A Fluorescence-Lifetime-Based Binding Assay for Class IIa Histone Deacetylases

Design and synthesis of peptides as stabilizers of histone deacetylase 4

Histone deacetylase 4 (HDAC4) contributes to gene repression by complex formation with HDAC3 and the corepressor silencing mediator for retinoid or thyroid hormone receptors (SMRT). We hypothesized that peptides derived from the class IIa specific binding site of SMRT would stabilize a specific conformation of its target protein and modulate its activity. Based on the SMRT-motif 1 (SM1) involved in the interaction of SMRT with HDAC4, we systematically developed cyclic peptides that exhibit Ki values that are 9 to 56 times lower than that of the linear SMRT peptide. The peptide macrocycles stabilize the wildtype of the catalytic domain of HDAC4 (cHDAC4) considerably better than its thermally more stable 'gain-of-function' (GOF) variant, cHDAC4-H976Y. Molecular docking and mutagenesis studies indicated that the cyclic peptides bind in a similar but not identical manner as the linear SMRT peptide to a discontinuous binding site. Ion mobility mass spectrometry showed no major changes in the protein fold upon peptide binding. Consistent with these results, preliminary hydrogen-deuterium exchange mass spectrometry measurements indicated only minor conformational changes. Taken together, the cyclic SMRT peptides most likely stabilize the apo form of cHDAC4.

Rapid Determination of Kinetic Constants for Slow-Binding Inhibitors and Inactivators of Human Histone Deacetylase 8

The kinetics and mechanism of drug binding to its target are critical to pharmacological efficacy. A high throughput (HTS) screen often results in hundreds of hits, of which usually only simple IC50 values are determined during reconfirmation. However, kinetic parameters such as residence time for reversible inhibitors and the kinact/KI ratio, which is the critical measure for evaluating covalent inactivators, are early predictive measures to assess the chances of success of the hits in the clinic. Using the promising cancer target human histone deacetylase 8 as an example, we present a robust method that calculates concentration-dependent apparent rate constants for the inhibition or inactivation of HDAC8 from dose-response curves recorded after different pre-incubation times. With these data, hit compounds can be classified according to their mechanism of action, and the relevant kinetic parameters can be calculated in a highly parallel fashion. HDAC8 inhibitors with known modes of action were correctly assigned to their mechanism, and the binding mechanisms of some hits from an internal HDAC8 screening campaign were newly determined. The oxonitriles SVE04 and SVE27 were classified as fast reversible HDAC8 inhibitors with moderate time-constant IC50 values of 4.2 and 2.6 µM, respectively. The hit compound TJ-19-24 and SAH03 behave like slow two-step inactivators or reversible inhibitors, with a very low reverse isomerization rate.

Access to Trifluoromethylketones from Alkyl Bromides and Trifluoroacetic Anhydride by Photocatalysis

Aliphatic trifluoromethyl ketones are a type of unique fluorine-containing subunit which play a significant role in altering the physical and biological properties of molecules. Catalytic methods to provide direct access to aliphatic trifluoromethyl ketones are highly desirable yet remain underdeveloped, partially owing to the high reactivity and instability of trifluoroacetyl radical. Herein, we report a photocatalytic synthesis of trifluoromethyl ketones from alkyl bromides with trifluoroacetic anhydride. The reaction features dual visible-light and halogen-atom-transfer catalysis, followed by an enabling radical-radical cross-coupling of an alkyl radical with a stabilized trifluoromethyl radical. The reaction provides straightforward access to aliphatic trifluoromethyl ketones from readily available and cost-effective alkyl halides and trifluoroacetic anhydride (TFAA).

[1,3]-Dioxolo[4,5-f]benzodioxole (DBD) Fluorescent Dyes; Synthesis, Properties, and Applications

In this review we give an overview of the syntheses and photophysical properties of the new class of fluorescent dyes based on a [1,3]-dioxolo[4,5-f]benzodioxole core and their derivatives. Starting from commercially available reactants (e.g., sesamol, 1,2,4,5-tetrachlorobenzene) the core units can be prepared in a simple manner. Then, the benzene core can be derivatized via lithiation and their photophysical properties can be adjusted as desired. The obtained fluorophores have an absorption range of 403–520 nm and an emission range of 495–665 nm. This class of fluorescent dyes is also characterized by a long fluorescence lifetime, a high stability towards photobleaching, large Stokes shifts, and small size. Thus, the DBD dyes are optimally suited for optical sensing.

1 Introduction

2 Synthesis

3 Properties

4 Applications

HDAC Inhibitors: Innovative Strategies for Their Design and Applications

Histone deacetylases (HDACs) are a large family of epigenetic metalloenzymes that are involved in gene transcription and regulation, cell proliferation, differentiation, migration, and death, as well as angiogenesis. Particularly, disorders of the HDACs expression are linked to the development of many types of cancer and neurodegenerative diseases, making them interesting molecular targets for the design of new efficient drugs and imaging agents that facilitate an early diagnosis of these diseases. Thus, their selective inhibition or degradation are the basis for new therapies. This is supported by the fact that many HDAC inhibitors (HDACis) are currently under clinical research for cancer therapy, and the Food and Drug Administration (FDA) has already approved some of them. In this review, we will focus on the recent advances and latest discoveries of innovative strategies in the development and applications of compounds that demonstrate inhibitory or degradation activity against HDACs, such as PROteolysis-TArgeting Chimeras (PROTACs), tumor-targeted HDACis (e.g., folate conjugates and nanoparticles), and imaging probes (positron emission tomography (PET) and fluorescent ligands).

Non-Hydroxamate Zinc-Binding Groups as Warheads for Histone Deacetylases

Histone deacetylases (HDACs) remove acetyl groups from acetylated lysine residues and have a large variety of substrates and interaction partners. Therefore, it is not surprising that HDACs are involved in many diseases. Most inhibitors of zinc-dependent HDACs (HDACis) including approved drugs contain a hydroxamate as a zinc-binding group (ZBG), which is by far the biggest contributor to affinity, while chemical variation of the residual molecule is exploited to create more or less selectivity against HDAC isozymes or other metalloproteins. Hydroxamates have a propensity for nonspecificity and have recently come under considerable suspicion because of potential mutagenicity. Therefore, there are significant concerns when applying hydroxamate-containing compounds as therapeutics in chronic diseases beyond oncology due to unwanted toxic side effects. In the last years, several alternative ZBGs have been developed, which can replace the critical hydroxamate group in HDACis, while preserving high potency. Moreover, these compounds can be developed into highly selective inhibitors. This review aims at providing an overview of the progress in the field of non-hydroxamic HDACis in the time period from 2015 to present. Formally, ZBGs are clustered according to their binding mode and structural similarity to provide qualitative assessments and predictions based on available structural information.

ALS-linked PFN1 variants exhibit loss and gain of functions in the context of formin-induced actin polymerization

Profilin-1 (PFN1) plays important roles in modulating actin dynamics through binding both monomeric actin and proteins enriched with polyproline motifs. Mutations in PFN1 have been linked to the neurodegenerative disease amyotrophic lateral sclerosis (ALS). However, whether ALS-linked mutations affect PFN1 function has remained unclear. To address this question, we employed an unbiased proteomics analysis in mammalian cells to identify proteins that differentially interact with mutant and wild-type (WT) PFN1. These studies uncovered differential binding between two ALS-linked PFN1 variants, G118V and M114T, and select formin proteins. Furthermore, both variants augmented formin-mediated actin assembly relative to PFN1 WT. Molecular dynamics simulations revealed mutation-induced changes in the internal dynamic couplings within an alpha helix of PFN1 that directly contacts both actin and polyproline, as well as structural fluctuations within the actin- and polyproline-binding regions of PFN1. These data indicate that ALS-PFN1 variants have the potential for heightened flexibility in the context of the ternary actin-PFN1-polyproline complex during actin assembly. Conversely, PFN1 C71G was more severely destabilized than the other PFN1 variants, resulting in reduced protein expression in both transfected and ALS patient lymphoblast cell lines. Moreover, this variant exhibited loss-of-function phenotypes in the context of actin assembly. Perturbations in actin dynamics and assembly can therefore result from ALS-linked mutations in PFN1. However, ALS-PFN1 variants may dysregulate actin polymerization through different mechanisms that depend upon the solubility and stability of the mutant protein.

HDAC7 Inhibition by Phenacetyl and Phenylbenzoyl Hydroxamates

The zinc-containing histone deacetylase enzyme HDAC7 is emerging as an important regulator of immunometabolism and cancer. Here, we exploit a cavity in HDAC7, filled by Tyr303 in HDAC1, to derive new inhibitors. Phenacetyl hydroxamates and 2-phenylbenzoyl hydroxamates bind to Zn²⁺ and are 50-2700-fold more selective inhibitors of HDAC7 than HDAC1. Phenylbenzoyl hydroxamates are 30-70-fold more potent HDAC7 inhibitors than phenacetyl hydroxamates, which is attributed to the benzoyl aromatic group interacting with Phe679 and Phe738. Phthalimide capping groups, including a saccharin analogue, decrease rotational freedom and provide hydrogen bond acceptor carbonyl/sulfonamide oxygens that increase inhibitor potency, liver microsome stability, solubility, and cell activity. Despite being the most potent HDAC7 inhibitors to date, they are not selective among class IIa enzymes. These strategies may help to produce tools for interrogating HDAC7 biology related to its catalytic site.

Kinetically selective and potent inhibitors of HDAC8

Histone deacetylase 8 (HDAC8) is an established and validated target for T-cell lymphoma and childhood neuroblastoma. The active site binding pocket of HDAC8 is highly conserved among all zinc-containing representatives of the histone deacetylase (HDAC) family. This explains that most HDACs are unselectively recognized by similar inhibitors featuring a zinc binding group (ZBG), a hydrophobic linker and a head group. In the light of this difficulty, the creation of isoenzyme-selectivity is one of the major challenges in the development of HDAC inhibitors. In a series of trifluoromethylketone inhibitors of HDAC8 compound 10 shows a distinct binding mechanism and a dramatically increased residence time (RT) providing kinetic selectivity against HDAC4. Combining the binding kinetics results with computational docking and binding site flexibility analysis suggests that 10 occupies the conserved catalytic site as well as an adjacent transient sub-pocket of HDAC8.

First total syntheses of the pro-resolving lipid mediators 7(S),13(R),20(S)-Resolvin T1 and 7(S),13(R)-Resolvin T4

The first total syntheses of the pro-resolving lipid mediators 7(S),13(R),20(S)-Resolvin T1 [7(S),13(R),20(S)-RvT1] and 7(S),13(R)-Resolvin T4 [7(S),13(R)-RvT4], derived from n-3 docosapentaenoic acid (n-3 DPA), are described. 7(S),13(R),20(S)-RvT1 was prepared from 7(S),13(R)-RvT4 via an enzymatic lipoxidase reaction. 7(S),13(R)-RvT4 was obtained by total synthesis where the chiral centers at C7 and C13 where introduced by a Noyori transfer hydrogenation and a chiral pool strategy respectively. Wittig reactions, Sonogashira coupling and Boland Zn(Cu/Ag) reduction were the key steps in the synthesis.

Photophysics of Acyl- and Ester-DBD Dyes: Quadrupole-Induced Solvent Relaxation Investigated by Transient Absorption Spectroscopy

A new generation of wavelength-tunable, fluorescent dyes, so-called DBD ([1,3]dioxolo[4,5- f][1,3]benzodioxole) dyes, were developed a few years ago, and they showed great potential as probes, for example, for fluorescence microscopy. However, their photophysics is not fully explored and leaves open questions regarding their large fluorescence Stokes shifts and sensitivity to solvent conditions of differently substituted DBD dyes. To improve the understanding of the influence of the substitution pattern of the DBD dyes on their respective photophysics, transient absorption spectroscopy (TAS) was used, that is, a pump-probe experiment on the femtosecond timescale. TAS allows measurements of excited states, ground state recovery, solvent relaxation, and fluorescence properties on time scales of up to several nanoseconds. Two different DBD dye samples were investigated: acyl- and ester-substituted DBD dyes. Experiments were carried out in solvents with different polarities using different excitation energies and at different viscosities. Based on the experimental data and theoretical calculations, we were able to determine the conformational changes of the molecule due to electronic excitation and were able to investigate solvent relaxation processes for both types of DBD dyes. By generalizing the theory for quadrupole-induced solvent relaxation developed by Togashi et al., we derived quadrupole moments of both molecules in the ground and excited state. Our data showed differences in the binding of polar solvent molecules to the dyes depending on the substituent on the DBD dye. In the case of water as the solvent, an additional efficient quenching process in the electronically excited state was revealed, which was indicated by the observation of solvated electrons in the TAS signals.

Determination of the binding mechanism of histone deacetylase inhibitors

This article places its focus on methods and tools enabling the elucidation of the mechanism by which ligands, small-molecule inhibitors, or substrates interact with zinc-containing bacterial or human members of the histone deacetylase family (HDACs). These methods include biochemical and biophysical approaches and can be subdivided into equilibrium and kinetic methods. More information about the exact mode of action can be obtained by combining these methods with specific mutant variants of the enzymes and/or series of structural similar ligands. All available equilibrium and kinetic data including additional information from 3D structures of HDAC-ligand complexes can be beneficially combined in a data analysis procedure called Integrated Global-Fit analysis eventually providing the most likely binding mechanism.

Synthesis and Characterization of a New Bifunctionalized, Fluorescent, and Amphiphilic Molecule for Recruiting SH-Containing Molecules to Membranes

This study describes the synthesis and characterization of an amphiphilic construct intended to recruit SH-containing molecules to membranes. The construct consists of 1) an aliphatic chain to enable anchoring within membranes, 2) a maleimide moiety to react with the sulfhydryl group of a soluble (bio)molecule, and 3) a fluorescence moiety to allow the construct to be followed by fluorescence spectroscopy and microscopy. It is shown that the construct can be incorporated into preformed membranes, thus allowing application of the approach with biological membranes. The close proximity between the fluorophore and the maleimide moiety within the construct causes fluorescence quenching. This allows monitoring of the reaction with SH-containing molecules by measurement of increases in fluorescence intensity and lifetime. Notably, the construct distributes into laterally ordered membrane domains of lipid vesicles, which is probably triggered by the length of its membrane anchor. The advantages of the new construct can be employed for several biological, biotechnological, and medicinal applications.

A highly HDAC6-selective inhibitor acts as a fluorescent probe

HDAC6 receives great attention because of its therapeutic potential for the treatment of various diseases.

Fluorescence lifetime based bioassays

Fluorescence lifetime (FLT) is a robust intrinsic property and material constant of fluorescent matter. Measuring this important physical indicator has evolved from a laboratory curiosity to a powerful and established technique for a variety of applications in drug discovery, medical diagnostics and basic biological research. This distinct trend was mainly driven by improved and meanwhile affordable laser and detection instrumentation on the one hand, and the development of suitable FLT probes and biological assays on the other. In this process two essential working approaches emerged. The first one is primarily focused on high throughput applications employing biochemical in vitro assays with no requirement for high spatial resolution. The second even more dynamic trend is the significant expansion of assay methods combining highly time and spatially resolved fluorescence data by fluorescence lifetime imaging. The latter approach is currently pursued to enable not only the investigation of immortal tumor cell lines, but also specific tissues or even organs in living animals. This review tries to give an actual overview about the current status of FLT based bioassays and the wide range of application opportunities in biomedical and life science areas. In addition, future trends of FLT technologies will be discussed.

Highly K+ -Selective Fluorescent Probes for Lifetime Sensing of K+ in Living Cells

The new K⁺ -selective fluorescent probes 1 and 2 were obtained by Cu^I -catalyzed 1,3-dipolar azide alkyne cycloaddition (CuAAC) reactions of an alkyne-substituted [1,3]dioxolo[4,5-f][1,3]benzodioxole (DBD) ester fluorophore with azido-functionalized N-phenylaza-18-crown-6 ether and N-(o-isopropoxy) phenylaza-18-crown-6 ether, respectively. Probes 1 and 2 allow the detection of K⁺ in the presence of Na⁺ in water by fluorescence enhancement (2.2 for 1 at 2000 mm K⁺ and 2.5 for 2 at 160 mm K⁺ ). Fluorescence lifetime measurements in the absence and presence of K⁺ revealed bi-exponential decay kinetics with similar lifetimes, however with different proportions changing the averaged fluorescence decay times (τ_f(av) ). For 1 a decrease of τ_f(av) from 12.4 to 9.3 ns and for 2 an increase from 17.8 to 21.8 ns was observed. Variation of the substituent in ortho position of the aniline unit of the N-phenylaza-18-crown-6 host permits the modulation of the K_d value for a certain K⁺ concentration. For example, substitution of H in 1 by the isopropoxy group (2) decreased the K_d value from >300 mm to 10 mm. 2 was chosen for studying the efflux of K⁺ from human red blood cells (RBC). Upon addition of the Ca²⁺ ionophor ionomycin to a RBC suspension in a buffer containing Ca²⁺ , the fluorescence of 2 slightly rose within 10 min, however, after 120 min a significant increase was observed.

Quantification of the Depolarization and Anisotropy of Fluorophore Stokes-Shifted Fluorescence, On-Resonance Fluorescence, and Rayleigh Scattering

Fluorophores are important but optically complicated photonic materials as they are simultaneous photon absorbers, emitters, and scatterers. Existing studies on fluorophore optical properties have been focused almost exclusively on its photon absorption and Stokes-shifted fluorescence (SSF) with scant information on the fluorophore photon scattering and on-resonance fluorescence (ORF). Presented herein is a unified theoretical framework and experimental approach for quantification of the fluorophore SSF, ORF, and scattering depolarization and anisotropy using a combination of fluorophore UV-vis, fluorescence emission, and resonance synchronous spectroscopic spectral measurements. A mathematical model for calculating fluorophore ORF and scattering cross sections has been developed that uses polystyrene nanoparticles as the external reference. The fluorophore scattering cross section is ∼10-fold smaller than its ORF counterparts for all the six model fluorophores, but more than 6 orders of magnitude larger than the water scattering cross section. Another finding is that the fluorophore ORF has a depolarization close to 1, while its Rayleigh scattering has zero depolarization. This enables the experimental separation of the fluorophore ORF and photon scattering features in the fluorophore resonance synchronous spectra. In addition to opening a new avenue for material characterization, the methods and insights derived from this study should be important for developing new analytical methods that exploit the fluorophore ORF and photon scattering properties.