Analysis of Flexibility and Hotspots in Bcl-xL and Mcl-1 Proteins for the Design of Selective Small-Molecule Inhibitors

Although Bcl-xL and Mcl-1, two antideath Bcl-2 members, have similar, flexible binding sites, they can achieve high binding selectivity to endogenous binding partners and synthetic small-molecule inhibitors. Here, we employed molecular dynamic (MD) simulations and hotspot analysis to investigate the conformational flexibility of these proteins and their binding hotspots at the binding sites. Backbone flexibility analyses indicate that the highest degree of flexibility in Mcl-1 is the α4 helical segment as opposed to the α3 helix in Bcl-xL among four helical segments in their binding sites. Furthermore, common and unique binding hotspots at both proteins were identified using small-molecule probes. These analyses can aid the design of potent and specific small-molecule inhibitors for these proteins

A learning-based end-to-end wireless communication system utilizing a deep neural network channel module

The existing end-to-end (E2E) wireless communication systems require fewer communication modules and have a simple processing signal flow, compared to conventional wireless communication systems. However, in the absence of a differentiable channel model, it is impossible to train transmitters, used in such systems, which makes impossible achieving optimal system performance. To solve this problem, E2E wireless communication systems, learned with conditional generative adversarial networks (CGANs) for channel modeling, have been proposed recently. Unfortunately, the CGAN training is prone to instability, slow convergence, and inaccurate channel modeling, which affects the system performance. To this end, a learning-based E2E wireless communication system, utilizing a deep neural network (DNN) channel module to model an unknown channel, is proposed in this paper. Simulation results show that the proposed DNN channel modeling has faster convergence, simpler network structure, and can reflect the behavior of real channels more accurately. In addition, the proposed learning-based E2E wireless communication system performs better, in terms of the bit error rate (BER) and block error rate (BLER), than the learning-based E2E wireless communication system, using CGAN as unknown channel, and a traditional communication system,designed based on the prior knowledge of the channel. Compared to these two systems, at high signal-to-noise ratio (SNR) values, the proposed system can achieve a SNR gain of at least 2 dB, in communication scenarios involving frequency-selective multi-path channels.</p

Potent and Selective Small-Molecule Inhibitors of cIAP1/2 Proteins Reveal That the Binding of Smac Mimetics to XIAP BIR3 Is Not Required for Their Effective Induction of Cell Death in Tumor Cells

Cellular inhibitor of apoptosis protein 1 and 2 (cIAP1/2) and X-linked inhibitor of apoptosis protein (XIAP) are key apoptosis regulators and promising new cancer therapeutic targets. This study describes a set of non-peptide, small-molecule Smac (second mitochondria-derived activator of caspases) mimetics that are selective inhibitors of cIAP1/2 over XIAP. The most potent and most selective compounds bind to cIAP1/2 with affinities in the low nanomolar range and show >1,000-fold selectivity for cIAP1 over XIAP. These selective cIAP inhibitors effectively induce degradation of the cIAP1 protein in cancer cells at low nanomolar concentrations and do not antagonize XIAP in a cell-free functional assay. They potently inhibit cell growth and effectively induce apoptosis at low nanomolar concentrations in cancer cells with a mechanism of action similar to that of other known Smac mimetics. Our study shows that binding of Smac mimetics to XIAP BIR3 is not required for effective induction of apoptosis in tumor cells by Smac mimetics. These potent and highly selective cIAP1/2 inhibitors are powerful tools in the investigation of the role of these IAP proteins in the regulation of apoptosis and other cellular processes

Discovery of Pyrrolo[2,3‑<i>c</i>]pyridines as Potent and Reversible LSD1 Inhibitors

Lysine specific demethylase 1 (LSD1) acts as an epigenetic eraser by specifically demethylating mono- and histone 3 lysine 4 (H3K4) and H3 lysine 9 (H3K9) residues. LSD1 has been pursued as a promising therapeutic target for the treatment of human cancer, and a number of LSD1 inhibitors have been advanced into clinical development. In the present study, we describe our discovery of pyrrolo[2,3-c]pyridines as a new class of highly potent and reversible LSD1 inhibitors, designed on the basis of a previously reported LSD1 inhibitor GSK-354. Among them, 46 shows an IC50 value of 3.1 nM in inhibition of LSD1 enzymatic activity and inhibits cell growth with IC50 values of 0.6 nM in the MV4;11 acute leukemia cell line and 1.1 nM in the H1417 small-cell lung cancer cell line. Compound 46 (LSD1-UM-109) is a novel, highly potent, and reversible LSD1 inhibitor and serves as a promising lead compound for further optimization

Discovery of Pyrrolo[2,3‑<i>c</i>]pyridines as Potent and Reversible LSD1 Inhibitors

Lysine specific demethylase 1 (LSD1) acts as an epigenetic eraser by specifically demethylating mono- and histone 3 lysine 4 (H3K4) and H3 lysine 9 (H3K9) residues. LSD1 has been pursued as a promising therapeutic target for the treatment of human cancer, and a number of LSD1 inhibitors have been advanced into clinical development. In the present study, we describe our discovery of pyrrolo[2,3-c]pyridines as a new class of highly potent and reversible LSD1 inhibitors, designed on the basis of a previously reported LSD1 inhibitor GSK-354. Among them, 46 shows an IC50 value of 3.1 nM in inhibition of LSD1 enzymatic activity and inhibits cell growth with IC50 values of 0.6 nM in the MV4;11 acute leukemia cell line and 1.1 nM in the H1417 small-cell lung cancer cell line. Compound 46 (LSD1-UM-109) is a novel, highly potent, and reversible LSD1 inhibitor and serves as a promising lead compound for further optimization

BM-1197 induces BAX/BAK-dependent apoptosis in MEF/<i>MCL1⁻</i>^/<i>−</i> cells.

<p>(A) <i>MCL1^−/−</i> cells were transfected with Bax- and/or Bak-specific siRNAs for 2 days then treated with BM-1197 for another 2 days. The growth-inhibitory activity of BM-1197 was evaluated by WST assay. Data are mean ± SD, and are representative of at least three independent experiments. (B) <i>MCL1^−/−</i> cells were transfected with mouse Bax- and/or Bak-specific siRNAs for 2 days then treated with BM-1197 (50 nM) for 20 h. Whole cell extracts were analyzed by immunoblotting.</p

BM-1197 induces BAX translocation, cytochrome c release and cell death in H146 cells.

<p>(A) CHAPS lysed whole cell extracts from BM-1197 (100 nM)-treated H146 cells were immunoprecipitated with conformation-sensitive Bax specific antibody 6A7, and immunoprecipitates were analyzed by immunoblotting. (B) H146 cells were treated with BM-1197 for 2 h and cytosolic fraction was isolated for immunoblotting. (C) Cells were treated with BM-1197 (100 nM) or ABT-263 (100 nM) for the indicated time points and whole cell extracts were analyzed by immunoblotting. (D) H146 cells were pretreated with DMSO or 40 µM of Z-VAD for 2 h, then treated with 200 nM of BM-1197 for 4 h for immunoblotting analysis. (E) Cells were treated with BM-1197 for 1 day and cell death was evaluated by trypan blue exclusion assay. Data are expressed as mean ± SD (n = 3).</p

Chemical structure and binding affinities of BM-1197.

<p>The binding affinities of BM-1197 and ABT-263 to Bcl-2 and Bcl-xL determined by fluorescence-polarization binding assay. Data are expressed as means ± SD (n≥3).</p

BM-1197 induces BAX translocation and cytochrome c release in MEF/<i>MCL1</i>^−/− cells.

<p>(A) Cells were treated with BM-1197 (50 nM) or ABT-263 (50 nM) for the indicated time points and whole cell extracts were analyzed by immunoblotting. (B) CHAPS lysed whole cell extracts from BM-1197 (50 nM)-treated <i>MCL1^−/−</i> cells were immunoprecipitated with conformation-sensitive Bax specific antibody 6A7, and immunoprecipitates were analyzed for Bax by immunoblotting. (C) <i>MCL1^−/−</i> cells were treated with BM-1197 (50 nM) for 30 min, then co-incubated with JC-1 (2 µg/ml) for an additional 30 min. Representative images are shown. (D) <i>MCL1^−/−</i> cells were treated with BM-1197 (50 nM) for 1 h and cytosolic fraction was isolated for immunoblotting. (E) MCL1<i>⁻</i>^/<i>−</i> cells were pretreated with DMSO or 40 µM of Z-VAD for 2 h, then treated with 100 nM of BM-1197 for 16 h and stained with Annexin V/PI for flow cytometry analysis.</p

Effects of MCL1 knockdown on BM-1197-induced apoptosis.

<p>(A) Cells were transduced with lentiviral particles containing scrambled (SCR) or MCL1-specific shRNAs for 2 days, then treated with BM-1197 for 2 days. The growth-inhibitory activity of BM-1197 was assessed by WST assay. Data are representative of three independent experiments. (B) Cells were transduced with lentiviral particles containing scrambled (SCR) or MCL1-specific shRNAs for 2 days then treated with BM-1197 (100 nM) for 20 h before harvested for immunoblotting.</p