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Mcl-1 is an anti-apoptotic protein overexpressed in hematological malignancies and several human solid tumors. Small molecule inhibition of Mcl-1 would offer an effective therapy to Mcl-1 mediated resistance. Subsequently, it has been the target of extensive research in the pharmaceutical industry. The discovery of a novel class of Mcl-1 small molecule inhibitors is described beginning with a simple biaryl sulfonamide hit derived from a high through put screen. A medicinal chemistry effort aided by SBDD generated compounds capable of disrupting the Mcl-1/Bid protein-protein interaction in vitro. The crystal structure of the Mcl-1 bound ligand represents a unique binding mode to the BH3 binding pocket where binding affinity is achieved, in part, through a sulfonamide oxygen/Arg263 interaction. The work highlights the some of the key challenges in designing effective protein-protein inhibitors for the Bcl-2 class of proteins.

A protein structure-guided drug design approach was employed to develop small molecule inhibitors of the BET family of bromodomains that were distinct from the known (+)-JQ1 scaffold class. These efforts led to the identification of a series of substituted benzopiperazines with structural features that enable interactions with many of the affinity-driving regions of the bromodomain binding site. Lipophilic efficiency was a guiding principle in improving binding affinity alongside drug-like physicochemical properties that are commensurate with oral bioavailability. Derived from this series was tool compound FT001, which displayed potent biochemical and cellular activity, translating to excellent in vivo activity in a mouse xenograft model (MV-4-11).

The central nervous system (CNS) is the major area that is affected by aging. Alzheimer's disease (AD), Parkinson's disease (PD), brain cancer, and stroke are the CNS diseases that will cost trillions of dollars for their treatment. Achievement of appropriate blood-brain barrier (BBB) penetration is often considered a significant hurdle in the CNS drug discovery process. On the other hand, BBB penetration may be a liability for many of the non-CNS drug targets, and a clear understanding of the physicochemical and structural differences between CNS and non-CNS drugs may assist both research areas. Because of the numerous and challenging issues in CNS drug discovery and the low success rates, pharmaceutical companies are beginning to deprioritize their drug discovery efforts in the CNS arena. Prompted by these challenges and to aid in the design of high-quality, efficacious CNS compounds, we analyzed the physicochemical property and the chemical structural profiles of 317 CNS and 626 non-CNS oral drugs. The conclusions derived provide an ideal property profile for lead selection and the property modification strategy during the lead optimization process. A list of substructural units that may be useful for CNS drug design was also provided here. A classification tree was also developed to differentiate between CNS drugs and non-CNS oral drugs. The combined analysis provided the following guidelines for designing high-quality CNS drugs: (i) topological molecular polar surface area of76 Å(2) (25-60 Å(2)), (ii) at least one (one or two, including one aliphatic amine) nitrogen, (iii) fewer than seven (two to four) linear chains outside of rings, (iv) fewer than three (zero or one) polar hydrogen atoms, (v) volume of 740-970 Å(3), (vi) solvent accessible surface area of 460-580 Å(2), and (vii) positive QikProp parameter CNS. The ranges within parentheses may be used during lead optimization. One violation to this proposed profile may be acceptable. The chemoinformatics approaches for graphically analyzing multiple properties efficiently are presented.

We describe the structure-activity relationship of the C7-position of pyrano[3,4-b]indole-based inhibitors of HCV NS5B polymerase. Further exploration of the allosteric binding site led to the discovery of the significantly more potent compounds 13 and 14.

Elaboration of the SAR around a series of 2,4-diaminopyrimidines led to a number of c-Met inhibitors in which kinase selectivity was modulated by substituents appended on the C4-aminobenzamide ring and the nature of the C2-aminoaryl ring. Further lead optimization of the C2-aminoaryl group led to benzoxazepine analogs whose pharmaceutical properties were modulated by the nature of the substituent on the benzoxazepine nitrogen. Tumor stasis (with partial regressions) were observed when an orally bioavailable analog was evaluated in a GTL-16 tumor xenograft mouse model. Subsequent PK/PD studies suggested that a metabolite contributed to the overall in vivo response.

We describe the structure-activity relationship of the C1-group of pyrano[3,4-b]indole based inhibitors of HCV NS5B polymerase. Further exploration of the allosteric binding site led to the discovery of the significantly more potent compound 12.

The scatter factor/hepatocyte growth factor (HGF)-c-Met axis is involved in the malignant phenotype of various tumor types via activation of a wide range of autocrine and paracrine processes. Autocrine activation of tumor cell c-Met receptors enhances tumor cell proliferation, angiogenesis, invasion/metastasis and resistance to apoptosis and cytotoxic therapies. In addition, tumor and stroma cell-derived HGF functions as a potent angiogenic factor. Therefore, the HGF-c-Met axis is critically involved in multiple facets of normal cellular growth and homeostasis and activated in a dysregulated manner in a variety of cancers. Consequently, inhibiting the HGF-c- Met axis would be anticipated to have potent anti-tumor effects in many cancers through multiple complimentary mechanisms including increased sensitivity to current cytotoxic chemo-and radiotherapies. The acceptance of c-Met as a tractable target for cancer therapy has fostered intensive drug discovery efforts across the pharmaceutical industry. This research has led to 20 published crystal structures (with and without ligands) that revealed two distinct binding modes for ATP-competitive inhibitors: Type I ligands which assumes a U shape geometry through interactions with both hinge and activation loop residue Y1230, and Type II ligands which adopt a more extended orientation, either binding a conventional DFG-out conformation or protein conformations with varying degrees of ‘DFG-out’ character. Nearly a dozen small molecule c-Met inhibitors have entered human clinical trials ranging from Type I inhibitors solely selective for c- Met to Type I inhibitors with broader kinase activities to Type II inhibitors with “spectrum selective” kinase activity. The identification, profiles and properties of these clinical candidates are summarized in this review.

toward kinase inhibitor discovery, with the result that several kinase inhibitors have been approved as drugs since 2001. The commercial success of imatinib (N-(4-methyl-3-(4-(pyridin-3yl)pyrimidin-2-ylamino)phenyl)-4-((4-methylpiperazin-1-l)methyl)benzamide) has provided a clear incentive for the continued pursuit of kinase inhibitor design.

The modern drug discovery process is steadily becoming more information driven. Structural, physicochemical and ADME-Tox property profiles of reference (successful) ligands, along with structural information of their target proteins, have been extremely useful for early-stage drug discovery. Recently, databases of known biologically active ligands (knowledge bases) have become more focused toward different protein-target classes. The number of new chemoinformatics tools used to analyze structures and properties of successful molecules has also increased enormously. Scientists in this area are exploring new physicochemical properties and appropriate drug sets to understand druglike properties. In this review, the various uses of the ligand knowledge bases in the drug discovery process have been critically reviewed.

A range of systems bearing hydroxy functions tethered to the molecular framework gives rise to a family of interesting radical cations, 5 + – 11 + , upon electron transfer to photo-excited cyanoaromatics. Geraniol ( 5 ), nerol ( 6 ), citronellol ( 7 ), chrysanthemol ( 8 ), homochrysanthemol ( 9 ), trans -1- o -hydroxyphenyl-2-phenylcyclopropane ( 10 ), and endo -5-hydroxymethylnorbornene ( 11 ), generate a series of mono-, bi-, or tricyclic ethers via a series of four- to seven-membered transition states. Two of the radical cations, 5 + and 6 + , undergo tandem cyclizations where 1,5- and/or 1,6-C–C cyclizations precede nucleophilic capture.

The syn dimer of cyclobuta- diene (tricyclo(4.2.0.0 2,5 )octa-3,7-diene, TOD) is subjected to ionization under different conditions and the resulting species are probed by optical and ESR spectroscopy. By means of quantum chemical modelling of the potential energy surfaces and the optical spectra, it is possible to assign the different products that arise spontaneously after ionization or after subsequent warming or illumination of the samples. Based on these findings, we propose a mechanistic scheme which involves a partitioning of the incipient radical cation of TOD between two electronic states. These two states engage in (near) activation- less decay to the more stable valence isomers, cyclooctatetraene (COT .a ) and a bis-cyclobutenylium radical cation BCB .a . The latter product undergoes further rearrangement, first to tetracy- clo(4.2.0.0 2,4 .0 3,5 )oct-7-ene (TCO .a ) and eventually to bicyclo(4.2.0)octa-2,4,7-tri- ene (BOT .a ) which can also be gener- ated photochemically from BCB .a or TCO .a . The surprising departure of syn- TOD .a from the least-motion reaction path leading to BOT .a can be traced to

Incorporation of trans-1,2-diphenylcyclopropane (1) and its 3,3-D2-isotopomer into the channels of a redox-active pentasil zeolite (Na-ZSM-5) resulted in the formation of exo,exo-1,3-diphenylallyl radical (2•) and its 2-D1 isotopomer, respectively. This conversion requires oxidation, ring opening, and deprotonation, in an unspecified sequence. The allyl radical 2• is also formed upon incorporation of trans-1,3-diphenylpropene (3). A comparison with the solution photochemistry, in the presence or absence of added base, shows the conversion of 1 into 2• to be a zeolite-specific reaction. Incorporation of arylcyclopropanes 9 (R = H, OCH3) into ZSM-5 generated trans-propenylbenzene radical cations 10•+ (R = H, OCH3); the 2,2-D2 isotopomer of 9 (R = OCH3) gave rise to three different isotopomers of 10•+ (R = OCH3).

The structure of phenylcyclopropane radical cation (1•+, R = H) is derived from CIDNP effects observed during the electron transfer reaction of 1 with chloranil. This species is an example of an elusive structure type. The secondary cyclopropane protons show significantly divergent hyperfine coupling constants due to an unprecedented stereoelectronic effect. Incorporation into a redox-active pentasil zeolite (Na−ZSM-5) converts 1 or its p-methoxy derivative (1, R = OCH3) to trans-propenylarene radical cations (2•+, R = H, OCH3).

The electron-transfer photochemistry of homochrysanthemol, 1, resulted exclusively in intramolecular "substitution" at the quaternary cyclopropane carbon, generating the five-membered cyclic ethers, 2 and 4. The alternative "addition" to the terminal carbon of the double bond, which would result in seven-membered cyclic ethers, 3 and 5, was not observed. Apparently, the five-membered transition state leading to 2 and 4 is significantly favored over the seven-membered one required for formation of 3 and 5. These results stand in interesting contrast to the previously established reaction pattern of chrysanthemol, 8, which is captured exclusively at the terminal vinyl carbon. The divergent regiochemistry of 1(*)(+) and 8(*)(+) (even though the tethers between vinylcyclopropane and alcohol functions differ only by a single CH(2) group) elucidates the principles governing the course of nucleophilic capture in radical cations.

The electron-transfer photochemistry of vinylcyclopropane (1) generates three ring-opened products, 2−4, each bearing a methoxy as well as a 4-cyanophenyl group. The products are ascribed to nucleophilic attack of methanol on the radical cation, 1•+. The attack is regioselective but not regiospecific; attack at the secondary cyclopropane carbons, leading to 2 and trans-3, is preferred; attack at the terminal vinylic carbon, yielding trans-4, occurs to a lesser extent. The potential surface of 1•+ was probed by ab initio calculations; 1•+ has two minima, anti- and syn-1•+; both have Cs symmetry and belong to the unusual structure type with two lengthened cyclopropane bonds. The calculations are in general agreement with the observed reaction pattern.

The radical cation of tricyclo[4.3.1.01,6]deca-2,4-diene (3) can be generated by electron transfer to 1,4-dicyanobenzene (DCB) in acetonitrile/methanol; the species is captured by regiospecific nucleophilic attack of methanol in the 2- (and 5-) position. On the other hand, the reaction shows little stereochemical preference. The resulting allylic radical reacts by aromatic substitution on the radical anion of DCB, the 3-position serving as the principal site of coupling. Remarkably, the cyclopropane function of 3•+ is not a target of nucleophilic attack, even though the secondary cyclopropane carbon has spin and charge density. The observed reaction is compatible with a theoretical model proposed by Shaik and Pross, which correlates radical cation reactivity with the spin density of the corresponding triplet state. The capture of 3•+ occurs in the position where both SOMO and LUMO have significant orbital coefficients.

The radical cations of three terpenes, sabinene, 1, and α-, 2, and β-thujene, 3, containing vinylcyclopropane functions held rigidly in either an anti- or syn-orientation, have been elucidated by CIDNP studies. The structures assigned to these species are discussed in view of their reactivities and compared with three simplified radical cations, 2-methylenebicyclo[3.1.0]hexane, 4, bicyclo[3.1.0]hex-2-ene, 5, and 5-methylbicyclo[3.1.0]hex-2-ene, 6, calculated by ab initio molecular orbital methods. © 1997 Elsevier Science Ltd.

Organic radical cations, generated by electron transfer from bi-or trifunctional donor terpenes to photo-excited acceptors, undergo a variety of intra- and intermolecular reactions, including nucleophilic capture and sigmatropic shifts, deprotonation, intramolecular nucleophilic capture, and various cyclizations.

The electron transfer photochemistry of optically pure (1R,3S)-(+)-cis-chrysanthemol (cis-2) results in the formation of (R)-5-(1-(p-cyanophenyl)-1-methylethyl)-2,2-dimethyl oxacyclohex-3-ene (4) w...

Members of the Bromodomain and Extra-Terminal (BET) family of bromodomain-containing proteins (BRD2, BRD3, BRD4, and BRDT) bind to acetylated lysine residues on histone tails and act as epigenetic readers to regulate chromatin structure and gene expression. In particular, BET family member BRD4 has been shown to positively regulate the expression of MYC and other critical cancer-associated genes through the localization of BRD4 to super-enhancer regulatory elements. Results from preclinical studies conducted using the small molecule tool BET inhibitor (+)-JQ1, and emerging data from clinical trials of BET inhibitors in leukemia and lymphoma patients, have provided support for the therapeutic potential of BET inhibitors in hematologic malignancies. A protein structure-guided drug design approach was employed to explore small molecule acetyl lysine mimetics and led to the identification of the BET inhibitor FT-1101, which is structurally unrelated to reported clinical-stage BET inhibitors in the (+)-JQ1 class. In biochemical binding assays, FT-1101 displayed equipotent inhibition of binding of both bromodomains in all four BET family members to a known bromodomain ligand (Kd ≤ 20 nM). In vitro, FT-1101 displayed potent anti-proliferative activity across a broad panel of human leukemia, lymphoma, and multiple myeloma cell lines, with 66 out of 123 cell lines having IC50 values < 500 nM. For the MV-4-11 acute myeloid leukemia cell line, the anti-proliferative activity of FT-1101 (IC50 = 40 nM) correlated with down-regulation of MYC gene and protein expression, suggesting that its anti-proliferative activity was at least in part due to suppression of MYC. Additionally, genome-wide mapping of BRD4 super-enhancer binding sites in MV-4-11 cells by ChIP-sequencing identified several potential pharmacodynamic biomarkers outside of the MYC signaling network. In vivo, in the MV-4-11 xenograft model, oral treatment with FT-1101 at its maximum tolerated dose resulted in significant tumor growth inhibition, including tumor regressions, on schedules ranging from once daily to once weekly, and similar activity was also observed in the THP-1 AML xenograft model. Superior in vivo efficacy in the MV-4-11 model was observed for FT-1101 relative to BET inhibitors of the (+)-JQ1 class. In vivo efficacy was associated with prolonged drug exposure and a >75% decrease in MYC gene expression in tumors that was sustained for at least 12 hours. FT-1101 also crossed the blood-brain barrier in mice, achieving a pharmacologically relevant free drug concentration in the brain. The promising preclinical profile of FT-1101 warranted its rapid progression into human clinical trials, and a Phase 1 study in patients with relapsed refractory acute leukemia or high-risk myelodysplastic syndrome is currently underway. Disclosures No relevant conflicts of interest to declare.

The Ras/RAF/MEK/ERK mitogen-activated protein kinase (MAPK) signaling pathway plays a central role in the regulation of cell growth, differentiation, and survival. Expression of mutant BRAF(V600E) results in constitutive activation of the MAPK pathway, which can lead to uncontrolled cellular growth. Herein, we describe an SAR optimization campaign around a series of quinazoline derived BRAF(V600E) inhibitors. In particular, the bioisosteric replacement of a metabolically sensitive tert-butyl group with fluorinated alkyl moieties is described. This effort led directly to the identification of a clinical candidate, compound 40 (CEP-32496). Compound 40 exhibits high potency against several BRAF(V600E)-dependent cell lines and selective cytotoxicity for tumor cell lines expressing mutant BRAF(V600E) versus those containing wild-type BRAF. Compound 40 also exhibits an excellent PK profile across multiple preclinical species. In addition, significant oral efficacy was observed in a 14-day BRAF(V600E)-dependent human Colo-205 tumor xenograft mouse model, upon dosing at 30 and 100 mg/kg BID.

Organic radical cations, generated by electron transfer from bi-or trifunctional donor terpenes to photo-excited acceptors, undergo a variety of intra- and intermolecular reactions, including nucleophilic capture and sigmatropic shifts, deprotonation, intramolecular nucleophilic capture, and various cyclizations.

toward kinase inhibitor discovery, with the result that several kinase inhibitors have been approved as drugs since 2001. The commercial success of imatinib (N-(4-methyl-3-(4-(pyridin-3yl)pyrimidin-2-ylamino)phenyl)-4-((4-methylpiperazin-1-l)methyl)benzamide) has provided a clear incentive for the continued pursuit of kinase inhibitor design.

Rhinoviruses are the most common infectious agents of humans. They are the principal etiologic agents of afebrile viral upper-respiratory-tract infections (the common cold). Human rhinoviruses (HRVs) comprise a genus within the familyPicornaviridae. There are >100 serotypically distinct members of this genus. In order to better understand their phylogenetic relationship, the nucleotide sequence for the major surface protein of the virus capsid, VP1, was determined for all known HRV serotypes and one untyped isolate (HRV-Hanks). Phylogenetic analysis of deduced amino acid sequence data support previous studies subdividing the genus into two species containing all but one HRV serotype (HRV-87). Seventy-five HRV serotypes and HRV-Hanks belong to species HRV-A, and twenty-five HRV serotypes belong to species HRV-B. Located within VP1 is a hydrophobic pocket into which small-molecule antiviral compounds such as pleconaril bind and inhibit functions associated with the virus capsid. Analyses of the amino acids that constitute this pocket indicate that the sequence correlates strongly with virus susceptibility to pleconaril inhibition. Further, amino acid changes observed in reduced susceptibility variant viruses recovered from patients enrolled in clinical trials with pleconaril were distinct from those that confer natural phenotypic resistance to the drug. These observations suggest that it is possible to differentiate rhinoviruses naturally resistant to capsid function inhibitors from those that emerge from susceptible virus populations as a result of antiviral drug selection pressure based on sequence analysis of the drug-binding pocket.