Fluorescence Polarization Binding Assay Research Articles

Two conserved arginine residues facilitate C-S bond cleavage and persulfide transfer in Suf family cysteine desulfurases.

Under conditions of oxidative stress or iron starvation, iron-sulfur cluster biogenesis in E. coli is initiated by the cysteine desulfurase, SufS, via the SUF pathway. SufS is a type II cysteine desulfurase that catalyzes the PLP-dependent breakage of an L-cysteine C-S bond to generate L-alanine and a covalent active site persulfide as products. The persulfide is transferred from SufS to SufE and then to the SufBC 2 D complex, which utilizes it in iron-sulfur cluster biogenesis. Several lines of evidence suggest two conserved arginine residues that line the solvent side of the SufS active site could be important for function. To investigate the mechanistic roles of R56 and R359, the residues were substituted using site-directed mutagenesis to obtain R56A/K and R359A/K SufS variants. Steady state kinetics indicated R56 and R359 have moderate defects in the desulfurase half reaction but major defects in the transpersulfurase step. Fluorescence polarization binding assays showed that the loss of activity was not due to a defect in forming the SufS/SufE complex. Structural characterization of R56A SufS shows loss of electron density for the α3-α4 loop at the R56/G57 positions, consistent with a requirement of R56 for proper loop conformation. The structure of R359A SufS exhibits a conformational change in the α3-α4 loop allowing R56 to enter the active site and mimics the residue's position in the PLP-cysteine aldimine structure. Taken together, the kinetic, binding, and structural data support a mechanism where R359 plays a role in linking SufS catalysis with modulation of the α3-α4 loop to promote a close-approach interaction of SufS and SufE conducive to persulfide transfer.

Substrate promiscuity of inositol 1,4,5-trisphosphate kinase driven by structurally-modified ligands and active site plasticity.

D-myo-inositol 1,4,5-trisphosphate (InsP3) is a fundamental second messenger in cellular Ca2+ mobilization. InsP3 3-kinase, a highly specific enzyme binding InsP3 in just one mode, phosphorylates InsP3 specifically at its secondary 3-hydroxyl group to generate a tetrakisphosphate. Using a chemical biology approach with both synthetised and established ligands, combining synthesis, crystallography, computational docking, HPLC and fluorescence polarization binding assays using fluorescently-tagged InsP3, we have surveyed the limits of InsP3 3-kinase ligand specificity and uncovered surprisingly unforeseen biosynthetic capacity. Structurally-modified ligands exploit active site plasticity generating a helix-tilt. These facilitated uncovering of unexpected substrates phosphorylated at a surrogate extended primary hydroxyl at the inositol pseudo 3-position, applicable even to carbohydrate-based substrates. Crystallization experiments designed to allow reactions to proceed in situ facilitated unequivocal characterization of the atypical tetrakisphosphate products. In summary, we define features of InsP3 3-kinase plasticity and substrate tolerance that may be more widely exploitable.

Small Molecule Antagonists of the DNA Repair ERCC1/XPA Protein-Protein Interaction.

The DNA excision repair protein ERCC1 and the DNA damage sensor protein, XPA are highly overexpressed in patient samples of cisplatin-resistant solid tumors including lung, bladder, ovarian, and testicular cancer. The repair of cisplatin-DNA crosslinks is dependent upon nucleotide excision repair (NER) that is modulated by protein-protein binding interactions of ERCC1, the endonuclease, XPF, and XPA. Thus, inhibition of their function is a potential therapeutic strategy for the selective sensitization of tumors to DNA-damaging platinum-based cancer therapy. Here, we report on new small-molecule antagonists of the ERCC1/XPA protein-protein interaction (PPI) discovered using a high-throughput competitive fluorescence polarization binding assay. We discovered a unique structural class of thiopyridine-3-carbonitrile PPI antagonists that block a truncated XPA polypeptide from binding to ERCC1. Preliminary hit-to-lead studies from compound 1 reveal structure-activity relationships (SAR) and identify lead compound 27 o with an EC50 of 4.7 μM. Furthermore, chemical shift perturbation mapping by NMR confirms that 1 binds within the same site as the truncated XPA67-80 peptide. These novel ERCC1 antagonists are useful chemical biology tools for investigating DNA damage repair pathways and provide a good starting point for medicinal chemistry optimization as therapeutics for sensitizing tumors to DNA damaging agents and overcoming resistance to platinum-based chemotherapy.

Examination of in vitro and in vivo antitumor activity of Menin-MLL inhibitor, D0060-319.

e15119 Background: Rearrangements of the mixed-lineage leukemia (MLL) gene result in the production of MLL fusion proteins, which occurs in 5-10% of acute leukemia in adults and > 70% of infant leukemia, respectively. Menin protein, encoded by the MEN1 gene, interacts with MLL fusion proteins to induce leukemia. D0060-319, a Menin-MLL inhibitor, shows a significant antitumor effect in vivo and in vitro. Methods: The fluorescence polarization (FP) binding assay to assess inhibition of D0060-319 to Menin-MLL interaction. The cross reactivity of 44 molecular targets was tested to assess their off-target binding potential. The anti-proliferative ability of D0060-319 was evaluated by CCK-8 in different cell lines. The in vivo anti-tumor effect of D0060-319 was evaluated in a human MV4-11 and MOLM-13 cell mouse xenograft tumor model. Briefly, five million MV4-11 cells or 500 thousand MOLM-13 cells were subcutaneously implanted the right flank of CB-17 SCID mice to establish cell mouse xenograft tumor model. When tumor volume reached 100-120mm3, the animals were grouped and administrated with D0060-319 at the dose of 25, 50, 75, 100 mg/kg or vehicle at twice daily for 21days. Tumor measurements and body weights were performed twice weekly to assess the antitumor efficacy and tolerability of D0060-319. Results: D0060-319 competitively binds Menin to inhibit the interaction with MLL fusion protein with IC50 of 7.46nM, has high antiproliferative activity in MV4-11 and MOLM-13 cell lines containing MLL fusion proteins with IC50 values of 4.0nM and 1.7nM, respectively. However, in Kasumi-1, K562, HL-60 and KG-1 cell lines lacking MLL rearrangement, D0060-319 antiproliferative activity with IC50 > 10 μM, indicating selectivity for leukemia cell lines containing MLL fusion proteins active. In the MV4-11 cell mouse xenograft tumor model, D0060-319 significantly inhibited tumor growth at the dose of 25mg/kg, with a tumor growth inhibition (TGI) rate of 82.97%, and other doses (50, 75 and 100mg/kg) tumor completely regressed. In the MOLM-13 cell mouse xenograft tumor model, a dose-dependent anti-tumor effect was observed after 14 days of administration, with TGIs of 81.08%, 88.47% and 90.26% at the dose of 50, 75 or 100 mg/kg, respectively. In both CDX models, no bodyweight loss was observed, suggesting that D0060-319 was well tolerated. Furthermore, off-target screening assays showed that D0060-319 did not cross-react with any of the 44 molecular targets at 10 μM, indicating that D0060-319 is highly selective, high-affinity for the MLL-binding pocket on Menin. Conclusions: In MLL-rearranged leukemia, D0060-319 showed high antitumor activity and good tolerability both in vitro and in vivo.

Bioinformatic prediction and experimental validation of RiPP recognition elements.

Ribosomally synthesized and post-translationally modified peptides (RiPPs) are a family of natural products for which discovery efforts have rapidly grown over the past decade. There are currently 38 known RiPP classes encoded by prokaryotes. Half of the prokaryotic RiPP classes include a protein domain called the RiPP Recognition Element (RRE) for successful installation of post-translational modifications on a RiPP precursor peptide. In most cases, the RRE domain binds to the N-terminal "leader" region of the precursor peptide, facilitating enzymatic modification of the C-terminal "core" region. The prevalence of the RRE domain renders it a theoretically useful bioinformatic handle for class-independent RiPP discovery; however, first-in-class RiPPs have yet to be isolated and experimentally characterized using an RRE-centric strategy. Moreover, with most known RRE domains engaging their cognate precursor peptide(s) with high specificity and nanomolar affinity, evaluation of the residue-specific interactions that govern RRE:substrate complexation is a necessary first step to leveraging the RRE domain for various bioengineering applications. This chapter details protocols for developing custom bioinformatic models to predict and annotate RRE domains in a class-specific manner. Next, we outline methods for experimental validation of precursor peptide binding using fluorescence polarization binding assays and in vitro enzyme activity assays. We anticipate the methods herein will guide and enhance future critical analyses of the RRE domain, eventually enabling its future use as a customizable tool for molecular biology.

Building and destroying synaptic bridges: How do Hevin/Sparcl1, SPARC, and MDGAs modify trans-synaptic neurexin-neuroligin interactions?

Astrocyte-secreted Hevin induces synapse formation by bridging the trans-synaptic organizers, neuroligins and neurexins. In this issue of Structure, Fan etal. (2021) elucidate the structural basis of Hevin's interaction with these molecules and reveal the competitive interplay between Hevin, SPARC, and MDGAs.

β-Thujaplicin Enhances TRAIL-Induced Apoptosis via the Dual Effects of XIAP Inhibition and Degradation in NCI-H460 Human Lung Cancer Cells.

Background: β-thujaplicin, a natural tropolone derivative, has anticancer effects on various cancer cells via apoptosis. However, the apoptosis regulatory proteins involved in this process have yet to be revealed. Methods: Trypan blue staining, a WST-8 assay, and a caspase-3/7 activity assay were used to investigate whether β-thujaplicin sensitizes cancer cells to TNF-related apoptosis-inducing ligand (TRAIL)-mediated apoptosis. Additionally, western blotting was performed to clarify the effects of β-thujaplicin on X-linked inhibitor of apoptosis protein (XIAP) in NCI-H460 cells and a fluorescence polarization binding assay was used to evaluate the binding-inhibitory activity of β-thujaplicin against XIAP-BIR3. Results: β- and γ-thujaplicins decreased the viability of NCI-H460 cells in a dose-dependent manner; they also sensitized the cells to TRAIL-induced cell growth inhibition and apoptosis. β-thujaplicin significantly potentiated the apoptosis induction effect of TRAIL on NCI-H460 cells, which was accompanied by enhanced caspase-3/7 activity. Interestingly, β-thujaplicin treatment in NCI-H460 cells decreased XIAP levels. Furthermore, β-thujaplicin was able to bind XIAP-BIR3 at the Smac binding site. Conclusions: These findings indicate that β-thujaplicin could enhance TRAIL-induced apoptosis in NCI-H460 cells via XIAP inhibition and degradation. Thus, the tropolone scaffold may be useful for designing novel nonpeptidic small-molecule inhibitors of XIAP and developing new types of anticancer drugs.

Creation of Fluorescent RXR Antagonists Based on CBTF-EE and Application to a Fluorescence Polarization Binding Assay.

Retinoid X receptor (RXR) ligands often bind in modes in which the carboxy group forms a hydrogen bond inside the ligand-binding pocket (LBP). However, our previously reported RXR antagonist, CBTF-EE (4a), binds with its carboxy group directed outside the LBP and its alkoxy side chain located inside the LBP. Here, we examined the binding modes of 4b and 4c bearing a nitrobenzoxadiazole (NBD) or boron-dipyrromethene (BODIPY) fluorophore, respectively, at the end of the alkoxy chain of 4a. Both compounds function as RXR antagonists. 4c, but not 4b, was available for a fluorescence polarization binding assay, indicating that rotation of BODIPY, but not NBD, is restricted in the bound state. The fluorescence findings, supported by docking simulations, suggest the fluorophores are located outside the LBP, so that the binding mode of 4b and 4c is different from that of 4a. The assay results were highly correlated with those of a [3H]9-cis-retinoic acid assay.

Binding affinity and synergy between agonists and peptides of the estrogen receptor‐beta (ERß) needed for arain‐selective SERB Activity

The estrogen receptor (ER) exist predominantly in two isoforms (ERα and ERß). Both are primarily activated by the naturally occurring hormone 17ß-Estradiol (E2) which regulates a variety of physiological processes. One of ER's major role is acting as key neuroprotective modulator for hippocampal plasticity in the brain. The ERß isoform is predominantly found in the brain, which makes it a promising drug target for memory consolidation. Selectivity for ERß over ERα is crucial to the development of drug leads, since ERα–induced cell proliferation results in risk of cancer. We have developed a selective and potent ERß agonist with in vivo efficacy for improving cognitive function within mice. A prior study determined that selectivity for ER is related to the ligand's ability to induce the conformational change necessary for the activation of transcription. Selective estrogen receptor modulators (SERMs) like raloxifene & tamoxifen are used to treat breast cancer by selectively targeting ERα in mammary tissue. This is done through the synergistic binding of coactivator proteins to the ER in the presence of an agonist. Similarly, it is predicted that selective estrogen beta agonists (SERBAs) have the ability to be tissue specific in the presence of specific coactivators. Through the use of computational modeling, a splice variant of SRC1 (steroid receptor coactivator-1), SRC1-4, was identified to be the most favorable brain-relevant peptide for ERß. This study determines the binding affinity of agonist for ERß and ERα in the presence and absence of SRC1-4. In addition we dive into the extent to which binding synergy between agonist and coactivator exist, which could lead to selective activity in the brain. The synergy associated with the conformational change is measured by ΔΔGsynergy based on binding affinity for both agonist and coactivator. The greater the synergy between the agonist and coactivator, the more promising the lead compound will be as a SERBA. Preliminary studies have been done for the binding of SRC1-4 using TR-FRET assays where the concentration of coactivator was varied. Fluorescence polarization (FP) studies were also utilized to determine a Kd. In these studies, FL-SRC1-4 remained constant while ERß-LBD concentrations varied in the presence of 1 μM (saturating) E2. The two methods are compared and contrasted. The same FP assay was completed again in the absence of E2 (no agonoism). This provides a binding affinity for SRC1-4 to the receptor when an agonist is not present. Computational modeling studies were performed to compare ER's affinity for SRC1-4 peptides over other coactivator peptides. 3 unlabeled peptides (SRC1-1, SRC1-3 and PGC1a) were used in a competitive FP binding assay with FL-SRC1-4. The data was consistent with prior data, indicating SRC1-4 has the highest affinity for ERß. The agonistic-synergy effect will be calculated through the measurement of E2 affinity for ERß in the presence and absence of SRC1-4. The comparison of ΔΔG(synergy) for ERß vs. ERα will ultimately provide a measurement of selectivity and synergy that is biologically relevant for SERB activity. Hanson, A. M. et al. A-C estrogens as potent and selective estrogen receptor-beta agonists (SERBAs) to enhance memory consolidation under low-estrogen conditions. J. Med. Chem.61, 4720–4738 (2018).

Novel amide and imidazole compounds as potent hematopoietic prostaglandin D2 synthase inhibitors

In seeking novel and potent small molecule hematopoietic prostaglandin D2 synthase (H-PGDS) inhibitors as potential therapies for PGD2-mediated diseases and conditions, we explored a series comprising multiple aryl/heteroaryl rings attached in a linear arrangement. Each compound incorporates an amide or imidazole “linker” between the pyrimidine or pyridine “core” ring and the “tail” ring system. We synthesized and screened twenty analogs by fluorescence polarization binding assay, thermal shift assay, glutathione S-transferase inhibition assay, and a cell-based assay measuring suppression of LPS-induced PGD2 stimulation. Amide analogs show ten-fold greater shift in the thermal shift assay in the presence of glutathione (GSH) versus the same assay run in the absence of GSH. The imidazole analogs did not produce a significant change in thermal shift between the two assay conditions, suggesting a possible stabilization effect of the amide linker in the synthase-GSH-inhibitor complex. Imidazole analog 23, (KMN-010034) demonstrates superior potency across the in vitro assays and good in vitro metabolic stability in both human and guinea pig liver microsomes.

Molecular mechanism for the interaction between human CPSF30 and hFip1.

Most eukaryotic pre-mRNAs must undergo 3'-end cleavage and polyadenylation prior to their export from the nucleus. A large number of proteins in several complexes participate in this 3'-end processing, including cleavage and polyadenylation specificity factor (CPSF) in mammals. The CPSF30 subunit contains five CCCH zinc fingers (ZFs), with ZF2-ZF3 being required for the recognition of the AAUAAA poly(A) signal. ZF4-ZF5 recruits the hFip1 subunit of CPSF, although the details of this interaction have not been characterized. Here we report the crystal structure of human CPSF30 ZF4-ZF5 in complex with residues 161-200 of hFip1 at 1.9 Å resolution, illuminating the molecular basis for their interaction. Unexpectedly, the structure reveals one hFip1 molecule binding to each ZF4 and ZF5, with a conserved mode of interaction. Our mutagenesis studies confirm that the CPSF30-hFip1 complex has 1:2 stoichiometry in vitro. Mutation of each binding site in CPSF30 still allows one copy of hFip1 to bind, while mutation of both sites abrogates binding. Our fluorescence polarization binding assays show that ZF4 has higher affinity for hFip1, with a Kd of 1.8 nM. We also demonstrate that two copies of the catalytic module of poly(A) polymerase (PAP) are recruited by the CPSF30-hFip1 complex in vitro, and both hFip1 binding sites in CPSF30 can support polyadenylation.

A novel GPER antagonist protects against the formation of estrogen-induced cholesterol gallstones in female mice

Many clinical studies and epidemiological investigations have clearly demonstrated that women are twice as likely to develop cholesterol gallstones as men, and oral contraceptives and other estrogen therapies dramatically increase that risk. Further, animal studies have revealed that estrogen promotes cholesterol gallstone formation through the estrogen receptor (ER) α, but not ERβ, pathway. More importantly, some genetic and pathophysiological studies have found that G protein-coupled estrogen receptor (GPER) 1 is a new gallstone gene, Lith18, on chromosome 5 in mice and produces additional lithogenic actions, working independently of ERα, to markedly increase cholelithogenesis in female mice. Based on computational modeling of GPER, a novel series of GPER-selective antagonists were designed, synthesized, and subsequently assessed for their therapeutic effects via calcium mobilization, cAMP, and ERα and ERβ fluorescence polarization binding assays. From this series of compounds, one new compound, 2-cyclohexyl-4-isopropyl-N-(4-methoxybenzyl)aniline (CIMBA), exhibits superior antagonism and selectivity exclusively for GPER. Furthermore, CIMBA reduces the formation of 17β-estradiol-induced gallstones in a dose-dependent manner in ovariectomized mice fed a lithogenic diet for 8 weeks. At 32 μg/day/kg CIMBA, no gallstones are found, even in ovariectomized ERα (-/-) mice treated with 6 μg/day 17β-estradiol and fed the lithogenic diet for 8 weeks. In conclusion, CIMBA treatment protects against the formation of estrogen-induced cholesterol gallstones by inhibiting the GPER signaling pathway in female mice. CIMBA may thus be a new agent for effectively treating cholesterol gallstone disease in women.

Protein Kinase A isoform dynamics and disease.

A number of disease mutations in the alpha and beta isoforms of Protein Kinase A have recently been identified. We model these mutations and investigate changes in conformational and protein/ligand interaction dynamics. Changes in partner protein and substrate interactions due to mutation is confirmed by fluorescence polarization binding and competition assays. Computational and biochemical approaches reveal a potential common mechanism among the mutations leading to kinase dysfunction.

A Tail of Night Owls: The Mammalian Cry1 C-Terminal Tail Controls Circadian Timing by Regulating its Association to CLOCK:BMAL1

Circadian rhythms are generated by a transcription-translation feedback loop that establishes cell-autonomous biological timing of ∼24-hours. A prevalent human variation in the core clock gene cryptochrome 1, Cry1Δ11, lengthens circadian period to cause Delayed Sleep Phase Disorder (DSPD). CRY1 has a 55 kDa photolyase homology region (PHR) followed by a ∼100 residue tail that is intrinsically disordered; the Δ11 variant lacks a short segment encoded by Exon 11 within its tail. Using fluorescence polarization binding assays and carbon detected NMR spectroscopy, we show here that the disordered tail of CRY1 interacts directly with its PHR, Furthermore we use fluorescence polarization and biolayer interferometry to show that Exon 11 is necessary and sufficient to disrupt the interaction between CRY1 and CLOCK, a subunit of the primary circadian transcription factor. Competition between PER2 and the tail for the CRY1 PHR suggests a regulatory role for the tail in the early morning, when CRY1 binds to CLOCK:BMAL1 on DNA independently of PER2. Discovery of this autoregulatory role for mammalian CRY1 highlights functional conservation with plant and insect cryptochromes, which also utilize PHR-tail interactions to reversibly control their activity.

Mechanistic Studies of the Kinase Domains of Class IV Lanthipeptide Synthetases.

Lanthipeptides, which belong to the superfamily of ribosomally synthesized and posttranslationally modified peptides (RiPPs), are associated with various interesting biological activities. Lanthipeptides can be subdivided into four classes that are defined by the characteristics of the corresponding posttranslational modification enzymes. Class IV lanthipeptide synthetases consist of an N-terminal lyase, a central kinase, and a C-terminal cyclase domain. Here, we present the first in-depth characterization of such a kinase domain from the globisporin maturation enzyme SgbL that originates from Streptomyces globisporus sp. NRRL B-2293. Catalytic residues were identified by alignments with homologues and structural modeling. Their roles were confirmed by employing proteins with Ala substitutions in in vitro modification and fluorescence polarization binding assays. Furthermore, the protein region that is binding the leader peptide was identified by hydrogen-deuterium exchange-mass spectrometry experiments. By fusion of this protein region to the maltose binding protein, a protein was generated that can specifically bind the SgbA leader peptide, albeit with reduced binding affinity compared to that of full length SgbL. Combined, the results of this study provide a firmer grasp of how lanthipeptide biosynthesis is accomplished by class IV synthetases and suggest by homology analysis that biosynthetic mechanisms are similar in class III lanthipeptide processing enzymes.

A NCAPG2-Derived Phosphopeptide Selectively Binds to the Polo-Box Domain of PLK1 and Inhibits Cancer Cell Proliferation

Polo-like kinase 1 (PLK1) serves as a regulator of cell cycle progression and is overexpressed in various human cancer cells. PLK1 contains a conserved polo-box domain (PBD) as well as a kinase domain (KD), like other members of the PLK family. The PBDs of the PLK family interact with phosphopeptides that contain highly conserved Ser-pSer/pThr (S-pS/T) motifs and play significant roles in substrate recognition and subcellular localization. The PBD of PLK1 has been regarded as a promising therapeutic target for cancer therapy. In this study, we investigated whether the phosphopeptide derived from NCAPG2 has a high binding specificity for the PLK1 PDB over those other highly similar PBDs, including PLK2, PLK3, and PLK5. We showed that the PBDs of PLKs have different binding affinities against CDC25c-, PBIP-, and NCAPG2-derived phosphopeptides using the fluorescence polarization binding assay. Unlike CDC25c-phosphopeptide, NCAPG2-phosphopeptide specifically bound to the PLK1 PBD with nanomolar affinity (Kd ~ 48.68 nM), and its specificity was similar to that of the PBIP-derived phosphopeptide. Some of these phosphopeptide-PBD interactions can be explained by calculating the binding free energies using the Molecular Mechanics Poisson–Boltzmann surface area (MM/PBSA). Additionally, NCAPG2-phosphopeptide suppressed the proliferation of cancer cells. The NCAPG2-derived phosphopeptide can be applicable to the discovery of highly selective protein–protein interaction inhibitors targeting the PBD of PLK1.

Family-Wide Characterization of Histone Binding Abilities of PHD Domains of AL Proteins in Arabidopsis thaliana.

Alfin1-like (AL) is a family of proteins homologous to the alfalfa Alfin1 in plant and bears an Alfin domain and a PHD domain at their N- and C-terminus, respectively. There are 7 AL proteins in Arabidopsis, and the PHD domains of most AL proteins are reported to bind to histone H3K4me3. Here we reported gene cloning, protein expression and purification of the PHD domains of all the AL family proteins in Arabidopsis. We then systematically characterized their histone binding abilities by quantitative isothermal titration calorimetry and fluorescence polarization binding assays. Our binding results indicate that all the PHD domains of the AL proteins bind to the histone H3K4me3 peptide with varying methylation state preference and binding affinities. Our study presented here provides the foundation for further studies of the peptide state-specific recognition by PHD domains of AL proteins.

Abstract 1654: Chemical and structure-guided optimization of BAX trigger site activators for cancer therapy

Abstract Cancer cells evade mitochondrial apoptosis most commonly by over-expressing anti-apoptotic BCL-2 proteins that suppress the activation of pro-apoptotic proteins. Pro-apoptotic BAX is a critical BCL-2 family effector protein that upon death stimuli is activated and induces mitochondrial outer membrane permeabilization that leads to cell death. The vast majority of cancer cells express wild-type BAX, therefore, direct BAX activation represents a potential therapeutic strategy in cancer. We previously presented the discovery of BTSA1 as a selective BAX activator with anti-leukemic activity and provided proof-of-concept for BAX as a druggable target in acute myeloid leukemia (AML) (Reyna et al, Cancer Cell, 2017). Here, we investigated chemical optimization of BTSA1 core scaffold to rationally optimize the potency and efficacy of the BAX trigger site activators in AML models. We designed compounds using a structural model of BTSA1 bound to the BAX trigger site that also fits with the previous established pharmacophore model. Synthesized compounds were evaluated for binding potency using a fluorescence polarization binding assay that measures compound competition of the fluorescein-label stapled BIM BH3 peptide from the BAX trigger site. Compounds with improved binding activity were evaluated for their potency in biochemical assays of BAX activation using isolated liposomal and mitochondrial membrane assays. Improved binding to BAX of BTSA1 derivatives correlated with better activation capacity. Moreover, compounds were evaluated for their efficacy in induction of BAX-mediated cell death in AML cell lines including Venetoclax-resistant cells. We have identified compounds with similar or superior cellular efficacy compared to BTSA1. Compounds were evaluated for ADME and in vivo pharmacokinetic profiles and these are compared to efficacy and pharmacodynamics data using in vivo AML xenograft models. Our work highlights our strategy for chemical and structure-guided optimization of BTSA1 demonstrating the potential for improved therapeutic induction of apoptosis in AML by BAX Trigger Site Activators. Citation Format: Denis E. Reyna, Felix Kopp, Evripidis Gavathiotis. Chemical and structure-guided optimization of BAX trigger site activators for cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1654.

Variations in Nuclear Localization Strategies Among Pol X Family Enzymes

The pol X family enzymes DNA polymerase β (pol β), DNA polymerase λ (pol λ), DNA polymerase μ (pol μ), and terminal deoxynucleotidyl transferase (TdT) have critical roles in DNA repair. Nevertheless, information about the structural basis of their nuclear import is limited. Recent studies revealed the unexpected presence of a functional NLS in DNA polymerase β, indicating the importance of active nuclear targeting, even for enzymes likely to leak in and out of the nucleus. Here we further explore the active nuclear transport of the three remaining human pol X enzymes by identifying and structurally characterizing their functional NLS sequences. We used X‐ray crystallography and fluorescence polarization binding assays to characterized the three pol X NLS sequences and their interactions with Importin α that lacks the Importin β binding domain (ImpαΔIBB). All three polymerases use NLS sequences located near their N‐terminus; the pol μ and TdT NLS sequences are monopartite, while pol λ utilizes a bipartite sequence, unique among the pol X family members. We confirmed the results by fluorescence‐based cellular localization studies, which also verified the bipartite nature of the pol λ NLS. This bipartite sequence, was somewhat unexpected, since NLS prediction programs either identified very low probability possibilities or completely failed to identify a potential NLS. Further validation of the identified NLS sequences was conducted by fluorescence polarization peptide‐binding to ImpαΔIBB, where TdT and pol λ demonstrated submicromolar dissociation constants, while pol μ had a low μM Kd value. Nuclear targeting is unique to each pol X family enzyme with variations in sequence context and affinity likely regulating the import and retention of these enzymes in the nuclear compartment.Support or Funding InformationThis work was supported by the Intramural Research Program of the NIH, National Institute of Environmental Health Sciences, project number ZIA ES050111 to REL.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Modulation of the Circadian Period: Searching for Isoform-Selective Cyclophilin Inhibitors

A dynamic, transcription-based oscillator coordinates physiological and behavioral processes with specific times in the 24-hour day, ultimately acting as a cellular clock. The transcription factor complex known as CLOCK:BMAL1 is at the core of this oscillator that generates circadian (about a day) rhythms. BMAL1 possesses a transactivation domain (TAD) that acts as a molecular switch to control the activation or repression state of CLOCK:BMAL1 and modulate circadian period. Recent findings from our lab have demonstrated that cis/trans isomerization about a Trp-Pro imide bond in the TAD is necessary for proper 24-hour circadian timekeeping. Members of the cyclophilin family, which possess peptidyl-prolyl isomerase (PPIase) activity, typically catalyze this intrinsically slow process in vivo. Use of the broad specificity cyclophilin inhibitor Cyclosporin A lengthens circadian rhythms and its persistent use as an immunosuppressant in transplant recipients is associated with deregulation of circadian rhythms. We found that a number of nuclear-localized cyclophilins exhibit robust catalytic activity on the BMAL1 TAD in vitro, yet the absence of isoform-selective inhibitors has made it difficult to tease out their respective contributions to circadian timekeeping. Here we present our initial studies on three nuclear-localized PPIases: PPIA, PPIE, and PPIH. Fluorescence polarization binding assays have allowed us to explore substrate binding in conjunction with 15N/1H ZZ NMR exchange assays that probe catalytic activity. Utilizing in silico ligand docking against high-resolution x-ray structures and NMR-based fragment-based drug discovery (FBDD), we aim to find isoform-selective inhibitors to better understand their role in circadian rhythms.