Computer-Aided Drug Design Tutorials: 4.2.

Docking with Glide

Background
Docking is a term that covers a large class of computer algorithms that attempt to find an optimal placement of
a rigid or flexible ligand in the receptor binding site. The ligands is typically a small molecule; peptide-protein
and protein-protein docking algorithms are currently under active development. Docking algorithms also
generate a score that attempts to distinguish between molecules that bind strongly in their optimal placement
from these that bind weakly. In this tutorial, you will learn to use the program Glide, which is developed and
sold by Schrodinger, LLC.
Schrodinger Molecular Modeling Environment
It would be nice if one could just feed the name of the PDB file as stored in the RCSB Protein Databank and a
SDF file defining nearly a million of lead-like compounds from a database such as ZINC into a docking
program, and sit back while the computer docks every compound to every binding pocket in the protein. In
reality, meaningful docking calculations require a careful preparation of receptor and ligand structures before
the docking programs can do their work. With Schrodinger Suite of programs, the bulk of receptor preparation
is carried out with the Protein Preparation Wizard while the ligand preparation is handled by Ligand
Preparation Wizard.
Glide Tutorial
The Glide program as well as the whole Schrodinger Suite comes with its own set of extensive tutorials (Quick
Start Guide) and user manuals. You should consult these when problems arise during your homework. For now,
you will follow a brief tutorial that was prepared by your instructor. The tutorial illustrates docking on nonnucleoside HIV reverse transcriptase inhibitors to the target protein. HIV reverse transcriptase is a a well-studies
protein that is targeted by several existing anti-AIDS drugs such as nevirapine and efavirenz, and etravirine.
One of the serious issues with HIV treatment is the emergence of drug resistance due to mutations; indeed
mutations resistant to existing non-nucleoside HIV reverse transcriptase inhibitors are known. It would thus be
interesting to develop analogs that can effectively inhibit these mutant forms of HIV reverse transcriptase.
Importing and Editing Molecules with Maestro
1. Type maestro to start the Maestro molecular visualization environment. This program also serves as the
interface to various modeling programs, such as the Protein Preparation Wizard and Glide. Maestro
offers quick access to most of these programs via the Applications menu. In addition, common task,
such as preparation of structures for docking are accessible via the Workflows menu.
2. From the Project menu, select Get PDB. Enter 1VRT for the PDB ID and hit Download to read in the
2.2 angstrom structure of HIV reverse transcriptase with bound drug nevirapine.
3. Maestro will perform the initial check for you, and display the results in color. Residues in grey are OK.
Residues in cyan are missing their neighbouring residues, which is not uncommon in case of flexible
loops; for rigorous docking studies one would attempt to model these loops. Residues in orange are nonstandard residues that oftentimes need to be dealt with before docking. Rotate the structure by dragging
while pressing the middle (wheel) button. Notice that nevirapine and one residue in protein are in
orange.

4. Closer examination reveals that the one unusual protein residue (residue name CSD at position 280) is
cysteine S-dioxide, also known as sulfinoalanine. This most likely formed by air-oxidation of Cys 280
during the protein purification and crystallization. You need to mutate this residue back to cysteine.
5. To mutate CSD 280, go to Edit, then Pick, and select Residues. Zoom in to CSD 280 by scrolling the
wheel forward. Left-click on one of the orange atoms; notice that all the atoms in this residue are now
selected. Hold down right mouse button to bring up a selection editing menu. Select Mutate residue and
then CYS. Note that the residue was mutated and is now colored grey. We are now ready to proceed to
Protein Preparation Wizard work flow with your receptor-ligand complex. Keep in mind that while
each PDB structure may present unique challenges, you can edit PDB files in Maestro or in text editor to
change or delete offending components.
Preparing Protein Structure for Docking
1. In order to be used as a receptor for docking, protein structures should be processed. Some of the typical
operations include (i) addition of hydrogen atoms, (ii) assignment atomic charges, (iii) elimination of
water molecules that are not involved in ligand binding, (iv) replacement of selenocysteins with
cysteins. The addition of hydrogens to sp3 carbons is trivial, but addition of polar hydrogens is more
complicated. For example, shall a Asp side chain in a hydrophobic pocket be protonated or kept anionic?
Or shall a particular His residue carry a proton on -nitrogen, -nitrogen, or on both nitrogens? Answer
to such questions usually require close examination of the environment around each of these residues.
Schrodinger Suite automates this work, and you can carry out the necessary preparation by launching the
Protein Preparation Wizard from the Workflows menu.
2. Under the Import and Process tab, you do not need to import a structure because you will be
processing the workspace structure. Examine the binding pocket around the ligand and notice that
several water molecules are interacting with the ligand. You want to keep these for now, but you may
want to eliminate some of them when docking larger analogs that would occupy the space where water
molecules are right now. Hit Preprocess. The preprocesing should take less than a minute to complete.
3. Under the Review and Modify tab, you see that HIV reverse transcriptase is composed of two chains,
that 5 water molecules were retained, and the structure contains an inhibitor and a Mg++ ion. You do not
need to do anything here today, but when you work with your own protein, you may want to generate
alternative tautomeric states of protein residues by pressing the Generate States button.
4. Under the Refine tab, assign H-bonds by considering different tautomeric states of histidines and
checking if the terminal amides of Asn and Gln are optimally oriented. Keep the option Sampling water
orientations checked and hit Optimize..., then Start. The optimization will take about a minute. Notice
that histidines are now explicitly labeled as HIS, HID, or HIE, and that some side chains carry a Flip
label.
5. Under the Refine tab, change the RMSD convergence criterion to 0.5 in order to save some time, and hit
Minimize..., then Start to minimize the structure. Notice that we are carrying out minimization in the
presence of bound ligand in order to avoid side chains moving into the cavity to which we hope to dock
our molecules. The minimization will take nearly 10 minutes.

Prepare Ligands to be Docked

1. Build the structure of nevirapine with Online SMILES Translator by National Institutes of Health. At the
website, sketch the molecule as a neutral species (it gets protonated at pH < 2.8). Select MOL and 3D
for output formats, and hit Translate. Save the structure (e.g. nevirapine.mol) in your directory as a 3D
MOL file. Repeat this process to generate an bioisosteric analog of your choice and save this with a
different file name (e.g. thio_nevirapine.mol).
2. In Maestro, under Applications, choose LigPrep.... In the File name line, hit Browse... and select the
structure file with nevirapine (e.g. nevirapine.mol). You do not need to change the ionization state,
desalt, or generate tautomers in this case. You may want to sample ring conformations and generate 2
low energy ring conformations. Hit Start ... and give a meaningful Name for your job (e.g.
Prep_nevirapine). The ligand preparation will take less than a minute, and the prepared ligand is now in
the file with .maegz extension. You can close the LigPrep window. Notice that the prepared ligands were
not incorporated into your workspace.

Generate the Grid

1. Under Edit, select Select Atoms, then Select .... In the Atom Selection dialog box, choose Residue
Type, and select NVP. Hit Add, and then OK to close the selection window. Notice that the bound
ligand is selected.
2. Click on the Representation tab in the top toolbar; notice that a new set of icons appears on the left
side. Select Ball-and-Stick representation, and click on any atom in the ligand. Notice that the ligand is
now easily visible. Deselect the ligand by clicking on an empty space.
3. Under Applications, select Glide, then Receptor Grid Generation.... A new window titled Receptor
Grid Generation opens. Make sure that Pick to identify ligand is checked, and click on any atom in
the ligand. Notice that green boxes surround selected ligand atoms.
4. Click on the Site tab and briefly examine the rectangular region for which the grid is generated. Then hit
Start, give a meaningful name (e.g. Grid_HIV_RT) for your job, and hit Start one more time to start the
grid generation. The grid generation takes about four minutes; you can examine Figure 1 of the article
High resolution structures of HIV-1 RT from four RT-inhibitor complexes until the calculation finishes.

5. You can close the Monitor window and the Receptor Grid Generation window. Keep the protein with
ligand in your workspace. (The last part is not really critical; because from now on you only need the
grid and ligand files, you could even close the Maestro program after saving your project)
Rigid Docking
1. Under Applications, select Glide, then Ligand Docking... A new window titled Ligand Docking
opens.
2. Under Settings tab, hit Browse and select the grid file you generated earlier (Grid_HIV_RT.zip, for
example). Select Dock rigidly for now; you can perform flexible docking later.
3. Under Ligands tab, hit Browse and select the prepared ligand file (Prep__t-out.maegz, for example).
4. Hit Start and give a meaningful name (e.g. Glide_HIVRT_nevirapine_rigid) to your job. Hit Start once
more to start the docking calculation. The standard precision rigid docking will complete in a few
seconds. Close the Monitor and Ligand Docking windows.
5. Under Project, select Show Table. A new window with results opens. The first four entries are your
prepared protein with the original ligand. The last set of entries include your receptor (without the
ligand) and the docked ligand poses. You can use Ctrl key on the keyboard to visualize multiple entries.
For example, compare how well does the docked ligand pose match the position of the original ligand.
Final Comments
Docking of the ligand that was originally present in the crystal structure to the same protein is one of the easiest
docking tasks. Many docking programs correctly identify a ligand pose very similar to the experimentally
observed pose as one with one with the highest score. The success of such re-docking does not always indicate
that the docking of novel compounds will be reliable with the same program. First, comparison of novel
compounds involves scoring of these compounds against each other; this step is not needed for docking a single
compound. Second, the shape of the binding pocket during docking of novel compounds is usually not allowed
to change to accommodate the novel ligand, and thus ligands larger than the original ligand may not fit into the
pocket according to the docking program. In reality, proteins are flexible, and it is likely that the active site will
change slightly to accommodate slightly larger ligands that otherwise make good contacts with the receptor. You
can prove this by trying to dock known HIV reverse transcriptase inhibitors. One source of relevant data here is
the Ph.D. thesis of R.C. Rizzo
Homework 1: Better HIV reverse transcriptase inhibitor
Check if the bioisostere that you had created earlier binds better than nevirapine according to Glide. If not, carry
out structural modification until you find a molecule that binds better. You can use either rigid or flexible
docking here. Keep in mind that when you compare different molecules, you want to run docking calculations
with the same setup. Recall that you only needed to generate the grid once.
Homework 2: Docking of Chorismate Mutase Inhibitors
Follow instructions in this tutorial as well as in the Glide Quick Start Guide to dock a set of chorismate mutase
ligands to the E. coli chorismate mutase using Glide. Use the same set of molecules that you used with DOCK.
Because of the small size of the enzyme and ligands, use the XP (extra precision) option when docking.

Compare the Glide and DOCK6 results, and briefly discuss the performance, and the ease of use of the two
programs.