Compound Libraries For Drug Discovery Research Articles

Fully automated screening of compound libraries in drug discovery using docking and molecular dynamics.

In the initial stage of drug discovery, hundreds of thousands of compounds are screened in high-throughput assays to find a small number of hits. To save time and resources, we develop a computational workflow that ranks drug candidates by their binding affinity to the target protein. First, all compounds in a library are docked to the protein. After this filtering step, the drug candidates with the poses scoring best are grouped into pairs, and their relative free energy of binding to the protein is calculated using the accelerated weight histogram method (AWH) for alchemical transformations. Thanks to random moves between λ-windows, a single AWH simulation samples the complete alchemical path connecting two ligands. The probability to visit a λ-window depends on its estimated free energy such that the sampling of the alchemical transformation and the free energy estimate improve each other in a positive feedback loop. To fully integrate docking and free energy calculations, we implemented routines that generate hybrid topologies for drug candidates without human intervention, i.e., they assign force field parameters (AMBER and CHARMM) to the compound and determine the smallest set of atoms to be alchemically transformed for a given compound pair. Being able to convert docking poses into input files for the molecular dynamics simulations in an automated fashion, we extensively test AWH's robustness to (sub-optimal) initial configurations on a benchmark with 13 proteins and approximately 500 ligand pairs for which experimental relative binding free energies are available. In return, free energies obtained from MD for protein-ligand complexes in the PDBbind data set are used as training data for a machine-learning model improving the scoring of docking poses such that both docking and free energy calculations benefit from integration in the workflow.

High-throughput screening of animal venoms for identification of compounds active on the cardiac Nav1.5 channel

Dysfunctions of the cardiac sodium channels (Nav1.5) have been associated with many cardiac diseases such as long QT syndrome or Brugada syndrome. In order to study the role of this channel in diseases or to restore function, molecules that specifically target this sodium channel are needed. Highly specific molecules for a given isoform of sodium channel are hard to discover with usual chemical libraries. Animal venoms, and especially spider venoms, contain each tens of peptides acting on ion channels and represent therefore interesting starting compound libraries for drug discovery. By screening spider venoms on Nav, we aimed to identify new toxins targeting specifically Nav1.5 channel which can be used as: – tools to study role of Nav1.5; – as pharmacological drug to prevent Nav1.5-related arrhythmias. For that purpose, 16 venoms isolated from spiders were first fractionated to generate libraries. Each fraction has been tested on several stable Nav cell lines using Syncropatch384PE system (Nanion) to ensure selectivity. False-positive fractions were excluded based on detection of material in HPLC and mass spectrometry analyses. We identified 10 native fractions active on Nav1.5. Among them, 5 inhibit sodium currents and 5 slow-down inactivation with increase in late sodium current. Theses fractions have been re-fractionated with a complementary purification approach until identification of isolated peptides. Validation of effects of these peptides on properties of Nav1.5 currents is ongoing. Sequences of positive hits are currently under study and chemical syntheses will be performed to get synthetic versions of these peptides. Complete pharmacological characterization of synthetic peptides is in progress. We developed a complete pipeline using automated patch-clamp that allows us to isolate and validate new toxins specific for human Nav1.5 sodium channel from large libraries of spider venoms.

Stereodivergent Synthesis through Catalytic Asymmetric Reversed Hydroboration.

The control of chemo-, regio-, diastereo-, and enantioselectivity is a central theme in organic synthesis. The capability to obtain the full set of stereoisomers of a molecule would significantly enhance the efficiency for the synthesis of natural product analogues and creation of chiral compound libraries for drug discovery. Despite the tremendous progress achieved in the field of asymmetric synthesis in the past decades, the precise control of both relative and absolute configurations in catalyst-controlled reactions that create multiple stereocenters remains a significant synthetic challenge. We report here the development of a catalyst-controlled hydroboration with hitherto unattainable selectivity. The Rh-catalyzed hydroboration of α, β-unsaturated carbonyl compounds with pinacolborane proceeds with high levels of regio-, diastereo-, and enantioselectivities to provide a hydroboration product with two vicinal stereocenters. Through the appropriate choice of substrate geometry ( E or Z) and ligand enantiomer ( S or R), all the possible diastereoisomers are readily accessible. The boron-containing products underwent many stereospecific transformations, thus providing a strategy for collective stereodivergent synthesis of diverse valuable chiral building blocks.

Ultrasensitive dynamic light scattering based nanobiosensor for rapid anticancer drug screening

Improved chemical library screens for drug modulators of a target protein are vital to advance precision medicine. Here, we describe an ultrasensitive dynamic light scattering (DLS) based biosensor using gold nanoparticles as plasmon-enhanced sensing probes to rapidly screen anticancer compounds. The nanobiosensor which consists of DNA-conjugated dumbbell-shaped gold nanoprobes can detect protein activities in drug-treated cells. We have validated the utility of our nanosensor to screen for compounds known to reactivate mutated tumor suppressor protein p53 for DNA binding in complex cellular context, which leads to significant increases in the hydrodynamic size of the nanoprobes through DLS measurement. This unique nanoplasmonic biosensor not only significantly enhances the DLS signal for specific biomolecular binding, but also effectively suppresses the background noise from irrelevant entities, which greatly improves sensitivity and reduces consumption of both sample and probe. In addition, a competition assay designed to evaluate the relative DNA binding affinities of p53 using the same sensing probes allows a concomitant assessment of responsive p53 pathways downstream or cell fate. Most critically, this nanosensor enables direct interrogation of endogenous protein activities following drug treatment in live cells, allowing simultaneous on-target validation during phenotypic screens. This DLS-based nanobiosensor is broadly applicable to other DNA binding molecules and/or proteins, and holds great potential for high-throughput screening campaigns utilizing both conventional and fragment-based compound libraries in drug discovery.

A carbohydrate-derived trifunctional scaffold for medicinal chemistry library synthesis

For the generation of compound libraries for drug discovery a central scaffold containing three exit vectors with defined chirality was devised starting from commercially available tri-O-acetyl-glucal. Surprisingly, the reaction of a 4-O-mesylate with sodium azide did not lead to the expected 4-azido-4-deoxy derivative but to a 3-azido-3-deoxy regioisomer via intermediate epoxide formation. The absolute stereochemical configuration of the final tetrahydropyran building block was proven by X-ray crystallography. This scaffold endowed with a carboxylic acid, a secondary alcohol, and an azide functionality may be connected to a DNA tag at any of the three distinct exit vectors, thus providing ready access to several different compound libraries.Â

Synthesis of Enantiomerically Pure 3-Substituted Piperazine-2-acetic Acid Esters as Intermediates for Library Production.

The piperazine heterocycle is broadly exploited in FDA-approved drugs and biologically active compounds, but its chemical diversity is usually limited to ring nitrogen substitutions, leaving the four carbon atoms underutilized. Using an efficient six-step synthesis, chiral amino acids were transformed into 3-substituted piperazine-2-acetic acid esters as diastereomeric mixtures whose cis and trans products (dr 0.56 → 2.2:1, respectively) could be chromatographically separated. From five amino acids (both antipodes) was obtained a complete matrix of 20 monoprotected chiral 2,3-disubstituted piperazines, each as a single absolute stereoisomer, all but one in multigram quantities. In keeping with our overall purpose of constructing more Csp3-enriched compound libraries for drug discovery, these diverse and versatile piperazines can be functionalized on either nitrogen atom, allowing them to be used as scaffolds for parallel library synthesis and as intermediates for the production of novel piperazine compounds.

Ligand-Controlled Palladium(II)-Catalyzed Regiodivergent Carbonylation of Alkynes: Syntheses of Indolo[3,2-c]coumarins and Benzofuro[3,2-c]quinolinones.

Regiodivergent syntheses of indolo[3,2-c]coumarins and benzofuro[3,2-c]quinolinones through a controllable palladium(II)-catalyzed carbonylative cyclization are established. The chemo- and regioselectivity are exclusively tuned by the ligand on the palladium catalyst. The rigid framework of the electron-deficient ligand promotes the O-attack/N-carbonylation cyclization leading to benzofuro[3,2-c]quinolinones, while a sterically bulky and electron-rich ligand facilitates N-attack/O-carbonylation cyclization to generate indolo[3,2-c]coumarins. Furthermore, various other nucleophiles are applicable for delivering a variety of indoloquinolinones, pyranoquinolones, and chromeno[3,4-c]quinolinones in one step, and serves as a method for creating compound libraries for drug discovery.

An Integrated Microfluidic Processor for DNA-Encoded Combinatorial Library Functional Screening

DNA-encoded synthesis is rekindling interest in combinatorial compound libraries for drug discovery and in technology for automated and quantitative library screening. Here, we disclose a microfluidic circuit that enables functional screens of DNA-encoded compound beads. The device carries out library bead distribution into picoliter-scale assay reagent droplets, photochemical cleavage of compound from the bead, assay incubation, laser-induced fluorescence-based assay detection, and fluorescence-activated droplet sorting to isolate hits. DNA-encoded compound beads (10-μm diameter) displaying a photocleavable positive control inhibitor pepstatin A were mixed (1920 beads, 729 encoding sequences) with negative control beads (58 000 beads, 1728 encoding sequences) and screened for cathepsin D inhibition using a biochemical enzyme activity assay. The circuit sorted 1518 hit droplets for collection following 18 min incubation over a 240 min analysis. Visual inspection of a subset of droplets (1188 droplets) yielded a 24% false discovery rate (1166 pepstatin A beads; 366 negative control beads). Using template barcoding strategies, it was possible to count hit collection beads (1863) using next-generation sequencing data. Bead-specific barcodes enabled replicate counting, and the false discovery rate was reduced to 2.6% by only considering hit-encoding sequences that were observed on >2 beads. This work represents a complete distributable small molecule discovery platform, from microfluidic miniaturized automation to ultrahigh-throughput hit deconvolution by sequencing.

Development of a Terpenoid Alkaloid-like Compound Library Based on the Humulene Skeleton.

Many natural terpenoid alkaloid conjugates show biological activity because their structures contain both sp3 -rich terpenoid scaffolds and nitrogen-containing alkaloid scaffolds. However, their biosynthesis utilizes a limited set of compounds as sources of the terpenoid moiety. The production of terpenoid alkaloids containing various types of terpenoid moiety may provide useful, chemically diverse compound libraries for drug discovery. Herein, we report the construction of a library of terpenoid alkaloid-like compounds based on Lewis-acid-catalyzed transannulation of humulene diepoxide and subsequent sequential olefin metathesis. Cheminformatic analysis quantitatively showed that the synthesized terpenoid alkaloid-like compound library has a high level of three-dimensional-shape diversity. Extensive pharmacological screening of the library has led to the identification of promising compounds for the development of antihypolipidemic drugs. Therefore, the synthesis of terpenoid alkaloid-like compound libraries based on humulene is well suited to drug discovery. Synthesis of terpenoid alkaloid-like compounds based on several natural terpenoids is an effective strategy for producing chemically diverse libraries.

Microwave Assisted Reactions in Organic Chemistry: A Review of Recent Advances

Revolution in organic compound synthesis has been promoted by microwave assisted organic syntheses (MAOS) by which small molecules are built up into large polymers in a fraction of time. The need for different organic compound libraries for drug discovery, biomaterial development, automated library screening; proteomics etc has supported the emergence of innovative technologies for rapid combinatorial organic synthesis using MAOS synthesis. In previous reviews on this subject the focus of MAOS has been on the process of MAOS reactions rather than the importance given to the related applications. This review focuses on solid-phase synthesis, biopolymer synthesis, applications in proteomics, parallel processing in microwave reactors and automated library generation by means of sequential microwave irradiation methods. This article has discussed the different applications of Microwave assisted synthesis of organic polymeric compounds most thoroughly by focusing on aspects of speed, reproducibility and scalability. From this review it is clearly identified that independent on the type of organic material, data consistently points out to MW as a novel and powerful tool which has enable synthesis of a number of new compounds and presents the need for future research in this area.

Nonlinear dimensionality reduction and mapping of compound libraries for drug discovery

Visualization of ‘chemical space’ and compound distributions has received much attraction by medicinal chemists as it may help to intuitively comprehend pharmaceutically relevant molecular features. It has been realized that for meaningful feature extraction from complex multivariate chemical data, such as compound libraries represented by many molecular descriptors, nonlinear projection techniques are required. Recent advances in machine-learning and artificial intelligence have resulted in a transfer of such methods to chemistry. We provide an overview of prominent visualization methods based on nonlinear dimensionality reduction, and highlight applications in drug discovery. Emphasis is on neural network techniques, kernel methods and stochastic embedding approaches, which have been successfully used for ligand-based virtual screening, SAR landscape analysis, combinatorial library design, and screening compound selection.

Evaluation of a New Preparative Supercritical Fluid Chromatography System for Compound Library Purification: The TharSFC SFC-MS Prep-100 System

Preparative HPLC-MS is often the method of choice for purification of small amounts (<100mg) of diverse new molecules, such as compound libraries for drug discovery. The method is robust, well proven, and widely applicable. In contrast, preparative supercritical fluid chromatography coupled with mass spectrometry (SFC-MS) has seen only slow acceptance for the same application--despite some potential scientific and economic advantages. One of the reasons for slow adoption of SFC-MS is the lack of well-proven, robust, and commercially available instrumentation. In early 2009, TharSFC (a Waters Company, Pittsburgh, PA) introduced a new fully integrated system for preparative SFC-MS: The SFC-MS Prep-100. We report herein an objective evaluation of the SFC-MS Prep-100, including tests for pump and autosampler performance, sample recovery, sample carryover, fraction triggering, detector/fraction collector synchronization, and overall robustness. Our results suggest that the SFC-MS Prep-100 represents a significant advance over previous generation instrumentation.

Aroma WaterLOGSY: a fast and sensitive screening tool for drug discovery

One-dimensional NMR spectroscopy has proven to be a powerful technique for screening compound libraries in drug discovery. We report a novel water ligand-observed gradient spectroscopy (WaterLOGSY) pulse sequence, named Aroma WaterLOGSY, that selectively detects aromatic WaterLOGSY signals from compounds or ligands. In the Aroma WaterLOGSY, water magnetization is untouched after water excitation and utilizes the whole period of the remaining pulse sequence to relax back to the +z direction. Due to the phase cycling design, the water magnetization is allowed to relax for the period of two full scans before it gets inverted again. Therefore, the recycle delay can be significantly shortened. Within similar experimental time, Aroma WaterLOGSY shows approximately two times higher sensitivity than the standard scheme. This method also allows the use of non-deuterated reagents, thereby accelerating experimental set-up time for ligand-binding studies.

Hit Triage Using Efficiency Indices after Screening of Compound Libraries in Drug Discovery

Fragment-based drug discovery (FBDD) is an important new tool to understand the molecule basis of ligand-biological target interactions. By combining optimal fragments, it is often possible to construct larger molecular weight compounds that have greater potency in a shorter period of time than can been achieved by the initial screening of larger molecular weight compound libraries. Alternatively, if screening of more traditional larger libraries has occurred, then it may be possible to analyze the data during the process of hit triage in such as way as to essentially adopt a fragment-based approach in reverse. In this review, we highlight general principles associated with the efficiency indices such as Ligand Efficiency (LE) in which screening data is normalized for biophysical properties such as molecular size. We further focus on the concept of Fit Quality (FQ), which standardizes LE values across molecular weight for more realistic, direct comparison. Using these simple concepts, one can apply FBDD routinely in the stage of hit triage when evaluating the data obtained after screening of compound libraries in drug discovery.

A fast, fully automated cell segmentation algorithm for high‐throughput and high‐content screening

High-throughput, high-content screening (HT-HCS) of large compound libraries for drug discovery imposes new constraints on image analysis algorithms. Time and robustness are paramount while accuracy is intrinsically statistical. In this article, a fast and fully automated algorithm for cell segmentation is proposed. The algorithm is based on a strong attachment to the data that provide robustness and have been validated on the HT-HCS of large compound libraries and different biological assays. We present the algorithm and its performance, a description of its advantages and limitations, and a discussion of its range of application.

Solid‐Phase Compound Library Synthesis in Drug Design and Development

AbstractFor Abstract see ChemInform Abstract in Full Text.

Combinatorial compound libraries for drug discovery: an ongoing challenge.

Almost 20 years of combinatorial chemistry have emphasized the power of numbers, a key issue for drug discovery in the current genomic era, in which it has been estimated that there might be more than 10,000 potential targets for which it would be desirable to have small-molecule modulators. Combinatorial chemistry is best described as the industrialization of chemistry; the chemistry has not changed, just the way in which it is now carried out, which is principally by exploiting instrumentation and robotics coupled to the extensive use of computers to efficiently control the process and analyse the vast amounts of resulting data. Many researchers have contributed to the general concepts as well as to the technologies in present use. However, some interesting challenges still remain to be solved, and these are discussed here in the context of the application of combinatorial chemistry to drug discovery.

Detection of small-molecule enzyme inhibitors with peptides isolated from phage-displayed combinatorial peptide libraries

Background: The rapidly expanding list of pharmacologically important targets has highlighted the need for ways to discover new inhibitors that are independent of functional assays. We have utilized peptides to detect inhibitors of protein function. We hypothesized that most peptide ligands identified by phage display would bind to regions of biological interaction in target proteins and that these peptides could be used as sensitive probes for detecting low molecular weight inhibitors that bind to these sites. Results: We selected a broad range of enzymes as targets for phage display and isolated a series of peptides that bound specifically to each target. Peptide ligands for each target contained similar amino acid sequences and competition analysis indicated that they bound one or two sites per target. Of 17 peptides tested, 13 were found to be specific inhibitors of enzyme function. Finally, we used two peptides specific for Haemophilus influenzae tyrosyl-tRNA synthetase to show that a simple binding assay can be used to detect small-molecule inhibitors with potencies in the micromolar to nanomolar range. Conclusions: Peptidic surrogate ligands identified using phage display are preferentially targeted to a limited number of sites that inhibit enzyme function. These peptides can be utilized in a binding assay as a rapid and sensitive method to detect small-molecule inhibitors of target protein function. The binding assay can be used with a variety of detection systems and is readily adaptable to automation, making this platform ideal for high-throughput screening of compound libraries for drug discovery.

The Importance of Automated Sample Management Systems in Realizing the Potential of Large Compound Libraries in Drug Discovery

Biomolecular screening is now enabled at a far greater scale than ever before due to the explosion of available libraries and targets. By the early '90s, however, it was becoming clear that the potential number of tests which could be done (theoretically the product of available test compounds multiplied by identified biological targets) was, in practice, being severely limited by the logistics of handling and preparing samples at rates exceeding 10,000 compounds per day. What was required was, in effect, a "sample supermarket" to feed screening research. This article describes the development of a solution to this problem, called Haystack, which was designed to be this sample supermarket, but with the addition of extensive use of robotics and computer based automation to reduce the scope for human error. The Haystack system consists of three broad types of modules which are: Sample Storage and Retrieval, Sample Dispensing and Preparation, and Sample Tracking and Data Management.