Competitive Fluorescence Polarization Assay Research Articles

A fluorescence polarization-based competition assay for measuring interactions between unlabeled ubiquitin chains and UCH37•RPN13

Ubiquitin chains regulate distinct signaling events through cooperative interactions with effector proteins and deubiquitinases. Measuring the strength of these interactions is often challenging; either large amounts of material are required or one of the binding partners must be labeled for detection. We sought to develop a label-free method for measuring binding of ubiquitin chains to the proteasome-associated deubiquitinase UCH37 and its binding partner RPN13. The method we describe here is based on a fluorescence polarization competition (FPcomp) assay in which fluorescent monoubiquitin is competed off the UCH37•RPN13 complex by the addition of unlabeled ubiquitin chains. We show that the UCH37•RPN13 complex displays higher affinity toward chains with more than two ubiquitin subunits. Removing the ubiquitin-binding PRU domain of RPN13 does not change affinities. These results suggest UCH37•RPN13 acts to selectively recruit proteins modified with long chains (>2 subunits) to the proteasome for degradation. We also demonstrate that the FPcomp assay is suitable for high-throughput screening, which is important considering both UCH37 and RPN13 are potential targets for cancer therapy.

Designed Metal‐Mediated Protein Dimerization

The specificity and stability of protein/protein interactions is of vital interest to the pharmaceutical and biotechnological industries. Incorporation of metal‐binding sites at target protein interfaces may be one approach to improve the specificity and affinity of naturally occurring and designed protein‐protein interactions. The main goal for this research was to generate a metal‐mediated protein interface and study the effects of interfacial modification on protein‐protein affinity. Our approach recently resulted in the creation of a high‐affinity, zinc‐mediated protein homodimer.Using a metal‐templated approach we engineered novel metal binding sites to generate a high affinity interaction using the β1 domain of Streptoccocal Protein G (Gβ1). Metal coordination enables focused surface redesign, allowing for the preservation of naturally occurring or designed interfaces. Incorporation of metal binding sites generates concerted interactions allowing for enhanced affinity and specificity for protein interactions. Our protein complex is driven by metal coordination through histidine side‐chains, allowing for a metal‐dependent interaction.Complex formation and assembly was evaluating using size exclusion chromatography and x‐ray crystallography. To accurately measure the molecular weight of the protein variants we have used size‐exclusion chromatography with multi‐angle light scattering (SEC‐MALS). This analytical technique first separates proteins based on size, and the molecular weight is determined from scattered laser light. The Gβ1 monomer and metal‐mediated dimers had molecular weight of 6.2 and 12.2–13.1 kDa, respectively. Crystal structure of the dimeric proteins proved the target design was achieved and that zinc was bound at the designed interface.We have also engineered a library of rationally designed proteins that contain mutations in proximity to the metal binding sites. The goal is to exploit and explore key thermodynamic parameters that are essential for protein complex formation. We measured the binding affinity of the metal‐mediated protein‐protein interactions using a fluorescence polarization competition assay. The measured affinities were stronger than 100 nM, which is both physiologically relevant and provides additional support for the design of high‐affinity metal‐mediated protein‐protein interactions.Support or Funding InformationThis work was supported by the Department of Defense and by the California Metabolic Research Foundation.Brian is a recipient of an Arne N. Wick Pre‐doctoral Research Fellowship from the California Metabolic Research Foundation.This abstract is from the Experimental Biology 2018 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

Direct Detection of Products from S-Adenosylmethionine-Dependent Enzymes Using a Competitive Fluorescence Polarization Assay.

S-Adenosylmethionine (AdoMet)-dependent methyltransferases (MTases) are an essential superfamily of enzymes that catalyze the transfer of a methyl group to several biomolecules. Alterations in the methylation of cellular components crucially impact vital biological processes, making MTases attractive drug targets for treating infectious diseases and diseases caused by overactive human-encoded MTases. Several methods have been developed for monitoring the activity of MTases, but most MTase assays have inherent limitations or are not amenable for high-throughput screening. We describe a universal, competitive fluorescence polarization (FP) assay that directly measures the production of S-adenosylhomocysteine (AdoHcy) from MTases. Our developed assay monitors the generation of AdoHcy by displacing a fluorescently labeled AdoHcy molecule complexed to a catalytically inert 5'-methylthioadenosine nucleosidase (MTAN-D198N) variant performed in a mix-and-read format. Producing the fluorescently labeled molecule involves a one-pot synthesis by combining AdoHcy with an amine-reactive rhodamine derivative, which possesses a Kd value of 11.3 ± 0.7 nM to MTAN-D198N. The developed competitive FP assay expresses a limit of detection for AdoHcy of 6 nM and exhibits a 34-fold preference to AdoHcy in comparison to AdoMet. We demonstrate the utility of the developed assay by performing a pilot screen with the NIH Clinical Collection as well as determining the kinetic parameters of l-histidine methylation for EgtD from Mycobacterium tuberculosis. Additionally, the developed assay is applicable to other AdoMet-dependent and ATP-dependent enzymes by detecting various adenosine-containing molecules including 5'-methylthioadenosine, AMP, and ADP.

Glycodendrimers as Chondroitin Sulfate Mimetics: Synthesis and Binding to Growth Factor Midkine.

Chondroitin sulfate (CS) is a member of the glycosaminoglycan (GAG) family, a class of polysaccharides implicated in relevant biological functions. The structural complexity of these carbohydrates demands the development of simple glycomimetics as useful tools to study the biological processes in which GAGs are involved. In this work we described the synthesis of the disaccharide unit of the CS-E (GlcA-GalNAc(4,6-di-OSO3 )), in a multivalent presentation. Using a fluorescence polarization competition assay we have demonstrated that a hexavalent dendrimer of this disaccharide interact with midkine, in the low micromolar range. This result highlights the potency of these disaccharide-displaying multivalent systems as interesting mimetics of longer and synthetically more complex GAG oligosaccharides.

JAK2 JH2 Fluorescence Polarization Assay and Crystal Structures for Complexes with Three Small Molecules.

A competitive fluorescence polarization (FP) assay is reported for determining binding affinities of probe molecules with the pseudokinase JAK2 JH2 allosteric site. The syntheses of the fluorescent 5 and 6 used in the assay are reported as well as Kd results for 10 compounds, including JNJ7706621, NVP-BSK805, and filgotinib (GLPG0634). X-ray crystal structures of JAK2 JH2 in complex with NVP-BSK805, filgotinib, and diaminopyrimidine 8 elucidate the binding poses.

The fungal natural product azaphilone-9 binds to HuR and inhibits HuR-RNA interaction in vitro.

The RNA-binding protein Hu antigen R (HuR) binds to AU-rich elements (ARE) in the 3’-untranslated region (UTR) of target mRNAs. The HuR-ARE interactions stabilize many oncogenic mRNAs that play important roles in tumorigenesis. Thus, small molecules that interfere with the HuR-ARE interaction could potentially inhibit cancer cell growth and progression. Using a fluorescence polarization (FP) competition assay, we identified the compound azaphilone-9 (AZA-9) derived from the fungal natural product asperbenzaldehyde, binds to HuR and inhibits HuR-ARE interaction (IC50 ~1.2 μM). Results from surface plasmon resonance (SPR) verified the direct binding of AZA-9 to HuR. NMR methods mapped the RNA-binding interface of HuR and identified the involvement of critical RNA-binding residues in binding of AZA-9. Computational docking was then used to propose a likely binding site for AZA-9 in the RNA-binding cleft of HuR. Our results show that AZA-9 blocks key RNA-binding residues of HuR and disrupts HuR-RNA interactions in vitro. This knowledge is needed in developing more potent AZA-9 derivatives that could lead to new cancer therapy.

Galactose-amidine derivatives as selective antagonists of galectin-9

The family of galectin proteins involved in adhesion, growth regulation, immunity, and inflammatory events are important targets for development of small molecule antagonists. Here, N-sulfonyl amidine galactopyranoside derivatives obtained via a multicomponent reaction between galactose alkyne derivatives, sulfonyl azides, and amines were evaluated as antagonists of galectin-1, -2, -3, -4N (N-terminal domain), -4C (C-terminal domain), -8N, -9N, and -9C in a competitive fluorescence polarization assay. Highly selective compounds against galectin-9N with up to 30-fold improved affinity compared to the reference methyl β-d-galactopyranoside were identified. Molecular dynamics simulation suggested that the selectivity and affinity for galectin-9N originate from the N-sulfonyl amidine moieties forming tridentate hydrogen bonds to two asparagine side chains and one phenyl stacking edge-to-face to an arginine side chain. These selective galectin-9N antagonists are of significant value as chemical tools for studying galectin-9 biology and chemistry as well as possible starting structures for the discovery of galectin-9-targeting drugs influencing, e.g., immune regulation.

Ribosomal binding and antibacterial activity of ethylene glycol-bridged apidaecin Api137 and oncocin Onc112 conjugates.

Recent surveillance data on antimicrobial resistance predict the beginning of the post-antibiotic era with pan-resistant bacteria even overcoming polymyxin as the last available treatment option. Thus, new substances using novel modes of antimicrobial action are urgently needed to reduce this health threat. Antimicrobial peptides are part of the innate immune system of most vertebrates and invertebrates and accepted as valid substances for antibiotic drug development efforts. Especially, short proline-rich antimicrobial peptides (PrAMP) of insect origin have been optimized for activity against Gram-negative strains. They inhibit protein expression in bacteria by blocking the 70S ribosome exit tunnel (oncocin-type) or the assembly of the 50S subunit (apidaecin-type binding). Thus, apidaecin analog Api137 and oncocin analog Onc112 supposedly bind to different nearby or possibly partially overlapping binding sites. Here, we synthesized Api137/Onc112-conjugates bridged by ethylene glycol spacers of different length to probe synergistic activities and binding modes. Indeed, the antimicrobial activities against Escherichia coli and Pseudomonas aeruginosa improved for some constructs, although the conjugates did not bind better to the 70S ribosome of E. coli than Api137 and Onc112 using 5(6)-carboxyfluorescein-labelled Api137 and Onc112 in a competitive fluorescence polarization assay. In conclusion, Api137/Onc112-conjugates showed increased antimicrobial activities against P. aeruginosa and PrAMP-susceptible and -resistant E. coli most likely because of improved membrane interactions, whereas the interaction to the 70S ribosome was most likely not improved relying still on the independent apidaecin- and oncocin-type binding modes. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.

Structure-based design of 3-carboxy-substituted 1,2,3,4-tetrahydroquinolines as inhibitors of myeloid cell leukemia-1 (Mcl-1).

Mcl-1 has recently emerged as an attractive target to expand the armamentarium in the war on cancer. Using structure-based design, 3-carboxy-substituted 1,2,3,4-tetrahydroquinolines were developed as a new chemotype to inhibit the Mcl-1 oncoprotein. The most potent compound inhibited Mcl-1 with a Ki of 120 nM, as determined by a fluorescence polarization competition assay. Direct binding was confirmed by 2D (1)H-(15)N HSQC NMR spectroscopy with (15)N-Mcl-1, which indicated that interactions with R263 and T266, and occupation of the p2 pocket are likely responsible for the potent binding affinity. The short and facile synthetic chemistry to access target molecules is expected to mediate lead optimization.

High-Throughput Screening for Ligands of the HEPN Domain of Sacsin.

Sacsin is a large protein implicated in the neurodevelopmental and neurodegenerative disease autosomal recessive spastic ataxia of Charlevoix-Saguenay (ARSACS), which features the loss of Purkinje neurons in the cerebellum. Although the domain architecture of sacsin suggests that it is a neuronal chaperone assisting in protein quality control, the precise function of sacsin remains elusive. Using fluorescence polarization (FP) assays, we confirmed that the HEPN domain of sacsin binds to nucleotides with low micromolar affinities. FP competition assays with a variety of nucleotides and nucleotide analogs revealed that the binding is primarily mediated by the phosphate groups of nucleotides. A high-throughput screen subsequently identified novel small molecule ligands of HEPN, providing new chemical probes for cell culture studies and drug development. Together, the results are consistent with the HEPN domain contributing to the functional activity of sacsin by binding to nucleotides or other multiply charged anionic compounds in neurons.

Synthesis and evaluation of geometric analogs of 1α,25-dihydroxyvitamin D2 as potential therapeutics

An improved convergent strategy was developed for the synthesis of the previously obtained side-chain extended and rigidified analogs of 1α,25-dihydroxyvitamin D2, PRI-1906 and PRI-1907. New (24Z) geometric isomers of the analogs, PRI-1916 and PRI-1917, were also obtained and identified. These side-chain isomers were separable by flash chromatography, as C-25 alcohols, from the synthetic precursors of PRI-1906 and PRI-1907, respectively. The structures of new analogs were determined by advanced techniques of 1H and 13C NMR, including COSY, HSQC and HMBC sequences. Binding affinities of the geometric analogs PRI-1906 and PRI-1916 and their respective C-26, C-27 homologs PRI-1907 and PRI-1917 for the full-length human vitamin D receptor were determined by a fluorescence polarization competition assay. The binding affinity of (24Z) methyl analog PRI-1906 was much higher than that of (24E) analog PRI-1906, while the affinity of (24Z) ethyl analog PRI-1917 was lower than that of the respective PRI-1907. Investigation of the metabolism of these compounds by human CYP24A1 revealed they are much more resistant to CYP24A1 than 1α,25-dihydroxyvitamin D2, indicating they could have longer-term biological effects on target tissues.

Two homoisoflavonoids act as peroxisome proliferator-activated receptor agonists

Polygonatum odoratum (Mill.) Druce is a well-known traditional Chinese medicine exerting multi-biological functions like removing dryness, promoting secretion of fluid, and quenching thirst, but its molecular mechanism is not fully understood. Peroxisome proliferator-activated receptor (PPAR) γ is a member of nuclear receptor superfamily, and its agonists are prescribed as anti-hyperglycemic drugs. In this study, homoisoflavonoids isolated from P. odoratum were evaluated for their activity against PPARγ by the fluorescence polarization competitive binding assay and transient transfection reporter assays. Primarily, the fluorescence polarization competitive binding assay results showed that 5,7-dihydroxy-6, 8-dimethyl-3-(4′-hydroxybenzyl)chroman-4-one (IC50 = 7 μM) and 5,7-dihydroxy-6-methyl-8-methoxy-3-(4′-hydroxybenzyl)chroman-4-one (IC50 = 12 μM) bound to PPARγ ligand-binding domain with fair binding affinity. Moreover, both homoisoflavonoids transactivated PPARγ-dependent promoters including PPRE (PPARγ response element), SHP, and ABCA1 gene promoters in dose-dependent manner. Further molecular modeling studies demonstrated that they interacted with PPARγ ligand-binding pocket in a similar manner as indeglitazar, a novel PPARγ agonist. All these results highly indicated that 5,7-dihydroxy-6, 8-dimethyl-3-(4′-hydroxybenzyl)chroman-4-one and 5,7-dihydroxy-6-methyl-8-methoxy-3-(4′-hydroxybenzyl)chroman-4-one are the active constituents of P. odoratum and act as PPARγ agonists.

Covalent small molecule inhibitors of Ca(2+)-bound S100B.

Elevated levels of the tumor marker S100B are observed in malignant melanoma, and this EF-hand-containing protein was shown to directly bind wild-type (wt) p53 in a Ca2+-dependent manner, dissociate the p53 tetramer, and inhibit its tumor suppression functions. Likewise, inhibiting S100B with small interfering RNA (siRNAS100B) is sufficient to restore wild-type p53 levels and its downstream gene products and induce the arrest of cell growth and UV-dependent apoptosis in malignant melanoma. Therefore, it is a goal to develop S100B inhibitors (SBiXs) that inhibit the S100B–p53 complex and restore active p53 in this deadly cancer. Using a structure–activity relationship by nuclear magnetic resonance approach (SAR by NMR), three persistent binding pockets are found on S100B, termed sites 1–3. While inhibitors that simultaneously bind sites 2 and 3 are in place, no molecules that simultaneously bind all three persistent sites are available. For this purpose, Cys84 was used in this study as a potential means to bridge sites 1 and 2 because it is located in a small crevice between these two deeper pockets on the protein. Using a fluorescence polarization competition assay, several Cys84-modified S100B complexes were identified and examined further. For five such SBiX–S100B complexes, crystallographic structures confirmed their covalent binding to Cys84 near site 2 and thus present straightforward chemical biology strategies for bridging sites 1 and 3. Importantly, one such compound, SC1982, showed an S100B-dependent death response in assays with WM115 malignant melanoma cells, so it will be particularly useful for the design of SBiX molecules with improved affinity and specificity.

Bisphenol A exerts estrogenic effects by modulating CDK1/2 and p38 MAP kinase activity.

Bisphenol A (BPA) is considered to be an endocrine disruptor, but the mechanisms by which it disrupts endocrine functions are poorly understood. Here, we have shown that BPA binds both estrogen receptor (ER)-α and ER-beta (ER-β) using a fluorescence polarization competitive binding assay. In addition, we found that BPA induced cell proliferation by modulating cell cycle-related genes in the MCF-7 human mammary cancer cell line. Moreover, using a BG1 luciferase ER transactivation assay, we found that BPA has estrogenic activity. Modulating the MAPK pathway by using an ERK inhibitor (PD98059) or a JNK inhibitor (SP600125) had no effect on the ability of BPA to induce estrogenic activity. However, the antiestrogen, ICI 182,780, and the p38 inhibitor, PD 169316 successfully blocked BPA-induced estrogenic activity. Our findings suggest that BPA mimics ER-dependent estrogenic activity by targeting proteins that regulate the cell cycle and p38 MAPK.

Synthesis and evaluation of iminocoumaryl and coumaryl derivatized glycosides as galectin antagonists

A collection of iminocoumarylmethyl glycoside derivatives have been prepared by copper-catalyzed multi-component reaction of carbohydrate propargyl derivatives, sulfonyl azides, and salicylaldehyde or o-hydroxy acetophenone. The method is simple, versatile to all three components, and exceptionally high yielding. The carbohydrate N-sulfonyl iminocoumarine hybrid molecules were evaluated for binding galectin-1, -2, -3, -4N, -4C, -7, -8N, -9N, and 9C using a competitive fluorescence polarization assay. Selective compounds were identified against galectin-3, 7, 8N, and 9N with up to 40-fold affinity enhancements relative to methyl α-d-galactopyranoside due to the coumarylmethyl moieties.

Fluorescence Polarization for the Evaluation of Small‐Molecule Inhibitors of PCAF BRD/Tat‐AcK50 Association

A fluorescence polarization competitive assay was developed to efficiently screen and evaluate inhibitors of PCAF bromodomain/Tat-AcK50 protein-peptide interaction. A series of pyridine 1-oxide derivatives were synthesized and evaluated. Some of the novel compounds, 2-(3-aminopropylamino) pyridine 1-oxide derivatives, could be effective inhibitors of PCAF bromodomain/Tat-AcK50 association. Specifically, 2-(3-aminopropylamino)-5-(hydroxymethyl)pyridine 1-oxide hydrochloride (15) and the 5-((3-aminopropylamino)methyl) derivative (20) were found to be effective ligands for the PCAF BRD pocket. First preliminary cellular studies indicate that these small-molecule inhibitors have lower cytotoxicities and are potential leads for the anti-HIV/AIDS therapeutic strategy by targeting host-cell protein PCAF BRD to block HIV replication.

Abstract 2455: BAM38 is a potent and selective pro-apoptotic BAX activator molecule that restores apoptosis in cancer cells.

Abstract Targeting key apoptosis regulators to overcome the apoptotic resistance of cancer cells is a highly attractive therapeutic strategy. The BCL-2 protein family includes both pro- and anti-apoptotic proteins that form a complex interaction network and regulate the critical balance between cellular life and death. BAX is a pro-apoptotic BCL-2 member that, when activated, undergoes a structural transformation, which converts BAX from an inactive conformation into a lethal one, creating mitochondrial pores. Although inactivating mutations in BAX have been identified with a very small frequency in tumors, cancer cells commonly ensure survival by overexpression of anti-apoptotic BCL-2 members, a feature that contributes to tumorigenesis and chemoresistance. Therefore, the vast majority of cancer cells contain functional but suppressed BAX. Our discovery of the BAX trigger site and BAX activator molecule 7 (BAM7), which directly triggers BAX activation and selective BAX-mediated cell death, provides a new opportunity for rational drug design to target BAX and promote cell death in tumors. Using an in silico structural similarity approach and a competitive fluorescence polarization assay, we identified a novel small molecule activator of BAX, BAM38, that has ten-fold improved binding potency compared to BAM7 and retains selectivity over anti-apoptotic BCL-2 proteins. NMR and molecular docking analysis demonstrates that BAM38 engages the BAX trigger site using increased complementary interactions. Biochemical assays indicate that BAM38 has correspondingly improved potency in triggering BAX conformational activation and BAX-mediated membrane permeabilization. In a panel of acute myeloid leukemia (AML) cells that overexpress distinct combinations of anti-apoptotic BCL-2 family proteins, BAM38 overcomes apoptotic blockade through induction of BAX-mediated apoptosis. We observe dose-dependent AML cell death that coincides with BAX translocation, cytochrome c release and caspase 3/7 activation. BAM38 synergizes with the BCL-2/BCL-XL inhibitor ABT-737 in resistant AML cells, highlighting the therapeutic potential of combined direct pharmacologic activation of BAX with targeted inhibition of anti-apoptotic BCL-2 and BCL-XL. Thus, our data suggest a novel small molecule approach to restoring cancer cell death by directly targeting BAX, and provides a lead molecule for further development into a next generation cancer therapeutic. Citation Format: Denis E. Reyna, Loren D. Walensky, Evripidis Gavathiotis. BAM38 is a potent and selective pro-apoptotic BAX activator molecule that restores apoptosis in cancer cells. [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 2455. doi:10.1158/1538-7445.AM2013-2455 Note: This abstract was not presented at the AACR Annual Meeting 2013 because the presenter was unable to attend.

Abstract 2471: Chemical optimization of direct and selective molecular activators of pro-apoptotic BAX for cancer therapy.

Abstract BAX is a pro-apoptotic BCL-2 family member that lies dormant in the cytosol until triggered by cellular stress to translocate to the mitochondria and form toxic oligomeric pores. The majority of cancer cells retain wild-type BAX and instead neutralize the death pathway by overexpressing anti-apoptotic BCL-2 family proteins. Thus, direct activation of BAX represents a pharmacologic opportunity to lower the apoptotic threshold in the setting of chemoresistance. Using a Stabilized Alpha-Helix of BCL-2 domain (SAHB) modeled after the BIM BH3 helix, we previously identified the “trigger site” for direct BAX activation at the confluence of alpha-helices 1 and 6. In silico screening for small molecule modulators of BAX led to our identification of BAX activator molecule 7 (BAM7), which selectively engages the trigger site and promotes BAX-mediated cell death (Gavathiotis et al, Nat Chem Biol, 2012). Here, we applied BAM7 to a panel of acute lymphoblastic leukemia cells and observe dose-responsive killing in the micromolar range. To improve the potency of anti-ALL activity, we undertook a systematic medicinal chemistry-based iteration of BAM7’s molecular features. A series of analogs demonstrate improved BAX binding activity based on a FITC-BIM SAHB/BAX competitive fluorescence polarization assay. The most potent binders were advanced to testing in a cellular model of anti-apoptotic protein-dependent chemoresistance. Whereas select BAM7 derivatives exhibited a potency similar to or greater than the BCL-2/BCL-XL inhibitor ABT-737 in a BCL-XL-dependent ALL cell line, the compounds significantly outperformed ABT-737 in the isogenic MCL-1-dependent ALL cells. Preliminary studies revealed favorable pharmacokinetic profiles for lead BAM7 derivatives, including oral bioavailability and central nervous system penetration. These early encouraging structure-activity relationship and pharmacokinetic data on chemically-optimized BAM7 analogs suggest that direct and selective activation of BAX may be a viable strategy for therapeutic induction of apoptosis in the context of cancer chemoresistance. Citation Format: Joseph A. Bellairs, Denis Reyna, Divakaramenon Sethumadhavan, Madhavi Neelagiri, Alex Broadhead, Christopher Baccei, Brian Koss, Joseph T. Opferman, Evripidis Gavathiotis, Loren D. Walensky. Chemical optimization of direct and selective molecular activators of pro-apoptotic BAX for cancer therapy. [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 2471. doi:10.1158/1538-7445.AM2013-2471

A Readily Applicable Strategy to Convert Peptides to Peptoid-based Therapeutics

Incorporation of unnatural amino acids and peptidomimetic residues into therapeutic peptides is highly efficacious and commonly employed, but generally requires laborious trial-and-error approaches. Previously, we demonstrated that C20 peptide has the potential to be a potential antiviral agent. Herein we report our attempt to improve the biological properties of this peptide by introducing peptidomimetics. Through combined alanine, proline, and sarcosine scans coupled with a competitive fluorescence polarization assay developed for identifying antiviral peptides, we enabled to pinpoint peptoid-tolerant peptide residues within C20 peptide. The synergistic benefits of combining these (and other) commonly employed methods could lead to a easily applicable strategy for designing and refining therapeutically-attractive peptidomimetics.

Novel pseudopeptides incorporating a benzodiazepine-based turn mimetic—targeting Mycobacterium tuberculosis ribonucleotide reductase

Peptides mimicking the C-terminus of the small subunit (R2) of Mycobacterium tuberculosis ribonucleotide reductase (RNR) can compete for binding to the large subunit (R1) and thus inhibit RNR activity. Moreover, it has been suggested that the binding of the R2 C-terminus is very similar in M. tuberculosis and Salmonella typhimurium. Based on modeling studies of a crystal structure of the holocomplex of the S. typhimurium enzyme, a benzodiazepine-based turn mimetic was identified and a set of novel compounds incorporating the benzodiazepine scaffold was synthesized. The compounds were evaluated in a competitive fluorescence polarization assay and in an RNR activity assay. These studies revealed that the compounds incorporating the benzodiazepine scaffold have the ability to compete for the M. tuberculosis R2 binding site with low-micromolar affinity.