Structural Determinants for the Binding of Morphinan Agonists to the μ-Opioid Receptor

Atomistic descriptions of the μ-opioid receptor (μOR) noncovalently binding with two of its prototypical morphinan agonists, morphine (MOP) and hydromorphone (HMP), are investigated using molecular dynamics (MD) simulations. Subtle differences between the binding modes and hydration properties of MOP and HMP emerge from the calculations. Alchemical free energy perturbation calculations show qualitative agreement with in vitro experiments performed in this work: indeed, the binding free energy difference between MOP and HMP computed by forward and backward alchemical transformation is 1.2±1.1 and 0.8±0.8 kcal/mol, respectively, to be compared with 0.4±0.3 kcal/mol from experiment. Comparison with an MD simulation of μOR covalently bound with the antagonist β-funaltrexamine hints to agonist-induced conformational changes associated with an early event of the receptor’s activation: a shift of the transmembrane helix 6 relative to the transmembrane helix 3 and a consequent loss of the key R165-T279 interhelical hydrogen bond. This finding is consistent with a previous proposal suggesting that the R165-T279 hydrogen bond between these two helices indicates an inactive receptor conformation.

[1]  M. Connor,et al.  Opioids: cellular mechanisms of tolerance and physical dependence. , 2005, Current opinion in pharmacology.

[2]  Alexander P. Lyubartsev,et al.  Derivation and Systematic Validation of a Refined All-Atom Force Field for Phosphatidylcholine Lipids , 2012, The journal of physical chemistry. B.

[3]  Carsten Kutzner,et al.  GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation. , 2008, Journal of chemical theory and computation.

[4]  B. Roux,et al.  The free energy landscapes governing conformational changes in a glutamate receptor ligand-binding domain. , 2007, Structure.

[5]  Paul Labute,et al.  The generalized Born/volume integral implicit solvent model: Estimation of the free energy of hydration using London dispersion instead of atomic surface area , 2008, J. Comput. Chem..

[6]  Berk Hess,et al.  LINCS: A linear constraint solver for molecular simulations , 1997, J. Comput. Chem..

[7]  Jan Hermans,et al.  Hydrophilicity of cavities in proteins , 1996 .

[8]  H. Loh,et al.  Opioid receptors: toward separation of analgesic from undesirable effects. , 2013, Trends in biochemical sciences.

[9]  J. Traynor,et al.  Opioid receptor interacting proteins and the control of opioid signaling. , 2014, Current pharmaceutical design.

[10]  G Vassart,et al.  ORL1, a novel member of the opioid receptor family , 1994, FEBS letters.

[11]  P. Labute.  proteins STRUCTURE O FUNCTION O BIOINFORMATICS Protonate3D: Assignment of ionization , 2013 .

[12]  Y. Cheng,et al.  Relationship between the inhibition constant (K1) and the concentration of inhibitor which causes 50 per cent inhibition (I50) of an enzymatic reaction. , 1973, Biochemical pharmacology.

[13]  Ruben Abagyan,et al.  The GPCR Network: a large-scale collaboration to determine human GPCR structure and function , 2012, Nature Reviews Drug Discovery.

[14]  P. Scheerer,et al.  A G protein-coupled receptor at work: the rhodopsin model. , 2009, Trends in biochemical sciences.

[15]  Andrei L. Lomize,et al.  OPM: Orientations of Proteins in Membranes database , 2006, Bioinform..

[16]  R. Dror,et al.  Improved side-chain torsion potentials for the Amber ff99SB protein force field , 2010, Proteins.

[17]  J. Åqvist,et al.  Ion-water interaction potentials derived from free energy perturbation simulations , 1990 .

[18]  T. Kenakin.  Functional Selectivity and Biased Receptor Signaling , 2011, Journal of Pharmacology and Experimental Therapeutics.

[19]  J. Violin,et al.  Biased ligands: pathway validation for novel GPCR therapeutics. , 2014, Current opinion in pharmacology.

[20]  John Hughes,et al.  Endogenous opioid peptides: multiple agonists and receptors , 1977, Nature.

[21]  Görel Sundström,et al.  Evolution of vertebrate opioid receptors , 2008, Proceedings of the National Academy of Sciences.

[22]  S. Ross,et al.  The Neurobiology of Addictive Disorders , 2009, Clinical neuropharmacology.

[23]  T. Schwartz,et al.  Molecular mechanism of 7TM receptor activation--a global toggle switch model. , 2006, Annual review of pharmacology and toxicology.

[24]  P. Kollman,et al.  How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? , 2000 .

[25]  B. Kuehn.  Prescription drug abuse rises globally. , 2007, JAMA.

[26]  Alexander P Lyubartsev,et al.  An Extension and Further Validation of an All-Atomistic Force Field for Biological Membranes. , 2012, Journal of chemical theory and computation.

[27]  Benjamin G Tehan,et al.  Unifying family A GPCR theories of activation. , 2014, Pharmacology & therapeutics.

[28]  X. Daura,et al.  Peptide Folding: When Simulation Meets Experiment , 1999 .

[29]  Junmei Wang,et al.  Development and testing of a general amber force field , 2004, J. Comput. Chem..

[30]  H. C. Andersen.  Molecular dynamics simulations at constant pressure and/or temperature , 1980 .

[31]  B. Roux,et al.  The Hidden Energetics of Ligand-Binding and Activation in a Glutamate Receptor , 2010, Nature Structural &Molecular Biology.

[32]  H. Akil,et al.  Key Residues Defining the μ‐Opioid Receptor Binding Pocket: A Site‐Directed Mutagenesis Study , 1997, Journal of neurochemistry.

[33]  S. Nosé,et al.  Constant pressure molecular dynamics for molecular systems , 1983 .

[34]  Makiko Suwa,et al.  Functional and Structural Overview of G-Protein-Coupled Receptors Comprehensively Obtained from Genome Sequences , 2011, Pharmaceuticals.

[35]  M. Spetea,et al.  The µ opioid receptor and ligands acting at the µ opioid receptor, as therapeutics and potential therapeutics. , 2014, Current pharmaceutical design.

[36]  M. Brownstein.  A brief history of opiates, opioid peptides, and opioid receptors. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[37]  Guodong Liu,et al.  A G Protein-Biased Ligand at the μ-Opioid Receptor Is Potently Analgesic with Reduced Gastrointestinal and Respiratory Dysfunction Compared with Morphine , 2013, The Journal of Pharmacology and Experimental Therapeutics.

[38]  Brigitte L. Kieffer,et al.  Loss of morphine-induced analgesia, reward effect and withdrawal symptoms in mice lacking the µ-opioid-receptor gene , 1996, Nature.

[39]  T Darden,et al.  New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations. , 1999, Structure.

[40]  Lenwood S. Heath,et al.  H++: a server for estimating pKas and adding missing hydrogens to macromolecules , 2005, Nucleic Acids Res..

[41]  L. Pardo,et al.  Crystal structure of the μ-opioid receptor bound to a morphinan antagonist , 2012, Nature.

[42]  Shuguang Yuan,et al.  The role of water and sodium ions in the activation of the μ-opioid receptor. , 2013, Angewandte Chemie.

[43]  Ben M. Webb,et al.  Comparative Protein Structure Modeling Using Modeller , 2006, Current protocols in bioinformatics.

[44]  M. Christie.  Cellular neuroadaptations to chronic opioids: tolerance, withdrawal and addiction , 2008, British journal of pharmacology.

[45]  L. Bohn,et al.  Functional selectivity of GPCR signaling in animals. , 2014, Current opinion in cell biology.

[46]  Gerrit Groenhof,et al.  GROMACS: Fast, flexible, and free , 2005, J. Comput. Chem..

[47]  W. L. Jorgensen,et al.  Comparison of simple potential functions for simulating liquid water , 1983 .

[48]  M. Parrinello,et al.  Polymorphic transitions in single crystals: A new molecular dynamics method , 1981 .

[49]  J. Kirkwood.  Statistical Mechanics of Fluid Mixtures , 1935 .

[50]  N. Tattrie,et al.  Maximum and minimum values for lecithin classes from various biological sources. , 1968, Canadian journal of biochemistry.

[51]  Adrian W. R. Serohijos,et al.  Structural basis for μ-opioid receptor binding and activation. , 2011, Structure.

[52]  S. Rasmussen,et al.  Crystal Structure of the β2Adrenergic Receptor-Gs protein complex , 2011, Nature.

[53]  Christian Kandt,et al.  LAMBADA and InflateGRO2: Efficient Membrane Alignment and Insertion of Membrane Proteins for Molecular Dynamics Simulations , 2012, J. Chem. Inf. Model..

[54]  Manfred J. Sippl,et al.  NQ-Flipper: recognition and correction of erroneous asparagine and glutamine side-chain rotamers in protein structures , 2007, Nucleic Acids Res..

[55]  H Weinstein,et al.  Functional role of a conserved motif in TM6 of the rat mu opioid receptor: constitutively active and inactive receptors result from substitutions of Thr6.34(279) with Lys and Asp. , 2001, Biochemistry.

[56]  G. Uhl,et al.  -mu opiate receptor. Charged transmembrane domain amino acids are critical for agonist recognition and intrinsic activity. , 1994, The Journal of biological chemistry.