2021 DOCK tutorial 2 with PDBID 2ZD1

Introduction

Learning Goals for this Tutorial

This tutorial will guide the student in performing a structure-based virtual screen of a large number of small molecule compounds (ligands) to assess the effectiveness of each in binding to a protein drug target (receptor) through the use of molecular docking. The student will additionally learn how to use tools to visualize and manipulate the components of a receptor-ligand complex, along with the results (docked ligand poses) of the virtual screen.

The techniques, computational tools, and biological system used in this tutorial are detailed below:

Techniques

Virtual Screening

vf

Molecular Docking

https://ringo.ams.stonybrook.edu/~rizzo/StonyBrook/teaching/AMS532_AMS535_AMS536/References/rizzo014.pdf

The DOCKING program specifically computes the interaction energy between the receptor and candidate ligand at different orientations. The ligand with the highest activity (usually the ideal candidate for a synthetic ligand or drug) would have the lowest computed energy.

Docking algorithms can be broadly classified as flexible (anchor and grow) or rigid. A rigid docking algorithm begins with a fully-formed ligand (whose structure is obtained from experiment) and allows for sampling of the rigid placement of the given experimental pose in the binding site of the receptor while varying the translational and rotational degrees of freedom of the whole ligand within the three spatial dimensions. Internal angle rotational degrees of freedom are not explicitly sampled with basic rigid docking.

Traditional flexible docking starts with a ligand scaffold, which is usually the largest substructure in a ligand, identified as such after the molecule is divided into substructures at its rotatable bonds. By a chosen method, such as Monte Carlo sampling or simulated annealing, multiple poses of this “anchor” substructure are then generated within the receptor binding pocket and scored. The next substructure’s layers of atoms are then added to the most favorable subset of initial anchor poses, and the process repeats until all the molecule is fully rebuilt within the receptor. This on-the-fly flexible conformer growth and minimization process is known as “anchor and grow.”

Conformal space search

A sequence of complexes of receptors and ligands in specific poses are constructed for subsequent evaluation by a set of scoring functions.

Scoring

zzz

Docking Assessment

zzz

Computational Tools

Protein DataBank (PDB)

A publicly-accessible database that houses downloadable 3-D structural information of proteins and other large biomolecules obtained mainly from X-ray crystallography and NMR experiments. This information is provided in a format that is easily manipulated by molecular visualization and modeling software. We will use the PDB to learn about and obtain the structure data for the reference protein-ligand complex used in this tutorial.

Organization Home: https://www.wwpdb.org/

Search Home: https://www.rcsb.org/

UCSF Chimera

Version 1.15 for Windows used in this tutorial.

https://www.cgl.ucsf.edu/chimera/

Seawulf

https://it.stonybrook.edu/help/kb/understanding-seawulf

DOCK

Version 6.9 used in this tutorial.

is one of the many tools available to computational biologists that predicts ligand binding geometries and interactions. The functions of DOCK 6.9 are diverse and have several general applications. A primary use of the program involves a virtual screening of thousands of molecules for an intended purpose. These purposes can include database screenings for molecules that inhibit enzyme activity, bind a particular protein, or even bind to larger complexes. As more versions of the program are released, new features are added such as the inclusion of solvation and receptor flexibility considerations in its calculations.

2ZD1: Crystal Structure of HIV-1 Reverse Transcriptase in Complex with Rilpivirine

, A Non-nucleoside RT Inhibitor 2ZD1 is the PDB code for the catalytic complex between human HMG-CoA reductase (HMGR) and Simvastatin. HMGR is considered a rate-controlling enzyme in the metabolic pathway responsible for the biosynthesis of cholesterol. Inhibitors of HMGR, known as statins, are often prescribed as treatment therapies for high cholesterol patients. While statins inhibit the catalytic effect of HMGR, they also provide other positive biochemical effects such as the stimulation of bone growth and anti-inflammatory responses. Studying statin binding using this complex can potentially aid in the discovery of drugs capable of producing these off-target effects.

Directory and File Setup

Before beginning the docking procedure, we will create a set of directories to store the various files we will be generating in an organized manner. We will also download the initial PDB file for the 2ZD1 complex from the RCSB PDB.

Notes:

• The directory and file nomenclature used throughout the tutorial is not required but is recommended for most efficient use of subsequently-provided commands and scripts.
• Italics are used in directory and file names to signify terms that may differ for each student.

1. Log in to Seawulf
2. Navigate to your personal student directory for AMS 536:

   cd /gpfs/projects/AMS536/year/students/name

3. Create a directory to store all files used and generated in this tutorial:

   mkdir dock_vs_2ZD1

4. Navigate into this new directory:

   cd dock_vs_2ZD1

5. Create all directories required for this tutorial:

   mkdir 01_structure   02_surface_spheres   03_grid_box   04_dock   05_virtual_screen   06_virtual_screen_mpi   07_cartesian_min   08_rescore

6. Download the PDB file to a local directory
7. Copy the PDB file to 01_structure using scp or rsync

Recommendations:

• Confirm the existence of all newly-created directories by executing the ls command
• Set up a dedicated local directory to store files that will be utilized in Chimera
• Set up an alias in .bashrc for an scp or rsync command that will allow for easy transfer of files between the relevant local and Seawulf directories

Receptor and Ligand Preparation

We will extract the individual receptor and ligand structure from our PDB file and add hydrogens and charges as appropriate.

Structure Verification

We will verify that the protein structure downloaded from the PDB aligns with the description in the submitted experimental paper.

1. Open the Chimera application.
2. Open the PDB file in Chimera:

   File -> Open, navigate to PDB file and clickOpen

   You should now be able to visualize the complex as shown below

   
3. Begin to prepare the receptor by deleting all non-receptor atoms, including those in water molecules, salts, and the ligand...

   Select -> Residue -> all nonstandard
Actions -> Atoms/Bonds -> Delete

   ...and any full receptor chains that are not of interest in the virtual screen and/or do not coordinate with the ligand.

   Select -> Chain -> B
Actions -> Atoms/Bonds -> Delete

4. Save the prepared receptor locally in .mol2 format.

   File -> Save mol2... -> "2ZD1_rec_nH.mol2"

5. Copy the mol2 file to the 01_structure directory using scp or rsync

Note that the file we have just created does not contain any hydrogen atoms. We will now generate a second receptor file with hydrogens and charge added to the molecule.

Begin to prepare the receptor by deleting all the non-receptor atoms. This also includes delete any chains in the receptor that are not of interest and or do not coordinate with the ligand.

Select -> Chain -> (Undesired chain) Actions -> Atoms/Bonds -> Delete. <p> Select -> Residue -> All-nonstandard Actions -> Atoms/Bonds -> Delete.

Save the prepared receptor locally in mol2 format. <p> File -> Save Mol2... -> "2ZD1_rec_nH.mol2"

Copy the mol2 file to <code> 01_structure using scp or rsync </ol> = test =