DNA Sliding Clamps as Therapeutic Targets

Abstract

Chromosomal DNA replication is achieved by an assembly of multi-protein complexes at the replication fork. DNA sliding clamps play an important role in this assembly and are essential for cell viability. Inhibitors of bacterial (β-clamp) and eukaryal DNA clamps, proliferating cell nuclear antigen (PCNA), have been explored for use as antibacterial and anti-cancer drugs, respectively. Inhibitors for bacterial β-clamps include modified peptides, small molecule inhibitors, natural products, and modified non-steroidal anti-inflammatory drugs. Targeting eukaryotic PCNA sliding clamp in its role in replication can be complicated by undesired effects on healthy cells. Some success has been seen in the design of peptide inhibitors, however, other research has focused on targeting PCNA molecules that are modified in diseased states. These inhibitors that are targeted to PCNA involved in DNA repair can sensitize cancer cells to existing anti-cancer therapeutics, and a DNA aptamer has also been shown to inhibit PCNA. In this review, studies in the use of both bacterial and eukaryotic sliding clamps as therapeutic targets are summarized.

Keywords: DNA clamp; DNA sliding clamp; PCNA; proliferating cell nuclear antigen; therapeutic; β-clamp.

Figure 1

DNA sliding clamps showing pseudo-hexameric symmetry and the central hole of the ring structure that accommodates double stranded DNA. (A) The Escherichia coli β-clamp dimer with one monomer colored blue and the other monomer orange. The three similar domains in each monomer are labeled Dom I, II, and III. One of the four IDCL loops is labeled. The peptide AcQADLF with its surface colored green shows the location of one of the binding pockets. The second binding pocket, notated by an arrow and dotted line is empty in this structure [PDBID: 4K30 (Zhao et al., 2013)]. (B) The human PCNA trimer with one monomer in orange, one in green and the third monomer colored blue. The two domains in one of the monomers are labeled Dom I and II. One of the three IDCLs is labeled. The FEN-1 PIP peptides are drawn in purple, with one of the ligands shown in molecular surface representation and the other two ligands as ribbons [PDBID: 1U7B (Bruning and Shamoo, 2004)]. Molecular rendering was made using Chimera (Pettersen et al., 2004).

Figure 2

Details of the peptide binding site on β-clamp. The surface residues in subsite 1 are colored in orange and subsite 2 in cyan. Residue labels in white are for the CBM peptide and labels in black are the β-clamp binding site residues. (A) Surface representation of the peptide binding pocket and stick figure of the AcQADLF peptide bound to E. coli β-clamp [PDBID: 4K3O (Zhao et al., 2013)]. (B) Surface representation of the E. coli β-clamp peptide binding pocket with a modified peptide competitive inhibitor, Ac-Q₁Cha₂D₃L₄(3,4)ClF₅ bound in the peptide pocket [PDBID: 3Q4L (Wolff et al., 2011)]. Molecular rendering was made using Chimera (Pettersen et al., 2004).

Figure 3

Details of the binding site on PCNA showing ligand interactions. (A) Surface representation of FEN-1 peptide bound to human PCNA [PDBID:1U7B (Bruning and Shamoo, 2004)]. Residue labels in white refer to the FEN-1 peptide and labels in black indicate PCNA binding site residues. (B) Surface representation of the PIP binding pocket of mono-ubiquitinated human PCNA with the small molecule inhibitor, T2AA bound [PDBID: 3WGW (Inoue et al., 2014)]. This inhibitor binds 2:1 to PCNA with the second binding site at the interface between the subunits (detail not shown). Molecular rendering was made using Chimera (Pettersen et al., 2004).