Breaking the oral barrier（4）

Discovery and Derivatization of the Cyclic Peptide PTG-200
The Discovery of PTG-200

In 2016, Protagonist disclosed a patent (WO2016011208) for an oral polypeptide inhibitor targeting IL-23R, which included several linear and cyclic peptide sequences capable of binding to IL-23R. Notably, the sequences presented in Table 3A of this patent closely resemble the structures previously obtained by MDL through phage display. The listed linear peptide sequences primarily contain the core structure -WQDYW- (as shown in the figure below). Among them, the most potent molecule (SEQ ID NO.4) achieved an IL-23R inhibitory concentration of 4.1 µM, with its structure formed by acetylating the N-terminus of MDL's Peptide 23.15.
It is worth mentioning that MDL and Protagonist once negotiated a collaboration on the IL-23R peptide in 2014, during which MDL shared its research information. In 2015, the two parties signed a confidentiality agreement, but the negotiations were terminated in October of the same year. Subsequent legal documents revealed that MDL filed a lawsuit against Protagonist in the U.S. District Court, alleging patent infringement by PTG-200, involving patents US 8946150 (MDL) and US 9624268 (Protagonist). In 2018, MDL's patent infringement claim was dismissed because Protagonist used these peptides to develop FDA-approved drugs for autoimmune diseases, which was protected under the safe harbor rule.

Returning to the focus of this article, Protagonist retained the - WQDYW core structure proposed by MDL in subsequent molecular modifications, but adopted different designs in the cyclization strategy. They introduced a Cys into the core sequence to form a conserved structure - CXX-WQCYW - (such as - CQTWQCYW -), and derived hundreds of peptides around this structure, increasing activity to nanomolar levels (as shown in the diagram below). In addition, Protagonist has also attempted various cyclization methods, including introducing a thioether bond between two Cys sites, using olefin metathesis reaction (RCM), and implementing amide bond cyclization strategies. However, experimental results indicate that peptides cyclic by disulfide or thioether bonds generally exhibit better activity than peptides cyclic by RCM or amide bonds.

The PK data of PTG-200 (compound C) is disclosed in the patent: after oral administration to rats at a dose of 20 mg/kg, the compound is mainly distributed in the gastrointestinal tissue, with extremely low systemic exposure. Among them, the AUC of small intestinal mucosa is 355 μ g · h/g, and that of colon mucosa is 77 μ g · h/g. However, the AUC in plasma is only 0.3 μ g · h/mL, with a recovery rate of 40% in feces. This compound exhibits good stability in various gastrointestinal fluids and reducing environments: its half-life is greater than 24 hours in simulated intestinal fluid (SIF), simulated gastric fluid (SGF), and human intestinal fluid, and it also has a half-life of over 2 hours in the reducing agent DTT. The SPR experiment results showed that it does not bind to IL-12R 1 alone, but can bind to the surface of IL-23R and IL-12R 1/IL-23R co expressed, with strong affinity and KD values of 2.42 nM and 2.56 nM, respectively.

Derivative of PTG-200

In 2017, Protagonist published its second patent for IL-23R peptide inhibitors (WO2017011820). This patent extends the skeleton of the first patent by 227 derived sequences (SEQ ID NO.1030-1256) and introduces structural units on the cyclic peptide that can prolong the half-life in vivo (as shown in the following figure). Pharmacokinetic studies have shown that after oral administration of 10mg/kg Peptide NO.1185 to rats, the concentration in plasma is much lower than that in small intestine and colon samples, and the recovery rate in feces reaches 20% after 24 hours. The safety evaluation showed that Peptide NO.1185 did not exhibit inhibitory effects on 44 targets including G protein coupled receptors, transporters, and ion channels at 10 µ M.

Subsequently, Protagonist published several derivative patents based on PTG-200 or Peptide NO.1185 structures, which further optimized activity and stability through structural derivations at different residue sites. Details of the related modifications can be found in patents WO2018136646, WO2020014646, WO2021007433, and WO2021146458. In addition, Protagonist has also applied for a patent (WO2018022937) covering a cyclic peptide IL-23R inhibitor containing 34 amino acids, which will not be further discussed in this article.