What makes a compound and allosteric modulator?

What makes a compound an allosteric modulator?Physicochemical profiling of allosteric regulators of proteins

Gerard JP van Westen Anna GaultonJohn P Overington

Background…

• Allosteric modulators enable small molecule modulation of targets that are infeasible to modulate orthosterically (e.g. Class B/C GPCRs).

• Allosteric modulators often considered as back-up strategy.

• Allosteric modulators to disturb PPIs?...

• Allosteric modulators are interesting drugs..

Background…

Göblyös, Anikó, and Ad P. IJzerman. "Allosteric modulation of adenosine receptors." Purinergic signalling 5.1 (2009): 51-61.

Background…•How do we define allostery?

Background…

• Idea: what can we learn from ChEMBL with regard to allosteric modulators?▫We should be able to retrieve literature on allosteric

modulation by searching for keywords in abstracts and titles of publications included in ChEMBL

Text mining approach• Searching for a number of terms (title and/or abstract):▫Uncompetitive▫un competitive‐▫Noncompetitive▫non competitive‐▫Allostery▫Alostery▫Activators▫Positive modulators▫Negative modulators▫Regulatory site▫NNRTI

▫Positive modulator▫Negative modulator▫Secondary binding site▫Secondary pocket▫Nonsubstrate▫Allosteric▫Allosterism▫Alosteric▫Alosterism▫ Indirectly inhibit▫ Indirectly activate

Retrieved records+/- 6,000 documents in the ‘Journal Articles’ table

± 900 documents were in ChEMBL

17,197 bioactivity points (primary assay)

414 targets (primary assay)

16,762 unique compounds

10 L1 Target classes

Bioactivity

TargetsChemistry

17 L2 Target classes

After initial round of curation+/- 6,000 documents in the ‘Journal Articles’ table

991 documents were from ChEMBL

18,273 bioactivity points (primary assay)

417 targets (primary assay)

17,829 unique compounds

10 L1 Target classes

Bioactivity

TargetsChemistry

17 L2 Target classes

After initial round of curation

Bioactivity

Retrieved records

Summarized..

Targets…

Targets• ChEMBL target class hierarchy

all protein binding compounds

Enzyme Membrane Receptor

HIV Reverse Transcriptase

7TM1 7TM2 7TM3

Adenosinereceptor

Metabotropic glutamate receptor

L0

L1

L2

L8Glucagon receptor

Target Distribution (L1)

Target Distribution (L2)

Targets Conclusions•Distribution of target classes differs between allosteric

and non-allosteric sets ▫Some targets are apparently much easier to hit via

allosteric modulation than via non-allosteric modulation (class C GPCRs).

• Allosteric modulation cannot be considered a cure-for-difficult targets

Chemistry…

Chemistry• Allosteric modulators have a slightly lower molecular

weight on average

Chemistry• Allosteric modulators have a slightly higher AlogP on

average

Chemistry•Hydrogen bonding (1)

Chemistry•Hydrogen bonding (2)

Chemistry• Additional properties

• So allosteric modulators:▫Smaller, more lipophilic / less hydrogen bonding potential

Chemistry

Chemistry• Allosteric modulators tend to

adhere slightly better to Lipinski’s rule of 5

▫no violations allowed : Allosteric: 75 % Non-Allosteric: 70 %

Chemistry

All compounds

Chemistry Conclusions•Difficult to draw firm conclusions on ‘allosteric

modulators’, properties target dependent▫Allosteric modulation and non-allosteric modulation of

targets can be considered different targets

• Still, some trends with regard to physicochemical properties can be spotted

Bioactivity…

Bioactivity• Allosteric modulators are very similar to non-allosteric

modulators with respect to bioactivity

• Their absolute affinity tends to be slightly lower on average ▫The binding efficiency index is similar due to the lower

molecular weight (log affinity/ MW (kDa))▫The surface efficiency index tends to be higher due to the

lower polar surface area (log affinity / PSA-2)

• Allosteric modulators occupy similar ‘high affinity’ hotspots as do orthosteric modulators

C. Abad-Zapatero. ”Ligand efficiency indexes for efficient drug discovery" Expert Opin. Drug. Dicov. 2 (2007): 469-489

Bioactivity

Shown is the median value of all compounds. Error is given by the median average deviation of the median (MAD)C. Abad-Zapatero. ”Ligand efficiency indexes for efficient drug discovery" Expert Opin. Drug. Dicov. 2 (2007): 469-489

Bioactivity•What is the cause for the lowered absolute affinity?▫… properties of binding pockets themselves▫… metabolites can make allosteric modulators and these

tend to be present at very high local concentrations▫…

• In any case we observe that the absolute affinity is lower… ▫hence assay read-outs should be adopted to properly reflect

this or possible (unoptimized) compounds can be missed

Bioactivity (Case study)

Kinases

Bioactivity (Case study) • Kinases form a slightly different story▫Allosteric modulators can also be ligand-mimetic, hence

peptides can be allosteric modulators in this case (opposite from class B GPCRs) Allosterics (peptides) Allosterics (small molecules)

▫Orthosteric ligands (usually atp-competitive) actually form a more converse class in this case

• Please remember this for later on..

So if Allosteric =/= Non-allosteric……then can we model this classification?

Allosteric =/= Orthosteric

Red is the model, Blue is random

Allosteric Models *•What properties are important? (L0)▫Property importance varies with target class

Target Level Class Allosteric

CompoundsOrthosteric Compounds ROC Sensitivity Specificity PPV NPV MCC

0 n/a 17,197 509,257 0.90 0.70 0.93 0.24 0.99 0.38

Allosteric property 1

Allosteric property 2

Allosteric property 3

Non-Allosteric Property 1

Non-Allosteric Property 2

Non-Allosteric Property 3

AlogP Aromatic Bonds Frac

Molecular Solubility *

Molecular Volume

Molecular Surface Area Molecular SASA

Note that molecular solubility is a log concentration value, hence larger values indicate compounds are less solubleNote that these models have been retrained and improved after manual curation (results pending)..

So, what about individual target classes…?

Allosteric Models•Models follow ChEMBL target class hierarchy

all protein binding compounds

Enzyme Membrane Receptor

HIV Reverse Transcriptase

7TM1 7TM2 7TM3

Adenosinereceptor

Metabotropic glutamate receptor

L0

L1

L2

L8Glucagon receptor

Allosteric Models•What properties are important? (L1):

Target Level Class Allosteric

CompoundsNon-allosteric Compounds ROC (OOB) Sensitivity Specificity PPV NPV MCC

1 Enzyme 8,445 212,885 0.91 0.75 0.93 0.29 0.99 0.43

Allosteric property 1

Allosteric property 2

Allosteric property 3

Non-Allosteric Property 1

Non-Allosteric Property 2

Non-Allosteric Property 3

AlogP Average Bondlength

Molecular Solubility *

Rotatable Bonds Frac

Polar Surface Area Hydrogen Frac

Note that molecular solubility is a log concentration value, hence larger values indicate compounds are less solubleNote that these models have been retrained and improved after manual curation (results pending)..

Allosteric Models• Sometimes the story is different (L1):▫Non-competitive with respect to regulator proteins,

competitive with regard to ions

Target Level Class Allosteric

CompoundsOrthosteric Compounds ROC (OOB) Sensitivity Specificity PPV NPV MCC

1 Ion Channel 1,974 23,871 0.93 0.77 0.93 0.50 0.98 0.58

Allosteric property 1

Allosteric property 2

Allosteric property 3

Non-Allosteric Property 1

Non-Allosteric Property 2

Non-Allosteric Property 3

Average Bondlength Hydrogen Frac Rotatable

Bonds FracAromatic Bonds

Frac N Count Frac AlogP

Note that molecular solubility is a log concentration value, hence larger values indicate compounds are less solubleNote that these models have been retrained and improved after manual curation (results pending)..

Allosteric Models (case study 1)

HIV Reverse Transcriptase

Allosteric Models (case study 1)

Class Allosteric Compounds

Orthosteric Compounds ROC (OOB) Sensitivity Specificity PPV NPV MCC

HIV RT 1,933 1,204 1.00 0.90 0.94 0.95 0.87 0.83

Allosteric Models (case study 1)

PropertyImportance (Accuracy)

Importance (Gini)

Correlation 'Allosteric’ Structure

O Count Frac 0.05 133.97 -0.47

Molecular PolarSurfaceArea 0.05 85.44 -0.37

CM#FCFP_6#885225145 0.04 70.80 0.37

AromaticBonds Frac 0.04 52.19 0.36

H_Acceptors Frac 0.03 54.14 -0.43

RotatableBonds_Frac 0.03 35.21 -0.30

RingBonds_Frac 0.02 29.05 0.38

Molecular Fractional PolarSurfaceArea 0.02 34.23 -0.40

ALogP 0.02 42.45 0.27

Allosteric Models (case study 2)

Class Allosteric Compounds

Orthosteric Compounds ROC (OOB) Sensitivity Specificity PPV NPV MCC

Protein Kinase B 248 755 1.00 0.91 0.99 0.97 0.97 0.23

Allosteric Models (case study 2)

PropertyImportance (Accuracy)

Importance (Gini)

Correlation 'Allosteric’ Structure

Molecular SASA 0.05 48.18 0.75Num Bonds 0.03 38.03 0.75

Molecular SurfaceArea 0.02 23.86 0.74

Molecular Volume 0.01 14.07 0.74

CM#FCFP_6#-874404860 0.01 6.20 0.78

Num RingAssemblies 0.01 7.75 0.03

AromaticBonds Frac 0.01 4.67 -0.60

CM#FCFP_6#266887156 0.01 16.73 0.28

Allosteric Models (case study 3)

Class Allosteric Compounds

Orthosteric Compounds ROC (OOB) Sensitivity Specificity PPV NPV MCC

Adenosine Receptors 697 9177 0.99 0.92 0.98 0.80 0.99 0.84

Allosteric Models (case study 2)

PropertyImportance (Accuracy)

Importance (Gini)

Correlation 'Allosteric’ Structure

Heteroatom Frac 0.01 104.93 -0.34

CM#FCFP_6#-1617833330 0.01 79.21 0.59

Average BondLength 0.01 28.96 0.21

Molecular Weight 0.01 10.24 -0.08

Molecular PolarSurfaceArea 0.01 12.05 -0.15

Molecular Volume 0.01 7.44 -0.08

Molecular SurfaceArea 0.01 9.08 -0.11

Molecular SASA 0.01 6.94 -0.09

Current work• Finalizing all models and sets ▫To be distributed with paper

• Scaffold and monomer profiling (ongoing)▫Allosterically biased versus non-allosterically biased

• Retrieving missed primary literature on allosteric modulators

• Application of models to: ▫Compound libraries (allosteric-like libraries)▫HTS hit lists

What makes a compound an allosteric modulator?Physicochemical profiling of allosteric regulators of proteins

Gerard JP van Westen Anna GaultonJohn P Overington