DFT-based ranking of zinc-binding groups in histone deacetylase inhibitors

Density functional theory (DFT) studies in HDAC-based chemotherapeutics: Current findings, case studies and future perspectives

Density Functional Theory (DFT) is a quantum chemical computational method used to predict and analyze the electronic properties of atoms, molecules, and solids based on the density of electrons rather than wavefunctions. It provides insights into the structure, bonding, and behavior of different molecules, including those involved in the development of chemotherapeutic agents, such as histone deacetylase inhibitors (HDACis). HDACs are a wide group of metalloenzymes that facilitate the removal of acetyl groups from acetyl-lysine residues situated in the N-terminal tail of histones. Abnormal HDAC recruitment has been linked to several human diseases, especially cancer. Therefore, it has been recognized as a prospective target for accelerating the development of anticancer therapies. Researchers have studied HDACs and its inhibitors extensively using a combination of experimental methods and diverse in-silico approaches such as machine learning and quantitative structure-activity relationship (QSAR) methods, molecular docking, molecular dynamics, pharmacophore mapping, and more. In this context, DFT studies can make significant contribution by shedding light on the molecular properties, interactions, reaction pathways, transition states, reactivity and mechanisms involved in the development of HDACis. This review attempted to elucidate the scope in which DFT methodologies may be used to enhance our comprehension of the molecular aspects of HDAC inhibitors, aiding in the rational design and optimization of these compounds for therapeutic applications in cancer and other ailments. The insights gained can guide experimental efforts toward developing more potent and selective HDAC inhibitors.

In silico and in vitro assessment of drugs potentially causing adverse effects by inhibiting CYP17A1

Cytochrome P450 enzymes (CYPs) play a crucial role in the metabolism and synthesis of various compound classes. While drug-metabolizing CYP enzymes are frequently investigated as anti-targets, the inhibition of CYP enzymes involved in adrenal steroidogenesis is not well studied. The steroidogenic enzyme CYP17A1 is a dual-function enzyme catalyzing hydroxylase and lyase reactions relevant for the biosynthesis of adrenal glucocorticoids and androgens. Inhibition of CYP17A1-hydroxylase leads to pseudohyperaldosteronism with subsequent excessive mineralocorticoid receptor activation, hypertension and hypokalemia. In contrast, specific inhibition of the lyase function might be beneficial for the treatment of prostate cancer by decreasing adrenal androgen levels. This study combined in silico and in vitro methods to identify drugs inhibiting CYP17A1. The most potent CYP17A1 inhibitors identified are serdemetan, mocetinostat, nolatrexed, liarozole, and talarozole. While some of these drugs are currently under investigation for the treatment of various cancers, their potential for the treatment of prostate cancer is yet to be explored. The DrugBank database was screened for CYP17A1 inhibitors, to increase the awareness for the risk of drug-induced pseudohyperaldosteronism and to highlight drugs so far unknown for their potential to cause side effects resulting from CYP17A1 inhibition.

The Zinc-Binding Group Effect: Lessons from Non-Hydroxamic Acid Vorinostat Analogs

Histone deacetylases (HDACs) are enzymes pursued as drug targets in various cancers and several non-oncological conditions, such as inflammation and neurodegenerative disorders. In the past decade, HDAC inhibitors (HDACi) have emerged as relevant pharmaceuticals, with many efforts devoted to the development of new representatives. However, the growing safety concerns regarding the established hydroxamic acid-based HDAC inhibitors tend to drive current research more toward the design of inhibitors bearing alternative zinc-binding groups (ZBGs). This Perspective presents an overview of all non-hydroxamic acid ZBGs that have been incorporated into the clinically approved prototypical HDACi, suberoylanilide hydroxamic acid (vorinostat). This provides the unique opportunity to compare the inhibition potential and biological effects of different ZBGs in a direct way, as the compounds selected for this Perspective differ only in their ZBG. To that end, different strategies used to select a ZBG, its properties, activity, and liabilities are discussed.

From Density Functional Theory to Conceptual Density Functional Theory and Biosystems

The position of conceptual density functional theory (CDFT) in the history of density functional theory (DFT) is sketched followed by a chronological report on the introduction of the various DFT descriptors such as the electronegativity, hardness, softness, Fukui function, local version of softness and hardness, dual descriptor, linear response function, and softness kernel. Through a perturbational approach they can all be characterized as response functions, reflecting the intrinsic reactivity of an atom or molecule upon perturbation by a different system, including recent extensions by external fields. Derived descriptors such as the electrophilicity or generalized philicity, derived from the nature of the energy vs. N behavior, complete this picture. These descriptors can be used as such or in the context of principles such as Sanderson’s electronegativity equalization principle, Pearson’s hard and soft acids and bases principle, the maximum hardness, and more recently, the minimum electrophilicity principle. CDFT has known an ever-growing use in various subdisciplines of chemistry: from organic to inorganic chemistry, from polymer to materials chemistry, and from catalysis to nanotechnology. The increasing size of the systems under study has been coped with thanks to methodological evolutions but also through the impressive evolution in software and hardware. In this flow, biosystems entered the application portfolio in the past twenty years with studies varying (among others) from enzymatic catalysis to biological activity and/or the toxicity of organic molecules and to computational peptidology. On the basis of this evolution, one can expect that “the best is yet to come”.

Theoretical Reactivity Study of Indol-4-Ones and Their Correlation with Antifungal Activity

Chemical reactivity descriptors of indol-4-ones obtained via density functional theory (DFT) and hard–soft acid–base (HSAB) principle were calculated to prove their contribution in antifungal activity. Simple linear regression was made for global and local reactivity indexes. Results with global descriptors showed a strong relationship between antifungal activity vs. softness (S) (r = 0.98) for series I (6, 7a–g), and for series II (8a–g) vs. chemical potential (µ), electronegativity (χ) and electrophilicity (ω) (r = 0.86), p < 0.05. Condensed reactivity descriptors s_k⁺, ω_k⁻ for different fragments had strong relationships for series I and II (r = 0.98 and r = 0.92). Multiple linear regression was statistically significant for S (r = 0.98), η (r = 0.91), and µ/ω (r = 0.91) in series I. Molecular electrostatic potential maps (MEP) showed negative charge accumulation around oxygen of carbonyl group and positive accumulation around nitrogen. Fukui function isosurfaces showed that carbons around nitrogen are susceptible to electrophilic attack, whereas the carbon atoms of the carbonyl and phenyl groups are susceptible to nucleophilic attack for both series. The above suggest that global softness in conjunction with softness and electrophilicity of molecular fragments in enaminone systems and pyrrole rings contribute to antifungal activity of indol-4-ones.

Impact of Phytochemicals and Dietary Patterns on Epigenome and Cancer

Cancer remains one of the leading causes of death around the world. Initially it is recognized as a genetic disease, but now it is known to involve epigenetic abnormalities along with genetic alterations. Epigenetics refers to heritable changes that are not encoded in the DNA sequence itself, but play an important role in the control of gene expression. It includes changes in DNA methylation, histone modifications, and RNA interference. Although it is heritable, environmental factors such as diet could directly influence epigenetic mechanisms in humans. This article will focus on the role of dietary patterns and phytochemicals that have been demonstrated to influence the epigenome and more precisely histone and non-histone proteins modulation by acetylation that helps to induce apoptosis and phosphorylation inhibition, which counteracts with cells proliferation. Recent developments discussed here enhance our understanding of how dietary intervention could be beneficial in preventing or treating cancer and improving health outcomes.

Synthesis, biological characterization and molecular modeling insights of spirochromanes as potent HDAC inhibitors

In the last decades, inhibitors of histone deacetylases (HDAC) have become an important class of anti-cancer agents. In a previous study we described the synthesis of spiro[chromane-2,4'-piperidine]hydroxamic acid derivatives able to inhibit histone deacetylase enzymes. Herein, we present our exploration for new derivatives by replacing the piperidine moiety with various cycloamines. The goal was to obtain highly potent compounds with a good in vitro ADME profile. In addition, molecular modeling studies unravelled the binding mode of these inhibitors.

Histone deacetylases: structural determinants of inhibitor selectivity

Histone deacetylases (HDACs) are epigenetic targets with an important role in cancer, neurodegeneration, inflammation, and metabolic disorders. Although clinically effective HDAC inhibitors have been developed, the design of inhibitors with the desired isoform(s) selectivity remains a challenge. Selective inhibitors could help clarify the function of each isoform, and provide therapeutic agents having potentially fewer adverse effects. Crystal structures of several HDACs have been reported, enabling structure-based drug design and providing important information to understand enzyme function. Here, we provide a comprehensive review of the structural information available on HDACs, discussing both conserved and isoform-specific structural and mechanistic features. We focus on distinctive aspects that help rationalize inhibitor selectivity, and provide structure-based recommendations for achieving the desired selectivity.

Application of QM/MM and QM methods to investigate histone deacetylase 8

Computational chemistry plays an important supporting role in the early stages of drug discovery research.

Inhibition and mechanism of HDAC8 revisited

Histone deacetylases (HDACs) have found intense interest as drug targets for a variety of diseases, but there is disagreement about basic aspects of the inhibition and mechanism of HDACs. QM/MM calculations of HDAC8 including a large QM region provide a model that is consistent with the available crystal structures and structure-activity relationships of different HDAC inhibitors. The calculations support a spontaneous proton transfer from a hydroxamic acid to an active site histidine upon binding to the zinc. The role of the H142/D176 catalytic dyad as the general base of the reaction is elucidated. The reasons for the disagreements between previous proposals are discussed. The results provide detailed insights into the unique mechanism of HDACs, including the role of the two catalytic dyads and function of the potassium near the active site. They also have important implications for the design of novel inhibitors for a number of HDACs such as the class IIa HDACs.

Inhibitory Activity of Linoleic Acid Isolated from Proso and Japanese Millet toward Histone Deacetylase

Linoleic acid was isolated from both the methanol extracts of proso and Japanese millet as a histone deacetylase inhibitor. It showed uncompetitive inhibitory activity toward histone deacetylase (IC(50)=0.51 mM) and potent cytotoxicity toward human leukemia K562 (IC(50)=68 microM) and prostate cancer LNCaP cells (IC(50)=193 microM). Millet containing linoleic acid might have anti-tumor activity.

Epigenetic molecular recognition: a biomolecular modeling perspective

The abnormal regulation of epigenetic protein families is associated with the onset and progression of various human diseases. However, epigenetic processes remain relatively obscure at the molecular level, thus preventing the rational design of chemical therapeutics. An array of robust computational and modeling approaches can complement experiments to shed light on the complex mechanisms of epigenetic molecular recognition and can guide medicinal chemists in designing selective and potent drug molecules. Herein we present a review of studies focused on epigenetic molecular recognition from a biomolecular modeling viewpoint. Although the known epigenetic targets are numerous, this review focuses on the more limited protein families on which computational modeling has been successfully applied. Therefore, we review three main topics: 1) histone deacetylases, 2) histone demethylases, and 3) histone tail dynamics. A brief review of the biological background and biomedical relevance is presented for each topic, followed by a detailed discussion of the computational studies and their relevance.

Computational exploration of zinc binding groups for HDAC inhibition

Histone deacetylases (HDACs) have emerged as important drug targets in epigenetics. The most common HDAC inhibitors use hydroxamic acids as zinc binding groups despite unfavorable pharmacokinetic properties. A two-stage protocol of M05-2X calculations of a library of 48 fragments in a small model active site, followed by QM/MM hybrid calculations of the full enzyme with selected binders, is used to prospectively select potential bidentate zinc binders. The energetics and interaction patterns of several zinc binders not previously used for the inhibition of HDACs are discussed.

Insights from comprehensive multiple receptor docking to HDAC8

A systematic investigation of the available crystal structures of HDAC8 and of the influence of different receptor structures and docking protocols is presented. The study shows that the open conformation of HDAC8 may be preferred by ligands with flexible surface binding groups, as such a conformation allows the ligands to minimize their exposure to solvent upon binding. This observation allowed us to rationalize the excellent potency of pyrazole-based inhibitors compared to that of isoxazole-based inhibitors.

A proton-shuttle reaction mechanism for histone deacetylase 8 and the catalytic role of metal ions

Zinc-dependent histone deacetylase 8 (HDAC8) catalyzes the removal of acetyl moieties from histone tails, and is critically involved in regulating chromatin structure and gene expression. The detailed knowledge of its catalytic process is of high importance since it has been established as a most promising target for the development of new antitumor drugs. By employing Born-Oppenheimer ab initio QM/MM molecular dynamics simulations and umbrella sampling, a state-of-the-art approach to simulate enzyme reactions, we have provided further evidence against the originally proposed general acid-base catalytic pair mechanism for Zinc-dependent histone deacetylases. Instead, our results indicated that HDAC8 employs a proton-shuttle catalytic mechanism, in which a neutral His143 first serves as the general base to accept a proton from the zinc-bound water molecule in the initial rate-determining nucleophilic attack step, and then shuttles it to the amide nitrogen atom to facilitate the cleavage of the amide bond. During the deacetylation process, the Zn(2+) ion changes its coordination mode and plays multiple catalytic roles. For the K(+) ion, which is located about 7 A from the catalytic Zn(2+) ion and conserved in class I and II HDACs, our simulations indicated that its removal would lead to the different transition state structure and a higher free energy reaction barrier for the rate-determining step. It is found that the existence of this conserved K(+) ion would enhance the substrate binding, increase the basicity of His143, strengthen the catalytic role of zinc ion, and improve the transition state stabilization by the enzyme environment.

Chemopreventive mechanisms of α-keto acid metabolites of naturally occurring organoselenium compounds

Previous studies on the chemopreventive mechanisms of dietary selenium have focused on its incorporation into antioxidative selenoproteins, such as glutathione peroxidase and thioredoxin reductase. Several studies, however, have revealed that dietary selenium in the form of L-selenomethionine and the 21st amino acid, selenocysteine, also have intrinsic anti-cancer properties. Biochemical mechanisms previously investigated to contribute to their anticancer effects involve β- and γ-lyase reactions. Some pyridoxal 5'-phosphate (PLP)-containing enzymes can catalyze a β-lyase reaction with Se-methyl-L-selenocysteine (MSC) generating pyruvate and ammonia. Other PLP-enzymes can catalyze a γ-lyase reaction with L-selenomethionine (SM) generating α-ketobutyrate and ammonia. In both cases, a purported third product is methylselenol (CH(3)SeH). Although not directly quantifiable, as a result of its extreme hydrophobicity and high vapor pressure, CH(3)SeH has been indirectly observed to act through the alteration of protein-sulfhydryl moieties on redox-responsive signal and transcription factors, thereby maintaining a non-proliferative intracellular environment. We have considered the possibility that α-keto acid analogues of MSC (i.e., methylselenopyruvate; MSP) and SM (i.e., α-keto-γ-methylselenobutyrate; KMSB), generated via a transamination and/or L-amino acid oxidase reaction may also be chemoprotective. Indeed, these compounds were shown to increase the level of histone-H3 acetylation in human prostate and colon cancer cells. MSP and KMSB structurally resemble butyrate, an inhibitor of several histone deacetylases. Thus, the seleno α-keto acid metabolites of MSC and SM, along with CH(3)SeH derived from β- and γ-lyase reactions, may be potential direct-acting metabolites of organoselenium that lead to de-repression of silenced tumor suppressor proteins and/or regulation of genes and signaling molecules.

Inside HDAC with HDAC inhibitors

Histone deacetylase inhibitors are a large group of diverse molecules intrinsically able to inhibit cell proliferation in various cancer cell lines. Their apoptotic effects have been linked to the modulation in the expression of several regulatory tumor suppressor genes caused by the modified status of histone acetylation, a key event in chromatin remodelling. As the initial histone deacetylase activity of HDAC has been extended to other proteins, the possible other biological mechanisms modified by HDAC inhibitor treatments are still to be clarified. The need for HDAC isoform selective inhibitors is an important issue to serve this goal. This review discusses the approaches proposed by several research groups working on the synthesis of HDAC inhibitors, based on modelling studies and the way these findings were used to obtain new HDAC inhibitors with possible isoform selectivity.

Enzymatic catalysis: the emerging role of conceptual density functional theory

Experimentalists and quantum chemists are living in a different world. A wealth of theoretical enzymology-related publications is hardly known by experimentalists, and vice versa. Our aim is to bring both worlds together and to show the powerful possibilities of a multidisciplinary approach to study subtle details of complicated enzymatic processes to a broad readership. MD simulations and QM/MM approaches often focus on the calculation of reaction paths based on activation energies, which is a time-consuming task. A valuable alternative is the reactivity descriptors founded in conceptual DFT like softness, electrophilicity, and the Fukui function, which describe the kinetic aspects of a reaction in terms of the response to perturbations in N and/or upsilon(r), typical for a chemical reaction, of the reagents in the ground state. As such, the relative energies at the beginning of the reaction predict a sequence of activation energies only based on the properties of the reactants (Figure 5 ). In 2003, Geerlings et al. published a key review giving a detailed description of the principles and concepts of conceptual DFT and highlighting its success to study generalized acid/base reactions including addition, substitution, and elimination reactions. Since the time that this review appeared, conceptual DFT has proven its strength in literally hundreds of papers with application to organic and inorganic reactions. Its role in unravelling enzymatic reaction mechanisms, in handling experimentally difficult accessible biochemical problems, and in the interpretation of biochemical experimental observations is emerging and very promising.

Alpha-keto acid metabolites of naturally occurring organoselenium compounds as inhibitors of histone deacetylase in human prostate cancer cells

Histone deacetylase (HDAC) inhibitors are gaining interest as cancer therapeutic agents. We tested the hypothesis that natural organoselenium compounds might be metabolized to HDAC inhibitors in human prostate cancer cells. Se-Methyl-L-selenocysteine (MSC) and selenomethionine are amino acid components of selenium-enriched yeast. In a cell-free system, glutamine transaminase K (GTK) and L-amino acid oxidase convert MSC to the corresponding alpha-keto acid, beta-methylselenopyruvate (MSP), and L-amino acid oxidase converts selenomethionine to its corresponding alpha-keto acid, alpha-keto-gamma-methylselenobutyrate (KMSB). Although methionine (sulfur analogue of selenomethionine) is an excellent substrate for GTK, selenomethionine is poorly metabolized. Structurally, MSP and KMSB resemble the known HDAC inhibitor butyrate. We examined androgen-responsive LNCaP cells and androgen-independent LNCaP C4-2, PC-3, and DU145 cells and found that these human prostate cancer cells exhibit endogenous GTK activities. In the corresponding cytosolic extracts, the metabolism of MSC was accompanied by the concomitant formation of MSP. In MSP-treated and KMSB-treated prostate cancer cell lines, acetylated histone 3 levels increased within 5 hours, and returned to essentially baseline levels by 24 hours, suggesting a rapid, transient induction of histone acetylation. In an in vitro HDAC activity assay, the selenoamino acids, MSC and selenomethionine, had no effect at concentrations up to 2.5 mmol/L, whereas MSP and KMSB both inhibited HDAC activity. We conclude that, in addition to targeting redox-sensitive signaling proteins and transcription factors, alpha-keto acid metabolites of MSC and selenomethionine can alter HDAC activity and histone acetylation status. These findings provide a potential new paradigm by which naturally occurring organoselenium might prevent the progression of human prostate cancer.

Synthesis and histone deacetylase inhibitory activity of largazole analogs: alteration of the zinc-binding domain and macrocyclic scaffold

Fourteen analogs of the marine natural product largazole have been prepared and assayed against histone deacetylases (HDACs) 1, 2, 3, and 6. Olefin cross-metathesis was used to efficiently access six variants of the side-chain zinc-binding domain, while adaptation of our previously reported modular synthesis allowed probing of the macrocyclic cap group.

Computational studies on the histone deacetylases and the design of selective histone deacetylase inhibitors

The catalytic activity of the histone deacetylase (HDAC) enzymes is directly relevant to the pathogenesis of cancer as well as several other diseases. HDAC inhibitors have been shown to have the potential to treat several types of cancers. The role of computational study of the HDAC enzymes is reviewed, with particular emphasis on the important role of molecular modeling to the development of HDAC inhibitors with improved efficacy and selectivity. The use of two computational approaches--one structure-based, and the second ligand-based--toward inhibitors against the different HDAC sub-classes, are summarized.

Identification of KD5170: a novel mercaptoketone-based histone deacetylase inhibitor

We report the identification of KD5170, a potent mercaptoketone-based Class I and II-histone deacetylase inhibitor that demonstrates broad spectrum cytotoxic activity against a range of human tumor-derived cell lines. KD5170 exhibits robust and sustained histone H3 hyperacetylation in HCT-116 xenograft tumors following single oral or i.v. dose and inhibition of tumor growth following chronic dosing.

KD5170, a novel mercaptoketone-based histone deacetylase inhibitor that exhibits broad spectrum antitumor activity in vitro and in vivo

Histone deacetylase (HDAC) inhibitors have garnered significant attention as cancer drugs. These therapeutic agents have recently been clinically validated with the market approval of vorinostat (SAHA, Zolinza) for treatment of cutaneous T-cell lymphoma. Like vorinostat, most of the small-molecule HDAC inhibitors in clinical development are hydroxamic acids, whose inhibitory activity stems from their ability to coordinate the catalytic Zn2+ in the active site of HDACs. We sought to identify novel, nonhydroxamate-based HDAC inhibitors with potentially distinct pharmaceutical properties via an ultra-high throughput small molecule biochemical screen against the HDAC activity in a HeLa cell nuclear extract. An alpha-mercaptoketone series was identified and chemically optimized. The lead compound, KD5170, exhibits HDAC inhibitory activity with an IC50 of 0.045 micromol/L in the screening biochemical assay and an EC50 of 0.025 micromol/L in HeLa cell-based assays that monitor histone H3 acetylation. KD5170 also exhibits broad spectrum classes I and II HDAC inhibition in assays using purified recombinant human isoforms. KD5170 shows significant antiproliferative activity against a variety of human tumor cell lines, including the NCI-60 panel. Significant tumor growth inhibition was observed after p.o. dosing in human HCT-116 (colorectal cancer), NCI-H460 (non-small cell lung carcinoma), and PC-3 (prostate cancer) s.c. xenografts in nude mice. In addition, a significant increase in antitumor activity and time to end-point occurred when KD5170 was combined with docetaxel in xenografts of the PC-3 prostate cancer cell line. The biological and pharmaceutical profile of KD5170 supports its continued preclinical and clinical development as a broad spectrum anticancer agent.