Brain-penetrant cyanoindane and cyanotetralin inhibitors of G2019S-LRRK2 kinase activity.

The G2019S variant of LRRK2, which causes an increase in kinase activity, is associated with the occurrence of Parkinson's disease (PD). Potent, mutation-selective, and brain penetrant inhibitors of LRRK2 can suppress the biological effects specific to G2019S-LRRK2 that cause pathogenicity. We report the discovery of a series of cyanoindane and cyanotetralin kinase inhibitors culminating in compound 34 that demonstrated selective inhibition of phosphorylation of LRRK2 in the mouse brain. These novel inhibitors may further enable the precision medicine path for future PD therapeutics.

Fine tuning for success in structure-based virtual screening.

Structure-based virtual screening plays a significant role in drug-discovery. The method virtually docks millions of compounds from corporate or public libraries into a binding site of a disease-related protein structure, allowing for the selection of a small list of potential ligands for experimental testing. Many algorithms are available for docking and assessing the affinity of compounds for a targeted protein site. The performance of affinity estimation calculations is highly dependent on the size and nature of the site, therefore a rationale for selecting the best protocol is required. To address this issue, we have developed an automated calibration process, implemented in a Knime workflow. It consists of four steps: preparation of a protein test set with structures and models of the target, preparation of a compound test set with target-related ligands and decoys, automatic test of 24 scoring/rescoring protocols for each target structure and model, and graphical display of results. The automation of the process combined with execution on high performance computing resources greatly reduces the duration of the calibration phase, and the test of many combinations of algorithms on various target conformations results in a rational and optimal choice of the best protocol. Here, we present this tool and exemplify its application in setting-up an optimal protocol for SBVS against Retinoid X Receptor alpha.

Cyclopropane derivatives as potential human serine racemase inhibitors: unveiling novel insights into a difficult target.

d-Serine is the co-agonist of NMDA receptors and binds to the so-called glycine site. d-Serine is synthesized by human serine racemase (SR). Over activation of NMDA receptors is involved in many neurodegenerative diseases and, therefore, the inhibition of SR might represent a novel strategy for the treatment of these pathologies. SR is a very difficult target, with only few compounds so far identified exhibiting weak inhibitory activity. This study was aimed at the identification of novel SR inhibitor by mimicking malonic acid, the best-known SR inhibitor, with a cyclopropane scaffold. We developed, synthesized, and tested a series of cyclopropane dicarboxylic acid derivatives, complementing the synthetic effort with molecular docking. We identified few compounds that bind SR in high micromolar range with a lack of significant correlation between experimental and predicted binding affinities. The thorough analysis of the results can be exploited for the development of more potent SR inhibitors.

LiGen: a high performance workflow for chemistry driven de novo design.

Tools for molecular de novo design are actively sought incorporating sets of chemical rules for fast and efficient identification of structurally new chemotypes endowed with a desired set of biological properties. In this paper, we present LiGen, a suite of programs which can be used sequentially or as stand-alone tools for specific purposes. In its standard application, LiGen modules are used to define input constraints, either structure-based, through active site identification, or ligand-based, through pharmacophore definition, to docking and to de novo generation. Alternatively, individual modules can be combined in a user-defined manner to generate project-centric workflows. Specific features of LiGen are the use of a pharmacophore-based docking procedure which allows flexible docking without conformer enumeration and accurate and flexible reactant mapping coupled with reactant tagging through substructure searching. The full description of LiGen functionalities is presented.

Use of experimental design to optimize docking performance: the case of LiGenDock, the docking module of LiGen, a new de novo design program.

On route toward a novel de novo design program, called LiGen, we developed a docking program, LiGenDock, based on pharmacophore models of binding sites, including a non-enumerative docking algorithm. In this paper, we present the functionalities of LiGenDock and its accompanying module LiGenPocket, aimed at the binding site analysis and structure-based pharmacophore definition. We also report the optimization procedure we have carried out to improve the cognate docking and virtual screening performance of LiGenDock. In particular, we applied the design of experiments (DoE) methodology to screen the set of user-adjustable parameters to identify those having the largest influence on the accuracy of the results (which ensure the best performance in pose prediction and in virtual screening approaches) and then to choose their optimal values. The results are also compared with those obtained by two popular docking programs, namely, Glide and AutoDock for pose prediction, and Glide and DOCK6 for Virtual Screening.

Discovery of a Potent, Selective, and Orally Bioavailable Tool Compound for Probing the Role of Lysophosphatidic Acid Type 2 Receptor Antagonists in Fibrotic Disorders.

Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal disease characterized by lung fibrosis leading to an irreversible decline of lung function. Current antifibrotic drugs on the market slow down but do not prevent the progression of the disease and are associated with tolerability issues. The involvement of lysophosphatidic acid receptor 2 (LPA2) in IPF is supported by LPA2 knockdown studies. To further validate the role of LPA2 receptors in modulating IPF and potentially other fibrotic processes, a potent and selective LPA2 receptor antagonist with a good pharmacokinetic (PK) profile is needed. Herein, we report the medicinal chemistry exploration that led to the discovery of a new class of highly potent and selective LPA2 antagonists. Among them, compound 58 exhibits excellent potency, selectivity, and oral PK profile, making it a suitable tool for probing the involvement of LPA2 receptors in IPF and other fibrotic processes.

Aspergillus fumigatus tryptophan metabolic route differently affects host immunity.

Indoleamine 2,3-dioxygenases (IDOs) degrade l-tryptophan to kynurenines and drive the de novo synthesis of nicotinamide adenine dinucleotide. Unsurprisingly, various invertebrates, vertebrates, and even fungi produce IDO. In mammals, IDO1 also serves as a homeostatic regulator, modulating immune response to infection via local tryptophan deprivation, active catabolite production, and non-enzymatic cell signaling. Whether fungal Idos have pleiotropic functions that impact on host-fungal physiology is unclear. Here, we show that Aspergillus fumigatus possesses three ido genes that are expressed under conditions of hypoxia or tryptophan abundance. Loss of these genes results in increased fungal pathogenicity and inflammation in a mouse model of aspergillosis, driven by an alternative tryptophan degradation pathway to indole derivatives and the host aryl hydrocarbon receptor. Fungal tryptophan metabolic pathways thus cooperate with the host xenobiotic response to shape host-microbe interactions in local tissue microenvironments.

Selective Inhibitors of G2019S-LRRK2 Kinase Activity.

Pathogenic variants in the leucine-rich repeat kinase 2 (LRRK2) gene have been identified that increase the risk for developing Parkinson's disease in a dominantly inherited fashion. These pathogenic variants, of which G2019S is the most common, cause abnormally high kinase activity, and compounds that inhibit this activity are being pursued as potentially disease-modifying therapeutics. Because LRRK2 regulates important cellular processes, developing inhibitors that can selectively target the pathogenic variant while sparing normal LRRK2 activity could offer potential advantages in heterozygous carriers. We conducted a high-throughput screen and identified a single selective compound that preferentially inhibited G2019S-LRRK2. Optimization of this scaffold led to a series of novel, potent, and highly selective G2019S-LRRK2 inhibitors.

Accepting the Invitation to Open Innovation in Malaria Drug Discovery: Synthesis, Biological Evaluation, and Investigation on the Structure-Activity Relationships of Benzo[b]thiophene-2-carboxamides as Antimalarial Agents.

Malaria eradication is a global health priority, but current therapies are not always suitable for providing a radical cure. Artemisinin has paved the way for the current malaria treatment, the so-called Artemisinin-based Combination Therapy (ACT). However, with the detection of resistance to ACT, innovative compounds active against multiple parasite species and at multiple life stages are needed. GlaxoSmithKline has recently disclosed the results of a phenotypic screening of an internal library, publishing a collection of 400 antimalarial chemotypes, termed the "Malaria Box". After analysis of the data set, we have carried out a medicinal chemistry campaign in order to define the structure-activity relationships for one of the released compounds, which embodies a benzothiophene-2-carboxamide core. Thirty-five compounds were prepared, and a description of the structural features responsible for the in vitro activity against different strains of P. falciparum, the toxicity, and the metabolic stability is herein reported.

Rational Design, Synthesis, and Preliminary Structure-Activity Relationships of α-Substituted-2-Phenylcyclopropane Carboxylic Acids as Inhibitors of Salmonella typhimurium O-Acetylserine Sulfhydrylase.

Cysteine is a building block for several biomolecules that are crucial for living organisms. The last step of cysteine biosynthesis is catalyzed by O-acetylserine sulfydrylase (OASS), a highly conserved pyridoxal 5'-phosphate (PLP)-dependent enzyme, present in different isoforms in bacteria, plants, and nematodes, but absent in mammals. Beside the biosynthesis of cysteine, OASS exerts a series of "moonlighting" activities in bacteria, such as transcriptional regulation, contact-dependent growth inhibition, swarming motility, and induction of antibiotic resistance. Therefore, the discovery of molecules capable of inhibiting OASS would be a valuable tool to unravel how this protein affects the physiology of unicellular organisms. As a continuation of our efforts toward the synthesis of OASS inhibitors, in this work we have used a combination of computational and spectroscopic approaches to rationally design, synthesize, and test a series of substituted 2-phenylcyclopropane carboxylic acids that bind to the two S. typhymurium OASS isoforms at nanomolar concentrations.

Uma revisita ao desejo do psicanalista em O banquete de Platão, segundo o legado de Freud e Lacan / A revisit to the analyst's desire at Plato's The banquet, according to the legacy of Freud and Lacan / Una revisita al deseo del psicoanalista en El banquete de Platón, de acuerdo con el legado de Freud y Lacan

Objetivamos compreender o termo desejo do psicanalista enquanto direção ética da psicanálise. Para isso, o texto partirá de contribuições da conceituação do termo desejo em Freud como introdução ao termo desejo do psicanalista nomeado por Lacan, lugar esvaziado de intenções pessoais e de promessas de felicidade ao seu analisante. Ao longo do trabalho, serão revisitados alguns pontos essenciais da clássica obra literária O banquete de Platão de acordo com Lacan, destacando a relação de Sócrates e Alcibíades como possibilidade de contraponto da práxis psicanalítica. Em uma correlação com essa práxis, Sócrates foi colocado no lugar de objeto perdido, objeto agalmático para Alcibíades, ocupando um lugar de objeto na transferência do amor depositado por este último. Diante da sua sustentação e do desejo de não ceder ao discurso sedutor deste participante, Sócrates relança-o ao seu próprio desejo, tal como é recomendado a um psicanalista na condução de um tratamento. Finalmente, esse exemplo irá nos levar a uma reflexão quanto ao rigor ético da psicanálise como norteadora do desejo do psicanalista (AU)

We aim to understand the term psychoanalyst's desire as an ethical direction of psychoanalysis. For this, the text will start from contributions of the conceptualization of the term desire in Freud as an introduction to the term desire of the psychoanalyst named by Lacan, a place emptied of his personal intentions and promises of happiness to his analysand. Throughout the work, some essential points of the classic literary work Plato's The banquet will be revisited by Lacan, highlighting the relationship between Socrates and Alcibiades as a possibility for counterpointing psychoanalytic praxis. In a correlation with this praxis, Socrates may have been placed in the place of a lost object, an agalmatic object for Alcibiades, who occupied an object`s place in the transference and love deposited by the latter. Given the support and desire not to give in to this participant's seductive speech, Socrates relaunches it to his own desire as recommended by a psychoanalyst when conducting a treatment. Finally, this example will enlighten us for a reflection on the ethical rigor of psychoanalysis as guiding the psychoanalyst's desire (AU)

Nuestro objetivo es entender el término deseo del psicoanalista como una dirección ética del psicoanálisis. Para esto, el texto comenzará con contribuciones de la conceptualización del término deseo en Freud como una introducción al término deseo del psicoanalista nombrado por Lacan, un lugar vaciado de sus intenciones personales y promesas de felicidad para su analizante. Se explorarán algunos puntos esenciales de la obra literaria clásica El banquete de Platón por Lacan, destacando la relación entre Sócrates y Alcibíades como una posibilidad de contrapunto a la praxis psicoanalítica. En una correlación con esta praxis, Sócrates puede haber sido colocado en el lugar de objeto perdido, objeto agalmático para Alcibíades, quien ocupó un lugar de objeto en la transferencia y el amor depositado por este último. Delante su apoyo y deseo de no ceder ante el discurso seductor de este participante, Sócrates lo relanza a su propio deseo según lo recomendado por un psicoanalista cuando realiza el tratamiento. Finalmente, este ejemplo nos iluminará para reflexionar sobre el rigor ético del psicoanálisis como guía para el deseo del psicoanalista (AU)

Further insights into the SAR of α-substituted cyclopropylamine derivatives as inhibitors of histone demethylase KDM1A.

Epigenetics alterations including histone methylation and acetylation, and DNA methylation, are thought to play important roles in the onset and progression of cancer in numerous tumour cell lines. Lysine-specific demethylase 1 (LSD1 or KDM1A) is highly expressed in different cancer types and inhibiting KDM1A activity seems to have high therapeutic potential in cancer treatment. In the recent years, several inhibitors of KDM1A have been prepared and disclosed. The majority of these derivatives were designed based on the structure of tranylcypromine, as the cyclopropane core is responsible for the covalent interaction between the inhibitor and the catalytic domain of KDM proteins. In this study, we have further extended the SAR regarding compounds 1a-e, which were recently found to inhibit KDM1A with good activity. The decoration of the phenyl ring at the ß-position of the cyclopropane ring with small functional groups, mostly halogenated, and in particular at the meta position, led to a significant improvement of the inhibitory activity against KDM1A, as exemplified by compound 44a, which has a potency in the low nanomolar range (31 nM).

2-Aminonicotinic acid 1-oxides are chemically stable inhibitors of quinolinic acid synthesis in the mammalian brain: a step toward new antiexcitotoxic agents.

3-Hydroxyanthranilic acid 3,4-dioxygenase (3-HAO) is the enzyme responsible for the production of the neurotoxic tryptophan metabolite quinolinic acid (QUIN). Elevated brain levels of QUIN are observed in several neurodegenerative diseases, but pharmacological investigation on its role in the pathogenesis of these conditions is difficult because only one class of substrate-analogue 3-HAO inhibitors, with poor chemical stability, has been reported so far. Here we describe the design, synthesis, and biological evaluation of a novel class of chemically stable inhibitors based on the 2-aminonicotinic acid 1-oxide nucleus. After the preliminary in vitro evaluation of newly synthesized compounds using brain tissue homogenate, we selected the most active inhibitor and showed its ability to acutely reduce the production of QUIN in the rat brain in vivo. These findings provide a novel pharmacological tool for the study of the mechanisms underlying the onset and propagation of neurodegenerative diseases.

Molecular dynamics simulations and docking studies on 3D models of the heterodimeric and homodimeric 5-HT(2A) receptor subtype.

BACKGROUND: G-protein coupled receptors may exist as functional homodimers, heterodimers and even as higher aggregates. In this work, we investigate the 5-HT(2A) receptor, which is a known target for antipsychotic drugs. Recently, 5-HT(2A) has been shown to form functional homodimers and heterodimers with the mGluR2 receptor. The objective of this study is to build up 3D models of the 5-HT(2A)/mGluR2 heterodimer and of the 5-HT(2A)-5-HT(2A) homodimer, and to evaluate the impact of the dimerization interface on the shape of the 5-HT(2A) binding pocket by using molecular dynamics simulations and docking studies. RESULTS AND DISCUSSION: The heterodimer, homodimer and monomeric 5-HT(2A) receptors were simulated by molecular dynamics for 40 ns each. The trajectories were clustered and representative structures of six clusters for each system were generated. Inspection of the these representative structures clearly indicate an effect of the dimerization interface on the topology of the binding pocket. Docking studies allowed to generate receiver operating characteristic curves for a set of 5-HT(2A) ligands, indicating that different complexes prefer different classes of 5-HT(2A) ligands. CONCLUSION: This study clearly indicates that the presence of a dimerization interface must explicitly be considered when studying G-protein coupled receptors known to exist as dimers. Molecular dynamics simulation and cluster analysis are appropriate tools to study the phenomenon.