The Potential of Micellar Media in the Synthesis of DNA-Encoded Libraries.

DNA-encoded library (DEL) technology has become widely used in drug discovery research. The construction of DELs requires robust organic transformations that proceed in aqueous media under mild conditions. Unfortunately, the application of water as reaction medium for organic synthesis is not evident due to the generally limited solubility of organic reagents. However, the use of surfactants can offer a solution to this issue. Oil-in-water microemulsions formed by surfactant micelles are able to localize hydrophobic reagents inside them, resulting in high local concentrations of the organic substances in an otherwise poorly solvated environment. This review provides a conceptual and critical summary of micellar synthesis possibilities that are well suited to DEL synthesis. Existing examples of micellar DEL approaches, together with a selection of micellar organic transformations fundamentally suitable for DEL are discussed.

Use of Biodegradable, Chitosan-Based Nanoparticles in the Treatment of Alzheimer's Disease.

Alzheimer's disease (AD) is a progressive neurodegenerative disorder that affects more than 24 million people worldwide and represents an immense medical, social and economic burden. While a vast array of active pharmaceutical ingredients (API) is available for the prevention and possibly treatment of AD, applicability is limited by the selective nature of the blood-brain barrier (BBB) as well as by their severe peripheral side effects. A promising solution to these problems is the incorporation of anti-Alzheimer drugs in polymeric nanoparticles (NPs). However, while several polymeric NPs are nontoxic and biocompatible, many of them are not biodegradable and thus not appropriate for CNS-targeting. Among polymeric nanocarriers, chitosan-based NPs emerge as biodegradable yet stable vehicles for the delivery of CNS medications. Furthermore, due to their mucoadhesive character and intrinsic bioactivity, chitosan NPs can not only promote brain penetration of drugs via the olfactory route, but also act as anti-Alzheimer therapeutics themselves. Here we review how chitosan-based NPs could be used to address current challenges in the treatment of AD; with a specific focus on the enhancement of blood-brain barrier penetration of anti-Alzheimer drugs and on the reduction of their peripheral side effects.

Cannabis Constituents and Acetylcholinesterase Interaction: Molecular Docking, In Vitro Studies and Association with CNR1 rs806368 and ACHE rs17228602.

The study documented here was aimed to find the molecular interactions of some of the cannabinoid constituents of cannabis with acetylcholinesterase (AChE). Molecular docking and LogP determination were performed to predict the AChE inhibitory effect and lipophilicity. AChE enzyme activity was measured in the blood of cannabis addicted human subjects. Further, genetic predisposition to cannabis addiction was investigated by association analysis of cannabinoid receptor 1 (CNR1) single nucleotide polymorphism (SNP) rs806368 and ACHE rs17228602 using restriction fragment length polymorphism (RFLP) method. All the understudied cannabis constituents showed promising binding affinities with AChE and are lipophilic in nature. The AChE activity was observed to be indifferent in cannabis addicted and non-addicted healthy controls. There was no significant association with CNR1 SNP rs806368 and ACHE rs17228602. The study concludes that in silico prediction for individual biomolecules of cannabis is different from in vivo physiological action in human subjects when all are present together. However, for a deeper mechanistic insight into these interactions and association, multi-population studies are suggested. Further studies to explore the inhibitory potential of different cannabis constituents for intended AChE inhibitor-based drug are warranted.

Novel continuous flow technology for the development of a nanostructured aprepitant formulation with improved pharmacokinetic properties.

The oral bioavailability of Aprepitant is limited by poor dissolution of the compound in the gastrointestinal tract which is more prominent in the fasted state resulting in significant positive food effect. Due to the low aqueous solubility of the active substance the product development has been focused on decreasing the particle size of the active compound down to the submicron range in order to overcome this disadvantageous pharmacokinetic property. The marketed drug consisting of wet-milled nanocrystals exhibits significantly higher oral bioavailability in the fasted state and reduced food effect when compared to the unformulated compound. We have developed a novel process for the production of a nanostructured Aprepitant formulation in which the generation of the nanosized particles takes place at molecular level. The process relies on controlled continuous flow precipitation of the compound from its solution in the presence of stabilizers. The precise control of the production parameters (mixing geometry, flow rates, temperature, etc.) allows to tailor the physicochemical properties and biological performance of the active compound. We have prepared a novel nanostructured Aprepitant formulation using this method and compared its physicochemical and pharmacokinetic properties with the reference compound and the marketed nanoformula. We found that our method produces a stable amorphous solid form comprising novel nanostructured particles having a particle size of less than 100 nm with instantaneous redispersibility characteristics and improved apparent solubility and permeability. In vivo beagle dog pharmacokinetic studies showed that the novel formula exhibited greatly improved pharmacokinetic characteristics when compared to the reference compound, while serum blood concentrations for the nanostructured formula and the wet-milled formula were similar. The marked food effect observed for the reference compound was practically eliminated by our formulation method. These results indicate that the novel continuous flow precipitation technology is a suitable tool to prepare nanostructured formulations with similar, or even superior in vitro and in vivo characteristics when compared to the industrial standard milling technology.

Medicinal chemistry of drugs with active metabolites following conjugation.

Authorities of Drug Administration in the United States of America approved about 5000 drugs for use in the therapy or management of several diseases. About two hundred of these drugs have active metabolites and the knowledge of their medicinal chemistry is important both in medical practice and pharmaceutical research. This review gives a detailed description of the medicinal chemistry of drugs with active metabolites generated after conjugation. This review focused on glucuronide-, acetyl-, sulphate- and phosphate-conjugation of drugs, converting the drug into an active metabolite. This conversion essentially changed the lipophilicity of the drug.

Phosphine-phosphite ligands: chelate ring size vs. activity and enantioselectivity relationships in asymmetric hydrogenation.

A series of new phosphine-phosphite ligands P(C)(n)OP (n = 1-4) have been synthesized and used for rhodium-catalyzed asymmetric hydrogenation of prochiral olefins in order to study the effect of the chelate ring size. Excellent ees (up to 97.5%) were obtained in the hydrogenation of dimethyl itaconate and an increase of activity and enantioselectivity was observed in the hydrogenation of (Z)-α-acetamidocinnamic acid methyl ester with the increasing length of the backbone of the ligands.

Stepwise aromatic nucleophilic substitution in continuous flow. Synthesis of an unsymmetrically substituted 3,5-diamino-benzonitrile library.

Aromatic or heteroaromatic ring precursors with 2-3 identical functionalities are often used in sequential derivatization depending on the reactivity difference or the selective execution of the reaction such as nucleophilic aromatic substitution. Continuous flow chemistry offers an enhanced parameter space (pressure and temperature) with rapid parameter optimization that ensures selectivity in many cases. We developed a flow chemistry procedure to carry out a stepwise aromatic nucleophilic substitution of difluoro-benzenes having an activating group in meta position to the fluorines. The mono-aminated products were obtained in high yield and selectivity in an extremely short reaction time, while applying higher temperature, longer reaction zone (or time), and employing higher excess of another amine reactant, the subsequent introduction of the second amino group was also successfully achieved leading to an unsymmetrically substituted 3,5-diamino-benzonitrile library.

Monitoring by HPLC of chamomile flavonoids exposed to rat liver microsomal metabolism.

Three major flavonoid chamomile components (quercetin, apigenin-7-O-glucoside and rutin) were subjected to oxidative metabolism by cytochrome P-450 of rat liver microsomal preparations. Changes over time in their respective concentrations were followed using reversed-phase HPLC with UV detection. No clean-up had to be applied as only the specific flavonoid had to be separated from the background components originating from the rat liver microsome.Neither the concentration of apigenin-7-O-glucoside nor that of the diglycoside rutin decreased during one hour of exposure to rat microsomal treatment. In contrast, the concentration of quercetin, a lipophilic aglycon, decreased.Our analytical HPLC results complement the in silico calculated lipophilicity (logP) of these compounds; the relatively high lipophilicity of quercetin appears to predispose it to oxidative metabolism in order to decrease its fat solubility. In contrast the much less lipophilic compounds apigenin-7-O-glucoside and rutin were resistant in vitro to microsomal treatment.

High-efficiency aminocarbonylation by introducing CO to a pressurized continuous flow reactor.

Halogenated aryl carboxylic acids were efficiently converted to the corresponding dicarboxylic acid monoamides by a one-step Pd-catalyzed aminocarbonylation in a micro/meso fluidic continuous flow reactor (X-Cube) operated at high pressure and high temperature with CO gas introduction. Reaction parameters (solvent, base, catalyst, pressure, temperature) were rapidly optimized in the reactions, which required less than 2 min. The method gave improved results over comparable batch techniques and is also suited to automated parallel syntheses of compound libraries.

Enhanced hit-to-lead process using bioanalogous lead evolution and chemogenomics: application in designing selective matrix metalloprotease inhibitors.

The authors describe an innovative approach for designing novel inhibitors. This approach effectively integrates the emerging chemogenomics concept of target-family-based drug discovery with bioanalogous design strategies, including privileged structures, molecular frameworks as well as bioisosteric and bioanalogous/isofunctional modifications. The authors applied this method in the design of selective inhibitors of matrix metalloproteases (MMPs), also referred to as matrixins, on the basis of a unique analysis of the ligand-target knowledge base, the 'matrixinome'. For this analysis, the authors created an annotated MMP database containing ∼ 300 inhibitors with their published activity profile. The ligand space was then arranged into a lead evolution tree, where the substructural transformations in each virtual step led to marked changes in the activity pattern. This allowed subtype-specific privileged fragments to be extracted as well as modifications, which improve activity and/or selectivity. Furthermore, the compounds with the preferred activity profile were correlated with sequence homology as well as binding site similarity within the target family, thereby leading to the identification of substructural modifications that turn non-selective, biohomologous structures into selective inhibitors. The matrixinomic application of the authors' approach, therefore, provides an example of how the combination of ligand space knowledge with sequence-related data can radically improve the outcome of the lead optimisation process to achieve higher selectivity within a given target family.

[Comparative chemical proteomics: simultaneous identification of disease-specific protein targets and their small molecule-binding partners, suitable as drug candidates]. / Osszehasonlító kémiai proteomika: Betegség-specifikus molekuláris célpontok és ezekre ható gyógyszerjelötek párhuzamos azonosítása.

The simultaneous identification of disease-specific protein targets and their small molecule binding partners, suitable as drug candidates, could radically reduce the timeline and costs of drug discovery and development. Comparative chemical proteomics provides a novel approach to achieve this goal through rapid detection of overexpressed proteins in diseased samples by the application of small molecule microarrays. The interacting small molecules enables direct affinity-based isolation and identification of the proteins. In the present paper we report comparative chemical proteomics studies on melanocytes and melanoma cell-lines, which led to the identification of 3 overexpressed proteins (e.g. -tubulin) together with their small molecule binding partner.

Explicit Diversity Index (EDI): a novel measure for assessing the diversity of compound databases.

A novel diversity assessment method, the Explicit Diversity Index (EDI), is introduced for druglike molecules. EDI combines structural and synthesis-related dissimilarity values and expresses them as a single number. As an easily interpretable measure, it facilitates the decision making in the design of combinatorial libraries, and it might assist in the comparison of compound sets provided by different manufacturers. Because of its rapid calculation algorithm, EDI enables the diversity assessment of in-house or commercial compound collections.

Solution-phase parallel synthesis of a pyridinium pyrazol-3-olate inner salt library using a three-component reaction.

We present here the discovery of a novel, versatile, multicomponent reaction leading to various 4-[4-(pyridinium-1-yl)-2,5-dioxo-2,5-dihydro-1H-pyrrol-3-yl]-2H-pyrazol-3-olate inner salts. The structure of the unusual zwitterionic inner salts was elucidated, and the scope of the novel reaction was investigated. After rapid optimization, the reaction was adapted to parallel synthesis, and an 800-membered compound library was produced.

Continuous-flow high pressure hydrogenation reactor for optimization and high-throughput synthesis.

This paper reports on a novel continuous-flow hydrogenation reactor and its integration with a liquid handler to generate a fully automated high-throughput hydrogenation system for library synthesis. The reactor, named the H-Cube, combines endogenous hydrogen generation from the electrolysis of water with a continuous flow-through system. The system makes significant advances over current batch hydrogenation reactors in terms of safety, reaction validation efficiency, and rates of reaction. The hydrogenation process is described along with a detailed description of the device's main parts. The reduction of a series of functional groups, varying in difficulty up to 70 degrees C and 70 bar are also described. The paper concludes with the integration of the device into an automated liquid handler followed by the reduction of a nitro compound in a high throughput manner. The system is fully automated and can conduct 5 reactions in the time it takes to perform and workup one reaction manually on a standard batch reactor.

A neural network based classification scheme for cytotoxicity predictions:Validation on 30,000 compounds.

Elimination of cytotoxic compounds in the early phases of drug discovery can save substantial amounts of research and development costs. An artificial neural network based approach using atomic fragmental descriptors has been developed to categorize compounds according to their in vitro human cytotoxicity. Fragmental descriptors were obtained from the Atomic7 linear logP calculation method implemented in Pallas PrologP program. We used cytotoxicity values obtained from an in-house screening campaign of a diverse set of 30,000 drug-like molecules. The training set included only the most and least toxic 12,998 compounds, however, cytotoxicity data for all compounds were used for validation. The proposed approach can be safely used for filtering out potentially cytotoxic candidates from the development pipeline before synthesis or assays during lead development or lead optimisation. The trained neural network misclassified less than 5% percent of the non-toxic and 9% of the toxic compounds.

Procedure for the parallel preparation of 3-imidazo[1,2-a]pyridin-3-yl-propionic acid derivatives involving Meldrum's acid.

We describe here an efficient and versatile method for the preparation of 3-imidazo[1,2-a]pyridin-3-yl-propionic acids involving, as a key step, a three-component Michael-type reaction. The extended and validated procedure allowed us to prepare various acids with three diversity points. The method was easily adaptable for parallel synthesis and an approximately 2000-membered 3-imidazo[1,2-a]pyridin-3-yl-propionic acid amide library was prepared in a semiautomated manner.

A neural network based prediction of octanol-water partition coefficients using atomic5 fragmental descriptors.

An artificial neural network based approach using Atomic5 fragmental descriptors has been developed to predict the octanol-water partition coefficient (logP). We used a pre-selected set of organic molecules from PHYSPROP database as training and test sets for a feedforward neural network. Results demonstrate the superiority of our non-linear model over the traditional linear method.

Development of chemically modified glass surfaces for nucleic acid, protein and small molecule microarrays.

Microarrays have become a widely used tool to investigate the living cell at different levels. DNA microarrays enable the expression analysis of thousand of genes simultaneously, while protein arrays investigate the properties and interactions of proteins with other proteins and with non-proteinaceous molecules. One crucial step in producing such microarrays is the permanent immobilization of samples on a solid surface. Our goal was to develop diverse linker systems capable of anchoring different biological samples, especially DNA and drug-like small molecules. We developed 6 different chemical surfaces having a 3-D-like linker system for biomolecule immobilization, and compared them to previously described immobilization strategies. The attachment chemistry utilizes the amino reactive properties of acrylic and epoxy functions. The capacity of the support was increased by creating a branching structure holding the reactive functions. The method of anchoring was investigated through a model reaction. From HPLC and mass spectrometry measurements we concluded that the covalent binding of DNA occurs through nucleobases. The tested systems offer the capability to permanently immobilize several biomolecular species in an array format.

In Silico and Ex silico ADME approaches for drug discovery.

The high attrition rate of drug candidates during clinical trials for poor pharmacokinetic and metabolic properties has created a need to do these studies as early as it is possible during the drug discovery process. In addition the most successful drug is often not the most potent one but the one that has the suitable level of potency, safety, and pharmacokinetics. Science and technology development during the last few years and the generation of last databases and information has created the basis for doing early experimental PK and ADME studies in addition to eADME. Similarly, testing safety features as early as possible is key to affordable drug discovery and development. Throughput and cost are crucial for early application. In silico methods have by far the highest throughput, followed by the in vitro and in vivo approaches. On the other hand, with regard to relevance and reliability of data the ranking is the opposite. The great challenge for in silico methods is generation of models that correlate more closely with in vivo systems. For the in vitro assays increasing the throughput is an absolute must. Ex silico methods that combine in silico predictions with experimental methods are new additions to the scientific repertoire (e.g. Chromatographic Hydrophobicity Index that is deduced from the reverse phase HPLC data can be used for calculation of lipophilicity). The emerging new approaches have clear impact on the design of early stage screening and combinatorial libraries. In addition to the Lipinski's rules descriptors such as number of rotatable bonds, number of aromatic rings, branching behavior and polar surface area (PSA) are commonly used is the drug design process.