A comprehensive evaluation of the potential binding poses of fentanyl and its analogs at the µ-opioid receptor

Computational and Structural Biotechnology Journal - Tập 20 - Trang 2309-2321 - 2022
Bing Xie1, Alexander Goldberg1, Lei Shi1
1Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse – Intramural Research Program, National Institutes of Health, Baltimore, MD 21224, USA

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Pasternak, 2013, Mu opioids and their receptors: evolution of a concept, Pharmacol Rev, 65, 1257, 10.1124/pr.112.007138

Stanley, 2014, The fentanyl story, J Pain, 15, 1215, 10.1016/j.jpain.2014.08.010

Baumann, 2018, Pharmacological research as a key component in mitigating the opioid overdose crisis, Trends Pharmacol Sci, 39, 995, 10.1016/j.tips.2018.09.006

The Drug Enforcement Administration's (DEA) special testing and research laboratory’s emerging trends program. DEA Emerging Threat Reports. 2020, May 1; Available from: https://ndews.umd.edu/resources/dea-emerging-threat-reports.

Comer, 2019, Fentanyl: Receptor pharmacology, abuse potential, and implications for treatment, Neurosci Biobehav Rev, 106, 49, 10.1016/j.neubiorev.2018.12.005

Haley, 2020, The opioid epidemic during the COVID-19 pandemic, JAMA, 324, 1615, 10.1001/jama.2020.18543

Schmid, 2017, Bias factor and therapeutic window correlate to predict safer opioid analgesics, Cell, 171, 1165, 10.1016/j.cell.2017.10.035

Ehrlich, 2019, Biased signaling of the mu opioid receptor revealed in native neurons, iScience, 14, 47, 10.1016/j.isci.2019.03.011

Gillis, 2020, Low intrinsic efficacy for G protein activation can explain the improved side effect profiles of new opioid agonists, Sci Signal, 13, 10.1126/scisignal.aaz3140

Stahl, 2021, Low intrinsic efficacy alone cannot explain the improved side effect profiles of new opioid agonists, Biochemistry

Kelly, 2021, The anomalous pharmacology of fentanyl, Br J Pharmacol

Subramanian, 2000, Molecular docking reveals a novel binding site model for fentanyl at the mu-opioid receptor, J Med Chem, 43, 381, 10.1021/jm9903702

Dosen-Micovic, 2006, Steric interactions and the activity of fentanyl analogs at the mu-opioid receptor, Bioorg Med Chem, 14, 2887, 10.1016/j.bmc.2005.12.010

Huang, 2015, Structural insights into micro-opioid receptor activation, Nature, 524, 315, 10.1038/nature14886

Manglik, 2012, Crystal structure of the micro-opioid receptor bound to a morphinan antagonist, Nature, 10.1038/nature10954

Koehl, 2018, Structure of the micro-opioid receptor-Gi protein complex, Nature, 558, 547, 10.1038/s41586-018-0219-7

Kapoor, 2020, Atomic-level characterization of the methadone-stabilized active conformation of µ-opioid receptor, Mol Pharmacol, 98, 475, 10.1124/mol.119.119339

Mafi, 2020, Mechanism of β-arrestin recruitment by the μ-opioid G protein-coupled receptor, Proc Natl Acad Sci U S A, 117, 16346, 10.1073/pnas.1918264117

Ellis, 2018, Predicting opioid receptor binding affinity of pharmacologically unclassified designer substances using molecular docking, PLoS ONE, 13, e0197734, 10.1371/journal.pone.0197734

Lipinski, 2019, Molecular dynamics of fentanyl bound to mu-opioid receptor, J Mol Model, 25, 144, 10.1007/s00894-019-3999-2

de Waal, 2020, Molecular mechanisms of fentanyl mediated beta-arrestin biased signaling, PLoS Comput Biol, 16, e1007394, 10.1371/journal.pcbi.1007394

Podlewska, 2020, Molecular modeling of µ opioid receptor ligands with various functional properties: PZM21, SR-17018, morphine, and fentanyl-simulated interaction patterns confronted with experimental data, Molecules, 25, 10.3390/molecules25204636

Ricarte, 2021, Structural assessment of agonist efficacy in the μ-opioid receptor: morphine and fentanyl elicit different activation patterns, J Chem Inf Model, 61, 1251, 10.1021/acs.jcim.0c00890

Vo, 2021, How mu-opioid receptor recognizes fentanyl, Nat Commun, 12, 984, 10.1038/s41467-021-21262-9

Eshleman, 2020, Affinity, potency, efficacy, selectivity, and molecular modeling of substituted fentanyls at opioid receptors, Biochem Pharmacol, 182, 10.1016/j.bcp.2020.114293

Ballesteros JA, Weinstein H. Modeling transmembrane helix contacts in GPCR. In: Biophysical Society Meeting. 1995. San Francisco, CA.

Van Bever, 1974, Synthetic analgesics. Synthesis and pharmacology of the diastereoisomers of N-(3-methyl-1-(2-phenylethyl)-4-piperidyl)-N-phenylpropanamide and N-(3-methyl-1-(1-methyl-2-phenylethyl)-4-piperidyl)-N-phenylpropanamide, J Med Chem, 17, 1047, 10.1021/jm00256a003

Zawilska, 2021, Carfentanil - from an animal anesthetic to a deadly illicit drug, Forensic Sci Int, 320, 10.1016/j.forsciint.2021.110715

Wax, 2003, Unexpected “gas” casualties in Moscow: a medical toxicology perspective, Ann Emerg Med, 41, 700, 10.1067/mem.2003.148

Jin, 1981, Studies on synthesis and relationship between analgesic activity and receptor affinity for 3-methyl fentanyl derivatives, Sci Sin, 24, 710

Xu, 1991, (+)-cis-3-methylfentanyl and its analogs bind pseudoirreversibly to the mu opioid binding site: evidence for pseudoallosteric modulation, Neuropharmacology, 30, 455, 10.1016/0028-3908(91)90006-W

Maguire, 1992, Pharmacological profiles of fentanyl analogs at mu, delta and kappa opiate receptors, Eur J Pharmacol, 213, 219, 10.1016/0014-2999(92)90685-W

Yeadon, 1988, Differences in the characteristics of opioid receptor binding in the rat and marmoset, J Pharm Pharmacol, 40, 736, 10.1111/j.2042-7158.1988.tb07008.x

Janssen, 1982, Potent, new analgesics, tailor-made for different purposes, Acta Anaesthesiol Scand, 26, 262, 10.1111/j.1399-6576.1982.tb01765.x

Leysen, 1983, [3H]Sufentanil, a superior ligand for mu-opiate receptors: binding properties and regional distribution in rat brain and spinal cord, Eur J Pharmacol, 87, 209, 10.1016/0014-2999(83)90331-X

Tollenaere, 1986, On conformation analysis, molecular graphics, fentanyl and its derivatives, Prog Drug Res, 30, 91

Leysen, 1978, Receptor binding properties in vitro and in vivo of some long-acting opiates, Arch Int Pharmacodyn Ther, 232, 243

Stahl, 1977, Receptor affinity and pharmacological potency of a series of narcotic analgesic, anti-diarrheal and neuroleptic drugs, Eur J Pharmacol, 46, 199, 10.1016/0014-2999(77)90334-X

Leysen, J, Laduron, P, and Niemegeers, C, Receptor binding properties in vitro and in vivo of new long acting narcotic analgesics. In: Characteristics and function of opioids. 1978, Elsevier North-Holland Biomedical Press Amsterdam. p. 479-482.

Flippenanderson, 1994, X-ray crystal-structures of potent opioid receptor ligands - etonitazene, cis-(+)-3-methylfentanyl, etorphine, diprenorphine, and buprenorphine, Heterocycles, 39, 751, 10.3987/COM-94-S(B)70

Xu, 1999, Opioid peptide receptor studies, 11: involvement of Tyr148, Trp318 and His319 of the rat mu-opioid receptor in binding of mu-selective ligands, Synapse, 32, 23, 10.1002/(SICI)1098-2396(199904)32:1<23::AID-SYN3>3.0.CO;2-N

Lesnik, 2020, Potential Energy Function for Fentanyl-Based Opioid Pain Killers, J Chem Inf Model, 60, 3566, 10.1021/acs.jcim.0c00185

Giannos, 2021, CHARMM force-field parameters for morphine, heroin, and oliceridine, and conformational dynamics of opioid drugs, J Chem Inf Model, 61, 3964, 10.1021/acs.jcim.1c00667

Roos, 2019, OPLS3e: extending force field coverage for drug-like small molecules, J Chem Theory Comput, 15, 1863, 10.1021/acs.jctc.8b01026

Lu, 2021, OPLS4: improving force field accuracy on challenging regimes of chemical space, J Chem Theory Comput, 10.1021/acs.jctc.1c00302

Bochevarov, 2013, Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences, Int J Quantum Chem, 113, 2110, 10.1002/qua.24481

Bowers, 2006, Scalable algorithms for molecular dynamics simulations on commodity clusters

Dijkstra, 1959, A note on two problems in connexion with graphs, Numer Math, 1, 269, 10.1007/BF01386390

Li, 2011, The VSGB 2.0 model: a next generation energy model for high resolution protein structure modeling, Proteins, 79, 2794, 10.1002/prot.23106

John, 2003, Comparative protein structure modeling by iterative alignment, model building and model assessment, Nucleic Acids Res, 31, 3982, 10.1093/nar/gkg460

Olsson, 2011, PROPKA3: consistent treatment of internal and surface residues in empirical pKa predictions, J Chem Theory Comput, 7, 525, 10.1021/ct100578z

Sherman, 2006, Novel procedure for modeling ligand/receptor induced fit effects, J Med Chem, 49, 534, 10.1021/jm050540c

Dror, 2011, Activation mechanism of the beta2-adrenergic receptor, Proc Natl Acad Sci U S A, 108, 18684, 10.1073/pnas.1110499108

Lane, 2020, Distinct inactive conformations of the dopamine D2 and D3 receptors correspond to different extents of inverse agonism, Elife, 9, 10.7554/eLife.52189

Humphrey W, Dalke A, Schulten K. VMD: visual molecular dynamics. J Mol Graph, 1996; 14(1): 33-8, 27-8.

Stolzenberg, S, Michino, M, LeVine, MV, Weinstein, H, and Shi, L, Computational approaches to detect allosteric pathways in transmembrane molecular machines. Biochim Biophys Acta, 2016; 1858(7 Pt B): 1652-62.

Michino, 2017, Toward understanding the structural basis of partial agonism at the dopamine D3 receptor, J Med Chem, 60, 580, 10.1021/acs.jmedchem.6b01148

Bick, 2017, Computational design of environmental sensors for the potent opioid fentanyl, Elife, 6, 10.7554/eLife.28909

Laio, 2002, Escaping free-energy minima, Proc Natl Acad Sci U S A, 99, 12562, 10.1073/pnas.202427399

Branduardi, 2013, String method for calculation of minimum free-energy paths in Cartesian space in freely-tumbling systems, J Chem Theory Comput, 9, 4140, 10.1021/ct400469w

Liu, 2011, Lipophilicity and its relationship with passive drug permeation, Pharm Res, 28, 962, 10.1007/s11095-010-0303-7

Mansour, 1997, Key residues defining the mu-opioid receptor binding pocket: a site-directed mutagenesis study, J Neurochem, 68, 344, 10.1046/j.1471-4159.1997.68010344.x

Bonner, 2000, Selectivity of mu-opioid receptor determined by interfacial residues near third extracellular loop, Eur J Pharmacol, 403, 37, 10.1016/S0014-2999(00)00578-1

Spivak, 1997, Naloxone activation of mu-opioid receptors mutated at a histidine residue lining the opioid binding cavity, Mol Pharmacol, 52, 983, 10.1124/mol.52.6.983

Katritch, 2014, Allosteric sodium in class A GPCR signaling, Trends Biochem Sci, 39, 233, 10.1016/j.tibs.2014.03.002

Lesnik, 2021, Opioid receptors and protonation-coupled binding of opioid drugs, Int J Mol Sci, 22, 10.3390/ijms222413353

Kelly, 2013, Efficacy and ligand bias at the mu-opioid receptor, Br J Pharmacol, 169, 1430, 10.1111/bph.12222

Tong, 2021, Large-scale analysis of bioactive ligand conformational strain energy by ab initio calculation, J Chem Inf Model, 61, 1180, 10.1021/acs.jcim.0c01197

Lalinde, 1990, Synthesis and pharmacological evaluation of a series of new 3-methyl-1,4-disubstituted-piperidine analgesics, J Med Chem, 33, 2876, 10.1021/jm00172a032

Abramyan, 2019, Computation-guided analysis of paroxetine binding to hSERT reveals functionally important structural elements and dynamics, Neuropharmacology, 161, 10.1016/j.neuropharm.2018.10.040