1. Design of PPI Modulators for Anti-inflammation and Anti-infective Research
May 2017

2. Overview
Protein-protein interactions (PPIs) represent a vast class of therapeutic targets both inside and outside the cell
Protein–protein interactions (PPIs) are involved in most cellular processes and influence biological functions - enzymatic activity, subcellular localization, and/or binding properties
The human interactome has been estimated to cover ~400,000 protein–protein interactions
High-resolution structures showed PPI interfaces are generally flat and large (roughly 1000–2000 A2 per side) and considered difficult to target
Mutational analysis of protein interfaces showed that not all residues at the PPI interface were critical but rather small “hot spots” conferred most of the binding energy (Arkin and Wells, 2004; Clackson and Wells, 1995). Hot spots tended to cluster at the center of the interface, to cover an area comparable to the size of a small molecule, to be hydrophobic, and to show conformational adaptivity
Modulation of PPIs provide a wealth of opportunities for therapeutic intervention in a broad range of disease conditions

3. Types of PPI by Interaction
Small interface and short peptide sequence for interaction
Partner proteins with secondary structure binding to a hydrophobic groove
Complex structure of interaction on both sides, multiple points of interaction
PPI come in many shapes and sizes
Most of the clinical-stage inhibitors target PPI primary interaction where the hot-spot residues are concentrated in small binding pockets (250 – 900 A2) and partner proteins are characterized by short primary sequences at the interface
PPI that contain a single unit of secondary structure, such as an alpha helix, binding to a hydrophobic groove
Globular interfaces, requiring tertiary structure on both sides of the PPI

4. Classification of PPI Modulators

5. Properties of the Known PPI Modulators (Examples)
Primary Epitope
Secondary Epitope
PPI Target/Partner
Compound MW
Oral BA
LFA1/ICAM1
Lifitergrast
615 -
cIAP/SMAC
GDC-0152
499
GDC-0917/CUDC-427
565 +
AT-406/SM-406
562
Birinapant
809
Bromodomain/histone
(+)-JQ-1
457
i-BET762
424
RVX-208
370 nd
Integrase/LEDGF
BI224436
443
PPI Target/Partner
Compound MW
Oral BA
BCL family/BH3
Navitoclax
975 +
ABT-199
868
MDM2/p53
RG7112
728
RG7388
616
MI-888
548
PDK1/PIF-tide
PS210
380 nd
Menin/MML
MIV-6R
418
MIV-2-2
416
P300 CH1 domain/HIF1
 OHM 1
495
nd 
Tertiary Epitope
PPI Target/Partner
Compound MW
Oral BA
IL-2/IL-2Ra
SP4206
663 nd
HPV11 E1/E2
BILH434
608
Historically, PPI inhibitors have been larger and more hydrophobic than typical orally available drugs
PPI oriented libraries with improved properties may enhance hit rate and ensure success in transition from “ligandability” into “druggability”

6. Examples of Anti-inflammatory PPI Modulators
Structure of IL-2 (white surface) bound to SP4206 green sticks; PDB: 1PY2)
SAR1118 (lifitegrast) inhibits binding of LFA1 (CD11a/CD18) to its ligand ICAM. The mechanism either involves binding directly to the ICAM site in the I domain of CD11a (Keating et al., 2006) or allosteric inhibition through binding to the I-like domain in CD18 (Shimaoka et al., 2003)

7. Examples of Anti-infective PPI Modulators
Structure of transactivation domain of E2 protein from HPV11 (white surface) bound to BILH 434 (green sticks; PDB: 1R6N)
Crystal structure of the dimerization interface of HIV integrase (white and cyan surface) bound to compound 16 (green sticks; PDB: 4NYF) with overlaid epitope from LEDGF (magenta; PDB: 2B4J). Compound 16 is a precursor to the clinical compound BI

8. Commercial Libraries Targeted at PPIs*
Supplier
No. of Compounds
Design Method
ChemDiv
125,000**
β-turn-, helix-, 3D-, peptidomimetics, macrocycles, spiro compounds
Otava Chemicals
1,330
decision trees
1,020
similarity search
520
β-turn mimetics
Asinex
7,000
shape analysis
ComInnex
custom
helix mimetics, macrocycles
Life Chemicals
850
machine learning
23,200
2D fingerprint similarity
4,300
rule-of-four
NQuix NA
* - Huggins et al; Chem Biol Jun 18; 22(6): 689–703
Overcoming Chemical, Biological, and Computational Challenges in the Development of Inhibitors Targeting Protein-Protein Interactions
** - Library size as published

9. Structure of ChemDiv PPI Library
Total Library size – 210K compounds

10. Turn Mimetics and Approaches for Targeting

11. Scaffolds of Known b-Turn Mimetics (Examples)

12. Principles of b-Turn Mimetics Design* (Example)
* - Witby, L.R. ; Boger, D.L. Comprehensive Peptidomimetic Libraries Targeting Protein-Protein Interactions. Acc. Chem. Res. 2012, 45, 1698 – 1709

13. ChemDiv’s b-Turn Mimetics (Examples)

14. Helix Mimetics and Approaches for Targeting
α-Helices are common protein secondary structure elements
Interacting residues occupy predominantly i, i+3 or i+4, and i+7 positions

15. Strategy for the Design of Helix Mimetics
mimicry of helix by polycyclic small molecule scaffolds
mimicry of side-chain residues on one face of the α-helix
three points of mimetics interaction with 7-ala helix at i, i+4 (or i+3) and i+7 positions
possible H-bond, hydrophobic, electrostatic or π-π-interaction
include hydrophilic and lipophilic regions in the scaffolds
avoid polycyclic aromatics (as terphenils). High Fsp3 i
i+4
i+7
Energy minimized poly- and 7-alanine
α-helix displaying i, i + 4, and i + 7 positions

16. Examples of Known Helix Mimetics
Most of the known alpha-helix mimetics have sub-optimal physicochemical properties

17. New Scaffolds of α-Helix Mimetics
Over 200 scaffold templates have been developed

18. In-silico Design Validation
lipophilic
ππ-interaction
H-bond MW
373.5
ClogP
2.23
PSA
56.25
H-donor 1
H-acceptor 6
Rot bond 7
Fsp3,%
66.7
Dipole
3.76
Max distance, Å
15.38
ionic bond
H-bonds
ionic bond
Energy minimized three-dimensional interaction with 7-ala (~100,000 iterations)
Indicated directions show the favorable H-bond formation (distance ~ 2-3Å )
Intermolecular forces were taken into account

19. Macrocyclic as PPI Modulators

20. Spiro Compounds as PPI Scaffolds (Examples)

21. Peptidomimetics: PLG-Mimetics Design Example
Evolution
modulator of the dopamine D2 receptor
Core alignment:
Green – starting PLG
violet – plg-01 scaffold

22. Library Statistics Parameter Value Total Library Size 210,000
Number of Scaffolds
2,599
Number of Unique Heterocycles
960
Singletones
2,539
Diversity, compounds
0.8160
Library size, number of scaffolds and number of unique heterocycles are updated constantly due to development of novel approaches to the design and in-house novel chemistries research
ChemDiv’s PPI Library is customizable for customer needs – screening throughput, specific interaction
Compounds can be cherry picked
Library will be formatted to customer specification – plates, racks, solutions, dry powder et cet
Diversity is calculated by Tonimoto algorithm

23. ChemDiv’s PPI Library Physicochemical Properties
Molecular Weight Distribution

24. ChemDiv’s PPI Library Physicochemical Properties
Hydrogen Bond Acceptors
Hydrogen Bond Donors
Rotational Bonds
N+O

25. ChemDiv’s PPI Library Physicochemical Properties
logP
logD
PSA

26. ChemDiv’s PPI Library Largest commercially available PPI library
Designed to cover most epitope, hot-spot interactions
Unique chemistry – strong IP potential
Customizable to customer needs
Size
Cherry-picking
Format options
Delivery options
Expandable from stock and synthesis
Attractively priced

27. Thank you!