# help in FEP calculations_binding free energy difference between 2 inhibitors

From: Bruno Luís Pinto de Oliveira (boliveira_at_itn.pt)
Date: Mon Sep 05 2011 - 13:08:58 CDT

Dear NAMD users,

Recently I put a post on the mailing list but received no answers.

Maybe I was not clear enough but I really need some orientation.

Can someone give me a little help please?

I copy and past again my last email.

Thank you

Bruno

In my group we have some organometallic complexes that have better affinity for an enzyme (iNOS) when compared with the free-metal ligands. For example:

Ligand have a Ki =178 uM

the corresponding rhenium complex have a ki = 84 uM (Ligand .... Re(CO)3; ligand coordenated to the Re(CO)3 fragment)

We are trying to rationalize why the coordenation of the Re(CO)3 core improves the affinity.

We did docking and molecular dynamics of both ligand and rhenium complex and it seems that the Re(CO)3 core is strongly stabilized by interactions with 3 polar and charged residues (R260, R380 and Q257) of the active pocket.

I did FEP calculation to estimate the difference in the binding energy between the Rhenium complex and the corresponding ligand. From the MD simulation (of the rhenium complex) using the last 3 ns I calculate the averaged structure. This averaged strcuture I have used in the FEP calculations.

Please let me know if I got the termodynamic cycle correctly

DeltaG1
Ligand .... Re(CO)3 : enzyme ---------> Ligand .... Re(CO)3 + enzyme
| DeltaG4 | DeltaG2
| |

Ligand : enzyme --------> Ligand + enzyme
DeltaG3

DDbind = DeltaG1 - Delta3 = DeltaG4 - DeltaG2

I calculate the "transformation" of the Rhenium complex into the ligand in water (DeltaG2 = -31,93 Kcal/mol) and in the protein (DeltaG4 = -31,05 Kcal/mol).

DeltDeltG = DeltaG4 - DeltaG2 = - 0,886 Kcal/mol

The obtained results are in good agreement with the experimental results.

Ligand X have a Ki =178 uM = -5,29 Kcal/mol

Ligand X .... Re(CO)3 ki = 84 uM -5,76 Kcal/mol

DeltDeltG = - 0,470 Kcal/mol (experimental)

My doubt is that in my case there isn´t any transformation as the ligand is exactly the same as the Rhenium complex but minus the Re(CO)3 core.

In my calculations I just did the Re(CO)3 core vanish. I need your advice or let's say your supervision. Can I use FEP in this particular case? Did I do something wrong? Can I considerer the results correct? A last question, fep calculates the standard deviations???

Any help is really appreciated.