In Silico Discovery of a Novel Potential Allosteric PI3Kα Inhibitor Incorporating 3-(2-Chloro-5-fluorophenyl)isoindolin-1-one to Target Head and Neck Squamous Cell Carcinoma

TL;DR

This study discovers a new potential drug, H-18, that could target a specific protein involved in head and neck cancer with fewer side effects than existing treatments.

Contribution

The paper introduces H-18, a novel allosteric PI3Kα inhibitor with high selectivity and improved safety for treating HNSCC.

Findings

H-18 showed a higher docking score with PI3Kα than RLY-2608, indicating stronger binding.

H-18 selectively interacts with key amino acids at the allosteric site of PI3Kα.

H-18 demonstrated good safety and pharmacokinetic properties suitable for drug development.

Abstract

PIK3CA mutations lead to abnormal activation of phosphatidylinositol 3-kinase alpha (PI3Kα), promoting the development of head and neck squamous cell carcinoma (HNSCC). Compared with traditional ATP-competitive PI3Kα inhibitors, such as Alpelisib, the allosteric inhibitor RLY-2608 has strong selectivity for mutant PI3Kα and does not cause the side effect of hyperglycemia (the main reason for the limited clinical application of ATP-competitive PI3Kα inhibitors). The development of novel allosteric PI3Kα inhibitors can significantly benefit patients with PIK3CA mutations. We used the scaffold hopping method to modify the structure of RLY-2608 to discover novel PI3Kα inhibitors with diverse structures and high selectivity. The results showed that the docking score between H-18 (35.9705 kcal/mol) and PI3Kα was higher than that between RLY-2608 (21.4709 kcal/mol) and PI3Kα, and that H-18 selectively targeted PI3Kα by interacting with key amino acids at the allosteric site. H-18 exhibited good safety characteristics and excellent pharmacokinetic properties. This study advances the development of PI3Kα allosteric inhibitors and provides new ideas for overcoming HNSCC.

Phosphatidylinositol 3-kinase alpha (PI3Kα) is frequently mutated in head and neck squamous cell carcinoma (HNSCC), leading to the constitutive activation of the PI3K/Akt pathway, which promotes tumor cell proliferation, survival, and metastasis. PI3Kα allosteric inhibitors demonstrate therapeutic potential as both monotherapy and combination therapy, particularly in patients with PIK3CA mutations or resistance to immunotherapy, through the precise targeting of mutant PI3Kα. Compared to ATP-competitive PI3Kα inhibitors such as Alpelisib, the allosteric inhibitor RLY-2608 exhibits enhanced selectivity for mutant PI3Kα while minimizing the inhibition of wild-type PI3Kα, thereby reducing side effects such as hyperglycemia. To date, no allosteric PI3Kα inhibitors have been approved for clinical use. To develop novel PI3Kα inhibitors with improved safety and efficacy, we employed a scaffold hopping approach to structurally modify RLY-2608 and constructed a compound library. Based on the structural information of the PI3Kα allosteric site, we conducted the systematic virtual screening of 11,550 molecules from databases to identify lead compounds. Through integrated approaches, including molecular docking studies, target validation, druggability evaluation, molecular dynamics simulations, and metabolic pathway and metabolite analyses, we successfully identified a promising novel allosteric PI3Kα inhibitor, H-18 (3-(2-chloro-5-fluorophenyl)isoindolin-1-one). H-18 has not been previously reported as a PI3Kα inhibitor, and provides an excellent foundation for subsequent lead optimization, offering a significant starting point for the development of more potent PI3Kα allosteric inhibitors.

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