what makes a compound and allosteric modulator?
TRANSCRIPT
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