Fragment‐based discovery of small molecule inhibitors of the HDGFRP2 PWWP domain

• Published in: FEBS letters 2024-10, Vol.598 (20), p.2533-2543
• Main Authors: Wei, Xiaoli, Li, Shuju, Li, Zihuan, Wang, Lei, Fan, Weiwei, Ruan, Ke, Gao, Jia
• Format: Article
• Language: English
• Subjects: Crystallography, X-Ray; Drug Discovery - methods; fragment‐based screening; hepatoma‐derived growth factor‐related protein 2; histone methylation readers; Humans; Models, Molecular; Protein Domains; PWWP domain; Pyrazoles - chemistry; Pyrazoles - pharmacology; Pyridines - chemistry; Pyridines - pharmacology; Quinoxalines - chemistry; Quinoxalines - pharmacology; Small Molecule Libraries - chemistry; Small Molecule Libraries - pharmacology
• ISSN: 0014-5793; 1873-3468; 1873-3468
• DOI: 10.1002/1873-3468.14981

The PWWP domain of hepatoma‐derived growth factor‐related protein 2 (HDGFRP2) recognizes methylated histones to initiate the recruitment of homologous recombination repair proteins to damaged silent genes. The combined depletion of HDGFRP2 and its paralog PSIP1 effectively impedes the onset and progression of diffuse intrinsic pontine glioma (DIPG). Here, we discovered varenicline and 4‐(4‐bromo‐1H‐pyrazol‐3‐yl) pyridine (BPP) as inhibitors of the HDGFRP2 PWWP domain through a fragment‐based screening method. The complex crystal structures reveal that both Varenicline and BPP engage with the aromatic cage of the HDGFRP2 PWWP domain, albeit via unique binding mechanisms. Notably, BPP represents the first single‐digit micromolar inhibitor of the HDGFRP2 PWWP domain with a high ligand efficiency. As a dual inhibitor targeting both HDGFRP2 and PSIP1 PWWP domains, BPP offers an exceptional foundation for further optimization into a chemical tool to dissect the synergetic function of HDGFRP2 and PSIP1 in DIPG pathogenesis. The PWWP domain of hepatoma‐derived growth factor‐related protein 2 (HDGFRP2) recognizes methylated histones to initiate the recruitment of homologous recombination repair proteins to damaged silent genes. We discovered 4‐(4‐bromo‐1H‐pyrazol‐3‐yl) pyridine (BPP) as an inhibitor of the HDGFRP2 PWWP domain through a fragment‐based screening, BPP offers an exceptional foundation for further optimization into a chemical tool to dissect the function of HDGFRP2.