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The development, scope and mechanism of general, efficient and atropdiastereoselective reactions leading to compounds having biaryl containing medium rings are reported. The process described outlines a pathway that will contribute to a systematic and comprehensive approach to exploring biology (chemical genetics).

A newly developed amide-containing receptor for [Zn.sup.2+], combined with a naphthalimide fluorophore, termed ZTRS is presented. The developed ZTRS could be applied to image intracellular [Zn.sup.2+] ions in the presence of iron ions and to detect zinc ions during the development of living zebrafish embryos.

It has been possible to identify readily synthesized substrates that experience two forms of medium ring-forming reactions producing two classes of complex structures, one patterned after the biaryl natural products and the other a metal-inserted variant.

It is still a significant challenge to develop a Zn2+-seIective fluorescent sensor with the ability to exclude the interference of some heavy and transition metal (HTM) ions such as Fe2+, Co2+, Ni2+, Cu2+, Cd2+, and Hg2+. Herein, we report a novel amide-containing receptor for Zn2+, combined with a naphthalimide fluorophore, termed ZTRS. The fluorescence, absorption detection, NMR, and IR studies indicated that ZTRS bound Zn2+ in an imidic acid tautomeric form of the amide/di-2-picolylamine receptor in aqueous solution, while most other HTM ions were bound to the sensor in an amide tautomeric form. Due to this differential binding mode, ZTRS showed excellent selectivity for Zn2+ over most competitive HIM ions with an enhanced fluorescence (22-fold) as well as a red-shift in emission from 483 to 514 nm. Interestingly, the ZTRS/Cd2+ complex showed an enhanced (21-fold) blue-shift in emission from 483 to 446 nm. Therefore, ZTRS discriminated in vitro and in vivo Zn2+ and Cd2+ with green and blue fluorescence, respectively. Due to the stronger affinity, Zn2+ could be ratiometrically detected in vitro and in viva with a large emission wavelength shift from 446 to 514 nm via a Cd2+ displacement approach. ZTRS was also successfully used to image intracellular Zn2+ ions in the presence of iron ions. Finally, we applied ZTRS to detect zinc ions during the development of living zebrafish embryos. [ABSTRACT FROM AUTHOR]

Methods that survey protein surfaces for binding hotspots can help to evaluate target tractability and guide exploration of potential ligand binding regions. Fragment Hotspot Maps builds upon interaction data mined from the CSD (Cambridge Structural Database) and exploits the idea of identifying hotspots using small chemical fragments, which is now widely used to design new drug leads. Prior to this publication, Fragment Hotspot Maps was only publicly available through a web application. To increase the accessibility of this algorithm we present the Hotspots API (application programming interface), a toolkit that offers programmatic access to the core Fragment Hotspot Maps algorithm, thereby facilitating the interpretation and application of the analysis. To demonstrate the package's utility, we present a workflow which automatically derives protein hydrogen-bond constraints for molecular docking with GOLD. The Hotspots API is available from https://github.com/prcurran/hotspots under the MIT license and is dependent upon the commercial CSD Python API.

The Sondheimer dialkyne reagent has previously been employed in strain-promoted double-click cycloadditions with bis-azide peptides to generate stapled peptide inhibitors of protein-protein interactions. The substituted variants of the Sondheimer dialkyne can be used to generate functionalized stapled peptide inhibitors with improved biological properties; however, this remains a relatively underdeveloped field. Herein, we report the synthesis of new substituted variants of Sondheimer dialkyne and their application in the stapling of p53-based diazido peptides to generate potent stapled peptide-based inhibitors of the oncogenic p53-MDM2 interaction. The functionalized stapled peptide formed from a meta -fluoro-substituted Sondheimer dialkyne was found to be the most potent inhibitor. Furthermore, through experimental studies and density functional theory calculations, we investigated the impact of the substituent on the strain-promoted double-click reactivity of Sondheimer dialkyne., Competing Interests: The authors declare no competing financial interest., (Copyright © 2020 American Chemical Society.)

Polo-like kinase 1 (PLK1) is a key regulator of mitosis and a recognized drug target for cancer therapy. Inhibiting the polo-box domain of PLK1 offers potential advantages of increased selectivity and subsequently reduced toxicity compared with targeting the kinase domain. However, many if not all existing polo-box domain inhibitors have been shown to be unsuitable for further development. In this paper, we describe a novel compound series, which inhibits the protein-protein interactions of PLK1 via the polo-box domain. We combine high throughput screening with molecular modeling and computer-aided design, synthetic chemistry, and cell biology to address some of the common problems with protein-protein interaction inhibitors, such as solubility and potency. We use molecular modeling to improve the solubility of a hit series with initially poor physicochemical properties, enabling biophysical and biochemical characterization. We isolate and characterize enantiomers to improve potency and demonstrate on-target activity in both cell-free and cell-based assays, entirely consistent with the proposed binding model. The resulting compound series represents a promising starting point for further progression along the drug discovery pipeline and a new tool compound to study kinase-independent PLK functions., Competing Interests: The authors declare the following competing financial interest(s): David Walker, Richard Boyce and Robert G. Boyle are employees and shareholders of Sentinel Oncology Ltd. Grahame McKenzie is an employee and shareholder of PhoreMost Ltd. Ashok R. Venkitaraman is a founder, shareholder and scientific advisor of Sentinel Oncology Ltd. and Phoremost Ltd. David Huggins is a founder and shareholder of Integrated Biomedical Solutions Ltd., (Copyright © 2019 American Chemical Society.)

Novel divergent methodology to access sp 3 -rich spirocyclic fragments is reported. First, a robust modular synthesis of bis-alkene amino ester building blocks was developed. Three different carbocycles and six heterocycles were then constructed to assemble eight spirocycles. Importantly, strategic exit vectors were incorporated within each scaffold to aid fragment growth and were elaborated via chemical modifications. Finally, computational methods demonstrate higher levels of rigidity, three-dimensionality, and structural diversity of the library compared to a commercial collection.

We report a double-click macrocyclization approach for the design of constrained peptide inhibitors having non-helical or extended conformations. Our targets are the tankyrase proteins (TNKS), poly(ADP-ribose) polymerases (PARP) that regulate Wnt signaling by targeting Axin for degradation. TNKS are deregulated in many different cancer types, and inhibition of TNKS therefore represents an attractive therapeutic strategy. However, clinical development of TNKS-specific PARP catalytic inhibitors is challenging due to off-target effects and cellular toxicity. We instead targeted the substrate-recognition domain of TNKS, as it is unique among PARP family members. We employed a two-component strategy, allowing peptide and linker to be separately engineered and then assembled in a combinatorial fashion via click chemistry. Using the consensus substrate-peptide sequence as a starting point, we optimized the length and rigidity of the linker and its position along the peptide. Optimization was further guided by high-resolution crystal structures of two of the macrocyclized peptides in complex with TNKS. This approach led to macrocyclized peptides with submicromolar affinities for TNKS and high proteolytic stability that are able to disrupt the interaction between TNKS and Axin substrate and to inhibit Wnt signaling in a dose-dependent manner. The peptides therefore represent a promising starting point for a new class of substrate-competitive inhibitors of TNKS with potential for suppressing Wnt signaling in cancer. Moreover, by demonstrating the application of the double-click macrocyclization approach to non-helical, extended, or irregularly structured peptides, we greatly extend its potential and scope, especially given the frequency with which such motifs mediate protein-protein interactions.

A computational ligand-mapping approach to detect protein surface pockets that interact with hydrophobic moieties is presented. In this method, we incorporated benzene molecules into explicit solvent molecular dynamics simulations of various protein targets. The benzene molecules successfully identified the binding locations of hydrophobic hot-spot residues and all-hydrocarbon cross-links from known peptidic ligands. They also unveiled cryptic binding sites that are occluded by side chains and the protein backbone. Our results demonstrate that ligand-mapping molecular dynamics simulations hold immense promise to guide the rational design of peptidic modulators of protein-protein interactions, including that of stapled peptides, which show promise as an exciting new class of cell-penetrating therapeutic molecules.

We map ligand binding sites on protein surfaces in molecular dynamics simulations using chlorobenzene as a probe molecule. The method was validated on four proteins. Two types of affinity maps that identified halogen and hydrophobic binding sites on proteins were obtained. Our method could prove useful for the discovery and development of halogenated inhibitors.

Tubulin modulating agents such as the taxanes are among the most effective antimitotic cancer drugs, although resistance and toxicity present significant problems in their clinical use. However, most tubulin modulators are derived from complex natural products, which can make modification of their structure to address these problems difficult. Here, we report the discovery of new antimitotic compounds with simple structures that can be rapidly synthesized, through the phenotypic screening of a diverse compound library for the induction of mitotic arrest. We first identified a compound, which induced mitotic arrest in human cells at submicromolar concentrations. Its simple structure enabled rapid exploration of activity, defining a biphenylacetamide moiety required for activity, A family of analogues was synthesized, yielding optimized compounds that caused mitotic arrest and cell death in the low nanomolar range, comparable to clinically used antimitotic agents. These compounds can be synthesized in 1-3 steps and good yields. We show that one such compound targets tubulin, partially inhibiting colchicine but not vinblastine binding, suggesting that it acts allosterically to the known colchicine-binding site. Thus, our results exemplify the use of phenotypic screening to identify novel antimitotic compounds from diverse chemical libraries and characterize a family of biphenylacetamides (biphenabulins) that show promise for further development.

Chemical diversity is a widely applied approach to select structurally diverse subsets of molecules, often with the objective of maximizing the number of hits in biological screening. While many methods exist in the area, few systematic comparisons using current descriptors in particular with the objective of assessing diversity in bioactivity space have been published, and this shortage is what the current study is aiming to address. In this work, 13 widely used molecular descriptors were compared, including fingerprint-based descriptors (ECFP4, FCFP4, MACCS keys), pharmacophore-based descriptors (TAT, TAD, TGT, TGD, GpiDAPH3), shape-based descriptors (rapid overlay of chemical structures (ROCS) and principal moments of inertia (PMI)), a connectivity-matrix-based descriptor (BCUT), physicochemical-property-based descriptors (prop2D), and a more recently introduced molecular descriptor type (namely, "Bayes Affinity Fingerprints"). We assessed both the similar behavior of the descriptors in assessing the diversity of chemical libraries, and their ability to select compounds from libraries that are diverse in bioactivity space, which is a property of much practical relevance in screening library design. This is particularly evident, given that many future targets to be screened are not known in advance, but that the library should still maximize the likelihood of containing bioactive matter also for future screening campaigns. Overall, our results showed that descriptors based on atom topology (i.e., fingerprint-based descriptors and pharmacophore-based descriptors) correlate well in rank-ordering compounds, both within and between descriptor types. On the other hand, shape-based descriptors such as ROCS and PMI showed weak correlation with the other descriptors utilized in this study, demonstrating significantly different behavior. We then applied eight of the molecular descriptors compared in this study to sample a diverse subset of sample compounds (4%) from an initial population of 2587 compounds, covering the 25 largest human activity classes from ChEMBL and measured the coverage of activity classes by the subsets. Here, it was found that "Bayes Affinity Fingerprints" achieved an average coverage of 92% of activity classes. Using the descriptors ECFP4, GpiDAPH3, TGT, and random sampling, 91%, 84%, 84%, and 84% of the activity classes were represented in the selected compounds respectively, followed by BCUT, prop2D, MACCS, and PMI (in order of decreasing performance). In addition, we were able to show that there is no visible correlation between compound diversity in PMI space and in bioactivity space, despite frequent utilization of PMI plots to this end. To summarize, in this work, we assessed which descriptors select compounds with high coverage of bioactivity space, and can hence be used for diverse compound selection for biological screening. In cases where multiple descriptors are to be used for diversity selection, this work describes which descriptors behave complementarily, and can hence be used jointly to focus on different aspects of diversity in chemical space.

Traditionally a pursuit of large pharmaceutical companies, high-throughput screening assays are becoming increasingly common within academic and government laboratories. This shift has been instrumental in enabling projects that have not been commercially viable, such as chemical probe discovery and screening against high-risk targets. Once an assay has been prepared and validated, it must be fed with screening compounds. Crafting a successful collection of small molecules for screening poses a significant challenge. An optimized collection will minimize false positives while maximizing hit rates of compounds that are amenable to lead generation and optimization. Without due consideration of the relevant protein targets and the downstream screening assays, compound filtering and selection can fail to explore the great extent of chemical diversity and eschew valuable novelty. Herein, we discuss the different factors to be considered and methods that may be employed when assembling a structurally diverse compound collection for screening. Rational methods for selecting diverse chemical libraries are essential for their effective use in high-throughput screens.

The regio- and stereoselective synthesis and subsequent Hiyama cross coupling of pentafluorophenyldimethylvinylsilanes has been developed, thus providing a convenient and robust method for the diversity-oriented synthesis of (E)-, (Z)- and alpha-disubstituted alkenes from terminal alkynes. Pentafluorophenyldimethylvinylsilanes undergo cross-coupling reactions with excellent selectivity and in good yields, offering an attractive alternative to existing masked silanols.

It is still a significant challenge to develop a Zn(2+)-selective fluorescent sensor with the ability to exclude the interference of some heavy and transition metal (HTM) ions such as Fe(2+), Co(2+), Ni(2+), Cu(2+), Cd(2+), and Hg(2+). Herein, we report a novel amide-containing receptor for Zn(2+), combined with a naphthalimide fluorophore, termed ZTRS. The fluorescence, absorption detection, NMR, and IR studies indicated that ZTRS bound Zn(2+) in an imidic acid tautomeric form of the amide/di-2-picolylamine receptor in aqueous solution, while most other HTM ions were bound to the sensor in an amide tautomeric form. Due to this differential binding mode, ZTRS showed excellent selectivity for Zn(2+) over most competitive HTM ions with an enhanced fluorescence (22-fold) as well as a red-shift in emission from 483 to 514 nm. Interestingly, the ZTRS/Cd(2+) complex showed an enhanced (21-fold) blue-shift in emission from 483 to 446 nm. Therefore, ZTRS discriminated in vitro and in vivo Zn(2+) and Cd(2+) with green and blue fluorescence, respectively. Due to the stronger affinity, Zn(2+) could be ratiometrically detected in vitro and in vivo with a large emission wavelength shift from 446 to 514 nm via a Cd(2+) displacement approach. ZTRS was also successfully used to image intracellular Zn(2+) ions in the presence of iron ions. Finally, we applied ZTRS to detect zinc ions during the development of living zebrafish embryos.

Using an atropdiastereoselective oxidative biaryl coupling as the key step, the total synthesis of the ellagitannin natural product sanguiin H-5 is reported. Both organomagnesium and organozinc based metalation methodologies were used to efficiently construct the strained medium-ring core of the natural product.

Bacteria "talk" with each other by using small molecules that enable individuals in a population to coordinate their behavior. This language is termed quorum sensing. Bacterial pathogens may use this language to decide when to attack a host organism; therefore, the development of artificial signals to interfere with this signal process has become an area of intense chemical research.

Cell-permeable small molecules can be used to modulate protein function selectively, rapidly, reversibly, and conditionally with temporal and quantitative control in biological systems. The identification of these chemical probes can require the screening of large numbers of small molecules. With the advent of new technologies, small-molecule high-throughput screening is widely available. This Review focuses on the emerging technologies of microarray screening platforms and high-content screening formats.