Discovery of Novel Class I Histone Deacetylase Inhibitors with Promising in Vitro and in Vivo Antitumor Activities

A successful structure-based design of novel cyclic depsipeptides that selectively target class I HDAC isoforms is described. Compound <b>11</b> has an IC₅₀ of 2.78 nM for binding to the HDAC1 protein, and the prodrugs <b>12</b> and <b>13</b> also exhibit promising antiproliferative activities in the nanomolar range against various cancer cell lines. Compounds <b>12</b> and <b>13</b> show more than 20-fold selectivity toward human cancer cells over human normal cells in comparison with romidepsin (FK228), demonstrating low probability of toxic side effects. In addition, compound <b>13</b> exhibits excellent in vivo anticancer activities in a human prostate carcinoma (Du145) xenograft model with no observed toxicity. Thus, prodrug <b>13</b> has therapeutic potential as a new class of anticancer agent for further clinical translation

Discovery of Novel Class I Histone Deacetylase Inhibitors with Promising in Vitro and in Vivo Antitumor Activities

A successful structure-based design of novel cyclic depsipeptides that selectively target class I HDAC isoforms is described. Compound <b>11</b> has an IC₅₀ of 2.78 nM for binding to the HDAC1 protein, and the prodrugs <b>12</b> and <b>13</b> also exhibit promising antiproliferative activities in the nanomolar range against various cancer cell lines. Compounds <b>12</b> and <b>13</b> show more than 20-fold selectivity toward human cancer cells over human normal cells in comparison with romidepsin (FK228), demonstrating low probability of toxic side effects. In addition, compound <b>13</b> exhibits excellent in vivo anticancer activities in a human prostate carcinoma (Du145) xenograft model with no observed toxicity. Thus, prodrug <b>13</b> has therapeutic potential as a new class of anticancer agent for further clinical translation

3‑Substituted‑<i>N</i>‑(4-Hydroxynaphthalen-1-yl)arylsulfonamides as a Novel Class of Selective Mcl‑1 Inhibitors: Structure-Based Design, Synthesis, SAR, and Biological Evaluation

Mcl-1, an antiapoptotic member of the Bcl-2 family of proteins, is a validated and attractive target for cancer therapy. Overexpression of Mcl-1 in many cancers results in disease progression and resistance to current chemotherapeutics. Utilizing high-throughput screening, compound <b>1</b> was identified as a selective Mcl-1 inhibitor and its binding to the BH3 binding groove of Mcl-1 was confirmed by several different, but complementary, biochemical and biophysical assays. Guided by structure-based drug design and supported by NMR experiments, comprehensive SAR studies were undertaken and a potent and selective inhibitor, compound <b>21</b>, was designed which binds to Mcl-1 with a <i>K</i>_i of 180 nM. Biological characterization of <b>21</b> showed that it disrupts the interaction of endogenous Mcl-1 and biotinylated Noxa-BH3 peptide, causes cell death through a Bak/Bax-dependent mechanism, and selectively sensitizes Eμ-myc lymphomas overexpressing Mcl-1, but not Eμ-myc lymphoma cells overexpressing Bcl-2. Treatment of human leukemic cell lines with compound <b>21</b> resulted in cell death through activation of caspase-3 and induction of apoptosis

PDB Ligand Conformational Energies Calculated Quantum-Mechanically

We present here a greatly updated version of an earlier study on the conformational energies of protein–ligand complexes in the Protein Data Bank (PDB) [Nicklaus et al. <i>Bioorg. Med. Chem</i>. <b>1995</b>, <i>3</i>, 411–428], with the goal of improving on all possible aspects such as number and selection of ligand instances, energy calculations performed, and additional analyses conducted. Starting from about 357,000 ligand instances deposited in the 2008 version of the Ligand Expo database of the experimental 3D coordinates of all small-molecule instances in the PDB, we created a “high-quality” subset of ligand instances by various filtering steps including application of crystallographic quality criteria and structural unambiguousness. Submission of 640 Gaussian 03 jobs yielded a set of about 415 successfully concluded runs. We used a stepwise optimization of internal degrees of freedom at the DFT level of theory with the B3LYP/6-31G­(d) basis set and a single-point energy calculation at B3LYP/6-311++G­(3df,2p) after each round of (partial) optimization to separate energy changes due to bond length stretches vs bond angle changes vs torsion changes. Even for the most “conservative” choice of all the possible conformational energiesthe energy difference between the conformation in which all internal degrees of freedom except torsions have been optimized and the fully optimized conformersignificant energy values were found. The range of 0 to ∼25 kcal/mol was populated quite evenly and independently of the crystallographic resolution. A smaller number of “outliers” of yet higher energies were seen only at resolutions above 1.3 Å. The energies showed some correlation with molecular size and flexibility but not with crystallographic quality metrics such as the Cruickshank diffraction-component precision index (DPI) and R_free-R, or with the ligand instance-specific metrics such as occupancy-weighted B-factor (OWAB), real-space R factor (RSR), and real-space correlation coefficient (RSCC). We repeated these calculations with the solvent model IEFPCM, which yielded energy differences that were generally somewhat lower than the corresponding vacuum results but did not produce a qualitatively different picture. Torsional sampling around the crystal conformation at the molecular mechanics level using the MMFF94s force field typically led to an increase in energy