Mechanism-based Irreversible Inhibitor Research Articles

Discovery of AZD4831, a Mechanism-Based Irreversible Inhibitor of Myeloperoxidase, As a Potential Treatment for Heart Failure with Preserved Ejection Fraction.

Myeloperoxidase is a promising therapeutic target for treatment of patients suffering from heart failure with preserved ejection fraction (HFpEF). We aimed to discover a covalent myeloperoxidase inhibitor with high selectivity for myeloperoxidase over thyroid peroxidase, limited penetration of the blood–brain barrier, and pharmacokinetics suitable for once-daily oral administration at low dose. Structure–activity relationship, biophysical, and structural studies led to prioritization of four compounds for in-depth safety and pharmacokinetic studies in animal models. One compound (AZD4831) progressed to clinical studies on grounds of high potency (IC50, 1.5 nM in vitro) and selectivity (>450-fold vs thyroid peroxidase in vitro), the mechanism of irreversible inhibition, and the safety profile. Following phase 1 studies in healthy volunteers and a phase 2a study in patients with HFpEF, a phase 2b/3 efficacy study of AZD4831 in patients with HFpEF started in 2021.

An in silico discovery of potential 3CL protease inhibitors of SARS-CoV-2 based upon inactivation of the cysteine 145-Histidine 41 catalytic dyad

Coronavirus disease 19 (COVID19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Currently, several countries are at risk of the pandemic caused by this virus. In the absence of any vaccine or virus-specific antiviral treatments, the need is to fast track search for potential drug candidates to combat the virus. Though there are known drugs that are being repurposed to fight against the SARS-CoV-2, there is a requirement for the virus-specific drugs at the earliest. One of the main drug targets of SARS-CoV-2 is an essential non-structural protein, 3CL protease, critical for the life cycle of the virus. We have used molecular docking studies to screen a chemically diverse set of small molecules to identify potential drug candidates to target this protein. Of the 22,630 molecules from varied small molecule libraries, based on the binding affinities and physicochemical properties, we finalized 30 molecules to be potential drug candidates. Eight of these molecules bind in a manner allowing for the scope of a nearly orthogonal backside nucleophilic attack on their suitably placed electrophilic carbonyl groups by the thiol group of cysteine residue 145, while remaining inside a 4 Ǻ distance range. It is interesting since carbonyl groups are known to be attacked in a similar fashion by external nucleophiles and can be relevant when considering these molecules as potential mechanism-based irreversible inhibitors of the 3CLPro. Further, ADMET analysis and Molecular dynamics simulations and available bioactive assays led to the identification of three molecules with high potential to be explored as drug candidates/lead molecules to target 3CLPro of SARS-CoV-2. Communicated by Ramaswamy H. Sarma

Hydride Abstraction as the Rate-Limiting Step of the Irreversible Inhibition of Monoamine Oxidase B by Rasagiline and Selegiline: A Computational Empirical Valence Bond Study.

Monoamine oxidases (MAOs) catalyze the degradation of a very broad range of biogenic and dietary amines including many neurotransmitters in the brain, whose imbalance is extensively linked with the biochemical pathology of various neurological disorders, and are, accordingly, used as primary pharmacological targets to treat these debilitating cognitive diseases. Still, despite this practical significance, the precise molecular mechanism underlying the irreversible MAO inhibition with clinically used propargylamine inhibitors rasagiline and selegiline is still not unambiguously determined, which hinders the rational design of improved inhibitors devoid of side effects current drugs are experiencing. To address this challenge, we present empirical valence bond QM/MM simulations of the rate-limiting step of the MAO inhibition involving the hydride anion transfer from the inhibitor α-carbon onto the N5 atom of the flavin adenin dinucleotide (FAD) cofactor. The proposed mechanism is strongly supported by the obtained free energy profiles, which confirm a higher reactivity of selegiline over rasagiline, while the calculated difference in the activation Gibbs energies of ΔΔG‡ = 3.1 kcal mol−1 is found to be in very good agreement with that from the measured literature kinact values that predict a 1.7 kcal mol−1 higher selegiline reactivity. Given the similarity with the hydride transfer mechanism during the MAO catalytic activity, these results verify that both rasagiline and selegiline are mechanism-based irreversible inhibitors and offer guidelines in designing new and improved inhibitors, which are all clinically employed in treating a variety of neuropsychiatric and neurodegenerative conditions.

A Simple Approach for Pilot Analysis of Time-dependent Enzyme Inhibition: Discrimination Between Mechanism-based Inactivation and Tight Binding Inhibitor Behavior

The increase in enzyme inhibition developed during prolonged incubation of an enzyme preparation with a chemical substance may be associated with both the non-covalent and also with covalent enzyme-inhibitor complex formation. The latter case involves catalytic conversion of a mechanism-based irreversible inhibitor (a poor substrate) into a reactive species forming covalent adduct(s) with the enzyme and thus irreversibly inactivating the enzyme molecule. Using a simple approach, based on comparison of enzyme inhibition after preincubation with a potential inhibitor at 4ºC or 37ºC we have analyzed inhibition of monoamine oxidase A (MAO A) by known MAO inhibitors pargyline and pirlindole (pyrazidol). MAO A inhibitory activity of pirlindole (reversible tight binding inhibitor of MAO A) assayed after mitochondrial wash was basically the same for the incubation at both 4ºC and 37ºC. In contrast to pirlindole, the effect of pargyline (mechanism based irreversible MAO inhibitor) strongly depended on the temperature of the incubation medium. At 37ºC the residual activity MAO A in the mitochondrial fraction after washing was significantly lower than in the mitochondrial samples incubated with pargyline at 4ºC. Results of this study suggest that using analysis of both time- and temperature-dependence of inhibition it is possible to discriminate mechanism-based irreversible inhibition and reversible tight binding inhibition of target enzym

Activity-Based Probes for Glycosidases: Profiling and Other Applications.

Glycosidases mediate the fragmentation of glycoconjugates in the body, including the vital recycling of endogenous molecules. Several inherited diseases in man concern deficiencies in lysosomal glycosidases degrading glycosphingolipids. Prominent is Gaucher disease caused by an impaired lysosomal β-glucosidase (glucocerebrosidase, GBA) and resulting in pathological lysosomal storage of glucosylceramide (glucocerebroside) in tissue macrophages. GBA is a retaining glucosidase with a characteristic glycosyl-enzyme intermediate formed during catalysis. Using the natural suicide inhibitor cyclophellitol as a lead, we developed mechanism-based irreversible inhibitors of GBA equipped with a fluorescent reporter. These reagents covalently link to the catalytic nucleophile residue of GBA and permit specific and sensitive visualization of active enzyme molecules. The amphiphilic activity-based probes (ABPs) allow in situ detection of active GBA in cells and organisms. Furthermore, they may be used to biochemically confirm the diagnosis of Gaucher disease and they might assist in screening for small compounds interacting with the catalytic pocket. While the focus of this chapter is ABPs for β-glucosidases and Gaucher disease, the described concept has meanwhile been extended to other retaining glycosidases and related disease conditions as well.

Abstract 1489: Targeting the mitochondrial enzyme proline dehydrogenase with a mechanism-based irreversible inhibitor induces selective mitochondrial stress and enhances breast cancer cell death under hypoxia

Abstract Proline dehydrogenase (PRODH) is a p53-inducible inner mitochondrial membrane flavoprotein functionally linked to electron transport for proline catabolism and intracellular ATP production, particularly under nutrient stress conditions. We have previously shown that in breast cancer cells, PRODH and glutaminase (GLS1) transcript levels are inversely correlated, supplying anaplerotic glutamate to triple-negative (GLS1) and luminal (PRODH) breast cancer subtypes by different means; and that siRNA knockdown or competitive inhibition of PRODH induces synthetic lethal interactions with both GLS1 inhibition and p53 upregulation in various malignant (ZR-75-1, DU4475, MCF7) but not normal (MCF10A) breast epithelial models. In the present study we have synthesized and structurally modeled a novel mechanism-based irreversible (suicide) inhibitor of PRODH, N-propargylglycine (PPG), that shows more than 2-fold greater capacity to inhibit PRODH activity in isolated mitochondrial assays when compared to competitive PRODH inhibitors (L-tetrahydrofuroic acid, THFA; or 5-oxo-2-tetrahydrofurancarboxylic acid, 5-oxo). Modeling human PRODH predicts a post-reactive PPG structure with PPG covalently linked to the enzyme pocket’s FAD moiety, producing pocket distortion that does not occur with competitive PRODH inhibitors. Reflecting PPG’s irreversible binding to PRODH, mitochondria isolated from PPG treated ZR-75-1 cells are unable to catabolize proline despite being able to efficiently catabolize malate; in contrast, isolated mitochondria from 5-oxo treated cells remain efficient at catabolizing both proline and malate. Unexpectedly, we observed that PPG but not the competitive inhibitors induces selective degradation of mitochondrial PRODH protein levels within 24 h of cell culture treatment followed by loss of other mitochondrial proteins like complex-I NDUFS1 but not by concomitant loss of cytosolic FAD-containing proteins like MTHRF. MitoTracker assays confirm the selective cellular loss of mitochondrial mass in ZR-75-1 cells within 24 h of PPG treatment. To confirm that suicide inhibition of PRODH can also induce synthetically lethal metabolic interactions, breast cancer cells (MCF7) were cultured under normoxic (20% O2) or hypoxic (1% O2) conditions and then treated with PPG and a p53 upregulator known to induce PRODH expression (MI-63). Cell viability demonstrated that during hypoxia PPG with p53 upregulation synergistically reduces cell survival at 48 h, confirming the synthetic lethality of this treatment combination. Altogether, these findings support the preclinical development of suicide PRODH inhibitors as potential cancer therapeutics capable of inducing mitochondrial stress, exploiting synthetically lethal metabolic conditions, and selectively enhancing cancer cell death. Citation Format: Gary K. Scott, Katya Frazier, Christina Yau, Beatrice Becker, Mauricio Ortega, Christopher C. Benz. Targeting the mitochondrial enzyme proline dehydrogenase with a mechanism-based irreversible inhibitor induces selective mitochondrial stress and enhances breast cancer cell death under hypoxia [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1489. doi:10.1158/1538-7445.AM2017-1489

Regulation of the nitric oxide oxidase activity of myeloperoxidase by pharmacological agents

The leukocyte-derived heme enzyme myeloperoxidase (MPO) is released extracellularly during inflammation and impairs nitric oxide (NO) bioavailability by directly oxidizing NO or producing NO-consuming substrate radicals. Here, structurally diverse pharmacological agents with activities as MPO substrates/inhibitors or antioxidants were screened for their effects on MPO NO oxidase activity in human plasma and physiological model systems containing endogenous MPO substrates/antioxidants (tyrosine, urate, ascorbate). Hydrazide-based irreversible/reversible MPO inhibitors (4-ABAH, isoniazid) or the sickle cell anaemia drug, hydroxyurea, all promoted MPO NO oxidase activity. This involved the capacity of NO to antagonize MPO inhibition by hydrazide-derived radicals and/or the ability of drug-derived radicals to stimulate MPO turnover thereby increasing NO consumption by MPO redox intermediates or NO-consuming radicals. In contrast, the mechanism-based irreversible MPO inhibitor 2-thioxanthine, potently inhibited MPO turnover and NO consumption. Although the phenolics acetaminophen and resveratrol initially increased MPO turnover and NO consumption, they limited the overall extent of NO loss by rapidly depleting H2O2 and promoting the formation of ascorbyl radicals, which inefficiently consume NO. The vitamin E analogue trolox inhibited MPO NO oxidase activity in ascorbate-depleted fluids by scavenging NO-consuming tyrosyl and urate radicals. Tempol and related nitroxides decreased NO consumption in ascorbate-replete fluids by scavenging MPO-derived ascorbyl radicals. Indoles or apocynin yielded marginal effects. Kinetic analyses rationalized differences in drug activities and identified criteria for the improved inhibition of MPO NO oxidase activity. This study reveals that widely used agents have important implications for MPO NO oxidase activity under physiological conditions, highlighting new pharmacological strategies for preserving NO bioavailability during inflammation.

Abstract PR10: A DNA hypomethylation signature predicts novel antitumor activity of LSD1 inhibition in SCLC

Abstract Epigenetic dysregulation has emerged as an important mechanism in cancer. Alterations in epigenetic machinery have become a major focus for new targeted therapies. The current report describes the discovery and biological activity of a cyclopropylamine containing inhibitor of Lysine Demethylase 1 (LSD1), GSK2879552. This small molecule is a potent, selective, orally bioavailable, mechanism-based irreversible inhibitor of LSD1. A proliferation screen of cell lines representing a number of tumor types indicated that small cell lung carcinoma (SCLC) is sensitive to LSD1 inhibition. The subset of SCLC lines that undergo growth inhibition in response to GSK2879552 exhibit DNA hypomethylation of a signature set of probes suggesting this may be used as a predictive biomarker of activity. This targeted mechanism coupled with a novel predictive biomarker make LSD1 inhibition an exciting potential therapy for SCLC, a highly prevalent, rarely cured, tumor type representing approximately 15% of all lung cancers. Citation Format: Helai Mohammad, Ryan Kruger. A DNA hypomethylation signature predicts novel antitumor activity of LSD1 inhibition in SCLC. [abstract]. In: Proceedings of the AACR Special Conference on Chromatin and Epigenetics in Cancer; Sep 24-27, 2015; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2016;76(2 Suppl):Abstract nr PR10.

Abstract 5402: A new anticancer strategy based on inhibiting mitochondrial proline dehydrogenase (PRODH) and exploiting synthetic lethal interactions with p53 restoration and/or glutaminase (GLS1) inhibition

Abstract From prokaryotes to the highest eukaryotes, proline is catabolized by a unique and structurally conserved flavoprotein, proline dehydrogenase (PRODH). In eukaryotes PRODH associates with the inner mitochondrial membrane and catalyzes the first and rate limiting catabolic step, transferring two electrons to the electron transport chain where they can produce ATP and/or reactive oxygen species (ROS). Following recognition that PRODH is one of the most strongly upregulated genes by the tumor suppressing protein, p53, its capacity to generate reactive oxygen species (ROS) and induce apoptosis initially qualified it as a tumor suppressing response, mediating the effects of p53 upregulation). However, we have definitively shown that while PRODH can induce mitochondrial ROS production it does so almost exclusively at other mitochondrial sites (e.g. complex I) via its anaplerotic glutamate production and not directly by itself. Furthermore, our recent studies indicate that PRODH critically supports breast cancer cell growth and survival by consuming proline for anaplerotic glutamate production, bypassing glutaminase (GLS1) to fuel oxidative phosphorylation and sustain ATP levels. We now show that PRODH knockdown, as well as its enzymatic inhibition by proline competitive inhibitors like L-tetrahydro-2-furoic acid (L-THFA) or (S)-5-oxo-2-tetrahydrofurancarboxylic acid (5-oxo), induce breast cancer cell apoptosis (cleaved PARP)and reduce viable cell growth within 48 h. Given that PRODH can provide an alternate source of mitochondrial glutamate for glutamine addicted and GLS1-dependent cancer cells, we evaluated the expression microarray profiles of 51 different human breast cancer lines and found a significant breast cancer subtype association with PRODH expression (luminal and HER2+ > basal-like), and also a strong inverse correlation between PRODH and GLS1 expression, suggesting that one or the other of these mitochondrial pathways is needed to feed breast cancer's anaplerotic addiction to glutamate. Consistent with our hypothesis of synthetic lethal interactions between PRODH, p53wt upregulation and glutamine addiction, we combined PRODH knockdown or enzymatic inhibition with either a p53wt restoring drug (e.g. MI-63, nutlin-3a) or a clinical glutaminase (GLS1) inhibitor (CB-839, Calithera) and observed synergistic induction of apoptosis and growth inhibition against malignant (e.g. MCF7, ZR-75-1, DU4475) but not normal (MCF10A) breast epithelial cells. Using an in vitro mitochondrial PRODH bioassay and a computationally based structural model of human PRODH's catalytic site, we are now designing new competitive and mechanism-based irreversible PRODH inhibitors capable of exploiting these synthetic lethal interactions to develop more effective and less toxic cancer therapy. Citation Format: Gary K. Scott, Justine Rutter, Katya Frazier, Daniel Rothschild, Christina Yau, Christopher Benz. A new anticancer strategy based on inhibiting mitochondrial proline dehydrogenase (PRODH) and exploiting synthetic lethal interactions with p53 restoration and/or glutaminase (GLS1) inhibition. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 5402. doi:10.1158/1538-7445.AM2015-5402

Identification of multiple structurally distinct, nonpeptidic small molecule inhibitors of protein arginine deiminase 3 using a substrate-based fragment method.

The protein arginine deiminases (PADs) are a family of enzymes that catalyze the post-translational hydrolytic deimination of arginine residues. Four different enzymologically active PAD subtypes have been characterized and exhibit tissue-specific expression and association with a number of different diseases. In this Article we describe the development of an approach for the reliable discovery of low molecular weight, nonpeptidic fragment substrates of the PADs that then can be optimized and converted to mechanism-based irreversible PAD inhibitors. The approach is demonstrated by the development of potent and selective inhibitors of PAD3, a PAD subtype implicated in the neurodegenerative response to spinal cord injury. Multiple structurally distinct inhibitors were identified with the most potent inhibitors having >10,000 min(-1) M(-1) k(inact)/K(I) values and ≥10-fold selectivity for PAD3 over PADs 1, 2, and 4.

Abstract SY35-03: Novel anti-tumor activity of targeted LSD1 inhibition

Abstract Lysine specific demethylase 1 (LSD1) is a histone H3K4me1/2 demethylase found in various transcriptional co-repressor complexes. These complexes include Histone Deacetylases (HDAC1/2) and Co-Repressor for Element-1-Silencing Transcription factor (CoREST). LSD1 mediated H3K4 demethylation can result in a repressive chromatin environment that silences gene expression and has been shown to play a role in development. LSD1 can interact with pluripotency factors in human embryonic stem cells and is essential for decommissioning enhancers in stem cell differentiation. Beyond embryonic settings, LSD1 is also critical for hematopoietic differentiation. LSD1 dysregulation plays a key role in cancer and LSD1 is overexpressed in multiple tumor types, including acute myeloid leukemia (AML). Recent literature suggests inhibition of LSD1 reactivates the all-trans retinoic acid differentiation pathway in AML. Together, these observations suggest LSD1 is an important regulator of the epigenome that modulates gene expression through post-translational modification of histones and its presence in transcriptional complexes. The current study describes the anti-tumor effects of a novel LSD1 inhibitor (GSK2879552). GSK2879552 is a potent, selective, mechanism-based irreversible inhibitor of LSD1 currently in clinical development. Screening of over 150 cancer cell lines revealed that while many tumor types appear resistant to LSD1 inhibition, specific tumor types were uniquely sensitive. For example, AML cells have a distinct requirement for LSD1, and LSD1 inhibition results in a prodifferentiation effect in this setting. Preclinical characterization of the anti-tumor activities of GSK2879552 both in vitro and in vivo in AML as well as the solid tumor setting will be discussed. All studies were conducted in accordance with the GSK Policy on the Care, Welfare and Treatment of Laboratory Animals and were reviewed the Institutional Animal Care and Use Committee either at GSK or by the ethical review process at the institution where the work was performed. Citation Format: Ryan G. Kruger. Novel anti-tumor activity of targeted LSD1 inhibition. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr SY35-03. doi:10.1158/1538-7445.AM2014-SY35-03

Effect of erlotinib on CYP3A activity, evaluated in vitro and by dual probes in patients with cancer

In vitro, erlotinib (0-30 µmol/l) and C-labelled midazolam (MDZ) (5 µmol/l) were incubated with human liver microsomes; separately, microsomes were preincubated with erlotinib (10 µmol/l) before the addition of MDZ. Results showed a time-dependent inhibition of MDZ metabolism by erlotinib, with a Ki of 7.5 µmol/l and an inactivation rate constant of 0.009/min. Patients with cancer (n=24) received a single oral dose of 7.5 mg MDZ and a single intravenous dose of 3 µCi [C-N-methyl] erythromycin on days 1, 8, 14 and 21. Patients also received 150 mg oral erlotinib daily from day 8 to day 14. Plasma concentrations of erlotinib and OSI-420 were determined on days 8 and 14; MDZ and 1'-hydroxymidazolam were determined on days 1, 8, 14 and 21. Coadministration of erlotinib resulted in a 4 and a 16% increase in CO2 on days 8 and 14, respectively, after the administration of erythromycin. The mean AUC0-last of MDZ decreased 17 and 34% after erlotinib treatment on day 8 and day 14, respectively. The half-life of MDZ and the AUC ratio of 1'-hydroxymidazolam to MDZ were not significantly changed. Although erlotinib may be a weak mechanism-based irreversible inhibitor of CYP3A4 in vitro, in vivo, erlotinib did not inhibit CYP3A-mediated metabolism, as determined by the erythromycin breath test and the MDZ pharmacokinetics. The mechanism for reduced exposure of MDZ is unclear, but may be because of an increase in intestinal metabolism or decreased absorption. These findings suggest that coadministration of erlotinib may not result in clinically relevant increases in exposure of CYP3A substrates.

Probing the Mechanism of Cyanobacterial Aldehyde Decarbonylase Using a Cyclopropyl Aldehyde

Cyanobacterial aldehyde decarbonylase (cAD) is a non-heme diiron oxygenase that catalyzes the conversion of fatty aldehydes to alkanes and formate. The mechanism of this chemically unusual reaction is poorly understood. We have investigated the mechanism of C1-C2 bond cleavage by cAD using a fatty aldehyde that incorporates a cyclopropyl group, which can act as a radical clock. When reacted with cAD, the cyclopropyl aldehyde produces 1-octadecene as the rearranged product, providing evidence for a radical mechanism for C-C bond scission. In an alternate pathway, the cyclopropyl aldehyde acts as a mechanism-based irreversible inhibitor of cAD through covalent binding of the alkyl chain to the enzyme.

Further characterization of a putative serine protease contributing to the γ-secretase cleavage of β-amyloid precursor protein

The 3-alkoxy-7-amino-4-chloro-isocoumarins JLK-6 and JLK-2 have been shown to markedly reduce the production of Amyloid β-peptide (Aβ) by Amyloid-β Precursor Protein (APP) expressing HEK293 cells by affecting the γ-secretase cleavage of APP, with no effect on the cleavage of the Notch receptor. This suggested that these compounds do not directly inhibit the presenilin-dependent γ-secretase complex but more likely interfere with an upstream target involved in γ-secretase-associated pathway. The mechanism of action of these compounds is unknown and there are high fundamental and therapeutical interests to unravel their target. Isocoumarin compounds were previously shown to behave as potent mechanism-based irreversible inhibitors of serine proteases, suggesting that the JLK-directed target could belong to such enzyme family. To get further insight into structure–activity relationships and to develop more potent isocoumarin derivatives, we have synthesized and evaluated a series of isocoumarin analogues with modifications at positions 3, 4 and 7. In particular, the 7-amino group was substituted with either acyl, urethane, alkyl or aryl groups, which could represent additional interaction sites. Altogether, the results highlighted the essential integrity of the 3-alkoxy-7-amino-4-chloro-isocoumarin scaffold for Aβ-lowering activity and supported the involvement of a serine protease, or may be more generally, a serine hydrolase. The newly reported 7-N-alkyl series produced the most active compounds with an IC50 between 10 and 30μM. Finally, we also explored peptide boronates, a series of reversible serine protease inhibitors, previously shown to also lower cellular Aβ production. The presented data suggested they could act on the same target or interfere with the same pathway as isocoumarins derivatives.

Mechanism-based inhibition of human Cytochrome P450-3A activity by grapefruit hybrids having low furanocoumarin content

A citrus breeding program aimed at developing low furanocoumarin (FC) grapefruit cultivars provided 40 grapefruit juice (GFJ) samples containing variable concentrations of FC derivatives, established as being mechanism-based (irreversible) inhibitors of human CYP3A isoforms.The principal inhibitory FCs were identified as 6′,7′-dihydroxybergamottin, along with a series of dimeric compounds (spiroesters) having high inhibitory potency.A random subset of the GFJ samples (n = 25) were tested as CYP3A inhibitors using an in vitro model based on human liver microsomal metabolism of the index substrate triazolam. The reciprocal values of in vitro 50% inhibitory concentrations (IC50) were highly correlated with concentrations of inhibitory FCs in the GFJ samples (r2 = 0.96). However the correlations were driven mainly by a few samples having high FC content and high reciprocal IC50 (corresponding to low IC50). Among the rest of the samples, the relationship was less robust.Further study is needed to determine how low the FC content needs to be (or how high the IC50 needs to be) to assure minimal risk of clinical interactions involving GFJ and CYP3A substrate drugs.

Looking glass mechanism-based inhibition of peptidylglycine α-amidating monooxygenase

Carboxyl-terminal amidation, a required post-translational modification for the bioactivation of many peptide hormones, entails sequential enzymatic action by peptidylglycine α-monooxygenase (PAM, EC 1.14.17.3) and peptidylamidoglycolate lyase (PGL, EC 4.3.2.5). We have previously demonstrated that PAM and PGL exhibit strict tandem reaction stereospecificities, with PAM producing exclusively α-hydroxyglycine moieties of absolute configuration ( S), and PGL being reactive only toward ( S)-α-hydroxyglycines, and we have also shown that PAM exhibits strict P 2-subsite stereospecificity toward both peptide substrates and peptidyl competitive inhibitors. Herein, it is reported that the inhibitory stereochemistry of olefinic mechanism-based amidation inhibitors differs from the strict subsite stereospecificity exhibited by PAM toward substrates and reversible competitive inhibitors. Kinetic analyses of mechanism-based irreversible inhibition of PAM by the ( S)- and ( R)-enantiomers of 5-acetamido-4-oxo-6-phenyl-2-hexenoic acid were carried out using the rigorous progress curve method. The two enantiomers were found to exhibit very similar values of K I and k inact and in both cases kinetic analysis confirmed that irreversible inhibition occurs strictly at the substrate binding site with no ESI complex being formed during the catalytic processing of these irreversible inhibitors. Molecular docking studies were carried out to help rationalize the sharp contrast in the stereospecificity of PAM toward irreversible inhibitors versus substrates and competitive inhibitors. The results revealed that, in contrast to substrates, both docked enantiomers of the olefinic irreversible inhibitors are well-positioned to undergo catalytic processing at the Cu center that gives rise to irreversible inhibition. Taken together, these results provide one of the first clear examples where the stereospecificity of a particular enzyme toward mechanism-based irreversible inhibitors differs from that for substrates and competitive inhibitors.

Inhibition of C5-cytosine-DNA-methyltransferases

Changes in the methylation pattern of genomic DNA, particularly hypermethylation of tumor suppressor genes, occur at early stages of tumor development. Errors in DNA methylation contribute to both initiation and progression of various cancers. This stimulates significant interest in searching for inhibitors of C5-DNA-methyltransferases (MTases). Here we review the known nucleoside mechanism-based reversible and irreversible inhibitors of the MTases, as well as non-nucleoside ones, and discuss their inhibitory mechanisms and application for MTase investigations and cancer therapy.

Synthesis of Fluoroneplanocin A

Fluoroneplanocin A, designed as a potent mechanism-based irreversible inhibitor of S-adenosylhomocysteine hydrolase (SAH), is synthesized from D-ribose via a key D-cyclopentenone intermediate. This intermediate is synthesized using a stereoselective Grignard reaction, a ring-closing metathesis (RCM) reaction, and oxidative rearrangement as key steps.

Synthesis and Evaluation of Substrate Analogues as Mechanism-Based Inhibitors of Type II Isopentenyl Diphosphate Isomerase

Type 2 isopentenyl diphosphate isomerase (IDI-2), which catalyzes the interconversion of isopentenyl diphosphate and dimethylallyl diphosphate, contains a tightly bound molecule of FMN. To probe the mechanism of the reaction, cyclopropyl and epoxy substrate analogues, designed to be mechanism-based irreversible inhibitors, were synthesized and evaluated with IDI-2 from Thermus thermophilus. The cyclopropyl analogues were alternative substrates. The epoxy analogue was an irreversible inhibitor, with kI = 0.37 +/- 0.07 min(-1) and KI = 1.4 +/- 0.3 microM. LC-MS studies revealed formation of an epoxide-FMN adduct.

Trans-2-Phenylcyclopropylamine Is a Mechanism-Based Inactivator of the Histone Demethylase LSD1

The catalytic domain of the flavin-dependent human histone demethylase lysine-specific demethylase 1 (LSD1) belongs to the family of amine oxidases including polyamine oxidase and monoamine oxidase (MAO). We previously assessed monoamine oxidase inhibitors (MAOIs) for their ability to inhibit the reaction catalyzed by LSD1 [Lee, M. G., et al. (2006) Chem. Biol. 13, 563-567], demonstrating that trans-2-phenylcyclopropylamine (2-PCPA, tranylcypromine, Parnate) was the most potent with respect to LSD1. Here we show that 2-PCPA is a time-dependent, mechanism-based irreversible inhibitor of LSD1 with a KI of 242 microM and a kinact of 0.0106 s-1. 2-PCPA shows limited selectivity for human MAOs versus LSD1, with kinact/KI values only 16-fold and 2.4-fold higher for MAO B and MAO A, respectively. Profiles of LSD1 activity and inactivation by 2-PCPA as a function of pH are consistent with a mechanism of inactivation dependent upon enzyme catalysis. Mass spectrometry supports a role for FAD as the site of covalent modification by 2-PCPA. These results will provide a foundation for the design of cyclopropylamine-based inhibitors that are selective for LSD1 to probe its role in vivo.