Establishing Drug Discovery and Identification of Hit Series for the Anti-apoptotic Proteins, Bcl-2 and Mcl-1.

We describe our work to establish structure- and fragment-based drug discovery to identify small molecules that inhibit the anti-apoptotic activity of the proteins Mcl-1 and Bcl-2. This identified hit series of compounds, some of which were subsequently optimized to clinical candidates in trials for treating various cancers. Many protein constructs were designed to identify protein with suitable properties for different biophysical assays and structural methods. Fragment screening using ligand-observed NMR experiments identified several series of compounds for each protein. The series were assessed for their potential for subsequent optimization using 1H and 15N heteronuclear single-quantum correlation NMR, surface plasmon resonance, and isothermal titration calorimetry measurements to characterize and validate binding. Crystal structures could not be determined for the early hits, so NMR methods were developed to provide models of compound binding to guide compound optimization. For Mcl-1, a benzodioxane/benzoxazine series was optimized to a K d of 40 µM before a thienopyrimidine hit series was identified which subsequently led to the lead series from which the clinical candidate S 64315 (MIK 665) was identified. For Bcl-2, the fragment-derived series were difficult to progress, and a compound derived from a published tetrahydroquinone compound was taken forward as the hit from which the clinical candidate (S 55746) was obtained. For both the proteins, the work to establish a portfolio of assays gave confidence for identification of compounds suitable for optimization.

S55746 is a novel orally active BCL-2 selective and potent inhibitor that impairs hematological tumor growth.

Escape from apoptosis is one of the major hallmarks of cancer cells. The B-cell Lymphoma 2 (BCL-2) gene family encodes pro-apoptotic and anti-apoptotic proteins that are key regulators of the apoptotic process. Overexpression of the pro-survival member BCL-2 is a well-established mechanism contributing to oncogenesis and chemoresistance in several cancers, including lymphoma and leukemia. Thus, BCL-2 has become an attractive target for therapeutic strategy in cancer, as demonstrated by the recent approval of ABT-199 (Venclexta™) in relapsed or refractory Chronic Lymphocytic Leukemia with 17p deletion. Here, we describe a novel orally bioavailable BCL-2 selective and potent inhibitor called S55746 (also known as BCL201). S55746 occupies the hydrophobic groove of BCL-2. Its selectivity profile demonstrates no significant binding to MCL-1, BFL-1 (BCL2A1/A1) and poor affinity for BCL-XL. Accordingly, S55746 has no cytotoxic activity on BCL-XL-dependent cells, such as platelets. In a panel of hematological cell lines, S55746 induces hallmarks of apoptosis including externalization of phosphatidylserine, caspase-3 activation and PARP cleavage. Ex vivo, S55746 induces apoptosis in the low nanomolar range in primary Chronic Lymphocytic Leukemia and Mantle Cell Lymphoma patient samples. Finally, S55746 administered by oral route daily in mice demonstrated robust anti-tumor efficacy in two hematological xenograft models with no weight lost and no change in behavior. Taken together, these data demonstrate that S55746 is a novel, well-tolerated BH3-mimetic targeting selectively and potently the BCL-2 protein.

Application of Off-Rate Screening in the Identification of Novel Pan-Isoform Inhibitors of Pyruvate Dehydrogenase Kinase.

Libraries of nonpurified resorcinol amide derivatives were screened by surface plasmon resonance (SPR) to determine the binding dissociation constant (off-rate, kd) for compounds binding to the pyruvate dehydrogenase kinase (PDHK) enzyme. Parallel off-rate measurements against HSP90 and application of structure-based drug design enabled rapid hit to lead progression in a program to identify pan-isoform ATP-competitive inhibitors of PDHK. Lead optimization identified selective sub-100-nM inhibitors of the enzyme which significantly reduced phosphorylation of the E1α subunit in the PC3 cancer cell line in vitro.

Unusual Childhood Waking as a Possible Precursor of the 1995 Kobe Earthquake.

Nearly 1,100 young students living in Japan at a range of distances up to 500 km from the 1995 Kobe M7 earthquake were interviewed. A statistically significant abnormal rate of early wakening before the earthquake was found, having exponential decrease with distance and a half value approaching 100 km, but decreasing much slower than from a point source such as an epicentre; instead originating from an extended area of more than 100 km in diameter. Because an improbably high amount of variance is explained, this effect is unlikely to be simply psychological and must reflect another mechanism-perhaps Ultra-Low Frequency (ULF) electromagnetic waves creating anxiety-but probably not (222)Rn excess. Other work reviewed suggests these conclusions may be valid for animals in general, not just children, but would be very difficult to apply for practical earthquake prediction.

Iodine-129 measurements in soil samples from Dolon village near the Semipalatinsk nuclear test site.

Dolon village, located about 60 km from the border of the Semipalatinsk nuclear test site, is known to be heavily contaminated by the first USSR atomic bomb test in August 1949. Soil samples around Dolon were taken in October 2005 in an attempt to evaluate internal thyroid dose arising from incorporation of radioiodine isotopes (mainly (131)I). Iodine-129 in soil was measured by using the technique of accelerator mass spectrometry. The (129)I/(127)I atom ratios measured were in the range from 3.3 x 10(-9) to 3.3 x 10(-7). These values were within the range of the current background level ( approximately 10(-9) to 10(-7)) in the environment, including contributions from the global fallout of atmospheric nuclear tests and local fallout of nuclear facilities. The (129)I atom accumulated level in soil ranged from 1.28 x 10(13) to 1.59 x 10(14) atoms m(-2), the average (8.0 x 10(13)) of which was higher than the background level of (2-5) x 10(13). From the relationship between (129)I and( 137)Cs (corrected for background and decay from 1949 to 2005) accumulated levels, the background level of (129)I and the (129)I/(137)Cs ratio around Dolon were estimated to be (6.4 +/- 0.4) x 10(13) atoms m(-2) and 0.25 +/- 0.16, respectively. This (129)I/(137)Cs ratio is almost similar to the fission yield ratio for (239)Pu fast fission (0.24).

Carbapenem antibiotic biosynthesis in Erwinia carotovora is regulated by physiological and genetic factors modulating the quorum sensing-dependent control pathway.

Erwinia carotovora produces the beta-lactam antibiotic, carbapenem, in response to a quorum sensing signalling molecule, N-(3-oxohexanoyl)-L-homoserine lactone (OHHL). We have mapped the OHHL-dependent promoter upstream of the first of the biosynthetic genes, carA. We have also analysed the effect on this promoter of the known genetic regulators of carbapenem expression, carR, carI (encoding homologues of LuxR and LuxI respectively) and hor (encoding a SlyA/MarR-like transcriptional regulator). We describe a previously unknown promoter located within the carA-H operon. This promoter does not respond to CarR and is required for quorum sensing-independent expression of the carbapenem resistance determinants encoded by the carFG genes. We have mapped the carR, carI and hor transcription start points, shown that CarR is positively autoregulated in the presence of OHHL, and have demonstrated negative feedback affecting transcription of carI. In addition, various environmental and physiological factors were shown to impinge on the transcription of the car biosynthetic genes. The nature of the carbon source and the temperature of growth influence carbapenem production by modulating the level of the OHHL signalling molecule, and thereby physiologically fine-tune the quorum sensing regulatory system.

The regulation of virulence in phytopathogenic Erwinia species: quorum sensing, antibiotics and ecological considerations.

Erwinia carotovora is a Gram-negative bacterial phytopathogen that causes soft-rot disease and potato blackleg. The organism is environmentally widespread and exhibits an opportunistic plant pathogenesis. The ability to secrete multiple plant cell wall-degrading enzymes is a key virulence trait and exoenzyme production is responsive to multiple environmental and physiological cues. One important cue is the cell population density of the pathogen. Cell density is monitored via an acylated homoserine lactone (acyl HSL) signalling molecule, which is thought to diffuse between Erwinia cells in a process now commonly known as 'quorum sensing'. This molecule also acts as the chemical communication signal controlling production of a broad-spectrum beta-lactam antibiotic (1-carbapen-2-em-3-carboxylic acid; carbapenem) synthesised in concert with exoenzyme elaboration, possibly for niche defence. In antibiotic production control, quorum sensing acts at the level of transcriptional activation of the antibiotic biosynthetic cluster. This is achieved via a dedicated LuxR-type protein, CarR that is bound to the signalling molecule. The molecular relay connecting acyl HSL production and exoenzyme induction is not clear, despite the identification of a multitude of global regulatory genes, including those of the RsmA/rsmB system, impinging on enzyme synthesis. Quorum sensing control mediated by acyl HSLs is widespread in Gram-negative bacteria and is responsible for the regulation of diverse phenotypes. Although there is still a paucity of meaningful information on acyl HSL availability and in-situ biological function, there is growing evidence that such molecules play significant roles in microbial ecology.

Preliminary results of using ESR to examine biofilms

This preliminary work shows ESR (Electron Spin Resonance) can be used to detect biofilms, particularly from Fe-metabolising bacteria. A film was detected by ESR as early as 1 day, hence possibly more sensitively than by fluorescent methods. Films can probably be detected as early as one hour. Spectra contain a very broad peak at g=2.13, probably due to ferrihydrite. Results of field experiments from streams and ponds in New Zealand and Japan, particularly the Minoh River, showed a general increase of ferrihydrite with time. Loss by exfoliation was later than 20 days. The rate of accumulation was faster in a nutrient-rich stagnant pond. Hematite (g=4.3) was often observed, magnetite (g=9) once, and usually small amounts of a common bacterial decay product. The latter was detected for at least 18 months film storage. ESR is a particularly good tool for observing the growth of oxic biofilms containing Fe-metabolising bacteria, and should be just as sensitive for observing Mn-metabolising bacteria in reducing conditions.