Structural Approach To Identify a Lead Scaffold That Targets the Translesion Synthesis Polymerase Rev1

Dash, Radha Charan; Ozen, Zuleyha; Rizzo, Alessandro A.; Lim, Socheata; Korzhnev, Dmitry M.; Hadden, M. Kyle

doi:10.1021/acs.jcim.8b00535

Cited by 17 publications

(44 citation statements)

References 42 publications

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“…[15] In addition, we performed extensive per-residue free energy decomposition profiling from molecular dynamics (MD) simulations of each analogue in complexw ith Rev1-CT to determine which amino acid residues are criticalf or high-affinity binding. [15] In addition, we performed extensive per-residue free energy decomposition profiling from molecular dynamics (MD) simulations of each analogue in complexw ith Rev1-CT to determine which amino acid residues are criticalf or high-affinity binding.…”

Section: Resultsmentioning

confidence: 99%

“…Our previous MD studies for the core PAP scaffold demonstratedt hat each compound interacts with Leu1159,A la1160, Leu1171, Gln1174, Trp1175, Ile1179,A sp1186, and Glu1189 either by hydrogen bondingo rh ydrophobic interactions ( Figure 1B). [15] Next, we used Glide XP to automatically generate af ourpoint e-pharmacophore hypothesis for each activec ompound complexed with Rev1-CT ( Figure 3). Analysis of the root-mean-square deviation (RMSD)b etween the averaged structure and the isolated ligandsi nc omplex with Rev1-CT demonstrated that both structures correlated well when superimposed (RMSD < 0.1 ).…”

Section: Resultsmentioning

confidence: 99%

“…[1,2,8,9] Severalo ft hese switching events are mediated by protein-protein interactions (PPIs) between the C-terminal domain of the Y-familyp olymerase Rev1 (Rev1-CT) and the Rev1 interacting regions (RIR) from the Y-familyp olymerases polh,p olk,p oli,a nd polz. [14][15][16] These compounds increase sensitivity to cisplatin and decrease cisplatin-mediated mutagenesis in human cancer cells, highlighting their potential as combination therapies for variousforms of cancer. [14][15][16] These compounds increase sensitivity to cisplatin and decrease cisplatin-mediated mutagenesis in human cancer cells, highlighting their potential as combination therapies for variousforms of cancer.…”

Section: Introductionmentioning

confidence: 99%

“…[15] The RIR motif contains ap eptide sequence consisting of two Phe residues flankedb ya nN -cap residue and four helixforming residues (-nFFhhhh-), which serve as a" recognition sequence" for binding to Rev1-CT. [10,11] This peptide motif orients the two Phe residues in the proper conformationt oi nteract with ah ydrophobic binding pocket and an adjacent surface groove on Rev1-CT ( Figure 1B). [15] The RIR motif contains ap eptide sequence consisting of two Phe residues flankedb ya nN -cap residue and four helixforming residues (-nFFhhhh-), which serve as a" recognition sequence" for binding to Rev1-CT. [10,11] This peptide motif orients the two Phe residues in the proper conformationt oi nteract with ah ydrophobic binding pocket and an adjacent surface groove on Rev1-CT ( Figure 1B).…”

Section: Introductionmentioning

confidence: 99%

“…[15] The RIR motif contains ap eptide sequence consisting of two Phe residues flankedb ya nN -cap residue and four helixforming residues (-nFFhhhh-), which serve as a" recognition sequence" for binding to Rev1-CT. [10,11] This peptide motif orients the two Phe residues in the proper conformationt oi nteract with ah ydrophobic binding pocket and an adjacent surface groove on Rev1-CT ( Figure 1B). [15] In this study,w eu sed the PAPs caffold to generate ap harmacophore that was used in a virtual screening effort to identify severala dditional small-molecule scaffolds that target the Rev1-CT/RIRP PI. [15] Additional studies on the PAPs caffold demonstrated that it disrupts the Rev1-CT/RIR PPI through directb inding interactions at the RIR interfaceo fR ev1-CT,a nd structurebased analogue design identified initial structure-activity rela-Translesions ynthesis (TLS) has emerged as am echanism through which several forms of cancer developa cquired resistance to first-line genotoxic chemotherapies by allowing replication to continue in the presence of damaged DNA.…”

Section: Introductionmentioning

confidence: 99%

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Virtual Pharmacophore Screening Identifies Small‐Molecule Inhibitors of the Rev1‐CT/RIR Protein–Protein Interaction

et al. 2019

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Translesion synthesis (TLS) has emerged as a mechanism through which several forms of cancer develop acquired resistance to first‐line genotoxic chemotherapies by allowing replication to continue in the presence of damaged DNA. Small molecules that inhibit TLS hold promise as a novel class of anticancer agents that can serve to enhance the efficacy of these front‐line therapies. We previously used a structure‐based rational design approach to identify the phenazopyridine scaffold as an inhibitor of TLS that functions by disrupting the protein–protein interaction (PPI) between the C‐terminal domain of the TLS DNA polymerase Rev1 (Rev1‐CT) and the Rev1 interacting regions (RIR) of other TLS DNA polymerases. To continue the identification of small molecules that disrupt the Rev1‐CT/RIR PPI, we generated a pharmacophore model based on the phenazopyridine scaffold and used it in a structure‐based virtual screen. In vitro analysis of promising hits identified several new chemotypes with the ability to disrupt this key TLS PPI. In addition, several of these compounds were found to enhance the efficacy of cisplatin in cultured cells, highlighting their anti‐TLS potential.

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Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

“…[15] The RIR motif contains ap eptide sequence consisting of two Phe residues flankedb ya nN -cap residue and four helixforming residues (-nFFhhhh-), which serve as a" recognition sequence" for binding to Rev1-CT. [10,11] This peptide motif orients the two Phe residues in the proper conformationt oi nteract with ah ydrophobic binding pocket and an adjacent surface groove on Rev1-CT ( Figure 1B). [15] In this study,w eu sed the PAPs caffold to generate ap harmacophore that was used in a virtual screening effort to identify severala dditional small-molecule scaffolds that target the Rev1-CT/RIRP PI. [15] Additional studies on the PAPs caffold demonstrated that it disrupts the Rev1-CT/RIR PPI through directb inding interactions at the RIR interfaceo fR ev1-CT,a nd structurebased analogue design identified initial structure-activity rela-Translesions ynthesis (TLS) has emerged as am echanism through which several forms of cancer developa cquired resistance to first-line genotoxic chemotherapies by allowing replication to continue in the presence of damaged DNA.…”

Section: Introductionmentioning

confidence: 99%

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Virtual Pharmacophore Screening Identifies Small‐Molecule Inhibitors of the Rev1‐CT/RIR Protein–Protein Interaction

et al. 2019

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Structure‐Based Drug Design of Phenazopyridine Derivatives as Inhibitors of Rev1 Interactions in Translesion Synthesis

et al. 2021

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Rev1 is a protein scaffold of the translesion synthesis (TLS) pathway, which employs low‐fidelity DNA polymerases for replication of damaged DNA. The TLS pathway helps cancers tolerate DNA damage induced by genotoxic chemotherapy, and increases mutagenesis in tumors, thus accelerating the onset of chemoresistance. TLS inhibitors have emerged as potential adjuvant drugs to enhance the efficacy of first‐line chemotherapy, with the majority of reported inhibitors targeting protein‐protein interactions (PPIs) of the Rev1 C‐terminal domain (Rev1‐CT). We previously identified phenazopyridine (PAP) as a scaffold to disrupt Rev1‐CT PPIs with Rev1‐interacting regions (RIRs) of TLS polymerases. To explore the structure‐activity relationships for this scaffold, we developed a protocol for co‐crystallization of compounds that target the RIR binding site on Rev1‐CT with a triple Rev1‐CT/Rev7R124A/Rev3‐RBM1 complex, and solved an X‐ray crystal structure of Rev1‐CT bound to the most potent PAP analogue. The structure revealed an unexpected binding pose of the compound and informed changes to the scaffold to improve its affinity for Rev1‐CT. We synthesized eight additional PAP derivatives, with modifications to the scaffold driven by the structure, and evaluated their binding to Rev1‐CT by microscale thermophoresis (MST). Several second‐generation PAP derivatives showed an affinity for Rev1‐CT that was improved by over an order of magnitude, thereby validating the structure‐based assumptions that went into the compound design.

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The Rev1-Polζ translesion synthesis mutasome: Structure, interactions and inhibition

Rizzo

Korzhnev

2019

The Enzymes

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DNA contains information that must be safeguarded, but also accessed for transcription and replication. To perform replication, eukaryotic cells use the B-family DNA polymerase enzymes Polδ and Polε, which are optimized for accuracy, speed, and processivity. The molecular basis of these high-performance characteristics causes these replicative polymerases to fail at sites of DNA damage (lesions), which would lead to genomic instability and cell death. To avoid this, cells possess additional DNA polymerases such as the Y-family of polymerases and the B-family member Polζ that can replicate over sites of DNA damage in a process called translesion synthesis (TLS). While able to replicate over DNA lesions, the TLS polymerases exhibit low-fidelity on undamaged DNA and, consequently, must be prevented from replicating DNA under normal circumstances and recruited only when necessary. The replicative bypass of most types of DNA lesions requires the consecutive action of these specialized TLS polymerases assembled into a dynamic multiprotein complex called the Rev1/Polζ mutasome. To this end, posttranslational modifications and a network of protein-protein interactions mediated by accessory domains/ subunits of the TLS polymerases control the assembly and rearrangements of the Rev1/Polζ mutasome and recruitment of TLS proteins to sites of DNA damage. This chapter focuses on the structures and interactions that control these processes underlying the function of the Rev1/Polζ mutasome, as well as the development of small molecule inhibitors of the Rev1/Polζ dependent TLS holding promise as a potential anticancer therapy.

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Structural Approach To Identify a Lead Scaffold That Targets the Translesion Synthesis Polymerase Rev1

Cited by 17 publications

References 42 publications

Virtual Pharmacophore Screening Identifies Small‐Molecule Inhibitors of the Rev1‐CT/RIR Protein–Protein Interaction

Virtual Pharmacophore Screening Identifies Small‐Molecule Inhibitors of the Rev1‐CT/RIR Protein–Protein Interaction

Structure‐Based Drug Design of Phenazopyridine Derivatives as Inhibitors of Rev1 Interactions in Translesion Synthesis

The Rev1-Polζ translesion synthesis mutasome: Structure, interactions and inhibition

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