This document outlines a computational modelling study of receptor-ligand complexes associated with fibromyalgia syndrome. The study builds 3D models of platelet-activating factor receptor (PAFr) and two lipid ligands, PC(14:0/0:0) and PC(16:0/0:0), that were observed to increase in fibromyalgia patients. Docking and molecular dynamics simulations were performed to analyze ligand binding and the receptor's conformational changes. The results found the ligands bind PAFr with similar energy to PAF and induce small conformational changes in key receptor domains, suggesting they may activate the receptor and contribute to fibromyalgia pathogenesis.

1. Computational Modelling of Receptor
Ligand complex associated to
Fibromyalgia Syndrome
Amit Kumar
amit369@gmail.com
27-05-2015

2. Outline
Quick Introduction to problem of Fibromyalgia
Motivation
Key players
Our methodological approach
Building Model
Docking
Molecular Dynamics
Results
Conclusion
2

3. Quick Introduction
3

4. Motivation
• Fibromyalgia pathogenesis unclear and no biomarkers.
• Observed increase PC(14:0/0:0) and PC(16:0/0:0) in FMS patients
noted using plasma lipidomic analysis approach metabolites.
• These metabolites had Platelet Activating Factor (PAF) like structure.
PAF : a potent phospholipid activator mediator of many leukocyte (White
Blood cell) functions, e.g. inflammation
4

5. Chemical structure of metabolites: lyso-
phosphocholines ligands
LMGP01050012: PC(14:O/O:O)
2 106 8 124
14
LMGP01050018: PC(16:O/O:O)
142 106 8 124
16
LMGP01020046: PAF (standard)
5

6. Search for Lipid ligands: Lipidomics Database
6

7. 3D-modelling-Ligands
7

8. CCCCCCCCCCCCCCCC(=O)OC[C@@H](O)COP([O-])(=O)OCC[N+](C)(C)C
3D modelling: Ligand
8

9. LMGP01050018: PC(16:O/O:O)
Download 3D file
9
3D modelling: Ligand

10. Geometry optimisation: Attempt to find
configuration of minimum energy of
molecule
3D modelling: Ligand
Free for academic use
10

11. 3D Modelling PAFr

12. 3D Models for PAFr and ligands
Starting structure:
Theoretical model PDBSum
database: 2b0x (Gui et. al
proteins 2005)
12

13. 3D Modelling for not known structures

14. DOCKING PAFr-Ligands
GLIDE, GOLD, MOE: Commercial
software

15. PAFR-Ligand Binding region
Ligands
∆G (Binding free
energy)
PAF -7.O kcal/mol
PC(14:O/O:O) -7.1 kcal/mol
PC(16:O/O:O) -5.1 kcal/mol
Docking Energy
15

16. Molecular Dynamics: 1

17. Molecular Dynamics: 2
http://portfolio.scistyle.com/Publication-Quality-Science-Figures17
(1)
(2)
(3)
(4)(5)
Empirical Force Field
equation
⬅️
Non-bonded terms
Bonded terms
Electrostatics
Van der Waals

18. Molecular Dynamics: 3
18
MD Engine3D
coordinates
Topology
file
Parameter
file
New 3D
coordinates at
different time
intervals
NAMD, AMBER, CHARMM, GROMACS, DLPOLY

19. TOPOLOGY File
Topology RESI ALA 0.00
GROUP
ATOM N NH1 -0.47 ! |
ATOM HN H 0.31 ! HN-N
ATOM CA CT1 0.07 ! | HB1
ATOM HA HB 0.09 ! | /
GROUP ! HA-CA--CB-HB2
ATOM CB CT3 -0.27 ! |
ATOM HB1 HA 0.09 ! | HB3
ATOM HB2 HA 0.09 ! O=C
ATOM HB3 HA 0.09 ! |
GROUP !
ATOM C C 0.51
ATOM O O -0.51
BOND CB CA N HN N CA
BOND C CA C +N CA HA CB HB1 CB HB2 CB HB3
DOUBLE O C
IMPR N -C CA HN C CA +N O
DONOR HN N
ACCEPTOR O C
c
ct1
ct3
nh1

20. PARAMETER File
BONDS
CT3 CT1 222.00 1.538
CT3 HA 322 1.1
CE1 CE1 440.000 1.3400
ANGLE
CT3 CT1 HB 30.000 110.00
CT3 CT1 C 48.00 123.50
HA CT3 CT1 32.00 112.20
NH1 CT1 HB 23.00 118.00
DIHEDRAL
CT3 CT1 C O O.2 1 180.0
HA CT3 CT1 NH1 0.5 2 180.0
c
ct1
ct3
ha
hb
nh1
o

21. Mimicking Biological membrane
Insertion of PAFr-ligand
complex into the membrane
⬅️
➡️
Start with a relaxed
membrane-water system

22. Movies

23. RMSD Analysis: LIGAND
Measure of the deviation between the
atoms (usually the backbone atoms)
with respect to starting structure

24. RMSD helix
Gui. et. al found large deviation of Helix 3 and Helix 6: Related to PAFr activation

25. Hydrogen Bond interactions

26. Binding Free Energy Calculation
MM-PBSA: Molecular Mechanics- Poisson
Bolzmann Surface Area
Gsolv = EPB/EGB + ECAVITY
EPB/EGB = the electrostatic contribution to the free
energy calculated by PB or GB
ECAVITY = nonpolar contribution to the solvation
free energy calculated by an empirical model. 26

27. Interaction Picture

28. Conclusions
PC(14:0/0:0) and PC(16:0/0:0) ligands are slightly more flexible than PAF, but
overall similar binding energy ~11 kcal/mol to PAFR.
RMSD variations in key intra-membrane domains smaller than in another MD investigation,
but show signals of a conformational change upon binding, which on turn could be linked to
receptor activation.
with PAF-like function, could role in the clinical manifestation of FMS.
New disease biomarkers and therapeutic targets in Fibromyalgia; aid to design new
diagnostic & therapeutic approaches & diets.