1
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Pro-Gly based dipeptide containing sulphonamide functionality, their antidiabetic, antioxidant, and anti-inflammatory activities. Synthesis, characterization and computational studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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2
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Li BY, Yang F, Zhang ZY, Shen YF, Wang T, Zhao L, Qin JC, Ling F, Wang GX. Quinoline, with the active site of 8-hydroxyl, efficiently inhibits Micropterus salmoides rhabdovirus (MSRV) infection in vitro and in vivo. JOURNAL OF FISH DISEASES 2022; 45:895-905. [PMID: 35445749 DOI: 10.1111/jfd.13615] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Revised: 03/17/2022] [Accepted: 03/24/2022] [Indexed: 06/14/2023]
Abstract
Micropterus salmoides rhabdovirus (MSRV) is an significant pathogen that causes high mortality and related economic losses in bass aquaculture. There is no effective or approved therapy to date. In this study, we evaluated the anti-MSRV effects of 22 quinoline derivatives in grass carp ovary (GCO) cells. Among these compounds, 8-hydroxyquinoline exhibited valid inhibition in decreasing MSRV nucleoprotein gene expression levels of 99.3% with a half-maximal inhibitory concentrations (IC50 ) value of 4.66 μM at 48 h. Moreover, 8-hydroxyquinoline significantly enhanced a protective effect in GCO cells by reducing the cytopathic effect (CPE). By comparing the anti-MSRV activity of 22 quinoline derivatives, we found that 8-hydroxyquinoline possessed the efficient active site of 8-hydroxyl and inhibited MSRV infection in vitro. For in vivo studies, 8-hydroxyquinoline via intraperitoneal injection exhibited an antiviral effect in MSRV-infected largemouth bass by substantially enhancing the survival rate by 15.0%. Importantly, the viral loads in the infected largemouth bass notably reduced in the spleen on the third days post-infection. Overall, 8-hydroxyquinoline was considered to be an efficient agent against MSRV in aquaculture.
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Affiliation(s)
- Bo-Yang Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Fei Yang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Zhong-Yu Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yu-Feng Shen
- Changzhou Agricultural Comprehensive Technology Extension Center, Changzhou, Jiangsu, China
| | - Tao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Liang Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Jia-Cheng Qin
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Fei Ling
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Gao-Xue Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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3
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Towards Quantum-Chemical Modeling of the Activity of Anesthetic Compounds. Int J Mol Sci 2021; 22:ijms22179272. [PMID: 34502179 PMCID: PMC8431746 DOI: 10.3390/ijms22179272] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Revised: 08/16/2021] [Accepted: 08/17/2021] [Indexed: 12/16/2022] Open
Abstract
The modeling of the activity of anesthetics is a real challenge because of their unique electronic and structural characteristics. Microscopic approaches relevant to the typical features of these systems have been developed based on the advancements in the theory of intermolecular interactions. By stressing the quantum chemical point of view, here, we review the advances in the field highlighting differences and similarities among the chemicals within this group. The binding of the anesthetics to their partners has been analyzed by Symmetry-Adapted Perturbation Theory to provide insight into the nature of the interaction and the modeling of the adducts/complexes allows us to rationalize their anesthetic properties. A new approach in the frame of microtubule concept and the importance of lipid rafts and channels in membranes is also discussed.
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4
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Regulation and drug modulation of a voltage-gated sodium channel: Pivotal role of the S4-S5 linker in activation and slow inactivation. Proc Natl Acad Sci U S A 2021; 118:2102285118. [PMID: 34260401 PMCID: PMC8285963 DOI: 10.1073/pnas.2102285118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Voltage-gated sodium channels initiate electric signals in cell communications. The S4–S5 linker between the voltage-sensing and pore modules transmits depolarization signals to trigger channel activation. The mechanisms of this action, however, remain elusive. By combining biophysical and computational approaches, we identify a critical residue, T140, in the S4–S5 linker of the bacterial sodium channel NaChBac, which plays a pivotal role in channel activation and drug modulation of slow inactivation. Specifically, we discovered conformation-dependent drug binding at this site and unveiled a toggling mode of action by T140, which switches interaction partners with different S6 residues to regulate channel activation and slow inactivation. These observations suggest the possibility of conformation-specific drugs targeting the gating machinery of voltage-gated ion channels. Voltage-gated sodium (NaV) channels control excitable cell functions. While structural investigations have revealed conformation details of different functional states, the mechanisms of both activation and slow inactivation remain unclear. Here, we identify residue T140 in the S4–S5 linker of the bacterial voltage-gated sodium channel NaChBac as critical for channel activation and drug effects on inactivation. Mutations at T140 either attenuate activation or render the channel nonfunctional. Propofol, a clinical anesthetic known to inhibit NaChBac by promoting slow inactivation, binds to a pocket between the S4–S5 linker and S6 helix in a conformation-dependent manner. Using 19F-NMR to quantify site-specific binding by saturation transfer differences (STDs), we found strong STDs in inactivated, but not activated, NaChBac. Molecular dynamics simulations show a highly dynamic pocket in the activated conformation, limiting STD buildup. In contrast, drug binding to this pocket promotes and stabilizes the inactivated states. Our results provide direct experimental evidence showing distinctly different associations between the S4–S5 linker and S6 helix in activated and inactivated states. Specifically, an exchange occurs between interaction partners T140 and N234 of the same subunit in activation, and T140 and N225 of the domain-swapped subunit in slow inactivation. The drug action on slow inactivation of prokaryotic NaV channels seems to have a mechanism similar to the recently proposed “door-wedge” action of the isoleucine-phenylalanine-methionine (IFM) motif on the fast inactivation of eukaryotic NaV channels. Elucidating this gating mechanism points to a possible direction for conformation-dependent drug development.
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5
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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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6
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Mechanistic basis of propofol-induced disruption of kinesin processivity. Proc Natl Acad Sci U S A 2021; 118:2023659118. [PMID: 33495322 DOI: 10.1073/pnas.2023659118] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Propofol is a widely used general anesthetic to induce and maintain anesthesia, and its effects are thought to occur through impact on the ligand-gated channels including the GABAA receptor. Propofol also interacts with a large number of proteins including molecular motors and inhibits kinesin processivity, resulting in significant decrease in the run length for conventional kinesin-1 and kinesin-2. However, the molecular mechanism by which propofol achieves this outcome is not known. The structural transition in the kinesin neck-linker region is crucial for its processivity. In this study, we analyzed the effect of propofol and its fluorine derivative (fropofol) on the transition in the neck-linker region of kinesin. Propofol binds at two crucial surfaces in the leading head: one at the microtubule-binding interface and the other in the neck-linker region. We observed in both the cases the order-disorder transition of the neck-linker was disrupted and kinesin lost its signal for forward movement. In contrast, there was not an effect on the neck-linker transition with propofol binding at the trailing head. Free-energy calculations show that propofol at the microtubule-binding surface significantly reduces the microtubule-binding affinity of the kinesin head. While propofol makes pi-pi stacking and H-bond interactions with the propofol binding cavity, fropofol is unable to make a suitable interaction at this binding surface. Therefore, the binding affinity of fropofol is much lower compared to propofol. Hence, this study provides a mechanism by which propofol disrupts kinesin processivity and identifies transitions in the ATPase stepping cycle likely affected.
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7
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White ER, Leace DM, Bedell VM, Bhanu NV, Garcia BA, Dailey WP, Eckenhoff RG. Synthesis and Characterization of a Diazirine-Based Photolabel of the Nonanesthetic Fropofol. ACS Chem Neurosci 2021; 12:176-183. [PMID: 33355437 PMCID: PMC7948515 DOI: 10.1021/acschemneuro.0c00667] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The mechanisms of general anesthetics have been debated in the literature for many years and continue to be of great interest. As anesthetic molecules are notoriously difficult to study due to their low binding affinities and multitude of binding partners, it is advantageous to have additional tools to study these interactions. Fropofol is a hydroxyl to fluorine-substituted propofol analogue that is able to antagonize the actions of propofol. Understanding fropofol's ability to antagonize propofol would facilitate further characterization of the binding interactions of propofol that may contribute to its anesthetic actions. However, the study of fropofol's molecular interactions has many of the same difficulties as its parent compound. Here, we present the synthesis and characterization of ortho-azi-fropofol (AziFo) as a suitable photoaffinity label (PAL) of fropofol that can be used to covalently label proteins of interest to characterize fropofol's binding interactions and their contribution to general anesthetic antagonism.
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Affiliation(s)
- E Railey White
- Perelman School of Medicine, Department of Anesthesiology and Critical Care, University of Pennsylvania, John Morgan Building, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - David M Leace
- Perelman School of Medicine, Department of Anesthesiology and Critical Care, University of Pennsylvania, John Morgan Building, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Victoria M Bedell
- Perelman School of Medicine, Department of Anesthesiology and Critical Care, University of Pennsylvania, John Morgan Building, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
| | - Natarajan V Bhanu
- Perelman School of Medicine, Department of Biochemistry and Biophysics, Smilow Center for Translational Research, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, United States
| | - Benjamin A Garcia
- Perelman School of Medicine, Department of Biochemistry and Biophysics, Smilow Center for Translational Research, University of Pennsylvania, 3400 Civic Center Boulevard, Philadelphia, Pennsylvania 19104, United States
| | - William P Dailey
- Department of Chemistry, University of Pennsylvania, 231 S. 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Roderic G Eckenhoff
- Perelman School of Medicine, Department of Anesthesiology and Critical Care, University of Pennsylvania, John Morgan Building, 3620 Hamilton Walk, Philadelphia, Pennsylvania 19104, United States
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8
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Wang Y, Ming XX, Zhang CP. Fluorine-Containing Inhalation Anesthetics: Chemistry, Properties and Pharmacology. Curr Med Chem 2020; 27:5599-5652. [DOI: 10.2174/0929867326666191003155703] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 08/27/2019] [Accepted: 09/05/2019] [Indexed: 02/07/2023]
Abstract
Studies on fluorinated inhalation anesthetics, including synthesis, physical chemistry and
pharmacology, have been summarized in this review. Retrospecting the history of inhalation anesthetics
revealed their increasing reliance on fluorine and ether structures. Halothane causes a rare but
severe immune-based hepatotoxicity, which was replaced by enflurane in the 1970s. Isoflurane replaced
enflurane in the 1980s, showing modest advantages (e.g. lower solubility, better metabolic
stability, and without convulsive predisposition). Desflurane and sevoflurane came into use in the
1990s, which are better anesthetics than isoflurane (less hepatotoxicity, lower solubility, and/or
markedly decreased pungency). However, they are still less than perfect. To gain more ideal inhalation
anesthetics, a large number of fluorinated halocarbons, polyfluorocycloalkanes, polyfluorocycloalkenes,
fluoroarenes, and polyfluorooxetanes, were prepared and their potency and toxicity were
evaluated. Although the pharmacology studies suggested that some of these agents produced anesthesia,
no further studies were continued on these compounds because they showed obvious lacking
as anesthetics. Moreover, the anesthetic activity cannot be simply predicted from the molecular
structures but has to be inferred from the experiments. Several regularities were found by experimental
studies: 1) the potency and toxicity of the saturated linear chain halogenated ether are enhanced
when its molecular weight is increased; 2) the margin of safety decreases and the recovery
time is prolonged when the boiling point of the candidate increases; and 3) compounds with an
asymmetric carbon terminal exhibit good anesthesia. Nevertheless, the development of new inhalation
anesthetics, better than desflurane and sevoflurane, is still challenging not only because of the
poor structure/activity relationship known so far but also due to synthetic issues.
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Affiliation(s)
- Yuzhong Wang
- The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST) & Key Laboratory of Oral Biomedicine Ministry of Education, School and Hospital of Stomatology, Wuhan University, 237 Luoyu Road, Wuhan 430079, China
| | - Xiao-Xia Ming
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan 430070, China
| | - Cheng-Pan Zhang
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 205 Luoshi Road, Wuhan 430070, China
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9
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Joyce RL, Beyer NP, Vasilopoulos G, Woll KA, Hall AC, Eckenhoff RG, Barman DN, Warren JD, Tibbs GR, Goldstein PA. Alkylphenol inverse agonists of HCN1 gating: H-bond propensity, ring saturation and adduct geometry differentially determine efficacy and potency. Biochem Pharmacol 2019; 163:493-508. [PMID: 30768926 DOI: 10.1016/j.bcp.2019.02.013] [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: 11/29/2018] [Accepted: 02/11/2019] [Indexed: 10/27/2022]
Abstract
BACKGROUND AND PURPOSE In models of neuropathic pain, inhibition of HCN1 is anti-hyperalgesic. 2,6-di-iso-propyl phenol (propofol) and its non-anesthetic congener, 2,6-di-tert-butyl phenol, inhibit HCN1 channels by stabilizing closed state(s). EXPERIMENTAL APPROACH Using in vitro electrophysiology and kinetic modeling, we systematically explore the contribution of ligand architecture to alkylphenol-channel coupling. KEY RESULTS When corrected for changes in hydrophobicity (and propensity for intra-membrane partitioning), the decrease in potency upon 1-position substitution (NCO∼OH >> SH >>> F) mirrors the ligands' H-bond acceptor (NCO > OH > SH >>> F) but not donor profile (OH > SH >>> NCO∼F). H-bond elimination (OH to F) corresponds to a ΔΔG of ∼4.5 kCal mol-1 loss of potency with little or no disruption of efficacy. Substitution of compact alkyl groups (iso-propyl, tert-butyl) with shorter (ethyl, methyl) or more extended (sec-butyl) adducts disrupts both potency and efficacy. Ring saturation (with the obligate loss of both planarity and π electrons) primarily disrupts efficacy. CONCLUSIONS AND IMPLICATIONS A hydrophobicity-independent decrement in potency at higher volumes suggests the alkylbenzene site has a volume of ≥800 Å3. Within this, a relatively static (with respect to ligand) H-bond donor contributes to initial binding with little involvement in generation of coupling energy. The influence of π electrons/ring planarity and alkyl adducts on efficacy reveals these aspects of the ligand present towards a face of the channel that undergoes structural changes during opening. The site's characteristics suggest it is "druggable"; introduction of other adducts on the ring may generate higher potency inverse agonists.
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Affiliation(s)
| | | | | | - Kellie A Woll
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
| | - Adam C Hall
- Smith College, Northampton, MA, United States
| | - Roderic G Eckenhoff
- University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, United States
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10
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Ibeji CU, Tolufashe GF, Ntombela T, Govender T, Maguire GEM, Lamichhane G, Kruger HG, Honarparvar B. The catalytic role of water in the binding site of l,d-transpeptidase 2 within acylation mechanism: A QM/MM (ONIOM) modelling. Tuberculosis (Edinb) 2018; 113:222-230. [PMID: 30514506 DOI: 10.1016/j.tube.2018.10.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 10/11/2018] [Accepted: 10/14/2018] [Indexed: 01/13/2023]
Abstract
Mycobacterium tuberculosis is the causative agent of Tuberculosis. Formation of 3 → 3 crosslinks in the peptidoglycan layer of M. tuberculosis is catalyzed by l,d-transpeptidases. These enzymes can confer resistance against classical β-lactams that inhibit enzymes that generate 4 → 3 peptidoglycan crosslinks. The focus of this study is to investigate the catalytic role of water molecules in the acylation mechanism of the β-lactam ring within two models; 4- and 6-membered ring systems using two-layered our Own N-layer integrated Molecular Mechanics ONIOM (B3LYP/6-311++G(2d,2p): AMBER) model. The obtained thermochemical parameters revealed that the 6-membered ring model best describes the inhibition mechanism of acylation which indicates the role of water in the preference of 6-membered ring reaction pathway. This finding is in accordance with experimental data for the rate-limiting step of cysteine protease with the same class of inhibitor and binding affinity for both inhibitors. As expected, the ΔG# results also reveal that the 6-membered ring reaction pathway is the most favourable. The electrostatic potential (ESP) and the natural bond orbital analysis (NBO) showed stronger interactions in 6-membered ring transition state (TS-6) mechanism involving water in the active site of the enzyme. This study could be helpful in the development of novel antibiotics against l,d-transpeptidase.
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Affiliation(s)
- Collins U Ibeji
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa; Department of Pure and Industrial Chemistry, Faculty of Physical Sciences, University of Nigeria, Nsukka, 410001, Enugu State, Nigeria
| | - Gideon F Tolufashe
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Thandokuhle Ntombela
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Thavendran Govender
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Glenn E M Maguire
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa; School of Chemistry and Physics, University of KwaZulu-Natal, Durban, 4041, South Africa
| | - Gyanu Lamichhane
- Center for Tuberculosis Research, Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, 21287, USA
| | - Hendrik G Kruger
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.
| | - Bahareh Honarparvar
- Catalysis and Peptide Research Unit, School of Health Sciences, University of KwaZulu-Natal, Durban, 4041, South Africa.
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11
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Fahrenbach VS, Bertaccini EJ. Insights Into Receptor-Based Anesthetic Pharmacophores and Anesthetic-Protein Interactions. Methods Enzymol 2018; 602:77-95. [PMID: 29588042 DOI: 10.1016/bs.mie.2018.01.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
General anesthetics are thought to allosterically bind and potentiate the inhibitory currents of the GABAA receptor through drug-specific binding sites. The physiologically relevant isoform of the GABAA receptor is a transmembrane ligand-gated ion channel consisting of five subunits (γ-α-β-α-β linkage) symmetrically arranged around a central chloride-conducting pore. Although the exact molecular structure of this heteropentameric GABAA receptor remains unknown, molecular modeling has allowed significant advancements in understanding anesthetic binding and action. Using the open-channel conformations of the homologous glycine and glutamate-gated chloride receptors as templates, a homology model of the GABAA receptor was constructed using the Discovery Studio computational chemistry software suite. Consensus structural alignment of the homology templates allowed for the construction of a three-dimensional heteropentameric GABAA receptor model with (γ2-β3-α1-β3-α1) subunit linkage. An anesthetic binding site was identified within the transmembrane α/β intersubunit space by the convergence of three residues shown to be essential for anesthetic activity in previous studies with mutant mice (β3-N265, β3-M286, α1-L232). Propofol derivatives docked into this binding site showed log-linear correlation with experimentally derived GABAA receptor potentiation (EC50) values, suggesting this binding site may be important for receptor activation. The receptor-based pharmacophore was analyzed with surface maps displaying the predominant anesthetic-protein interactions, revealing an amphiphilic binding cavity incorporating the three residues involved in anesthetic modulation. Quantum mechanics calculations of the bonding patterns found in complementary high-resolution receptor systems further elucidated the complex nature of anesthetic-protein interactions.
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Affiliation(s)
- Victoria S Fahrenbach
- Stanford University School of Medicine, Stanford, CA, United States; Palo Alto VA Health Care System, Palo Alto, CA, United States
| | - Edward J Bertaccini
- Stanford University School of Medicine, Stanford, CA, United States; Palo Alto VA Health Care System, Palo Alto, CA, United States.
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12
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Looking Back, Looking Forward at Halogen Bonding in Drug Discovery. Molecules 2017; 22:molecules22091397. [PMID: 28837116 PMCID: PMC6151711 DOI: 10.3390/molecules22091397] [Citation(s) in RCA: 117] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 08/18/2017] [Indexed: 11/25/2022] Open
Abstract
Halogen bonding has emerged at the forefront of advances in improving ligand: receptor interactions. In particular the newfound ability of this extant non-covalent-bonding phenomena has revolutionized computational approaches to drug discovery while simultaneously reenergizing synthetic approaches to the field. Here we survey, via examples of classical applications involving halogen atoms in pharmaceutical compounds and their biological hosts, the unique advantages that halogen atoms offer as both Lewis acids and Lewis bases.
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