Monte Carlo methods for small molecule high-throughput experimentation

By analogy with Monte Carlo algorithms, we propose new strategies for design and redesign of small molecule libraries in high-throughput experimentation, or combinatorial chemistry. Several Monte Carlo methods are examined, including Metropolis, three types of biased schemes, and composite moves that include swapping or parallel tempering. Among them, the biased Monte Carlo schemes exhibit particularly high efficiency in locating optimal compounds. The Monte Carlo strategies are compared to a genetic algorithm approach. Although the best compounds identified by the genetic algorithm are comparable to those from the better Monte Carlo schemes, the diversity of favorable compounds identified is reduced by roughly 60%.     

Triarylpyridines: a versatile small molecule scaffold for G-quadruplex recognition

The triarylpyridines are potent G-quadruplex ligands that are highly discriminating against duplex DNA and show promising selectivity between intramolecular quadruplexes.     

Chemical protein synthesis-assisted high-throughput screening strategies for d-peptides in drug discovery

_D-peptides are recognized as a new class of synthetic chemical drugs and they possess many interesting advantages such as high enzymatic stability,improved oral bioavailability,as well as high binding affinity and specificity.Recently,_D-peptide drugs have been attracting increasing attention in both academic and industrial researches over recent years.One _D-peptide etelcalcetide has even entered the market that targets the calcium(Ca²⁺)-sensing recepto...     

Using a lipase as a high-throughput screening method for measuring the enantiomeric excess of allylic acetates

This report describes a high-throughput method for measuring the enantiomeric excess of allylic acetates. Such methods are useful tools for screening libraries of potential catalysts for enantioselective reactions. This technique, which is called EMDee for an enzymatic method for determining enantiomeric excess, uses the lipase from Pseudomonas cepacia to hydrolyze the (R) enantiomer of an allylic acetate, while the (S) enantiomer does not react. The rate of the reaction is monitored by measuring the acetic acid that is produced during the hydrolysis reaction with a pH indicator. Using the Michaelis-Menten equation, the rate of the reaction can be correlated with the concentration of the (R) enantiomer. This method can process 88 samples in less that 30 min.     

Polymer-micelle incarcerated scandium as a polymer-supported catalyst for high-throughput organic synthesis

A novel immobilization technique for Sc(OTf)3, a polymer-micelle incarcerated (PMI) method, has been developed. PMI Sc(OTf)3 is highly active in several fundamental carbon-carbon bond-forming reactions. The catalyst is recovered quantitatively by simple filtration and reused several times without loss of catalytic activity, and no Sc leaching was observed in all reactions (<0.1 ppm). In addition, several solvents are available, and these aspects are suitable for high-throughput organic synthesis (HTOS). To the best of our knowledge, this is the first example of immobilization of Lewis acids utilizing polymer micelles.     

Enantioselective fluorescent recognition of a soluble "supported" chiral acid: toward a new method for chiral catalyst screening

The long-chain aliphatic-group-substituted mandelic acid 3c, which is soluble only in THF and insoluble in water and many polar/nonpolar organic solvents, has been synthesized. This unique solubility allows 3c to be easily isolated from reaction mixtures and makes it potentially useful for catalyst screening. The fluorescent sensors (R)- and (S)-1 can be used to determine the ees of various samples of 3c generated from a series of catalyst screening experiments. The fluorescence measurements correlate well with the conventional HPLC-chiral column analysis. This work demonstrates that the enantioselective fluorescent recognition of organic substrates can lead to a fundamentally new method for chiral catalyst screening. [reaction: see text]     

A fluorescence polarization based screening assay for identification of small molecule inhibitors of the PICK1 PDZ domain

PDZ (PSD-95/Discs-large/ZO-1 homology) domains represent putative targets in several diseases including cancer, stroke, addiction and neuropathic pain. Here we describe the application of a simple and fast screening assay based on fluorescence polarization (FP) to identify inhibitors of the PDZ domain in PICK1 (protein interacting with C kinase 1). We screened 43,380 compounds for their ability to inhibit binding of an Oregon Green labeled C-terminal dopamine transporter peptide (OrG-DAT C13) to purified PICK1 in solution. The assay was highly reliable with excellent screening assay parameters (Z'≈0.7 and Z≈0.6). Out of ~200 compounds that reduced FP to less than 80% of the control wells, six compounds were further characterized. The apparent affinities of the compounds were determined in FP competition binding experiments and ranged from ~5.0 μM to ~193 μM. Binding to the PICK1 PDZ domain was confirmed for five of the compounds (CSC-03, CSC-04, CSC-43, FSC-231 and FSC-240) in a non-fluorescence based assay by their ability to inhibit pull-down of PICK1 by a C-terminal DAT GST fusion protein. CSC-03 displayed the highest apparent affinity (5.0 μM) in the FP assay, and was according to fluorescence resonance energy transfer (FRET) experiments capable of inhibiting the interaction between the C-terminus of the GluR2 subunit of the AMPA-type glutamate receptor and PICK1 in live cells. Additional experiments suggested that CSC-03 most likely is an irreversible inhibitor but with specificity for PICK1 since it did not bind three different PDZ domains of PSD-95. Summarized, our data suggest that FP based screening assays might be a widely applicable tool in the search for small molecule inhibitors of PDZ domain interactions.     

Back to basics: label-free technologies for small molecule screening

Small molecule high-throughput screening in drug discovery today is dominated by techniques which are dependent upon artificial labels or reporter systems. While effective, these approaches can be affected by certain experimental limitations, such as conformational restrictions imposed by the selected label or compound fluorescence/quenching. Label-free approaches potentially address many of these issues by allowing researchers to investigate more native systems without fluorescence- or luminescence-based readouts. However, due to throughput and expense constraints, label-free methods have been largely relegated to a supporting role as the basis of secondary assays. In this review, we describe recent improvements in impedance-based, optical biosensor-based, automated patch clamp and mass spectrometry technologies that have enhanced their ease of use and throughput and, hence, their utility for primary screening of small- to medium-sized compound libraries. The ultimate maturation of these techniques will enable drug discovery researchers to screen large chemical libraries against minimally manipulated biological systems.     

Fluorescence polarization immunoassays and related methods for simple, high-throughput screening of small molecules

Fluorescence polarization immunoassay (FPIA) is a homogeneous (without separation) competitive immunoassay method based on the increase in fluorescence polarization (FP) of fluorescent-labeled small antigens when bound by specific antibody. The minimum detectable quantity of FPIAs with fluorescein label (about 0.1 ng analyte) is comparable with chromatography and ELISA methods, although this may be limited by sample matrix interference. Because of its simplicity and speed, FPIA is readily automated and therefore suitable for high-throughput screening (HTS) in a variety of application areas. Systems that involve binding of ligands to receptor proteins are also susceptible to analysis by analogous FP methods employing fluorescent-labeled ligand and HTS applications have been developed, notably for use in candidate drug screening.     

Unmodified methodologies in target discovery for small molecule drugs: A rising star

Target discovery, involving target identification and validation, is the prerequisite for drug discovery and screening. Novel methodologies and technologies for the precise discovery and confirmation of drug targets are powerful tools in understanding the disease, looking for a drug and elucidating the mechanism of drug treatment. Among the common target identification and confirmation methods, the modified method is time-consuming and laborious, which may reduce or change the activity of natural products. The unmodified methods developed in recent years without chemical modification have gradually become an important means of studying drug targets. A wide range of unmodified approaches have been reported, introducing and analyzing the recent emerging methodologies and technologies. This review highlights the advantages and limitations of these methods for the application of drug target discovery and presents an overview of their contributions to the target discovery of small molecule drugs. The application and future development trends of methodologies in target discovery are also prospected to provide a reference for drug target research.     

X-ray fluorescence as a method of monitoring metal catalyst content during the purification of carbon nanotubes

There have been several studies that suggest that catalyst metals in carbon nanotubes (CNTs) may pose a health threat. As there are many potential applications of CNTs in medicine, it is important to be able to quantitatively determine the amount of metal catalyst contained in a CNT sample. The relative catalyst content of carbon nanotube samples synthesized via arc-discharge has been determined at various stages of the purification process using X-ray fluorescence (XRF) analysis. Purification was achieved by immersing samples in heated nitric acid. The intensities of the nickel K_α X-rays were studied to determine the relative catalyst content in the samples. Scanning electron microscopy (SEM) images of purified nanotubes have been compared to the images of a sample that has been irradiated by 0-15 keV bremsstrahlung in order to determine if the XRF analysis of the nanotubes is in any way destructive. No obvious structural defects were observed as the result of irradiation.     

A general microcantilever surface modification method using a multilayer for biospecific recognition

The key to microcantilever surface modification technology is to selectively modify one side of a microcantilever surface with molecular recognition layers. In this paper, we report a general microcantilever modification method using a multilayer film.     

Accelerated discovery of novel high-performance zinc-ion battery cathode materials by combining high-throughput screening and experiments

Aqueous zinc ion batteries (AZIBs) have attracted much attention in recent years due to their high safety, low cost, and decent electrochemical performance. However, the traditional electrodes development process requires tedious synthesis and testing procedures, which reduces the efficiency of developing high-performance battery devices. Here, we proposed a high-throughput screening strategy based on first-principles calculations to aid the experimental development of high-performance spinel cathode materials for AZIBs. We obtained 14 spinel materials from 12,047 Mn/Zn-O based materials by examining their structures and whether they satisfy the basic properties of electrodes. Then their band structures and density of states, open circuit voltage and volume expansion rate, ionic diffusion coefficient and energy barrier were further evaluated by first-principles calculations, resulting in five potential candidates. One of the promising candidates identified, Mg₂MnO₄, was experimentally synthesized, characterized and integrated into an AZIB based cell to verify its performance as a cathode. The Mg₂MnO₄ cathode exhibits excellent cycling stability, which is consistent with the theoretically predicted low volume expansion. Moreover, at high current density, the Mg₂MnO₄ cathode still exhibits high reversible capacity and excellent rate performance, indicating that it is an excellent cathode material for AZIBs. Our work provides a new approach to accelerate the development of high-performance cathodes for AZIBs and other ion batteries.     

A general synthetic method for the formation of arylaminotetrazoles using natural natrolite zeolite as a new and reusable heterogeneous catalyst

An efficient method for preparation of arylaminotetrazoles is reported using natrolite zeolite as a natural catalyst. Generally, isomer of 5-arylamino-1H-tetrazole can be obtained from arylcyanamides carrying electron-withdrawing substituent on aryl ring and as the electropositivity of substituent is increased, the product is shifted toward the isomer of 1-aryl-5-amino-1H-tetrazole. This method has the advantages of high yields, simple methodology, short reaction times and easy work-up. The catalyst can be recovered by simple filtration and reused in good yields.     

Energetics of a protein disorder–order transition in small molecule recognition

Many proteins recognise other proteins via mechanisms that involve the folding of intrinsically disordered regions upon complex formation. Here we investigate how the selectivity of a drug-like small molecule arises from its modulation of a protein disorder-to-order transition. Binding of the compound AM-7209 has been reported to confer order upon an intrinsically disordered ‘lid’ region of the oncoprotein MDM2. Calorimetric measurements revealed that truncation of the lid region of MDM2 increases the apparent dissociation constant of AM-7209 250-fold. By contrast, lid truncation has little effect on the binding of the ligand Nutlin-3a. Insights into these differential binding energetics were obtained via a complete thermodynamic analysis that featured adaptive absolute alchemical free energy of binding calculations with enhanced-sampling molecular dynamics simulations. The simulations reveal that in apo MDM2 the ordered lid state is energetically disfavoured. AM-7209, but not Nutlin-3a, shows a significant energetic preference for ordered lid conformations, thus shifting the balance towards ordering of the lid in the AM-7209/MDM2 complex. The methodology reported herein should facilitate broader targeting of intrinsically disordered regions in medicinal chemistry.

Molecular simulations and biophysical measurements elucidate why the ligand AM-7209 orders a disordered region of the protein MDM2 on binding. This work expands strategies available to medicinal chemists for targeting disordered proteins.     

Iridium as a general catalyst for the decarbonylative addition of aldehydes to alkynes

A general catalytic system for the decarbonylative addition reaction of aldehydes with alkynes is developed by using an iridium catalyst system. Both aromatic and aliphatic aldehydes reacted with terminal alkynes efficiently to give the corresponding olefination products in high yields and up to 11:1 E/Z selectivity.     

Synergetic activation of carbon dioxide molecule using phenylazomethine dendrimers as a catalyst

Phenylazomethine dendrimers bearing a cobalt porphyrin core act as catalysts for CO₂ reduction in the presence of a strong Lewis acid such as lanthanide trifluoromethanesulfonate (Ln(OTf)₃). We investigated the catalytic activity using electrochemical measurements (cyclic voltammetry) on a glassy carbon electrode in a DMF solution. Dissolving CO₂ gas into the solution, the cyclic voltammograms displayed an irreversible increase of the cathodic current. This result suggests the catalytic reduction of CO₂. The redox potential (–1.3 V versus Fc/Fc⁺) at which the catalytic behavior was observed is 1.1 V higher than that catalyzed by cobalt tetraphenylporphyrin (CoTPP). The generation number (n) dependence of the dendrimer catalysts showed the maximum activity at n = 3. A significant decrease of the activity for the largest dendrimer (n = 4) indicates a steric effect, which prevents transmission of the substrate (CO₂ molecule) and electrons to the catalytic center (cobalt porphyrin core). For more efficient catalysis, a novel open-shell dendrimer having a pocket on one side of the molecule was designed and synthesized. Because the accessibility to the core in the opened shell improved, this dendrimer exhibited the highest catalytic activity. These results suggest that tuning of the local domain around the cobalt porphyrin center would lead to a decisive solution for further activation of the CO₂ molecule. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 44: 5229–5236, 2006