Discovery and optimization of novel constrained pyrrolopyridone BET family inhibitors

Novel conformationally constrained BET bromodomain inhibitors have been developed. These inhibitors were optimized in two similar, yet distinct chemical series, the 6-methyl-1H-pyrrolo[2,3-c]pyridin-7(6H)-ones (A) and the 1-methyl-1H-pyrrolo[2,3-c]pyridin-7(6H)-ones (B). Each series demonstrated excellent activity in binding and cellular assays, and lead compounds from each series demonstrated significant efficacy in in vivo tumor xenograft models.     

MTMR9 Increases MTMR6 Enzyme Activity, Stability, and Role in Apoptosis

Myotubularin-related protein 6 (MTMR6) is a catalytically active member of the myotubularin (MTM) family, which is composed of 14 proteins. Catalytically active myotubularins possess 3-phosphatase activity dephosphorylating phosphatidylinositol-3-phoshate and phosphatidylinositol-3,5-bisphosphate, and some members have been shown to form homomers or heteromeric complexes with catalytically inactive myotubularins. We demonstrate that human MTMR6 forms a heteromer with an enzymatically inactive member myotubularin-related protein 9 (MTMR9), both in vitro and in cells. MTMR9 increased the binding of MTMR6 to phospholipids without changing the lipid binding profile. MTMR9 increased the 3-phosphatase activity of MTMR6 up to 6-fold. We determined that MTMR6 is activated up to 28-fold in the presence of phosphatidylserine liposomes. Together, MTMR6 activity in the presence of MTMR9 and assayed in phosphatidylserine liposomes increased 84-fold. Moreover, the formation of this heteromer in cells resulted in increased protein levels of both MTMR6 and MTMR9, probably due to the inhibition of degradation of both proteins. Furthermore, co-expression of MTMR6 and MTMR9 decreased etoposide-induced apoptosis, whereas decreasing both MTMR6 and MTMR9 by RNA interference led to increased cell death in response to etoposide treatment when compared with that seen with RNA interference of MTMR6 alone. Thus, MTMR9 greatly enhances the functions of MTMR6.Myotubularin proteins are a family of 14 proteins with the canonical dual specificity protein tyrosine phosphatase active site CX₅R motif (1–3). Eight members of the myotubularin family possess catalytic activity, dephosphorylating phosphatidylinositol 3-phosphate (PtdIns-3-P)⁴ and phosphatidylinositol 3,5-bisphosphate (PtdIns-3,5-P₂) at the D-3 position, and six members are not catalytically active because they lack the conserved cysteine residue in the protein tyrosine phosphatase motif that is required for activity. Interest in this group of proteins originated from the genetic evidence linking myotubularin, the founding member of this family, to myotubular myopathy, an X-linked disorder characterized by severe hypotonia and generalized muscle weakness (4). Subsequently, mutations in MTMR2 and in its inactive binding partner MTMR13 were linked to a subset of Charcot-Marie-Tooth disease type 4B, a demyelinating neurodegenerative disorder (5, 6).Despite near identical substrate specificity, biochemical and genetic evidence supports the hypothesis that myotubularin proteins are not redundant and have unique functions within cells (2, 7–9). The mechanisms by which loss of function of myotubularin proteins produce diseases are not known. Current evidence supports the hypothesis that each myotubularin protein regulates a specific pool of PtdIns-3-P and/or PtdIns-3,5-P₂, which in turn regulates a variety of cellular functions. Differences in tissue expression and subcellular localization play a role in the specificity of different myotubularins (10–15).The functions of myotubularin proteins are altered by the formation of heteromers between catalytically active and inactive members of the family. The initial biochemical purification of MTM1 demonstrated the presence of MTM1 homodimers and MTM1-3-phosphatase adapter protein (3PAP) heteromers (16), which was later described as MTMR12 (15, 17). MTMR2 was found to form heteromers with MTMR5 (13) and MTMR13 (18), and MTMR7 formed heteromers with MTMR9 (19). In each case, a catalytically active myotubularin protein interacted with an inactive protein. Heteromerization generated two important effects: increased catalytic activity of the active component (13, 15, 19, 20) and targeting of the heteromer to specific subcellular locations (15). Mutations in the inactive member MTMR13 result in a similar phenotype in patients as the mutations in its catalytically active binding partner MTMR2, indicating an indispensable role for the catalytically inactive subunit (21).Myotubularin proteins can be grouped into subfamilies based on homology. Closely related MTMR6, MTMR7, and MTMR8 comprise such a subfamily. We have previously characterized the interaction between mouse MTMR7 and MTMR9 proteins (19). In this report, we characterize the interaction between human MTMR6 and MTMR9. MTMR6 and MTMR9 have been shown to form a heteromeric complex in mouse and Caenorhabditis elegans (19, 22). MTMR6 has been shown to inhibit the activity of a calcium-activated potassium channel (type KCa3.1) (23, 24). Two screening experiments implicate MTMR6 as a regulator of apoptosis. By RNA microarray analysis, increased MTMR6 expression was observed in B cell chronic lymphoid leukemia cells with increased resistance to irradiation-induced apoptosis (25), whereas in an RNA interference screen in HeLa cells, decreased MTMR6 expression promoted apoptosis (26).Here we show that MTMR6 interacts with MTMR9 in vitro and in human cells. This interaction increases the phospholipid binding and enzymatic activity of MTMR6 in vitro. Co-expression of either subunit in cells dramatically increased the protein levels of the individual binding partners, suggesting that heteromer formation increases the stability of the proteins. Finally, MTMR9 was found to potentiate the effects of MTMR6 on apoptosis.     

High-resolution phylogenetic analysis of southeastern Europe traces major episodes of paternal gene flow among Slavic populations

The extent and nature of southeastern Europe (SEE) paternal genetic contribution to the European genetic landscape were explored based on a high-resolution Y chromosome analysis involving 681 males from seven populations in the region. Paternal lineages present in SEE were compared with previously published data from 81 western Eurasian populations and 5,017 Y chromosome samples. The finding that five major haplogroups (E3b1, I1b* (xM26), J2, R1a, and R1b) comprise more than 70% of SEE total genetic variation is consistent with the typical European Y chromosome gene pool. However, distribution of major Y chromosomal lineages and estimated expansion signals clarify the specific role of this region in structuring of European, and particularly Slavic, paternal genetic heritage. Contemporary Slavic paternal gene pool, mostly characterized by the predominance of R1a and I1b* (xM26) and scarcity of E3b1 lineages, is a result of two major prehistoric gene flows with opposite directions: the post-Last Glacial Maximum R1a expansion from east to west, the Younger Dryas-Holocene I1b* (xM26) diffusion out of SEE in addition to subsequent R1a and I1b* (xM26) putative gene flows between eastern Europe and SEE, and a rather weak extent of E3b1 diffusion toward regions nowadays occupied by Slavic-speaking populations.     

Expression of glycolytic isoenzymes in activated human peripheral lymphocytes: cell cycle analysis using flow cytometry

Human peripheral lymphocytes activated with concanavalin A and phorbol myristate ester exhibit an increase in glycolysis on a time-course similar to that for DNA synthesis. Elevated glycolysis is accompanied by increased specific activities of the glycolytic enzymes. Increased enzyme activities are accounted for by the appearance of specific isoenzyme forms (muscle forms) normally expressed in rapidly growing tumor cells or in growth-stimulated cells. In the present study we analyzed the expression of the glycolytic isoenzymes during cell cycle progression of activated human lymphocytes using two-parameter (DNA and protein) flow cytometry. Time-course studies and analysis of subpopulations prepared by elutriation centrifugation showed that the inducible isoenzymes are expressed at low levels or not at all in G0 cells. They are expressed first during the G0 to G1 transition or in early G1. However, expression increases throughout G1, reaching a maximum in S-phase. Thus, induction of glycolytic isoenzymes provides an excellent marker of T-cell activation and progression toward DNA synthesis.     

A platelet secretion pathway mediated by cGMP-dependent protein kinase

Platelet secretion (exocytosis) is critical in amplifying platelet activation, in stabilizing thrombi, and in arteriosclerosis and vascular remodeling. The signaling mechanisms leading to secretion have not been well defined. We have shown previously that cGMP-dependent protein kinase (PKG) plays a stimulatory role in platelet activation via the glycoprotein Ib-IX pathway. Here we show that PKG also plays an important stimulatory role in mediating aggregation-dependent platelet secretion and secretion-dependent second wave platelet aggregation, particularly those induced via Gq-coupled agonist receptors, the thromboxane A2 (TXA2) receptor, and protease-activated receptors (PARs). PKG I knock-out mouse platelets and PKG inhibitor-treated human platelets showed diminished aggregation-dependent secretion and also showed a diminished secondary wave of platelet aggregation induced by a TXA2 analog and thrombin receptor-activating peptides that were rescued by the granule content ADP. Low dose collagen-induced platelet secretion and aggregation were also reduced by PKG inhibitors. Furthermore PKG I knockout and PKG inhibitors significantly attenuated activation of the Gi pathway that is mediated by secreted ADP. These data unveil a novel PKG-dependent platelet secretion pathway and a mechanism by which PKG promotes platelet activation.     

Frequencies of mtDNA haplogroups in southeastern Europe--Croatians, Bosnians and Herzegovinians, Serbians, Macedonians and Macedonian Romani

Mitochondrial DNA polymorphisms were analyzed in of 1,610 randomly chosen adult men from 11 different regions from southeastern Europe (Croatians, Bosnians and Herzegovinians, Serbians, Macedonians and Macedonian Romani). MtDNA HVS-I region together with RFLP sites diagnostic for main Euroasian and African mtDNA haplogroups were typed to determine haplogroup frequency distribution. The most frequent haplogroup in studied populations was H with the exception of Macedonian Romani among whom the most frequent were South Asian (Indian) specific variants of haplogroup M. The multidimensional scaling plot showed two clusters of populations and two outliers (Macedonian Romani and the most distant from mainland Croatian island of Korcula). The first cluster was formed by populations from three Croatian islands (Hvar, Krk and Brac) and the second cluster was formed by Macedonians, Serbians, Croatians from mainland and coast, Herzegovinians, Bosnians, Slovenians, Poles and Russians. The present analysis does not address a precise evaluation of phylogenetic relations of studied populations although some conclusions about historical migrations could be noticed. More extended conclusions will be possible after deeper phylogenetic and statistical analyses.     

Impact assessment of risk parameters of underground coal mining on the environment

Coal is an important energy source but it has a significant negative impact on the environmental processes. This paper analyses the impact, measurement, and input of parameters representing potential environmental polluters in the information system (IS).

The methodology of recording and systematization includes the following parameters: coal deposits; climate parameters; roads; rivers; land and surrounding objects; air polluters; water polluters; and soil polluters. Methods for calculating land deformation, air polluter emissions, and noise impact are also presented.

Based on the number and specificity of analyzed data, the paper provides a concept of the IS and an overview of environmental impact of underground coal mine technological units. The concept was used to present the results of a research conducted at the underground coal mine “Soko” in Serbia.

The results of this research can help many potential users realize their goals. Those goals are preventive by nature, since negative environmental impact can be predicted, which enables the environmental protection experts to take appropriate measures.     

Diurnal fluctuations of protein contents and the pH dependence of β<Subscript>2</Subscript>-microglobulin stability in urine

Diurnal fluctuations of protein excretion into urine and the effect of urinary pH on the urinary protein concentrations were studied in patients with various kidney diseases. The diurnal kinetics of γ-immunoglobulin, transferrin, albumin, α₁-microglobulin, γ-immunoglobulin light chains, and the retinol-binding protein proved to positively correlate with the diurnal fluctuations of proteinuria and to negatively correlate with urinary pH. Diurnal changes in urinary β₂-microglobulin content did not correlate with those of any other protein. Oral bicarbonate intake alkalinized the urine, increased the urinary β₂-microglobulin content, and led to a direct correlation between β₂-microglobulin excretion and excretion of other low-molecular proteins. Thus, proteinuria, single protein excretion, and urinary pH displayed diurnal rhythmicity in the patients; β₂-microglobulin was unstable in acid urine and its urinary level depended on the urinary pH.