Binding of Chlorinated Phenylacrylonitriles to the Aryl Hydrocarbon Receptor: Computational Docking and Molecular Dynamics Simulations

The development of ligands capable of binding to the aryl hydrocarbon receptor (AhR) and hijacking its signaling pathway is of potential use for the design of novel agents against breast cancer. To guide the synthesis of new compounds and characterize their binding to the AhR, we employed homology modeling, ligand docking, and molecular dynamics simulations. As there is currently no crystallographic information available for the structure of the AhR’s ligand-binding PAS-B domain, a homology model was developed. The location of the binding site was identified by scanning the model for concave areas and comparing them to known ligand-binding sites in proteins related to the AhR, such as the CLOCK:BMAL1 transcriptional activator complex and the hypoxia-inducible factor-2α (HIF-2α). Docking of several chlorinated phenylacrylonitriles was performed with the modeling suite MOE, identifying π-π stacking, hydrophobic, and van der Waals interactions as the driving forces for binding, an observation consistent with the hydrophobic nature of the site. Molecular dynamics simulations with one of the compounds for 100 ns verified the overall stability of a docking-predicted pose and revealed the presence of interacting water molecules in the vicinity of the ligand. Given the buried location of the ligand in the core of the receptor, this observation was somewhat unexpected, but it explained a slight shift of the ligand pose seen during the simulation

Chalcones: Potential Anticancer Agents

Chalcones in their various guises have been considered either valid and critically important lead compounds in the development of novel anticancer agents or as pan assay interference compounds, PAINS. Medicinal chemistry is replete with exemplars from both “camps” progressing to clinical utility. Chalcones offer a simple starting point for the development of specific compounds with high levels of activity toward key biological targets. Chalcones have been shown to display a wide array of anticancer compounds. This chapter seeks to offer an overview of key examples in an effort to encourage further reading and research in development in this intriguing space

Recent Developments in the Use of Flow Hydrogenation in the Field of Medicinal Chemistry

This chapter focuses on recent applications of flow hydrogenation in medicinal chemistry. Flow reactors can enhance laboratory safety, reducing the risks associated with pyrophoric catalysts, due to their containment in catalyst cartridges or omnifit columns. Flow hydrogenation reduces the risks arising from hydrogen gas, with either hydrogen generated in situ from water, or precise management of the gas flow rate through tube-in-tube reactors. There is an increasing body of evidence that flow hydrogenation enhances reduction outcomes across nitro, imine, nitrile, amide, azide, and azo reductions, together with de-aromatisation and hydrodehalogenation. In addition, olefin, alkyne, carbonyl, and benzyl reductions have been widely examined. Further, protocols involving multistage flow reactions involving hydrogenation are highlighted

An introduction to classical molecular dynamics simulation for experimental scattering users

Classical molecular dynamics simulations are a common component of multi-modal analyses from scattering measurements, such as small-angle scattering and diffraction. Users of these experimental techniques often have no formal training in the theory and practice of molecular dynamics simulation, leading to the possibility of these simulations being treated as a "black box" analysis technique. In this article, we describe an open educational resource (OER) designed to introduce classical molecular dynamics to users of scattering methods. This resource is available as a series of interactive web pages, which can be easily accessed by students, and as an open source software repository, which can be freely copied, modified, and redistributed by educators. The topic covered in this OER includes classical atomistic modelling, parameterising interatomic potentials, molecular dynamics simulations, typical sources of error, and some of the approaches to using simulations in the analysis of scattering data.Comment: Electronic Supplementary Information (ESI) available: All analysis/plotting scripts and figure files, allowing for a fully reproducible, and automated, analysis workflow for the work presented is available at \url{https://github.com/arm61/sim_and_scat_paper} (DOI: 10.5281/zenodo.2556826) under a CC BY-SA 4.0 licens

Mechanisms of tethering and cargo transfer during epididymosome-sperm interactions

Abstract Background The mammalian epididymis is responsible for the provision of a highly specialized environment in which spermatozoa acquire functional maturity and are subsequently stored in preparation for ejaculation. Making important contributions to both processes are epididymosomes, small extracellular vesicles released from the epididymal soma via an apocrine secretory pathway. While considerable effort has been focused on defining the cargo transferred between epididymosomes and spermatozoa, comparatively less is known about the mechanistic basis of these interactions. To investigate this phenomenon, we have utilized an in vitro co-culture system to track the transfer of biotinylated protein cargo between mouse epididymosomes and recipient spermatozoa isolated from the caput epididymis; an epididymal segment that is of critical importance for promoting sperm maturation. Results Our data indicate that epididymosome-sperm interactions are initiated via tethering of the epididymosome to receptors restricted to the post-acrosomal domain of the sperm head. Thereafter, epididymosomes mediate the transfer of protein cargo to spermatozoa via a process that is dependent on dynamin, a family of mechanoenzymes that direct intercellular vesicle trafficking. Notably, upon co-culture of sperm with epididymosomes, dynamin 1 undergoes a pronounced relocation between the peri- and post-acrosomal domains of the sperm head. This repositioning of dynamin 1 is potentially mediated via its association with membrane rafts and ideally locates the enzyme to facilitate the uptake of epididymosome-borne proteins. Accordingly, disruption of membrane raft integrity or pharmacological inhibition of dynamin both potently suppress the transfer of biotinylated epididymosome proteins to spermatozoa. Conclusion Together, these data provide new mechanistic insight into epididymosome-sperm interactions with potential implications extending to the manipulation of sperm maturation for the purpose of fertility regulation

Next-generation of BBQ analogues that selectively target breast cancer

We previously reported on the interaction of 10-chloro-7H-benzo[de]benzo[4,5]imidazo[2,1-a]isoquinolin-7-one (10-Cl-BBQ) with the Aryl hydrocarbon Receptor (AhR) and selective growth inhibition in breast cancer cell lines. We now report on a library of BBQ analogues with substituents on the phenyl and naphthyl rings for biological screening. Herein, we show that absence of the phenyl Cl of 10-Cl-BBQ to produce the simple BBQ molecule substantially enhanced the growth inhibitory effect with GI50 values of 0.001–2.1 μM in select breast cancer cell lines MCF-7, T47D, ZR-75-1, SKBR3, MDA-MB-468, BT20, BT474 cells, while having modest effects of 2.1–7 μM in other cell lines including HT29, U87, SJ-G2, A2780, DU145, BE2-C, MIA, MDA-MB-231 or normal breast cells, MCF10A (3.2 μM). The most potent growth inhibitory effect of BBQ was observed in the triple negative cell line, MDA-MB-468 with a GI50 value of 0.001 μM, presenting a 3,200-fold greater response than in the normal MCF10A breast cells. Additions of Cl, CH3, CN to the phenyl ring and ring expansion from benzoimidazole to dihydroquinazoline hindered the growth inhibitory potency of the BBQ analogues by blocking potential sites of CYP1 oxidative metabolism, while addition of Cl or NO2 to the naphthyl rings restored potency. In a cell-based reporter assay all analogues induced 1.2 to 10-fold AhR transcription activation. Gene expression analysis confirmed the induction of CYP1 oxygenases by BBQ. The CYP1 inhibitor α-naphthoflavone, and the SULT1A1 inhibitor quercetin significantly reduced the growth inhibitory effect of BBQ, confirming the importance of both phase I and II metabolic activation for growth inhibition. Conventional molecular modelling/docking revealed no significant differences between the binding poses of the most and least active analogues. More detailed DFT analysis at the DSD-PBEP86/Def-TZVPP level of theory could not identify significant geometric or electronic changes which would account for this varied AhR activation. Generation of Fukui functions at the same level of theory showed that CYP1 metabolism will primarily occur at the phenyl head group of the analogues, and substituents within this ring lead to lower cytotoxicity