Docking

Docking
n

The study of multi-molecular complexes

Common use: to study the interactions
between proteins and small molecules (often
inhibitors) in order to design improved
ligands for that protein

Challenges
n

The lowest energy conformation of a molecule

is dependent on its environment
n

Pure/Complex Crystal Comparison

The conformation of a small molecule may

change when bound to a protein
The conformation of a protein may change when
bound to a small molecule
Water molecules may mediate interactions

The stability of the complex is best reflected by

the Gibbs free energy (G) for the process
mol1s + mol2s <=> mol1:mol2:s
3

Nicklaus et al., Conformational Changes of

Small Molecules Binding to Proteins,
Bioorg. Med. Chem., 1995, 3(4), 411-428

Challenges
CH3
N
HO2C

H
N

N
N

NH2

N
NH2

CO2HO

The lowest energy conformation of a molecule

is dependent on its environment
n

methotrexate

The conformation of a small molecule may

change when bound to a protein
The conformation of a protein may change when
bound to a small molecule
Water molecules may mediate interactions

The stability of the complex is best reflected by

the Gibbs free energy (G) for the process
mol1s + mol2s <=> mol1:mol2:s
6

Protein Structural Changes

HIV Protease Dimer
HIV Protease Dimer

ligand (spacefilling)

no ligand

Challenges
n

The lowest energy conformation of a molecule

is dependent on its environment
n

Water-bridged Drug Binding

The conformation of a small molecule may

change when bound to a protein
The conformation of a protein may change when
bound to a small molecule
Water molecules may mediate interactions

The stability of the complex is best reflected by

the Gibbs free energy (G) for the process
mol1s + mol2s <=> mol1:mol2:s

n
n

Download 1AAQ from the Protein DataBank

Isolate the inhibitor (abbreviated PSI in the
sequence editor) and residues proximal to it
Identify the position of the water molecule
(will just be an oxygen atom as hydrogens
are not present)
Identify likely hydrogen bonding partners of
the water molecule (you should find four)

10

Challenges
n

The lowest energy conformation of a molecule

is dependent on its environment
n

Binding Free Energy

The conformation of a small molecule may

change when bound to a protein
The conformation of a protein may change when
bound to a small molecule
Water molecules may mediate interactions

The stability of the complex is best reflected by

the Gibbs free energy (G) for the process
mol1s + mol2s <=> mol1:mol2:s
11

Relationship between G and dissociation

constant (Kd):
n
n

G = RT ln Kd
Therefore small differences in G give large
differences in Kd

Contributions to G
n
n

G=H-TS
H (enthalpy) includes electrostatic and steric
(van derWaals) interactions
S (entropy) changes as degrees of freedom are
restrained and solvent rearrangements occur
12

Contributions to Enthalpy
n

Electrostatic interactions
n
n
n

n
n
n

Multipole Interactions
n

Ionic interactions (E=qiqj/rij)

Charge-dipole and dipole-dipole interactions
Multipole interactions (with ions, dipoles or other
multipoles)
Dipole-induced dipole interactions
Dispersion or van derWaals interactions
Hydrogen Bonds

Aromatic rings are examples of multipoles

Concentration of negative charges

Concentration of positive charges

Steric interactions

Aromatic rings interact favorably with cations

(cation-pi or ion-quadrupole interactions) and
other aromatic rings (pi-pi or quadrupolequadrupole interactions)

13

14

Multipole Interaction Example

Close-up
Magenta: part of actinomycin
Blues: part of one DNA strand
Oranges: part of the other DNA strand

DNA Interaction with Actinomycin

15

16

Contributions to Entropy
n

Translational and rotational entropy

n

n
n
n

Contributions to Entropy
n

small molecules in solution have freedom to rotate

(defined by 3 degrees of freedom) and translate (defined
by 3 degrees of freedom)
Translations and rotations within a protein binding pocket
are very restricted
These result in a negative entropy change

Conformational entropy
Hydrophobic effect
Solvent reorganization

Translational and rotational entropy

Conformational entropy
n

n
n
17

Single bonds in solvated molecules have a

torsional degree of freedom
Torsional rotation is restricted in protein active
sites
This is also a negative entropy change

Hydrophobic effect
Solvent reorganization
18

Contributions to Entropy
n
n
n

Translational and rotational entropy

Conformational entropy
Hydrophobic effect
n

Contributions to Entropy
n
n

polar solvent molecules form an organized solvation shell

around nonpolar molecules in order to optimize favorable
interactions with other polar solvent molecules
a greater number of equivalent arrangements are possible
in the absence of the nonpolar molecule
a positive entropy change thus occurs when a nonpolar
molecule transfers from aqueous solution to a protein
binding site

n
n

Translational and rotational entropy

Conformational entropy
Hydrophobic effect
Solvent reorganization
electrostatic interactions between a polar solute
and solvent will produce an ordered solvent shell
association of polar solute molecules (drug +
protein) results in a favorable (positive) entropy
change for the solvent

Solvent reorganization
19

20

General Docking Algorithms

Common Docking Simplifications

n

Protein Conformation
n
n

Rigid (MOE, DOCK, Autodock)

Limited protein sidechain flexibility (Flexi-dock)

Ligand Conformation

Binding Free Energy

n
n
n
n

1.

Generate a relative orientation for the two

molecules
A.
B.

Fully flexible

2.

Grid-based interaction energy (MOE, Autodock)

Shape complementarity (DOCK)
Functional group complementarity (DOCK)
Empirical (SCORE )

Evaluate or score the orientation

A.
B.

3.

Randomly with subsequent optimization (MOE)

Matched to protein surface (DOCK, Autodock)
Grid-based
Empirical

Repeat

21

Grid-Based Dock Scoring

n

Protein Grids

Possible interactions with the protein are precomputed

n

22

A grid of points that occupies the same volume as the

protein is generated
Steric and electrostatic interactions with the protein at
each point are computed

The ligand orientation is scored by summing

interactions at grid points contacting the ligand
Neglected
n
n
n

Solvation changes upon binding

Entropy changes upon binding
Protein conformational changes
23

24

Class Exercise II
n

Docking in VHTS

See handout

HTS: High Throughput Screening

n

VHTS: Virtual High Throughput Screening

n

25

Very rapid (and qualitative) means to screen

libraries of chemical structures for biological
activity
Represented a potential elimination of
computational chemistry in the pharmaceutical
industry
Very rapid (and approximate) docking methods
designed to evaluate libraries of compounds to
enrich elaborated libraries with active compounds
26

Reading
n

The Organic Chemistry of Drug Design and

Drug Action, Second Edition
n
n

2.2H, 2.4 Problem 19-21

3.2B

Textbook of Drug Design and Discovery,

Third Edition
n

Chapter 2

27