1
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Talhout R, Leventhal AM. Coolants, organic acids, flavourings and other additives that facilitate inhalation of tobacco and nicotine products: implications for regulation. Tob Control 2024:tc-2024-058738. [PMID: 39256038 DOI: 10.1136/tc-2024-058738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2024] [Accepted: 08/19/2024] [Indexed: 09/12/2024]
Abstract
To inform regulatory policy, this article summarises findings on inhalation facilitation from the ninth report of the WHO Study Group on Tobacco Product Regulation. Some additives counteract the harshness and bitterness of tobacco and nicotine product aerosols, making them easier to inhale. Additives that promote inhalability may perpetuate and increase the use of inhaled tobacco and nicotine products, especially by young people. Thus, as a class, additives that facilitate inhalation are an important regulatory target to prevent tobacco and nicotine product uptake. We defined inhalation facilitation as modifications to products during manufacturing that enhance the sensory experience and (potentially) behaviours associated with inhalation (eg, deeper puffs, faster inhalation, larger puff volume, shorter intervals in between puffs and use episodes). Evidence review showed that: (a) menthol and synthetic coolants decrease irritation caused by aerosol constituents by activating sensory perception receptors (eg, cooling receptors) and may promote dependence in inexperienced users; (b) acid additives and sugars, which lower the pH of aerosols and shift nicotine from free-base to protonated salt forms, reduce harshness and increase blood nicotine yield; (c) e-cigarette flavourings perceived as sweet or fruity reduce subjective bitterness, increase attractiveness and may escalate use, although their effects on perceived harshness are inconclusive; (d) sugars in tobacco impart sweet sensations, but limited industry-independent data preclude strong conclusions for sugars' roles in inhalation facilitation. Given these findings, WHO policy recommendations suggest that regulators might consider banning ingredients that facilitate inhalation in all commercial inhaled tobacco and nicotine products.
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Affiliation(s)
- Reinskje Talhout
- Centre for Health Protection, Dutch National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Adam M Leventhal
- Preventive Medicine, Keck School of Medicine of the University of Southern California, Los Angeles, California, USA
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2
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Infield DT, Schene ME, Galpin JD, Ahern CA. Genetic Code Expansion for Mechanistic Studies in Ion Channels: An (Un)natural Union of Chemistry and Biology. Chem Rev 2024. [PMID: 39207057 DOI: 10.1021/acs.chemrev.4c00306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Ion channels play central roles in biology and human health by catalyzing the transmembrane flow of electrical charge. These proteins are ideal targets for genetic code expansion (GCE) methods because it is feasible to measure ion channel activity from miniscule amounts of protein and to analyze the resulting data via rigorous, established biophysical methods. In an ideal scenario, the encoding of synthetic, noncanonical amino acids via GCE allows the experimenter to ask questions inaccessible to traditional methods. For this reason, GCE has been successfully applied to a variety of ligand- and voltage-gated channels wherein extensive structural, functional, and pharmacological data exist. Here, we provide a comprehensive summary of GCE as applied to ion channels. We begin with an overview of the methods used to encode noncanonical amino acids in channels and then describe mechanistic studies wherein GCE was used for photochemistry (cross-linking; caged amino acids) and atomic mutagenesis (isosteric manipulation of charge and aromaticity; backbone mutation). Lastly, we cover recent advances in the encoding of fluorescent amino acids for the real-time study of protein conformational dynamics.
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Affiliation(s)
- Daniel T Infield
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Miranda E Schene
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Jason D Galpin
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, Iowa 52242, United States
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3
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Nuruzzaman M, Colella BM, Nizam ZM, Cho IJ, Zagorski J, Ohata J. Redox-neutral, metal-free tryptophan labeling of polypeptides in hexafluoroisopropanol (HFIP). RSC Chem Biol 2024; 5:d4cb00142g. [PMID: 39234575 PMCID: PMC11368038 DOI: 10.1039/d4cb00142g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 08/23/2024] [Indexed: 09/06/2024] Open
Abstract
Despite the unmet needs for chemical tools to study biological roles of tryptophan in living systems, there has been a lack of chemical modification methods for tryptophan residues that can be used in cellular environments. Driven by a preliminary computational study of our previous research, this work experimentally examined our hypotheses to translate the metal-catalyzed tryptophan modification method in hexafluoroisopropanol (HFIP) into a metal-free process. While one of the hypotheses merely confirmed the superiority of the thiophene-ethanol reagent developed in the previous report, the second hypothesis resulted in the identification of a trifluoroborate salt and an acidic ionic liquid as alternatives for the catalysis. Labeling of lysates of a human cell line was achieved with the acidic ionic liquid catalyst, where negative impacts of the tryptophan labeling and HFIP medium on the cellular samples were apparently insignificant. Because the labeling process does not require any redox mediators and is a formal redox-neutral reaction, the metal-free approach would be of use for tryptophan biology research potentially related to their various redox roles.
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Affiliation(s)
- Mohammad Nuruzzaman
- Department of Chemistry, North Carolina State University Raleigh North Carolina 27695 USA
| | - Brandon M Colella
- Department of Chemistry, North Carolina State University Raleigh North Carolina 27695 USA
| | - Zeinab M Nizam
- Department of Chemistry, North Carolina State University Raleigh North Carolina 27695 USA
| | - Isaac JiHoon Cho
- Department of Chemistry, North Carolina State University Raleigh North Carolina 27695 USA
| | - Julia Zagorski
- Department of Chemistry, North Carolina State University Raleigh North Carolina 27695 USA
| | - Jun Ohata
- Department of Chemistry, North Carolina State University Raleigh North Carolina 27695 USA
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4
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Talandashti R, Moqadam M, Reuter N. Model Mechanism for Lipid Uptake by the Human STARD2/PC-TP Phosphatidylcholine Transfer Protein. J Phys Chem Lett 2024; 15:8287-8295. [PMID: 39143857 PMCID: PMC11331517 DOI: 10.1021/acs.jpclett.4c01743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2024] [Revised: 07/11/2024] [Accepted: 07/16/2024] [Indexed: 08/16/2024]
Abstract
The human StAR-related lipid transfer domain protein 2 (STARD2), also known as phosphatidylcholine (PC) transfer protein, is a single-domain lipid transfer protein thought to transfer PC lipids between intracellular membranes. We performed extensive μs-long molecular dynamics simulations of STARD2 of its apo and holo forms in the presence or absence of complex lipid bilayers. The simulations in water reveal ligand-dependent conformational changes. In the 2 μs-long simulations of apo STARD2 in the presence of a lipid bilayer, we observed spontaneous reproducible PC lipid uptake into the protein hydrophobic cavity. We propose that the lipid extraction mechanism involves one to two metastable states stabilized by choline-tyrosine or choline-tryptophane cation-π interactions. Using free energy perturbation, we evaluate that PC-tyrosine cation-π interactions contribute 1.8 and 2.5 kcal/mol to the affinity of a PC-STARD2 metastable state, thus potentially providing a significant decrease of the energy barrier required for lipid desorption.
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Affiliation(s)
- Reza Talandashti
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Mahmoud Moqadam
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
| | - Nathalie Reuter
- Department
of Chemistry, University of Bergen, Bergen 5020, Norway
- Computational
Biology Unit, Department of Informatics, University of Bergen, Bergen 5020, Norway
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5
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López-Sánchez U, Munro LJ, Ladefoged LK, Pedersen AJ, Brun CC, Lyngby SM, Baud D, Juillan-Binard C, Pedersen MG, Lummis SCR, Bang-Andersen B, Schiøtt B, Chipot C, Schoehn G, Neyton J, Dehez F, Nury H, Kristensen AS. Structural determinants for activity of the antidepressant vortioxetine at human and rodent 5-HT 3 receptors. Nat Struct Mol Biol 2024; 31:1232-1242. [PMID: 38698207 DOI: 10.1038/s41594-024-01282-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 03/19/2024] [Indexed: 05/05/2024]
Abstract
Vortioxetine (VTX) is a recently approved antidepressant that targets a variety of serotonin receptors. Here, we investigate the drug's molecular mechanism of operation at the serotonin 5-HT3 receptor (5-HT3R), which features two properties: VTX acts differently on rodent and human 5-HT3R, and VTX appears to suppress any subsequent response to agonists. Using a combination of cryo-EM, electrophysiology, voltage-clamp fluorometry and molecular dynamics, we show that VTX stabilizes a resting inhibited state of the mouse 5-HT3R and an agonist-bound-like state of human 5-HT3R, in line with the functional profile of the drug. We report four human 5-HT3R structures and show that the human receptor transmembrane domain is intrinsically fragile. We also explain the lack of recovery after VTX administration via a membrane partition mechanism.
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Affiliation(s)
- Uriel López-Sánchez
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
- Program in Cellular and Molecular Medicine, Boston Children's Hospital and Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Lachlan Jake Munro
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | | | - Anders Juel Pedersen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Christian Colding Brun
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Signe Meisner Lyngby
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Delphine Baud
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | | | | | - Sarah C R Lummis
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | | | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Aarhus, Denmark
| | - Christophe Chipot
- Université de Lorraine, CNRS, LPCT, Nancy, France
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy, France
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Guy Schoehn
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Jacques Neyton
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France
| | - Francois Dehez
- Université de Lorraine, CNRS, LPCT, Nancy, France
- Laboratoire International Associé CNRS and University of Illinois at Urbana-Champaign, Vandoeuvre-les-Nancy, France
| | - Hugues Nury
- University Grenoble Alpes, CNRS, CEA, IBS, Grenoble, France.
| | - Anders S Kristensen
- Department of Drug Design and Pharmacology, University of Copenhagen, Copenhagen, Denmark.
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6
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Zhang Z, Yang Q, Dong Y, Wang L, Niu R, Xia J, Bi Y, Liu G. Sirtuin 2 regulates neutrophil functions through NAD + synthesis pathway in virus infection. iScience 2024; 27:110184. [PMID: 38974970 PMCID: PMC11226967 DOI: 10.1016/j.isci.2024.110184] [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: 01/11/2024] [Revised: 04/12/2024] [Accepted: 06/01/2024] [Indexed: 07/09/2024] Open
Abstract
Neutrophils play an important role in antiviral immunity, but the underlying mechanisms remain unclear. Here, we found that SIRT2 deficiency inhibited the infiltration of neutrophils, as well as the secretion of inflammatory cytokines and the formation of neutrophil extracellular traps (NETs), ameliorating disease symptoms during acute respiratory virus infection. Mechanistically, SIRT2 deficiency upregulates quinolinic acid (QA)-producing enzyme 3-hydroxyanthranilate oxygenase (3-HAO) and leads to expression of quinolinate phosphoribosyltransferase (QPRT), which promotes the synthesis of QA for NAD+ and limits viral infection when de novo NAD+ synthesis is blocked. Tryptophan-2,3-oxygenase expressed in epithelial cells metabolizes tryptophan to produce kynurenine and 3-hydroxyaminobenzoic acid, which is a source of intracellular QA in neutrophils. Thus, our findings reveal a previously unrecognized QPRT-mediated switch in NAD+ metabolism by exploiting neutrophil-derived QA as an alternative source of replenishing intracellular NAD+ pools induced by SIRT2 to regulate neutrophil functions during virus infection, with implications for future immunotherapy approaches.
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Affiliation(s)
- Zhiyuan Zhang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Qiuli Yang
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yingjie Dong
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Likun Wang
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing 100071, China
| | - Ruiying Niu
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Jingxuan Xia
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yujing Bi
- State Key Laboratory of Pathogen and Biosecurity, Academy of Military Medical Science, Beijing 100071, China
| | - Guangwei Liu
- Key Laboratory of Cell Proliferation and Regulation Biology, Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
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7
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Söllner J, Derler I. Genetic code expansion, an emerging tool in the Ca 2+ ion channel field. J Physiol 2024; 602:3297-3313. [PMID: 38695316 DOI: 10.1113/jp285840] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Accepted: 04/15/2024] [Indexed: 07/17/2024] Open
Abstract
Various methods for characterizing binding forces as well as for monitoring and remote control of ion channels are still emerging. A recent innovation is the direct incorporation of unnatural amino acids (UAAs) with corresponding biophysical or biochemical properties, which are integrated using genetic code expansion technology. Minimal changes to natural amino acids, which are achieved by chemical synthesis of corresponding UAAs, are valuable tools to provide insight into the contributions of physicochemical properties of side chains in binding events. To gain unique control over the conformational changes or function of ion channels, a series of light-sensitive, chemically reactive and posttranslationally modified UAAs have been developed and utilized. Here, we present the existing UAA tools, their mode of action, their potential and limitations as well as their previous applications to Ca2+-permeable ion channels.
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Affiliation(s)
- Julia Söllner
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz, Austria
| | - Isabella Derler
- Institute of Biophysics, JKU Life Science Center, Johannes Kepler University Linz, Linz, Austria
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8
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Ganguly T, Das S, Maity D, Baitalik S. Luminescent Ruthenium-Terpyridine Complexes Coupled with Stilbene-Appended Naphthalene, Anthracene, and Pyrene Motifs Demonstrate Fluoride Ion Sensing and Reversible Trans-Cis Photoisomerization. Inorg Chem 2024; 63:6883-6897. [PMID: 38567656 DOI: 10.1021/acs.inorgchem.4c00339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
A new family of luminescent heteroleptic Ru(II)-terpyridine complexes coupled with stilbene-appended naphthalene, anthracene, and pyrene motifs is reported. Each of the complexes features moderately intense emission at room temperature having a lifetime of 16.7 ns for naphthalene and 11.4 ns for anthracene, while a substantially elevated lifetime of 8.3 μs was observed for the pyrene derivative. All the three complexes display a reversible couple in the positive potential window due to Ru2+/Ru3+ oxidation but multiple reversible and/or quasi-reversible peaks in the negative potential domain because of the reduction of the terpyridine moieties. All the complexes selectively sense F- among the studied anions via the intermediary of different noncovalent interactions. The interaction event is monitored through absorption, emission, and 1H and 19F NMR spectroscopy. Additionally, upon utilizing the stilbene motif, reversible trans-cis isomerization of the complexes has been undertaken upon alternate treatment of visible and UV light so that the complexes can act as potential photomolecular switches. We also carried out the anion sensing characterization of the cis form of the complexes. Theoretical calculation employing density functional theory is also executed for a selective complex (naphthalene derivative) to elucidate different noncovalent interactions that are operative during the complex-fluoride interplay.
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Affiliation(s)
- Tanusree Ganguly
- Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata 700032, India
| | - Soumi Das
- Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata 700032, India
| | - Dinesh Maity
- Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata 700032, India
- Department of Chemistry, Katwa College, Purba Bardhaman, West Bengal 713130, India
| | - Sujoy Baitalik
- Department of Chemistry, Inorganic Chemistry Section, Jadavpur University, Kolkata 700032, India
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9
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Suating P, Ewe MB, Kimberly LB, Arman HD, Wherritt DJ, Urbach AR. Peptide recognition by a synthetic receptor at subnanomolar concentrations. Chem Sci 2024; 15:5133-5142. [PMID: 38577360 PMCID: PMC10988627 DOI: 10.1039/d4sc01122h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 03/07/2024] [Indexed: 04/06/2024] Open
Abstract
This paper describes the discovery and characterization of a dipeptide sequence, Lys-Phe, that binds to the synthetic receptor cucurbit[8]uril (Q8) in neutral aqueous solution with subnanomolar affinity when located at the N-terminus. The thermodynamic and structural basis for the binding of Q8 to a series of four pentapeptides was characterized by isothermal titration calorimetry, NMR spectroscopy, and X-ray crystallography. Submicromolar binding affinity was observed for the peptides Phe-Lys-Gly-Gly-Tyr (FKGGY, 0.3 μM) and Tyr-Leu-Gly-Gly-Gly (YLGGG, 0.2 μM), whereas the corresponding sequence isomers Lys-Phe-Gly-Gly-Tyr (KFGGY, 0.3 nM) and Leu-Tyr-Gly-Gly-Gly (LYGGG, 1.2 nM) bound to Q8 with 1000-fold and 170-fold increases in affinity, respectively. To our knowledge, these are the highest affinities reported between a synthetic receptor and an unmodified peptide. The high-resolution crystal structures of the Q8·Tyr-Leu-Gly-Gly-Gly and Q8·Leu-Tyr-Gly-Gly-Gly complexes have enabled a detailed analysis of the structural determinants for molecular recognition. The high affinity, sequence-selectivity, minimal size of the target binding site, reversibility in the presence of a competitive guest, compatibility with aqueous media, and low toxicity of Q8 should aid in the development of applications involving low concentrations of target polypeptides.
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Affiliation(s)
- Paolo Suating
- Department of Chemistry, Trinity University 1 Trinity Place San Antonio TX 78212 USA
| | - Marc B Ewe
- Department of Chemistry, Trinity University 1 Trinity Place San Antonio TX 78212 USA
| | - Lauren B Kimberly
- Department of Chemistry, Trinity University 1 Trinity Place San Antonio TX 78212 USA
| | - Hadi D Arman
- Department of Chemistry, University of Texas at San Antonio 1 UTSA Circle San Antonio TX 78249 USA
| | - Daniel J Wherritt
- Department of Chemistry, University of Texas at San Antonio 1 UTSA Circle San Antonio TX 78249 USA
| | - Adam R Urbach
- Department of Chemistry, Trinity University 1 Trinity Place San Antonio TX 78212 USA
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10
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Munafó JP, Biscussi B, Obiol D, Costabel M, Bouzat C, Murray AP, Antollini S. New Multitarget Molecules Derived from Caffeine as Potentiators of the Cholinergic System. ACS Chem Neurosci 2024; 15:994-1009. [PMID: 38407056 DOI: 10.1021/acschemneuro.3c00710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
Cholinergic deficit is a characteristic factor of several pathologies, such as myasthenia gravis, some types of congenital myasthenic syndromes, and Alzheimer's Disease. Two molecular targets for its treatment are acetylcholinesterase (AChE) and nicotinic acetylcholine receptor (nAChR). In previous studies, we found that caffeine behaves as a partial nAChR agonist and confirmed that it inhibits AChE. Here, we present new bifunctional caffeine derivatives consisting of a theophylline ring connected to amino groups by different linkers. All of them were more potent AChE inhibitors than caffeine. Furthermore, although some of them also activated muscle nAChR as partial agonists, not all of them stabilized nAChR in its desensitized conformation. To understand the molecular mechanism underlying these results, we performed docking studies on AChE and nAChR. The nAChR agonist behavior of the compounds depends on their accessory group, whereas their ability to stabilize the receptor in a desensitized state depends on the interactions of the linker at the binding site. Our results show that the new compounds can inhibit AChE and activate nAChR with greater potency than caffeine and provide further information on the modulation mechanisms of pharmacological targets for the design of novel therapeutic interventions in cholinergic deficit.
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Affiliation(s)
- Juan Pablo Munafó
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur and Consejo Nacional de Investigaciones Científicas y Técnicas, Camino La Carrindanga km 7, Bahía Blanca 8000, Argentina
| | - Brunella Biscussi
- Instituto de Química del Sur, Departamento de Química, Universidad Nacional del Sur and Consejo Nacional de Investigaciones Científicas y Técnicas, Avda. Alem 1253, Bahía Blanca 8000, Argentina
| | - Diego Obiol
- Grupo de Biofísica, Instituto de Física del Sur, Departamento de Física, Universidad Nacional del Sur and Consejo Nacional de Investigaciones Científicas y Técnicas, Avda. Alem 1253, Bahía Blanca 8000, Argentina
| | - Marcelo Costabel
- Grupo de Biofísica, Instituto de Física del Sur, Departamento de Física, Universidad Nacional del Sur and Consejo Nacional de Investigaciones Científicas y Técnicas, Avda. Alem 1253, Bahía Blanca 8000, Argentina
| | - Cecilia Bouzat
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur and Consejo Nacional de Investigaciones Científicas y Técnicas, Camino La Carrindanga km 7, Bahía Blanca 8000, Argentina
| | - Ana Paula Murray
- Instituto de Química del Sur, Departamento de Química, Universidad Nacional del Sur and Consejo Nacional de Investigaciones Científicas y Técnicas, Avda. Alem 1253, Bahía Blanca 8000, Argentina
| | - Silvia Antollini
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur and Consejo Nacional de Investigaciones Científicas y Técnicas, Camino La Carrindanga km 7, Bahía Blanca 8000, Argentina
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11
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Guzman-Vallejos MS, Ramirez-Cando LJ, Aguayo L, Ballaz SJ. Molecular Docking Analysis at the Human α7-nAChR and Proliferative and Evoked-Calcium Changes in SH-SY5Y Cells by Imidacloprid and Acetamiprid Insecticides. Neurotox Res 2024; 42:16. [PMID: 38376791 DOI: 10.1007/s12640-024-00697-0] [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: 11/06/2023] [Revised: 01/24/2024] [Accepted: 02/14/2024] [Indexed: 02/21/2024]
Abstract
Acetamiprid (ACE) and Imidacloprid (IMI) are widely-used neonicotinoid insecticides (NNIs) with functional activity at human acetylcholine nicotinic receptors and, therefore, with putative toxic effects. The objective of this study was the evaluation of the interactions between NNIs and α7-nAChR, as this receptor keeps intracellular Ca2+ ([Ca2+]i) to an optimum for an adequate neuronal functioning. Possible interactions between NNIs and the cryo-EM structure of the human α-7 nAChR were identified by molecular docking. Additionally, NNI effects were analyzed in neuroblastoma SH-SY5Y cells, as they naturally express α-7 nAChRs. Functional studies included proliferative/cytotoxic effects (MTT test) in undifferentiated SH-SY-5Y cells and indirect measurements of [Ca2+]i transients in retinoic acid-differentiated SH-SY-5Y cells loaded with Fluo-4 AM. Docking analysis showed that the binding of IMI and ACE occurred at the same aromatic cage that the specific α-7 nAChR agonist EVP-6124. IMI showed a better docking strength than ACE. According to the MTT assays, low doses (10-50 µM) of IMI better than ACE stimulated neuroblastoma cell proliferation. At higher doses (250-500 µM), IMI also prevailed over ACE and dose-dependently triggered more abrupt fluorescence changes due to [Ca2+]i mobilization in differentiated SH-SY5Y neurons. Indeed, only IMI blunted nicotine-evoked intracellular fluorescence stimulation (i.e., nicotine cross-desensitization). Summarizing, IMI demonstrated a superior docking strength and more robust cellular responses compared to ACE, which were likely associated with a stronger activity at α-7nAChRs. Through the interaction with α-7nAChRs, IMI would demonstrate its high neurotoxic potential for humans. More research is needed for investigating the proliferative effects of IMI in neuroblastoma cells.
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Affiliation(s)
| | - Lenin J Ramirez-Cando
- School of Biological Sciences & Engineering, Universidad Yachay Tech, Urcuquí, Ecuador
| | - Luis Aguayo
- School of Biological Sciences, Universidad de Concepcion, Concepción, Chile
| | - Santiago J Ballaz
- School of Medicine, Universidad Espíritu Santo, Ave. Samborondón 5, Samborondón, 0901952, Ecuador.
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12
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Schene ME, Infield DT, Ahern CA. Expression and purification of fluorinated proteins from mammalian suspension culture. Methods Enzymol 2024; 696:341-354. [PMID: 38658087 DOI: 10.1016/bs.mie.2024.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The site-specific encoding of noncanonical amino acids allows for the introduction of rationalized chemistry into a target protein. Of the methods that enable this technology, evolved tRNA and synthetase pairs offer the potential for expanded protein production and purification. Such an approach combines the versatility of solid-phase peptide synthesis with the scalable features of recombinant protein production. We describe the large scale production and purification of eukaryotic proteins bearing fluorinated phenylalanine in mammalian suspension cell preparations. Downstream applications of this approach include scalable recombinant protein preparation for ligand binding assays with small molecules and ligands, protein structure determination, and protein stability assays.
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Affiliation(s)
- Miranda E Schene
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Daniel T Infield
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA
| | - Christopher A Ahern
- Department of Molecular Physiology and Biophysics, University of Iowa, Iowa City, IA, USA.
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13
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Rusali LE, Lopez-Hernandez AM, Kremiller KM, Kulkarni GC, Gour A, Straub CJ, Argade MD, Peters CJ, Sharma A, Toll L, Cippitelli A, Riley AP. Synthesis of α3β4 Nicotinic Acetylcholine Receptor Modulators Derived from Aristoquinoline That Reduce Reinstatement of Cocaine-Seeking Behavior. J Med Chem 2024; 67:529-542. [PMID: 38151460 PMCID: PMC10872344 DOI: 10.1021/acs.jmedchem.3c01758] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Growing evidence suggests that inhibition of the α3β4 nicotinic acetylcholine receptor (nAChR) represents a promising therapeutic strategy to treat cocaine use disorder. Recently, aristoquinoline (1), an alkaloid from Aristotelia chilensis, was identified as an α3β4-selective nAChR inhibitor. Here, we prepared 22 derivatives of 1 and evaluated their ability to inhibit the α3β4 nAChR. These studies revealed structure-activity trends and several compounds with increased potency compared to 1 with few off-target liabilities. Additional mechanistic studies indicated that these compounds inhibit the α3β4 nAChR noncompetitively, but do not act as channel blockers, suggesting they are negative allosteric modulators. Finally, using a cocaine-primed reinstatement paradigm, we demonstrated that 1 significantly attenuates drug-seeking behavior in an animal model of cocaine relapse. The results from these studies further support a role for the α3β4 nAChR in the addictive properties of cocaine and highlight the possible utility of aristoquinoline derivatives in treating cocaine use disorder.
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Affiliation(s)
- Lisa E. Rusali
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL 60612, United States
| | - Ana M. Lopez-Hernandez
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL 60612, United States
| | - Kyle M. Kremiller
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL 60612, United States
| | - Gauri C. Kulkarni
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612, United States
| | - Abhishek Gour
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL 32610, United States
| | - Carolyn J. Straub
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL 60612, United States
| | - Malaika D. Argade
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL 60612, United States
| | - Christian J. Peters
- Department of Anatomy and Cell Biology, College of Medicine, University of Illinois Chicago, Chicago, IL 60612, United States
| | - Abhisheak Sharma
- Department of Pharmaceutics, College of Pharmacy, University of Florida, Gainesville, FL 32610, United States
| | - Lawrence Toll
- Biomedical Science Department, Charles E. Schmidt College of Medicine, Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, FL 33458, United States
| | - Andrea Cippitelli
- Biomedical Science Department, Charles E. Schmidt College of Medicine, Stiles-Nicholson Brain Institute, Florida Atlantic University, Jupiter, FL 33458, United States
| | - Andrew P. Riley
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Illinois Chicago, Chicago, IL 60612, United States
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14
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Huo K, Yang Y, Yang T, Zhang W, Shao J. Identification of Drug Targets and Agents Associated with Ferroptosis-related Osteoporosis through Integrated Network Pharmacology and Molecular Docking Technology. Curr Pharm Des 2024; 30:1103-1114. [PMID: 38509680 PMCID: PMC11348511 DOI: 10.2174/0113816128288225240318045050] [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: 10/19/2023] [Revised: 02/16/2024] [Accepted: 02/29/2024] [Indexed: 03/22/2024]
Abstract
BACKGROUND Osteoporosis is a systemic bone disease characterized by progressive reduction of bone mineral density and degradation of trabecular bone microstructure. Iron metabolism plays an important role in bone; its imbalance leads to abnormal lipid oxidation in cells, hence ferroptosis. In osteoporosis, however, the exact mechanism of ferroptosis has not been fully elucidated. OBJECTIVE The main objective of this project was to identify potential drug target proteins and agents for the treatment of ferroptosis-related osteoporosis. METHODS In the current study, we investigated the differences in gene expression of bone marrow mesenchymal stem cells between osteoporosis patients and normal individuals using bioinformatics methods to obtain ferroptosis-related genes. We could predict their protein structure based on the artificial intelligence database of AlphaFold, and their target drugs and binding sites with the network pharmacology and molecular docking technology. RESULTS We identified five genes that were highly associated with osteoporosis, such as TP53, EGFR, TGFB1, SOX2 and MAPK14, which, we believe, can be taken as the potential markers and targets for the diagnosis and treatment of osteoporosis. Furthermore, we observed that these five genes were highly targeted by resveratrol to exert a therapeutic effect on ferroptosis-related osteoporosis. CONCLUSION We examined the relationship between ferroptosis and osteoporosis based on bioinformatics and network pharmacology, presenting a promising direction to the pursuit of the exact molecular mechanism of osteoporosis so that a new target can be discovered for the treatment of osteoporosis.
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Affiliation(s)
- Kailun Huo
- Postgraduate Training Base in Shanghai Gongli Hospital, Ningxia Medical University, Yinchuan, Ningxia Hui-Autonomous Region 750004, China
| | - Yiqian Yang
- Postgraduate Training Base in Shanghai Gongli Hospital, Ningxia Medical University, Yinchuan, Ningxia Hui-Autonomous Region 750004, China
| | - Tieyi Yang
- Department of Orthopedics, Shanghai Pudong New Area Gongli Hospital, Shanghai 200135, China
- School of Gongli Hospital Medical Technology, University of Shanghai for Science and Technology, Shanghai 200093, China
| | - Weiwei Zhang
- Department of Urology, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Jin Shao
- Department of Orthopedics, Shanghai Pudong New Area Gongli Hospital, Shanghai 200135, China
- School of Gongli Hospital Medical Technology, University of Shanghai for Science and Technology, Shanghai 200093, China
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15
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Sam S, Sung S, Kim D. Sensitive Detection of Biomolecular Adsorption by a Low-Density Surfactant Layer Using Sum-Frequency Vibrational Spectroscopy. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:17412-17419. [PMID: 38050679 DOI: 10.1021/acs.langmuir.3c02546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/06/2023]
Abstract
Small molecules or proteins interact with a biomembrane in various ways for molecular recognition, structure stabilization, and transmembrane signaling. In this study, 1,2-dipalmitoyl-3-trimethylammonium-propane (DPTAP), having a choline group, was used to investigate this interaction by using sum-frequency vibrational spectroscopy. The sum-frequency spectrum characteristic of a neat monolayer changed to that of a bare air/water interface at a larger molecular area of the DPTAP molecules due to local laser heating. Upon introduction of the aromatic molecules in the subphase at around 120 Å2 per molecule, the sum-frequency signal suddenly reappeared due to molecular adhesion, and this was utilized to probe the adsorption of the aromatic ring molecules in the water subphase to the choline headgroup of the DPTAP by cation-π interaction. The onset concentrations of this sum-frequency signal change allowed a comparison of the relative interaction strengths between different aromatic molecules. A zwitterionic surfactant molecule (DPPC) was found to interact weakly compared to the cationic DPTAP molecule.
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Affiliation(s)
- Sokhuoy Sam
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul, 04107, Korea
| | - Siheon Sung
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul, 04107, Korea
| | - Doseok Kim
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul, 04107, Korea
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16
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Afshinpour M, Smith LA, Chakravarty S. AQcalc: A web server that identifies weak molecular interactions in protein structures. Protein Sci 2023; 32:e4762. [PMID: 37596782 PMCID: PMC10503417 DOI: 10.1002/pro.4762] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/25/2023] [Accepted: 08/15/2023] [Indexed: 08/20/2023]
Abstract
Weak molecular interactions play an important role in protein structure and function. Computational tools that identify weak molecular interactions are, therefore, valuable for the study of proteins. Here, we present AQcalc, a web server (https://aqcalcbiocomputing.com/) that can be used to identify anion-quadrupole (AQ) interactions, which are weak interactions involving aromatic residue (Trp, Tyr, and Phe) ring edges and anions (Asp, Glu, and phosphate ion) both within proteins and at their interfaces (protein-protein, protein-nucleic acids, and protein-lipid bilayer). AQcalc identifies AQ interactions as well as clusters involving AQ, cation-π, and salt bridges, among others. Utilizing AQcalc we analyzed weak interactions in protein models, even in the absence of experimental structures, to understand the contributions of weak interactions to deleterious structural changes, including those associated with oncogenic and germline disease variants. We identified several deleterious variants with disrupted AQ interactions (comparable in frequency to cation-π disruptions). Amyloid fibrils utilize AQ to bury anions at frequencies that far exceed those observed for globular proteins. AQ interactions were detected three and five times more frequently than the hydrogen-bonded AQ (HBAQ) in fibril structures and protein-lipid bilayer interfaces, respectively. By contrast, AQ and HBAQ interactions were detected with similar frequencies in globular proteins. Collectively, these findings suggest AQcalc will be effective in facilitating fine structural analysis. As other web utilities designed to identify protein residue interaction networks do not report AQ interactions, wide use of AQcalc will enrich our understanding of residue interaction networks and facilitate hypothesis testing by identifying and experimentally characterizing these comparably weak but important interactions.
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Affiliation(s)
- Maral Afshinpour
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
| | - Logan A. Smith
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
| | - Suvobrata Chakravarty
- Department of Chemistry & BiochemistrySouth Dakota State UniversityBrookingsSouth DakotaUSA
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17
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Grillberger K, Cöllen E, Trivisani CI, Blum J, Leist M, Ecker GF. Structural Insights into Neonicotinoids and N-Unsubstituted Metabolites on Human nAChRs by Molecular Docking, Dynamics Simulations, and Calcium Imaging. Int J Mol Sci 2023; 24:13170. [PMID: 37685977 PMCID: PMC10487998 DOI: 10.3390/ijms241713170] [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: 07/28/2023] [Revised: 08/10/2023] [Accepted: 08/12/2023] [Indexed: 09/10/2023] Open
Abstract
Neonicotinoid pesticides were initially designed in order to achieve species selectivity on insect nicotinic acetylcholine receptors (nAChRs). However, concerns arose when agonistic effects were also detected in human cells expressing nAChRs. In the context of next-generation risk assessments (NGRAs), new approach methods (NAMs) should replace animal testing where appropriate. Herein, we present a combination of in silico and in vitro methodologies that are used to investigate the potentially toxic effects of neonicotinoids and nicotinoid metabolites on human neurons. First, an ensemble docking study was conducted on the nAChR isoforms α7 and α3β4 to assess potential crucial molecular initiating event (MIE) interactions. Representative docking poses were further refined using molecular dynamics (MD) simulations and binding energy calculations using implicit solvent models. Finally, calcium imaging on LUHMES neurons confirmed a key event (KE) downstream of the MIE. This method was also used to confirm the predicted agonistic effect of the metabolite descyano-thiacloprid (DCNT).
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Affiliation(s)
- Karin Grillberger
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
| | - Eike Cöllen
- In Vitro Toxicology and Biomedicine, University of Konstanz, 78457 Konstanz, Germany
| | | | - Jonathan Blum
- In Vitro Toxicology and Biomedicine, University of Konstanz, 78457 Konstanz, Germany
| | - Marcel Leist
- In Vitro Toxicology and Biomedicine, University of Konstanz, 78457 Konstanz, Germany
| | - Gerhard F. Ecker
- Department of Pharmaceutical Sciences, University of Vienna, 1090 Vienna, Austria
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18
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Papke RL, Quadri M, Gulsevin A. Silent agonists for α7 nicotinic acetylcholine receptors. Pharmacol Res 2023; 190:106736. [PMID: 36940890 DOI: 10.1016/j.phrs.2023.106736] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/10/2022] [Revised: 03/07/2023] [Accepted: 03/14/2023] [Indexed: 03/23/2023]
Abstract
We discuss models for the activation and desensitization of α7 nicotinic acetylcholine receptors (nAChRs) and the effects of efficacious type II positive allosteric modulators (PAMs) that destabilize α7 desensitized states. Type II PAMs such as PNU-120596 can be used to distinguish inactive compounds from silent agonists, compounds that produce little or no channel activation but stabilize the non-conducting conformations associated with desensitization. We discuss the effects of α7 nAChRs in cells of the immune system and their roles in modulating inflammation and pain through what has come to be known as the cholinergic anti-inflammatory system (CAS). Cells controlling CAS do not generate ion channel currents but rather respond to α7 drugs by modulating intracellular signaling pathways analogous to the effects of metabotropic receptors. Metabotropic signaling by α7 receptors appears to be mediated by receptors in nonconducting conformations and can be accomplished by silent agonists. We discuss electrophysiological structure-activity relationships for α7 silent agonists and their use in cell-based and in vivo assays for CAS regulation. We discuss the strongly desensitizing partial agonist GTS-21 and its effectiveness in modulation of CAS. We also review the properties of the silent agonist NS6740, which is remarkably effective at maintaining α7 receptors in PAM-sensitive desensitized states. Most silent agonists bind to sites overlapping those for orthosteric agonists, but some appear to bind to allosteric sites. Finally, we discuss α9⁎ nAChRs and their potential role in CAS, and ligands that will be useful in defining and distinguishing the specific roles of α7 and α9 in CAS.
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Affiliation(s)
- Roger L Papke
- Department of Pharmacology and Therapeutics, University of Florida, PO Box 100267 Gainesville, FL 32610 USA (RLP); Olon S.p.A., Strada Rivoltana, Km 6/7 - 20053 Rodano (MI) - ITALY (MQ); Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA, 37212 (AG).
| | - Marta Quadri
- Department of Pharmacology and Therapeutics, University of Florida, PO Box 100267 Gainesville, FL 32610 USA (RLP); Olon S.p.A., Strada Rivoltana, Km 6/7 - 20053 Rodano (MI) - ITALY (MQ); Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA, 37212 (AG)
| | - Alican Gulsevin
- Department of Pharmacology and Therapeutics, University of Florida, PO Box 100267 Gainesville, FL 32610 USA (RLP); Olon S.p.A., Strada Rivoltana, Km 6/7 - 20053 Rodano (MI) - ITALY (MQ); Department of Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, Tennessee, USA, 37212 (AG)
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19
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Das BK, Chakraborty D. Deciphering the competitive inhibition of dihydropteroate synthase by 8 marcaptoguanine analogs: enhanced potency in phenylsulfonyl fragments. J Biomol Struct Dyn 2022; 40:13083-13102. [PMID: 34581241 DOI: 10.1080/07391102.2021.1981452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The emergence of sulfa-drug resistance and reduced efficacy of pterin-based analogs towards Dihydropteroate synthase (DHPS) inhibition dictate a pressing need of developing novel antimicrobial agents for immune-compromised patients. Recently, a series of 8-Marcaptoguanin (8-MG) derivatives synthesized for 6-Hydroxymethyl-7,8-dihydropterin pyrophosphokinase (experimental KD ∼ 100-.0.36) showed remarkable homology with the pteroic-acid and serve as a template for product antagonism in DHPS. The present work integrates ligand-based drug discovery techniques with structure-based docking, enhanced MD simulation, and MM/PBSA techniques to demonstrate the essential features of 8-MG analogs which make it a potent inhibitor for DHPS. The delicate balance in hydrophilic, hydrophobic substitutions on the 8-MG core is the crucial signature for DHPS inhibition. It is found that the dynamic interactions of active compounds are mainly dominated by consistent hydrogen bonding network with Asp 96, Asn 115, Asp 185, Ser 222, Arg 255 and π-π stacking, π-cation interactions with Phe 190, Lys 221. Further, two new 8-MG compounds containing N-phenylacetamide (compound S1, ΔGbind-eff = -62.03 kJ/mol) and phenylsulfonyl (compound S3, ΔGbind-eff = -71.29 kJ/mol) fragments were found to be the most potent inhibitor of DHPS, which stabilize the flexible pABA binding loop, thereby increasing their binding affinity. MM/PBSA calculation shows electrostatic energy contribution to be the principal component in stabilizing the inhibitors in the binding pocket. This fact is further confirmed by the higher energy barrier obtained in umbrella sampling for this class of inhibitors.
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Affiliation(s)
- Bratin Kumar Das
- Biophysical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Karnataka, Mangalore, India
| | - Debashree Chakraborty
- Biophysical and Computational Chemistry Laboratory, Department of Chemistry, National Institute of Technology Karnataka, Mangalore, India
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20
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Wang X, Pavlović RZ, Finnegan TJ, Karmakar P, Moore CE, Badjić JD. Rapid Access to Chiral and Tripodal Cavitands from β-Pinene. Chemistry 2022; 28:e202202416. [PMID: 36168151 PMCID: PMC9797447 DOI: 10.1002/chem.202202416] [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: 08/03/2022] [Indexed: 12/31/2022]
Abstract
We report Pd-catalyzed cyclotrimerization of (+)-α-bromoenone, obtained from monoterpene β-pinene, into an enantiopure cyclotrimer. This C3 symmetric compound has three bicyclo[3.1.1]heptane rings fused to its central benzene with each ring carrying a carbonyl group. The cyclotrimer undergoes diastereoselective threefold alkynylation with the lithium salts of five terminal alkynes (41-63 %, de=4-83 %). The addition enabled a rapid synthesis of a small library of novel chiral cavitands that, in shape, resemble a tripod stand. These molecular tripods include a tris-bicycloannelated benzene head attached to three alkyne legs twisted in one direction to form a nonpolar cavity with polar groups as feet. Tripods with methylpyridinium and methylisoquinolinium legs, respectively, form inclusion complexes with anti-inflammatory and chiral drugs (R)/(S)-ibuprofen and (R)/(S)-naproxen. The mode of binding shows drug molecules docked in the cavity of the host through ion-ion, cation-π, and C-H-π contacts that, in addition of desolvation, give rise to complexes having millimolar to micromolar stability in water. Our findings open the door to creating a myriad of enantiopure tripods with tunable functions that, in the future, might give novel chemosensors, catalysts or sequestering agents.
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Affiliation(s)
- Xiuze Wang
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th Avenue43210, OhioColumbusUSA
| | - Radoslav Z. Pavlović
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th Avenue43210, OhioColumbusUSA
| | - Tyler J. Finnegan
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th Avenue43210, OhioColumbusUSA
| | - Pratik Karmakar
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th Avenue43210, OhioColumbusUSA
- Department of ChemistryKing Mongkut's University of Technology Thonburi (KMUTT)126 Pracha Uthit Rd., Bang ModThung Khru, Bangkok10140Thailand
| | - Curtis E. Moore
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th Avenue43210, OhioColumbusUSA
| | - Jovica D. Badjić
- Department of Chemistry and BiochemistryThe Ohio State University100 West 18th Avenue43210, OhioColumbusUSA
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21
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Batista VS, Gonçalves AM, Nascimento-Júnior NM. Pharmacophore Mapping Combined with dbCICA Reveal New Structural Features for the Development of Novel Ligands Targeting α4β2 and α7 Nicotinic Acetylcholine Receptors. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27238236. [PMID: 36500328 PMCID: PMC9735964 DOI: 10.3390/molecules27238236] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Revised: 11/04/2022] [Accepted: 11/10/2022] [Indexed: 11/29/2022]
Abstract
The neuronal nicotinic acetylcholine receptors (nAChRs) belong to the ligand-gated ion channel (GLIC) group, presenting a crucial role in several biological processes and neuronal disorders. The α4β2 and α7 nAChRs are the most abundant in the central nervous system (CNS), being involved in challenging diseases such as epilepsy, Alzheimer's disease, schizophrenia, and anxiety disorder, as well as alcohol and nicotine dependencies. In addition, in silico-based strategies may contribute to revealing new insights into drug design and virtual screening to find new drug candidates to treat CNS disorders. In this context, the pharmacophore maps were constructed and validated for the orthosteric sites of α4β2 and α7 nAChRs, through a docking-based Comparative Intermolecular Contacts Analysis (dbCICA). In this sense, bioactive ligands were retrieved from the literature for each receptor. A molecular docking protocol was developed for all ligands in both receptors by using GOLD software, considering GoldScore, ChemScore, ASP, and ChemPLP scoring functions. Output GOLD results were post-processed through dbCICA to identify critical contacts involved in protein-ligand interactions. Moreover, Crossminer software was used to construct a pharmacophoric map based on the most well-behaved ligands and negative contacts from the dbCICA model for each receptor. Both pharmacophore maps were validated by using a ROC curve. The results revealed important features for the ligands, such as the presence of hydrophobic regions, a planar ring, and hydrogen bond donor and acceptor atoms for α4β2. Parallelly, a non-planar ring region was identified for α7. These results can enable fragment-based drug design (FBDD) strategies, such as fragment growing, linking, and merging, allowing an increase in the activity of known fragments. Thus, our results can contribute to a further understanding of structural subunits presenting the potential for key ligand-receptor interactions, favoring the search in molecular databases and the design of novel ligands.
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Affiliation(s)
- Victor S. Batista
- Laboratory of Medicinal Chemistry, Organic Synthesis and Molecular Modeling (LaQMedSOMM), Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University (Unesp), Rua Professor Francisco Degni, 55, Jardim Quitandinha, Araraquara 14800-060, SP, Brazil
| | - Adriano Marques Gonçalves
- Laboratory of Medicinal Chemistry, Organic Synthesis and Molecular Modeling (LaQMedSOMM), Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University (Unesp), Rua Professor Francisco Degni, 55, Jardim Quitandinha, Araraquara 14800-060, SP, Brazil
- Department of Biological and Health Sciences, University of Araraquara (Uniara), Rua Carlos Gomes, 1217, Centro, Araraquara 14801-340, SP, Brazil
| | - Nailton M. Nascimento-Júnior
- Laboratory of Medicinal Chemistry, Organic Synthesis and Molecular Modeling (LaQMedSOMM), Department of Biochemistry and Organic Chemistry, Institute of Chemistry, São Paulo State University (Unesp), Rua Professor Francisco Degni, 55, Jardim Quitandinha, Araraquara 14800-060, SP, Brazil
- Correspondence:
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22
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Xia X, Zhou F, Xu J, Wang Z, Lan J, Fan Y, Wang Z, Liu W, Chen J, Feng S, Tu Y, Yang Y, Chen L, Fang H. Unexpectedly efficient ion desorption of graphene-based materials. Nat Commun 2022; 13:7247. [PMID: 36434112 PMCID: PMC9700706 DOI: 10.1038/s41467-022-35077-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 11/18/2022] [Indexed: 11/27/2022] Open
Abstract
Ion desorption is extremely challenging for adsorbents with superior performance, and widely used conventional desorption methods involve high acid or base concentrations and large consumption of reagents. Here, we experimentally demonstrate the rapid and efficient desorption of ions on magnetite-graphene oxide (M-GO) by adding low amounts of Al3+. The corresponding concentration of Al3+ used is reduced by at least a factor 250 compared to conventional desorption method. The desorption rate reaches ~97.0% for the typical radioactive and bivalent ions Co2+, Mn2+, and Sr2+ within ~1 min. We achieve effective enrichment of radioactive 60Co and reduce the volume of concentrated 60Co solution by approximately 10 times compared to the initial solution. The M-GO can be recycled and reused easily without compromising its adsorption efficiency and magnetic performance, based on the unique hydration anionic species of Al3+ under alkaline conditions. Density functional theory calculations show that the interaction of graphene with Al3+ is stronger than with divalent ions, and that the adsorption probability of Al3+ is superior than that of Co2+, Mn2+, and Sr2+ ions. This suggests that the proposed method could be used to enrich a wider range of ions in the fields of energy, biology, environmental technology, and materials science.
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Affiliation(s)
- Xinming Xia
- grid.203507.30000 0000 8950 5267School of Physical Science and Technology, Ningbo University, 315211 Ningbo, China ,grid.443483.c0000 0000 9152 7385Department of Optical Engineering, Zhejiang Prov Key Lab Carbon Cycling Forest Ecosy, College of Environmental and Resource Sciences, Zhejiang A&F University, 311300 Hangzhou, China ,grid.268415.cSchool of Physical Science and Technology & Microelectronics Industry Research Institute, Yangzhou University, 225009 Yangzhou, China
| | - Feng Zhou
- Radiation Monitoring Technical Center of Ministry of Environmental Protection, State Environmental Protection Key Laboratory of Radiation monitoring, Key Laboratory of Radiation Monitoring of Zhejiang Province, 310012 Hangzhou, China
| | - Jing Xu
- grid.443483.c0000 0000 9152 7385Department of Optical Engineering, Zhejiang Prov Key Lab Carbon Cycling Forest Ecosy, College of Environmental and Resource Sciences, Zhejiang A&F University, 311300 Hangzhou, China
| | - Zhongteng Wang
- grid.443483.c0000 0000 9152 7385Department of Optical Engineering, Zhejiang Prov Key Lab Carbon Cycling Forest Ecosy, College of Environmental and Resource Sciences, Zhejiang A&F University, 311300 Hangzhou, China
| | - Jian Lan
- grid.443483.c0000 0000 9152 7385Department of Optical Engineering, Zhejiang Prov Key Lab Carbon Cycling Forest Ecosy, College of Environmental and Resource Sciences, Zhejiang A&F University, 311300 Hangzhou, China
| | - Yan Fan
- grid.443483.c0000 0000 9152 7385Department of Optical Engineering, Zhejiang Prov Key Lab Carbon Cycling Forest Ecosy, College of Environmental and Resource Sciences, Zhejiang A&F University, 311300 Hangzhou, China
| | - Zhikun Wang
- grid.443483.c0000 0000 9152 7385Department of Optical Engineering, Zhejiang Prov Key Lab Carbon Cycling Forest Ecosy, College of Environmental and Resource Sciences, Zhejiang A&F University, 311300 Hangzhou, China
| | - Wei Liu
- grid.443483.c0000 0000 9152 7385Department of Optical Engineering, Zhejiang Prov Key Lab Carbon Cycling Forest Ecosy, College of Environmental and Resource Sciences, Zhejiang A&F University, 311300 Hangzhou, China
| | - Junlang Chen
- grid.443483.c0000 0000 9152 7385Department of Optical Engineering, Zhejiang Prov Key Lab Carbon Cycling Forest Ecosy, College of Environmental and Resource Sciences, Zhejiang A&F University, 311300 Hangzhou, China
| | - Shangshen Feng
- grid.443483.c0000 0000 9152 7385Department of Optical Engineering, Zhejiang Prov Key Lab Carbon Cycling Forest Ecosy, College of Environmental and Resource Sciences, Zhejiang A&F University, 311300 Hangzhou, China
| | - Yusong Tu
- grid.268415.cSchool of Physical Science and Technology & Microelectronics Industry Research Institute, Yangzhou University, 225009 Yangzhou, China
| | - Yizhou Yang
- grid.28056.390000 0001 2163 4895Department of Physics, East China University of Science and Technology, 200237 Shanghai, China
| | - Liang Chen
- grid.203507.30000 0000 8950 5267School of Physical Science and Technology, Ningbo University, 315211 Ningbo, China
| | - Haiping Fang
- grid.28056.390000 0001 2163 4895Department of Physics, East China University of Science and Technology, 200237 Shanghai, China ,grid.410726.60000 0004 1797 8419Wenzhou Institute, University of Chinese Academy of Sciences, 325000 Wenzhou, Zhejiang China
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23
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Li Z, Chan KC, Nickels JD, Cheng X. Electrostatic Contributions to the Binding Free Energy of Nicotine to the Acetylcholine Binding Protein. J Phys Chem B 2022; 126:8669-8679. [PMID: 36260486 PMCID: PMC10056799 DOI: 10.1021/acs.jpcb.2c04641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Biomolecular binding relies on specific attractive interactions between two partner molecules, including electrostatics, dispersion, hydrophobicity, and solvation. Assessing the contributions of electrostatic interactions to binding is key to the understanding of ligand binding mechanisms and the design of improved biomolecular binders. For example, nicotine is a well-known agonist of nicotinic acetylcholine receptors (nAChRs), but the molecular mechanisms for the differential action of nicotine on brain and muscle nAChRs remain elusive. In this work, we have chosen the acetylcholine binding protein (AChBP) in complex with nicotine as a model system to interrogate the electrostatic contributions to nicotine binding. Our absolute binding free energy simulations confirm that nicotine binds AChBP predominantly in its protonated (charged) form. By comparing energetic contributions from decomposed interactions for either neutral or charged nicotine, our calculations shed light on the nature of the binding of nicotine to the AChBP. The preferred binding of charged nicotine over neutral nicotine originates from its stronger electrostatic interactions with AChBP, a cation-π interaction to a tryptophan residue and a hydrogen bond between nicotine and the backbone carbonyl of the tryptophan, whereas the major force driving the binding process appears to be van der Waals interactions. The various nonelectrostatic terms can also indirectly modulate the electrostatic interactions through fine-tuning the binding pose of the ligand in the binding site, providing an explanation of why the binding specificity of nicotine to the brain versus muscle nAChRs is driven by electrostatic interaction, given that the immediate binding site residues, including the key tryptophan residue, are identical in the two receptors.
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Affiliation(s)
- Zoe Li
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio43210, United States
| | - Kevin C Chan
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio43210, United States
| | - Jonathan D Nickels
- Department of Chemical and Environmental Engineering, University of Cincinnati, Cincinnati, Ohio45221, United States
| | - Xiaolin Cheng
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy at The Ohio State University, Columbus, Ohio43210, United States
- Translational Data Analytics Institute (TDAI) at The Ohio State University, Columbus, Ohio43210, United States
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24
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Cerdan AH, Peverini L, Changeux JP, Corringer PJ, Cecchini M. Lateral fenestrations in the extracellular domain of the glycine receptor contribute to the main chloride permeation pathway. SCIENCE ADVANCES 2022; 8:eadc9340. [PMID: 36240268 PMCID: PMC9565810 DOI: 10.1126/sciadv.adc9340] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Glycine receptors (GlyRs) are ligand-gated ion channels mediating signal transduction at chemical synapses. Since the early patch-clamp electrophysiology studies, the details of the ion permeation mechanism have remained elusive. Here, we combine molecular dynamics simulations of a zebrafish GlyR-α1 model devoid of the intracellular domain with mutagenesis and single-channel electrophysiology of the full-length human GlyR-α1. We show that lateral fenestrations between subunits in the extracellular domain provide the main translocation pathway for chloride ions to enter/exit a central water-filled vestibule at the entrance of the transmembrane channel. In addition, we provide evidence that these fenestrations are at the origin of current rectification in known anomalous mutants and design de novo two inward-rectifying channels by introducing mutations within them. These results demonstrate the central role of lateral fenestrations on synaptic neurotransmission.
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Affiliation(s)
- Adrien H. Cerdan
- Institut de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Channel-Receptors Unit, Paris, France
| | - Laurie Peverini
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Channel-Receptors Unit, Paris, France
| | - Jean-Pierre Changeux
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Channel-Receptors Unit, Paris, France
- Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA, USA
- Collège de France, Paris, France
| | - Pierre-Jean Corringer
- Institut Pasteur, Université Paris Cité, CNRS UMR 3571, Channel-Receptors Unit, Paris, France
| | - Marco Cecchini
- Institut de Chimie de Strasbourg, UMR7177, CNRS, Université de Strasbourg, F-67083 Strasbourg Cedex, France
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25
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Sam S, Sung S, Krem S, Park S, Hwang DS, Kim D. Sum-Frequency Vibrational Spectroscopic Study of the Cation-π Interaction: Amine and Guanidine. J Phys Chem B 2022; 126:7621-7626. [PMID: 36166344 DOI: 10.1021/acs.jpcb.2c05709] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The cation-π interaction is an interaction between a positively charged cation and π electrons in an aromatic group of a molecule. It is considered to play key roles in signal transduction, stabilization of the protein structure, enzyme catalysis in biology, and wet adhesion and biomolecular condensation. In this study, octadecylguanidine hydrochloride (ODG) and octadecylamine (ODA) having guanidine and amine headgroups, respectively, are found to interact with π molecules (phenol or indole) as investigated by sum-frequency vibrational spectroscopy. ODG is unstable and does not form a neat monolayer on the water surface. However, after adding π molecules into subphase water, it becomes more stable against dissolution as evidenced by the appearance of its CHx peaks and a CH peak of the aromatic ring in the sum-frequency spectrum. Unlike ODG, ODA forms a stable monolayer on the water surface at a neutral pH. After adding π molecules into the solution, the amine-π interaction promotes the protonation of the amine headgroup and the penetration of the π molecules makes the ODA monolayer more disordered. Indole is found to be more effective in binding with the ODG as compared to phenol.
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Affiliation(s)
- Sokhuoy Sam
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Korea
| | - Siheon Sung
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Korea
| | - Sona Krem
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Korea
| | - Sohee Park
- Division of Environmental Science and Engineering (DESE), Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Namgu, Pohang 37673, Korea
| | - Dong Soo Hwang
- Division of Environmental Science and Engineering (DESE), Pohang University of Science and Technology (POSTECH), 77 Cheongam-ro, Namgu, Pohang 37673, Korea
| | - Doseok Kim
- Department of Physics, Sogang University, 35, Baekbeom-ro, Mapo-gu, Seoul 04107, Korea
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26
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Knox HJ, Rego Campello H, Lester HA, Gallagher T, Dougherty DA. Characterization of Binding Site Interactions and Selectivity Principles in the α3β4 Nicotinic Acetylcholine Receptor. J Am Chem Soc 2022; 144:16101-16117. [PMID: 36006801 DOI: 10.1021/jacs.2c06495] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Nicotinic acetylcholine receptors (nAChRs) play an important role in neurotransmission and are also involved in addiction and several disease states. There is significant interest in therapeutic targeting of nAChRs; however, achieving selectivity for one subtype over others has been a longstanding challenge, given the close structural similarities across the family. Here, we characterize binding interactions in the α3β4 nAChR subtype via structure-function studies involving noncanonical amino acid mutagenesis and two-electrode voltage clamp electrophysiology. We establish comprehensive binding models for both the endogenous neurotransmitter ACh and the smoking cessation drug cytisine. We also use a panel of C(10)-substituted cytisine derivatives to probe the effects of subtle changes in the ligand structure on binding. By comparing our results to those obtained for the well-studied α4β2 subtype, we identify several features of both the receptor and agonist structure that can be utilized to enhance selectivity for either α3β4 or α4β2. Finally, we characterize binding interactions of the α3β4-selective partial agonist AT-1001 to determine factors that contribute to its selectivity. These results shed new light on the design of selective nAChR-targeted ligands and can be used to inform the design of improved therapies with minimized off-target effects.
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Affiliation(s)
- Hailey J Knox
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | | | - Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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27
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Shao J, Kuiper BP, Thunnissen AMWH, Cool RH, Zhou L, Huang C, Dijkstra BW, Broos J. The Role of Tryptophan in π Interactions in Proteins: An Experimental Approach. J Am Chem Soc 2022; 144:13815-13822. [PMID: 35868012 PMCID: PMC9354243 DOI: 10.1021/jacs.2c04986] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
![]()
In proteins, the amino acids Phe, Tyr, and especially
Trp are frequently
involved in π interactions such as π–π, cation−π,
and CH−π bonds. These interactions are often crucial
for protein structure and protein–ligand binding. A powerful
means to study these interactions is progressive fluorination of these
aromatic residues to modulate the electrostatic component of the interaction.
However, to date no protein expression platform is available to produce
milligram amounts of proteins labeled with such fluorinated amino
acids. Here, we present a Lactococcus lactis Trp
auxotroph-based expression system for efficient incorporation (≥95%)
of mono-, di-, tri-, and tetrafluorinated, as well as a methylated
Trp analog. As a model protein we have chosen LmrR, a dimeric multidrug
transcriptional repressor protein from L. lactis. LmrR binds aromatic drugs, like daunomycin and riboflavin, between
Trp96 and Trp96′ in the dimer interface. Progressive fluorination
of Trp96 decreased the affinity for the drugs 6- to 70-fold, clearly
establishing the importance of electrostatic π–π
interactions for drug binding. Presteady state kinetic data of the
LmrR–drug interaction support the enthalpic nature of the interaction,
while high resolution crystal structures of the labeled protein–drug
complexes provide for the first time a structural view of the progressive
fluorination approach. The L. lactis expression system
was also used to study the role of Trp68 in the binding of riboflavin
by the membrane-bound riboflavin transport protein RibU from L. lactis. Progressive fluorination of Trp68 revealed a
strong electrostatic component that contributed 15–20% to the
total riboflavin-RibU binding energy.
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Affiliation(s)
- Jinfeng Shao
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Bastiaan P Kuiper
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Andy-Mark W H Thunnissen
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Robbert H Cool
- Department of Chemical and Pharmaceutical Biology, University of Groningen, Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | - Liang Zhou
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Chenxi Huang
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Bauke W Dijkstra
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Jaap Broos
- Groningen Biomolecular Science and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
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28
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Kumar S, Choudhary M. Copper(II) Schiff base complex derived from salen ligand: structural investigation, Hirshfeld surface analysis, anticancer and anti-SARS-CoV-2. J Biomol Struct Dyn 2022:1-24. [DOI: 10.1080/07391102.2022.2076155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sunil Kumar
- Department of Chemistry, National Institute of Technology Patna, Patna, Bihar, India
| | - Mukesh Choudhary
- Department of Chemistry, National Institute of Technology Patna, Patna, Bihar, India
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29
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Mesoy SM, Bridgland-Taylor M, Lummis SCR. Mutations of the nACh Receptor M4 Helix Reveal Different Phenotypes in Different Expression Systems: Could Lipids be Responsible? Front Physiol 2022; 13:850782. [PMID: 35600303 PMCID: PMC9116227 DOI: 10.3389/fphys.2022.850782] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2022] [Accepted: 03/31/2022] [Indexed: 11/18/2022] Open
Abstract
The role of the outermost helix (M4) in the pentameric ligand-gated ion channel (pLGIC) family is currently not fully understood. It is known that M4 is important for receptor assembly, possibly via interactions with neighboring M1 and M3 helices. M4 can also transmit information on the lipid content of the membrane to the gating mechanism, and it may form a link to the extracellular domain via the Cys-loop. Our previous study examining the α4β2 nACh receptor M4 helix using HEK cells indicated M4 here is more sensitive to change than those of other pLGIC. Many of these other studies, however, were performed in Xenopus oocytes. Here we examine the nine previously identified nonfunctional α4β2 nACh receptor M4 mutant receptors using this system. The data reveal that seven of these mutant receptors do function when expressed in oocytes, with only 2, the conserved Asp at the intracellular end of M4 and a Phe in the center, having a similar phenotype (nonfunctional) in both HEK cells and oocytes. The oocyte data are more consistent with studies in other pLGIC and demonstrate the importance of the expression system used. Of the many differences between these two expression systems, we suggest that the different lipid content of the plasma membrane is a possible candidate for explaining these discrepancies.
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Affiliation(s)
- Susanne M. Mesoy
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, United Kingdom
| | - Matthew Bridgland-Taylor
- Clinical Pharmacology and Safety Sciences, Biopharmaceuticals R&D, AstraZeneca, Cambridge, United Kingdom
| | - Sarah C. R. Lummis
- Department of Biochemistry, University of Cambridge, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Sarah C. R. Lummis,
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30
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Song W, Li Q, Wang T, Li Y, Fan T, Zhang J, Wang Q, Pan J, Dong Q, Sun ZS, Wang Y. Putative complement control protein CSMD3 dysfunction impairs synaptogenesis and induces neurodevelopmental disorders. Brain Behav Immun 2022; 102:237-250. [PMID: 35245678 DOI: 10.1016/j.bbi.2022.02.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 02/10/2022] [Accepted: 02/26/2022] [Indexed: 12/23/2022] Open
Abstract
Recent studies have reported that complement-related proteins modulate brain development through regulating synapse processes in the cortex. CSMD3 belongs to a group of putative complement control proteins. However, its role in the central nervous system and synaptogenesis remains largely unknown. Here we report that CSMD3 deleterious mutations occur frequently in patients with neurodevelopmental disorders (NDDs). Csmd3 is predominantly expressed in cortical neurons of the developing cortex. In mice, Csmd3 disruption induced retarded development and NDD-related behaviors. Csmd3 deficiency impaired synaptogenesis and neurogenesis, allowing fewer neurons reaching the cortical plate. Csmd3 deficiency also induced perturbed functional networks in the developing cortex, involving a number of downregulated synapse-associated genes that influence early synaptic organization and upregulated genes related to immune activity. Our study provides mechanistic insights into the endogenous regulation of complement-related proteins in synaptic development and supports the pathological role of CSMD3 in NDDs.
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Affiliation(s)
- Wei Song
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Quan Li
- School of Life Sciences, Hebei University, Baoding 071002, China
| | - Tao Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China
| | - Yuanyuan Li
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Tianda Fan
- Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China
| | - Jianghong Zhang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qingqing Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinrong Pan
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Qiwen Dong
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhong Sheng Sun
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China; School of Life Sciences, Hebei University, Baoding 071002, China; Institute of Genomic Medicine, Wenzhou Medical University, Wenzhou 325000, China; State Key Laboratory of Integrated Management of Pest Insects and Rodents, Chinese Academy of Sciences, Beijing 100101, China.
| | - Yan Wang
- Beijing Institutes of Life Science, Chinese Academy of Sciences, Beijing 100101, China; CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing 100049, China.
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31
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Geng H, Zhang P, Peng Q, Cui J, Hao J, Zeng H. Principles of Cation-π Interactions for Engineering Mussel-Inspired Functional Materials. Acc Chem Res 2022; 55:1171-1182. [PMID: 35344662 DOI: 10.1021/acs.accounts.2c00068] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Supramolecular assembly is commonly driven by noncovalent interactions (e.g., hydrogen bonding, electrostatic, hydrophobic, and aromatic interactions) and plays a predominant role in multidisciplinary research areas ranging from materials design to molecular biology. Understanding these noncovalent interactions at the molecular level is important for studying and designing supramolecular assemblies in chemical and biological systems. Cation-π interactions, initially found through their influence on protein structure, are generally formed between electron-rich π systems and cations (mainly alkali, alkaline-earth metals, and ammonium). Cation-π interactions play an essential role in many biological systems and processes, such as potassium channels, nicotinic acetylcholine receptors, biomolecular recognition and assembly, and the stabilization and function of biomacromolecular structures. Early fundamental studies on cation-π interactions primarily focused on computational calculations, protein crystal structures, and gas- and solid-phase experiments. With the more recent development of spectroscopic and nanomechanical techniques, cation-π interactions can be characterized directly in aqueous media, offering opportunities for the rational manipulation and incorporation of cation-π interactions into the design of supramolecular assemblies. In 2012, we reported the essential role of cation-π interactions in the strong underwater adhesion of Asian green mussel foot proteins deficient in l-3,4-dihydroxyphenylalanine (DOPA) via direct molecular force measurements. In another study in 2013, we reported the experimental quantification and nanomechanics of cation-π interactions of various cations and π electron systems in aqueous solutions using a surface forces apparatus (SFA).Over the past decade, much progress has been achieved in probing cation-π interactions in aqueous solutions, their impact on the underwater adhesion and cohesion of different soft materials, and the fabrication of functional materials driven by cation-π interactions, including surface coatings, complex coacervates, and hydrogels. These studies have demonstrated cation-π interactions as an important driving force for engineering functional materials. Nevertheless, compared to other noncovalent interactions, cation-π interactions are relatively less investigated and underappreciated in governing the structure and function of supramolecular assemblies. Therefore, it is imperative to provide a detailed overview of recent advances in understanding of cation-π interactions for supramolecular assembly, and how these interactions can be used to direct supramolecular assembly for various applications (e.g., underwater adhesion). In this Account, we present very recent advances in probing and applying cation-π interactions for mussel-inspired supramolecular assemblies as well as their structural and functional characteristics. Particular attention is paid to experimental characterization techniques for quantifying cation-π interactions in aqueous solutions. Moreover, the parameters responsible for modulating the strengths of cation-π interactions are discussed. This Account provides useful insights into the design and engineering of smart materials based on cation-π interactions.
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Affiliation(s)
- Huimin Geng
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
| | - Peiyu Zhang
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
| | - Qiongyao Peng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
| | - Jiwei Cui
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
| | - Jingcheng Hao
- Key Laboratory of Colloid and Interface Chemistry of the Ministry of Education, School of Chemistry and Chemical Engineering, and the State Key Laboratory of Microbial Technology, Shandong University, Jinan, Shandong 250100, China
| | - Hongbo Zeng
- Department of Chemical and Materials Engineering, University of Alberta, Edmonton, Alberta T6G 1H9, Canada
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32
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Espinoza-Derout J, Shao XM, Lao CJ, Hasan KM, Rivera JC, Jordan MC, Echeverria V, Roos KP, Sinha-Hikim AP, Friedman TC. Electronic Cigarette Use and the Risk of Cardiovascular Diseases. Front Cardiovasc Med 2022; 9:879726. [PMID: 35463745 PMCID: PMC9021536 DOI: 10.3389/fcvm.2022.879726] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Accepted: 03/11/2022] [Indexed: 12/12/2022] Open
Abstract
Electronic cigarettes or e-cigarettes are the most frequently used tobacco product among adolescents. Despite the widespread use of e-cigarettes and the known detrimental cardiac consequences of nicotine, the effects of e-cigarettes on the cardiovascular system are not well-known. Several in vitro and in vivo studies delineating the mechanisms of the impact of e-cigarettes on the cardiovascular system have been published. These include mechanisms associated with nicotine or other components of the aerosol or thermal degradation products of e-cigarettes. The increased hyperlipidemia, sympathetic dominance, endothelial dysfunction, DNA damage, and macrophage activation are prominent effects of e-cigarettes. Additionally, oxidative stress and inflammation are unifying mechanisms at many levels of the cardiovascular impairment induced by e-cigarette exposure. This review outlines the contribution of e-cigarettes in the development of cardiovascular diseases and their molecular underpinnings.
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Affiliation(s)
- Jorge Espinoza-Derout
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, Los Angeles, CA, United States
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Xuesi M. Shao
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, Los Angeles, CA, United States
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Candice J. Lao
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, Los Angeles, CA, United States
| | - Kamrul M. Hasan
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, Los Angeles, CA, United States
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Juan Carlos Rivera
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, Los Angeles, CA, United States
| | - Maria C. Jordan
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Valentina Echeverria
- Research and Development Service, Bay Pines VA Healthcare System, Bay Pines, FL, United States
- Laboratorio de Neurobiología, Facultad de Ciencias de la Salud, Universidad San Sebastián, Concepción, Chile
| | - Kenneth P. Roos
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Amiya P. Sinha-Hikim
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, Los Angeles, CA, United States
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Theodore C. Friedman
- Division of Endocrinology, Metabolism and Molecular Medicine, Department of Internal Medicine, Charles R. Drew University of Medicine and Science, Los Angeles, CA, United States
- David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
- Friends Research Institute, Cerritos, CA, United States
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33
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Zhao H, Liu C, Ding W, Tang L, Fang Y, Chen Y, Hu L, Yuan Y, Fang D, Lin S. Manipulating Cation-π Interactions with Genetically Encoded Tryptophan Derivatives. J Am Chem Soc 2022; 144:6742-6748. [PMID: 35380832 DOI: 10.1021/jacs.1c12944] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cation-π interactions are the major noncovalent interactions for molecular recognition and play a central role in a broad area of chemistry and biology. Despite tremendous success in understanding the origin and biological importance of cation-π interactions, the design and synthesis of stronger cation-π interactions remain elusive. Here, we report an approach that greatly increases the binding energy of cation-π interactions by replacing Trp in the aromatic box with an electron-rich Trp derivative using the genetic code expansion strategy. The binding affinity between histone H3K4me3 and its reader is increased more than eightfold using genetically encoded 6-methoxy-Trp. Furthermore, through a systematic engineering process, we construct an H3K4me3 Super-Reader with single-digit nM affinity for H3K4me3 detection and imaging. More broadly, this approach paves the way for manipulating cation-π interactions for a variety of applications.
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Affiliation(s)
- Hongxia Zhao
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Chao Liu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Wenlong Ding
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ling Tang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yu Fang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Yulin Chen
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Linzhen Hu
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China
| | - Ying Yuan
- Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Dong Fang
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.,Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China
| | - Shixian Lin
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou 310058, China.,Department of Medical Oncology, The Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310058, China.,Cancer Center, Zhejiang University, Hangzhou 310058, China
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Lin CY, Romei MG, Mathews II, Boxer SG. Energetic Basis and Design of Enzyme Function Demonstrated Using GFP, an Excited-State Enzyme. J Am Chem Soc 2022; 144:3968-3978. [PMID: 35200017 PMCID: PMC9014791 DOI: 10.1021/jacs.1c12305] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The past decades have witnessed an explosion of de novo protein designs with a remarkable range of scaffolds. It remains challenging, however, to design catalytic functions that are competitive with naturally occurring counterparts as well as biomimetic or nonbiological catalysts. Although directed evolution often offers efficient solutions, the fitness landscape remains opaque. Green fluorescent protein (GFP), which has revolutionized biological imaging and assays, is one of the most redesigned proteins. While not an enzyme in the conventional sense, GFPs feature competing excited-state decay pathways with the same steric and electrostatic origins as conventional ground-state catalysts, and they exert exquisite control over multiple reaction outcomes through the same principles. Thus, GFP is an "excited-state enzyme". Herein we show that rationally designed mutants and hybrids that contain environmental mutations and substituted chromophores provide the basis for a quantitative model and prediction that describes the influence of sterics and electrostatics on excited-state catalysis of GFPs. As both perturbations can selectively bias photoisomerization pathways, GFPs with fluorescence quantum yields (FQYs) and photoswitching characteristics tailored for specific applications could be predicted and then demonstrated. The underlying energetic landscape, readily accessible via spectroscopy for GFPs, offers an important missing link in the design of protein function that is generalizable to catalyst design.
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Affiliation(s)
- Chi-Yun Lin
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Matthew G Romei
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Irimpan I Mathews
- Stanford Synchrotron Radiation Lightsource, 2575 Sand Hill Road, Menlo Park, California 94025, United States
| | - Steven G Boxer
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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Conformational transitions and ligand-binding to a muscle-type nicotinic acetylcholine receptor. Neuron 2022; 110:1358-1370.e5. [PMID: 35139364 DOI: 10.1016/j.neuron.2022.01.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 11/02/2021] [Accepted: 01/10/2022] [Indexed: 12/15/2022]
Abstract
Fast synaptic communication requires receptors that respond to the presence of neurotransmitter by opening an ion channel across the post-synaptic membrane. The muscle-type nicotinic acetylcholine receptor from the electric fish, Torpedo, is the prototypic ligand-gated ion channel, yet the structural changes underlying channel activation remain undefined. Here we use cryo-EM to solve apo and agonist-bound structures of the Torpedo nicotinic receptor embedded in a lipid nanodisc. Using both a direct biochemical assay to define the conformational landscape and molecular dynamics simulations to assay flux through the pore, we correlate structures with functional states and elucidate the motions that lead to pore activation of a heteromeric nicotinic receptor. We highlight an underappreciated role for the complementary subunit in channel gating, establish the structural basis for the differential agonist affinities of α/δ versus α /γ sites, and explain why nicotine is less potent at muscle nicotinic receptors compared to neuronal ones.
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Nichols AL, Blumenfeld Z, Fan C, Luebbert L, Blom AEM, Cohen BN, Marvin JS, Borden PM, Kim CH, Muthusamy AK, Shivange AV, Knox HJ, Campello HR, Wang JH, Dougherty DA, Looger LL, Gallagher T, Rees DC, Lester HA. Fluorescence activation mechanism and imaging of drug permeation with new sensors for smoking-cessation ligands. eLife 2022; 11:e74648. [PMID: 34982029 PMCID: PMC8820738 DOI: 10.7554/elife.74648] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 01/03/2022] [Indexed: 12/16/2022] Open
Abstract
Nicotinic partial agonists provide an accepted aid for smoking cessation and thus contribute to decreasing tobacco-related disease. Improved drugs constitute a continued area of study. However, there remains no reductionist method to examine the cellular and subcellular pharmacokinetic properties of these compounds in living cells. Here, we developed new intensity-based drug-sensing fluorescent reporters (iDrugSnFRs) for the nicotinic partial agonists dianicline, cytisine, and two cytisine derivatives - 10-fluorocytisine and 9-bromo-10-ethylcytisine. We report the first atomic-scale structures of liganded periplasmic binding protein-based biosensors, accelerating development of iDrugSnFRs and also explaining the activation mechanism. The nicotinic iDrugSnFRs detect their drug partners in solution, as well as at the plasma membrane (PM) and in the endoplasmic reticulum (ER) of cell lines and mouse hippocampal neurons. At the PM, the speed of solution changes limits the growth and decay rates of the fluorescence response in almost all cases. In contrast, we found that rates of membrane crossing differ among these nicotinic drugs by >30-fold. The new nicotinic iDrugSnFRs provide insight into the real-time pharmacokinetic properties of nicotinic agonists and provide a methodology whereby iDrugSnFRs can inform both pharmaceutical neuroscience and addiction neuroscience.
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Affiliation(s)
- Aaron L Nichols
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Zack Blumenfeld
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Keck School of Medicine, University of Southern CaliforniaLos AngelesUnited States
| | - Chengcheng Fan
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Laura Luebbert
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
- Institute of Biology, Leiden UniversityLeidenNetherlands
| | - Annet EM Blom
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Bruce N Cohen
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Jonathan S Marvin
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Philip M Borden
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | - Charlene H Kim
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Anand K Muthusamy
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Amol V Shivange
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Hailey J Knox
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | | | - Jonathan H Wang
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
| | - Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
| | - Loren L Looger
- Janelia Research Campus, Howard Hughes Medical InstituteAshburnUnited States
| | | | - Douglas C Rees
- Division of Chemistry and Chemical Engineering, California Institute of TechnologyPasadenaUnited States
- Howard Hughes Medical Institute, California Institute of TechnologyPasadenaUnited States
| | - Henry A Lester
- Division of Biology and Biological Engineering, California Institute of TechnologyPasadenaUnited States
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Fabiani C, Biscussi B, Munafo JP, Murray AP, Corradi J, Antollini SS. NEW SYNTHETIC CAFFEINE ANALOGS AS MODULATORS OF THE CHOLINERGIC SYSTEM. Mol Pharmacol 2021; 101:154-167. [PMID: 34969831 DOI: 10.1124/molpharm.121.000415] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 12/26/2021] [Indexed: 11/22/2022] Open
Abstract
Alzheimer's disease (AD) is a multifactorial neurodegenerative disorder. Since cholinergic deficit is a major factor in this disease, two molecular targets for its treatment are the acetylcholinesterase (AChE) and the nicotinic acetylcholine receptors (nAChRs). Given that caffeine is a natural compound that behaves as an AChE inhibitor and as a partial agonist of nAChRs, the aim of this work was to synthetize more potent bifunctional caffeine analogs that modulate these two molecular targets. To this end, a theophylline structure was connected to a pyrrolidine structure through a methylene chain of different lengths (3 to 7 carbon atoms) to give compounds 7-11 All caffeine derivatives inhibited the AChE, of which compound 11 showed the strongest effect. Electrophysiological studies showed that all compounds behave as agonists of the muscle and the neuronal α7 nAChR with greater potency than caffeine. To explore if the different analogs could affect the nAChR conformational state, the nAChR conformational-sensitive probe crystal violet (CrV) was used. Compounds 9 and 10 conduced the nAChR to a different conformational state comparable with a control nAChR desensitized state. Finally, molecular docking experiments showed that all derivatives interacted with both the catalytic and anionic sites of AChE and with the orthosteric binding site of the nAChR. Thus, the new synthetized compounds can inhibit the AChE and activate muscle and α7 nAChRs with greater potency than caffeine, which suggests that they could be useful leaders for the development of new therapies for the treatment of different neurological diseases. Significance Statement In this work we synthetized caffeine derivatives which can inhibit the AChE and activate both muscle and α7 nAChRs with higher potency than caffeine. These analogs can be divided into two groups: a non-desensitizing and a desensitizing nAChR group. From the nAChR-non desensitizing group, we propose compound 11 as the most interesting analog for further studies since it inhibits AChE with the highest potency and activates the nAChRs in the picomolar range without inducing receptor desensitization.
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Affiliation(s)
- Camila Fabiani
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur y Consejo Nacional de Investigaciones Científicas y Técnicas, Camino La Carrindanga km 7, Argentina
| | - Brunella Biscussi
- Instituto de Química del Sur, Departamento de Química, Universidad Nacional del Sur y Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Alem 1253, Argentina
| | - Juan Pablo Munafo
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur y Consejo Nacional de Investigaciones Científicas y Técnicas, Camino La Carrindanga km 7, Argentina
| | - Ana Paula Murray
- Instituto de Química del Sur, Departamento de Química, Universidad Nacional del Sur y Consejo Nacional de Investigaciones Científicas y Técnicas, Av. Alem 1253, Argentina
| | - Jeremias Corradi
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur y Consejo Nacional de Investigaciones Científicas y Técnicas, Camino La Carrindanga km 7, Argentina
| | - Silvia Susana Antollini
- Instituto de Investigaciones Bioquímicas de Bahía Blanca, Departamento de Biología, Bioquímica y Farmacia, Universidad Nacional del Sur y Consejo Nacional de Investigaciones Científicas y Técnicas, Camino La Carrindanga km 7, Argentina
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38
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Timsit Y, Grégoire SP. Towards the Idea of Molecular Brains. Int J Mol Sci 2021; 22:ijms222111868. [PMID: 34769300 PMCID: PMC8584932 DOI: 10.3390/ijms222111868] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 10/24/2021] [Accepted: 10/28/2021] [Indexed: 02/06/2023] Open
Abstract
How can single cells without nervous systems perform complex behaviours such as habituation, associative learning and decision making, which are considered the hallmark of animals with a brain? Are there molecular systems that underlie cognitive properties equivalent to those of the brain? This review follows the development of the idea of molecular brains from Darwin’s “root brain hypothesis”, through bacterial chemotaxis, to the recent discovery of neuron-like r-protein networks in the ribosome. By combining a structural biology view with a Bayesian brain approach, this review explores the evolutionary labyrinth of information processing systems across scales. Ribosomal protein networks open a window into what were probably the earliest signalling systems to emerge before the radiation of the three kingdoms. While ribosomal networks are characterised by long-lasting interactions between their protein nodes, cell signalling networks are essentially based on transient interactions. As a corollary, while signals propagated in persistent networks may be ephemeral, networks whose interactions are transient constrain signals diffusing into the cytoplasm to be durable in time, such as post-translational modifications of proteins or second messenger synthesis. The duration and nature of the signals, in turn, implies different mechanisms for the integration of multiple signals and decision making. Evolution then reinvented networks with persistent interactions with the development of nervous systems in metazoans. Ribosomal protein networks and simple nervous systems display architectural and functional analogies whose comparison could suggest scale invariance in information processing. At the molecular level, the significant complexification of eukaryotic ribosomal protein networks is associated with a burst in the acquisition of new conserved aromatic amino acids. Knowing that aromatic residues play a critical role in allosteric receptors and channels, this observation suggests a general role of π systems and their interactions with charged amino acids in multiple signal integration and information processing. We think that these findings may provide the molecular basis for designing future computers with organic processors.
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Affiliation(s)
- Youri Timsit
- Aix Marseille Université, Université de Toulon, CNRS, IRD, MIO UM110, 13288 Marseille, France
- Research Federation for the Study of Global Ocean Systems Ecology and Evolution, FR2022/Tara GOSEE, 3 rue Michel-Ange, 75016 Paris, France
- Correspondence:
| | - Sergeant-Perthuis Grégoire
- Institut de Mathématiques de Jussieu—Paris Rive Gauche (IMJ-PRG), UMR 7586, CNRS-Université Paris Diderot, 75013 Paris, France;
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Zhang L, Shi G, Peng B, Gao P, Chen L, Zhong N, Mu L, Zhang L, Zhang P, Gou L, Zhao Y, Liang S, Jiang J, Zhang Z, Ren H, Lei X, Yi R, Qiu Y, Zhang Y, Liu X, Wu M, Yan L, Duan C, Zhang S, Fang H. Novel 2D CaCl crystals with metallicity, room-temperature ferromagnetism, heterojunction, piezoelectricity-like property and monovalent calcium ions. Natl Sci Rev 2021; 8:nwaa274. [PMID: 34691690 PMCID: PMC8310769 DOI: 10.1093/nsr/nwaa274] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Revised: 10/29/2020] [Accepted: 10/29/2020] [Indexed: 11/12/2022] Open
Abstract
Under ambient conditions, the only known valence state of calcium ions is +2, and the corresponding crystals with calcium ions are insulating and nonferromagnetic. Here, using cryo-electron microscopy, we report direct observation of two-dimensional (2D) CaCl crystals on reduced graphene oxide (rGO) membranes, in which the calcium ions are only monovalent (i.e. +1). Remarkably, metallic rather than insulating properties are displayed by those CaCl crystals. More interestingly, room-temperature ferromagnetism, graphene-CaCl heterojunction, coexistence of piezoelectricity-like property and metallicity, as well as the distinct hydrogen storage and release capability of the CaCl crystals in rGO membranes are experimentally demonstrated. We note that such CaCl crystals are obtained by simply incubating rGO membranes in salt solutions below the saturated concentration, under ambient conditions. Theoretical studies suggest that the formation of those abnormal crystals is attributed to the strong cation-π interactions of the Ca cations with the aromatic rings in the graphene surfaces. The findings highlight the realistic potential applications of such abnormal CaCl material with unusual electronic properties in designing novel transistors and magnetic devices, hydrogen storage, catalyzers, high-performance conducting electrodes and sensors, with a size down to atomic scale.
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Affiliation(s)
- Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Guosheng Shi
- Shanghai Applied Radiation Institute, Shanghai University, Shanghai 200444, China
| | - Bingquan Peng
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Pengfei Gao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Liang Chen
- Department of Optical Engineering, Zhejiang A&F University, Hangzhou 311300, China
| | - Ni Zhong
- Key Laboratory of Polar Materials and Devices of Ministry of Education, East China Normal University, Shanghai 200241, China
| | - Liuhua Mu
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Lijuan Zhang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Peng Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Lu Gou
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yimin Zhao
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Shanshan Liang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jie Jiang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Zejun Zhang
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Hongtao Ren
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Xiaoling Lei
- Department of Physics, East China University of Science and Technology, Shanghai 200237, China
| | - Ruobing Yi
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Yinwei Qiu
- Department of Optical Engineering, Zhejiang A&F University, Hangzhou 311300, China
| | - Yufeng Zhang
- College of Physical Science and Technology, Xiamen University, Xiamen 361005, China
| | - Xing Liu
- Shanghai Applied Radiation Institute, Shanghai University, Shanghai 200444, China
| | - Minghong Wu
- Shanghai Applied Radiation Institute, Shanghai University, Shanghai 200444, China
| | - Long Yan
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Chungang Duan
- Key Laboratory of Polar Materials and Devices of Ministry of Education, East China Normal University, Shanghai 200241, China
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi'an Jiaotong University, Xi'an 710049, China
| | - Haiping Fang
- Department of Physics, East China University of Science and Technology, Shanghai 200237, China
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Nicotine Exacerbates TAAD Formation Induced by Smooth Muscle-Specific Deletion of the TGF- β Receptor 2. J Immunol Res 2021; 2021:6880036. [PMID: 34646889 PMCID: PMC8505064 DOI: 10.1155/2021/6880036] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 09/04/2021] [Indexed: 01/22/2023] Open
Abstract
Tobacco smoke is an established risk factor for thoracic aortic aneurysms and dissections (TAAD). However, little is known about its underlying mechanisms due to the lack of validated animal models. The present study developed a mouse model that may be utilized to investigate exacerbation of TAAD formation by mimetics of tobacco smoke. TAADs were created via inducible deletion of smooth muscle cell-specific Tgfbr2 receptors. Using this model, the first set of experiments evaluated the efficacy of nicotine salt (34.0 mg/kg/day), nicotine free base (NFB, 5.0 mg 90-day pellets), and cigarette smoke extract (0.1 ml/mouse/day). Compared with their respective control groups, only NFB pellets promoted TAAD dilation (23 ± 3% vs. 12 ± 2%, P = 0.014), and this efficacy was achieved at a cost of >50% acute mortality. Infusion of NFB with osmotic minipumps at extremely high, but nonlethal, doses (15.0 or 45.0 mg/kg/day) failed to accelerate TAAD dilation. Interestingly, costimulation with β-aminopropionitrile (BAPN) promoted TAAD dilation and aortic rupture at dosages of 3.0 and 45.0 mg/kg/day, respectively, indicating that BAPN sensitizes the response of TAADs to NFB. In subsequent analyses, the detrimental effects of NFB were associated with clustering of macrophages, neutrophils, and T-cells in areas with structural destruction, enhanced matrix metalloproteinase- (MMP-) 2 production, and pathological angiogenesis with attenuated fibrosis in the adventitia. In conclusion, modeling nicotine exacerbation of TAAD formation requires optimization of chemical form, route of delivery, and dosage of the drug as well as the pathologic complexity of TAADs. Under the optimized conditions of the present study, chronic inflammation and adventitial mal-remodeling serve as critical pathways through which NFB exacerbates TAAD formation.
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Mizumura K, Gon Y. Iron-Regulated Reactive Oxygen Species Production and Programmed Cell Death in Chronic Obstructive Pulmonary Disease. Antioxidants (Basel) 2021; 10:antiox10101569. [PMID: 34679704 PMCID: PMC8533398 DOI: 10.3390/antiox10101569] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 09/30/2021] [Accepted: 09/30/2021] [Indexed: 01/01/2023] Open
Abstract
Chronic obstructive pulmonary disease (COPD) is characterized by persistent respiratory symptoms and airflow limitation. However, the pathogenesis of COPD remains unclear. Currently, it is known to involve the loss of alveolar surface area (emphysema) and airway inflammation (bronchitis), primarily due to exposure to cigarette smoke (CS). CS causes epithelial cell death, resulting in pulmonary emphysema. Moreover, CS induces iron accumulation in the mitochondria and cytosol, resulting in programmed cell death. Although apoptosis has long been investigated as the sole form of programmed cell death in COPD, accumulating evidence indicates that a regulated form of necrosis, called necroptosis, and a unique iron-dependent form of non-apoptotic cell death, called ferroptosis, is implicated in the pathogenesis of COPD. Iron metabolism plays a key role in producing reactive oxygen species (ROS), including mitochondrial ROS and lipid peroxidation end-products, and activating both necroptosis and ferroptosis. This review outlines recent studies exploring CS-mediated iron metabolism and ROS production, along with the regulation of programmed cell death in COPD. Elucidating the mechanisms of these pathways may provide novel therapeutic targets for COPD.
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Zhao LX, Wang ZX, Peng JF, Zou YL, Hui YZ, Chen YZ, Gao S, Fu Y, Ye F. Design, synthesis, and herbicidal activity of novel phenoxypyridine derivatives containing natural product coumarin. PEST MANAGEMENT SCIENCE 2021; 77:4785-4798. [PMID: 34161678 DOI: 10.1002/ps.6523] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 04/30/2021] [Accepted: 06/23/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND In recent years, protoporphyrinogen oxidase (PPO, EC 1.3.3.4) inhibitors have been widely studied as important agricultural herbicides. Our research focused on the design and synthesis of novel PPO inhibitor herbicides, through linking of a diphenylether pyridine bioisostere structure to substituted coumarins, which aims to enhance environmental and crop safety while retaining high efficacy. RESULTS A total of 21 compounds were synthesized via acylation reactions and all compounds were characterized using infrared, 1 H NMR, 13 C NMR, and high-resolution mass spectra. The respective configurations of compounds IV-6 and IV-12 were also confirmed using single crystal X-ray diffraction. The bioassay results showed that the title compounds displayed notable herbicidal activity, particularly compound IV-6 which displayed better herbicidal activity in greenhouse and field experiments, crop selectivity and safety for cotton and soybean compared with the commercial herbicide oxyfluorfen. CONCLUSION The work revealed that compound IV-6 deserves further attention as a candidate structure for a novel and safe herbicide. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Li-Xia Zhao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, China
| | - Zhi-Xin Wang
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, China
| | - Jian-Feng Peng
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, China
| | - Yue-Li Zou
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, China
| | - Yong-Zhuo Hui
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, China
| | - Yong-Zheng Chen
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, China
| | - Shuang Gao
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, China
| | - Ying Fu
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, China
| | - Fei Ye
- Department of Chemistry, College of Arts and Sciences, Northeast Agricultural University, Harbin, China
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Pursuing High-Resolution Structures of Nicotinic Acetylcholine Receptors: Lessons Learned from Five Decades. Molecules 2021; 26:molecules26195753. [PMID: 34641297 PMCID: PMC8510392 DOI: 10.3390/molecules26195753] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Revised: 09/19/2021] [Accepted: 09/20/2021] [Indexed: 01/04/2023] Open
Abstract
Since their discovery, nicotinic acetylcholine receptors (nAChRs) have been extensively studied to understand their function, as well as the consequence of alterations leading to disease states. Importantly, these receptors represent pharmacological targets to treat a number of neurological and neurodegenerative disorders. Nevertheless, their therapeutic value has been limited by the absence of high-resolution structures that allow for the design of more specific and effective drugs. This article offers a comprehensive review of five decades of research pursuing high-resolution structures of nAChRs. We provide a historical perspective, from initial structural studies to the most recent X-ray and cryogenic electron microscopy (Cryo-EM) nAChR structures. We also discuss the most relevant structural features that emerged from these studies, as well as perspectives in the field.
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44
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Horenstein NA, Stokes C, Papke RL. Sulfonium Ligands of the α7 nAChR. Molecules 2021; 26:5643. [PMID: 34577114 PMCID: PMC8464850 DOI: 10.3390/molecules26185643] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Revised: 09/13/2021] [Accepted: 09/13/2021] [Indexed: 11/16/2022] Open
Abstract
The α7 nicotinic acetylcholine receptor (nAChR) is an important target given its role in cognitive function as well as in the cholinergic anti-inflammatory pathway, where ligands that are effective at stabilizing desensitized states of the receptor are of particular interest. The typical structural element associated with a good desensitizer is the ammonium pharmacophore, but recent work has identified that a trivalent sulfur, in the positively charged sulfonium form, can substitute for the nitrogen in the ammonium pharmacophore. However, the breadth and scope of employing the sulfonium group is largely unexplored. In this work, we have surveyed a disparate group of sulfonium compounds for their functional activity with α7 as well as other nAChR subtypes. Amongst them, we found that there is a wide range of ability to induce α7 desensitization, with 4-hydroxyphenyldimethylsulfonium and suplatast sulfonium salts being the most desensitizing. The smallest sulfonium compound, trimethylsulfonium, was a partial agonist for α7 and other neuronal nAChR. Molecular docking into the α7 receptor extracellular domain revealed preferred poses in the orthosteric binding site for all but one compound, with typical cation-pi interactions as seen with traditional ammonium compounds. A number of the compounds tested may serve as useful platforms for further development of α7 desensitizing ability and for receptor subtype selectivity.
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Affiliation(s)
| | - Clare Stokes
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610-0267, USA; (C.S.); (R.L.P.)
| | - Roger L. Papke
- Department of Pharmacology and Therapeutics, University of Florida, Gainesville, FL 32610-0267, USA; (C.S.); (R.L.P.)
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45
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Breunig SL, Tirrell DA. Incorporation of proline analogs into recombinant proteins expressed in Escherichia coli. Methods Enzymol 2021; 656:545-571. [PMID: 34325798 DOI: 10.1016/bs.mie.2021.05.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Proline residues are unique in the extent to which they constrain the conformational space available to the protein backbone. Because the conformational preferences of proline cannot be recapitulated by any of the other proteinogenic amino acids, standard mutagenesis approaches that seek to introduce new chemical functionality at proline positions unavoidably perturb backbone flexibility. Here, we detail the incorporation of proline analogs into recombinant proteins in Escherichia coli via a residue-specific mutagenesis strategy. This approach results in global replacement of proline residues with high yields of the recombinant protein of interest, minimal genetic manipulation, and maintenance of backbone conformational constraints.
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Affiliation(s)
- Stephanie L Breunig
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, United States
| | - David A Tirrell
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, United States.
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46
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Al Mughram MH, Catalano C, Bowry JP, Safo MK, Scarsdale JN, Kellogg GE. 3D Interaction Homology: Hydropathic Analyses of the "π-Cation" and "π-π" Interaction Motifs in Phenylalanine, Tyrosine, and Tryptophan Residues. J Chem Inf Model 2021; 61:2937-2956. [PMID: 34101460 DOI: 10.1021/acs.jcim.1c00235] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Three-dimensional (3D) maps of the hydropathic environments of protein amino acid residues are information-rich descriptors of preferred conformations, interaction types and energetics, and solvent accessibility. The interactions made by each residue are the primary factor for rotamer selection and the secondary, tertiary, and even quaternary protein structure. Our evolving basis set of environmental data for each residue type can be used to understand the protein structure. This work focuses on the aromatic residues phenylalanine, tyrosine, and tryptophan and their structural roles. We calculated and analyzed side chain-to-environment 3D maps for over 70,000 residues of these three types that reveal, with respect to hydrophobic and polar interactions, the environment around each. After binning with backbone ϕ/ψ and side chain χ1, we clustered each bin by 3D similarities between map-map pairs. For each of the three residue types, four bins were examined in detail: one in the β-pleat, two in the right-hand α-helix, and one in the left-hand α-helix regions of the Ramachandran plot. For high degrees of side chain burial, encapsulation of the side chain by hydrophobic interactions is ubiquitous. The more solvent-exposed side chains are more likely to be involved in polar interactions with their environments. Evidence for π-π interactions was observed in about half of the residues surveyed [phenylalanine (PHE): 53.3%, tyrosine (TYR): 34.1%, and tryptophan (TRP): 55.7%], but on an energy basis, this contributed to only ∼4% of the total. Evidence for π-cation interactions was observed in 14.1% of PHE, 8.3% of TYR, and 26.8% of TRP residues, but on an energy basis, this contributed to only ∼1%. This recognition of even these subtle interactions in the 3D hydropathic environment maps is key support for our interaction homology paradigm of protein structure elucidation and possibly prediction.
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Affiliation(s)
- Mohammed H Al Mughram
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States
| | - Claudio Catalano
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States
| | - John P Bowry
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States
| | - Martin K Safo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
| | - J Neel Scarsdale
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
| | - Glen E Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, Virginia 23298-0540, United States.,Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia 23284-2030, United States.,Institute of Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, Virginia 23298-0133, United States
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47
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Structure and gating mechanism of the α7 nicotinic acetylcholine receptor. Cell 2021; 184:2121-2134.e13. [PMID: 33735609 DOI: 10.1016/j.cell.2021.02.049] [Citation(s) in RCA: 142] [Impact Index Per Article: 47.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/13/2021] [Accepted: 02/22/2021] [Indexed: 12/13/2022]
Abstract
The α7 nicotinic acetylcholine receptor plays critical roles in the central nervous system and in the cholinergic inflammatory pathway. This ligand-gated ion channel assembles as a homopentamer, is exceptionally permeable to Ca2+, and desensitizes faster than any other Cys-loop receptor. The α7 receptor has served as a prototype for the Cys-loop superfamily yet has proven refractory to structural analysis. We present cryo-EM structures of the human α7 nicotinic receptor in a lipidic environment in resting, activated, and desensitized states, illuminating the principal steps in the gating cycle. The structures also reveal elements that contribute to its function, including a C-terminal latch that is permissive for channel opening, and an anionic ring in the extracellular vestibule that contributes to its high conductance and calcium permeability. Comparisons among the α7 structures provide a foundation for mapping the gating cycle and reveal divergence in gating mechanisms in the Cys-loop receptor superfamily.
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48
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Prevost MS, Bouchenaki H, Barilone N, Gielen M, Corringer PJ. Concatemers to re-investigate the role of α5 in α4β2 nicotinic receptors. Cell Mol Life Sci 2021; 78:1051-1064. [PMID: 32472188 PMCID: PMC11071962 DOI: 10.1007/s00018-020-03558-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 05/15/2020] [Accepted: 05/22/2020] [Indexed: 01/08/2023]
Abstract
Nicotinic acetylcholine receptors (nAChRs) are pentameric ion channels expressed in the central nervous systems. nAChRs containing the α4, β2 and α5 subunits are specifically involved in addictive processes, but their functional architecture is poorly understood due to the intricacy of assembly of these subunits. Here we constrained the subunit assembly by designing fully concatenated human α4β2 and α4β2α5 receptors and characterized their properties by two-electrodes voltage-clamp electrophysiology in Xenopus oocytes. We found that α5-containing nAChRs are irreversibly blocked by methanethiosulfonate (MTS) reagents through a covalent reaction with a cysteine present only in α5. MTS-block experiments establish that the concatemers are expressed in intact form at the oocyte surface, but that reconstitution of nAChRs from loose subunits show inefficient and highly variable assembly of α5 with α4 and β2. Mutational analysis shows that the concatemers assemble both in clockwise and anticlockwise orientations, and that α5 does not contribute to ACh binding from its principal (+) site. Reinvestigation of suspected α5-ligands such as galantamine show no specific effect on α5-containing concatemers. Analysis of the α5-D398N mutation that is linked to smoking and lung cancer shows no significant effect on the electrophysiological function, suggesting that its effect might arise from alteration of other cellular processes. The concatemeric strategy provides a well-characterized platform for mechanistic analysis and screening of human α5-specific ligands.
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Affiliation(s)
- Marie S Prevost
- Unité Récepteurs-Canaux, Institut Pasteur, UMR 3571, CNRS, 75015, Paris, France
| | - Hichem Bouchenaki
- Unité Récepteurs-Canaux, Institut Pasteur, UMR 3571, CNRS, 75015, Paris, France
| | - Nathalie Barilone
- Unité Récepteurs-Canaux, Institut Pasteur, UMR 3571, CNRS, 75015, Paris, France
| | - Marc Gielen
- Unité Récepteurs-Canaux, Institut Pasteur, UMR 3571, CNRS, 75015, Paris, France.
- Sorbonne Université, 21, rue de l'école de médecine, 75006, Paris, France.
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49
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Zhou W, Guan Z. Ion Channels in Anesthesia. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1349:401-413. [DOI: 10.1007/978-981-16-4254-8_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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50
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Bilonda MK, Mammino L. Computational studies of biologically active alkaloids of plant origin: an overview. PHYSICAL SCIENCES REVIEWS 2020. [DOI: 10.1515/psr-2019-0132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Abstract
Computational studies nowadays constitute a crucial source of information for drug development, because they provide information on many molecular properties and also enable predictions of the properties of not-yet-synthesized compounds. Alkaloids are a vast group of natural products exhibiting a variety of biological activities, many of which are interesting for drug development. On the other hand, computational studies of biologically active alkaloids have so far mostly focused on few particularly relevant or “popular” molecules, such as quinine, caffeine, or cocaine, with only few works on the other molecules. The present work offers an overview of existing computational studies on alkaloid molecules, from the earliest ones to the most recent, and considering all the theoretical approaches with which studies have been performed (both quantum mechanics and molecular dynamics). The considered studies are grouped according to their objectives and outcomes, such as conformational analysis of alkaloid molecules, effects of selected solvents on their properties, docking studies aimed at better understanding of the interactions between alkaloid molecules and biological targets, studies focusing on structure activity relationships, and computational studies performed to confirm experimental results. It is concluded that it would be important that computational studies on many other alkaloid molecules are performed and their results made available, covering their different classes as well as the variety of their biological activities, to attain better understanding of the properties not only of individual molecules, but also of groups of related molecules and of the overall alkaloids family.
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Affiliation(s)
- Mireille K. Bilonda
- School of Mathematical and Natural Sciences, University of Venda , Thohoyandou , South Africa
- Faculty of Science, University of Kinshasa , Kinshasa , Democratic Republic of Congo
| | - Liliana Mammino
- School of Mathematical and Natural Sciences, University of Venda , Thohoyandou , South Africa
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