A series of 138 nonchiral 3-amidinobenzyl-1H-indole-2-carboxamides and analogues as inhibitors of the blood coagulation enzyme factor Xa (fXa) were designed, synthesized, and investigated by X-ray structure analysis and 3D quantitative structure-activity relationship (QSAR) studies (CoMFA, CoMSIA) in order to identify important protein-ligand interactions responsible for biological affinity and selectivity. Several compounds from this series are highly potent and selective inhibitors of this important enzyme linking extrinsic and intrinsic coagulation pathways. To rationalize biological affinity and to provide guidelines for further design, all compounds were docked into the factor Xa binding site. Those docking studies were based on X-ray structures of factor Xa in complex with literature-known inhibitors. It was possible to validate those binding modes by four X-ray crystal structures of representative ligands in factor Xa, while one ligand was additionally crystallized in trypsin to rationalize requirements for selective factor Xa inhibition. The 3D-QSAR models based on a superposition rule derived from these docking studies were validated using conventional and cross-validated r(2) values using the leave-one-out method and repeated analyses using two randomly chosen cross-validation groups plus randomization of biological activities. This led to consistent and highly predictive 3D-QSAR models with good correlation coefficients for both CoMFA and CoMSIA, which were found to correspond to experimentally determined factor Xa binding site topology in terms of steric, electrostatic, and hydrophobic complementarity. Subsets selected as smaller training sets using 2D fingerprints and maximum dissimilarity methods resulted in 3D-QSAR models with remarkable correlation coefficients and a high predictive power. The final quantitative SAR information agrees with all experimental data for the binding topology and thus provides reasonable activity predictions for novel factor Xa inhibitors.

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Using a focused screening approach, acyl ureas have been discovered as a new class of inhibitors of human liver glycogen phosphorylase (hlGPa). The X-ray structure of screening hit 1 (IC50 = 2 microM) in a complex with rabbit muscle glycogen phosphorylase b reveals that 1 binds at the AMP site, the main allosteric effector site of the dimeric enzyme. A first cycle of chemical optimization supported by X-ray structural data yielded derivative 21, which inhibited hlGPa with an IC50 of 23 +/- 1 nM, but showed only moderate cellular activity in isolated rat hepatocytes (IC50 = 6.2 microM). Further optimization was guided by (i) a 3D pharmacophore model that was derived from a training set of 24 compounds and revealed the key chemical features for the biological activity and (ii) the 1.9 angstroms crystal structure of 21 in complex with hlGPa. A second set of compounds was synthesized and led to 42 with improved cellular activity (hlGPa IC50 = 53 +/- 1 nM; hepatocyte IC50 = 380 nM). Administration of 42 to anaesthetized Wistar rats caused a significant reduction of the glucagon-induced hyperglycemic peak. These findings are consistent with the inhibition of hepatic glycogenolysis and support the use of acyl ureas for the treatment of type 2 diabetes.

More than 50 % of all drug targets are membrane proteins. [1] Recent progress in membrane protein crystallography has made a few of these targets amenable to established structurebased design methods.[2] However, crystallization of a membrane protein target remains a challenge, and medicinal chemists must rely on ligand-based design approaches for the targets that do not crystallize. These approaches can benefit from the knowledge of the bioactive conformation of the ligand conformation and the relative orientation of different chemotypes in the receptor binding site (cross-chemotype alignments). The generation of hypotheses for the bioactive conformation and cross-chemotype alignments depend on the availability of sufficient data on ligand structure-activity relationships (SARs). Herein, we demonstrate that these insights can be derived in the absence of protein-ligand crystal structures by straightforward ligand-based approaches relying on NMR spectroscopy. We show that a qualitative and fast analysis of INPHARMA NMR data [3,4] can be used within the timelines of the drug-discovery process without extended modeling and detailed data interpretation. We performed this study using intact biological membranes rather than reconstituted proteins [5,6] to eliminate solubilization-related artefacts, to expand the applicability to receptors that do not tolerate solubilization, and to significantly enhance the speed of the method. Here we demonstrate that a straightforward ligand-based NMR approach can be used to establish a nonradioactive binding assay for a Gprotein-coupled receptor (GPCR) and to give access to the relative orientation of multiple chemotypes supporting ligand-based drug design.

Glycogen phosphorylase (GP) is a validated target for the treatment of type 2 diabetes. Here we describe highly potent GP inhibitors, AVE5688, AVE2865, and AVE9423. The first two compounds are optimized members of the acyl urea series. The latter represents a novel quinolone class of GP inhibitors, which is introduced in this study. In the enzyme assay, both inhibitor types compete with the physiological activator AMP and act synergistically with glucose. Isothermal titration calorimetry (ITC) shows that the compounds strongly bind to nonphosphorylated, inactive GP (GPb). Binding to phosphorylated, active GP (GPa) is substantially weaker, and the thermodynamic profile reflects a coupled transition to the inactive (tense) conformation. Crystal structures confirm that the three inhibitors bind to the AMP site of tense state GP. These data provide the first direct evidence that acyl urea and quinolone compounds are allosteric inhibitors that selectively bind to and stabilize the inactive conformation of the enzyme. Furthermore, ITC reveals markedly different thermodynamic contributions to inhibitor potency that can be related to the binding modes observed in the cocrystal structures. For AVE5688, which occupies only the lower part of the bifurcated AMP site, binding to GPb (Kd = 170 nM) is exclusively enthalpic (Delta H = -9.0 kcal/mol, TDelta S = 0.3 kcal/mol). The inhibitors AVE2865 (Kd = 9 nM, Delta H = -6.8 kcal/mol, TDelta S = 4.2 kcal/mol) and AVE9423 (Kd = 24 nM, Delta H = -5.9 kcal/mol, TDelta S = 4.6 kcal/mol) fully exploit the volume of the binding pocket. Their pronounced binding entropy can be attributed to the extensive displacement of solvent molecules as well as to ionic interactions with the phosphate recognition site.

Acyl ureas were discovered as a novel class of inhibitors for glycogen phosphorylase, a molecular target to control hyperglycemia in type 2 diabetics. This series is exemplified by 6-{2,6-Dichloro-4-[3-(2-chloro-benzoyl)-ureido]-phenoxy}-hexanoic acid, which inhibits human liver glycogen phosphorylase a with an IC 50 of 2.0 mM. Here we analyze four crystal structures of acyl urea derivatives in complex with rabbit muscle glycogen phosphorylase b to elucidate the mechanism of inhibition of these inhibitors. The structures were determined and refined to 2.26Å resolution and demonstrate that the inhibitors bind at the allosteric activator site, where the physiological activator AMP binds. Acyl ureas induce conformational changes in the vicinity of the allosteric site. Our findings suggest that acyl ureas inhibit glycogen phosphorylase by direct inhibition of AMP binding and by indirect inhibition of substrate binding through stabilization of the T 0 state.

More than 50 % of all drug targets are membrane proteins. [1] Recent progress in membrane protein crystallography has made a few of these targets amenable to established structurebased design methods.[2] However, crystallization of a membrane protein target remains a challenge, and medicinal chemists must rely on ligand-based design approaches for the targets that do not crystallize. These approaches can benefit from the knowledge of the bioactive conformation of the ligand conformation and the relative orientation of different chemotypes in the receptor binding site (cross-chemotype alignments). The generation of hypotheses for the bioactive conformation and cross-chemotype alignments depend on the availability of sufficient data on ligand structure-activity relationships (SARs). Herein, we demonstrate that these insights can be derived in the absence of protein-ligand crystal structures by straightforward ligand-based approaches relying on NMR spectroscopy. We show that a qualitative and fast analysis of INPHARMA NMR data [3,4] can be used within the timelines of the drug-discovery process without extended modeling and detailed data interpretation. We performed this study using intact biological membranes rather than reconstituted proteins [5,6] to eliminate solubilization-related artefacts, to expand the applicability to receptors that do not tolerate solubilization, and to significantly enhance the speed of the method. Here we demonstrate that a straightforward ligand-based NMR approach can be used to establish a nonradioactive binding assay for a Gprotein-coupled receptor (GPCR) and to give access to the relative orientation of multiple chemotypes supporting ligand-based drug design.

The therapeutic success of peptidic GLP-1 receptor agonists for treatment of type 2 diabetes mellitus (T2DM) motivated our search for orally bioavailable small molecules that can activate the GLP-1 receptor (GLP-1R) as a well-validated target for T2DM. Here, the discovery and characterization of a potent and selective positive allosteric modulator (PAM) for GLP-1R based on a 3,4,5,6-tetrahydro-1H-1,5-epiminoazocino­[4,5-b]­indole scaffold is reported. Optimization of this series from HTS was supported by a GLP-1R ligand binding model. Biological in vitro testing revealed favorable ADME and pharmacological profiles for the best compound 19. Characterization by in vivo pharmacokinetic and pharmacological studies demonstrated that 19 activates GLP-1R as positive allosteric modulator (PAM) in the presence of the much less active endogenous degradation product GLP1(9–36)­NH2 of the potent endogenous ligand GLP-1(7–36)­NH2. While these data suggest the potential of small molecule GLP-1R PAMs for T2DM treatment, further optimization is still required towards a clinical candidate.