GPCR orthosteric site simulation

Introduction

The GPCR package aims to find the binding path of a small molecule to the orthosteric site of a G protein-coupled receptor.

Initially, the software will place the ligand all around the user-defined initial site and create a simulation box encompassing the initial and orthosteric sites. The simulation will be performed with a slight bias towards ligand’s SASA as well as high constraints on all alpha carbons to avoid the collapse of the structure due to the lack of the membrane. Finally, ranked binding modes of the small molecule will be retrieved to the user.

Inputs

  • protein-ligand PDB file

  • input.yaml specifying orthosteric and initial sites of atom

Defaults

  • iterations: 50

  • pele steps: 8

  • epsilon: 0.25

  • constraint level: 3 (backbone is constrained every 5 carbon alpha atoms with 5 kcal/mol constant)

Recommendations

  1. We suggest using at least 50 CPUs.

  2. The simulation will take around 3h on average.

1. Complex Preparation

Prepare the system with Protein Preparation Wizard. We would usually recommend protonating the protein (obligatory), deleting water molecules more than 5Å away from ligands and ions as well as filling in missing loops and side chains. The system must contain the protein and the ligand, however, the latter can be placed anywhere as its position will be automatically randomised all around the specified initial site atom.

2. Input Preparation

Prepare the input file input.yml:

system: "complex.pdb" # Ligand-protein complex
resname: "LIG" # Ligand residue name in system
chain: "L" # Ligand chain ID
seed: 1234
gpcr_orth: true # Set defaults for GPCR simulation
orthosteric_site: "A:114:CG" # Atom in the orthosteric site (chain ID:residue number:atom name)
initial_site: "A:310:CD" # Atom in the initial site
cpus: 50

For more optional flags please refer to optional flags.

3. Run simulation

To run the system launch the simulation with the following command:

python -m pele_platform.main input.yml

4. Output

Raw output

Trajectory and report files for each simulation are located in working_folder/output. That’s where you can find detailed information on each snapshot (PDB file, binding energy, metrics, etc.).

Selected poses

Clusters

Upon completion of the simulation, all trajectories are clustered based on ligand heavy atom coordinates. Then, a cluster representative with the best binding energy (or metric of your choice) is selected. Ranked cluster representatives can be found in:

working_folder/results/clusters

Best snapshots

In addition, top 100 structures with the best binding energy (or metric of your choice) are retrieved. This is done to ensure the clustering algorithm did not skip any valuable results. They are stored in:

working_folder/results/top_poses