REPLACE: a route from PPI peptides to drug-like inhibitors

Rather than blocking ATP binding, PPI Pharmaceuticals targets protein-protein interactions that allosterically regulate kinase activity and other non-catalytic functions — interfaces long considered undruggable.

The problem

Cancer is second only to heart disease in total mortality.

The numbers

1.6M+

New U.S. cancer diagnoses / year

Cancer remains second only to heart disease in total mortality.

~500K

U.S. cancer deaths / year

Highlights the persistent need for better-targeted therapies.

~80K

Prostate patients needing better options

Approximate cohort cited for improved treatment need.

$100K+

Cost per course of treatment

FDA approved drugs can cost over $100,000/course of treatment

Estimated Incidence and Mortality of Common Cancers

Estimated incidence and mortality of common cancers
	Prostate / Breast		Lung		Colorectal
	Prostate / Breast Men	Prostate / Breast Women	Lung Men	Lung Women	Colorectal Men	Colorectal Women
Incidence	238,590(28%)	232,340(29%)	118,080(14%)	110,110(14%)	73,680(9%)	69,140(9%)
Mortality	29,720(10%)	39,620(15%)	87,260(28%)	72,220(26%)	26,300(9%)	24,530(9%)

U.S. estimates shown in the company overview for prostate, breast, lung, and colorectal cancers. Percentages are each figure’s share of all cancers for that sex.

World War I soldiers in a front-line trench, the setting in which mustard agents were first used — Many chemotherapy agents have been in use for decades and very toxic drugs.

Molecular model of an early chemotherapy agent — Many chemotherapy agents have been in use for decades and very toxic drugs.

The solution

A new era in cancer treatment

REPLACE converts peptidic protein-protein interaction determinants into selective oncology inhibitors.

Time magazine cover, 28 May 2001, on drugs that target tumors — Time, 28 May 2001

The REPLACE strategy

Structure-guided conversion of binding determinants

Map the PPI interface

Identify binding determinants from SAR, crystal structures, and substrate peptides that mediate allosteric or non-catalytic kinase functions.

Build FLIP / REPLACE libraries

Truncate peptide leads, select fragments by docking and scoring, and synthesize focused libraries that preserve critical contacts while shrinking molecular weight.

Optimize to drug-like inhibitors

Iterate N- and C-terminal caps, peptide minimization, and phosphomimetic design to yield selective, cell-active small molecules for preclinical models.

REPLACE Strategy Overview

REPLACE scheme for the Cdc25c phosphosubstrate, from N-cap identification through N-cap and C-cap optimization and peptide minimization

Projects

Potential Drug targets in the Human Genome

Of roughly 5–10,000 potential drug targets in the human genome, traditional pharma typically focuses on highly druggable pockets — the low-hanging fruit. Higher-risk interfaces, including many protein-protein interactions, were long avoided for lack of methodology. The McInnes laboratory developed REPLACE to make more of these targets accessible to drug development.

SM targets
Highly druggable catalytic pockets — the low-hanging fruit traditional pharma already works on.
Biologics
Antibodies and related modalities covering a smaller set of extracellular targets.
“Undruggable”
The large remainder, including many protein-protein interfaces. This is where REPLACE is aimed.

Many companies pursue cancer drug development; high attrition (~99%) means the field needs multiple approaches. REPLACE uniquely positions PPI Pharmaceuticals against kinase PPI interfaces that ATP-site and biologic strategies do not fully cover.

REPLACE Technology

Letters A–D mark the path from a peptidic ligand, through fragment replacement, to a small-molecule inhibitor.

Discovery of ABBApolin PBD inhibitors

(Alkyl Benzamido Benzoic Acids)

REPLACE scheme from the Cdc25c phosphosubstrate Leu-Leu-Cys-Ser-pThr-Pro-Asn-Gly-Leu through N-cap identification, N-cap optimization and peptide minimization, then C-cap identification and optimization to a phosphomimetic that reaches a cryptic pocket

Discovery of Abbapolins

PLK1 is a sought-after drug target in oncology – ATP competitive kinase inhibitors are problematic
Potent peptidic inhibitors of the Polo-Box Domain have been identified
REPLACE, a validated strategy for targeting PPI’s has been successfully applied to discover non-peptidic PBD inhibitors
Abbapolins, inhibit PLK1 kinase activity, lead to PLK1 degradation and furthermore block PLK1 dimerization.
In vivo proof of concept for REPLACE mediated conversion of peptides into drug-like compounds
Next generation PLK1 Inhibitors – synergize with ATP Inhibitors?

Chapagai et al., J. Med. Chem., 2021, 64, 9916.
Craig et al., Eur. J. Med. Chem., 2022, 227:113926.

In vivo proof of concept for REPLACE

Abbapolin PK and xenograft activity

Pharmacokinetic properties for orally dosed abbapolins 6369 and 6190
PK properties for orally dosed abbapolins
PK Parameters	Compound ID
	6369	6190
Dose (mg/kg)	50	50
Cmax (μmol/L)	0.0429	89.8
t½ (hr)	1.63	4.88
Tmax (hr)	1	1
AUC0–8 (h·μg/L)	0.1414	295.04
Total body clearance (μg/hr)	812.08	0.17
Elimination constant (hr−1)	0.42	0.14
Cellular IC50 (μM)	1.1 ± 0.092	2.13