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Sendri N, Singh S, Sharma B, Purohit R, Bhandari P. Effect of co-pigments on anthocyanins of Rhododendron arboreum and insights into interaction mechanism. Food Chem 2023; 426:136571. [PMID: 37331145 DOI: 10.1016/j.foodchem.2023.136571] [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: 02/07/2023] [Revised: 05/24/2023] [Accepted: 06/05/2023] [Indexed: 06/20/2023]
Abstract
The impact of intermolecular copigmentation between five phenolic acids, two flavonoid and three amino acids with R. arboreum anthocyanins (ANS) and its isolated cyanidin-3-O-monoglycosides were investigated through experimental and theoretical approach. On addition of different copigments, phenolic acid induced strong hyperchromic (0.26-0.55 nm) and bathochromic shift (6.6-14.2 nm). The color intensity and stability of ANS with, storage at 4 °C & 25 °C, sunlight, oxidation and heat were evaluated by chromaticity, anthocyanin content, kinetic and structural simulation analysis. The strongest copigmentation reaction was observed with narningin (NA) and also showed high thermostability and highest half-life i.e. 3.39 h-1.24 h at 90-160 °C. The cyanidin-3-O-monoglycosides were analysed for their copigmentation effect and observations revealed that NA displayed best copigmentation effect to cyanidin-3-O-arabinoside (B) followed by cyanidin-3-O-galactoside (A), and cyanidin-3-O-rhamnoside (C). Additionally, structural simulation and steered molecular dynamics insights NA is the most favourable co-pigment involving π-π stacking and H-bonding.
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Affiliation(s)
- Nitisha Sendri
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Sarvpreet Singh
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Bhanu Sharma
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Rituraj Purohit
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Pamita Bhandari
- CSIR-Institute of Himalayan Bioresource Technology, Palampur, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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2
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Bertaccini EJ. Anesthesia, Coming of Age in the World of Modern In Silico Drug Design. Anesthesiology 2023; 138:129-131. [PMID: 36629466 DOI: 10.1097/aln.0000000000004445] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Edward J Bertaccini
- Department of Anesthesiology, Pain and Perioperative Medicine, Stanford University School of Medicine, Stanford, California; and Department of Anesthesiology, Palo Alto VA Health Care System, Palo Alto, California
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3
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Nin-Hill A, Mueller NPF, Molteni C, Rovira C, Alfonso-Prieto M. Photopharmacology of Ion Channels through the Light of the Computational Microscope. Int J Mol Sci 2021; 22:12072. [PMID: 34769504 PMCID: PMC8584574 DOI: 10.3390/ijms222112072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Revised: 10/31/2021] [Accepted: 11/02/2021] [Indexed: 12/13/2022] Open
Abstract
The optical control and investigation of neuronal activity can be achieved and carried out with photoswitchable ligands. Such compounds are designed in a modular fashion, combining a known ligand of the target protein and a photochromic group, as well as an additional electrophilic group for tethered ligands. Such a design strategy can be optimized by including structural data. In addition to experimental structures, computational methods (such as homology modeling, molecular docking, molecular dynamics and enhanced sampling techniques) can provide structural insights to guide photoswitch design and to understand the observed light-regulated effects. This review discusses the application of such structure-based computational methods to photoswitchable ligands targeting voltage- and ligand-gated ion channels. Structural mapping may help identify residues near the ligand binding pocket amenable for mutagenesis and covalent attachment. Modeling of the target protein in a complex with the photoswitchable ligand can shed light on the different activities of the two photoswitch isomers and the effect of site-directed mutations on photoswitch binding, as well as ion channel subtype selectivity. The examples presented here show how the integration of computational modeling with experimental data can greatly facilitate photoswitchable ligand design and optimization. Recent advances in structural biology, both experimental and computational, are expected to further strengthen this rational photopharmacology approach.
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Affiliation(s)
- Alba Nin-Hill
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain; (A.N.-H.); (C.R.)
| | - Nicolas Pierre Friedrich Mueller
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany;
- Faculty of Mathematics and Natural Sciences, Heinrich-Heine-University Düsseldorf, Universitätsstr. 1, 40225 Düsseldorf, Germany
| | - Carla Molteni
- Physics Department, King’s College London, London WC2R 2LS, UK;
| | - Carme Rovira
- Departament de Química Inorgànica i Orgànica (Secció de Química Orgànica) and Institut de Química Teòrica i Computacional (IQTCUB), Universitat de Barcelona, 08028 Barcelona, Spain; (A.N.-H.); (C.R.)
- Institució Catalana de Recerca i Estudis Avançats (ICREA), 08020 Barcelona, Spain
| | - Mercedes Alfonso-Prieto
- Institute for Advanced Simulations IAS-5 and Institute of Neuroscience and Medicine INM-9, Computational Biomedicine, Forschungszentrum Jülich, 52425 Jülich, Germany;
- Cécile and Oskar Vogt Institute for Brain Research, University Hospital Düsseldorf, Medical Faculty, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
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Identification of Dihydromyricetin and Metabolites in Serum and Brain Associated with Acute Anti-Ethanol Intoxicating Effects in Mice. Int J Mol Sci 2021; 22:ijms22147460. [PMID: 34299083 PMCID: PMC8307506 DOI: 10.3390/ijms22147460] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 07/07/2021] [Accepted: 07/09/2021] [Indexed: 01/01/2023] Open
Abstract
Dihydromyricetin is a natural bioactive flavonoid with unique GABAA receptor activity with a putative mechanism of action to reduce the intoxication effects of ethanol. Although dihydromyricetin's poor oral bioavailability limits clinical utility, the promise of this mechanism for the treatment of alcohol use disorder warrants further investigation into its specificity and druggable potential. These experiments investigated the bioavailability of dihydromyricetin in the brain and serum associated with acute anti-intoxicating effects in C57BL/6J mice. Dihydromyricetin (50 mg/kg IP) administered 0 or 15-min prior to ethanol (PO 5 g/kg) significantly reduced ethanol-induced loss of righting reflex. Total serum exposures (AUC0→24) of dihydromyricetin (PO 50 mg/kg) via oral (PO) administration were determined to be 2.5 µM × h (male) and 0.7 µM × h (female), while intraperitoneal (IP) administration led to 23.8-fold and 7.2- increases in AUC0→24 in male and female mice, respectively. Electrophysiology studies in α5β3γ2 GABAA receptors expressed in Xenopus oocytes suggest dihydromyricetin (10 µM) potentiates GABAergic activity (+43.2%), and the metabolite 4-O-methyl-dihydromyricetin (10 µM) negatively modulates GABAergic activity (-12.6%). Our results indicate that administration route and sex significantly impact DHM bioavailability in mice, which is limited by poor absorption and rapid clearance. This correlates with the observed short duration of DHM's anti-intoxicating properties and highlights the need for further investigation into mechanism of DHM's potential anti-intoxicating properties.
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Yuan X, Zhang D, Mao S, Wang Q. Filling the Gap in Understanding the Mechanism of GABA AR and Propofol Using Computational Approaches. J Chem Inf Model 2021; 61:1889-1901. [PMID: 33823589 DOI: 10.1021/acs.jcim.0c01290] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
γ-Aminobutyric acid type-A receptors (GABAARs) play a critical role in neural transmission by mediating the inhibitory neural firing and are the target of many psychiatric drugs. Among them, propofol is one of the most widely used and important general anesthetics in clinics. Recent advances in structural biology revealed the structure of a human GABAAR in both open and closed states. Yet, the detailed mechanism of the receptor and propofol remains to be fully understood. Therefore, in this study, based on the previous successes in structural biology, a variety of computational techniques were applied to fill the gap between previous experimental studies. This study investigated the ion-conducting mechanism of GABAAR, predicted the possible binding mechanism of propofol, and revealed a new motion mechanism of transmembrane domain (TMD) helices. We hope that this study may contribute to future studies on ion-channel receptors, general anesthetics, and drug development.
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Affiliation(s)
- Xinghang Yuan
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Di Zhang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Shengjun Mao
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
| | - Qiantao Wang
- Key Laboratory of Drug-Targeting and Drug Delivery System of the Education Ministry and Sichuan Province, Sichuan Engineering Laboratory for Plant-Sourced Drug and Sichuan Research Center for Drug Precision Industrial Technology, West China School of Pharmacy, Sichuan University, Chengdu 610041, China
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Borghese CM, Wang HYL, McHardy SF, Messing RO, Trudell JR, Harris RA, Bertaccini EJ. Modulation of α1β3γ2 GABA A receptors expressed in X. laevis oocytes using a propofol photoswitch tethered to the transmembrane helix. Proc Natl Acad Sci U S A 2021; 118:e2008178118. [PMID: 33593898 PMCID: PMC7923644 DOI: 10.1073/pnas.2008178118] [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] [Indexed: 11/18/2022] Open
Abstract
Tethered photoswitches are molecules with two photo-dependent isomeric forms, each with different actions on their biological targets. They include reactive chemical groups capable of covalently binding to their target. Our aim was to develop a β-subunit-tethered propofol photoswitch (MAP20), as a tool to better study the mechanism of anesthesia through the GABAA α1β3γ2 receptor. We used short spacers between the tether (methanethiosulfonate), the photosensitive moiety (azobenzene), and the ligand (propofol), to allow a precise tethering adjacent to the putative propofol binding site at the β+α- interface of the receptor transmembrane helices (TMs). First, we used molecular modeling to identify possible tethering sites in β3TM3 and α1TM1, and then introduced cysteines in the candidate positions. Two mutant subunits [β3(M283C) and α1(V227C)] showed photomodulation of GABA responses after incubation with MAP20 and illumination with lights at specific wavelengths. The α1β3(M283C)γ2 receptor showed the greatest photomodulation, which decreased as GABA concentration increased. The location of the mutations that produced photomodulation confirmed that the propofol binding site is located in the β+α- interface close to the extracellular side of the transmembrane helices. Tethering the photoswitch to cysteines introduced in the positions homologous to β3M283 in two other subunits (α1W288 and γ2L298) also produced photomodulation, which was not entirely reversible, probably reflecting the different nature of each interface. The results are in agreement with a binding site in the β+α- interface for the anesthetic propofol.
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Affiliation(s)
- Cecilia M Borghese
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712;
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712
| | - Hua-Yu L Wang
- Center for Innovative Drug Discovery, University of Texas at San Antonio, San Antonio, TX 78249
| | - Stanton F McHardy
- Center for Innovative Drug Discovery, University of Texas at San Antonio, San Antonio, TX 78249
| | - Robert O Messing
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712
| | - James R Trudell
- Department of Anesthesia, Stanford University, Palo Alto, CA 94305
- Beckman Program for Molecular and Genetic Medicine, Stanford University, Palo Alto, CA 94305
| | - R Adron Harris
- Waggoner Center for Alcohol and Addiction Research, The University of Texas at Austin, Austin, TX 78712
- Department of Neuroscience, The University of Texas at Austin, Austin, TX 78712
| | - Edward J Bertaccini
- Department of Anesthesia, Stanford University, Palo Alto, CA 94305
- Department of Anesthesia, Palo Alto VA Health Care System, Palo Alto Division, Palo Alto, CA 94304
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Discovery of the EL-0052 as a potential anesthetic drug. Comput Struct Biotechnol J 2021; 19:710-718. [PMID: 33510871 PMCID: PMC7817531 DOI: 10.1016/j.csbj.2021.01.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Revised: 01/03/2021] [Accepted: 01/05/2021] [Indexed: 01/13/2023] Open
Abstract
As a γ-aminobutyric acid A receptor (GABAAR) inhibitor, etomidate fulfills several characteristics of an ideal anesthetic agent, such as rapid onset with rapid clearance and high potency, along with cardiovascular stability. Unfortunately, etomidate has been reported to inhibit CYP11B1 at hypnotic doses, which is associated with a marked increase in patient deaths due to this unexpected off-target effect. In this study, molecular docking was used to simulate the binding mode of etomidate with GABAAR and CYP11B1. Based on the in-depth analysis of the binding mode, strong electron-withdrawing group on the C4 position of the imidazole ring was introduced to reduce the charge density of the nitrogen, which is beneficial in reducing the coordination bond between the imidazole nitrogen and heme iron in CYP11B1, as well as in reducing the adrenocortical suppression. Based on the results of ADMET property prediction, MEP analysis, and molecular docking simulation, 4-fluoroetomidate (EL-0052) was designed and synthesized. In vivo studies in rats and mice confirmed that EL-0052 had the efficacy similar to etomidate, but without adrenocortical suppression. These findings suggested that EL-0052 was superior to etomidate and support the continued development of EL-0052 as a preclinical candidate as an anesthetic.
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Wei W, Champion C, Barigye SJ, Liu Z, Labute P, Moitessier N. Use of Extended-Hückel Descriptors for Rapid and Accurate Predictions of Conjugated Torsional Energy Barriers. J Chem Inf Model 2020; 60:3534-3545. [DOI: 10.1021/acs.jcim.0c00440] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wanlei Wei
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal H3A 0B8, Québec, Canada
| | - Candide Champion
- Chemical Computing Group Incorporation, 1010 Sherbrooke St. W., Montreal H3A 2R7, Québec, Canada
| | - Stephen J. Barigye
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal H3A 0B8, Québec, Canada
| | - Zhaomin Liu
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal H3A 0B8, Québec, Canada
| | - Paul Labute
- Chemical Computing Group Incorporation, 1010 Sherbrooke St. W., Montreal H3A 2R7, Québec, Canada
| | - Nicolas Moitessier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal H3A 0B8, Québec, Canada
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Wei W, Champion C, Liu Z, Barigye SJ, Labute P, Moitessier N. Torsional Energy Barriers of Biaryls Could Be Predicted by Electron Richness/Deficiency of Aromatic Rings; Advancement of Molecular Mechanics toward Atom-Type Independence. J Chem Inf Model 2019; 59:4764-4777. [PMID: 31430147 DOI: 10.1021/acs.jcim.9b00585] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Biaryl molecules are ubiquitous pharmacophores found in natural products and pharmaceuticals. In spite of this, existing molecular mechanics force fields are unable to accurately reproduce their torsional energy profiles, except for a few well-parametrized cases. This effectively limits the ability of structure-based drug design methods to correctly identify hits involving biaryls with confidence (e.g., during virtual screening, employing docking and/or molecular dynamics simulations). Continuing in our endeavor to quantify organic chemistry principles, we showed that the torsional energy profile of biaryl compounds could be computed on-the-fly based on the electron richness/deficiency of the aromatic rings. This method, called H-TEQ 4.0, was developed using a set of 131 biaryls. It was subsequently validated on a separate set of 100 diverse biaryls, including multisubstituted, bicyclic and tricyclic druglike molecules, and produced an average root-mean-square error (RMSE) of 0.95 kcal·mol-1. For comparison, GAFF2 produced an RMSE of 3.88 kcal·mol-1, owing to problems associated with the transferability of torsion parameters. The success of H-TEQ 4.0 provided further evidence that force fields could transition to become atom-type independent, providing that the correct chemical principles are used. Overall, this method solved the problem of transferability of biaryl torsion parameters, while simultaneously improving the overall accuracy of the force field.
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Affiliation(s)
- Wanlei Wei
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montréal , Quebec , Canada H3A 0B8
| | - Candide Champion
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montréal , Quebec , Canada H3A 0B8
| | - Zhaomin Liu
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montréal , Quebec , Canada H3A 0B8
| | - Stephen J Barigye
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montréal , Quebec , Canada H3A 0B8
| | - Paul Labute
- Chemical Computing Group Inc. , 1010 Sherbrooke Street West , Montréal , Quebec , Canada H3A 2R7
| | - Nicolas Moitessier
- Department of Chemistry , McGill University , 801 Sherbrooke Street West , Montréal , Quebec , Canada H3A 0B8
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McGrath M, Pence A, Raines DE. Computational Approaches to Anesthetic Drug Discovery. Trends Pharmacol Sci 2019; 40:809-811. [PMID: 31623940 DOI: 10.1016/j.tips.2019.09.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 09/12/2019] [Indexed: 11/25/2022]
Abstract
All currently available general anesthetics produce potentially deadly side effects. Unfortunately, few approaches have been developed to design safer ones, despite important advances in anesthetic mechanisms research. Cayla and colleagues recently showed that computational methods can be used to identify anesthetic lead compounds devoid of specific side effects.
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Affiliation(s)
- Megan McGrath
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Andrea Pence
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Douglas E Raines
- Department of Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA.
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