naveena yanamala, kalyan c. tirupula and judith klein-seetharaman
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Preferential Binding of Allosteric Modulators to Active and Inactive Conformational States of Metabotropic Glutamate Receptors. Naveena Yanamala, Kalyan C. Tirupula and Judith Klein-Seetharaman. - PowerPoint PPT PresentationTRANSCRIPT
Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260, USA
Preferential Binding of Allosteric Preferential Binding of Allosteric Modulators to Active and Inactive Modulators to Active and Inactive
Conformational States of Conformational States of Metabotropic Glutamate ReceptorsMetabotropic Glutamate Receptors
Naveena Yanamala, Kalyan C. Tirupula and Judith Klein-Seetharaman
InCoB 2007
G-Protein Coupled ReceptorsG-Protein Coupled Receptors
EMBO J. 18: 1723-1729 (1999)
GPCR family is pharmacologically important.
• 7 transmembrane helices
• Bind to diverse ligands • Major classes include
• Family A Rhodopsin like
• Family B Secretin like
• Family C Glutamate receptor
like
Rhodopsin Rhodopsin
Only atomic level structure available is for Rhodopsin
h
Cytoplasmic side
Extracellular side
b. Isin et al, Proteins 65, 970 (Dec 1, 2006).
h Trans-membrane
a. Palczewski et al, Science 289(5480), 739 (2004)
Metabotropic Glutamate Receptors Metabotropic Glutamate Receptors (mGluR’s)(mGluR’s)
Glutamate is the most important excitatory neurotransmitter in the brain
mGluR function: modulatory Class C GPCR, very limited homology to rhodopsinmGluR’s are sub-divided based on sequence similarity
Group I ( mGluR1 and mGluR5 ) Group II ( mGluR2 and mGluR3 ) Group III ( mGluR4, mGluR6, mGluR7 and mGluR8 )
Potential drug targets for neurological & neurodegenerative diseases
mGluR LigandsmGluR Ligands
Modified : http://www.npsp.com/img/img_mGluR_diag.jpg
Competitive
Allosteric Positive modulator enhances
response to glutamate Negative modulator suppresses
response to glutamate
Glutamate binding siteAllosteric Ligand
binding siteCompetitive Ligand binding site
Open QuestionOpen Question
Do positive and negative modulators bind differentially to the active and inactive conformations of the receptors?
ApproachApproach1. Dark state rhodopsin crystal structure
2. Light activated rhodopsin model (ANM)
Docked models
Critical residues within 5Å
1. Homology models for inactive states of mGluR subtypes
2. Homology models for active states of mGluR subtypes
1. Generated Alignment of TM regions using ClustalX.
2. Modeler for Homology Modeling
3. MolProbity, Procheck
4. Docking using ArgusDock3.0
5. Selection of best model based on energy and buried surface
6. Analysis of binding pocket
Ligands DockedLigands DockedLigands for which the nature of
their allosteric effects on mGluR’s experimentally known were analyzed:(A) EM-TBPC (B) Ro67-7476
(C) Ro01-6128 (D) Ro67-4853
(E) R214127 (F) triazafluorenone
(G) CPCCOEt (H) YM298198
(I) MPEP (J) SIB-1757
(K) SIB-1893 (L) Fenobam
(M) MTEP (N) DFB-3,3`
(O) PTEB (P) NPS2390
(Q) CPPHA (R) 5MPEP
(S) MPEPy (T) PHCCC
(U) AMN082
Ligands bind at a region between 3,5,6 & 7 TM’s
Ligand Binding Site Ligand Binding Site Inactive mGluR5 Model
Docked with MPEPActive mGluR5 Model
Docked with MPEP
Binding EnergiesBinding EnergiesPositive Modulator
Negative Modulator
Neutral
1. mGluR1 – I2. mGluR2 – II3. mGluR5 – I4. mGluR4 – III5. mGluR7 - III
Binding energies for the active and inactive models favor positive and negative
modulators, respectively.
23
5
1 1 1
11
1
1
11 1
33 3
3
33 3 3 4
Act
ive-
Inac
tive
Bin
din
g E
ner
gy
(kca
l/mo
l)
Ligand binding pocket overlaps with that of rhodopsin
mGluR’s vs Rhodopsin (5Å)mGluR’s vs Rhodopsin (5Å)Rhodopsin Inactive Model
Rhodopsin Active Model
mGluR5 Inactive Model
mGluR5 Active Model
Example: Positive Modulator for mGluR5: 3,3-DFBExample: Negative Modulator for mGluR5: MPEP
3,3-Difluorobenzaldazine 2-methyl-6-((3-methoxyphenyl)ethynyl)-pyridine
Validation of Docking ResultsValidation of Docking Results
Predicted binding site fits well with experimental results
Model Validation: Comparison Model Validation: Comparison with MPEP Experimental Studieswith MPEP Experimental Studies
*. P. Malherbe et al., Mol Pharmacol 64, 823 (Oct, 2003) Residues not predicted Additional Residues predicted Residues predicted
MPEP Data *mGluR5/MPEPActive Model
mGluR5/MPEP Inactive Model
TM3Arg-647, Pro-654, Tyr-658
Arg-647, Ile-650 ,Tyr-658
Arg-647, Ile-650, Pro-654, Tyr-658
EC2 Asn-733
Arg-726, Glu-727,Ile-731, Cys-732,Asn-733, Asn-736
Ile-731, Cys-732, Asn-733
TM5 Leu-743Leu-737, Leu-743, Pro-742 Pro-742, Leu-743
TM6
Thr-780, Trp-784, Phe-787, Val-788, Tyr-791
Trp-784, Phe-787,Val-788 Trp-784, Phe-787
TM7 Met-801, Ala-809Met-801, Cys-802,Ser-804, Val-805
Thr-800, Met-801, Cys-802, Ser-804, Val-805
Predicted binding site fits well with experimental results
Model Validation: Comparison to Model Validation: Comparison to 3,3`-DFB Experimental Studies 3,3`-DFB Experimental Studies
*. A. Muhlemann et al., Eur J Pharmacol 529: 95 (2006) Residues not predicted Additional Residues predicted Residues predicted
3,3’-DFB Data *mGluR5/3,3’-DFB
Active ModelmGluR5/3,3’-DFB Inactive
Model
TM3Arg-647, Pro-654, Ser-657, Tyr-658 Arg-647, Pro-654, Tyr-658
Arg-647, Pro-654, Ser-657, Tyr-658
EC2 Asn-733Arg-726, Ile-731, Cys-732, Asn-733
Cys-732, Asn-733, Thr-734, Asn-736
TM5 Leu-743Leu-737, Gly-738, Leu-743, Gly-744, Pro-742 Leu-743
TM6
Thr-780, Trp-784, Phe-787, Val-788, Tyr-791 Trp-784, Phe-787, Val-788
Thr-780, Trp-784, Phe-787, Cys-781, Leu-785, Val-788, Tyr-791
TM7 Met-801Thr-800, Met-801, Cys-802, Ser-804 Met-801, Ser-804
W784, R647, L743, Y658, and F787 were found to be part of the binding pocket regardless of the type of modulator and
conformation of the receptor.
Summary of Comparison between Summary of Comparison between MPEP and 3,3’DFB Binding PocketsMPEP and 3,3’DFB Binding Pockets
MPEP
3,3`-DFB
Ligand docked to active model
Ligand docked to Inactive model
ConclusionsConclusionsHigh overlap between experimentally determined and
predicted binding pockets validate that bovine rhodopsin can be used as template for predicting the distantly related mGluR GPCR family members.
Allosteric ligand binding pockets of mGluR’s overlap with retinal binding pocket of rhodopsin.
mGluR allosteric modulation occurs via stabilization of different conformations analogous to those identified in rhodopsin.
The models predict the residues which might have a critical role in imparting selectivity and high potency, specific to mGluR-ligand interactions.
Future WorkFuture Work
Building a queryable database with simple rule based classifier
Setting up experimental platforms to further validate our predictions
AcknowledgementsAcknowledgements
Kalyan TirupulaGraduate Student
Molecular Biophysics and Structural Biology
Graduate Program
University of Pittsburgh
Dr. Judith Klein-SeetharamanAssistant Professor
Department of Structural Biology
University of Pittsburgh
Thank You Thank You
Questions ?
Compare GADock & ShapeDockCompare GADock & ShapeDock
Robust & GeneralSlow, hard to define
convergenceNot reproducible
(Stochastic)Can get caught in a local
minima
Some ligand/binding site types may cause problems
Fast!ReproducibleFormally explores all
minima
GADock ShapeDock
Slide from http://www.planaria-software.com
•Begin with the published XScore parameters.[1]
•Begin with Wang’s data set of 100 protein-ligand structures.[2]
•Remove incorrect structures to get a final training set of 84 structures:
39 hydrophilic, 20 hydrophobic, 25 mixed
•Modify H-bond parameters & other new parameters to improve correlation of score of x-ray
pose and experiment binding free.
[1] “Further development and validation of empirical scoring functions for structure-based binding affinity prediction” Wang, R, Lai, L, and Wang, S. J. Comp. Aided Mol. Design 16, 11-26, 2002
[2] “Comparative Evaluation of 11 Scoring Functions for Molecular Docking” Renxiao Wang, Yipin Lu, and Shaomeng Wang. J. Med. Chem. 2003, 46, 2287-2303
Parameterization & ValidationParameterization & Validation
Slide from http://www.planaria-software.com
Dock the training set using the ShapeDock engine.
Parameterization & Validation
Slide from http://www.planaria-software.com
Neuraminidase DockingsNeuraminidase DockingsShapeDockShapeDock
9 of the 10 structures reproduced the experimental binding mode.
Correlation of predicted and measured binding affinities
R2 = 0.70Ave. RMSD = 1.55 Angstroms
-12
-11
-10
-9
-10 -9 -8 -7 -6 -5 -4 -3 -2
log IC50
AS
co
re S
co
re (kcal
/mo
l)
[1] “The Effect of Small Changes in Protein Structure on Predicted Binding Modes of Known Inhibitors of Influenza Virus Neruaminidase: PMF-Scoring in Dock4” Ingo Muegge, Med. Chem. Res. 9, 1999, 490-500. Slide from http://www.planaria-software.com
AScore an empirical scoring function
AScore is based on terms taken from the HPScore piece of XScore [1]
[1] “Further development and validation of empirical scoring functions for structure-based binding affinity prediction” Wang, R, Lai, L, and Wang, S. J. Comp. Aided Mol. Design 16, 11-26, 2002
Gbind = Gvdw + Ghydrophobic + GH-bond + GH-bond (chg) + Gdeformation + G0
Gvdw = CVDW VDW
Ghydrophobic = Chydrophobic HP
GH-bond = CH-bond HB
GH-bond (chg-chg & chg-neutral) = CH-bond(chg) HB
Gdeformation = Crotor RT
G0 = Cregression
Slide from http://www.planaria-software.com