Methodology:

1. Open 1HSG.pdb with Discovery Studio. Remove the water molecules

2. Cut and paste the ligan molecule(indinavir) from the protein to a ne 3D
windo save ligand as indinavir.pdb and receptor without ligand as HSG.pdb
3. Open HSG.pdb with Autodock Tools(ADT)c= Click Cl and change color by
atom type edit Hydrogen Add Click GridMacromolecules
ChooseHSGSelect molecule HSG click Ok and save
4. Click Grid grid Box Spacing=1.00, x=16, y=25 and z=4 and dimensions
as 30Close without saving Edit deletedelete molecule Select HSG
Delete molecule and Continue

B.Preparing Ligand

1. Open Indinavir.pdb with Autodock Tools(ADT)c= Click Cl and change color

by atom type edit Hydrogen Add Click GridMacromolecules
ChooseHSGSelect molecule HSG click Ok and save
2. Click LigandTorsion tree Choose torsions should be 14 torsions seen.
3. Click Grid grid Box Spacing=1.00, x=16, y=25 and z=4 and dimensions
as 30Close without saving
4. Click Ligand Output Sve as PDBQT as indinavir.pdbqt

C.Preparing docking configuration

1. Open wordpad Type script based on page 37 of lab manual and x=16, y=25
and z=4 [center_x,y,z]and size_x,y,z as 30Save file as indinavir.txt.

D.Run Autodock Vina

1. Go to start menu Run Type cmd

2. In the command prompt Type filename exp12type dir to see all files in
desktop
3. Type Program Files\The Scripps Research Institute\Vina\vina.exe config
indinavir.txt log indinavir.log, click enter
4. Ind_all.pdbqt and indinavir.log file will be generated containing calculated
affinities
5. Visualize docking result in Pymol by loading HSG.pdb, indinavir.pdb and
indinavir_all.pdbqt and play the modes given

For Nelfinavir:

1. Use chemsketch to create nelfinavir ligand and save as nelfinavir.molOpen

file in Discovery studio- Check the bonds andStuctureClean Geometry
to optimize structure Save as nelfinavir.pdbRepeat B till D in creating
the nelfinavir.txt change the out= nelfi_all.pdbqt.
Questions:

1. Qualitatively how good are the docked structure?

Table 1: Docked structure mode 1 to 9 (from left to right)

Table 2: Docked structure Scores

We employ docking as the prediction of the three dimensional structure of the

particular macromolecular complex as it would occur in a living organism. Docking
only produces probable candidate structures and they are ranked by methods such
as scoring functions to identify structures that are most likely to occur in nature.
From our results for indinavir docked strutures(refer table 1), the first mode(1)
gives the most similar to the already given ligand orientation. The second and third
mode still looks similar with small deviations from original. But starting from mode
4 everything looks very messy or disoriented. We can also see that as the energy
becomes less negative (from mode 4 to mode 9), the disorientation increases. In
accordance to thermodynamics, yes, the lowest energy(most negative) structure is
most stable just like our indinavir of mode 1 is most stable as the original position.
There are deviation at C33-36( The area circled). Therefore we can say that the
docked structures are just averagely good. Also to be noted the run time the 9
structures was 30 sec, supposingly proportional to the number of protein structures
in consideration.

2. Is the crystal binding mode reproduced? If not or if there is a difference, what

could be the reason? Is it the best conformation according to AutoDock Vina?

The crystal binding mode wasnt reproduced actually the major difference as in
question 1 is around C33-36. Also to be noted indinavir has 14 active torsions. We
also know indinavir has 12 rotatable bonds. Theoretically, the more rotatable bonds
in the ligand, the more difficult it will be to find good binding modes in repeated
docking experiments. This is why there is a difference in structure.

The docking accuracy was evaluated in terms of the root mean square deviation
(RMSD) between the docked position and the experimentally determined position
for the ligand. The energy scores of the conformers were then merged for each
ligand. A total of 9 modes obtained. The conformer with the lowest score
represented the best docked ligand that is the mode 1 with affinity of -11.5kcal/mol,
and rmsd of 0 .
 3. Perform molecular docking of nelfinavir into HIV-1 protease. Based on
indinavir docking, dock nelfinavir into HIV-1 protease and discuss your
results?

Table 4: Nelfinavir docking mode 1 to mode 9

 Table 4: Nelfinavir docking scores

The score for the best conformer of nelvinavir is -10.1kcal/mol at 0 rmsd which is
actually more negative than indinavir. Making indinavir a better protease inhibitor
since it has lower energy thus it is more stable. Besides, Nelfinavir has 12 active
torsions based on our results log file. It has rotatable bond count of 10. Making this
less flexible than indinavir. We also see that only the docked structure can binds to
the structure rather than the original ligand. Also all the docked structures vary from
the original ligand if compared to nelfinavir at least had one slightly similar
structure.

Conclusions:

1. Docking results in a few crucial files namely Log file which is a log file describing
the tasks performed and noting any warnings or errors. A DockedLigand.pdb file
that has the best (i.e. lowest docking scores) poses of the docked ligand in PDB
format. Also a DockedLigand.log file containing the Vina docking scores for these
best poses. Hereby, poses with similar docking scores should be treated as equally
likely. As well as a ligand.pdbqt file having the target ligand in PDBQT format.

2. PDBQT is a file type which stores the atomic coordinates, partial charges and
AutoDock atom types, for both the receptor and the ligand.

3.Indinavir is more stable than nelfinavir.

4. The best conformer of nelvinavir is -10.1kcal/mol at 0 rmsd

5. The best conformer for indinavir is of affinity -11.5kcal/mol, and rmsd of 0 .

References:

1. http://en.wikipedia.org/wiki/Macromolecular_docking

2.
http://graylab.jhu.edu/pyrosetta/downloads/documentation/Workshop7_PyRosetta_D
ocking.pdf

3. http://autodock.scripps.edu/faqs-help/tutorial/using-autodock-with-
autodocktools/UsingAutoDockWithADT_v2e.pdf
4. http://ashujo.wordpress.com/2007/05/05/how-do-you-choose-a-good-crystal-
structure-for-docking/

5. http://docking.utmb.edu/faq.php