Generating Synthetically Accessible Ligands by De Novo Design

Synthetic Sprout

A Peter Johnson Krisztina Boda

Attilla TingJon Baber

SPROUT is the De Novo design system developed in Leeds

SPROUT components

Identification of potential interaction sites complementary to the receptor, ie H bonding, hydrophobic sites, metal co-ordination sites etc.

Automated docking of small fragments at the interaction sites.

Generation of hypothetical structures by linking the docked fragments together.

Tools for scoring, sorting and navigating the answer set.

Example: 3D shapes of sites

H-bond acceptor site

H-bond donor site

Hydrogen Bond Sites

Boundary Surface

Docking of small fragments at target sites

Target sites are generated either by SPROUT module HIPPO (or similar system) or come from a pharmacophore hypothesis.

Small fragments with complementary functionality are selected by the user and automatically docked into the target site(s).

In addition to these small fragments, it is also possible to dock large fragments which are known to satisfy several of the target sites. Such a large fragment can then act as a “seed” for further growth.

A successful dock must place the small fragment at the target site with the correct orientation to satisfy any directional constraints.

The docking process is very fast and uses a novel hierarchical least squares optimisation procedure.

Structure generationThe SPIDER module links the target sites together in a pairwise fashion to make complete molecular structures which satisfy target sites. It does this by sequentially adding new fragments in an exhaustive fashion.

There is no element of random choice in this process, which means that various heuristics have to be adopted to avoid a combinatorial explosion.

The main approximations employed are:There is a sampling of all the possible conformations about single bonds.Growth is only permitted from atoms/bonds which are closest to the target site which is to be reached

Main algorithm of SPIDER

Multiphase heuristic graph search on a forest ( set of trees)Two trees are searched and removed in each phase and a new tree generated which contains skeletons connections both set of sites

Each phase consists of a bi-directional searchBreadth First Search (BFS)Depth First Search (DFS)

Typical saving bi-directional search 10 successors, 6 level: 2x103 << 106

Connection of Partial Structures

Common template is located in two structures (one from each tree)

Structures are overlayed by the common template

Combined structure is docked to the united set of target sites also considering the steric constraints of the receptor site

Side effect joins are axamined for validity (e.g. fusion on figure)

Navigating the answer sets

Estimated binding energy score Ranking final de novo set Ranking and pruning (with caution)

intermediate trees to reduce combinatorial problem.

Estimated ease of synthesis score Ranking final de novo answer set Too slow (~1 structure per minute) to be

useful for intermediate pruning Need faster methods for intermediate

pruning

Recent Advances Parallelization of structure generation

– Farm of SG’s or pcs– SPROUT server – BEOWOLF cluster currently 11

dual processor 600Mhz Pentium III VLSPROUT screens virtual libraries SYNSPROUT generates synthetically

accessible ligands Receptor SPROUT generates potential

synthetic receptors for small movecules

The perennial modellers problem

Hypothetical ligands, including those predicted to bind very strongly, have no practical value unless they can be readily synthesised.

Our attempts to provide solutions:

CAESA post design estimation of synthetic accessibility

SynSPROUT synthetic constraints built into the de novo design process

VLSPROUT even greater synthetic constraints – only members of a specific virtual library are generated

Synthetic Sprout Approach

Pool of readily available starting materials, e.g. subset of ACD

Knowledge Base of reliable high yielding reactions, e.g. esterification,amide formation, reductive amination..

Readily synthesablePutative ligand structures

VIRTUAL SYNTHESISIN RECEPTOR CAVITY

Creation of Starting Material Libraries Obvious Classes eg amino acids “Drug like” starting materials selected by

hand “Drug like” starting materials generated

automatically by retrosynthetic analysis of drug databases

12

O

OOH

3

EXPLANATION Ether FormationIF EtherTHEN disconnect bond between 2 and 3 add-atom O[Hs=1], Cl, Br 3 with – add-hydrogen to 2END-THEN

EXPLANATION Ether FormationIF EtherTHEN disconnect bond between 2 and 3 add-atom O[Hs=1], Cl, Br 3 with – add-hydrogen to 2END-THEN

12

O

OH

3O

N

S

O

NH

O O

13

2

4

O

OOH

EXPLANATION Amide FormationIF AmideTHEN disconnect bond between 1 and 3 add-atom O[Hs=1] to 1 with – add-hydrogen to 2END-THEN

N

S

O

NH2

O O

13

2

4

O

OOH

EXPLANATION Amide FormationIF AmideTHEN disconnect bond between 1 and 3 add-atom O[Hs=1] to 1 with – add-hydrogen to 2END-THEN

N

S

O

NH

O O

13

2

4

O

O

EXPLANATION Amide FormationIF AmideTHEN disconnect bond between 1 and 3 add-atom O[Hs=1] to 1 with – add-hydrogen to 2END-THEN

N

S

O

NH

O OH

O

O

EXPLANATION Amide FormationIF AmideTHEN disconnect bond between 1 and 3 add-atom O[Hs=1] to 1 with – add-hydrogen to 2END-THEN

N

S

O

NH

O OH

O

O1

2

4

3

Retro-Synthetic Knowledge BaseRetro-Synthetic Rule

N

S

O

NH2

O O

EXPLANATION Amide FormationIF AmideTHEN disconnect bond between 1 and 3 add-atom O[Hs=1] to 1 with – add-hydrogen to 2END-THEN

O

OOH

EXPLANATION Ether FormationIF EtherTHEN disconnect bond between 2 and 3 add-atom O[Hs=1], Cl, Br 3 with – add-hydrogen to 2END-THEN

12 O

HO,Cl,Br OH

3O

EXPLANATION Ether FormationIF EtherTHEN disconnect bond between 2 and 3 add-atom O[Hs=1], Cl, Br 3 with – add-hydrogen to 2END-THEN

12 O

HO,Cl,Br OH

3OH

EXPLANATION Ether FormationIF EtherTHEN disconnect bond between 2 and 3 add-atom O[Hs=1], Cl, Br 3 with – add-hydrogen to 2END-THEN

OH

Cl

Br

OH

O

OH

OH

O

Cl

OH

O

Br

Automatic Template LibraryGeneration

Synthetic Template Library

CorinaCorina

OmegaOmega

SyntheticKnowledge Base• Functional groups

SyntheticKnowledge Base• Functional groups

PerceptionKnowledge Bases•Aromatic•Normalisation•Hybridisation•H-bonding properties

Single 3D ConformerGeneration

Multiple ConformerGeneration

2D Drug-like Structures

Retro-SyntheticKnowledge BaseRetro-SyntheticKnowledge Base

Fragmentation

Filter

Clustering

Ring PerceptionRing Perception

Retro-Synthetic rules Retro-Synthetic rules

Retro-synthetic patterns Retro-synthetic patterns

Automatic Chemical Perception Information

Perceived – Aromatic atoms and

bonds– Normalised bonds– Hybridisation including

induced hybridisation– H-Donors / Acceptors– Number of hydrogens

attached to an atom– Number of connections to

an atom– Number of available

electron pairs– Charge at an atom

CHEMICAL-LABEL <NitrogenWithLP--SP2>X[SPCENTRE=2]-N[HS=0,1,2];[SPCENTRE=3]EXPLANATION N with lone pair next to sp2 centre behaves as sp2.IF NitrogenWithLP--SP2THEN set-av-eps 2 to 0 set-hybridisation 2 to 2END-THEN

Example from Hybridisation knowledgebase

Rule based system where rules are encoded using the PATRAN language

(similar to SMILES)

Perception - Binding Properties

O Single atom based Vs C Functional group based

– D - H donor– A - H acceptor– J - Joinable*– H - Hydrophobic– N - None

O - original method C - current method

* According to reaction knowledge base

Synthetic Template

Primary Amine (Donor)

Carboxylic Acid(Acceptor)

Phenol(Acceptor-Donor)

NN

N

OO

OA

A

AD H

A

D

H

A

A

Synthetic Knowledge BaseSynthetic Rules

EXPLANATION Amide Formation 1IF Carboxylic Acid INTER Primary AmineTHEN destroy-atom 3 form-bond - between 1 and 5 change-hybridization 5 to SP2Dihedral 0 0Dihedral 0 180 Bond-length 1.35END-THEN

Joining Rules• Steps of formation• Hybridization change• Bond type• Bond length• Dihedral angles/penalties

OH

O

N

H

H

+

4

51

2

3

O

NH

O OH

NH2

NH2 OH

1. Dock selected fragments to each site 2. Select two sites for connection

NH2 OH

DF Searchtowards acceptor site

O OH

NH2

O

O

OH

PrimaryAmine

CarboxylicAcid O

OH

NH

OH2

ReductiveAmination

O

OH

ONH2 OH

Carbonyl

PrimaryAmine

O OH

N

O

N OH

1

2

O

NH

OH

OH

O OH

NH

O

O

O

O

OH

Overlapping common fragmentO OH

NH2BF Searchtowards donor site

O OH

NH

O

O

1AmideFormation

Acceptor Site

Donor site

De-novo DesignUsing Synthetic Sprout

O OH

N

O

O

1

O

OH

N OH2

2.Reductive Amination ( Carbonyl - Primary Amine )

1.Amide Formation ( Carboxylic Acid -Primary Amine )

New Problems - Hybridisation change

(SP3 SP2)

SP3 SP2

Hybridisation change in Amide Formation 2.( Carboxylic Acid - Secondary Amine )

Secondary Amine Nitrogen becomes SP2

Hybridisation change (SP2 SP3)

SP2

SP3

Carbonyl Carbon becomes SP2

Hybridisation change in Reductive Amination 1.( Carbonyl - Primary Amine )

Selection of Synthetic Reactions

Amide Formation Ether Formation Ullman reaction Amine Alkylation Ester Formation Aldol Wittig Imine C-S-C Formation Reductive Amination

CDK2

Docked:890

Docked:780Docked:935

Docked:358

1534

1079

71

Library :300 fragments/1055 conformations

Run time : 10 h

12

3

4

5

1 Amide Alkylation 2 ( Secondary Amide – Primary Alkyl Halide )2 Wittig Reaction ( Carbonyl = Primary Alkyl Halide )3 Ether Formation 1 ( Alcohol - Alcohol )4 & 5 Amine Alkylation 1 (Primary Amine - Primary Alkyl Halide )

Act Score : -7.80

SynSPROUTCurrent status

Works well for small starting material libraries (low hundreds).

Several libraries now built including amino acid library for peptide generation. Library from MDDR being built.

Potential for suggesting starting points for new combinatorial libraries

Future work

Extend types of chemistry allowed

Develop algorithms which would permit the use of libraries of hundreds of thousands of starting materials (such as ACD).

Parallelisation helps but on its own is not sufficient to cope with the inevitable combinatorial explosion.

Acknowledgements

Co-workers :Krisztina Boda Attilla TingJon Baber

Special thanks to Open Eye Scientific Software for providing access to OMEGA