Identification of , an Orally Bioavailable Compound that Inhibits the DNA Polymerase Activity of Polθ

DNA polymerase theta (Polθ) is an attractive synthetic lethal target for drug discovery, predicted to be efficacious against breast and ovarian cancers harboring BRCA-mutant alleles. Here, we describe our hit-to-lead efforts in search of a selective inhibitor of human Polθ (encoded by POLQ). A high-throughput screening campaign of 350,000 compounds identified an 11 micromolar hit, giving rise to the N2-substituted fused pyrazolo series, which was validated by biophysical methods. Structure-based drug design efforts along with optimization of cellular potency and ADME ultimately led to the identification of RP-6685: a potent, selective, and orally bioavailable Polθ inhibitor that showed in vivo efficacy in an HCT116 BRCA2-/- mouse tumor xenograft model.

Discovery and Structural Characterization of Small Molecule Binders of the Human CTLH E3 Ligase Subunit GID4

Targeted protein degradation (TPD) strategies exploit bivalent small molecules to bridge substrate proteins to an E3 ubiquitin ligase to induce substrate degradation. Few E3s have been explored as degradation effectors due to a dearth of E3-binding small molecules. We show that genetically induced recruitment to the GID4 subunit of the CTLH E3 complex induces protein degradation. An NMR-based fragment screen followed by structure-guided analog elaboration identified two binders of GID4, 16 and 67, with K_d values of 110 and 17 μM in vitro. A parallel DNA-encoded library (DEL) screen identified five binders of GID4, the best of which, 88, had a K_d of 5.6 μM in vitro and an EC₅₀ of 558 nM in cells with strong selectivity for GID4. X-ray co-structure determination revealed the basis for GID4–small molecule interactions. These results position GID4-CTLH as an E3 for TPD and provide candidate scaffolds for high-affinity moieties that bind GID4.

Discovery of an Orally Bioavailable and Selective PKMYT1 Inhibitor, RP-6306

PKMYT1 is a regulator of CDK1 phosphorylation and is a compelling therapeutic target for the treatment of certain types of DNA damage response cancers due to its established synthetic lethal relationship with CCNE1 amplification. To date, no selective inhibitors have been reported for this kinase that would allow for investigation of the pharmacological role of PKMYT1. To address this need compound 1 was identified as a weak PKMYT1 inhibitor. Introduction of a dimethylphenol increased potency on PKMYT1. These dimethylphenol analogs were found to exist as atropisomers that could be separated and profiled as single enantiomers. Structure-based drug design enabled optimization of cell-based potency. Parallel optimization of ADME properties led to the identification of potent and selective inhibitors of PKMYT1. RP-6306 inhibits CCNE1-amplified tumor cell growth in several preclinical xenograft models. The first-in-class clinical candidate RP-6306 is currently being evaluated in Phase 1 clinical trials for treatment of various solid tumors.

Bora phosphorylation substitutes in trans for T-loop phosphorylation in Aurora A to promote mitotic entry

Polo-like kinase 1 (Plk1) is instrumental for mitotic entry and progression. Plk1 is activated by phosphorylation on a conserved residue Thr210 in its activation segment by the Aurora A kinase (AURKA), a reaction that critically requires the co-factor Bora phosphorylated by a CyclinA/B-Cdk1 kinase. Here we show that phospho-Bora is a direct activator of AURKA kinase activity. We localize the key determinants of phospho-Bora function to a 100 amino acid region encompassing two short Tpx2-like motifs and a phosphoSerine-Proline motif at Serine 112, through which Bora binds AURKA. The latter substitutes in trans for the Thr288 phospho-regulatory site of AURKA, which is essential for an active conformation of the kinase domain. We demonstrate the importance of these determinants for Bora function in mitotic entry both in Xenopus egg extracts and in human cells. Our findings unveil the activation mechanism of AURKA that is critical for mitotic entry.

Functional characterization of a PROTAC directed against BRAF mutant V600E

The RAF family kinases function in the RAS-ERK pathway to transmit signals from activated RAS to the downstream kinases MEK and ERK. This pathway regulates cell proliferation, differentiation and survival, enabling mutations in RAS and RAF to act as potent drivers of human cancers. Drugs targeting the prevalent oncogenic mutant BRAF(V600E) have shown great efficacy in the clinic, but long-term effectiveness is limited by resistance mechanisms that often exploit the dimerization-dependent process by which RAF kinases are activated. Here, we investigated a proteolysis-targeting chimera (PROTAC) approach to BRAF inhibition. The most effective PROTAC, termed P4B, displayed superior specificity and inhibitory properties relative to non-PROTAC controls in BRAF(V600E) cell lines. In addition, P4B displayed utility in cell lines harboring alternative BRAF mutations that impart resistance to conventional BRAF inhibitors. This work provides a proof of concept for a substitute to conventional chemical inhibition to therapeutically constrain oncogenic BRAF.

Identification and characterization of the first fragment hits for SETDB1 Tudor domain

SET domain bifurcated protein 1 (SETDB1) is a human histone-lysine methyltransferase which is amplified in human cancers and was shown to be crucial in the growth of non-small and small cell lung carcinoma. In addition to its catalytic domain, SETDB1 harbors a unique tandem tudor domain which recognizes histone sequences containing both methylated and acetylated lysines, and likely contributes to its localization on chromatin. Using X-ray crystallography and NMR spectroscopy fragment screening approaches, we have identified the first small molecule fragment hits that bind to histone peptide binding groove of the Tandem Tudor Domain (TTD) of SETDB1. Herein, we describe the binding modes of these fragments and analogues and the biophysical characterization of key compounds. These confirmed small molecule fragments will inform the development of potent antagonists of SETDB1 interaction with histones.

Crystal structure of native α-L-rhamnosidase from Aspergillus terreus

α-L-Rhamnosidases cleave terminal nonreducing α-L-rhamnosyl residues from many natural rhamnoglycosides. This makes them catalysts of interest for various biotechnological applications. The X-ray structure of the GH78 family α-L-rhamnosidase from Aspergillus terreus has been determined at 1.38 Å resolution using the sulfur single-wavelength anomalous dispersion phasing method. The protein was isolated from its natural source in the native glycosylated form, and the active site contained a glucose molecule, probably from the growth medium. In addition to its catalytic domain, the α-L-rhamnosidase from A. terreus contains four accessory domains of unknown function. The structural data suggest that two of these accessory domains, E and F, might play a role in stabilizing the aglycon portion of the bound substrate.

Identification of a fragment-like small molecule ligand for the methyl-lysine binding protein, 53BP1

Improving our understanding of the role of chromatin regulators in the initiation, development, and suppression of cancer and other devastating diseases is critical, as they are integral players in regulating DNA integrity and gene expression. Developing small molecule inhibitors for this target class with cellular activity is a crucial step toward elucidating their specific functions. We specifically targeted the DNA damage response protein, 53BP1, which uses its tandem tudor domain to recognize histone H4 dimethylated on lysine 20 (H4K20me2), a modification related to double-strand DNA breaks. Through a cross-screening approach, we identified UNC2170 (1) as a micromolar ligand of 53BP1, which demonstrates at least 17-fold selectivity for 53BP1 as compared to other methyl-lysine (Kme) binding proteins tested. Structural studies revealed that the tert-butyl amine of UNC2170 anchors the compound in the methyl-lysine (Kme) binding pocket of 53BP1, making it competitive with endogenous Kme substrates. X-ray crystallography also demonstrated that UNC2170 binds at the interface of two tudor domains of a 53BP1 dimer. Importantly, this compound functions as a 53BP1 antagonist in cellular lysates and shows cellular activity by suppressing class switch recombination, a process which requires a functional 53BP1 tudor domain. These results demonstrate that UNC2170 is a functionally active, fragment-like ligand for 53BP1.

Carborane-based carbonic anhydrase inhibitors: insight into CAII/CAIX specificity from a high-resolution crystal structure, modeling, and quantum chemical calculations

Carborane-based compounds are promising lead structures for development of inhibitors of carbonic anhydrases (CAs). Here, we report structural and computational analysis applicable to structure-based design of carborane compounds with selectivity toward the cancer-specific CAIX isoenzyme. We determined the crystal structure of CAII in complex with 1-methylenesulfamide-1,2-dicarba-closo-dodecaborane at 1.0 Å resolution and used this structure to model the 1-methylenesulfamide-1,2-dicarba-closo-dodecaborane interactions with CAIX. A virtual glycine scan revealed the contributions of individual residues to the energy of binding of 1-methylenesulfamide-1,2-dicarba-closo-dodecaborane to CAII and CAIX, respectively.

Identification of carbonic anhydrase I immunodominant epitopes recognized by specific autoantibodies which indicate an improved prognosis in patients with malignancy after autologous stem cell transplantation

This work employs an epitope mapping of carbonic anhydrase (CA), isoform I (CA I), for detection of the main immunodominant epitopes. Our interest has arisen from an observed spontaneous tumor regression in patients who developed an aplastic anemia type syndrome after a high-dose therapy with autologous stem cell transplantation and whose sera contained high titer of anti carbonic anhydrase (anti-CA) autoantibodies. There are many indications that the presence of these autoantibodies may provide significant survival benefit for the patients. Western blot analysis confirmed strong immunoreactivity of the patients' sera with several CA isoforms and the CA I has been selected for our study as a highly abundant and widely distributed isoform. The applied analytical approach consists of specific fragmentation of CA I protein followed by immunospecific isolation of peptides reacting with polyclonal anti-CA I autoantibodies of patients in spontaneous remission. We improved the standard epitope mapping schema by incorporating the benefits of magnetic carriers and biomagnetic separation techniques. Mass spectrometry has been applied for detection and identification of epitopes and the acquired results were verified by bioinformatic tools. The candidate epitopes of CA I (NVGHS, DGLAV, SSEQL, and SLKPI) are discussed herein as potential therapeutic targets. This work highlights the usefulness of the epitope mapping technique based on magnetic microspheres for effective and rapid determination of immunodominant epitopes of the target protein.

The "Presodium" Hydrogen Evolution at the Dropping Mercury Electrode Catalysed by Simple Cysteine Peptides

"Presodium" catalytic currents at dropping mercury electrode of cysteine, cysteinylglycine, γ-glutamylcysteine and reduced glutathione were systematically studied in weakly alkaline solutions. They consist in shifts to positive potentials of current due to reduction of the blank solution, and, under some conditions, also in formation of "catalytic prewaves". The two cases have been qualitatively interpreted as based on a suggested common mechanism, differing by the occurrence of weak catalyst adsorption in the prewave case. The catalytic activity depends on the catalyst itself (concentration, structure, conformation at the electrode, partial protonation/ionisation, partial hydrophobic/hydrophilic character) as well as on the solution (pH, ionic strength, nature and concentration of components).

Technical advance: the DNA-binding activity of gal4 is inhibited by methylation of the gal4 binding site in plant chromatin

Derivatives of the Saccharomyces cerevisiae transcription factor Gal4 which act as effective transcription activators in yeast, Drosophila, mammalian cells and plant protoplasts are shown to direct expression from a GUS reporter construct when expressed in transgenic tobacco. However, in comparison to 35S-GUS controls, Gal4-mediated expression of the reporter gene was relatively weak and extremely variable. GUS expression was lost as plants matured and it was almost undetectable in most of their progeny. Gal4-mediated gene expression could be restored by treating tissues with 5-aza-cytidine, implicating cytosine methylation in the loss of Gal4-mediated expression. Restoration of reporter expression was not accompanied by an increase in steady-state levels of the activator transcript. We propose that the DNA-binding activity of Gal4 is sensitive to methylation of its binding site in plant chromatin. The Gal4-DNA co-crystal predicts that 5-methylcytosine at either of the outer two positions of the binding site will effectively prevent Gal4 binding. We show that these positions become extensively methylated in transgenic plants and that methylation of Gal4-binding sites interferes with Gal4 binding in vitro. These observations suggest that the Gal4 DNA-binding domain is intrinsically sensitive to cytosine methylation and that, despite the success of Gal4-based expression systems in yeast and Drosophila, Gal4 is not ideal for use in plant gene expression technology.

Voltammetry on mercury and carbon electrodes as a tool for studies of metallothionein interactions with metal ions

Rabbit liver Cd-metallothionein (CdMT) and Cd-complex of synthetically prepared pentapeptide (gamma-Glu-Cys)2-Gly were studied as examples of animal and plant metallothioneins. Using hanging mercury electrode, cathodic stripping voltammetry after adsorptive accumulation of the Cd(II)-SR complex at different potentials, is suitable for estimating changes occurring in metal coordination due to the presence of metal ions such as Zn2+, Cu2+, Hg2+ or excessive Cd2+. Conditions under which similar behaviour can be observed for both CdMT and Cd-pentapeptide complex are specified. On carbon electrodes, detailed study of reduction processes of Cd(II)-SR complexes is prevented by occurrence of a large catalytic current; oxidation processes are more suitable for study at these electrodes. Carbon composite paste electrode (10% SiO2) allows deposition of Cd(II)-SR complex during its reduction, as was demonstrated with Cd-cysteine, CdMT or Cd-pentapeptide complex. After deposition, oxidation peak of the uncomplexed Cd2+ ions and one or two oxidation peaks corresponding to a formation of the RS-Cd(II) complex are observed. Also, similarly as on Hg electrode, it was observed that excessive Cd2+ or Zn2+ ions influence oxidation peaks of the RS-Cd(II) complex formation. Combination of measurements on mercury electrode and composite paste electrode is recommended for studies of metallothionein interactions with metal ions or other metal complexes.

Environmental specimen banking in the Czech Republic: a pilot study

In recognition of the importance of environmental specimen banking (ESB) as an important component of the described ongoing real-time environmental and health-related monitoring programmes, a proposal for a planned ESB pilot study in the Czech Republic is presented. Selection of biomonitors, analytes, sampling techniques and sites is discussed, especially with regard to the possible harmonization with ESB already operational abroad. Availability of validated analytical techniques for determination of up to 30 elements using nuclear and spectroscopic techniques, including speciation of several metals, and of the most important organic pollutants employing various chromatographic techniques in biological and environmental samples is demonstrated.

Interlaboratory analysis of IRM NSC-21 Compost Vitahum

The preparation of internal reference material NSC-21 Compost Vitahum, including its stabilization, homogeneity testing, and evaluation of an interlaboratory comparison in which 19 laboratories took part using several analytical methods is described. From the results of the intercomparison, consensus values were derived for the contents of Cd, Cu, Ni, Pb, and Zn, whereas for As, Co, Cr, Fe, Hg and Mn, information values were derived. Bimodal distribution of the As and Cr results was obtained, presumably because of incomplete dissolution of the elements from the matrix if insufficiently aggressive decomposition procedures were employed. Some problems encountered were elucidated by application of neutron activation analysis (NAA) in its nondestructive and destructive (radiochemical) modes.

[Present problems of environmental contamination with so-called heavy metals]

Till recently the true state and quality of the environment was kept secret. False pretension of a better state is one of the reasons not only for the poor state of our living environment but also for the poor health status of the population. The authors discuss the contemporary process of contamination and pollution of the environment as a result of economic activities and pays special attention to so-called heavy metals.

The surgical treatment of high myopia: comparison of epikeratoplasty, keratomileusis and minus power anterior chamber lenses

Seventy high myopic eyes (-8.00 to -28.00 diopters) with epikeratoplasty (n = 29), myopic non-freeze keratomileusis (n = 26) or minus power anterior chamber intraocular lenses in phakic eyes (n = 15) were operated by two surgeons and were evaluated retrospectively. Results are reported at the 6-month postoperative interval. Eyes treated with epikeratoplasty had an average preoperative spherical equivalent of the cycloplegic refraction of -17.80 D (range -12.00 to -28.00 D). At 6 months, 66.6% of eyes were within 3 D of emmetropia and 7.4% of eyes had an uncorrected visual acuity of 20/40 or more. Average preoperative spectacle visual acuity was 20/50 (0.39); it was 20/50 (0.37) at both 6 and 24 months. Between 6 and 24 months, 32.2% of eyes had a change in refraction of 1.00 D or more. Two lenticules were removed. Eyes treated with non-freeze keratomileusis had an average preoperative refraction of -10.0 D (range -8 to -15 D). At 6 months, 61.5% of eyes were within 3.00 D of emmetropia and 30.7% of eyes had an uncorrected visual acuity of 20/40 or better. Average preoperative spectacle visual acuity was 20/30 (0.67), and 6 and 12 months afterward it was 20/30-20/40 (0.57) and 20/30 (0.66) respectively. Between 6 and 12 months, 8.3% of eyes, had a change in refraction of 1.00 D or more. Eyes treated with minus power anterior chamber lenses had an average preoperative refraction of -17.30 D (range -12.50 to -20.00 D).(ABSTRACT TRUNCATED AT 250 WORDS)

Polarography of the oxytocin and vasopressin synthetic analogs

Small changes in the molecules of the oxytocin and vasopressin synthetic analogs bring about considerable changes in their polarographic behaviour within the entire potential interval available (+0·5 to -2·0 V VS SCE). In the study of the polarographic activity of ten peptides we used classical, differential pulse and alternating current polarography and cyclic voltammetry. Liquid chromatographic separation studies of the peptides on the reverse phase complemented the electrochemical investigation. Hydrophobicity showed to be the parameter which decisively influences the polarographic behaviour of the studied peptides. Strong interaction of the SS and S-carba analogs with the electrode material (mercury) has been observed and surface activity of the SH-forms of the peptides at negative potentials has been confirmed. The importance of various functional groups in the peptide molecule for the catalytic activity in hydrogen evolution at negative potentials is discussed.

[Experimental control of the process of lead absorption and deposition in domestic ducks]

A trial was conducted with 40 domestic ducks of the White Pekin breed at the age of 40 days: thirty pieces of lead shot were introduced as a single dose in the gizzard. The process of lead resorption and deposition was found not to be significantly influenced by the therapeutic treatments nor changes in the composition of feed. A week after the administration of shot a significant increase was recorded in the content of lead to 4.32 mg in liver, to 11.36 mg in kidney and to 1.15 mg in muscle (the respective values for the control animals were 0.07, 0.11 and 0.06 mg per kg). At the end of the trial after three weeks of treatment and administration of experimental diets, no significant differences were recorded in lead content in liver, kidney and muscle between the untreated and treated ducks nor ducks fed experimental diets.