PARP1: Structural insights and pharmacological targets for inhibition

Abstract

Poly(ADP-ribose) polymerase 1 (PARP1, also known as ADPRT1) is a multifunctional human ADP-ribosyltransferase. It plays a role in multiple DNA repair pathways, including the base excision repair (BER), non-homologous end joining (NHEJ), homologous recombination (HR), and Okazaki-fragment processing pathways. In response to DNA strand breaks, PARP1 covalently attaches ADP-ribose moieties to arginine, glutamate, aspartate, cysteine, lysine, and serine acceptor sites on both itself and other proteins. This signal recruits DNA repair proteins to the site of DNA damage. PARP1 binding to these sites enhances ADP-ribosylation via allosteric communication between the distant DNA binding and catalytic domains. In this review, we provide a general overview of PARP1 and emphasize novel potential approaches for pharmacological inhibition. Clinical PARP1 inhibitors bind the catalytic pocket, where they directly interfere with ADP-ribosylation. Some inhibitors may further enhance potency by "trapping" PARP1 on DNA via an allosteric mechanism, though this proposed mode of action remains controversial. PARP1 inhibitors are used clinically to treat some cancers, but resistance is common, so novel pharmacological approaches are urgently needed. One approach may be to design novel small molecules that bind at inter-domain interfaces that are essential for PARP1 allostery. To illustrate these points, this review also includes instructive videos showing PARP1 structures and mechanisms.

Keywords: Cancer; Chemotherapy; DNA repair; Drug resistance; PARP1; Review.

Figure 1.. PARP1 domains and subdomains.

The protein schematic (above) was generated with the help of PROSITE [159]. The protein structure (below) shows PARP1 bound to DNA (PDB: 4DQY). The zinc finger 2 (Zn2) and BRCA C-terminus (BRCT) subdomains are not shown, as they are not present in the crystal structure. See Video S1 for an additional review of these PARP1 domains.

Figure 2.. Interdomain interfaces.

Select residues are shown as sticks. (A) PARP1 (PDB: 4DQY) with red boxes encompassing three critical interdomain interfaces. (B) The Zn1-Zn3 interface. K97 (Zn1) is omitted, as it was not resolved. (C) The Zn1-WGR-HD interface. (D) The HD-WGR-Zn3 interface. See ref. [51] for more details, and Video S2 for an additional review of these PARP1 interfaces.

Figure 3.. Critical CAT interfaces (4R6E:A).

Select residues are shown as sticks. (A) and (B) Two views of the interfaces between the HD (light orange) and ART subdomain (brownish orange), marked with red boxes. The PARPi niraparib (yellow sticks) binds the NI site. (C) The interface between the HD αD helix and the ART ASL. (D) The interface between the HD αF helix and the ART αJ helix. Figure adapted with rights and permissions from ref. [74]. See Video S3 for an additional review of these interfaces.

Figure 4. . Catalytic binding site.

(A) BAD (sticks), an NAD+ analog, bound to the catalytic pocket (PDB: 6BHV:A). The catalytic triad (purple) binds to and catabolizes NAD+. Y907 and the catalytic-triad residue Y896 position the benzamide moiety via π-π stacking interactions. NAD+ likely binds the catalytic pocket in a similar orientation. (B) Niraparib (cyan sticks) bound to the catalytic pocket (PDB: 4R6E:A). Niraparib forms contacts with both the HD (light orange) and the ART (reddish orange). Select residues that interact with niraparib are shown as colored sticks.

Figure 5.. Differences in veliparib and UKTT-15 binding to the CAT domain.

(A) Veliparib (cyan, 2RD6:A) does not interact with the HD. (B) UKTT-15, a veliparib analog (green, 6VKO:A), displaces the HD αF helix. See Video S3 for further discussion.

Figure 6.. The four FDA-approved PARPi.

Chemical structures are shown together with the generic names, companies, and years of FDA approval. Nicotinamide, a NAD+ moiety, is shown to illustrate the chemical similarities between the PARPi and the endogenous ligand.

Figure 7.. FTMap-detected hot spots (PDB: 4DQY).

(A) Molecular fragments used to identify hot spots are shown as blue spheres. There are two hot spots at the Zn1-Zn3 interface and two in the catalytic pocket. (B) The pocket volumes of the Zn1-Zn3 interface hot spot (top left) and the Zn1-WGR-HD interface hot spot (bottom center) are shown as transparent yellow surfaces, calculated using POVME2 [160]. See Video S4 for further discussion.