Large-Scale Assessment of Binding Free Energy Calculations in Active Drug Discovery Projects.

Accurate ranking of compounds with regards to their binding affinity to a protein using computational methods is of great interest to pharmaceutical research. Physics-based free energy calculations are regarded as the most rigorous way to estimate binding affinity. In recent years, many retrospective studies carried out both in academia and industry have demonstrated its potential. Here, we present the results of large-scale prospective application of the FEP+ method in active drug discovery projects in an industry setting at Merck KGaA, Darmstadt, Germany. We compare these prospective data to results obtained on a new diverse, public benchmark of eight pharmaceutically relevant targets. Our results offer insights into the challenges faced when using free energy calculations in real-life drug discovery projects and identify limitations that could be tackled by future method development. The new public data set we provide to the community can support further method development and comparative benchmarking of free energy calculations.

Synthesis and SAR development of quinoline analogs as novel P2X7 receptor antagonists.

The P2X7 receptor (P2X7R) plays an important role in diverse conditions associated with tissue damage and inflammation, suggesting that the human P2X7R (hP2X7R) is an attractive therapeutic target. In the present study, the synthesis and structure-activity relationship (SAR) of a novel series of quinoline derivatives as P2X7R antagonists are described herein. These compounds exhibited mechanistic activity (YO PRO) in an engineered HEK293 expressing hP2X7R as well as a functional response (IL-1ß) in human THP-1 (hTHP-1) cellular assays. Compound 19 was identified as the most promising compound in this series with excellent cellular potency, low liver microsomal clearance, good permeability and low efflux ratio. In addition, this compound also displayed good pharmacokinetic properties and acceptable brain permeability (Kp,uu of 0.37).

SAR and evaluation of novel 5H-benzo[c][1,8]naphthyridin-6-one analogs as Aurora kinase inhibitors.

Several potent Aurora kinase inhibitors derived from 5H-benzo[c][1,8]naphthyridin-6-one scaffold were identified. A crystal structure of Aurora kinase A in complex with an initial hit revealed a binding mode of the inhibitor within the ATP binding site and provided insight for structure-guided compound optimization. Subsequent SAR campaign provided a potent and selective pan Aurora inhibitor, which demonstrated potent target modulation and antiproliferative effects in the pancreatic cell line, MIAPaCa-2. Furthermore, this compound inhibited phosphorylation of histone H3 (pHH3) in mouse bone morrow upon oral administration, which is consistent with inhibition of Aurora kinase B activity.

Synthesis and evaluation of a gamma-lactam as a highly selective EP2 and EP4 receptor agonist.

Gamma-lactam analogs (2) of EP(4) receptor agonists were identified by substitution of the pyrazolidinone ring (1) with a pyrrolidinone ring. Several compounds (such as 2a, 2h) with high potency, selectivity and acceptable PK profiles were discovered. These were assessed in animal models of ovulation induction and bronchoconstriction.

Synthesis and evaluation of novel pyrazolidinone analogs of PGE2 as EP2 and EP4 receptors agonists.

Replacement of the hydroxy cyclopentanone ring in PGE(2) with chemically more stable heterocyclic rings and substitution of the unsaturated alpha-alkenyl chain with a metabolically more stable phenethyl chain led to the development of potent and selective analogs of PGE(2). Compound 10f showed the highest potency and selectivity for EP(4) the receptor.

Discovery of novel prostaglandin analogs of PGE2 as potent and selective EP2 and EP4 receptor agonists.

Analogs of PGE(2) with introduction of diene groups at the omega-side chain have been synthesized and evaluated for their binding affinity for EP(2) and EP(4) receptors. An optimized analog (compound 9b) showed high potency and selectivity for the EP(4) receptor over other known receptors.

Design and Development of the First Peptide-Chelating Bisphosphane Bioconjugate from a Novel Functionalized Phosphorus(III) Hydride Synthon.

Remarkable oxidative stability is shown by the carboxylate-functionalized primary bisphosphane 1. Compound 1 can be used in conjugation reactions with biomolecules for functionalization through the COOH group without prior protection of PH2 groups. A novel water-soluble bisphosphane was obtained by reaction of the PH2 groups of 1 with formaldehyde under mild conditions.

Chemistry of Bifunctional Photoprobes. 1. Perfluoroaryl Azido Functionalized Phosphorus Hydrazides as Novel Photoreactive Heterobifunctional Chelating Agents: High Efficiency Nitrene Insertion on Model Solvents and Proteins.

Synthesis and evaluation of a new class of photochemically activated heterobifunctional chelating agents for protein modification is described. Selective functionalization of perfluoroaryl azides by versatile phosphorus hydrazide ligating systems 2 and 3 for the complexation of transition metals and analogous radiometals form the basis for these new agents. The utility of the photogenerated precursors from these bifunctional agents to form covalent attachments is demonstrated through examination of C-H bond insertion on cyclohexane. Representative amide-coupled phosphorus hydrazides 5 and 6 provide >78% insertion of the probe into unactivated C-H bonds of cyclohexane with short photolysis times. Photoconjugation of the photoactivable heterobifunctional chelating agent 6 and its Pd metalated analog 7 with HSA is also evaluated. The uncomplexed chelate appears to add to HSA with high efficiency, consistent with the observed 82% bond insertion into model solvents. Covalent attachment of 7, evaluated through the use of (109)Pd, was estimated to be between 49% and 74% with the uncertainty arising because of prephotolysis association of the (109)Pd complex with HSA. The application of in situ (19)F NMR to distinguish between bond insertion and noninsertion processes is demonstrated. These results suggest that functionalized perfluoroaryl azido phosphorus hydrazides may find utility as heterobifunctional photolabeling agents for attaching radionuclides to proteins and antibodies.

Synthesis and Coordination Chemistry of the First Water-Soluble Dithio-Bis(phosphine) Ligands [(HOH(2)C)(2)P(CH(2))(2)S-X-S(CH(2))(2)P(CH(2)OH)(2)] (X = (CH(2))(3) or C(6)H(4)). X-ray Crystal Structure of [Pd(HOH(2)C)(2)P(CH(2))(2)S(CH(2))(3)S(CH(2))(2)P(CH(2)OH)(2)](Cl)(2)(1).

The thioether-functionalized, water-soluble, bis(phosphines) (HOH(2)C)(2)PCH(2)CH(2)S(CH(2))(3)SCH(2)CH(2)P(CH(2)OH)(2) (9) and C(6)H(4){1,2-SCH(2)CH(2)P(CH(2)OH)(2)}(2) (10) were synthesized in near quantitative yields by the formylation of the appropriate phosphine hydrides in the presence of formaldehyde in ethanol. The reactions of 9 and 10 with Pt(COD)Cl(2) and Pd(C(6)H(5)CN)(2)Cl(2) in biphasic media (aqueous/organic) produced the water-soluble Pt(II) and Pd(II) complexes [Pt(HOH(2)C)(2)P(CH(2))(2)S(CH(2))(3)S(CH(2))(2)P(CH(2)OH)(2)](Cl)(2) (11), [Pd(HOH(2)C)(2)P(CH(2))(2)S(CH(2))(3)S(CH(2))(2)P(CH(2)OH)(2)](Cl)(2) (12), [Pt{(C(6)H(4)){1,2-S(CH(2))(2)P(CH(2)OH)(2)}(2)}](Cl)(2) (13), and [Pd{(C(6)H(4)){1,2-S(CH(2))(2)P(CH(2)OH)(2)}(2)}](Cl)(2) (14) in near quantitative yields. The X-ray crystal structure of 12 confirms a square-planar Pd(II) structure for this new generation of water-soluble transition metal complexes. All of the complexes were characterized by MS, (1)H, (13)C, and (31)P NMR spectroscopy. X-ray data for 12: triclinic, P&onemacr;, a = 9.9761(6) Å, b = 10.2049(7) Å, c = 11.6954(7) Å, alpha = 67.730(10) degrees, beta = 69.943(10) degrees, gamma = 79.828(10) degrees, Z = 2, R = 0.0307 (R(w) = 0.0797).