Drug-target residence time (τ), one of the main determinants of drug efficacy, remains highly challenging to predict computationally and, therefore, is usually not considered in the early stages of drug design. Here, we present an efficient computational method, τ-random acceleration molecular dynamics (τRAMD), for the ranking of drug candidates by their residence time and obtaining insights into ligand-target dissociation mechanisms. We assessed τRAMD on a data set of 70 diverse drug-like ligands of the N-terminal domain of HSP90α, a pharmaceutically important target with a highly flexible binding site, obtaining computed relative residence times with an accuracy of about 2.3τ for 78% of the compounds and less than 2.0τ within congeneric series. Analysis of dissociation trajectories reveals features that affect ligand unbinding rates, including transient polar interactions and steric hindrance. These results suggest that τRAMD will be widely applicable as a computationally efficient aid to improving drug residence times during lead optimization.

We here report on non-equilibrium targeted Molecular Dynamics simulations as tool for the estimation of protein-ligand unbinding kinetics. With this method, we furthermore investigate the molecular basis determining unbinding rates, correlating simulations with experimental data from SPR kinetics measurements and X-ray crystallography on two small molecule compound libraries bound to the N-terminal domain of the chaperone Hsp90. Within the investigated libraries, we find ligand conformational changes and protein-ligand nonbonded interactions as discriminators for unbinding rates. Ligands with flexible chemical scaffold may remain longer at the protein target if they need to pass through extended conformations upon unbinding, or if they exhibit strong electrostatic and/or van der Waals interactions with the target. Ligands with rigid chemical scaffold can exhibit longer residence times if they need to perform any kind of conformational change for unbinding, while electrostatic interactions with the protein can facilitate unbinding. Our resultsshow that understanding the unbinding pathway and the protein-ligand interactions along this path is crucial for the prediction of small molecule ligands with defined unbinding kinetics. Supporting InformationFour supporting tables, nine supporting figures and additional references (PDF) SMILES annotations (CSV) Accession CodesThe crystallographic coordinates of novel compounds are deposited in the Protein Data Bank under the accession codes 5LRL (2d) and 5LO1 (2j). Authors will release the atomic coordinates and experimental data upon article publication.

UMP kinase catalyses the phosphorylation of UMP by ATP to yield UDP and ADP. In prokaryotes, the reaction is carried out by a hexameric enzyme, activated by GTP and inhibited by UTP. In the present study, Streptococcus pneumoniae UMP kinase was studied as a target for antibacterial research and its interest was confirmed by the demonstration of the essentiality of the gene for cell growth. In the presence of MnCl 2 or MgCl 2 , the saturation kinetics of recombinant purified UMP kinase was hyperbolic for UMP (K m = 0.1 mM) and sigmoidal for ATP (the substrate concentration at half-saturation S 0.5 = 9.4 + − 0.7 mM and n = 1.9 + − 0.1 in the presence of MgCl 2 ). GTP increased the affinity for ATP and decreased the Hill coefficient (n). UTP decreased the affinity for ATP and only slightly increased the Hill coefficient.The k cat (175 + − 13 s −1 in the presence of MgCl 2 ) was not affected by the addition of GTP or UTP, whose binding site was shown to be different from the active site. The hydrodynamic radius of the protein similarly decreased in the presence of ATP or GTP. There was a shift in the pH dependence of the activity when the ATP concentration was switched from low to high. These results support the hypothesis of an allosteric transition from a conformation with low affinity for ATP to a form with high affinity, which would be induced by the presence of ATP or GTP.

Several extracts from Epilobium parviflorum, a plant used in Central Europe for the treatment of prostate disorders, were evaluated in a biochemical assay with 5-alpha-reductase. The aqueous extract displaying inhibition of the enzyme was analyzed, the fraction responsible for this activity was purified, and the active compound identified as a macrocyclic tannin, oenothein B (1).

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The HGF/MET pathway is frequently activated in a variety of cancer types. Several selective small molecule inhibitors of the MET kinase are currently in clinical evaluation, in particular for NSCLC, liver, and gastric cancer patients. We report herein the discovery of a series of triazolopyridazines that are selective inhibitors of wild-type (WT) MET kinase and several clinically relevant mutants. We provide insight into their mode of binding and report unprecedented crystal structures of the Y1230H variant. A multiparametric chemical optimization approach allowed the identification of compound 12 (SAR125844) as a development candidate. In this chemical series, absence of CYP3A4 inhibition was obtained at the expense of satisfactory oral absorption. Compound 12, a promising parenteral agent for the treatment of MET-dependent cancers, promoted sustained target engagement at tolerated doses in a human xenograft tumor model. Preclinical pharmacokinetics conducted in several species were predictive for the observed pharmacokinetic behavior of 12 in cancer patients.

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We have identified two spiro-oxindole-based modulators -compounds A and B- of the MDM2-p53 protein-protein interaction that display suitable pharmacological properties for human clinical testing (1) and a high affinity to the N-terminal domain of human MDM2. For instance, in fluorescence polarization (FP) displacement assay using N-terminal domain of human MDM2 and a p53-based peptide (2), compounds A and B display Ki values of 5 and 5,9 nM, respectively, while Nutlin 3 shows a Ki value of 80,3 nM. The superior binding activity of the spiro-oxindole derivatives was confirmed by isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR). Having established their binding activities for the human target and in order to properly address potential on-target adverse effects in preclinical settings, we cloned MDM2 N-terminal domains of monkey, dog, rat and mouse. Sequencing analysis showed that, while the rat data from NCBI Reference Sequence database (3) is inaccurate, there is a high identity between human and monkey sequences. FP displacement assays were developed using MDM2 N-terminal domains of dog, rat and mouse which matched above-mentioned N-terminal domain of human MDM2. Ki value determinations revealed that the binding affinities of compounds A and B but not of Nutlin 3 significantly shifted to higher values by using both rodent MDM2 while, by using canine MDM2, they were similar to the ones determined with human MDM2. These findings were unexpected since MDM2 N-terminal domain sequences are conserved between rodent and non-rodent species. Cellular p53 activation data obtained with Nutlin 3, compounds A and B in a panel of monkey, dog, rat and mouse cell lines were consistent with the biochemical findings and confirmed that compounds A and B are modest p53 activators in rodent cells. In line with the results obtained in cellular settings, acute in vivo induction of p53-dependent transactivation by compounds A and B was significantly weaker in mouse spleen than in human xenografted tumor samples. In conclusion, these data demonstrate that compounds A and B both display high affinity against human MDM2 and that modulators of the MDM2-p53 protein-protein interaction can exhibit inter-species selectivity. These findings should be taken into consideration in the assessment of the tolerabily of MDM2-p53 antagonists in preclinical settings. 1. Wang S. et al., AACR, Orlando FL, 2011, Abstract LB-204 2. Ding K. et al, J. Am. Chem. Soc. 127, 10130-1, 2005. 3. http://www.ncbi.nlm.nih.gov/protein/NP_001101569.1 Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4648. doi:1538-7445.AM2012-4648