Mannich Base PIP-199 Is a Chemically Unstable Pan-Assay Interference Compound

Abstract

Mannich base PIP-199 is the only reported smallmolecule inhibitor of the Fanconi anemia complementation group M-RecQ-mediated genome instability protein (FANCM-RMI), a protein−protein interaction that governs genome instability in the genetic disorders Fanconi anemia and Bloom's syndrome. PIP-199 and analogues with the same indole-derived Mannich base scaffold have been used as tool compounds in diverse biological studies. We report the first published synthesis of PIP-199 and its analogues, demonstrating that PIP-199 immediately decomposes in common aqueous buffers and some organic solvents. Neither PIP-199 nor its more hydrolytically stable analogues show any observable activity in binding and competitive biophysical assays for FANCM-RMI. We conclude that PIP-199 is not an effective tool compound for biological studies and that apparent cellular activity likely arises from the nonspecific toxicity of breakdown products. More generally, apparent inhibitors that share this Mannich scaffold potentially represent a new family of pan-assay interference compounds (PAINS) that should be thoroughly assessed for aqueous stability prior to use in biological studies.

Novel Skeletal Rearrangements of the Tigliane Diterpenoid Core

“…Compound 3a could be stored as a frozen DMSO or benzene solution, but much to our regret, was unstable under the cellular or enzyme assay conditions, and therefore not a suitable tool compound for bioactivity studies. 21 No specific degradation product could be isolated, but it does not seem unrealistic to assume that rearrangements similar to those observed in the 20-protected derivatives could take place, compounded by the presence of a free 20-hydroxy. In summary, due to unforeseen instability issues associated with the presence of a carbonyl function at C-5, our attempts to shed light on the role of the C-5 hydroxy group in the activity of epoxytiglianes have substantially failed.…”

“…Compound 3a could be stored as a frozen DMSO or benzene solution, but much to our regret, was unstable under the cellular or enzyme assay conditions, and therefore not a suitable tool compound for bioactivity studies. 21 No specific degradation product could be isolated, but it does not seem unrealistic to assume that rearrangements similar to those observed in the 20-protected derivatives could take place, compounded by the presence of a free 20-hydroxy.…”

Telomere-related DNA damage response pathways in cancer therapy: prospective targets

“…AZD0156, an ATM inhibitor, has been used to treat ALT neuroblastomas and overcomes chemotherapy resistance ( Koneru et al, 2021 ). As an inhibitor of the FANCM-BTR interaction ( Wu et al, 2023 ), PIP-199 may be selectively toxic to ALT cancer cells ( Lu et al, 2019 ), rendering it a potential therapeutic target. Tetra-Pt (bpy), a cisplatin derivative that targets telomeric G-quadruplexes, severely inhibits the growth of ALT cell xenograft tumors, indicating that it may be a novel oncotherapeutic agent for targeting ALT cancer cells ( Zheng et al, 2017 ).…”