Discovery of a potent inhibitor of replication protein a protein-protein interactions using a fragment-linking approach

Replication protein A (RPA), the major eukaryotic single-stranded DNA (ssDNA)-binding protein, is involved in nearly all cellular DNA transactions. The RPA N-terminal domain (RPA70N) is a recruitment site for proteins involved in DNA-damage response and repair. Selective inhibition of these protein-protein interactions has the potential to inhibit the DNA-damage response and to sensitize cancer cells to DNA-damaging agents without affecting other functions of RPA. To discover a potent, selective inhibitor of the RPA70N protein-protein interactions to test this hypothesis, we used NMR spectroscopy to identify fragment hits that bind to two adjacent sites in the basic cleft of RPA70N. High-resolution X-ray crystal structures of RPA70N-ligand complexes revealed how these fragments bind to RPA and guided the design of linked compounds that simultaneously occupy both sites. We have synthesized linked molecules that bind to RPA70N with submicromolar affinity and minimal disruption of RPA's interaction with ssDNA.

Discovery of Protein-Protein Interaction Inhibitors of Replication Protein A

Replication Protein A (RPA) is a ssDNA binding protein that is essential for DNA replication and repair. The initiation of the DNA damage response by RPA is mediated by protein-protein interactions involving the N-terminal domain of the 70 kDa subunit with partner proteins. Inhibition of these interactions increases sensitivity towards DNA damage and replication stress and may therefore be a potential strategy for cancer drug discovery. Towards this end, we have discovered two lead series of compounds, derived from hits obtained from a fragment-based screen, that bind to RPA70N with low micromolar affinity and inhibit the binding of an ATRIP-derived peptide to RPA. These compounds may offer a promising starting point for the discovery of clinically useful RPA inhibitors.

Tyrosinase Inhibitors: A Perspective

Due to its integral role in the biosynthesis of melanin in all kingdoms of life, tyrosinase has become an extremely important target for inhibition in several sectors of research including agricultural and cosmetic research. Inhibitors of tyrosinase have made it to the market in the cosmetics industry, but their use has been limited due to conflicting efficacy and potential toxicity, which has led to several small molecules being removed from the market. Undaunted, researchers have continued to pursue tyrosinase inhibitors with varying degrees of success. These pursuits have built an impressive and rich library of research. This review is intended to provide a perspective of the past twenty years (2003-2023) of research on tyrosinase inhibitors by highlighting exemplar molecules and developments.

Selective inhibitors of bacterial phosphopantothenoylcysteine synthetase

Bacterial phosphopantothenolycysteine synthetase (PPCS) catalyzes the formation of phosphopantothenoylcysteine (PPC) from (R)-phosphopantothenate, l-cysteine, and cytidine-5'-triphosphate (CTP) and has been shown to be essential for growth and survival. The reaction proceeds through a phosphopantothenoyl cytidylate, mixed anhydride intermediate. Both structural and kinetic characterization studies on PPCS have shown differences in the nucleobase binding site between the bacterial and human enzyme. We report for the first time the design and synthesis of mimics of the phosphopantothenoyl cytidylate, which proved to be potent inhibitors of PPCS. These compounds were evaluated in vitro against PPCS from human and several species of bacteria and showed marked selectivity (up to 1000-fold) toward the bacterial enzymes. A phosphodiester intermediate mimic was the most potent of the compounds synthesized and displayed slow-onset, tight-binding kinetics toward E. faecalis PPCS.

Surface reengineering of RPA70N enables cocrystallization with an inhibitor of the replication protein A interaction motif of ATR interacting protein

Replication protein A (RPA) is the primary single-stranded DNA (ssDNA) binding protein in eukaryotes. The N-terminal domain of the RPA70 subunit (RPA70N) interacts via a basic cleft with a wide range of DNA processing proteins, including several that regulate DNA damage response and repair. Small molecule inhibitors that disrupt these protein-protein interactions are therefore of interest as chemical probes of these critical DNA processing pathways and as inhibitors to counter the upregulation of DNA damage response and repair associated with treatment of cancer patients with radiation or DNA-damaging agents. Determination of three-dimensional structures of protein-ligand complexes is an important step for elaboration of small molecule inhibitors. However, although crystal structures of free RPA70N and an RPA70N-peptide fusion construct have been reported, RPA70N-inhibitor complexes have been recalcitrant to crystallization. Analysis of the P61 lattice of RPA70N crystals led us to hypothesize that the ligand-binding surface was occluded. Surface reengineering to alter key crystal lattice contacts led to the design of RPA70N E7R, E100R, and E7R/E100R mutants. These mutants crystallized in a P212121 lattice that clearly had significant solvent channels open to the critical basic cleft. Analysis of X-ray crystal structures, target peptide binding affinities, and (15)N-(1)H heteronuclear single-quantum coherence nuclear magnetic resonance spectra showed that the mutations do not result in perturbations of the RPA70N ligand-binding surface. The success of the design was demonstrated by determining the structure of RPA70N E7R soaked with a ligand discovered in a previously reported molecular fragment screen. A fluorescence anisotropy competition binding assay revealed this compound can inhibit the interaction of RPA70N with the peptide binding motif from the DNA damage response protein ATRIP. The implications of the results are discussed in the context of ongoing efforts to design RPA70N inhibitors.

Diphenylpyrazoles as replication protein a inhibitors

Replication Protein A is the primary eukaryotic ssDNA binding protein that has a central role in initiating the cellular response to DNA damage. RPA recruits multiple proteins to sites of DNA damage via the N-terminal domain of the 70 kDa subunit (RPA70N). Here we describe the optimization of a diphenylpyrazole carboxylic acid series of inhibitors of these RPA-protein interactions. We evaluated substituents on the aromatic rings as well as the type and geometry of the linkers used to combine fragments, ultimately leading to submicromolar inhibitors of RPA70N protein-protein interactions.

Identification and Optimization of Anthranilic Acid Based Inhibitors of Replication Protein A

Replication protein A (RPA) is an essential single-stranded DNA (ssDNA)-binding protein that initiates the DNA damage response pathway through protein-protein interactions (PPIs) mediated by its 70N domain. The identification and use of chemical probes that can specifically disrupt these interactions is important for validating RPA as a cancer target. A high-throughput screen (HTS) to identify new chemical entities was conducted, and 90 hit compounds were identified. From these initial hits, an anthranilic acid based series was optimized by using a structure-guided iterative medicinal chemistry approach to yield a cell-penetrant compound that binds to RPA70N with an affinity of 812 nm. This compound, 2-(3- (N-(3,4-dichlorophenyl)sulfamoyl)-4-methylbenzamido)benzoic acid (20 c), is capable of inhibiting PPIs mediated by this domain.

Characterization and kinetics of phosphopantothenoylcysteine synthetase from Enterococcus faecalis

The enzyme phosphopantothenoylcysteine synthetase (PPCS) catalyzes the nucleotide-dependent formation of phosphopantothenoylcysteine from (R)-phosphopantothenate and L-cysteine in the biosynthetic pathway leading to the formation of the essential biomolecule, coenzyme A. The Enterococcus faecalis gene coaB encodes a novel monofunctional PPCS which has been cloned into pET23a and expressed in Escherichia coli BL21 AI. The heterologous expression system yielded 30 mg of purified PPCS per liter of cell culture. The purified enzyme chromatographed as a homodimer of 28 kDa subunits on Superdex HR 200 gel filtration resin. The monofunctional protein displayed a nucleotide specificity for cytidine 5'-triphosphate (CTP) analogous to that seen for bifunctional PPCS expressed by most prokaryotes. Kinetic characterization, utilizing initial velocity and product inhibition studies, found the mechanism of PPCS to be Bi Uni Uni Bi Ping-Pong, with the nucleotide CTP binding first and CMP released last. Michaelis constants were 156, 17, and 86 microM for CTP, (R)-phosphopantothenate, and L-cysteine, respectively, and the k(cat) was 2.9 s(-1). [carboxyl-(18)O]Phosphopantothenate was prepared by hydrolysis of methyl pantothenate with Na(18)OH, followed by enzymatic phosphorylation with E. faecalis pantothenate kinase (PanK). The fate of the carboxylate oxygen of labeled phosphopantothenate, during the course of the PPCS-catalyzed reaction with CTP and L-cysteine, was monitored by (31)P NMR spectroscopy. The results show that the carboxylate oxygen of the phosphopantothenate is recovered with the CMP formed during the reaction, indicative of the formation of a phosphopantothenoyl cytidylate catalytic intermediate, which is consistent with the kinetic mechanism.

Recent advancements in the discovery of protein-protein interaction inhibitors of replication protein A

Due to the relatively high rate of DNA damage that can occur during cell cycle progression, the DNA damage response (DDR) pathway is critical for the survival of eukaryotic cells. Replication protein A (RPA) is an essential cell cycle checkpoint protein that mediates the initiation of the DDR by binding to single-stranded DNA (ssDNA) and recruiting response partners via protein-protein interactions (PPIs). This important role of RPA in initiating the DDR and cell survival has led to interest within the scientific community to investigate RPA as a potential cancer drug discovery target. To this end, RPA inhibitors have been explored via a variety of methods. This review summarizes the structure and function of RPA and highlights recent efforts to discover inhibitors of RPA-protein interactions.

Concise Modular Synthesis of Thalassotalic Acids A-C

The novel N-acyldehydrotyrosine analogues known as thalassotalic acids A-C were isolated from a marine bacterium by Deering et al. in 2016. These molecules were shown to have tyrosinase inhibition activity and thus are an attractive set of molecules for further study and optimization. To this end, a concise and modular synthesis has been devised and executed to produce thalassotalic acids A-C and two unnatural analogues. This synthesis has confirmed the identity and inhibitory data of thalassotalic acids A-C, more potent synthetic analogues (IC₅₀ = 65 μM), and provides a route for further structure-activity relationship studies to optimize these molecules.

Current Progress in the Chemoenzymatic Synthesis of Natural Products

Natural products, with their array of structural complexity, diversity, and biological activity, have inspired generations of chemists and driven the advancement of techniques in their total syntheses. The field of natural product synthesis continuously evolves through the development of methodologies to improve stereoselectivity, yield, scalability, substrate scope, late-stage functionalization, and/or enable novel reactions. One of the more interesting and unique techniques to emerge in the last thirty years is the use of chemoenzymatic reactions in the synthesis of natural products. This review highlights some of the recent examples and progress in the chemoenzymatic synthesis of natural products from 2019–2022.

Abstract 2473: Fragment-based discovery of inhibitors of replication protein A protein-protein interactions

Replication Protein A (RPA) is a heterotrimeric protein that binds to and protects ssDNA and plays an integral role in initiating the cellular response to DNA damage. This response is mediated via protein-protein interactions between a basic cleft on the RPA70N subunit and a number of protein partners, including ATRIP, Rad9, Mre11, and p53. RNAi against RPA has shown an expected toxicity against cancer cell lines, possibly due to abrogation of the ssDNA binding function of RPA. Specific disruption of the protein-protein interactions between the RPA07N subunit and its binding partners has the potential to produce a more selective cytotoxic response in cancer cells. To more accurately dissect the therapeutic relevance of disrupting only the protein-protein interaction functions of RPA, we sought to discover potent small molecule probes that bind to the basic cleft of RPA70N.

Inhibition of protein-protein interactions is considered a difficult task. An NMR-based fragment screen has identified more than 130 fragment molecules that bind to the RPA70N protein-protein interaction cleft with affinities that range from 500 μM to 2 mM and corresponding ligand efficiencies from 0.18 to 0.30. Selected fragments, representing several distinct chemotypes, have been optimized for binding to the protein. Using X-ray crystallography, the binding modes of these fragments have been defined. Fragments were found to bind primarily to two main sites within the basic cleft of RPA70N. Additional structure-guided optimizations have been carried out and ternary co-crystal structures have been generated to guide fragment linking strategies. Together, these activities have led to the creation of multiple lead series of inhibitors of the RPA:ATRIP interaction, with binding affinities improved by several fold over the initial fragments. The SAR and biological activities of the fragments and lead compounds will be discussed.

Citation Format: Alex G. Waterson, James D. Patrone, J. Phillip Kennedy, Nicholas F. Pelz, Andreas O. Frank, Bhavatarini Vandgamudi, Michael D. Feldkamp, Elaine M. Souza-Fagundes, Olivia W. Rossanese, Walter J. Chazin, Stephen W. Fesik. Fragment-based discovery of inhibitors of replication protein A protein-protein interactions. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2473. doi:10.1158/1538-7445.AM2013-2473

Abstract 3695: Discovery of probes to evaluate the disruption of the protein-protein interactions mediated by RPA70N

Replication Protein A (RPA) is a major regulator of checkpoint activation and enhanced DNA repair in cancer cells. In response to genotoxic stress, the RPA complex binds to and protects ssDNA while serving as a scaffold to recruit critical checkpoint and DNA-damage response proteins through the N-terminal region of the 70 kDa subunit of RPA (RPA70N). RNAi against RPA has shown an expected toxicity against cancer cell lines. However, specific disruption of the RPA protein-protein interactions mediated by the RPA70N domain has the potential to produce selective killing of cancer cells without of cytotoxicity due to interference with its ssDNA-binding function. In order to accurately examine the therapeutic relevance of the inhibition of RPA function, we have sought to discover potent probe molecules that disrupt the interactions between RPA70N and its binding partners.

Here we describe the discovery of molecules to probe RPA function using complementary fragment-based and traditional high-throughput screening techniques. SAR studies and structure-based design concepts used to optimize the lead series of interest will be discussed along with the biochemical and cellular results obtained with the compounds.

Citation Format: Alex G. Waterson, Phillip Kennedy, James D. Patrone, Nicholas F. Pelz, Andreas O. Frank, Bhavatarini Vangamudi, DeMarco V. Camper, Elaine M. Souza-Fagundes, Michael D. Feldkamp, Edward T. Olejniczak, Olivia W. Rossanese, Walter J. Chazin, Stephen W. Fesik. Discovery of probes to evaluate the disruption of the protein-protein interactions mediated by RPA70N. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 3695. doi:10.1158/1538-7445.AM2015-3695