Frontiers in Medicinal Chemistry 2015: Meet the Experts of MedChem near the Cradle of Medicinal and Pharmaceutical Chemistry.

Pioneering inspiration: Right next to the former laboratories of Johannes Hartmann, the first so-called "Professor of Chymiatrie", the 2015 Frontiers in Medicinal Chemistry meeting was held last March at Philipps University in Marburg, Germany. Herein we give readers an idea of what it was like to attend the conference, which was organized jointly by the DPhG, GDCh, and SCS. Along with the lectures, we also describe the poster sessions, social program, and awards.

N-acyl derivatives of 4-phenoxyaniline as neuroprotective agents.

Neuronal cell death is the main cause behind the progressive loss of brain function in age-related neurodegenerative disorders such as Alzheimer's and Parkinson's diseases. Despite the differing etiologies of these neurological diseases, the underlying neuronal damage is triggered by common mechanisms such as oxidative stress, impaired calcium homeostasis, and disrupted mitochondrial integrity and function. In particular, mitochondrial fragmentation, mitochondrial membrane permeability, and the release of death-promoting factors into the cytosol have been revealed as the "point of no return" in programmed cell death in neurons. Recent studies revealed a pivotal role for the pro-apoptotic Bcl-2-family protein Bid in models of neuronal cell death, which confirmed Bid as a potential drug target. Herein, we present N-acyl-substituted derivatives of 4-phenoxyaniline that were screened for their potential to attenuate Bid-mediated neurotoxicity. These compounds provided significant protection against glutamate- and Bid-induced toxicity in cultured neurons. Substitution of the amino group in the 4-phenoxyaniline scaffold with 4-piperidine carboxylic acid and N-hydroxyethyl-4-piperidine carboxylic acid yielded compounds that displayed significant neuroprotective activity at concentrations as low as 1 µM. Furthermore, findings of a tBid-overexpression assay and real-time measurements of cell impedance support the hypothesis that these compounds indeed address the Bid protein.

Novel N-phenyl-substituted thiazolidinediones protect neural cells against glutamate- and tBid-induced toxicity.

Mitochondrial demise is a key feature of progressive neuronal death contributing to acute and chronic neurological disorders. Recent studies identified a pivotal role for the BH3-only protein B-cell lymphoma-2 interacting domain death antagonist (Bid) for such mitochondrial damage and delayed neuronal death after oxygen-glucose deprivation, glutamate-induced excitotoxicity, or oxidative stress in vitro and after cerebral ischemia in vivo. Therefore, we developed new N-phenyl-substituted thiazolidine-2,4-dione derivatives as potent inhibitors of Bid-dependent neurotoxicity. The new compounds 6, 7, and 16 were identified as highly protective by extensive screening in a model of glutamate toxicity in immortalized mouse hippocampal neurons (HT-22 cells). These compounds significantly prevent truncated Bid-induced toxicity in the neuronal cell line, providing strong evidence that inhibition of Bid was the underlying mechanism of the observed protective effects. Furthermore, Bid-dependent hallmarks of mitochondrial dysfunction, such as loss of mitochondrial membrane potential, ATP depletion, as well as impairments in mitochondrial respiration, are significantly prevented by compounds 6, 7, and 16. Therefore, the present study identifies a class of N-phenyl thiazolidinediones as novel Bid-inhibiting neuroprotective agents that provide promising therapeutic perspectives for neurodegenerative diseases, in which Bid-mediated mitochondrial damage and associated intrinsic death pathways contribute to the underlying progressive loss of neurons.

Congeneric but still distinct: how closely related trypsin ligands exhibit different thermodynamic and structural properties.

A congeneric series of benzamidine-type ligands with a central proline moiety and a terminal cycloalkyl group--linked by a secondary amine, ether, or methylene bridge--was synthesized as trypsin inhibitors. This series of inhibitors was investigated by isothermal titration calorimetry, crystal structure analysis in two crystal forms, and molecular dynamics simulations. Even though all of these congeneric ligands exhibited essentially the same affinity for trypsin, their binding profiles at the structural, dynamic, and thermodynamic levels are very distinct. The ligands display a pronounced enthalpy/entropy compensation that results in a nearly unchanged free energy of binding, even though individual enthalpy and entropy terms change significantly across the series. Crystal structures revealed that the secondary amine-linked analogs scatter over two distinct conformational families of binding modes that occupy either the inside or of the outside the protein's S3/S4 specificity pocket. In contrast, the ether-linked and methylene-linked ligands preferentially occupy the hydrophobic specificity pocket. This also explains why the latter ligands could only be crystallized in the conformationally restricting closed crystal form whereas the derivative with the highest residual mobility in the series escaped our attempts to crystallize it in the closed form; instead, a well-resolved structure could only be achieved in the open form with the ligand in disordered orientation. These distinct binding modes are supported by molecular dynamics simulations and correlate with the shifting enthalpic/entropic signatures of ligand binding. The examples demonstrate that, at the molecular level, binding modes and thermodynamic binding signatures can be very different even for closely related ligands. However, deviating binding profiles provide the opportunity to optimally address a given target.

Proteases of Plasmodium falciparum as potential drug targets and inhibitors thereof.

Malaria, caused by protozoa of the genus Plasmodium, remains one of the most dreadful infectious diseases worldwide killing more than 1 million people per year. The emergence of multidrug-resistant parasites highly demands a steadfast and continuous search not only for new targets but also for new anti-infectives addressing the known ones. As proteases in general have been proven to be excellent drug targets and the development of inhibitors has frequently resulted in approved drugs, this review will only focus on the proteases of Plasmodium falciparum as drug targets. The completion of the sequencing of the Plasmodium falciparum genome in 2002 lead to the discovery of nearly 100 putative proteases encoded therein. Within this review, only those proteases and inhibitors thereof will be discussed in more detail, in which their biological function has been determined undoubtedly or in those cases, in which the development of specific inhibitors has significantly contributed to the understanding of the underlying biological role of the respective protease thus validating the role as promising drug target.

More than a simple lipophilic contact: a detailed thermodynamic analysis of nonbasic residues in the s1 pocket of thrombin.

The field of medicinal chemistry aims to design and optimize small molecule leads into drug candidates that may positively interfere with pathological disease situations in humans or combat the growth of infective pathogens. From the plethora of crystal structures of protein-inhibitor complexes we have learned how molecules recognize each other geometrically, but we still have rather superficial understanding of why they bind to each other. This contribution surveys a series of 26 thrombin inhibitors with small systematic structural differences to elucidate the rationale for their widely deviating binding affinity from 185 microM to 4 nM as recorded by enzyme kinetic measurements. Five well-resolved (resolution 2.30 - 1.47 A) crystal structures of thrombin-inhibitor complexes and an apo-structure of the uncomplexed enzyme (1.50 A) are correlated with thermodynamic data recorded by isothermal titration calorimetry with 12 selected inhibitors from the series. Taking solubility data into account, the variation in physicochemical properties allows conclusions to be reached about the relative importance of the enthalpic binding features as well as to estimate the importance of the parameters more difficult to capture, such as residual ligand entropy and desolvation properties. The collected data reveal a comprehensive picture of the thermodynamic signature that explains the so far poorly understood attractive force experienced by m-chloro-benzylamides to thrombin.

FTree query construction for virtual screening: a statistical analysis.

FTrees (FT) is a known chemoinformatic tool able to condense molecular descriptions into a graph object and to search for actives in large databases using graph similarity. The query graph is classically derived from a known active molecule, or a set of actives, for which a similar compound has to be found. Recently, FT similarity has been extended to fragment space, widening its capabilities. If a user were able to build a knowledge-based FT query from information other than a known active structure, the similarity search could be combined with other, normally separate, fields like de-novo design or pharmacophore searches. With this aim in mind, we performed a comprehensive analysis of several databases in terms of FT description and provide a basic statistical analysis of the FT spaces so far at hand. Vendors' catalogue collections and MDDR as a source of potential or known "actives", respectively, have been used. With the results reported herein, a set of ranges, mean values and standard deviations for several query parameters are presented in order to set a reference guide for the users. Applications on how to use this information in FT query building are also provided, using a newly built 3D-pharmacophore from 57 5HT-1F agonists and a published one which was used for virtual screening for tRNA-guanine transglycosylase (TGT) inhibitors.

Expect the unexpected or caveat for drug designers: multiple structure determinations using aldose reductase crystals treated under varying soaking and co-crystallisation conditions.

In structure-based drug design, accurate crystal structure determination of protein-ligand complexes is of utmost importance in order to elucidate the binding characteristics of a putative lead to a given target. It is the starting point for further design hypotheses to predict novel leads with improved properties. Often, crystal structure determination is regarded as ultimate proof for ligand binding providing detailed insight into the specific binding mode of the ligand to the protein. This widely accepted practise relies on the assumption that the crystal structure of a given protein-ligand complex is unique and independent of the protocol applied to produce the crystals. We present two examples indicating that this assumption is not generally given, even though the composition of the mother liquid for crystallisation was kept unchanged: Multiple crystal structure determinations of aldose reductase complexes obtained under varying crystallisation protocols concerning soaking and crystallisation exposure times were performed resulting in a total of 17 complete data sets and ten refined crystal structures, eight in complex with zopolrestat and two complexed with tolrestat. In the first example, a flip of a peptide bond is observed, obviously depending on the crystallisation protocol with respect to soaking and co-crystallisation conditions. This peptide flip is accompanied by a rupture of an H-bond formed to the bound ligand zopolrestat. The indicated enhanced local mobility of the complex is in agreement with the results of molecular dynamics simulations. As a second example, the aldose reductase-tolrestat complex is studied. Unexpectedly, two structures could be obtained: one with one, and a second with four inhibitor molecules bound to the protein. They are located in and near the binding pocket facilitated by crystal packing effects. Accommodation of the four ligand molecules is accompanied by pronounced shifts concerning two helices interacting with the additional ligands.

Evaluation of in vivo endoscopic autofluorescence spectroscopy in gastric cancer.

BACKGROUND: The aim of this study was to evaluate light-induced autofluorescence spectroscopy for the in vivo diagnosis of gastric cancer. METHODS: A total of 344 endogenous fluorescence spectra were obtained from normal (164) and cancerous gastric mucosa (180) in 15 patients with pure adenocarcinoma and in 16 patients with gastric cancer containing signet-ring cells. A special light source capable of delivering either white or violet-blue light for the excitation of tissue autofluorescence via the endoscope was used. Endogenous fluorescence spectra emitted by the tissue were collected with a fiberoptic probe and analyzed with a spectrograph. RESULTS: Gastric adenocarcinoma exhibits specific changes in the emitted fluorescence spectra as compared with normal gastric mucosa. By algorithmic classification of the spectra, a sensitivity of 84%, specificity of 87%, a likelihood ratio for a positive test of 6.5 and for a negative test of 0.18 were obtained for the diagnosis of pure adenocarcinoma of the stomach. However, gastric cancer with signet-ring cells exhibits great variation in emitted autofluorescence spectra as compared with normal mucosa. The sensitivity for the diagnosis of all carcinomas containing signet-ring cells was 55%, specificity 85%, the likelihood ratio for a positive test was 3.7 and for a negative test, 0.53. The diagnostic value decreases with increasing numbers of signet-ring cells and tumor grade. CONCLUSIONS: Light-induced autofluorescence spectroscopy is a new and promising bio-optical technique for the endoscopic in vivo diagnosis of gastric adenocarcinoma. The poor diagnostic accuracy for signet-ring cell carcinoma may be explained by the diffuse and frequent submucosal growth of this tumor and the presence of collagen fibers.

Endoscopic light-induced autofluorescence spectroscopy for the diagnosis of colorectal cancer and adenoma.

To evaluate the new, bio-optical method of light-induced autofluorescence spectroscopy for the endoscopic in-vivo diagnosis of (pre)-cancerous lesions of the colorectum, 311 endogenous fluorescence spectra were obtained from normal, adenomatous and cancerous colorectal tissue in 11 patients with cancer, six patients with familial adenomatous polyposis, and six patients with multiple adenomatous polyps. A light source delivered either white or violet-blue light for excitation of tissue autofluorescence via a flexible endoscope. Endogenous fluorescence spectra emitted by the tissue were picked up with a fiberoptic probe and analysed with a spectrograph. Biopsies were taken for definitive classification of the spectra. Rectal cancer (n=11) as well as adenomas with severe dysplasia (n=19) showed specific differences between the emitted fluorescence spectra as compared with normal mucosa and hyperplastic polyps. Having applied a mathematical algorithm to the spectra, a sensitivity of 96% and a specificity of 93% were obtained for the diagnosis of rectal cancer. The equivalent values for the diagnosis of dysplastic ademomas were 98 and 89%, respectively. Light-induced autofluorescence spectroscopy is a new and promising bio-optical procedure for the endoscopic in-vivo diagnosis of colorectal cancer and dysplasia.