DOCKING SCHEME.

CONFORMATIONAL EXPLORATION
The ligand is placed in the binding site and different poses are
generated
In one run, a given number of searches is performed and the lowest
energetic complex is kept, N cycles are repeated

Systematic search methods quimics

canvis
Meller
"lents"

 Exhaustive
.

 Fragmentation (e.g
FlexX, DOCK) "docking peces
Iligand"
del
reconstruccio
I

 Conformational "buscar per conf .

"

ensemble Iligand per separat nomes d'alg corf

docking
.

proteina
: .

de la
, minims fora centre

Random or Stochastic methods deterministal

, no ac+iU)

 Monte Carlo based (e.g. AutoDock

molt
USA + Vina, ICM, ROSETTALIGAND)
 Genetic Algorithms based (e.g
AutoDock, GOLD, rDock)
 Tabu search methods
 Swarm methods colonies
->
insectes ...

Simulació Biomolecular Docking 8

 DOCKING SCHEME.
CONFORMATIONAL EXPLORATION. Example.
Autodock docking parameters input file. GA-based search.

Simulació Biomolecular Docking 9

 DOCKING SCHEME.
CALCULATION OF BINDING ENERGY (OR SCORE)
Irw + electrostatical

For each pose a binding energy is evaluated: score

The score allows ranking of poses of the same ligand

as well as different ligands between them

Force-field based
 GoldScore (Verdonk 2003)
 AutoDock (Morris 1998)
ens quedem amb termes
VDW + electro .

Empirical scoring function , Fitting

 Glide (Halgren 2004, Friesner 2004)
 ChemScore (Eldridge 1997)
 AutoDock Vina
 AutoDock (semi-empirical:Huey 2007)

Knowledge-based scoring function Developments are

 DrugScore (Gohlke 2000, Velec 2005) explored based on
 Gold/ASP (Mooij 2005) Machine Learning, QM
"Fitting" peroamb estadistica conjunt scores…
de dades (
Consensus
Simulació Biomolecular Salmaso & Moro, Frontiers in Pharmacology (2018) Docking 10
 DOCKING SCHEME.
CALCULATION OF BINDING ENERGY (OR SCORE)
1. Force-Field Based l

Explicit energetical terms V bonding= k b l− l0 2

provided by simplified
molecular mechanics force
fields
V bending = k b θ− θ0 2
Energy of the complex is
calculated based on the
energetic terms provided by
the FF
V torsion= A [ 1− cosnτ φ]

Mostly derived from AMBER

or CHARMM FF
qi q j
V Electrostatic= ∑ ∑
i ji εr ij
Slightly easier to
parameterize than the other
approaches V VDW= 4εij [σ ij /r ij 12 − σij /r ij 6 ]
Simulació Biomolecular Docking 11
 DOCKING SCHEME.
CALCULATION OF BINDING ENERGY (OR SCORE)

2. Scoring from empirical interactions:

Score is a linear combination of weighted single

interactions parametrized to fit known data
set

The types of interactions:

hydrogen bonds
electrostatic interactions
hydrophobic contacts
solvent exclusion volume
electrostatic interactions
...

Simulació Biomolecular Docking 12

 DOCKING SCHEME.
CALCULATION OF BINDING ENERGY (OR SCORE)
2. Scoring from empirical interactions:

E.g. Autodock4.2

Training-set:
190 known
protein-ligand
complexes

Image extracted
from Autodock
user guide.

Simulació Biomolecular Docking 13

 DOCKING SCHEME.
CALCULATION OF BINDING ENERGY (OR SCORE)
2. Scoring from empirical interactions:

E.g. Autodock (cont)

The force field includes six pair-wise evaluations (V) and an estimate
of the conformational entropy lost upon binding (ΔSconf):

where L refers to the “ligand” and P refers to the “protein”

Each of the pair-wise energetic terms includes evaluations for dispersion/repulsion,

hydrogen bonding, electrostatics, and desolvation:

The weighting constants W have been optimized to calibrate the empirical

free energy based on a set of experimentally determined binding constants
Simulació Biomolecular Docking 14
 DOCKING SCHEME.
CALCULATION OF BINDING ENERGY (OR SCORE)
2. Scoring from empirical interactions: GOLD -
polars
viNA <
apOlarS

E.g. Autodock Vina (which is different from Autodock!)

Training-set: 190 known

protein-ligand complexes
estr
qualitat ? RMSD d'una .

coneguda
teorica -coneguda

 Vina uses a different “philosophy” for the scoring function.

 And also a different method for the conformational search: Iterated Local Search global
optimizer, a succession of steps consisting of a mutation and a local optimization are
taken, with each step being accepted according to the Metropolis criterion (Monte Carlo).
Simulació Biomolecular Docking 15
 DOCKING SCHEME.
CALCULATION OF BINDING ENERGY (OR SCORE)
2. Scoring from empirical interactions:
E.g. Autodock Vina (cont)

 Vina uses a different philosophy for the scoring function.

 The binding energy is predicted as the sum of distance-dependent atom pair interactions:

where:

with r being the interatomic distance and Ri and Rj are the radii of the atoms in the pair.

 Every atom pair interacts through a steric

interaction given by the first three terms of
the equation. Also, depending on the atom
type, there could be hydrophobic and non-
directional H-bonding interactions, given
by the last two terms of the equation.

Simulació Biomolecular Docking 16

 DOCKING SCHEME.
FINALIZATION AND OUTPUT

The end of the full docking Calculation of

experiment provides: physicochemical properties of
the binding site

The n solutions provided by the

n runs
Their associated calculated Generation of
protein-ligand complexes
energies
Their ranking
Clustering analysis of the
solutions (if desired)
Estimation of the
binding energy

Analysis of the results and post

analysis can be carried out.
Ranking of poses /
Ranking of ligands

Simulació Biomolecular Docking 17

 DOCKING SCHEME.
FINALIZATION AND OUTPUT
Example: Gold run with
standard GA parameter
request

All poses
20
dockings
representats si hi ha molta flexibilitat ,

la
>variabilitat no necess .
Emenor=
s'assembla mes !
que

criteri quimic
de bona
varies sols .

energia possibles
Best pose .vs.
experimental

Simulació Biomolecular Docking 18

 DOCKING SCHEME.
FINALIZATION AND OUTPUT. ANALYSIS
A good analysis of the results is key for both qualitative and
quantitative interpretation

In general: the highest number of runs is performed the most likely the
experiment is valuable, but the harder it is to analyze and more time
consuming it is
encompres d'1 geom
Different tools are used to perform complete analysis:
.

bona , familia
-

"clusters"

Clustering: low energy solutions are packed in structural families based on

an structural parameter (usually RMSD between poses)

Filtering: eliminate a series of poses based on known information

Rescoring: for the given solutions, calculate the score using a different
scoring function trying to better discriminate poses.
Molecular dynamics: search for local rearrangement upon ligand binding
and ensuring stability of predicted complex. "refinement"
Simulació Biomolecular Docking 19
 DOCKING SCHEME.
FINALIZATION AND OUTPUT. ANALYSIS
In vitro and in vivo values can be used to +

e0 .

correlate with docking analysis:

Binding energies (e.g. calorimetry)

KD
exp .

sovint 0 9 pot venir

:

R2 molt ,

molta dependencia amb les

de la bioquimica o
part
cond .
exp .

modelitzaci

Ki (an indication of how potent an inhibitor is; it is the

concentration required to produce half maximum inhibition)
IC50 (half maximal inhibitory concentration) is a
measure of the potency of a substance in inhibiting a
specific biological or biochemical function. IC50 is a
quantitative measure that indicates how much of a
particular inhibitory substance (e.g. drug) is needed to
inhibit, in vitro, a given biological process or biological
component by 50%.

Mutagenesis data to help identify interacting

residues impacte de mutacions
…
Simulació Biomolecular Docking 20
 DOCKING SOME CONSIDERATIONS
The approximations (none flexible protein, score, parameterization, etc…)
used in molecular dockings can lead to many pitfalls which are typically:
Only one or some of the lowest 10 solutions reproduce an interesting binding
mode but not necessarily the most stable one
All orientations seem random, no clear pattern can be found
Difference in energy between the different runs are very small
…
It is crucial to know the limitation of the method!
Yet, sometimes is the only possible first step to start the modelization of a
complex system.

Although molecular docking algorithms are in constant improvement, some

properties require more development than others, especially the entropic
ones:
Solvation and desolvation
Structural and energetical impact of pre-organization and re-organization

Simulació Biomolecular Docking 21