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What makes a compound and allosteric modulator?
1. What makes a compound an
allosteric modulator?
Physicochemical profiling of allosteric
regulators of proteins
Gerard JP van Westen
Anna Gaulton
John P Overington
2. 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..
3. Background…
Göblyös, Anikó, and Ad P. IJzerman. "Allosteric modulation of adenosine receptors." Purinergic signalling 5.1 (2009): 51-61.
5. 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
6. 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
7. 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
8. 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
16. 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
26. 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
28. 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
29. 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
30. 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
32. 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..
33. So if Allosteric =/= Non-allosteric…
…then can we model this
classification?
37. Allosteric Models
• Models follow ChEMBL target class hierarchy
all protein binding compounds
Enzyme Membrane Receptor
HIV
Reverse
Transcriptase
7TM1 7TM2 7TM3
Adenosine
receptor
Metabotropic
glutamate receptor
L0
L1
L2
L8Glucagon
receptor
38. Allosteric Models
• What properties are important? (L1):
Target
Level
Class
Allosteric
Compounds
Non-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 soluble
Note that these models have been retrained and improved after manual curation (results pending)..
39. Allosteric Models
• Sometimes the story is different (L1):
▫ Non-competitive with respect to regulator proteins,
competitive with regard to ions
Target
Level
Class
Allosteric
Compounds
Orthosteric
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 Frac
Aromatic Bonds
Frac
N Count Frac AlogP
Note that molecular solubility is a log concentration value, hence larger values indicate compounds are less soluble
Note that these models have been retrained and improved after manual curation (results pending)..
47. 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
48. What makes a compound an
allosteric modulator?
Physicochemical profiling of allosteric
regulators of proteins
Gerard JP van Westen
Anna Gaulton
John P Overington