ligand-binding domain of the nAChRs and more recently the extracellular domain of human α9 nAChRs, have been reported. These studies have shed light on the diverse molecular mechanisms of ligand-binding at neuronal nAChR subtypes and uncovered critical insights useful for rational drug design. This review provides a comprehensive overview and perspectives obtained from structure and function studies of diverse plant and animal toxins and their associated inhibitory mechanisms at neuronal nAChRs.
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Affiliation(s)
| | | | - Richard J. Lewis
- Centre for Pain Research, Institute for Molecular Bioscience, The University of Queensland, St Lucia, QLD, Australia
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15
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Zhu X, Pan S, Xu M, Zhang L, Yu J, Yu J, Wu Y, Fan Y, Li H, Kasheverov IE, Kudryavtsev DS, Tsetlin VI, Xue Y, Zhangsun D, Wang X, Luo S. High Selectivity of an α-Conotoxin LvIA Analogue for α3β2 Nicotinic Acetylcholine Receptors Is Mediated by β2 Functionally Important Residues. J Med Chem 2020; 63:13656-13668. [PMID: 33196189 DOI: 10.1021/acs.jmedchem.0c00975] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The α3β2 and α3β4 nicotinic acetylcholine receptors (nAChRs) are widely expressed in the central and peripheral nervous systems, playing critical roles in various physiological processes and in such pathologies as addiction to nicotine and other drugs of abuse. α-Conotoxin LvIA, which we previously isolated from Conus lividus, modestly discriminates α3β2 and α3β4 rat nAChRs exhibiting a ∼17-fold tighter binding to the former. Here, alanine scanning resulted in two more selective analogues [N9A]LvIA and [D11A]LvIA, the former having a >2000-fold higher selectivity for α3β2. The determined crystal structures of [N9A]LvIA and [D11A]LvIA bound to the acetylcholine-binding protein (AChBP) were followed by homologous modeling of the complexes with the α3β2 and α3β4 nAChRs and by receptor mutagenesis, which revealed Phe106, Ser108, Ser113, and Ser168 residues in the β2 subunit as essential for LvIA binding. These results may be useful for the design of novel compounds of therapeutic potential targeting α3β2 nAChRs.
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Affiliation(s)
- Xiaopeng Zhu
- Medical School, Guangxi University, Nanning 530004, China.,Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Laboratory for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Si Pan
- The Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, Tsinghua University, Beijing 100084, China
| | - Manyu Xu
- The Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, Tsinghua University, Beijing 100084, China
| | - Lu Zhang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Laboratory for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Jinfang Yu
- The Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, Tsinghua University, Beijing 100084, China
| | - Jinpeng Yu
- Medical School, Guangxi University, Nanning 530004, China
| | - Yong Wu
- Medical School, Guangxi University, Nanning 530004, China
| | - Yingxu Fan
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Haonan Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Laboratory for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Igor E Kasheverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russia.,Sechenov First Moscow State Medical University, Institute of Molecular Medicine, Trubetskaya Street 8, bld. 2, Moscow 119991, Russia
| | - Denis S Kudryavtsev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russia
| | - Victor I Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, Moscow 117997, Russia.,PhysBio of MePhi, Kashirskoe Ave. 31, Moscow 115409, Russia
| | - Yi Xue
- Tsinghua-Peking Joint Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Dongting Zhangsun
- Medical School, Guangxi University, Nanning 530004, China.,Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Laboratory for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, Tsinghua University, Beijing 100084, China
| | - Sulan Luo
- Medical School, Guangxi University, Nanning 530004, China.,Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Laboratory for Marine Drugs of Haikou, School of Life and Pharmaceutical Sciences, Hainan University, Haikou 570228, China
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16
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Shah B, Sindhikara D, Borrelli K, Leffler AE. Water Thermodynamics of Peptide Toxin Binding Sites on Ion Channels. Toxins (Basel) 2020; 12:toxins12100652. [PMID: 33053750 PMCID: PMC7599640 DOI: 10.3390/toxins12100652] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 09/21/2020] [Accepted: 10/09/2020] [Indexed: 12/20/2022] Open
Abstract
Peptide toxins isolated from venomous creatures, long prized as research tools due to their innate potency for ion channels, are emerging as drugs as well. However, it remains challenging to understand why peptide toxins bind with high potency to ion channels, to identify residues that are key for activity, and to improve their affinities via mutagenesis. We use WaterMap, a molecular dynamics simulation-based method, to gain computational insight into these three questions by calculating the locations and thermodynamic properties of water molecules in the peptide toxin binding sites of five ion channels. These include an acid-sensing ion channel, voltage-gated potassium channel, sodium channel in activated and deactivated states, transient-receptor potential channel, and a nicotinic receptor whose structures were recently determined by crystallography and cryo-electron microscopy (cryo-EM). All channels had water sites in the peptide toxin binding site, and an average of 75% of these sites were stable (low-energy), and 25% were unstable (medium or high energy). For the sodium channel, more unstable water sites were present in the deactivated state structure than the activated. Additionally, for each channel, unstable water sites coincided with the positions of peptide toxin residues that previous mutagenesis experiments had shown were important for activity. Finally, for the sodium channel in the deactivated state, unstable water sites were present in the peptide toxin binding pocket but did not overlap with the peptide toxin, suggesting that future experimental efforts could focus on targeting these sites to optimize potency.
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Affiliation(s)
- Binita Shah
- Schrödinger, Inc. 120 W. 45th St, New York, NY 10036, USA; (B.S.); (D.S.); (K.B.)
- PhD Program in Biological and Biomedical Sciences, Division of Medical Sciences, Harvard Medical School, Boston, MA 02115, USA
| | - Dan Sindhikara
- Schrödinger, Inc. 120 W. 45th St, New York, NY 10036, USA; (B.S.); (D.S.); (K.B.)
| | - Ken Borrelli
- Schrödinger, Inc. 120 W. 45th St, New York, NY 10036, USA; (B.S.); (D.S.); (K.B.)
| | - Abba E. Leffler
- Schrödinger, Inc. 120 W. 45th St, New York, NY 10036, USA; (B.S.); (D.S.); (K.B.)
- Correspondence:
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17
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Gulsevin A, Meiler J. An Investigation of Three-Finger Toxin-nAChR Interactions through Rosetta Protein Docking. Toxins (Basel) 2020; 12:E598. [PMID: 32947868 PMCID: PMC7551183 DOI: 10.3390/toxins12090598] [Citation(s) in RCA: 4] [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: 08/11/2020] [Revised: 09/11/2020] [Accepted: 09/12/2020] [Indexed: 12/14/2022] Open
Abstract
Three-finger toxins (3FTX) are a group of peptides that affect multiple receptor types. One group of proteins affected by 3FTX are nicotinic acetylcholine receptors (nAChR). Structural information on how neurotoxins interact with nAChR is limited and is confined to a small group of neurotoxins. Therefore, in silico methods are valuable in understanding the interactions between 3FTX and different nAChR subtypes, but there are no established protocols to model 3FTX-nAChR interactions. We followed a homology modeling and protein docking protocol to address this issue and tested its success on three different systems. First, neurotoxin peptides co-crystallized with acetylcholine binding protein (AChBP) were re-docked to assess whether Rosetta protein-protein docking can reproduce the native poses. Second, experimental data on peptide binding to AChBP was used to test whether the docking protocol can qualitatively distinguish AChBP-binders from non-binders. Finally, we docked eight peptides with known α7 and muscle-type nAChR binding properties to test whether the protocol can explain the differential activities of the peptides at the two receptor subtypes. Overall, the docking protocol predicted the qualitative and some specific aspects of 3FTX binding to nAChR with reasonable success and shed light on unknown aspects of 3FTX binding to different receptor subtypes.
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Affiliation(s)
- Alican Gulsevin
- Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA;
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN 37212, USA;
- Institute for Drug Discovery, Leipzig University Medical School, 04103 Leipzig, Germany
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18
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Li X, Liu H, Gao C, Li Y, Jia D, Yang Y, Yang J, Wei Z, Jiang T, Yu R. ConoMode, a database for conopeptide binding modes. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2020; 2020:5880464. [PMID: 32754758 PMCID: PMC7402919 DOI: 10.1093/database/baaa058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/23/2020] [Accepted: 07/07/2020] [Indexed: 11/24/2022]
Abstract
ConoMode is a database for complex three-dimensional (3D) structures of conopeptides binding with their target proteins. Conopeptides, a large family of peptides from the venom of marine snails of the Conus genus, have exceptionally diverse sequences, and their high specificity to block ion channels makes them crucial as drug leads and tools for physiological studies. ConoMode is a specialized archive for the collection of 3D coordinate data for the conopeptides and their binding target proteins from published literature and the Protein Data Bank. These 3D structures can be determined using experimental methods such as X-ray crystallography and electron microscopy and computational methods including docking, homology modeling and molecular dynamics simulations. The binding modes for the conopeptides determined using computational modeling must be validated based on experimental data. The 3D coordinate data from ConoMode can be searched, visualized, downloaded and uploaded. Currently, ConoMode manages 19 conopeptide sequences (from 10 Conus species), 15 protein sequences and 37 3D structures. ConoMode utilizes a modern technical framework to provide a good user experience on mobile devices with touch interaction features. Furthermore, the database is fully optimized for unstructured data and flexible data models. Database URL: http://conomode.qnlm.ac/conomode/conomode/index
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Affiliation(s)
- Xiao Li
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Hao Liu
- Department of Computer Science and Technology, Ocean University of China, Qingdao 266100, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Chunxiao Gao
- Department of Computer Science and Technology, Ocean University of China, Qingdao 266100, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Yangyang Li
- Department of Computer Science and Technology, Ocean University of China, Qingdao 266100, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Dongning Jia
- Department of Computer Science and Technology, Ocean University of China, Qingdao 266100, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Yanbo Yang
- Department of Computer Science and Technology, Ocean University of China, Qingdao 266100, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Jinbo Yang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Zhiqiang Wei
- Department of Computer Science and Technology, Ocean University of China, Qingdao 266100, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Tao Jiang
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China.,Qingdao National Laboratory for Marine Science and Technology, Qingdao 266003, China
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19
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Gulsevin A, Papke RL, Horenstein N. In Silico Modeling of the α7 Nicotinic Acetylcholine Receptor: New Pharmacological Challenges Associated with Multiple Modes of Signaling. Mini Rev Med Chem 2020; 20:841-864. [PMID: 32000651 PMCID: PMC8719523 DOI: 10.2174/1389557520666200130105256] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022]
Abstract
The α7 nicotinic acetylcholine receptor is a homopentameric ion-channel of the Cys-loop superfamily characterized by its low probability of opening, high calcium permeability, and rapid desensitization. The α7 receptor has been targeted for the treatment of the cognitive symptoms of schizophrenia, depression, and Alzheimer's disease, but it is also involved in inflammatory modulation as a part of the cholinergic anti-inflammatory pathway. Despite its functional importance, in silico studies of the α7 receptor cannot produce a general model explaining the structural features of receptor activation, nor predict the mode of action for various ligand classes. Two particular problems in modeling the α7 nAChR are the absence of a high-resolution structure and the presence of five potentially nonequivalent orthosteric ligand binding sites. There is wide variability regarding the templates used for homology modeling, types of ligands investigated, simulation methods, and simulation times. However, a systematic survey focusing on the methodological similarities and differences in modeling α7 has not been done. In this work, we make a critical analysis of the modeling literature of α7 nAChR by comparing the findings of computational studies with each other and with experimental studies under the main topics of structural studies, ligand binding studies, and comparisons with other nAChR. In light of our findings, we also summarize current problems in the field and make suggestions for future studies concerning modeling of the α7 receptor.
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Affiliation(s)
- Alican Gulsevin
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, United States
| | - Roger L Papke
- Department of Pharmacology and Therapeutics, University of Florida, P.O. Box 100267, Gainesville, FL 32610, United States
| | - Nicole Horenstein
- Department of Chemistry, University of Florida, P.O. Box 117200, Gainesville, FL, 32611-7200, United States
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20
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Jin AH, Muttenthaler M, Dutertre S, Himaya SWA, Kaas Q, Craik DJ, Lewis RJ, Alewood PF. Conotoxins: Chemistry and Biology. Chem Rev 2019; 119:11510-11549. [PMID: 31633928 DOI: 10.1021/acs.chemrev.9b00207] [Citation(s) in RCA: 161] [Impact Index Per Article: 32.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The venom of the marine predatory cone snails (genus Conus) has evolved for prey capture and defense, providing the basis for survival and rapid diversification of the now estimated 750+ species. A typical Conus venom contains hundreds to thousands of bioactive peptides known as conotoxins. These mostly disulfide-rich and well-structured peptides act on a wide range of targets such as ion channels, G protein-coupled receptors, transporters, and enzymes. Conotoxins are of interest to neuroscientists as well as drug developers due to their exquisite potency and selectivity, not just against prey but also mammalian targets, thereby providing a rich source of molecular probes and therapeutic leads. The rise of integrated venomics has accelerated conotoxin discovery with now well over 10,000 conotoxin sequences published. However, their structural and pharmacological characterization lags considerably behind. In this review, we highlight the diversity of new conotoxins uncovered since 2014, their three-dimensional structures and folds, novel chemical approaches to their syntheses, and their value as pharmacological tools to unravel complex biology. Additionally, we discuss challenges and future directions for the field.
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Affiliation(s)
- Ai-Hua Jin
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Markus Muttenthaler
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia.,Institute of Biological Chemistry, Faculty of Chemistry , University of Vienna , 1090 Vienna , Austria
| | - Sebastien Dutertre
- Département des Acides Amines, Peptides et Protéines, Unité Mixte de Recherche 5247, Université Montpellier 2-Centre Nationale de la Recherche Scientifique , Institut des Biomolécules Max Mousseron , Place Eugène Bataillon , 34095 Montpellier Cedex 5 , France
| | - S W A Himaya
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Richard J Lewis
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
| | - Paul F Alewood
- Institute for Molecular Bioscience , The University of Queensland , Brisbane Queensland 4072 , Australia
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21
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Lebedev DS, Kryukova EV, Ivanov IA, Egorova NS, Timofeev ND, Spirova EN, Tufanova EY, Siniavin AE, Kudryavtsev DS, Kasheverov IE, Zouridakis M, Katsarava R, Zavradashvili N, Iagorshvili I, Tzartos SJ, Tsetlin VI. Oligoarginine Peptides, a New Family of Nicotinic Acetylcholine Receptor Inhibitors. Mol Pharmacol 2019; 96:664-673. [PMID: 31492697 DOI: 10.1124/mol.119.117713] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/26/2019] [Indexed: 12/28/2022] Open
Abstract
Many peptide ligands of nicotinic acetylcholine receptors (nAChRs) contain a large number of positively charged amino acid residues, a striking example being conotoxins RgIA and GeXIVA from marine mollusk venom, with an arginine content of >30%. To determine whether peptides built exclusively from arginine residues will interact with different nAChR subtypes or with their structural homologs such as the acetylcholine-binding protein and ligand-binding domain of the nAChR α9 subunit, we synthesized a series of R3, R6, R8, and R16 oligoarginines and investigated their activity by competition with radioiodinated α-bungarotoxin, two-electrode voltage-clamp electrophysiology, and calcium imaging. R6 and longer peptides inhibited muscle-type nAChRs, α7 nAChRs, and α3β2 nAChRs in the micromolar range. The most efficient inhibition of ion currents was detected for muscle nAChR by R16 (IC50 = 157 nM) and for the α9α10 subtype by R8 and R16 (IC50 = 44 and 120 nM, respectively). Since the R8 affinity for other tested nAChRs was 100-fold lower, R8 appears to be a selective antagonist of α9α10 nAChR. For R8, the electrophysiological and competition experiments indicated the existence of two distinct binding sites on α9α10 nAChR. Since modified oligoarginines and other cationic molecules are widely used as cell-penetrating peptides, we studied several cationic polymers and demonstrated their nAChR inhibitory activity. SIGNIFICANT STATEMENT: By using radioligand analysis, electrophysiology, and calcium imaging, we found that oligoarginine peptides are a new group of inhibitors for muscle nicotinic acetylcholine receptors (nAChRs) and some neuronal nAChRs, the most active being those with 16 and 8 Arg residues. Such compounds and other cationic polymers are cell-penetrating tools for drug delivery, and we also demonstrated the inhibition of nAChRs for several of the latter. Possible positive and negative consequences of such an action should be taken into account.
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Affiliation(s)
- Dmitry S Lebedev
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
| | - Elena V Kryukova
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
| | - Igor A Ivanov
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
| | - Natalia S Egorova
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
| | - Nikita D Timofeev
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
| | - Ekaterina N Spirova
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
| | - Elizaveta Yu Tufanova
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
| | - Andrei E Siniavin
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
| | - Denis S Kudryavtsev
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
| | - Igor E Kasheverov
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
| | - Marios Zouridakis
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
| | - Ramaz Katsarava
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
| | - Nino Zavradashvili
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
| | - Ia Iagorshvili
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
| | - Socrates J Tzartos
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
| | - Victor I Tsetlin
- Department of Molecular Neuroimmune Signaling, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia (D.S.L., E.V.K., I.A.I., N.S.E., N.D.T., E.N.S., E.Y.T., A.E.S., D.S.K., I.E.K., V.I.T.); Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece (M.Z., S.J.T.); Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia (I.E.K.); Institute of Chemistry and Molecular Engineering, Agricultural University of Georgia, Kakha Bendukidze University Campus, Tbilisi, Georgia (R.K., N.Z., I.I.); and PhysBio of MePhI, Moscow, Russia (V.I.T.)
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22
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Li R, Li X, Jiang J, Tian Y, Liu D, Zhangsun D, Fu Y, Wu Y, Luo S. Interaction of rat α9α10 nicotinic acetylcholine receptor with α-conotoxin RgIA and Vc1.1: Insights from docking, molecular dynamics and binding free energy contributions. J Mol Graph Model 2019; 92:55-64. [PMID: 31330438 DOI: 10.1016/j.jmgm.2019.06.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2019] [Revised: 06/25/2019] [Accepted: 06/27/2019] [Indexed: 12/12/2022]
Abstract
The α9α10 nicotinic acetylcholine receptor (nAChR) is an effective therapeutic target for neuropathic pain. α-Conotoxin RgIA and Vc1.1 are two well-known peptides blocking α9α10 nAChR potently and selectively, which have been extensively investigated as drug candidates. Several key residues were established in previous experimental research. However, the mechanism of the specific interaction still needs to be elucidated in more detail. In this work, we explored the interaction mechanism between RgIA/Vc1.1 and rat α9α10 nAChR using docking and molecular dynamics (MD) simulations. Energy and network analysis programs were used to reveal key residues responsible for their interaction. Our results indicated that the most critical residues were in accord with previous studies. Importantly, several novel residues, including Tyr95, Trp151 in α9 (+)α10 (-) interface as well as Tyr196, Arg59in α10 (+)α9 (-) interface, were found in our models. Furthermore, we analyzed noncovalent interaction energies between RgIA/Vc1.1 and rat α9α10 nAChR. The results showed that three negatively charged residues (Glu197 in α10 subunit, Asp168 in α9 subunit and Asp205 in α10 subunit) were involved in the interaction between RgIA and rat α9α10 nAChR. In contrast, the interaction between Vc1.1 and rat α9α10 nAChR was mediated by the positively charged residues Arg59, Arg81 in α9 (-) subunit. These findings provided further insights into the molecular mechanisms of interaction between RgIA and Vc1.1 and rat α9α10 nAChR.
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Affiliation(s)
- Rui Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Xincan Li
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Jiemei Jiang
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Yuanyuan Tian
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Danrui Liu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Donting Zhangsun
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Ying Fu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China
| | - Yong Wu
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China.
| | - Sulan Luo
- Key Laboratory of Tropical Biological Resources of Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, Hainan, 570228, China.
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23
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Morales Duque H, Campos Dias S, Franco OL. Structural and Functional Analyses of Cone Snail Toxins. Mar Drugs 2019; 17:md17060370. [PMID: 31234371 PMCID: PMC6628382 DOI: 10.3390/md17060370] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 06/16/2019] [Accepted: 06/17/2019] [Indexed: 12/12/2022] Open
Abstract
Cone snails are marine gastropod mollusks with one of the most powerful venoms in nature. The toxins, named conotoxins, must act quickly on the cone snails´ prey due to the fact that snails are extremely slow, reducing their hunting capability. Therefore, the characteristics of conotoxins have become the object of investigation, and as a result medicines have been developed or are in the trialing process. Conotoxins interact with transmembrane proteins, showing specificity and potency. They target ion channels and ionotropic receptors with greater regularity, and when interaction occurs, there is immediate physiological decompensation. In this review we aimed to evaluate the structural features of conotoxins and the relationship with their target types.
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Affiliation(s)
- Harry Morales Duque
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF 70.790-160, Brazil.
| | - Simoni Campos Dias
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF 70.790-160, Brazil.
| | - Octávio Luiz Franco
- Centro de Análises Proteômicas e Bioquímicas, Programa de Pós-Graduação em Ciências Genômicas e Biotecnologia, Universidade Católica de Brasília, Brasília-DF 70.790-160, Brazil.
- S-inova Biotech, Programa de Pós-Graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande-MS 79.117-900, Brazil.
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24
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Malde AK, Hill TA, Iyer A, Fairlie DP. Crystal Structures of Protein-Bound Cyclic Peptides. Chem Rev 2019; 119:9861-9914. [DOI: 10.1021/acs.chemrev.8b00807] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alpeshkumar K. Malde
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Abishek Iyer
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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25
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Zouridakis M, Papakyriakou A, Ivanov IA, Kasheverov IE, Tsetlin V, Tzartos S, Giastas P. Crystal Structure of the Monomeric Extracellular Domain of α9 Nicotinic Receptor Subunit in Complex With α-Conotoxin RgIA: Molecular Dynamics Insights Into RgIA Binding to α9α10 Nicotinic Receptors. Front Pharmacol 2019; 10:474. [PMID: 31118896 PMCID: PMC6504684 DOI: 10.3389/fphar.2019.00474] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 04/15/2019] [Indexed: 12/20/2022] Open
Abstract
The α9 subunit of nicotinic acetylcholine receptors (nAChRs) exists mainly in heteropentameric assemblies with α10. Accumulating data indicate the presence of three different binding sites in α9α10 nAChRs: the α9(+)/α9(−), the α9(+)/α10(−), and the α10(+)/α9(−). The major role of the principal (+) side of the extracellular domain (ECD) of α9 subunit in binding of the antagonists methyllylcaconitine and α-bungarotoxin was shown previously by the crystal structures of the monomeric α9-ECD with these molecules. Here we present the 2.26-Å resolution crystal structure of α9-ECD in complex with α-conotoxin (α-Ctx) RgIA, a potential drug for chronic pain, the first structure reported for a complex between an nAChR domain and an α-Ctx. Superposition of this structure with those of other α-Ctxs bound to the homologous pentameric acetylcholine binding proteins revealed significant similarities in the orientation of bound conotoxins, despite the monomeric state of the α9-ECD. In addition, ligand-binding studies calculated a binding affinity of RgIA to the α9-ECD at the low micromolar range. Given the high identity between α9 and α10 ECDs, particularly at their (+) sides, the presented structure was used as template for molecular dynamics simulations of the ECDs of the human α9α10 nAChR in pentameric assemblies. Our results support a favorable binding of RgIA at α9(+)/α9(−) or α10(+)/α9(−) rather than the α9(+)/α10(−) interface, in accordance with previous mutational and functional data.
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Affiliation(s)
- Marios Zouridakis
- Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
| | | | - Igor A Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Igor E Kasheverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Moscow, Russia
| | - Victor Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,PhysBio of MEPhI, Moscow, Russia
| | - Socrates Tzartos
- Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece.,Department of Pharmacy, University of Patras, Patras, Greece
| | - Petros Giastas
- Department of Neurobiology, Hellenic Pasteur Institute, Athens, Greece
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26
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Mansbach RA, Travers T, McMahon BH, Fair JM, Gnanakaran S. Snails In Silico: A Review of Computational Studies on the Conopeptides. Mar Drugs 2019; 17:E145. [PMID: 30832207 PMCID: PMC6471681 DOI: 10.3390/md17030145] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Revised: 02/21/2019] [Accepted: 02/22/2019] [Indexed: 12/26/2022] Open
Abstract
Marine cone snails are carnivorous gastropods that use peptide toxins called conopeptides both as a defense mechanism and as a means to immobilize and kill their prey. These peptide toxins exhibit a large chemical diversity that enables exquisite specificity and potency for target receptor proteins. This diversity arises in terms of variations both in amino acid sequence and length, and in posttranslational modifications, particularly the formation of multiple disulfide linkages. Most of the functionally characterized conopeptides target ion channels of animal nervous systems, which has led to research on their therapeutic applications. Many facets of the underlying molecular mechanisms responsible for the specificity and virulence of conopeptides, however, remain poorly understood. In this review, we will explore the chemical diversity of conopeptides from a computational perspective. First, we discuss current approaches used for classifying conopeptides. Next, we review different computational strategies that have been applied to understanding and predicting their structure and function, from machine learning techniques for predictive classification to docking studies and molecular dynamics simulations for molecular-level understanding. We then review recent novel computational approaches for rapid high-throughput screening and chemical design of conopeptides for particular applications. We close with an assessment of the state of the field, emphasizing important questions for future lines of inquiry.
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Affiliation(s)
- Rachael A Mansbach
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Timothy Travers
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Benjamin H McMahon
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - Jeanne M Fair
- Biosecurity and Public Health Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
| | - S Gnanakaran
- Theoretical Biology and Biophysics Group, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
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27
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Mutagenesis of α-Conotoxins for Enhancing Activity and Selectivity for Nicotinic Acetylcholine Receptors. Toxins (Basel) 2019; 11:toxins11020113. [PMID: 30781866 PMCID: PMC6409848 DOI: 10.3390/toxins11020113] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 02/10/2019] [Accepted: 02/11/2019] [Indexed: 02/04/2023] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) are found throughout the mammalian body and have been studied extensively because of their implication in a myriad of diseases. α-Conotoxins (α-CTxs) are peptide neurotoxins found in the venom of marine snails of genus Conus. α-CTxs are potent and selective antagonists for a variety of nAChR isoforms. Over the past 40 years, α-CTxs have proven to be valuable molecular probes capable of differentiating between closely related nAChR subtypes and have contributed greatly to understanding the physiological role of nAChRs in the mammalian nervous system. Here, we review the amino acid composition and structure of several α-CTxs that selectively target nAChR isoforms and explore strategies and outcomes for introducing mutations in native α-CTxs to direct selectivity and enhance binding affinity for specific nAChRs. This review will focus on structure-activity relationship studies involving native α-CTxs that have been rationally mutated and molecular interactions that underlie binding between ligand and nAChR isoform.
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Kryukova EV, Ivanov IA, Lebedev DS, Spirova EN, Egorova NS, Zouridakis M, Kasheverov IE, Tzartos SJ, Tsetlin VI. Orthosteric and/or Allosteric Binding of α-Conotoxins to Nicotinic Acetylcholine Receptors and Their Models. Mar Drugs 2018; 16:md16120460. [PMID: 30469507 PMCID: PMC6315749 DOI: 10.3390/md16120460] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 11/09/2018] [Accepted: 11/20/2018] [Indexed: 12/19/2022] Open
Abstract
α-Conotoxins from Conus snails are capable of distinguishing muscle and neuronal nicotinic acetylcholine receptors (nAChRs). α-Conotoxin RgIA and αO-conotoxin GeXIVA, blocking neuronal α9α10 nAChR, are potential analgesics. Typically, α-conotoxins bind to the orthosteric sites for agonists/competitive antagonists, but αO-conotoxin GeXIVA was proposed to attach allosterically, judging by electrophysiological experiments on α9α10 nAChR. We decided to verify this conclusion by radioligand analysis in competition with α-bungarotoxin (αBgt) on the ligand-binding domain of the nAChR α9 subunit (α9 LBD), where, from the X-ray analysis, αBgt binds at the orthosteric site. A competition with αBgt was registered for GeXIVA and RgIA, IC50 values being in the micromolar range. However, high nonspecific binding of conotoxins (detected with their radioiodinated derivatives) to His6-resin attaching α9 LBD did not allow us to accurately measure IC50s. However, IC50s were measured for binding to Aplysia californica AChBP: the RgIA globular isomer, known to be active against α9α10 nAChR, was more efficient than the ribbon one, whereas all three GeXIVA isomers had similar potencies at low µM. Thus, radioligand analysis indicated that both conotoxins can attach to the orthosteric sites in these nAChR models, which should be taken into account in the design of analgesics on the basis of these conotoxins.
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Affiliation(s)
- Elena V Kryukova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
| | - Igor A Ivanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
| | - Dmitry S Lebedev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
| | - Ekaterina N Spirova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
| | - Natalia S Egorova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
| | - Marios Zouridakis
- Department of Neurobiology, Hellenic Pasteur Institute, 127, Vas. Sofias ave., Athens 115 21, Greece.
| | - Igor E Kasheverov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
- Institute of Molecular Medicine, Sechenov First Moscow State Medical University, Trubetskaya Street 8, bld. 2, 119991 Moscow, Russia.
| | - Socrates J Tzartos
- Department of Neurobiology, Hellenic Pasteur Institute, 127, Vas. Sofias ave., Athens 115 21, Greece.
| | - Victor I Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia.
- PhysBio of MEPhI, Kashirskoye Ave., 31, 115409 Moscow, Russia.
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Kuzmenkov AI, Vassilevski AA. Labelled animal toxins as selective molecular markers of ion channels: Applications in neurobiology and beyond. Neurosci Lett 2018; 679:15-23. [DOI: 10.1016/j.neulet.2017.10.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 10/23/2017] [Accepted: 10/25/2017] [Indexed: 12/12/2022]
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Abraham N, Lewis RJ. Neuronal Nicotinic Acetylcholine Receptor Modulators from Cone Snails. Mar Drugs 2018; 16:E208. [PMID: 29899286 PMCID: PMC6024932 DOI: 10.3390/md16060208] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Revised: 05/25/2018] [Accepted: 06/06/2018] [Indexed: 12/15/2022] Open
Abstract
Marine cone snails are a large family of gastropods that have evolved highly potent venoms for predation and defense. The cone snail venom has exceptional molecular diversity in neuropharmacologically active compounds, targeting a range of receptors, ion channels, and transporters. These conotoxins have helped to dissect the structure and function of many of these therapeutically significant targets in the central and peripheral nervous systems, as well as unravelling the complex cellular mechanisms modulated by these receptors and ion channels. This review provides an overview of α-conotoxins targeting neuronal nicotinic acetylcholine receptors. The structure and activity of both classical and non-classical α-conotoxins are discussed, along with their contributions towards understanding nicotinic acetylcholine receptor (nAChR) structure and function.
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Affiliation(s)
- Nikita Abraham
- IMB Centre for Pain Research, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia.
| | - Richard J Lewis
- IMB Centre for Pain Research, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, QLD 4072, Australia.
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Slagboom J, Otvos RA, Cardoso FC, Iyer J, Visser JC, van Doodewaerd BR, McCleary RJR, Niessen WMA, Somsen GW, Lewis RJ, Kini RM, Smit AB, Casewell NR, Kool J. Neurotoxicity fingerprinting of venoms using on-line microfluidic AChBP profiling. Toxicon 2018; 148:213-222. [PMID: 29730150 DOI: 10.1016/j.toxicon.2018.04.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Revised: 04/22/2018] [Accepted: 04/25/2018] [Indexed: 11/27/2022]
Abstract
Venoms from snakes are rich sources of highly active proteins with potent affinity towards a variety of enzymes and receptors. Of the many distinct toxicities caused by envenomation, neurotoxicity plays an important role in the paralysis of prey by snakes as well as by venomous sea snails and insects. In order to improve the analytical discovery component of venom toxicity profiling, this paper describes the implementation of microfluidic high-resolution screening (HRS) to obtain neurotoxicity fingerprints from venoms that facilitates identification of the neurotoxic components of envenomation. To demonstrate this workflow, 47 snake venoms were profiled using the acetylcholine binding protein (AChBP) to mimic the target of neurotoxic proteins, in particular nicotinic acetylcholine receptors (nAChRs). In the microfluidic HRS system, nanoliquid chromatographic (nanoLC) separations were on-line connected to both AChBP profiling and parallel mass spectrometry (MS). For virtually all neurotoxic elapid snake venoms tested, we obtained bioactivity fingerprints showing major and minor bioactive zones containing masses consistent with three-finger toxins (3FTxs), whereas, viperid and colubrid venoms showed little or no detectable bioactivity. Our findings demonstrate that venom interactions with AChBP correlate with the severity of neurotoxicity observed following human envenoming by different snake species. We further, as proof of principle, characterized bioactive venom peptides from a viperid (Daboia russelli) and an elapid (Aspidelaps scutatus scutatus) snake by nanoLC-MS/MS, revealing that different toxin classes interact with the AChBP, and that this binding correlates with the inhibition of α7-nAChR in calcium-flux cell-based assays. The on-line post-column binding assay and subsequent toxin characterization methodologies described here provide a new in vitro analytic platform for rapidly investigating neurotoxic snake venom proteins.
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Affiliation(s)
- Julien Slagboom
- AIMMS Division of BioMolecular Analysis, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
| | - Reka A Otvos
- AIMMS Division of BioMolecular Analysis, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands; Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, Vrije Universiteit, Amsterdam, The Netherlands.
| | - Fernanda C Cardoso
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, Queensland, 4072, Australia.
| | - Janaki Iyer
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 16 Science Drive 4, 117558, Singapore
| | - Jeroen C Visser
- AIMMS Division of BioMolecular Analysis, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
| | - Bjorn R van Doodewaerd
- AIMMS Division of BioMolecular Analysis, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
| | - Ryan J R McCleary
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 16 Science Drive 4, 117558, Singapore; Department of Biological Sciences, Stetson University, 421 N. Woodland Blvd, Unit 8264, DeLand, FL, 32723, USA.
| | - Wilfried M A Niessen
- AIMMS Division of BioMolecular Analysis, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands; hyphen MassSpec, Margrietstraat 34, 2215 HJ, Voorhout, The Netherlands.
| | - Govert W Somsen
- AIMMS Division of BioMolecular Analysis, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
| | - Richard J Lewis
- Institute for Molecular Bioscience, The University of Queensland, 306 Carmody Road, St Lucia, Brisbane, Queensland, 4072, Australia.
| | - R Manjunatha Kini
- Department of Biological Sciences, Faculty of Science, National University of Singapore, 16 Science Drive 4, 117558, Singapore.
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, Vrije Universiteit, Amsterdam, The Netherlands.
| | - Nicholas R Casewell
- Alistair Reid Venom Research Unit, Parasitology Department, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK; Research Centre for Drugs and Diagnostics, Liverpool School of Tropical Medicine, Pembroke Place, Liverpool, L3 5QA, UK.
| | - Jeroen Kool
- AIMMS Division of BioMolecular Analysis, Vrije Universiteit Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands.
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α-Conotoxins to explore the molecular, physiological and pathophysiological functions of neuronal nicotinic acetylcholine receptors. Neurosci Lett 2017; 679:24-34. [PMID: 29199094 DOI: 10.1016/j.neulet.2017.11.063] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/28/2017] [Accepted: 11/29/2017] [Indexed: 12/22/2022]
Abstract
The vast diversity of neuronal nicotinic acetylcholine subunits expressed in the central and peripheral nervous systems, as well as in non-neuronal tissues, constitutes a formidable challenge for researchers and clinicians to decipher the role of particular subtypes, including complex subunit associations, in physiological and pathophysiological functions. Many natural products target the nAChRs, but there is no richer source of nicotinic ligands than the venom of predatory gastropods known as cone snails. Indeed, every single species of cone snail was shown to produce at least one type of such α-conotoxins. These tiny peptides (10-25 amino acids), constrained by disulfide bridges, proved to be unvaluable tools to investigate the structure and function of nAChRs, some of them having also therapeutic potential. In this review, we provide a recent update on the pharmacology and subtype specificity of several major α-conotoxins.
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Hung A, Kuyucak S, Schroeder CI, Kaas Q. Modelling the interactions between animal venom peptides and membrane proteins. Neuropharmacology 2017; 127:20-31. [PMID: 28778835 DOI: 10.1016/j.neuropharm.2017.07.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 07/18/2017] [Accepted: 07/31/2017] [Indexed: 12/19/2022]
Abstract
The active components of animal venoms are mostly peptide toxins, which typically target ion channels and receptors of both the central and peripheral nervous system, interfering with action potential conduction and/or synaptic transmission. The high degree of sequence conservation of their molecular targets makes a range of these toxins active at human receptors. The high selectivity and potency displayed by some of these toxins have prompted their use as pharmacological tools as well as drugs or drug leads. Molecular modelling has played an essential role in increasing our molecular-level understanding of the activity and specificity of animal toxins, as well as engineering them for biotechnological and pharmaceutical applications. This review focuses on the biological insights gained from computational and experimental studies of animal venom toxins interacting with membranes and ion channels. A host of recent X-ray crystallography and electron-microscopy structures of the toxin targets has contributed to a dramatic increase in the accuracy of the molecular models of toxin binding modes greatly advancing this exciting field of study. This article is part of the Special Issue entitled 'Venom-derived Peptides as Pharmacological Tools.'
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Affiliation(s)
- Andrew Hung
- School of Science, RMIT University, GPO Box 2476, Melbourne, Victoria 3001, Australia
| | - Serdar Kuyucak
- School of Physics, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Christina I Schroeder
- Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia
| | - Quentin Kaas
- Institute for Molecular Bioscience, The University of Queensland, Brisbane 4072, Australia.
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Screening and Validation of Highly-Efficient Insecticidal Conotoxins from a Transcriptome-Based Dataset of Chinese Tubular Cone Snail. Toxins (Basel) 2017; 9:toxins9070214. [PMID: 28684723 PMCID: PMC5535161 DOI: 10.3390/toxins9070214] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/29/2017] [Accepted: 06/30/2017] [Indexed: 12/23/2022] Open
Abstract
Most previous studies have focused on analgesic and anti-cancer activities for the conotoxins identified from piscivorous and molluscivorous cone snails, but little attention has been devoted to insecticidal activity of conotoxins from the dominant vermivorous species. As a representative vermivorous cone snail, the Chinese tubular cone snail (Conus betulinus) is the dominant Conus species inhabiting the South China Sea. We sequenced related venom transcriptomes from C. betulinus using both the next-generation sequencing and traditional Sanger sequencing technologies, and a comprehensive library of 215 conotoxin transcripts was constructed. In our current study, six conotoxins with potential insecticidal activity were screened out from our conotoxin library by homologous search with a reported positive control (alpha-conotoxin ImI from C. imperialis) as the query. Subsequently, these conotoxins were synthesized by chemical solid-phase and oxidative folding for further insecticidal activity validation, such as MTT assay, insect bioassay and homology modeling. The final results proved insecticidal activities of our achieved six conotoxins from the transcriptome-based dataset. Interestingly, two of them presented a lot of high insecticidal activity, which supports their usefulness for a trial as insecticides in field investigations. In summary, our present work provides a good example for high throughput development of biological insecticides on basis of the accumulated genomic resources.
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Dutertre S, Nicke A, Tsetlin VI. Nicotinic acetylcholine receptor inhibitors derived from snake and snail venoms. Neuropharmacology 2017. [PMID: 28623170 DOI: 10.1016/j.neuropharm.2017.06.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The nicotinic acetylcholine receptor (nAChR) represents the prototype of ligand-gated ion channels. It is vital for neuromuscular transmission and an important regulator of neurotransmission. A variety of toxic compounds derived from diverse species target this receptor and have been of elemental importance in basic and applied research. They enabled milestone discoveries in pharmacology and biochemistry ranging from the original formulation of the receptor concept, the first isolation and structural analysis of a receptor protein (the nAChR) to the identification, localization, and differentiation of its diverse subtypes and their validation as a target for therapeutic intervention. Among the venom-derived compounds, α-neurotoxins and α-conotoxins provide the largest families and still represent indispensable pharmacological tools. Application of modified α-neurotoxins provided substantial structural and functional details of the nAChR long before high resolution structures were available. α-bungarotoxin represents not only a standard pharmacological tool and label in nAChR research but also for unrelated proteins tagged with a minimal α-bungarotoxin binding motif. A major advantage of α-conotoxins is their smaller size, as well as superior selectivity for diverse nAChR subtypes that allows their development into ligands with optimized pharmacological and chemical properties and potentially novel drugs. In the following, these two groups of nAChR antagonists will be described focusing on their respective roles in the structural and functional characterization of nAChRs and their development into research tools. In addition, we provide a comparative overview of the diverse α-conotoxin selectivities that can serve as a practical guide for both structure activity studies and subtype classification. This article is part of the Special Issue entitled 'Venom-derived Peptides as Pharmacological Tools.'
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Affiliation(s)
- Sébastien Dutertre
- Institut des Biomolécules Max Mousseron, UMR 5247, Université Montpellier - CNRS, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France
| | - Annette Nicke
- Walther Straub Institute for Pharmacology and Toxicology, Ludwig-Maximilians-Universität, Nußbaumstr. 26, 80336 Munich, Germany.
| | - Victor I Tsetlin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya str.16/10, Moscow 117999, Russian Federation
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Cuny H, Yu R, Tae HS, Kompella SN, Adams DJ. α-Conotoxins active at α3-containing nicotinic acetylcholine receptors and their molecular determinants for selective inhibition. Br J Pharmacol 2017; 175:1855-1868. [PMID: 28477355 DOI: 10.1111/bph.13852] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 04/13/2017] [Accepted: 04/24/2017] [Indexed: 01/22/2023] Open
Abstract
Neuronal α3-containing nicotinic acetylcholine receptors (nAChRs) in the peripheral nervous system (PNS) and non-neuronal tissues are implicated in a number of severe disease conditions ranging from cancer to cardiovascular diseases and chronic pain. However, despite the physiological characterization of mouse models and cell lines, the precise pathophysiology of nAChRs outside the CNS remains not well understood, in part because there is a lack of subtype-selective antagonists. α-Conotoxins isolated from cone snail venom exhibit characteristic individual selectivity profiles for nAChRs and, therefore, are excellent tools to study the determinants for nAChR-antagonist interactions. Given that human α3β4 subtype selective α-conotoxins are scarce and this is a major nAChR subtype in the PNS, the design of new peptides targeting this nAChR subtype is desirable. Recent studies using α-conotoxins RegIIA and AuIB, in combination with nAChR site-directed mutagenesis and computational modelling, have shed light onto specific nAChR residues, which determine the selectivity of the α-conotoxins for the human α3β2 and α3β4 subtypes. Publications describing the selectivity profile and binding sites of other α-conotoxins confirm that subtype-selective nAChR antagonists often work through common mechanisms by interacting with the same structural components and sites on the receptor. LINKED ARTICLES This article is part of a themed section on Nicotinic Acetylcholine Receptors. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v175.11/issuetoc.
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Affiliation(s)
- Hartmut Cuny
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, NSW, Australia.,Victor Chang Cardiac Research Institute, Developmental and Stem Cell Biology Division, Sydney, NSW, Australia
| | - Rilei Yu
- Key Laboratory of Marine Drugs, Chinese Ministry of Education, School of Medicine and Pharmacy, Ocean University of China, Qingdao, China.,Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Han-Shen Tae
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, NSW, Australia
| | - Shiva N Kompella
- Faculty of Pharmacy, University of Sydney, Sydney, NSW, Australia
| | - David J Adams
- Illawarra Health and Medical Research Institute (IHMRI), University of Wollongong, Wollongong, NSW, Australia
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Xu M, Zhu X, Yu J, Yu J, Luo S, Wang X. The crystal structure of Ac-AChBP in complex with α-conotoxin LvIA reveals the mechanism of its selectivity towards different nAChR subtypes. Protein Cell 2017; 8:675-685. [PMID: 28585176 PMCID: PMC5563285 DOI: 10.1007/s13238-017-0426-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 04/27/2017] [Indexed: 12/15/2022] Open
Abstract
The α3* nAChRs, which are considered to be promising drug targets for problems such as pain, addiction, cardiovascular function, cognitive disorders etc., are found throughout the central and peripheral nervous system. The α-conotoxin (α-CTx) LvIA has been identified as the most selective inhibitor of α3β2 nAChRs known to date, and it can distinguish the α3β2 nAChR subtype from the α6/α3β2β3 and α3β4 nAChR subtypes. However, the mechanism of its selectivity towards α3β2, α6/α3β2β3, and α3β4 nAChRs remains elusive. Here we report the co-crystal structure of LvIA in complex with Aplysia californica acetylcholine binding protein (Ac-AChBP) at a resolution of 3.4 Å. Based on the structure of this complex, together with homology modeling based on other nAChR subtypes and binding affinity assays, we conclude that Asp-11 of LvIA plays an important role in the selectivity of LvIA towards α3β2 and α3/α6β2β3 nAChRs by making a salt bridge with Lys-155 of the rat α3 subunit. Asn-9 lies within a hydrophobic pocket that is formed by Met-36, Thr-59, and Phe-119 of the rat β2 subunit in the α3β2 nAChR model, revealing the reason for its more potent selectivity towards the α3β2 nAChR subtype. These results provide molecular insights that can be used to design ligands that selectively target α3β2 nAChRs, with significant implications for the design of new therapeutic α-CTxs.
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Affiliation(s)
- Manyu Xu
- The Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, Tsinghua University, Beijing, 100084, China
| | - Xiaopeng Zhu
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, 570228, China
| | - Jinfang Yu
- The Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, Tsinghua University, Beijing, 100084, China
| | - Jinpeng Yu
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, 570228, China
| | - Sulan Luo
- Key Laboratory of Tropical Biological Resources, Ministry of Education, Key Lab for Marine Drugs of Haikou, Hainan University, Haikou, 570228, China.
| | - Xinquan Wang
- The Ministry of Education Key Laboratory of Protein Science, School of Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Collaborative Innovation Center for Biotherapy, Tsinghua University, Beijing, 100084, China.
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Abraham N, Healy M, Ragnarsson L, Brust A, Alewood PF, Lewis RJ. Structural mechanisms for α-conotoxin activity at the human α3β4 nicotinic acetylcholine receptor. Sci Rep 2017; 7:45466. [PMID: 28361878 PMCID: PMC5374441 DOI: 10.1038/srep45466] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Accepted: 03/01/2017] [Indexed: 01/22/2023] Open
Abstract
Nicotinic acetylcholine receptors (nAChR) are therapeutic targets for a range of human diseases. α-Conotoxins are naturally occurring peptide antagonists of nAChRs that have been used as pharmacological probes and investigated as drug leads for nAChR related disorders. However, α-conotoxin interactions have been mostly characterised at the α7 and α3β2 nAChRs, with interactions at other subtypes poorly understood. This study provides novel structural insights into the molecular basis for α-conotoxin activity at α3β4 nAChR, a therapeutic target where subtype specific antagonists have potential to treat nicotine addiction and lung cancer. A co-crystal structure of α-conotoxin LsIA with Lymnaea stagnalis acetylcholine binding protein guided the design and functional characterisations of LsIA analogues that identified the minimum pharmacophore regulating α3β4 antagonism. Interactions of the LsIA R10F with β4 K57 and the conserved -NN- α-conotoxin motif with β4 I77 and I109 conferred α3β4 activity to the otherwise inactive LsIA. Using these structural insights, we designed LsIA analogues with α3β4 activity. This new understanding of the structural basis of protein-protein interactions between α-conotoxins and α3β4 may help rationally guide the development of α3β4 selective antagonists with therapeutic potential.
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Affiliation(s)
- Nikita Abraham
- IMB Centre for Pain Research, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Michael Healy
- IMB Centre for Pain Research, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Lotten Ragnarsson
- IMB Centre for Pain Research, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Andreas Brust
- IMB Centre for Pain Research, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Paul F Alewood
- IMB Centre for Pain Research, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Richard J Lewis
- IMB Centre for Pain Research, Institute for Molecular Bioscience, The University of Queensland, St. Lucia, Queensland 4072, Australia
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High-Affinity α-Conotoxin PnIA Analogs Designed on the Basis of the Protein Surface Topography Method. Sci Rep 2016; 6:36848. [PMID: 27841338 PMCID: PMC5107951 DOI: 10.1038/srep36848] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 10/21/2016] [Indexed: 11/08/2022] Open
Abstract
Despite some success for small molecules, elucidating structure-function relationships for biologically active peptides - the ligands for various targets in the organism - remains a great challenge and calls for the development of novel approaches. Some of us recently proposed the Protein Surface Topography (PST) approach, which benefits from a simplified representation of biomolecules' surface as projection maps, which enables the exposure of the structure-function dependencies. Here, we use PST to uncover the "activity pattern" in α-conotoxins - neuroactive peptides that effectively target nicotinic acetylcholine receptors (nAChRs). PST was applied in order to design several variants of the α-conotoxin PnIA, which were synthesized and thoroughly studied. Among the best was PnIA[R9, L10], which exhibits nanomolar affinity for the α7 nAChR, selectivity and a slow wash-out from this target. Importantly, these mutations could hardly be delineated by "standard" structure-based drug design. The proposed combination of PST with a set of experiments proved very efficient for the rational construction of new bioactive molecules.
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Residues Responsible for the Selectivity of α-Conotoxins for Ac-AChBP or nAChRs. Mar Drugs 2016; 14:md14100173. [PMID: 27727162 PMCID: PMC5082321 DOI: 10.3390/md14100173] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 09/20/2016] [Accepted: 09/21/2016] [Indexed: 12/22/2022] Open
Abstract
Nicotinic acetylcholine receptors (nAChRs) are targets for developing new drugs to treat severe pain, nicotine addiction, Alzheimer disease, epilepsy, etc. α-Conotoxins are biologically and chemically diverse. With 12–19 residues and two disulfides, they can be specifically selected for different nAChRs. Acetylcholine-binding proteins from Aplysia californica (Ac-AChBP) are homologous to the ligand-binding domains of nAChRs and pharmacologically similar. X-ray structures of the α-conotoxin in complex with Ac-AChBP in addition to computer modeling have helped to determine the binding site of the important residues of α-conotoxin and its affinity for nAChR subtypes. Here, we present the various α-conotoxin residues that are selective for Ac-AChBP or nAChRs by comparing the structures of α-conotoxins in complex with Ac-AChBP and by modeling α-conotoxins in complex with nAChRs. The knowledge of these binding sites will assist in the discovery and design of more potent and selective α-conotoxins as drug leads.
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