Selective and Bioavailable HDAC6 2-(Difluoromethyl)-1,3,4-oxadiazole Substrate Inhibitors and Modeling of Their Bioactivation Mechanism.

Histone deacetylase 6 (HDAC6) is a unique member of the HDAC family mainly targeting cytosolic nonhistone substrates, such as α-tubulin, cortactin, and heat shock protein 90 to regulate cell proliferation, metastasis, invasion, and mitosis in tumors. We describe the identification and characterization of a series of 2-(difluoromethyl)-1,3,4-oxadiazoles (DFMOs) as selective nonhydroxamic acid HDAC6 inhibitors. By comparing structure-activity relationships and performing quantum mechanical calculations of the HDAC6 catalytic mechanism, we show that potent oxadiazoles are electrophilic substrates of HDAC6 and propose a mechanism for the bioactivation. We also observe that the inherent electrophilicity of the oxadiazoles makes them prone to degradation in water solution and the generation of potentially toxic products cannot be ruled out, limiting the developability for chronic diseases. However, the oxadiazoles demonstrate high oral bioavailability and low in vivo clearance and are excellent tools for studying the role of HDAC6 in vitro and in vivo in rats and mice.

HDAC6 inhibitor ACY-1083 shows lung epithelial protective features in COPD.

Airway epithelial damage is a common feature in respiratory diseases such as COPD and has been suggested to drive inflammation and progression of disease. These features manifest as remodeling and destruction of lung epithelial characteristics including loss of small airways which contributes to chronic airway inflammation. Histone deacetylase 6 (HDAC6) has been shown to play a role in epithelial function and dysregulation, such as in cilia disassembly, epithelial to mesenchymal transition (EMT) and oxidative stress responses, and has been implicated in several diseases. We thus used ACY-1083, an inhibitor with high selectivity for HDAC6, and characterized its effects on epithelial function including epithelial disruption, cytokine production, remodeling, mucociliary clearance and cell characteristics. Primary lung epithelial air-liquid interface cultures from COPD patients were used and the impacts of TNF, TGF-ß, cigarette smoke and bacterial challenges on epithelial function in the presence and absence of ACY-1083 were tested. Each challenge increased the permeability of the epithelial barrier whilst ACY-1083 blocked this effect and even decreased permeability in the absence of challenge. TNF was also shown to increase production of cytokines and mucins, with ACY-1083 reducing the effect. We observed that COPD-relevant stimulations created damage to the epithelium as seen on immunohistochemistry sections and that treatment with ACY-1083 maintained an intact cell layer and preserved mucociliary function. Interestingly, there was no direct effect on ciliary beat frequency or tight junction proteins indicating other mechanisms for the protected epithelium. In summary, ACY-1083 shows protection of the respiratory epithelium during COPD-relevant challenges which indicates a future potential to restore epithelial structure and function to halt disease progression in clinical practice.

Advances in the design of new types of inhaled medicines.

Inhalation of small molecule drugs has proven very efficacious for the treatment of respiratory diseases due to enhanced efficacy and a favourable therapeutic index compared with other dosing routes. It enables targeted delivery to the lung with rapid onset of therapeutic action, low systemic drug exposure, and thereby reduced systemic side effects. An increasing number of pharmaceutical companies and biotechs are investing in new modalities-for this review defined as therapeutic molecules with a molecular weight >800Da and therefore beyond usual inhaled small molecule drug-like space. However, our experience with inhaled administration of PROTACs, peptides, oligonucleotides (antisense oligonucleotides, siRNAs, miRs and antagomirs), diverse protein scaffolds, antibodies and antibody fragments is still limited. Investigating the retention and metabolism of these types of molecules in lung tissue and fluid will contribute to understanding which are best suited for inhalation. Nonetheless, the first such therapeutic molecules have already reached the clinic. This review will provide information on the physiology of healthy and diseased lungs and their capacity for drug metabolism. It will outline the stability, aggregation and immunogenicity aspects of new modalities, as well as recap on formulation and delivery aspects. It concludes by summarising clinical trial outcomes with inhaled new modalities based on information available at the end of 2021.

Mechanism-Based Insights into Removing the Mutagenicity of Aromatic Amines by Small Structural Alterations.

Aromatic and heteroaromatic amines (ArNH2) are activated by cytochrome P450 monooxygenases, primarily CYP1A2, into reactive N-arylhydroxylamines that can lead to covalent adducts with DNA nucleobases. Hereby, we give hands-on mechanism-based guidelines to design mutagenicity-free ArNH2. The mechanism of N-hydroxylation of ArNH2 by CYP1A2 is investigated by density functional theory (DFT) calculations. Two putative pathways are considered, the radicaloid route that goes via the classical ferryl-oxo oxidant and an alternative anionic pathway through Fenton-like oxidation by ferriheme-bound H2O2. Results suggest that bioactivation of ArNH2 follows the anionic pathway. We demonstrate that H-bonding and/or geometric fit of ArNH2 to CYP1A2 as well as feasibility of both proton abstraction by the ferriheme-peroxo base and heterolytic cleavage of arylhydroxylamines render molecules mutagenic. Mutagenicity of ArNH2 can be removed by structural alterations that disrupt geometric and/or electrostatic fit to CYP1A2, decrease the acidity of the NH2 group, destabilize arylnitrenium ions, or disrupt their pre-covalent transition states with guanine.

Fragment-Based Discovery of Novel Allosteric MEK1 Binders.

The MEK1 kinase plays a critical role in key cellular processes, and as such, its dysfunction is strongly linked to several human diseases, particularly cancer. MEK1 has consequently received considerable attention as a drug target, and a significant number of small-molecule inhibitors of this kinase have been reported. The majority of these inhibitors target an allosteric pocket proximal to the ATP binding site which has proven to be highly druggable, with four allosteric MEK1 inhibitors approved to date. Despite the significant attention that the MEK1 allosteric site has received, chemotypes which have been shown structurally to bind to this site are limited. With the aim of discovering novel allosteric MEK1 inhibitors using a fragment-based approach, we report here a screening method which resulted in the discovery of multiple allosteric MEK1 binders, one series of which was optimized to sub-µM affinity for MEK1 with promising physicochemical and ADMET properties.

Theoretical Studies of the Mechanism of Carbamoylation of Nucleobases by Isocyanates.

Isocyanates with the -N═C═O functional group are highly reactive compounds. They are used in various industrial applications and have been found as possible metabolites of hydroxamic acids. Isocyanates interact with biopolymers and are notorious mutagens. Mutagenic effects of isocyanates are caused by the formation of covalent adducts with nucleobases of DNA, primarily cytosines, through carbamoylation of NH2 groups to give the corresponding urea. The mechanism of carbamoylation of nucleobases by aryl isocyanates is studied by high-level density functional theory calculations. Three possible pathways are analyzed. It is demonstrated that the reaction follows the stepwise pathway, which starts with the formation of a π-complex followed by a rate-determining C-N covalent bond formation via the reactive tautomeric imine forms of the nucleobases. The reaction proceeds further through two consecutive proton transfers mediated by water molecules to give the final adduct. The predicted activation free energies of the rate-determining step in water agree with experimental data. In line with experiments, the reactivity of isocyanates toward nucleobases decreases in the order cytosine > adenine > guanine, and we rationalize this order of reactivity by the fall of their basicity and destabilization of the imine forms. Activation barriers of the alternative concerted pathways are higher than that of the preferred stepwise mechanism, and the match to experiment is poor. The kinetic effect of adding electron-withdrawing or electron-donating groups to the aryl group of aryl isocyanate is minute, which suggests that mutagenicity of isocyanates is determined exclusively by the reactivity of the -N═C═O group and as such cannot be removed by structural alterations of the adjacent aryl.

Discovery of the Oral Leukotriene C4 Synthase Inhibitor (1S,2S)-2-({5-[(5-Chloro-2,4-difluorophenyl)(2-fluoro-2-methylpropyl)amino]-3-methoxypyrazin-2-yl}carbonyl)cyclopropanecarboxylic Acid (AZD9898) as a New Treatment for Asthma.

While bronchodilators and inhaled corticosteroids are the mainstay of asthma treatment, up to 50% of asthmatics remain uncontrolled. Many studies show that the cysteinyl leukotriene cascade remains highly activated in some asthmatics, even those on high-dose inhaled or oral corticosteroids. Hence, inhibition of the leukotriene C4 synthase (LTC4S) enzyme could provide a new and differentiated core treatment for patients with a highly activated cysteinyl leukotriene cascade. Starting from a screening hit (3), a program to discover oral inhibitors of LTC4S led to (1S,2S)-2-({5-[(5-chloro-2,4-difluorophenyl)(2-fluoro-2-methylpropyl)amino]-3-methoxypyrazin-2-yl}carbonyl)cyclopropanecarboxylic acid (AZD9898) (36), a picomolar LTC4S inhibitor (IC50 = 0.28 nM) with high lipophilic ligand efficiency (LLE = 8.5), which displays nanomolar potency in cells (peripheral blood mononuclear cell, IC50,free = 6.2 nM) and good in vivo pharmacodynamics in a calcium ionophore-stimulated rat model after oral dosing (in vivo, IC50,free = 34 nM). Compound 36 mitigates the GABA binding, hepatic toxicity signal, and in vivo toxicology findings of an early lead compound 7 with a human dose predicted to be 30 mg once daily.

A Phenotypic Screening Approach Using Human Treg Cells Identified Regulators of Forkhead Box p3 Expression.

Regulatory T (Treg) cells, expressing the transcription factor forkhead box p3 (FOXP3), are the key cells regulating peripheral autoreactive T lymphocytes by suppressing effector T cells. FOXP3+ Treg cells play essential roles controlling immune responses in autoimmune diseases and cancer. Several clinical approaches (e.g., polyclonal expansion of Treg cells with anti-CD3 and anti-CD28 coated beads in the presence of drugs) are under evaluation. However, expression of FOXP3, recognized as the master regulator of Treg cells, in induced Treg cells have been shown to be instable, and molecular targets involved in regulating FOXP3 expression and Treg cell function have not been well-defined. Thus, new targets directly regulating FOXP3 expression and the expression of its downstream genes (e.g., cytotoxic T-lymphocyte-associated protein 4 (CTLA4)) have the potential to stabilize the Treg cell phenotype and function. This report describes the development of an automated medium-throughput 384-well plate flow cytometry phenotypic assay meauring the protein expression of FOXP3 and CTLA4 in human Treg cells. Screening a library of 4213 structurally diverse compounds allowed us to identify a variety of compounds regulating FOXP3 and CTLA4 expression. Further evaluation of these and related small molecules, followed by confirmation using siRNA-mediated gene knockdown, revealed three targets: euchromatic histone-lysine N-methyltransferase (EHMT2) and glycogen synthase kinase 3 alpha/beta (GSK3α/ß) as potent positive regulators of FOXP3 expression, and bromodomain and extra-terminal domain (BET) inhibitors as negative regulators of FOXP3 and CTLA4 expression. These targets have potential implications for establishing novel therapies for autoimmune diseases and cancer.

Discovery of a Novel Oral Glucocorticoid Receptor Modulator (AZD9567) with Improved Side Effect Profile.

Synthetic glucocorticoids (GC) are essential for the treatment of a broad range of inflammatory diseases. However, their use is limited by target related adverse effects on, e.g., glucose homeostasis and bone metabolism. Starting from a nonsteroidal GR ligand (4) that is a full agonist in reporter gene assays, we exploited key functional triggers within the receptor, generating a range of structurally diverse partial agonists. Of these, only a narrow subset exhibited full anti-inflammatory efficacy and a significantly reduced impact on adverse effect markers in human cell assays compared to prednisolone. This led to the discovery of AZD9567 (15) with excellent in vivo efficacy when dosed orally in a rat model of joint inflammation. Compound 15 is currently being evaluated in clinical trials comparing the efficacy and side effect markers with those of prednisolone.

Theoretical studies of the second step of the nitric oxide synthase reaction: Electron tunneling prevents uncoupling.

Nitric oxide (NO·) is a messenger molecule with diverse physiological roles including host defense, neurotransmission and vascular function. The synthesis of NO· from l-arginine is catalyzed by NO-synthases and occurs in two steps through the intermediary Nω-hydroxy-l-arginine (NHA). In both steps the P450-like reaction cycle is coupled with the redox cycle of the cofactor tetrahydrobiopterin (H4B). The mechanism of the second step is studied by Density Functional Theory calculations to ascertain the canonical sequence of proton and electron transfer (PT and ET) events. The proposed mechanism is controlled by the interplay of two electron donors, H4B and NHA. Consistent with experimental data, the catalytic cycle proceeds through the ferric-hydroperoxide complex (Cpd 0) and the following aqua-ferriheme resting state, and involves interim partial oxidation of H4B. The mechanism starts with formation of Cpd 0 from the ferrous-dioxy reactant complex by PT from the C-ring heme propionate coupled with hole transfer to H4B through the highest occupied π-orbital of NHA as a bridge. This enables PT from NHA+· to the proximal oxygen leading to the shallow ferriheme-H2O2 oxidant. Subsequent Fenton-like peroxide bond cleavage triggered by ET from the NHA-derived iminoxy-radical leads to the protonated Cpd II diradicaloid singlet stabilized by spin delocalization in H4B, and the closed-shell coordination complex of HO- with iminoxy-cation. The complex is converted to the transient C-adduct, which releases intended products upon PT to the ferriheme-HO- complex coupled with ET to the H4B+·. Deferred ET from the substrate or undue ET from/to the cofactor leads to side products.

Theoretical studies of the mechanism of N-hydroxylation of primary aromatic amines by cytochrome P450 1A2: radicaloid or anionic?

Primary aromatic and heteroaromatic amines are notoriously known as potential mutagens and carcinogens. The major event of the mechanism of their mutagenicity is N-hydroxylation by P450 enzymes, primarily P450 1A2 (CYP1A2), which leads to the formation of nitrenium ions that covalently modify nucleobases of DNA. Energy profiles of the NH bond activation steps of two possible mechanisms of N-hydroxylation of a number of aromatic amines by CYP1A2, radicaloid and anionic, are studied by dispersion-corrected DFT calculations. The classical radicaloid mechanism is mediated by H-atom transfer to the electrophilic ferryl-oxo intermediate of the P450 catalytic cycle (called Compound I or Cpd I), whereas the alternative anionic mechanism involves proton transfer to the preceding nucleophilic ferrous-peroxo species. The key structural features of the catalytic site of human CYP1A2 revealed by X-ray crystallography are maintained in calculations. The obtained DFT reaction profiles and additional calculations that account for nondynamical electron correlation suggest that Cpd I has higher thermodynamic drive to activate aromatic amines than the ferrous-peroxo species. Nevertheless, the anionic mechanism is demonstrated to be consistent with a variety of experimental observations. Thus, energy of the proton transfer from aromatic amines to the ferrous-peroxo dianion splits aromatic amines into two classes with different mutagenicity mechanisms. Favorable or slightly unfavorable barrier-free proton transfer is inherent in compounds that undergo nitrenium ion mediated mutagenicity. Monocyclic electron-rich aromatic amines that do not follow this mutagenicity mechanism show significantly unfavorable proton transfer. Feasibility of the entire anionic mechanism is demonstrated by favorable Gibbs energy profiles of both chemical steps, NH bond activation, and NO bond formation. Taken together, results suggest that the N-hydroxylation of aromatic amines in CYP1A2 undergoes the anionic mechanism. Possible reasons for the apparent inability of Cpd I to activate aromatic amines in CYP1A2 are discussed.

Theoretical studies of chemical reactivity of metabolically activated forms of aromatic amines toward DNA.

The metabolism of aromatic and heteroaromatic amines (ArNH2) results in nitrenium ions (ArNH⁺) that modify nucleobases of DNA, primarily deoxyguanosine (dG), by forming dG-C8 adducts. The activated amine nitrogen in ArNH⁺ reacts with the C8 of dG, which gives rise to mutations in DNA. For the most mutagenic ArNH2, including the majority of known genotoxic carcinogens, the stability of ArNH⁺ is of intermediate magnitude. To understand the origin of this observation as well as the specificity of reactions of ArNH⁺ with guanines in DNA, we investigated the chemical reactivity of the metabolically activated forms of ArNH2, that is, ArNHOH and ArNHOAc, toward 9-methylguanine by DFT calculations. The chemical reactivity of these forms is determined by the rate constants of two consecutive reactions leading to cationic guanine intermediates. The formation of ArNH⁺ accelerates with resonance stabilization of ArNH⁺, whereas the formed ArNH⁺ reacts with guanine derivatives with the constant diffusion-limited rate until the reaction slows down when ArNH⁺ is about 20 kcal/mol more stable than PhNH⁺. At this point, ArNHOH and ArNHOAc show maximum reactivity. The lowest activation energy of the reaction of ArNH⁺ with 9-methylguanine corresponds to the charge-transfer π-stacked transition state (π-TS) that leads to the direct formation of the C8 intermediate. The predicted activation barriers of this reaction match the observed absolute rate constants for a number of ArNH⁺. We demonstrate that the mutagenic potency of ArNH2 correlates with the rate of formation and the chemical reactivity of the metabolically activated forms toward the C8 atom of dG. On the basis of geometric consideration of the π-TS complex made of genotoxic compounds with long aromatic systems, we propose that precovalent intercalation in DNA is not an essential step in the genotoxicity pathway of ArNH2. The mechanism-based reasoning suggests rational design strategies to avoid genotoxicity of ArNH2 primarily by preventing N-hydroxylation of ArNH2.

Explanation for main features of structure-genotoxicity relationships of aromatic amines by theoretical studies of their activation pathways in CYP1A2.

Aromatic and heteroaromatic amines (ArNH(2)) represent a class of potential mutagens that after being metabolically activated covalently modify DNA. Activation of ArNH(2) in many cases starts with N-hydroxylation by P450 enzymes, primarily CYP1A2. Poor understanding of structure-mutagenicity relationships of ArNH(2) limits their use in drug discovery programs. Key factors that facilitate activation of ArNH(2) are revealed by exploring their reaction intermediates in CYP1A2 using DFT calculations. On the basis of these calculations and extensive analysis of structure-mutagenicity data, we suggest that mutagenic metabolites are generated by ferric peroxo intermediate, (CYP1A2)Fe(III)-OO(-), in a three-step heterolytic mechanism. First, the distal oxygen of the oxidant abstracts proton from H-bonded ArNH(2). The subsequent proximal protonation of the resulting (CYP1A2)Fe(III)-OOH weakens both the O-O and the O-H bonds of the oxidant. Heterolytic cleavage of the O-O bond leads to N-hydroxylation of ArNH(-) via S(N)2 mechanism, whereas cleavage of the O-H bond results in release of hydroperoxy radical. Thus, our proposed reaction offers a mechanistic explanation for previous observations that metabolism of aromatic amines could cause oxidative stress. The primary drivers for mutagenic potency of ArNH(2) are (i) binding affinity of ArNH(2) in the productive binding mode within the CYP1A2 substrate cavity, (ii) resonance stabilization of the anionic forms of ArNH(2), and (iii) exothermicity of proton-assisted heterolytic cleavage of N-O bonds of hydroxylamines and their bioconjugates. This leads to a strategy for designing mutagenicity free ArNH(2): Structural alterations in ArNH(2), which disrupt geometric compatibility with CYP1A2, hinder proton abstraction, or strongly destabilize the nitrenium ion, in this order of priority, prevent genotoxicity.

Increasing selectivity of CC chemokine receptor 8 antagonists by engineering nondesolvation related interactions with the intended and off-target binding sites.

The metabolic stability and selectivity of a series of CCR8 antagonists against binding to the hERG ion channel and cytochrome Cyp2D6 are studied by principal component analysis. It is demonstrated that an efficient way of increasing metabolic stability and selectivity of this series is to decrease compound lipophilicity by engineering nondesolvation related attractive interactions with CCR8, as rationalized by three-dimensional receptor models. Although such polar interactions led to increased compound selectivity, such a strategy could also jeopardize the DMPK profile of compounds. However, once increased potency is found, the lipophilicity can be readjusted by engineering hydrophobic substituents that fit to CCR8 but do not fit to hERG. Several such lipophilic fragments are identified by two-dimensional fragment-based QSAR analysis. Electrophysiological measurements and site-directed mutagenesis studies indicated that the repulsive interactions of these fragments with hERG are caused by steric hindrances with residue F656.

Aryl Radical Endo Cyclization of Enamidines. Selective Preparation of Trans and Cis Fused Octahydrobenzo[f]quinolines.

Aryl radicals from N-protected 6-[2-(2-halophenyl)ethyl]-1,2,3,4-tetrahydropyridines and 6-[3-(2-halophenyl)propyl]-1,2,3,4-tetrahydropyridines undergo intramolecular cyclization onto the enamide/enamidine double bond by 6-endo and 7-endo closure, respectively. In the 6-endo cyclization the trans/cis ratio of the formed N-protected octahydrobenzo[f]quinoline can be controlled, and selective synthesis of either the trans or the cis isomer can be achieved with triphenyltin hydride and tris(trimethylsilyl)silicon hydride, respectively. In the 7-endo cyclization to N-protected octahydro-1H-benzo[3,4]cyclohepta[1,2-b]pyridine, the trans fused isomer predominates, although the selectivity is low. The oxidized cyclization products, with a restored enamide/enamidine double bond, are formed at low concentrations of tris(trimethylsilyl)silicon hydride.

Intramolecular Enantioselective Palladium-Catalyzed Heck Arylation of Cyclic Enamides.

Palladium-catalyzed intramolecular cyclization of N-formyl-6-[3-(2-iodophenyl)propyl]-1,2,3,4-tetrahydropyridine (1a) and N-formyl-6-[2-(2-iodophenyl)ethyl]-1,2,3,4-tetrahydropyridine (1b) in the presence of AsPh(3) resulted in formation of the spiro compounds N-formyl-3,3',4,4'-tetrahydrospiro[naphthalene-1(2H),2'(1'H)-pyridine] (2a) and N-formyl-3',4'-dihydrospiro[indan-1,2'(1'H)-pyridine] (2b), respectively, and in the presence of PPh(3) and TlOAc in the spiro compounds N-formyl-3,4,5',6'-tetrahydrospiro[naphthalene-1(2H),2'(1'H)-pyridine] (3a) and N-formyl-5',6'-dihydrospiro[indan-1,2'(1'H)-pyridine] (3b), respectively. Cyclization of N-formyl-6-(3-{2-[(trifluoromethanesulfonyl)oxy]phenyl}propyl)-1,2,3,4-tetrahydropyridine (7) in presence of a chiral (phosphinoaryl)oxazoline ((S)-8) resulted in formation of (R)-3a and (R)-N-formyl-1',3,4,6'-tetrahydrospiro[naphthalene-1(2H),2'(3'H)-pyridine] ((R)-6a) in high enantiomeric excesses, 87% and >99%, respectively, and in good yield. The oxazoline ligand (S)-8 furnished higher enantiomeric excesses and improved regioselectivities than (R)-BINAP.

Controlled Double-Bond Migration in Palladium-Catalyzed Intramolecular Arylation of Enamidines.

Palladium-catalyzed intramolecular cyclization of N-(N'-tert-butylformimidoyl)-6-[2-(2-iodophenyl)ethyl]-1,2,3,4-tetrahydropyridine (1a) and N-(N'-tert-butylformimidoyl)-6-[3-(2-iodophenyl)propyl]-1,2,3,4-tetrahydropyridine (1b) respectively results in formation of spiro compounds 1'-(N-tert-butylformimidoyl)-3',4'-dihydrospiro[indan-1,2'(1'H)-pyridine] (4a), 1'-(N-tert-butylformimidoyl)-1',6'-dihydrospiro[indan-1,2'(3'H)-pyridine] (5a), and 1'-(N-tert-butylformimidoyl)-5',6'-dihydrospiro[indan-1,2'(1'H)-pyridine] (6a) and 1'-(N-tert-butylformimidoyl)-3,3',4,4'-tetrahydrospiro[naphthalene-1(2H),2'(1'H)-pyridine] (4b), 1'-(N-tert-butylformimidoyl)-1',3,4,6'-tetrahydrospiro[naphthalene-1(2H),2'(3'H)-pyridine] (5b), and 1'-(N-tert-butylformimidoyl)-3,4,5',6'-tetrahydrospiro[naphthalene-1(2H),2'(1'H)-pyridine] (6b). The double-bond migration process can be controlled, and any of the three double-bond isomers can be prepared by employing proper ligands. A combination of BINAP and the amidine function was required to obtain the isomers 5a and 5b with the double bond in the homoallylic position relative to the aryl group. An electrospray ionization mass spectrometric study was conducted to support suggested reaction intermediates.