A new class of conformationally rigid analogues of 4-amino-5-halopentanoic acids, potent inactivators of gamma-aminobutyric acid aminotransferase

Identification of novel C-15 fluoro isosteviol derivatives for GABA-AT inhibition by in silico investigations

CONTEXT

The treatment of epilepsy is associated with the inhibition of γ-aminobutyric acid-aminotransferase (GABA-AT), which suppresses the concentration of a key neurotransmitter GABA. Isosteviol, a natural bioactive molecule, has been reported to possess an anticonvulsant property. In this work, we first reported a series of C-15 fluoro isosteviol analogs which are bearing different functional groups at C-16 to investigate the interactions with GABA-AT by applying molecular docking and molecular dynamic simulation approach. The results revealed that all fluoro isosteviol analogs displayed a greater binding affinity than references vigabatrin, an FDA-approved GABA-AT inactivator, and CPP-115, which has Orphan Drug Designation status, and positioned at the same binding site as references. Furthermore, molecular dynamic (MD) simulation studies on minimum (A1), maximum (E1) binding energy score of fluoro isosteviol analogs, and isosteviol (G1) revealed their stable complex formation in terms of RMSD, RMSF, RG, and hydrogen bond formation. All analogs were found to have drug-like nature, non-toxic, >80% absorption, and the majority tend to penetrate brain-blood-barrier (BBB). The investigations found in this study can help in the development of isosteviol derivatives as drugs for the treatment of epilepsy.

METHODS

The two-dimensional (2D) ligand structures were drawn using ChembioDraw Ultra 14.0. Molecular docking with Autodock4 and molecular dynamic simulation with GROMACS version 2020.1 were performed. The CHARMM27 all-atom force field was applied for writing the topology. Biovia Discovery Studio DS2021 was used for viewing and analyzing the protein-ligand complexes. The data generated from molecular dynamic simulation trajectories were plotted using the Origin® 8 software. The Open Babel software was utilized for extracting SMILEs files of all the fluoro isosteviol analogs. The drug-likeness and ADMET of the molecules were evaluated by SwissADME and ADMETlab 2.0 web tools.

Structural and Mechanistic Basis for the Inactivation of Human Ornithine Aminotransferase by (3S,4S)-3-Amino-4-fluorocyclopentenecarboxylic Acid

Ornithine aminotransferase (OAT) is overexpressed in hepatocellular carcinoma (HCC), and we previously showed that inactivation of OAT inhibits the growth of HCC. Recently, we found that (3S,4S)-3-amino-4-fluorocyclopentenecarboxylic acid (5) was a potent inactivator of γ-aminobutyric acid aminotransferase (GABA-AT), proceeding by an enamine mechanism. Here we describe our investigations into the activity and mechanism of 5 as an inactivator of human OAT. We have found that 5 exhibits 10-fold less inactivation efficiency (kinact/KI) against hOAT than GABA-AT. A comprehensive mechanistic study was carried out to understand its inactivation mechanism with hOAT. pKa and electrostatic potential calculations were performed to further support the notion that the α,β-unsaturated alkene of 5 is critical for enhancing acidity and nucleophilicity of the corresponding intermediates and ultimately responsible for the improved inactivation efficiency of 5 over the corresponding saturated analogue (4). Intact protein mass spectrometry and the crystal structure complex with hOAT provide evidence to conclude that 5 mainly inactivates hOAT through noncovalent interactions, and that, unlike with GABA-AT, covalent binding with hOAT is a minor component of the total inhibition which is unique relative to other monofluoro-substituted derivatives. Furthermore, based on the results of transient-state measurements and free energy calculations, it is suggested that the α,β-unsaturated carboxylate group of PLP-bound 5 may be directly involved in the inactivation cascade by forming an enolate intermediate. Overall, compound 5 exhibits unusual structural conversions which are catalyzed by specific residues within hOAT, ultimately leading to an enamine mechanism-based inactivation of hOAT through noncovalent interactions and covalent modification.

2-Oxa-5-azabicyclo[2.2.1]heptane as a Platform for Functional Diversity: Synthesis of Backbone-Constrained γ-Amino Acid Analogues

We communicate a versatile synthetic approach to C-3 disubstituted 2-oxa-5-azabicyclo[2.2.1]heptanes as carbon-atom bridged morpholines, starting with 4R-hydroxy-l-proline as a chiron. Attaching an acetic acid moiety on the C-3 carbon of the 2-oxa-5-azabicyclo[2.2.1]heptane core reveals the framework of an embedded γ-amino butyric acid (GABA). Variations in the nature of the substituent on the tertiary C-3 atom with different alkyls or aryls led to backbone-constrained analogues of the U.S. Food and Drug Administration-approved drugs baclofen and pregabalin.

Asymmetric Synthesis of Heterocyclic Chloroamines and Aziridines by Enantioselective Protonation of Catalytically Generated Enamines

We report a method for the synthesis of chiral vicinal chloroamines via asymmetric protonation of catalytically generated prochiral chloroenamines using chiral Brønsted acids. The process is highly enantioselective, with the origin of asymmetry and catalyst substituent effects elucidated by DFT calculations. We show the utility of the method as an approach to the synthesis of a broad range of heterocycle-substituted aziridines by treatment of the chloroamines with base in a one-pot process, as well as the utility of the process to allow access to vicinal diamines.

Positive Predictive Value Surfaces as a Complementary Tool to Assess the Performance of Virtual Screening Methods

BACKGROUND

Since their introduction in the virtual screening field, Receiver Operating Characteristic (ROC) curve-derived metrics have been widely used for benchmarking of computational methods and algorithms intended for virtual screening applications. Whereas in classification problems, the ratio between sensitivity and specificity for a given score value is very informative, a practical concern in virtual screening campaigns is to predict the actual probability that a predicted hit will prove truly active when submitted to experimental testing (in other words, the Positive Predictive Value - PPV). Estimation of such probability is however, obstructed due to its dependency on the yield of actives of the screened library, which cannot be known a priori.

OBJECTIVE

To explore the use of PPV surfaces derived from simulated ranking experiments (retrospective virtual screening) as a complementary tool to ROC curves, for both benchmarking and optimization of score cutoff values.

METHODS

The utility of the proposed approach is assessed in retrospective virtual screening experiments with four datasets used to infer QSAR classifiers: inhibitors of Trypanosoma cruzi trypanothione synthetase; inhibitors of Trypanosoma brucei N-myristoyltransferase; inhibitors of GABA transaminase and anticonvulsant activity in the 6 Hz seizure model.

RESULTS

Besides illustrating the utility of PPV surfaces to compare the performance of machine learning models for virtual screening applications and to select an adequate score threshold, our results also suggest that ensemble learning provides models with better predictivity and more robust behavior.

CONCLUSION

PPV surfaces are valuable tools to assess virtual screening tools and choose score thresholds to be applied in prospective in silico screens. Ensemble learning approaches seem to consistently lead to improved predictivity and robustness.

Turnover and Inactivation Mechanisms for (S)-3-Amino-4,4-difluorocyclopent-1-enecarboxylic Acid, a Selective Mechanism-Based Inactivator of Human Ornithine Aminotransferase

The inhibition of human ornithine δ-aminotransferase (hOAT) is a potential therapeutic approach to treat hepatocellular carcinoma. In this work, (S)-3-amino-4,4-difluorocyclopent-1-enecarboxylic acid (SS-1-148, 6) was identified as a potent mechanism-based inactivator of hOAT while showing excellent selectivity over other related aminotransferases (e.g., GABA-AT). An integrated mechanistic study was performed to investigate the turnover and inactivation mechanisms of 6. A monofluorinated ketone (M10) was identified as the primary metabolite of 6 in hOAT. By soaking hOAT holoenzyme crystals with 6, a precursor to M10 was successfully captured. This gem-diamine intermediate, covalently bound to Lys292, observed for the first time in hOAT/ligand crystals, validates the turnover mechanism proposed for 6. Co-crystallization yielded hOAT in complex with 6 and revealed a novel noncovalent inactivation mechanism in hOAT. Native protein mass spectrometry was utilized for the first time in a study of an aminotransferase inactivator to validate the noncovalent interactions between the ligand and the enzyme; a covalently bonded complex was also identified as a minor form observed in the denaturing intact protein mass spectrum. Spectral and stopped-flow kinetic experiments supported a lysine-assisted E2 fluoride ion elimination, which has never been observed experimentally in other studies of related aminotransferase inactivators. This elimination generated the second external aldimine directly from the initial external aldimine, rather than the typical E1cB elimination mechanism, forming a quinonoid transient state between the two external aldimines. The use of native protein mass spectrometry, X-ray crystallography employing both soaking and co-crystallization methods, and stopped-flow kinetics allowed for the detailed elucidation of unusual turnover and inactivation pathways.

Theoretical and Mechanistic Validation of Global Kinetic Parameters of the Inactivation of GABA Aminotransferase by OV329 and CPP-115

((S)-3-Amino-(difluoromethylenyl)cyclopent-1-ene-1-carboxylic acid (OV329) is a recently discovered inactivator of γ-aminobutyric acid aminotransferase (GABA-AT), which has 10 times better inactivation efficiency than its predecessor, CPP-115, despite the only structural difference being an endocyclic double bond in OV329. Both compounds are mechanism-based enzyme inactivators (MBEIs), which inactivate GABA-AT by a similar mechanism. Here, a combination of a variety of computational chemistry tools and experimental methods, including quantum mechanical (QM) calculations, molecular dynamic simulations, progress curve analysis, and deuterium kinetic isotope effect (KIE) experiments, are utilized to comprehensively study the mechanism of inactivation of GABA-AT by CPP-115 and OV329 and account for their experimentally obtained global kinetic parameters k_inact and K_I. Our first key finding is that the rate-limiting step of the inactivation mechanism is the deprotonation step, and according to QM calculations and the KIE experiments, k_inact accurately represents the enhancement of the rate-limiting step for the given mechanism. Second, the present study shows that the widely used simple QM models do not accurately represent the geometric criteria that are present in the enzyme for the deprotonation step. In contrast, QM cluster models successfully represent both the ground state destabilization and the transition state stabilization, as revealed by natural bond orbital analysis. Furthermore, the globally derived K_I values for both of the inactivators represent the inhibitor constants for the initial binding complexes (K_d) and indicate the inactivator competition with the substrate according to progress curve analysis and the observed binding isotope effect. The configurational entropy loss accounts for the difference in K_I values between the inactivators. The approach we describe in this work can be employed to determine the validity of globally derived parameters in the process of MBEI optimization for given inactivation mechanisms.

Synthesis of complex unnatural fluorine-containing amino acids

The area of fluorinated amino acid synthesis has seen rapid growth over the past decade. As reports of singly fluorinated natural amino acid derivatives have grown, researchers have turned their attention to develop methodology to access complex proteinogenic examples. A variety of reaction conditions have been employed in this area, exploiting new advances in the wider synthetic community such as photocatalysis and palladium cross-coupling. In addition, novel fluorinated functional groups have also been incorporated into amino acids, with SFX and perfluoro moieties now appearing with more frequency in the literature. This review focuses on synthetic methodology for accessing complex non-proteinogenic amino acids, along with amino acids containing multiple fluorine atoms such as CF3, SF5 and perfluoroaromatic groups.

Mechanism-Based Design of 3-Amino-4-Halocyclopentenecarboxylic Acids as Inactivators of GABA Aminotransferase

Aminotransferases are pyridoxal 5'-phosphate-dependent enzymes that catalyze reversible transamination reactions between an amino acid and an α-keto acid, playing a critical role in cellular nitrogen metabolism. It is evident that γ-aminobutyric acid aminotransferase (GABA-AT), which balances the levels of inhibitory and excitatory neurotransmitters, has emerged as a promising therapeutic target for epilepsy and cocaine addiction based on mechanism-based inactivators (MBIs). In this work, we established an integrated approach using computational simulation, organic synthesis, biochemical evaluation, and mass spectrometry to facilitate our design and mechanistic studies of MBIs, which led to the identification of a new cyclopentene-based analogue (6a), 25-times more efficient as an inactivator of GABA-AT compared to the parent compound (1R,3S,4S)-3-amino-4-fluorocyclopentane carboxylic acid (FCP, 4).

A Remarkable Difference That One Fluorine Atom Confers on the Mechanisms of Inactivation of Human Ornithine Aminotransferase by Two Cyclohexene Analogues of γ-Aminobutyric Acid

Human ornithine aminotransferase (hOAT), a pyridoxal 5'-phosphate-dependent enzyme, plays a critical role in the progression of hepatocellular carcinoma (HCC). Pharmacological selective inhibition of hOAT has been shown to be a potential therapeutic approach for HCC. Inspired by the discovery of the nonselective aminotransferase inactivator (1R,3S,4S)-3-amino-4-fluoro cyclopentane-1-carboxylic acid (1), in this work, we rationally designed, synthesized, and evaluated a novel series of fluorine-substituted cyclohexene analogues, thereby identifying 8 and 9 as novel selective hOAT time-dependent inhibitors. Intact protein mass spectrometry and protein crystallography demonstrated 8 and 9 as covalent inhibitors of hOAT, which exhibit two distinct inactivation mechanisms resulting from the difference of a single fluorine atom. Interestingly, they share a similar turnover mechanism, according to the mass spectrometry-based analysis of metabolites and fluoride ion release experiments. Molecular dynamics (MD) simulations and electrostatic potential (ESP) charge calculations were conducted, which elucidated the significant influence of the one-fluorine difference on the corresponding intermediates, leading to two totally different inactivation pathways. The novel addition-aromatization inactivation mechanism for 9 contributes to its significantly enhanced potency, along with excellent selectivity over other aminotransferases.

Applications of fluorine-containing amino acids for drug design

Fluorine-containing amino acids are becoming increasingly prominent in new drugs due to two general trends in the modern pharmaceutical industry. Firstly, the growing acceptance of peptides and modified peptides as drugs; and secondly, fluorine editing has become a prevalent protocol in drug-candidate optimization. Accordingly, fluorine-containing amino acids represent one of the more promising and rapidly developing areas of research in organic, bio-organic and medicinal chemistry. The goal of this Review article is to highlight the current state-of-the-art in this area by profiling 42 selected compounds that combine fluorine and amino acid structural elements. The compounds under discussion represent pharmaceutical drugs currently on the market, or in clinical trials as well as examples of drug-candidates that although withdrawn from development had a significant impact on the progress of medicinal chemistry and/or provided a deeper understanding of the nature and mechanism of biological action. For each compound, we present features of biological activity, a brief history of the design principles and the development of the synthetic approach, focusing on the source of tailor-made amino acid structures and fluorination methods. General aspects of the medicinal chemistry of fluorine-containing amino acids and synthetic methodology are briefly discussed.

Efficient metal-free aminoiodination of alkenes with N-fluorobenzenesulfonimide under mild conditions

A novel regioselective and stereoselective transition-metal-free aminoiodination of alkenes through an iodonium intermediate using NFSI as both the oxidant and amino precursor under mild conditions with a broad alkene scope is disclosed.

Copper-Catalysed Bromoamination of Maleimides using NBS as the Bromine Source

CuBr2-catalysed bromoamination of maleimides has been achieved in THF with alkylamines and N-bromosuccinimide as nitrogen and bromine sources respectively. The reaction conditions were optimised. A series of bromoamination products such as 3-amino-4-bromomaleimides was synthesised with satisfactory yields. Furthermore, a plausible mechanism of the bromoamination of maleimides was discussed.

Synthesis of ( S)-3-Amino-4-(difluoromethylenyl)-cyclopent-1-ene-1-carboxylic Acid (OV329), a Potent Inactivator of γ-Aminobutyric Acid Aminotransferase

( S)-3-Amino-4-(difluoromethylenyl)cyclopent-1-ene-1-carboxylic acid (OV329, 1) is being developed for the treatment of epilepsy and addiction. The previous 14-step synthesis of OV329 was low yielding, involved an unselective α-elimination to form the cyclopentene, required the use of tert-butyllithium, and produced toxic selenium byproducts in the penultimate step. A new synthesis, which avoids the aforementioned issues, was carried out on large scale, reducing the step count from 14 to 9 steps and increasing the overall yield from 3.7% to 8.1%.

Design and Mechanism of GABA Aminotransferase Inactivators. Treatments for Epilepsies and Addictions

When the brain concentration of the inhibitory neurotransmitter γ-aminobutyric acid (GABA) diminishes below a threshold level, the excess neuronal excitation can lead to convulsions. This imbalance in neurotransmission can be corrected by inhibition of the enzyme γ-aminobutyric acid aminotransferase (GABA-AT), which catalyzes the conversion of GABA to the excitatory neurotransmitter l-glutamic acid. It also has been found that raising GABA levels can antagonize the rapid elevation and release of dopamine in the nucleus accumbens, which is responsible for the reward response in addiction. Therefore, the design of new inhibitors of GABA-AT, which increases brain GABA levels, is an important approach to new treatments for epilepsy and addiction. This review summarizes findings over the last 40 or so years of mechanism-based inactivators (unreactive compounds that require the target enzyme to catalyze their conversion to the inactivating species, which inactivate the enzyme prior to their release) of GABA-AT with emphasis on their catalytic mechanisms of inactivation, presented according to organic chemical mechanism, with minimal pharmacology, except where important for activity in epilepsy and addiction. Patents, abstracts, and conference proceedings are not covered in this review. The inactivation mechanisms described here can be applied to the inactivations of a wide variety of unrelated enzymes.

Chiral N,N′-dioxide-Sc(NTf2)3 complex-catalyzed asymmetric bromoamination of chalones with N-bromosuccinimide as both bromine and amide source

A chiral N,N′-dioxide-Sc(NTf₂)₃ complex catalytic system has been developed to catalyze the asymmetric bromoamination reaction of chalones with N-bromosuccinimide.

Crystal structure of 2-(bromomethyl)-4-(4-chlorophenyl)-1-tosylpyrrolidine, C18H19BrClNO2S2

C18H19BrClNO2S2, monoclinic, P21/c (no. 14), a = 21.324(6) Å, b = 5.8597(16) Å, c = 14.966(4) Å, β = 95.558(5)°, V = 1861.2(9) Å3, Z = 4, R gt (F) = 0.0454, wR ref (F 2) = 0.1258, T = 296(2) K.

Visible-light promoted intermolecular halofunctionalization of alkenes with N-halogen saccharins

A simple and efficient visible-light promoted intermolecular haloamination and haloetherification of alkenes was reported.

A Versatile Organocatalytic Approach for the Synthesis of Enantioenriched gem-Difluorinated Compounds

The combination of a practical and highly enantioselective organocatalytic reaction, which allows the stereoselective introduction of a benzodithiol group, with a fluorination step, gives a new and effective strategy for the stereoselective synthesis of difluorinated building blocks. The benzodithiol group is a versatile and chameleonic group that can be further functionalized before fluorination, giving customized and tailored useful synthetic strategies. As an example of the application of this facile strategy, the effective enantioselective synthesis of difluoroarundic acid is described.

Catalytic enantioselective bromoamination of allylic alcohols

An enantioselective bromoamination of allylic alcohols has been developed for the first time using a newly designed cinchona-derived thiourea as the catalyst and N,N-dibromo-4-nitrobenzenesulfonamide as a bromine and amine source.

Iodine-mediated regioselective C–N and C–I bond formation of alkenes

Iodine mediated intermolecular C–N and C–I bonds formation of alkenes was realized. A series of alkenes could be converted into the aminoiodination products, which are versatile building blocks in organic synthesis and medicinal chemistry.

Organocatalytic stereoselective iodoamination of alkenes

A new chiral thiohydantoin catalyst is used for the stereoselective iodoamination of alkenes. N-iodosuccinimide as the source of the electrophilic iodine is activated by catalytic amounts of different additives which also influence the regioselectivity of some cyclizations.

Halonium ion triggered rearrangement of unsaturated benzo-annulated bi- and tricyclic sulfonamides

The halonium ion mediated 1,2-Wagner-Meerwein-type rearrangement of a series of benzo-fused bi- and tricyclic sulfonamides is reported. During this rearrangement the carbon-carbon bond that migrates was selectively set in the intramolecular Mizoroki-Heck (IHR) synthesis of the starting materials. Consequently, this method constitutes a means to access the regioisomeric series of cyclic sulfonamides not observed during the Mizoroki-Heck reaction.

Iron-catalyzed asymmetric haloamination reactions

The first iron(III)/N,N'-dioxide-catalyzed asymmetric haloamination of 3-alkylidene- and 3-arylidene-indolin-2-ones was developed, affording the corresponding chiral oxindole derivatives bearing vicinal haloamine substituents with excellent results (up to 99% yield, 99% ee, >19 : 1 dr). This iron catalyst also exhibits perfect enantioselectivity for chalcone derivatives. The cooperative activation of the substrate and the reagent in concert guarantees the high stereoselectivity.

Catalytic Aminohalogenation of Alkenes and Alkynes

Catalytic aminohalogenation methods enable the regio- and stereoselective vicinal difunctionalization of alkynes, allenes and alkenes with amine and halogen moieties. A range of protocols and reaction mechanisms including organometallic, Lewis base, Lewis acid and Brønsted acid catalysis have been disclosed, enabling the regio- and stereoselective synthesis of halogen-functionalized acyclic amines and nitrogen heterocycles. Recent advances including aminofluorination and catalytic enantioselective aminohalogenation reactions are summarized in this review.

Lewis basic selenium catalyzed chloroamidation of olefins using nitriles as the nucleophiles

A Lewis base catalyzed chloroamidation of olefinic substrates was achieved using diphenyl selenide as the catalyst. The reaction conditions are mild and suitable for a wide range of substrates including those which are acid labile.

Chiral β-Iodoamines by Urea-Catalyzed Iodocyclization of Trichloroacetimidates

Highly enantioselective vicinal iodoamination of olefins is accomplished through the iodocyclization of alkenyl trichloroacetimidates catalyzed by a new chiral Schiff-base urea derivative. The resulting products are converted readily to a variety of polyfunctional amine-containing chiral building blocks.

Synthesis and evaluation of novel heteroaromatic substrates of GABA aminotransferase

Two principal neurotransmitters are involved in the regulation of mammalian neuronal activity, namely, γ-aminobutyric acid (GABA), an inhibitory neurotransmitter, and L-glutamic acid, an excitatory neurotransmitter. Low GABA levels in the brain have been implicated in epilepsy and several other neurological diseases. Because of GABA's poor ability to cross the blood-brain barrier (BBB), a successful strategy to raise brain GABA concentrations is the use of a compound that does cross the BBB and inhibits or inactivates GABA aminotransferase (GABA-AT), the enzyme responsible for GABA catabolism. Vigabatrin, a mechanism-based inactivator of GABA-AT, is currently a successful therapeutic for epilepsy, but has harmful side effects, leaving a need for improved GABA-AT inactivators. Here, we report the synthesis and evaluation of a series of heteroaromatic GABA analogues as substrates of GABA-AT, which will be used as the basis for the design of novel enzyme inactivators.

Highly enantioselective electrophilic α-bromination of enecarbamates: chiral phosphoric acid and calcium phosphate salt catalysts

Metal-free chiral phosphoric acids and chiral calcium phosphates both catalyze highly enantio- and diastereoselective electrophilic α-bromination of enecarbamates to provide an atom-economical synthesis of enantioenriched vicinal haloamines. Either enantiomer can be formed in good yield with excellent diastereo- and enantioselectivity simply by switching the catalyst from a phosphoric acid to its calcium salt.