Parallel Synthesis Techniques Research Articles

New Reductive Mediators for Expanding Array-Based Parallel Synthesis

Microelectrode arrays are powerful analytical tools for monitoring interactions between biological molecules in real-time. By placing members of a molecular library at defined electrodes, one can easily screen interactions with biological targets in the supernatant through simple electrochemical impedance experiments. However, one of the limitations to using arrays with very high electrode densities is the requirement of functionalizing each individual electrode (commonly over 12500/cm2) with a member of the molecular library to be tested. The Moeller Lab seeks to bypass this road block by developing synthetic tools that would allow for synthesis of the combinatorial library directly on the array surface through parallel synthesis techniques. One of the key features of any parallel synthesis strategy is protecting group orthogonality. The ability to selectively cleave one protecting group in the presence of various other protecting group moieties allows for diversification of a core scaffold in a site-specific manner. To this end, the Moeller Lab has utilized electrochemical methods to site-selectively generate acids, bases, Ce(IV), Ru(VII), Os(VIII), Cr(VI), Pd(0), Pd(II), Cu(I), Cu(II), quinones, H2, and Sc(III) at defined electrodes on a microelectrode array. In order to expand this toolset further, we are investigating protecting groups that are reductively cleavable, such as p-nitrobenzyl carbonates and carbamates. The reduction potential of these groups is readily tunable by modifying the substitution on the aromatic ring, giving rise to a small library of cleavable groups with different reduction potentials. One of the challenges towards using these groups on the arrays, however, is selection of an appropriate reductive mediator to shuttle electrons from the electrode at the array surface to the substrates localized on the outside of a polymer coating over the array. While oxidative mediators are relatively well-characterized and easy to come by, reductive mediators often require multistep syntheses to obtain and are less known than their oxidative counterparts. We hypothesize that these reductively cleavable protecting groups can be mediated by the aryl ring moiety present in the protecting group (e.g. p-nitrobenzene for a p-nitrobenzyl carbamate-protected amine). Addition of an alkyl substituent (such as the methylene in the carbamate) to an aryl ring makes the reduction potential of the aryl ring more negative by ~200 mV. Thus the free aryl ring should be able to serve as the mediator for reductive cleavage of the protecting group. In support of this hypothesis, we have shown that we can deprotect a p-nitrobenzyl carbamate-protected amine site-selectively on a microelectrode array using p-nitrobenzene as the mediator. In addition, CV studies of a p-nitrobenzyl-protected amine substrate show that p-nitrobenzene is able to transfer electrons to the substrate -- the reduction wave of the mediator disappears when substrate is added. Thus by optimizing these mediated reactions on the microelectrode arrays and in solution, we hope to introduce a new family of reductive mediators and protecting groups to the synthetic community. Figure 1

TunableQ-enhanced LC dual-band filtering at microwave frequencies in 0.13 µm SiGe BiCMOS

AbstractThis paper presents an activeQ-enhanced LC dual-band band-pass filtering approach using parallel synthesis techniques at X- and Ku-bands in 0.13µm SiGe BiCMOS technology. By employing two independently tunable parallel LC-tanks with either in-phase and out-of-phase addition, independently tunable dual-band filtering is achieved. For higher out-of-band (OOB) attenuation, subtraction of the two 2nd-order bandpass filter is implemented. The two bands are independently tunable in terms ofQand center frequency. The dual-band filter at 9.7 GHz and 13.9 GHz achieves a normalized dynamic range of 165–154.5 dB.Hz with an OOB attenuation of >50 dB below 3 GHz. In between the two bands, the attenuation is 22 dB when the two passbands have 200 MHz bandwidth each. The total group delay is 0.8 ns and 1.9 ns forQof 20 and 50, respectively. The filter achieves better OOB rejection with wider band channels at X- and Ku-bands compared with state of the art integrated filters. The filter consumes 115–130 mW of DC power. The core die area is 0.53 × 0.7 mm2.

Discovery of the First Thumb Pocket 1 NS5B Polymerase Inhibitor (BILB 1941) with Demonstrated Antiviral Activity in Patients Chronically Infected with Genotype 1 Hepatitis C Virus (HCV)

Combinations of direct acting antivirals (DAAs) that have the potential to suppress emergence of resistant virus and that can be used in interferon-sparing regimens represent a preferred option for the treatment of chronic HCV infection. We have discovered allosteric (thumb pocket 1) non-nucleoside inhibitors of HCV NS5B polymerase that inhibit replication in replicon systems. Herein, we report the late-stage optimization of indole-based inhibitors, which began with the identification of a metabolic liability common to many previously reported inhibitors in this series. By use of parallel synthesis techniques, a sparse matrix of inhibitors was generated that provided a collection of inhibitors satisfying potency criteria and displaying improved in vitro ADME profiles. "Cassette" screening for oral absorption in rat provided a short list of potential development candidates. Further evaluation led to the discovery of the first thumb pocket 1 NS5B inhibitor (BILB 1941) that demonstrated antiviral activity in patients chronically infected with genotype 1 HCV.

Synthesis of a Drug-Like Focused Library of Trisubstituted Pyrrolidines Using Integrated Flow Chemistry and Batch Methods

A combination of flow and batch chemistries has been successfully applied to the assembly of a series of trisubstituted drug-like pyrrolidines. This study demonstrates the efficient preparation of a focused library of these pharmaceutically important structures using microreactor technologies, as well as classical parallel synthesis techniques, and thus exemplifies the impact of integrating innovative enabling tools within the drug discovery process.

Supportedp-Toluenesulfonic Acid as a Highly Robust and Eco-Friendly Isocyanide Scavenger

We document here the use of polymer-supported p-toluenesulfonic acid as a highly effective, robust, economical and eco-friendly isocyanide scavenger. The herein described strategy circumvent the intense and repulsive odor of volatile isocyanides, enabling simplified and odorless workup and purifications. The usefulness of the new scavengers has been validated in a set of diverse isocyanide-based organic transformations and this approach is also amenable to parallel synthesis techniques.

Discovery of benzimidazole-diamide finger loop (Thumb Pocket I) allosteric inhibitors of HCV NS5B polymerase: Implementing parallel synthesis for rapid linker optimization

Previously described SAR of benzimidazole-based non-nucleoside finger loop (Thumb Pocket I) inhibitors of HCV NS5B polymerase was expanded. Prospecting studies using parallel synthesis techniques allowed the rapid identification of novel cinnamic acid right-hand sides that provide renewed opportunities for further optimization of these inhibitors. Novel diamide derivatives such as 44 exhibited comparable potency (enzymatic and cell-based HCV replicon) as previously described tryptophan-based inhibitors but physicochemical properties (e.g., aqueous solubility and lipophilicity) have been improved, resulting in molecules with reduced off-target liabilities (CYP inhibition) and increased metabolic stability.

5-Aroyl-3,4-dihydropyrimidin-2-one Library Generation via Automated Sequential and Parallel Microwave-assisted Synthesis Techniques

An efficient two-step synthetic pathway toward the preparation of diversely substituted 5-aroyl-3,4-dihydropyrimidin-2-ones is realized. The protocol involves an initial trimethylsilyl chloride-mediated Biginelli multicomponent reaction involving S-ethyl acetothioacetate, aromatic aldehydes, and ureas as building blocks to generate a set of 3,4-dihydropyrimidine-5-carboxylic acid thiol esters. These thiol esters serve as starting materials for a subsequent Pd-catalyzed Cu-mediated Liebeskind-Srogl cross-coupling reaction with boronic acids to provide the desired 5-aroyl-3,4-dihydropyrimidin-2-one derivatives. Both steps were performed using microwave heating in sealed vessels, either in an automated sequential or parallel format using dedicated microwave reactor instrumentation. A diverse library of 30 5-aroyl-3,4-dihydropyrimidin-2-ones was prepared with commercially available aldehyde, urea, and boronic acid building blocks as starting materials.

Determination of chemical composition and molar mass distribution of random styrene-ethyl acrylate copolymers by high-throughput liquid chromatography

AbstractSynthesis and characterization of random copolymers by spectroscopic and chromatographic techniques are normally slow and expensive because most measurements are conducted consecutively and no high-throughput techniques are used. In the present work parallel synthesis and high-throughput analytical techniques for random styrene-ethyl acrylate copolymers were developed. With combinatorial methods, high-throughput instruments and a better design of experiments, the molar mass and chemical composition analyses were carried out simultaneously with time savings of more than 90% as compared to conventional set-ups. The chemical heterogeneity of high-conversion styrene-ethyl acrylate copolymers was determined successfully by fast gradient HPLC. Determination of the average composition was carried out via selective UV detection in size exclusion chromatography. The results were verified by 1H NMR and calculations based on the copolymerisation parameters. Differential scanning calorimetry and optical microscopy techniques were used for determination of the phase separation behaviour of the copolymers and correlated with the chemical heterogeneity.

Parallel, Solution Phase Synthesis of Dihydropyridine Miticides Via a Versatile Multicomponent Reaction

A novel class of highly active dihydropyridine miticides was prepared using a multicomponent reaction process. The initial lead was rapidly optimized using solution phase parallel synthesis techniques and a positional scanning approach. Detailed structure-activity relationships were developed for the amino and carbonyl components of the molecule and used to select the best candidates for broad field testing. The chemistry, biology and toxicology of these compounds will be presented along with numerous structural variants of the reaction products.

A Stand-Alone Monitoring System for Reliable Unattended Operation of a Commercial Preparative LC/MS Purification System

Commercially available preparative liquid chromatograph/mass spectrometer (LC/MS) systems are commonly used in drug discovery research to purify large numbers of compounds made by parallel synthesis techniques. The systems in our lab are comprised of individual instruments that communicate continuously with control software in order to collect specific compounds based on mass triggering. Over time, communication errors may cause improper system operation, and excessive pressure during injection may cause system damage or a leak. The risks of sample loss and safety hazards precluded unattended overnight operation of the purification systems. A stand-alone monitoring system was developed to ensure proper purification system operation. Custom sensors and software are used to identify failures and remotely control power to the purification system. In response to a failure, the monitoring system will either shut down the purification system or, if possible, selectively reboot an instrument to allow continued operation. With the creation of the monitoring system, the purification system can be run unattended with

3‐(2‐Pyrrolidin‐1‐ylethyl)‐5‐(1,2,3,6‐tetrahydropyridin‐4‐yl)‐1H‐indole Derivatives as High Affinity Human 5‐HT1B/1D Ligands.

AbstractFor Abstract see ChemInform Abstract in Full Text.

An Efficient Parallel Synthesis of Capsazepine and Capsazepine Analogs

Capsazepine (CPZ, 1) is a well-known vanilloid receptor (VR1) antagonist that has been cited widely used in the literature. However the current synthetic methods used for the total synthesis of CPZ are lengthy, involve multiple purification steps, and produce low yields. Here we describe a new and highly efficient synthesis of benzazepine 3, a synthetic precursor of CPZ, in only two steps and 59% overall yield from a commercially available tetralone 2 via a Schmidt reaction as a key step. Moreover, we apply parallel synthesis techniques to prepare CPZ and CPZ analogs. Our approach enables the possibility of preparing larger, and more diverse libraries of CPZ analogs.

Integration of Combinatorial Synthesis, Rapid Screening, and Computational Modeling in Biomaterials Development

AbstractSummary: The advent of high‐throughput combinatorial synthesis techniques in drug discovery has stimulated efforts to apply these techniques to the discovery of biomaterials. To be of practical utility, combinatorial approaches to biomaterials design require (i) the availability of parallel synthesis techniques to generate libraries of polymers, (ii) efficient assays for the rapid characterization of biorelevant material properties, and (iii) computational methods to efficiently model different biological responses in the presence of polymers. Here we report the integration of these methodologies and illustrate the potential of this approach to accelerate the development of new biomaterials. The parallel synthesis of a library of 112 biodegradable polyarylates has been reported previously. This library was used to develop efficient screening techniques to determine biorelevant polymer properties (fibrinogen adsorption, gene expression in macrophages, growth of fetal rat lung fibroblasts (RLFs)). A Surrogate (semiempirical) Model was developed (i) to determine molecular‐scale polymer properties that correlate to various biological responses, and (ii) to predict fibrinogen adsorption and RLF growth on polymeric surfaces. For 38 out of 45 polymers, the model predicted the amount of fibrinogen adsorbed correctly within the error of the experimental measurements. The growth of rat lung fibroblasts was correctly predicted by the model for 41 out of 48 polymers. The correlation factor between the model's predicted values and the experimentally determined data was 0.54 ± 0.09 and 0.69 ± 0.12 for fibrinogen adsorption and RLF growth, respectively. The results presented here demonstrate the utility of combinatorial and computational approaches for the rational design of polymers for biomedical applications.Design of the library of polyarylates, which are copolymers of a diacid and a diphenol. Chemical diversity was created by variations in the structure of the diacid (marked as “Y”) and the pendent chain (marked as “R”).magnified imageDesign of the library of polyarylates, which are copolymers of a diacid and a diphenol. Chemical diversity was created by variations in the structure of the diacid (marked as “Y”) and the pendent chain (marked as “R”).

3-(2-Pyrrolidin-1-ylethyl)-5-(1,2,3,6-tetrahydropyridin-4-yl)-1H-indole derivatives as high affinity human 5-HT 1B/1D ligands

A series of 3-(2-pyrrolidin-1-ylethyl)-5-(1,2,3,6-tetrahydropyridin-4-yl)-1H-indole derivatives ( 2) has been prepared using parallel synthesis techniques, and their structure–activity relationships studied. High affinity human 5-HT 1B/1D (h5-HT 1B/1D) ligands have been identified.

Semisynthetic macrolide antibacterials derived from tylosin. Synthesis and structure-activity relationships of novel desmycosin analogues.

A series of 20-O-substituted and 3,20-di-O-substituted derivatives of desmycosin were synthesized and their biological properties were evaluated. In particular, we have synthesized numerous side chain modified analogues of desmycosin as well as some analogues possessing a combination of modified side chain and alternative C-3 substituents. Thus, alpha,beta-unsaturated analogues of desmycosin (2), tylosin (1), 10,11,12,13-tetrahydrotylosin (11), and 2,3-didehydrodesmycosin (13) were prepared from the corresponding aldehydes by a Wittig reaction with the stabilized ylides (a-d), generating a trans-double bond, followed by modified Pfitzner-Moffat oxidation of the C-3 hydroxyl group. To evaluate the importance of the C-3 position of desmycosin for biological activity, the C-3 substituted derivatives were synthesized by a standard sequence of protective group chemistry followed by Wittig reaction and esterification as the key steps. For the attachment of the C-3 ester functionality, a mixed anhydride protocol was adopted. Reaction proceeded smoothly to give corresponding esters in yields ranging from 70 to 80%. Base- and acid-catalyzed rearrangement products including desmycosin 8,20-aldols (24a and 24b) and desmycosin 3,19-aldol (25) are also described. Parallel array synthesis and purification techniques allowed for the rapid exploration of structure-activity relationships within this class and for the improvement in potency. In vitro evaluation of these derivatives demonstrated good antimicrobial activity against Gram-positive bacteria for most of the compounds. The present derivatives of 16-membered macrolides were active against MLS(B)-resistant strains that were inducibly resistant, but not those constitutively resistant to erythromycin.

Applications of Parallel Synthesis to Lead Optimization

Parallel synthesis of focused compound libraries for hit confirmation and lead optimization are certainly important drivers for shortening the lead discovery phase in the pharmaceutical and crop protection industries. In this article we show with permission of Roche and Syngenta three real case studies where Polyphor synthesized focused libraries for lead validation and optimization using high-throughput parallel synthesis and purification techniques. The three examples differ significantly in the synthetic strategies which were employed as well as in the chemical complexity of the final products. A multigeneration approach towards insecticidal triazines, the application of a sequential three-component reaction towards insecticidal and fungicidal thiazoles and finally a multistep synthesis approach of advanced building blocks followed by a two-step final derivatization towards novel antiviral N-hydroxy-indolin-2-ones are presented. In all cases 100–200 analogues were synthesized using parallel synthesis in solution followed by purification of the final products by parallel flash or high-throughput (unattended) HPLC (coupled to MS) within four months. Promising biological results were obtained in all three cases.

Asymmetric rhodium carbene insertion into the SiH bond: identification of new dirhodium(II) carboxylate catalysts using parallel synthesis techniques

Decomposition of methyl 2-diazophenylacetate in the presence of silanes and a chiral dirhodium(II) catalyst results in SiH insertion of the intermediate carbenoid with varying degrees of enantioselectivity. New chiral dirhodium(II) carboxylate catalysts were identified using solution phase parallel synthesis techniques.

Identification of a pharmacophore for thrombopoietic activity of small, non-peptidyl molecules. 2. Rational design of naphtho[1,2-d]imidazole thrombopoietin mimics.

The invention of a new class of naphtho[1,2-d]imidazole thrombopoietin mimics based on a pharmacophore hypothesis for small-molecule thrombopoietic agonists is discussed. Parallel array synthesis and purification techniques allowed for the rapid exploration of structure-activity relationships within this class and for the improvement in TPO mimetic potencies and efficacies.

Parallel synthesis of tri- and tetrasubstituted ureas from carbamoyl imidazolium salts.

A method for producing tri- and tetrasubstituted ureas from carbamoyl imidazolium salts is presented. Carbamoyl imidazolium salts are prepared from the reaction of N,N carbonyldiimidazole (CDI) with secondary amines, followed by alkylation with iodomethane. These stable salts can be stored for extended periods and are effective electrophilic carbamoylation reagents. Primary and secondary amines add to carbamoyl imidazolium salts at room temperature to give tri- and tetrasubstituted ureas in excellent yields. This reaction was used to synthesize ureas using both liquid-liquid extraction and solid-phase extraction (cation exchange) purification techniques. Liquid-liquid extraction affords the product ureas more cleanly than cationic exchange. A series of urea compounds were synthesized using parallel synthesis techniques in high yields and with suitable purity for routine in vitro biological tests. These studies validate the utility of carbamoyl imidazolium salts as useful building blocks for combinatorial library synthesis.

Novel potent antagonists of human neuropeptide Y Y5 receptor. Part 1: 2-oxobenzothiazolin-3-acetic acid derivatives

Novel NPY-Y5 antagonist FR73966 was discovered by screening of our in-house chemical library. The analogues were prepared by application of parallel synthesis techniques. Some of the resulting 2-oxobenzothiazolin-3-acetic acid derivatives exhibited nanomolar binding affinity for human NPY-Y5 receptors.