Targeting protein-protein interactions in the DNA damage response pathways for cancer chemotherapy

Abstract

Cellular DNA damage response (DDR) is an extensive signaling network that orchestrates DNA damage recognition, repair and avoidance, cell cycle progression and cell death. DDR alteration is a hallmark of cancer, with the deficiency in one DDR capability often compensated by a dependency on alternative pathways endowing cancer cells with survival and growth advantage. Targeting these DDR pathways has provided multiple opportunities for the development of cancer therapies. Traditional drug discovery has mainly focused on catalytic inhibitors that block enzyme active sites, which limits the number of potential drug targets within the DDR pathways. This review article describes the emerging approach to the development of cancer therapeutics targeting essential protein-protein interactions (PPIs) in the DDR network. The overall strategy for the structure-based design of small molecule PPI inhibitors is discussed, followed by an overview of the major DNA damage sensing, DNA repair, and DNA damage tolerance pathways with a specific focus on PPI targets for anti-cancer drug design. The existing small molecule inhibitors of DDR PPIs are summarized that selectively kill cancer cells and/or sensitize cancers to front-line genotoxic therapies, and a range of new PPI targets are proposed that may lead to the development of novel chemotherapeutics.

Fig. 1. SBDD flowchart for PPI inhibitors.

Fig. 2. PIKK family DDR kinases, ATR, ATM, and DNA-PK, and their representative substrates in a DDR signaling cascade.

Fig. 3. Pharmaceutical disruption of the Mdm2–p53 PPI. (A) Schematic of p53 stabilization by a small molecule inhibitor. (B) Nutlin-3 and RG7112 structures. (C) Nutlin-3 (cyan) (PDB: 4J3E) and RG7112 (yellow) (PDB: 4IPF) in complex with the p53 binding site of Mdm2.

Fig. 4. HR and NHEJ, the two major NHEJ pathways. For NHEJ, DSB ends are recognized by Ku, which binds and activates DNA-PKcs. DNA nucleases and X-family polymerases Pol λ or μ remodel DSB ends. The DSBs are ligated by the ligation complex containing Lig IV, XLF, PAXX, and XRCC4. For HR, ends are resected by the MRN/BRCA1/CtIP complex and then various nucleases, resulting in long stretches of RPA-coated ssDNA. RPA is replaced by Rad51 in a BRCA2 dependent manner, and Rad51 facilitates strand invasion of a homologous DNA sequence, which is used as a template for DNA synthesis. After synthesis, the resulting HR intermediates are resolved and the ends are ligated.

Fig. 5. Inhibitors of DSB repair by (A) NHEJ and (B) HR.

Fig. 6. Schematic of NER, BER, and MMR. (A) gg-NER begins with recognition of a helix-distorting lesion by XPC/HR23B/CETN2, which recruits TFIIH to unwind DNA around the lesion. RPA binds the undamaged ssDNA strand, while XPA/XPF/ERCC1 recognizes the damage and, along with XPG associated with TFIIH, cuts DNA fragment around the lesion. A polymerase fills the gap and XRCC1-Lig3 ligates the newly synthesized DNA. (B) BER. One of 11 DNA glycosylases recognizes DNA damage and excises modified base, creating abasic site. In the short-patch BER, APE1 nicks DNA next to abasic site, and Polβ fills a single nucleotide gap and removes abasic sugar by its dRP lyase activity. In the long-parch BER. Polβ or Polδ/ε synthetizes longer DNA stretch, creating a flap removed by FEN1. The final nick is sealed by XRCC1-Lig3 or Lig1. (C) MMR. A mismatch or a deletion-insertion loop is recognized by MutSα or MutSβ. MutL binds MutS and recruits Exo1, which excises the mismatch. The gap is filled by Polδ and nick ligated by Lig1.

Fig. 7. Inhibitors of NER PPIs that target XPA-ERCC1 (top) and XPF-ERCC1 (bottom) complex formation.

Fig. 8. Two step Rev1/Polζ-dependent TLS. After PCNA monoubiquitination by Rad6/Rad18, an inserter Y-family TLS polymerase replaces a replicative polymerase, Polδ or Polε, and inserts nucleotides across the DNA lesion. The extender TLS polymerase Polζ continues replication past the site of DNA damage.

Fig. 9. Inhibitors of TLS PPIs between (A) Y-family TLS polymerases and ub-PCNA, (B) Rev7 and Rev3-RBM, (C) Rev1-CT and RIR motifs, and (D) Rev1-CT and Rev7.

Kerry Silva McPherson

Dmitry M. Korzhnev