The organic chemistry of mechanism-based enzyme inhibition: a chemical approach to drug design

The Biotin Biosynthetic Pathway in Mycobacterium tuberculosis is a Validated Target for the Development of Antibacterial Agents

Mycobacterium tuberculosis, responsible for Tuberculosis (TB), remains the leading cause of mortality among infectious diseases worldwide from a single infectious agent, with an estimated 1.7 million deaths in 2016. Biotin is an essential cofactor in M. tuberculosis that is required for lipid biosynthesis and gluconeogenesis. M. tuberculosis relies on de novo biotin biosynthesis to obtain this vital cofactor since it cannot scavenge sufficient biotin from a mammalian host. The biotin biosynthetic pathway in M. tuberculosis has been well studied and rigorously genetically validated providing a solid foundation for medicinal chemistry efforts. This review examines the mechanism and structure of the enzymes involved in biotin biosynthesis and ligation, summarizes the reported genetic validation studies of the pathway, and then analyzes the most promising inhibitors and natural products obtained from structure-based drug design and phenotypic screening.

Rational Optimization of Mechanism-Based Inhibitors through Determination of the Microscopic Rate Constants of Inactivation

Mechanism-based inhibitors (MBIs) are widely employed in chemistry, biology, and medicine because of their exquisite specificity and sustained duration of inhibition. Optimization of MBIs is complicated because of time-dependent inhibition resulting from multistep inactivation mechanisms. The global kinetic parameters k_inact and K_I have been used to characterize MBIs, but they provide far less information than is commonly assumed, as shown by derivation and simulation of these parameters. We illustrate an alternative and more rigorous approach for MBI characterization through determination of the individual microscopic rate constants. Kinetic analysis revealed the rate-limiting step of inactivation of the PLP-dependent enzyme BioA by dihydro-(1,4)-pyridone 1. This knowledge was subsequently applied to rationally design a second-generation inhibitor scaffold with a nearly optimal maximum inactivation rate (0.48 min^-1).

Pharmaceuticals as emerging contaminants and their removal from water. A review

The main objective of this study was to conduct an exhaustive review of the literature on the presence of pharmaceutical-derived compounds in water and on their removal. The most representative pharmaceutical families found in water were described and related water pollution issues were analyzed. The performances of different water treatment systems in the removal of pharmaceuticals were also summarized. The water treatment technologies were those based on conventional systems (chlorine, chlorine dioxide, wastewater treatment plants), adsorption/bioadsorption on activated carbon (from lotus stalks, olive-waste cake, coal, wood, plastic waste, cork powder waste, peach stones, coconut shell, rice husk), and advanced oxidation processes by means of ozonation (O₃, O₃/H₂O₂, O₃/activated carbon, O₃/biological treatment), photooxidation (UV, UV/H₂O₂, UV/K₂S₂O₈, UV/TiO₂, UV/H₂O₂/TiO₂, UV/TiO₂/activated carbon, photo-Fenton), radiolysis (e-Beam, ⁶⁰Co, ¹³⁷Cs. Additives used: H₂O₂, SO₃²⁻, HCO₃⁻, CH₃₋OH, CO₃²⁻, or NO₃⁻), and electrochemical processes (Electrooxidation without and with active chlorine generation). The effect of these treatments on pharmaceutical compounds and the advantages and disadvantages of different methodologies used were described. The most important parameters of the above water treatment systems (experimental conditions, removal yield, pharmaceutical compound mineralization, TOC removal, toxicity evolution) were indicated. The key publications on pharmaceutical removal from water were summarized.

Synthesis of stereo (R and S) and geometric (E and Z) isomers of [18F]fluoro-beta-fluoromethylene-m-tyrosine derivatives: in vivo probes of central dopaminergic function

Fluorination of pure R and S enantiomers of (E)-beta-fluoromethylene-m-tyrosine [(E)-FMMT] and its racemic geometric isomer, (Z)-beta-fluoromethylene-m-tyrosine [(Z)-FMMT] with [18F]acetyl hypofluorite ([18F]AcOF) gave a mixture of aromatic ring fluorinated products and a pair of diastereomeric products of addition across the exocyclic double bond. Semipreparative high performance liquid chromatography (HPLC) enabled a complete separation and isolation of these products, namely, 6-[18F]fluoro, 2-[18F]fluoro, and 2,6-[18F]difluoro (E)-FMMT and (Z)-FMMT derivatives. No attempt was made to isolate the individual components of the addition product. Pure racemic 4-[18F]fluoro-(E)-beta-fluoromethylene-m-tyrosine was also synthesized from a substituted (E)-FMMT precursor involving a fluorodestannylation reaction with [18F]F2. The availability of stereo (R and S) isomers of 6-[18F]fluoro and 2-[18F]fluoro (E)-FMMT and those of the racemic (Z)-FMMT along with 4-[18F]fluoro-(E)-beta-fluoromethylene-m-tyrosine would now enable a systematic investigation of the central monoamine oxidase/aromatic amino acid decarboxylase enzyme system with positron emission tomography.

Synthetic inhibitors of elastase

For more than two decades investigators around the world, in both academic and industrial institutions, have been developing inhibitors of human neutrophil elastase. A number of very elegant and insightful strategies have been reported. In the case of reversible peptidic inhibitors, this has resulted in the identification of some extremely potent compounds with dissociation constants in the 10(-11) M range. This is quite an accomplishment considering that these low molecular-weight inhibitors are only tri- and tetrapeptides. In the case of the heterocyclic-based inhibitors, the challenge of balancing the heterocycle's inherent reactivity and aqueous stability with the stability of the enzyme-inhibitor adduct has been meet by either using a latent, reactive functionality which is only activated within the enzyme, or by incorporating features which selectively obstruct deacylation but have little effect on the enzyme acylation step. The underlying goal of this research has been the identification of agents to treat diseases associated with HNE. Several animal models have been developed for evaluating the in vivo activity of elastase inhibitors, and compounds have been shown to be effective in all of these models by the intravenous, intratrachael or oral routes of administration. However, only a very small percentage of compounds have possessed all the necessary properties, including lack of toxicity, for progression into the clinic. The peptidyl TFMK ICI 200,880 (25-12) has many of the desired characteristics of a drug to treat the diseases associated with HNE: chemical stability, in vitro and in vivo activity, a long duration of action, and adequate metabolic stability. Currently ICI 200,880 is the only low molecular-weight HNE inhibitor known to be undergoing clinical trials, and may be the compound which finally demonstrates the clinical utility of a synthetic HNE inhibitor.

Inactivation of gamma-aminobutyric acid aminotransferase by (Z)-4-amino-2-fluorobut-2-enoic acid

(Z)-4-Amino-2-fluorobut-2-enoic acid (1) is shown to be a mechanism-based inactivator of pig brain gamma-aminobutyric acid aminotransferase. Approximately 750 inactivator molecules are consumed prior to complete enzyme inactivation. Concurrent with enzyme inactivation is the release of 708 +/- 79 fluoride ions; transamination occurs 737 +/- 15 times per inactivation event. Inactivation of [3H]pyridoxal 5'-phosphate ([3H]PLP) reconstituted GABA aminotransferase by 1 followed by denaturation releases [3H]PMP with no radioactivity remaining attached to the protein. A similar experiment carried out with 4-amino-5-fluoropent-2-enoic acid [Silverman, R. B., Invergo, B. J., & Mathew, J. (1986) J. Med. Chem. 29, 1840-1846] as the inactivator produces no [3H]PMP; rather, another radioactive species is released. These results support an inactivation mechanism for 1 that involves normal catalytic isomerization followed by active site nucleophilic attack on the activated Michael acceptor. A general hypothesis for predicting the inactivation mechanism (Michael addition vs enamine addition) of GABA aminotransferase inactivators is proposed.

Synthesis and enzymic hydrolysis of cyclic peptides containing an anthranilic acid residue

Two cyclic peptides cyclo (Phe-MeAnt-Glyn) with MeAnt = 5-methyl-anthranilic acid residue, n = 4 (3b) and n = 6 (4b), have been synthesized in solution and their reaction with alpha-chymotrypsin analyzed. The polyglycyl chain was prepared by the phosphazo method; cyclization at the Gly-Phe site occurred in good yield using the azide method. Catalysis of the hydrolysis of peptides 3b and 4b by alpha-chymotrypsin was characterized at 37 degrees by the apparent second-order rate constants kcat/Km 0.12 and 1.15 M-1 S-1, respectively, in agreement with the usual acceleration observed upon enlargement of the size of the peptidic ring in cyclic peptides. alpha-Chymotrypsin specifically split the Phe-MeAnt amide bond in cyclopeptide 4b. This specific orientation suggests that analogous structures with a functionalized methylene group instead of the methyl substituent can be used in the design of suicide substrates for serine proteases.

Kinetics of suicide substrate:enzyme inactivation. Methylenecyclopropaneacetyl-CoA and general acyl-CoA dehydrogenase

Kinetics of inactivation of general acyl-CoA dehydrogenase from pig kidney by methylenecyclopropaneacetyl-CoA have been analyzed using the theoretical treatment and exact steady-state kinetic solutions reported by Tatsunami (Tatsunami, S., Yago, N., and Hosoe, M. (1981) Biochim. Biophys. Acta 662, 226-235). Thus practical application of these analytical solutions for an important class of enzyme:substrate reactions has been demonstrated for the first time.

Metabolism of 2-(2-thienyl)allylamine hydrochloride in the rat: identification of a novel metabolite

A novel metabolite, 2-(2-thienyl)propionic acid, is formed in vivo from 2-(2-thienyl)allylamine hydrochloride. Mass spectral analysis suggested 2-(2-thienyl)propionic acid formation involves loss of the amine moiety followed by reduction of the olefinic group.

Mechanism of inactivation of gamma-aminobutyrate aminotransferase by 4-amino-5-fluoropentanoic acid. First example of an enamine mechanism for a gamma-amino acid with a partition ratio of 0

The mechanism of inactivation of pig brain gamma-aminobutyric acid aminotransferase (GABA-T) by (S)-4-amino-5-fluoropentanoic acid (1, R = CH2CH2COOH, X = F) previously proposed [Silverman, R. B., & Levy, M. A. (1981) Biochemistry 20, 1197-1203] is revised. apo-GABA-T is reconstituted with [4-3H]pyridoxal 5'-phosphate and inactivated with 1 (R = CH2CH2COOH, X = F). Treatment of inactivated enzyme with base followed by acid denaturation leads to the complete release of radioactivity as 6-[2-hydroxy-3-methyl-6-(phosphonoxymethyl)-4-pyridinyl]-4-oxo-5-+ ++hexenoic acid (4, R = CH2CH2COOH). Alkaline phosphatase treatment of this compound produces dephosphorylated 4 (R = CH2CH2COOH). These results support a mechanism that was suggested by Metzler and co-workers [Likos, J. J., Ueno, H., Feldhaus, R. W., & Metzler, D. E. (1982) Biochemistry 21, 4377-4386] for the inactivation of glutamate decarboxylase by serine O-sulfate (Scheme I, pathway b, R = COOH, X = OSO3-).

Studies of the inactivation of human placental aromatase by 17 alpha-ethynyl-substituted 10 beta-hydroperoxy and related 19-nor steroids

The inactivation of human placental aromatase by 17 alpha-ethynyl-10 beta-hydroperoxy-17 beta-hydroxy-4-estren-3-one (SCH 10015) was investigated. In either the presence or absence of added NADPH, SCH 10015 (Ki = 41 microM) caused a time-dependent loss of aromatase activity (e.g. 50% loss after 20 min with 20 microM SCH 10015). Evidence for the oxidation of an active site sulfhydryl group as the molecular basis for SCH 10015 inactivation is presented. The contraceptive 17 alpha-ethynyl-substituted 19-nor steroids, norethisterone (Ki = 48 microM) and norethynodrel (Ki = 38 microM), were evaluated and found not to inactivate aromatase, suggesting that the potential conversion of either compound to SCH 10015 did not occur to a significant extent in these microsomal incubations. It is speculated that the previously observed potent contraceptive effects of SCH 10015 may have been the result of irreversible inhibition of estrogen biosynthesis.

Identification of the amino acid bound to the labile adduct formed during inactivation of monoamine oxidase by 1-phenylcyclopropylamine

Three reactions are carried out on the reversible adduct formed when 1-phenylcyclopropylamine (1-PCPA) inactivates monoamine oxidase (MAO) in order to determine the identity of the amino acid involved in reversible adduct formation. Raney nickel treatment yields trans-beta-methyl[14C]styrene, the compound that would result from carbon-sulfur bond reduction of a (3-hydroxy-3-phenyl-propyl)cysteine adduct. A 5,5'-dithiobis(2-nitrobenzoic acid) assay for cysteine residues indicates that upon reversible inactivation of MAO by 1-PCPA, one cysteine is lost. The third reaction involves sodium periodate and hydrogen peroxide oxidation, but no definitive result is obtained. The first two reactions provide evidence that the amino acid residue involved in reversible adduct formation is a cysteine.