tim cheeseright, cresset, 'introducing fragment growing in fieldstere and other cool stuff

Evaluating Bioisosteric Replacements Taking the Whole Molecule into Account

Mark Mackey

Current Versions

Product GUI CLI Next release

FieldScreen (Virtual Screening) 2.6.0 2.6.0 Q1 2012

FieldStere (Bioisosteric groups) 2.0.0 2.1.0 October 2011

FieldAlign (Ligand alignment and design) 3.0.1 3.0.1 Q4 2011 (as Molecular Architect)

FieldTemplater (3D pharmacophore determination)

3.0.0 - Q2/3 2012

FieldView (Viewer) 2.0.2 - Q1 2012

XedTools (Conformations, Ligand Minimizer)

- 2.6.0 Q1 2012

NN

Br

F FF

SH2NO

O

Field Points

Condensed representation of electrostatic, hydrophobic and shape properties (“protein’s view”)

> Molecular Field Extrema (“Field Points”)

3D Molecular Electrostatic

Potential (MEP)

Field Points= Positive = Negative= Shape= Hydrophobic

2D

H-bond donor

H-bond acceptor

Hydrophobes

Aromatic p cloud

‘H acceptor’

Aromatic in-plane

‘H donor’

-ve ionic

+ve ionic

“Stickiest” surfaces (high vdW)

N

NH

O

O

OH H

H

Explanatory Power of Fields

Field points give you new insights into your molecule

= Positive = Negative= Shape= Hydrophobic

Field point size show importance

FieldStere

> Finding bioisosteres by replacing sections of the molecule

Rofecoxib

Valdecoxib

Etoricoxib

12nM

FieldStere’s Approach

1 Select a region to replace and remove these atoms

FieldStere’s Approach

1 Select a region to replace and remove these atoms2 Search database for matching fragments

(geometric search only)(search runs on fragment conformations)

1 Select a region to replace and remove these atoms2 Search database for matching fragments

(geometric search only)(search runs on fragment conformations)

3 Form Products(minimise and add Field Points)

FieldStere’s Approach

1 Select a region to replace and remove these atoms2 Search database for matching fragments

(geometric search only)(search runs on fragment conformations)

3 Form Products(minimise and add Field Points)

4 Score

FieldStere’s Approach

0.88

> Produces more diverse, non-obvious bioisosteres> Avoids fragment scoring

limitations> Allows for electronic influence

of replacing a moiety on the rest of the molecule and vice versa

> Allows for neighbouring group effects

Whole-Molecule Scoring Advantages

OO

S OO

SN

S OO

NN

Database of Replacement Moieties

> Series of commercial compounds> fragmented and recombined

> Resultant moieties placed into separate databases based on frequency> V. Common

> Common

> Less Common

> Rare

> Very Rare

> Frequency roughly correlates with synthesizability

> Add your own database containing proprietary moieties

Example - COX-2

> Search for Bioisosteres for cyclic lactone of Rofecoxib

O O

SO

O

aromatic atoms only

Actives:9 of the first 10 clusters21 of the first 30 clusters

Search Common Dbs

87,225 frags

Cluster, Result Nos

Cluster id

FieldStere result 2D sim closest lit compd

10,12 0.52 Same, 60nM

13,19 0.509

7nM

32, 104 0.48 None

COX-2 Results

Cluster, Result Nos

Cluster id

FieldStere result 2D sim closest lit compd

1,1 0.646

2,2 0.531

6.5uM

5,5 0.500 Same, 10nM

9,11 0.532

70nM

ON

SO

O

ON

SO

OH2N

ON

NNS

SO

O

NNS

SO

O

NNS

F

NS

N

N

SO

O

NS

N

N

S

SO

O

S

O NH2

SO

OH2N

S

O O

N

SO

O

N

SO

O

F

F

SO

O

F

F

F

N NN

N

SO

O

N NN

N

COX-2 Results

Product Space

Target Result 5 Result 1,484

Cross Scoring

> Separate target and reference for scoring

> Bring in interactions from a parallel series> Multiple series using different parts of a binding site

> Optimize a low activity series using a high activity “template”

> Grow molecules> Mimic interactions of alternative series

> Fragment growing

S

N

S

O

O

N

N

1 Select a region to replace and remove these atoms2 Search database for matching fragments

(geometric search only)(search runs on fragment conformations)

3 Form Products(minimise and add Field Points)

4 Score

FieldStere’s Approach

0.680.78

Cross scoring example - BACE

> Multiple known actives for BACE

> Binding site has flexibility> Ligand based methods less sensitive to protein

movements

> Ligands interact with the catalytic Aspartates differently

> PDB 2IQG - Hydroxyethylamine based inhibitor> Complex chemistry> Chiral

> PDB 3L59 - Small guanidine based inhibitor> Excellent interactions with

Asp’s

BACE Experiment

NH

O

N

O

NH2+

I

F

F

OH

N

Cl

NH

O NH2+

2IQG - Detail

3L59 - Detail

Can we use 3L59 to improve 2IQG ?

> Use 2IQG as the “Target”

> Score replacements against 3L59 - the “Reference”

NH

O

N

O

NH2+

I

F

F

OH

Region to be replaced

Only accept replacements with Carbon here

Preliminary Results

NH

O

N

O

F

F

SH2N

+HN

NH

O

N

O

F

F

NH

N NN

NH

O

N

O

F

F

O

NH+

NH

O

N

O

F

F

O

H2+

N

NH

O

N

O

F

F

N

NH3+

NH

O

N

O

F

F

NHN

H2+

N

HNH

O

N

O

NH2+

I

F

F

OH

Result 18 Result 31

Result 55 Result 83Result 42

Result 110

Cross Scoring 2 - Fragment Growing

> FieldStere version 3.0.0 fragment growth example:

1. P38 kinase bound to a fragment fluorescent probe PDB:3K3I specific to the ‘DFG-out’ conformation

2. ‘DFG-in’ example with specificity towards the ‘Gly’ flipped hinge PDB:3ROC and/or 3HUB

> Selectivity potentially to be gained by combining ‘Gly flip’ and ‘DFG-out’ in one molecule

> Can we use the new version of FieldStere to grow the DFG-out fragment into the DFG-in hinge?*

*we realize we don’t want to develop a fluorescent probe….but… as an illustration of utility it is OK. We also have a number of more reasonable edits of this fragment….

Fragment in DFG-out pocket, PDB:3K3I

predominant hingeconformation

+Gly hinge flip ligand_1, PDB:3ROC

Hinge Gly flip

+Gly hinge flip ligand_2, PDB:3HUB

Hinge Gly flip

Fieldstere input

> Target was PDB: 3K3I

> Reference was PDB: 3ROC

> 20/80 scoring T to R

> All databases

> Accurate settings

> Size limit on fragment removed

> Fragments limited to 3 rotatable bonds

> Fragment must contain a ring

Structure Rank Sim Structure Rank Sim

1 0.528 11 0.492

4 0.507 13 0.489

6 0.501 53 0.476

Fieldstere output: 2D mols

Fieldstere output: 3D mols

Fragment and reference Rank 4 Rank 6

Rank 11 Rank 13 Rank 53

Fieldstere output: 3D mols and Fields

Fragment and reference Rank 4 Rank 6

Rank 11 Rank 13 Rank 53

Fieldstere output: 3D overlay

> References and Rank 6

Outcome

> Fragment growth both possible and a facile process using FieldStere

> Interesting and sensible candidate molecules generated

> Many more options available for increasing diversity of the output

mark@cresset-bmd.com

Questions welcomed