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Volumn 30, Issue , 2016, Pages 14-21

Guiding lead optimization with GPCR structure modeling and molecular dynamics

Author keywords

[No Author keywords available]

Indexed keywords

G PROTEIN COUPLED RECEPTOR; MELANIN CONCENTRATING HORMONE RECEPTOR 1; MELANIN CONCENTRATING HORMONE RECEPTOR 1 ANTAGONIST; OREXIN 2 RECEPTOR; OREXIN RECEPTOR ANTAGONIST; POTASSIUM CHANNEL HERG; SEROTONIN 2C AGONIST; SEROTONIN 2C RECEPTOR; WATER; LIGAND; PROTEIN BINDING;

EID: 84978531774     PISSN: 14714892     EISSN: 14714973     Source Type: Journal    
DOI: 10.1016/j.coph.2016.06.004     Document Type: Review
Times cited : (27)

References (49)
  • 1
    • 84947032095 scopus 로고    scopus 로고
    • Structures of G protein-coupled receptors reveal new opportunities for drug discovery
    • Important review that describes recent breakthroughs in GPCR crystallography and how this new information changed the way we approach GPCR drug-discovery.
    • 1• Cooke, R.M., Brown, A.J., Marshall, F.H., Mason, J.S., Structures of G protein-coupled receptors reveal new opportunities for drug discovery. Drug Discov Today 20 (2015), 1355–1364 Important review that describes recent breakthroughs in GPCR crystallography and how this new information changed the way we approach GPCR drug-discovery.
    • (2015) Drug Discov Today , vol.20 , pp. 1355-1364
    • Cooke, R.M.1    Brown, A.J.2    Marshall, F.H.3    Mason, J.S.4
  • 2
    • 84891751622 scopus 로고    scopus 로고
    • The druggable genome: evaluation of drug targets in clinical trials suggests major shifts in molecular class and indication
    • 2 Rask-Andersen, M., Masuram, S., Schioth, H.B., The druggable genome: evaluation of drug targets in clinical trials suggests major shifts in molecular class and indication. Annu Rev Pharmacol Toxicol 54 (2014), 9–26.
    • (2014) Annu Rev Pharmacol Toxicol , vol.54 , pp. 9-26
    • Rask-Andersen, M.1    Masuram, S.2    Schioth, H.B.3
  • 3
    • 0037082324 scopus 로고    scopus 로고
    • Target validation of G-protein coupled receptors
    • 3 Wise, A., Gearing, K., Rees, S., Target validation of G-protein coupled receptors. Drug Discov Today 7 (2002), 235–246.
    • (2002) Drug Discov Today , vol.7 , pp. 235-246
    • Wise, A.1    Gearing, K.2    Rees, S.3
  • 6
    • 84939156572 scopus 로고    scopus 로고
    • Thematic minireview series: new directions in G protein-coupled receptor pharmacology
    • 6 Dohlman, H.G., Thematic minireview series: new directions in G protein-coupled receptor pharmacology. J Biol Chem 290 (2015), 19469–19470.
    • (2015) J Biol Chem , vol.290 , pp. 19469-19470
    • Dohlman, H.G.1
  • 7
    • 84939180100 scopus 로고    scopus 로고
    • From G Protein-coupled receptor structure resolution to rational drug design
    • Important review that outlines some of the approaches used in GPCR structure-based drug design and describes technical solutions that have accelerated GPCR crystallography as well as some of the salient findings from structures that are relevant to drug discovery.
    • 7•• Jazayeri, A., Dias, J.M., Marshall, F.H., From G Protein-coupled receptor structure resolution to rational drug design. J Biol Chem 290 (2015), 19489–19495 Important review that outlines some of the approaches used in GPCR structure-based drug design and describes technical solutions that have accelerated GPCR crystallography as well as some of the salient findings from structures that are relevant to drug discovery.
    • (2015) J Biol Chem , vol.290 , pp. 19489-19495
    • Jazayeri, A.1    Dias, J.M.2    Marshall, F.H.3
  • 8
    • 84930870342 scopus 로고    scopus 로고
    • Structure versus function – the impact of computational methods on the discovery of specific GPCR-ligands
    • 8 Bermudez, M., Wolber, G., Structure versus function – the impact of computational methods on the discovery of specific GPCR-ligands. Bioorg Med Chem 23 (2015), 3907–3912.
    • (2015) Bioorg Med Chem , vol.23 , pp. 3907-3912
    • Bermudez, M.1    Wolber, G.2
  • 9
    • 84942250868 scopus 로고    scopus 로고
    • The role of experimental and computational structural approaches in 7TM drug discovery
    • 9 Topiol, S., Sabio, M., The role of experimental and computational structural approaches in 7TM drug discovery. Expert Opin Drug Discov 10 (2015), 1071–1084.
    • (2015) Expert Opin Drug Discov , vol.10 , pp. 1071-1084
    • Topiol, S.1    Sabio, M.2
  • 11
    • 84899888407 scopus 로고    scopus 로고
    • How drugs are developed and approved by the FDA: current process and future directions
    • 11 Ciociola, A.A., Cohen, L.B., Kulkarni, P., the FDARMCotACoG. How drugs are developed and approved by the FDA: current process and future directions. Am J Gastroenterol 109 (2014), 620–623.
    • (2014) Am J Gastroenterol , vol.109 , pp. 620-623
    • Ciociola, A.A.1    Cohen, L.B.2    Kulkarni, P.3
  • 12
    • 84903776217 scopus 로고    scopus 로고
    • Modelling three-dimensional protein structures for applications in drug design
    • 12 Schmidt, T., Bergner, A., Schwede, T., Modelling three-dimensional protein structures for applications in drug design. Drug Discov Today 19 (2014), 890–897.
    • (2014) Drug Discov Today , vol.19 , pp. 890-897
    • Schmidt, T.1    Bergner, A.2    Schwede, T.3
  • 13
    • 84903535031 scopus 로고    scopus 로고
    • Multiparameter optimization in CNS drug discovery: design of pyrimido[4,5-d]azepines as potent 5-hydroxytryptamine 2C (5-HT(2)C) receptor agonists with exquisite functional selectivity over 5-HT(2)A and 5-HT(2)B receptors
    • 13 Storer, R.I., Brennan, P.E., Brown, A.D., Bungay, P.J., Conlon, K.M., Corbett, M.S., DePianta, R.P., Fish, P.V., Heifetz, A., Ho, D.K., et al. Multiparameter optimization in CNS drug discovery: design of pyrimido[4,5-d]azepines as potent 5-hydroxytryptamine 2C (5-HT(2)C) receptor agonists with exquisite functional selectivity over 5-HT(2)A and 5-HT(2)B receptors. J Med Chem 57 (2014), 5258–5269.
    • (2014) J Med Chem , vol.57 , pp. 5258-5269
    • Storer, R.I.1    Brennan, P.E.2    Brown, A.D.3    Bungay, P.J.4    Conlon, K.M.5    Corbett, M.S.6    DePianta, R.P.7    Fish, P.V.8    Heifetz, A.9    Ho, D.K.10
  • 14
    • 84937731056 scopus 로고    scopus 로고
    • What can we learn from molecular dynamics simulations for GPCR drug design?
    • Important article that describes the application of molecular dynamics simulations in GPCR drug discovery programs, their scope and limitations. The application of MD to GPCR SBDD is exemplified by two selected case studies: discovery of small molecule antagonists of the human CC chemokine receptor 3 and a detailed investigation of the interplay between receptor dynamics and solvation for the binding of small molecules to the human muscarinic acetylcholine receptor 3.
    • 14•• Tautermann, C.S., Seeliger, D., Kriegl, J.M., What can we learn from molecular dynamics simulations for GPCR drug design?. Computat Struct Biotechnol J 13 (2015), 111–121 Important article that describes the application of molecular dynamics simulations in GPCR drug discovery programs, their scope and limitations. The application of MD to GPCR SBDD is exemplified by two selected case studies: discovery of small molecule antagonists of the human CC chemokine receptor 3 and a detailed investigation of the interplay between receptor dynamics and solvation for the binding of small molecules to the human muscarinic acetylcholine receptor 3.
    • (2015) Computat Struct Biotechnol J , vol.13 , pp. 111-121
    • Tautermann, C.S.1    Seeliger, D.2    Kriegl, J.M.3
  • 15
    • 84906933886 scopus 로고    scopus 로고
    • GPCR structures in drug design, emerging opportunities with new structures
    • 15 Tautermann, C.S., GPCR structures in drug design, emerging opportunities with new structures. Bioorg Med Chem Lett 24 (2014), 4073–4079.
    • (2014) Bioorg Med Chem Lett , vol.24 , pp. 4073-4079
    • Tautermann, C.S.1
  • 16
    • 84971264657 scopus 로고    scopus 로고
    • Application of an integrated GPCR SAR-modelling platform to explain the activation selectivity of human 5-HT2C over 5-HT2B
    • 16 Heifetz, A., Storer, R.I., McMurray, G., James, T., Morao, I., Aldeghi, M., Bodkin, M.J., Biggin, P.C., Application of an integrated GPCR SAR-modelling platform to explain the activation selectivity of human 5-HT2C over 5-HT2B. ACS Chem Biol 11 (2016), 1372–1382.
    • (2016) ACS Chem Biol , vol.11 , pp. 1372-1382
    • Heifetz, A.1    Storer, R.I.2    McMurray, G.3    James, T.4    Morao, I.5    Aldeghi, M.6    Bodkin, M.J.7    Biggin, P.C.8
  • 17
    • 84947484341 scopus 로고    scopus 로고
    • New paradigms in GPCR drug discovery
    • 17 Jacobson, K.A., New paradigms in GPCR drug discovery. Biochem Pharmacol 98 (2015), 541–555.
    • (2015) Biochem Pharmacol , vol.98 , pp. 541-555
    • Jacobson, K.A.1
  • 18
    • 84888266137 scopus 로고    scopus 로고
    • Toward an understanding of agonist binding to human Orexin-1 and Orexin-2 receptors with G-protein-coupled receptor modeling and site directed mutagenesis
    • 18 Heifetz, A., Barker, O., Morris, G.B., Law, R.J., Slack, M., Biggin, P.C., Toward an understanding of agonist binding to human Orexin-1 and Orexin-2 receptors with G-protein-coupled receptor modeling and site directed mutagenesis. Biochemistry 52 (2013), 8246–8260.
    • (2013) Biochemistry , vol.52 , pp. 8246-8260
    • Heifetz, A.1    Barker, O.2    Morris, G.B.3    Law, R.J.4    Slack, M.5    Biggin, P.C.6
  • 23
    • 84893954062 scopus 로고    scopus 로고
    • Molecular control of delta-opioid receptor signalling
    • Highly important research that describes the solution of the high-resolution X-ray crystal structure of the human δ-opioid receptor, revealing the presence and fundamental role of a sodium ion and water molecule network in mediating allosteric control of receptor functional selectivity and constitutive activity.
    • 23•• Fenalti, G., Giguere, P.M., Katritch, V., Huang, X.P., Thompson, A.A., Cherezov, V., Roth, B.L., Stevens, R.C., Molecular control of delta-opioid receptor signalling. Nature 506 (2014), 191–196 Highly important research that describes the solution of the high-resolution X-ray crystal structure of the human δ-opioid receptor, revealing the presence and fundamental role of a sodium ion and water molecule network in mediating allosteric control of receptor functional selectivity and constitutive activity.
    • (2014) Nature , vol.506 , pp. 191-196
    • Fenalti, G.1    Giguere, P.M.2    Katritch, V.3    Huang, X.P.4    Thompson, A.A.5    Cherezov, V.6    Roth, B.L.7    Stevens, R.C.8
  • 25
    • 84857748866 scopus 로고    scopus 로고
    • Rapid and accurate prediction and scoring of water molecules in protein binding sites
    • 25 Ross, G.A., Morris, G.M., Biggin, P.C., Rapid and accurate prediction and scoring of water molecules in protein binding sites. PLoS ONE, 7, 2012, e32036.
    • (2012) PLoS ONE , vol.7 , pp. e32036
    • Ross, G.A.1    Morris, G.M.2    Biggin, P.C.3
  • 26
    • 84896258501 scopus 로고    scopus 로고
    • A cavity corrected 3D-RISM functional for accurate solvation free energies
    • 26 Truchon, J.F., Pettitt, B.M., Labute, P., A cavity corrected 3D-RISM functional for accurate solvation free energies. J Chem Theory Comput 10 (2014), 934–941.
    • (2014) J Chem Theory Comput , vol.10 , pp. 934-941
    • Truchon, J.F.1    Pettitt, B.M.2    Labute, P.3
  • 27
    • 84880564425 scopus 로고    scopus 로고
    • Water network perturbation in ligand binding: adenosine A(2A) antagonists as a case study
    • 27 Bortolato, A., Tehan, B.G., Bodnarchuk, M.S., Essex, J.W., Mason, J.S., Water network perturbation in ligand binding: adenosine A(2A) antagonists as a case study. J Chem Inf Model 53 (2013), 1700–1713.
    • (2013) J Chem Inf Model , vol.53 , pp. 1700-1713
    • Bortolato, A.1    Tehan, B.G.2    Bodnarchuk, M.S.3    Essex, J.W.4    Mason, J.S.5
  • 28
    • 33745880692 scopus 로고    scopus 로고
    • Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase
    • 28 Frembgen-Kesner, T., Elcock, A.H., Computational sampling of a cryptic drug binding site in a protein receptor: explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase. J Mol Biol 359 (2006), 202–214.
    • (2006) J Mol Biol , vol.359 , pp. 202-214
    • Frembgen-Kesner, T.1    Elcock, A.H.2
  • 30
    • 84896920576 scopus 로고    scopus 로고
    • Exploiting protein intrinsic flexibility in drug design, protein conformational dynamics
    • K.-I. Han X. Zhang M.-J. Yang Springer International Publishing
    • 30 Lukman, S., Verma, C., Fuentes, G., Exploiting protein intrinsic flexibility in drug design, protein conformational dynamics. Han, K.-I., Zhang, X., Yang, M.-J., (eds.) Advances in experimental medicine and biology, vol 805, 2014, Springer International Publishing, 245–269.
    • (2014) Advances in experimental medicine and biology , vol.805 , pp. 245-269
    • Lukman, S.1    Verma, C.2    Fuentes, G.3
  • 31
    • 84962419910 scopus 로고    scopus 로고
    • Interplay between two allosteric sites and their influence on agonist binding in human mu opioid receptor
    • 31 Bartuzi, D., Kaczor, A.A., Matosiuk, D., Interplay between two allosteric sites and their influence on agonist binding in human mu opioid receptor. J Chem Inf Model 56 (2016), 563–570.
    • (2016) J Chem Inf Model , vol.56 , pp. 563-570
    • Bartuzi, D.1    Kaczor, A.A.2    Matosiuk, D.3
  • 32
    • 77952756998 scopus 로고    scopus 로고
    • LowModeMD – implicit low-mode velocity filtering applied to conformational search of macrocycles and protein loops
    • 32 Labute, P., LowModeMD – implicit low-mode velocity filtering applied to conformational search of macrocycles and protein loops. J Chem Inf Model 50 (2010), 792–800.
    • (2010) J Chem Inf Model , vol.50 , pp. 792-800
    • Labute, P.1
  • 33
    • 84947998906 scopus 로고    scopus 로고
    • Activation and allosteric modulation of human mu opioid receptor in molecular dynamics
    • 33 Bartuzi, D., Kaczor, A.A., Matosiuk, D., Activation and allosteric modulation of human mu opioid receptor in molecular dynamics. J Chem Inf Model 55 (2015), 2421–2434.
    • (2015) J Chem Inf Model , vol.55 , pp. 2421-2434
    • Bartuzi, D.1    Kaczor, A.A.2    Matosiuk, D.3
  • 34
    • 84924158533 scopus 로고    scopus 로고
    • Site Identification by Ligand Competitive Saturation (SILCS) simulations for fragment-based drug design
    • 34 Faller, C.E., Raman, E.P., MacKerell, A.D. Jr., Guvench, O., Site Identification by Ligand Competitive Saturation (SILCS) simulations for fragment-based drug design. Methods Mol Biol 1289 (2015), 75–87.
    • (2015) Methods Mol Biol , vol.1289 , pp. 75-87
    • Faller, C.E.1    Raman, E.P.2    MacKerell, A.D.3    Guvench, O.4
  • 35
    • 58449131873 scopus 로고    scopus 로고
    • The role of binding kinetics in therapeutically useful drug action
    • 35 Swinney, D.C., The role of binding kinetics in therapeutically useful drug action. Curr Opin Drug Discov Dev 12 (2009), 31–39.
    • (2009) Curr Opin Drug Discov Dev , vol.12 , pp. 31-39
    • Swinney, D.C.1
  • 38
    • 84901827515 scopus 로고    scopus 로고
    • Drug-target residence time—a case for G protein-coupled receptors
    • This article outlines and exemplifies the importance of drug-target residence times of GPCR drugs. The authors propose that drug-target RT should be taken into account as an additional parameter in the lead selection and optimization process. This should ultimately lead to an increased number of candidate drugs moving to the preclinical development phase and onto the market. This review contains examples of the kinetic behavior of GPCR ligands with improved in vivo efficacy and summarizes methods for assessing drug-target RT.
    • 38•• Guo, D., Hillger, J.M., Ijzerman, A.P., Heitman, L.H., Drug-target residence time—a case for G protein-coupled receptors. Med Res Rev 34 (2014), 856–892 This article outlines and exemplifies the importance of drug-target residence times of GPCR drugs. The authors propose that drug-target RT should be taken into account as an additional parameter in the lead selection and optimization process. This should ultimately lead to an increased number of candidate drugs moving to the preclinical development phase and onto the market. This review contains examples of the kinetic behavior of GPCR ligands with improved in vivo efficacy and summarizes methods for assessing drug-target RT.
    • (2014) Med Res Rev , vol.34 , pp. 856-892
    • Guo, D.1    Hillger, J.M.2    Ijzerman, A.P.3    Heitman, L.H.4
  • 39
    • 84863228021 scopus 로고    scopus 로고
    • Functional efficacy of adenosine A2A receptor agonists is positively correlated to their receptor residence time
    • 39 Guo, D., Mulder-Krieger, T., Ijzerman, A.P., Heitman, L.H., Functional efficacy of adenosine A2A receptor agonists is positively correlated to their receptor residence time. Br J Pharm 166 (2012), 1846–1859.
    • (2012) Br J Pharm , vol.166 , pp. 1846-1859
    • Guo, D.1    Mulder-Krieger, T.2    Ijzerman, A.P.3    Heitman, L.H.4
  • 40
    • 84942244553 scopus 로고    scopus 로고
    • On the ‘micro’-pharmacodynamic and pharmacokinetic mechanisms that contribute to long-lasting drug action
    • 40 Vauquelin, G., On the ‘micro’-pharmacodynamic and pharmacokinetic mechanisms that contribute to long-lasting drug action. Expert Opin Drug Discov, 2015, 1–14.
    • (2015) Expert Opin Drug Discov , pp. 1-14
    • Vauquelin, G.1
  • 41
    • 77950197835 scopus 로고    scopus 로고
    • The dynamics of drug–target interactions: drug–target residence time and its impact on efficacy and safety
    • 41 Copeland, R.A., The dynamics of drug–target interactions: drug–target residence time and its impact on efficacy and safety. Expert Opin Drug Discov 5 (2010), 305–310.
    • (2010) Expert Opin Drug Discov , vol.5 , pp. 305-310
    • Copeland, R.A.1
  • 42
    • 84939780109 scopus 로고    scopus 로고
    • Ligand residence time at G-protein-coupled receptors – why we should take our time to study it
    • 42 Hoffmann, C., Castro, M., Rinken, A., Leurs, R., Hill, S.J., Vischer, H.F., Ligand residence time at G-protein-coupled receptors – why we should take our time to study it. Mol Pharmacol 88 (2015), 552–560.
    • (2015) Mol Pharmacol , vol.88 , pp. 552-560
    • Hoffmann, C.1    Castro, M.2    Rinken, A.3    Leurs, R.4    Hill, S.J.5    Vischer, H.F.6
  • 43
    • 78650514081 scopus 로고    scopus 로고
    • Novel 6,7,8,9-tetrahydro-5H-1,4,7,10a-tetraaza-cyclohepta[f]indene analogues as potent and selective 5-HT(2C) agonists for the treatment of metabolic disorders
    • 43 Tye, H., Mueller, S.G., Prestle, J., Scheuerer, S., Schindler, M., Nosse, B., Prevost, N., Brown, C.J., Heifetz, A., Moeller, C., et al. Novel 6,7,8,9-tetrahydro-5H-1,4,7,10a-tetraaza-cyclohepta[f]indene analogues as potent and selective 5-HT(2C) agonists for the treatment of metabolic disorders. Bioorg Med Chem Lett 21 (2011), 34–37.
    • (2011) Bioorg Med Chem Lett , vol.21 , pp. 34-37
    • Tye, H.1    Mueller, S.G.2    Prestle, J.3    Scheuerer, S.4    Schindler, M.5    Nosse, B.6    Prevost, N.7    Brown, C.J.8    Heifetz, A.9    Moeller, C.10
  • 44
    • 33846017361 scopus 로고    scopus 로고
    • Drugs and valvular heart disease
    • 44 Roth, B.L., Drugs and valvular heart disease. N Engl J Med 356 (2007), 6–9.
    • (2007) N Engl J Med , vol.356 , pp. 6-9
    • Roth, B.L.1
  • 45
    • 84977595019 scopus 로고    scopus 로고
    • National Institutes of Health Update: translating basic behavioral science into new pediatric obesity interventions
    • 45 Czajkowski, S.M., National Institutes of Health Update: translating basic behavioral science into new pediatric obesity interventions. Pediatr Clin North Am 63 (2016), 389–399.
    • (2016) Pediatr Clin North Am , vol.63 , pp. 389-399
    • Czajkowski, S.M.1
  • 46
    • 84878186205 scopus 로고    scopus 로고
    • Fighting obesity with a sugar-based library: discovery of novel MCH-1R antagonists by a new computational-VAST approach for exploration of GPCR binding sites
    • 46 Heifetz, A., Barker, O., Verquin, G., Wimmer, N., Meutermans, W., Pal, S., Law, R.J., Whittaker, M., Fighting obesity with a sugar-based library: discovery of novel MCH-1R antagonists by a new computational-VAST approach for exploration of GPCR binding sites. J Chem Inf Model 53 (2013), 1084–1099.
    • (2013) J Chem Inf Model , vol.53 , pp. 1084-1099
    • Heifetz, A.1    Barker, O.2    Verquin, G.3    Wimmer, N.4    Meutermans, W.5    Pal, S.6    Law, R.J.7    Whittaker, M.8
  • 47
    • 84930926195 scopus 로고    scopus 로고
    • Recent trends in orexin research – 2010 to 2015
    • 47 Boss, C., Roch, C., Recent trends in orexin research – 2010 to 2015. Bioorg Med Chem Lett 25 (2015), 2875–2887.
    • (2015) Bioorg Med Chem Lett , vol.25 , pp. 2875-2887
    • Boss, C.1    Roch, C.2
  • 49
    • 84859906798 scopus 로고    scopus 로고
    • Study of human Orexin-1 and -2 -G-protein-coupled receptors with novel and published antagonists by modeling, molecular dynamics simulations, and site-directed mutagenesis
    • 49 Heifetz, A., Morris, G.B., Biggin, P.C., Barker, O., Fryatt, T., Bentley, J., Hallett, D., Manikowski, D., Pal, S., Reifegerste, R., et al. Study of human Orexin-1 and -2 -G-protein-coupled receptors with novel and published antagonists by modeling, molecular dynamics simulations, and site-directed mutagenesis. Biochemistry 51 (2012), 3178–3197.
    • (2012) Biochemistry , vol.51 , pp. 3178-3197
    • Heifetz, A.1    Morris, G.B.2    Biggin, P.C.3    Barker, O.4    Fryatt, T.5    Bentley, J.6    Hallett, D.7    Manikowski, D.8    Pal, S.9    Reifegerste, R.10


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