Bcl-2 ͉ melanoma ͉ Bax ͉ Bak ͉ caspase

A genome wide search for new BH3-containing Bcl-2 family members was conducted using position weight matrices (PWM) and identified a large (480 kDa), novel BH3-only protein, originally called LASU1 (now also known as Ureb-1, E3 histone , ARF-BP1, and Mule). We demonstrated that LASU1 is an E3 ligase that ubiquitinated Mcl-1 in vitro and was required for its proteasome-dependent degradation in HeLa cells. Of note, the BH3 domain of LASU1 interacted with Mcl-1 but not with Bcl-2 or Bcl-Xl. A competing BH3-ligand derived from Bim interacted with Mcl-1 and prevented its interaction with LASU1 in HeLa cells, causing elevation of the steady-state levels of Mcl-1. This suggests that the unliganded form of Mcl-1 is sensitive to LASU1-mediated degradation of Mcl-1.

A facile and sensitive mass spectrometric method has been developed for the dereplication of natural products. The method provides information about the molecular formula and substructure of a precursor molecule and its fragments, which are invaluable aids in dereplication of natural products at their early stages of purification and characterization. Collision-induced MS/MS technique is used to fragment a precursor ion into several product ions, and individual product ions are selected and subjected to collision-induced MS/MS/MS analysis. This method enables the identification of the fragmentation pathway of a precursor molecule from its first-generation fragments (MS/MS), through to the nth generation product ions (MSn). It also allows for the identification of the corresponding neutral products released (neutral losses). Elements used in the molecular formula analysis include C, H, N, O, and S, as most natural products are constituted by these five elements. High-resolution mass separation and accurate mass measurements afforded the unique identification of molecular formula of small neutral products. Through sequential add-up of the molecular formulas of the small neutral products, the molecular formula of the precursor ion and its productions were uniquely determined. The molecular formula of the precursor molecule was then reversely used to identify or confirm the molecular formula of the neutral products and that of the productions. The molecular formula of the neutral fragments allowed for the identification of substructures, leading to a rapid and efficient characterization of precursor natural product. The method was applied to paclitaxel (C47H51NO14; 853 amu) to identify its molecular formula and its substructures, and to characterize its potential fragmentation pathways. The method was further validated by correctly identifying the molecular formula of minocycline (C23H27N3O7; 457 amu) and piperacillin (C23H27N5O7S; 517 amu).

RNA editing, catalyzed by the multiprotein editosome complex, is an essential step for the expression of most mitochondrial genes in trypanosomatid pathogens. It has been shown previously that Trypanosoma brucei RNA editing ligase 1 (TbREL1), a core catalytic component of the editosome, is essential in the mammalian life stage of these parasitic pathogens. Because of the availability of its crystal structure and absence from human, the adenylylation domain of TbREL1 has recently become the focus of several studies for designing inhibitors that target its adenylylation pocket. Here, we have studied new and existing inhibitors of TbREL1 to better understand their mechanism of action. We found that these compounds are moderate to weak inhibitors of adenylylation of TbREL1 and in fact enhance adenylylation at higher concentrations of protein. Nevertheless, they can efficiently block deadenylylation of TbREL1 in the editosome and, consequently, result in inhibition of the ligation step of RNA editing. Further experiments directly showed that the studied compounds inhibit the interaction of the editosome with substrate RNA. This was supported by the observation that not only the ligation activity of TbREL1 but also the activities of other editosome proteins such as endoribonuclease, terminal RNA uridylyltransferase, and uridylate-specific exoribonuclease, all of which require the interaction of the editosome with the substrate RNA, are efficiently inhibited by these compounds. In addition, we found that these compounds can interfere with the integrity and/or assembly of the editosome complex, opening the exciting possibility of using them to study the mechanism of assembly of the editosome components.Trypanosoma brucei, Trypanosoma cruzi, and Leishmania major are three major trypanosomatid pathogens that cause hundreds of thousands of deaths and infect millions of people in tropical and subtropical areas of the world (1). Current trypanocidal drugs have a number of limitations such as high rate of toxicity, low rate of efficacy, and drug resistance (2, 3). Therefore, it is important to look for a drug that is effective and does not produce harmful side effects. RNA editing is a unique posttranscriptional modification of mitochondrial mRNAs that is shared in all trypanosomatid pathogens (4, 5). Modification of specific editing sites, dictated by complementary guide RNAs (gRNAs), 5 constitutes essential steps to ensure the production of translatable mRNAs that encode essential components of the mitochondrial respiratory system. Although gRNAs specify the number of uridylates (Us) to be added or deleted by base pairing at each editing block (6, 7), a 1.6-MDa multiprotein complex, the editosome, is responsible for catalysis of different steps of RNA editing. Although the complete composition of the editosome is being elucidated, most purified functional editosomes contain over 20 proteins (8,9). The editosomes differ in their compositions, having at least three different complexes that sediment at ϳ20 S on glycerol gradie...

We carried out docking and molecular dynamics simulations on ABT-737 and obatoclax, which are inhibitors of the Bcl-2 family of proteins. We modeled the binding mode of ABT-737 with Bcl-x(L) , Bcl-2, and Mcl-1 and examined their dynamical behavior. We found that the binding of the chlorobiphenyl end of ABT-737 was quite stable across all three proteins. However, the phenylpiperazine linker group was dramatically more mobile in Mcl-1 compared to either Bcl-x(L) or Bcl-2. The S-phenyl group at the p4 binding site was well-anchored in Bcl-x(L) and Bcl-2 but was somewhat more mobile in Mcl-1 although the phenyl ring itself on average stayed close to the p4 binding site in Mcl-1. This greater mobility is likely due to the greater openness of the p3 and p4 binding sites on Mcl-1. The calculated binding free energies were consistent with the much weaker binding affinity of ABT-737 for Mcl-1. Obatoclax was predicted to bind at the p1 and p2 binding sites of Mcl-1 and the binding mode was quite stable during the molecular dynamics simulation with Mcl-1 wrapping around the molecule. The modeled binding mode suggests that obatoclax is able to inhibit all three proteins because it makes use of the p1 and p2 binding sites alone, which is a fairly narrow groove in all three proteins unlike the p4 binding site, which is much broader in Mcl-1.

Automated software was developed to analyze the molecular formula of organic molecules and peptides based on high-resolution MS/MS spectroscopic data. The software was validated with 96 compounds including a few small peptides in the mass range of 138-1569 Da containing the elements carbon, hydrogen, nitrogen and oxygen. A Micromass Waters Q-TOF Ultima Global mass spectrometer was used to measure the molecular masses of precursor and fragment ions. Our software assigned correct molecular formulas for 91 compounds, incorrect molecular formulas for 3 compounds, and no molecular formula for 2 compounds. The obtained 95% success rate indicates high reliability of the software. The mass accuracy of the precursor ion and the fragment ions, which is critical for the success of the analysis, was high, i.e. the accuracy and the precision of 850 data were 0.0012 Da and 0.0016 Da, respectively. For the precursor and fragment ions below 500 Da, 60% and 90% of the data showed accuracy within #0.001 Da and #0.002 Da, respectively. The precursor and fragment ions above 500 Da showed slightly lower accuracy, i.e. 40% and 70% of them showed accuracy within #0.001 Da and #0.002 Da, respectively. The molecular formulas of the precursor and the fragments were further used to analyze possible mass spectrometric fragmentation pathways, which would be a powerful tool in structural analysis and identification of small molecules. The method is valuable in the rapid screening and identification of small molecules such as the dereplication of natural products, characterization of drug metabolites, and identification of small peptide fragments in proteomics. The analysis was also extended to compounds that contain a chlorine or bromine atom.

Obatoclax (GX15-070), a synthetic small molecule pan-Bcl-2 family inhibitor, is currently under investigation in multiple Phase II trials directed at hematologic and solid tumor malignancies. Inhibition of pro-survival Bcl-2 members antagonizes their ability to neutralize the death effectors Bax and Bak, which are required for obatoclax-induced cellular toxicity. The hydrophobic character of obatoclax is consistent with its predicted occupation of a hydrophobic pocket in the lower region of the Bcl-2 BH3 binding groove. Based on comparisons with the published results of 10 known small molecule inhibitors, obatoclax is computationally predicted to have a significant binding affinity for Bcl-2 (Ki = 220 nanoM). A recent report (Zhai et al., Cell Death Differ. 2006 13: 1419-21), describing the interactions of synthetic BH3 peptides with Bcl-2 family proteins by fluorescence polarization in aqueous medium (PBS), indicated that obatoclax selectively antagonizes such interactions for all pro-survival members tested (Bcl-2, Bcl-Xl, Mcl-1, Bcl-w, A1, and Bcl-b), but did not affect control protein interactions. IC50s for obatoclax ranged from 1 to 7 microM. Under the aqueous conditions of this assay, however, obatoclax is largely insoluble and therefore this report likely underestimates the potency of the compound. In situ, Bcl-2 proteins reside integrated in the hydrophobic membranes of mitochondria and ER. We took advantage of the fact that Mcl-1 constitutively interacts with Bak in the mitochondrial outer membrane, thus presenting the opportunity to investigate the potency of obatoclax in situ on a native Bcl-2 protein-protein interaction. Employing chemical crosslinking to detect Mcl-1/Bak dimers in intact mitochondria, obatoclax was found to disrupt these interactions with an IC50 less than 10 nanoM, similar to that observed for inhibition by synthetic BH3 peptides corresponding to Noxa and Bim. In contrast to Bim peptide, which induced release of cytochrome c from isolated mitochondria, obatoclax did not, indicating that it is a sensitizer rather than an activator of the intrinsic mitochondrial apoptosis program. Bax or Bak are toxic to yeast cells, but are restrained by either Mcl-1, Bcl-2, Bcl-Xl, or Bcl-w. In each case, obatoclax treatment re-instated Bax or Bak toxicity, confirming the pan-inhibitor properties of the compound. Among Bcl-2 proteins, Mcl-1 rapidly turns over at steady state and is subject to ubiquitin-mediated degradation by the 26S proteasome. Not surprisingly, the proteasome inhibitor bortezomib significantly enhances Mcl-1 protein levels in various settings, including mantle cell lymphoma (MCL) cells. Bortezomib also induced Noxa upregulation in MCL, and obatoclax and Noxa appeared to cooperate to displace Bak from Mcl-1. As predicted, obatoclax and bortezomib exhibited synergistic toxicity in MCL lines in vitro and in cells derived from MCL patients ex vivo. Collectively, therefore, a biochemical rationale has been established to interrogate obatoclax-bortezomib combinations in clinical trials directed at mantle cell lymphoma.