Discovery and SAR of Novel 2,3-Dihydroimidazo[1,2-c]quinazoline PI3K Inhibitors: Identification of Copanlisib (BAY 80-6946)

The phosphoinositide 3‐kinase (PI3K) pathway is aberrantly activated in many disease states, including tumor cells, either by growth factor receptor tyrosine kinases or by the genetic mutation and amplification of key pathway components. A variety of PI3K isoforms play differential roles in cancers. As such, the development of PI3K inhibitors from novel compound classes should lead to differential pharmacological and pharmacokinetic profiles and allow exploration in various indications, combinations, and dosing regimens. A screening effort aimed at the identification of PI3Kγ inhibitors for the treatment of inflammatory diseases led to the discovery of the novel 2,3‐dihydroimidazo[1,2‐c]quinazoline class of PI3K inhibitors. A subsequent lead optimization program targeting cancer therapy focused on inhibition of PI3Kα and PI3Kβ. Herein, initial structure–activity relationship findings for this class and the optimization that led to the identification of copanlisib (BAY 80‐6946) as a clinical candidate for the treatment of solid and hematological tumors are described.

Antibacterial inhibitors of Gram-positive thymidylate kinase: structure-activity relationships and chiral preference of a new hydrophobic binding region

Thymidylate kinase (TMK), an essential enzyme in bacterial DNA biosynthesis, is an attractive therapeutic target for the development of novel antibacterial agents, and we continue to explore TMK inhibitors with improved potency, protein binding, and pharmacokinetic potential. A structure-guided design approach was employed to exploit a previously unexplored region in Staphylococcus aureus TMK via novel interactions. These efforts produced compound 39, with 3 nM IC50 against S. aureus TMK and 2 μg/mL MIC against methicillin-resistant S. aureus (MRSA). This compound exhibits a striking inverted chiral preference for binding relative to earlier compounds and also has improved physical properties and pharmacokinetics over previously published compounds. An example of this new series was efficacious in a murine S. aureus infection model, suggesting that compounds like 39 are options for further work toward a new Gram-positive antibiotic by maintaining a balance of microbiological potency, low clearance, and low protein binding that can result in lower efficacious doses.

In vivo validation of thymidylate kinase (TMK) with a rationally designed, selective antibacterial compound

There is an urgent need for new antibacterials that pinpoint novel targets and thereby avoid existing resistance mechanisms. We have created novel synthetic antibacterials through structure-based drug design that specifically target bacterial thymidylate kinase (TMK), a nucleotide kinase essential in the DNA synthesis pathway. A high-resolution structure shows compound TK-666 binding partly in the thymidine monophosphate substrate site, but also forming new induced-fit interactions that give picomolar affinity. TK-666 has potent, broad-spectrum Gram-positive microbiological activity (including activity against methicillin-resistant Staphylococcus aureus and vancomycin-resistant Enterococcus), bactericidal action with rapid killing kinetics, excellent target selectivity over the human ortholog, and low resistance rates. We demonstrate in vivo efficacy against S. aureus in a murine infected-thigh model. This work presents the first validation of TMK as a compelling antibacterial target and provides a rationale for pursuing novel clinical candidates for treating Gram-positive infections through TMK.

On the total synthesis and determination of the absolute configuration of rishirilide B: exploitation of subtle effects to control the sense of cycloaddition of o-quinodimethides

The total synthesis of racemic rishirilide B has been accomplished. The synthesis serves to define the relative relationships of its stereogenic centers. Also, starting with readily available chiral pool, ent-rishirilide B was synthesized, thereby demonstrating that natural configuration of rishirilide B. The defining step in our total synthesis is the facile cycloreversion of the bis(siloxy)benzocyclobutane and the intermolecular o-quinodimethide Diels-Alder cycloaddition. We believe that the tight regiochemical guidance in this step arises from a meshing of the electron-donating effects of the symmetry-perturbing aromatic OTBS group of the o-quinodimethide diene with the reactivity differential of the dienophile (enedione), modulated by the hydroxyl group at the alpha-position. The validity of the hypothesis of hydroxy-directed activation of its vicinal ketone function in the context of the enedione dienophile warrants further study. This type of activation may find broader applications in distinguishing reactivity profiles of key closely related functional groups in organic substrates.

The origin of endo stereoselectivity in the hetero-Diels-Alder reactions of aldehydes with ortho-xylylenes: CH-pi, pi-pi, and steric effects on stereoselectivity

Theoretical studies of stereoselectivity have been carried out with B3LYP and MP2 calculations. The high endo selectivity of hetero-Diels-Alder reactions of ortho-xylylenes with acetaldehydes is shown to result from attractive CH-pi interactions between alkyl groups of the aldehyde and the aromatic ring in the transition states of the reaction. For the hetero-Diels-Alder reactions of ortho-xylylenes with benzaldehyde, the stereoselectivity is shown to be mainly governed by the attractive pi-pi interactions between the phenyl rings of the benzaldehyde and the ortho-xylylene. MP2 calculations are necessary to reproduce the stabilizing dispersion interactions.