Many novel structural features impart a robust catalase activity to KatG that is absent from all other members of its superfamily. The conformationally dynamic “Arg switch” and oxidizable “proximal Trp” have both figured prominently in investigations of KatG structure and mechanism, but the full scope of their contributions to catalysis remains unclear. The switch (R418) appears to regulate active-site intramolecular electron transfer. The proximal Trp (W321) is a conspicuous site of radical formation, but W321•+ does not appear to participate directly in the KatG catalase cycle. To explore the extent to which these residues may cooperate in KatG’s catalase activity, we generated R418N and W321F/R418N KatG and compared their catalytic and spectroscopic properties to wt KatG. R418N KatG showed pH-independent susceptibility to H2O2-based inactivation, whereas wt KatG only showed this response under conditions where the Arg switch would be oriented away from the active site (i.e., low pH). Peroxidatic electron donors (PxEDs) prevented inactivation of wt and R418N KatG regardless of pH; however, protection of R418N KatG activity by this mechanism produced at least ten-fold greater extents of PxED oxidation. Elimination of the proximal Trp in addition to the Arg switch (i.e., W321F/R418N KatG) resulted in a near complete inability to sustain H2O2 degradation. Remarkably, W321F KatG showed resistance to H2O2-dependent inactivation indistinguishable from wt at pH 7 (i.e., when the Arg switch is oriented toward the active site) but sensitivity to H2O2-dependent inactivation indistinguishable from W321F/R418N KatG at pH 5 (i.e., when the Arg switch is oriented away from the active site). These data suggest loss of the Arg switch (either by mutagenesis or conformationally due to environmental pH) results in a KatG that is substantially compromised in the sustained degradation of H2O2. This can be overcome provided that KatG retains its ability to utilize the proximal Trp as a site of protein-based oxidation and has a PxED available to repair protein oxidation events. However, if both the Arg switch and the proximal Trp are absent, rapid H2O2-dependent inactivation is observed, and PxEDs are unable to effectively intervene to preserve KatG’s catalase activity.

Bifunctional catalase-peroxidase (KatG) features a posttranslational methionine-tyrosine-tryptophan (MYW) crosslinked cofactor crucial for its catalase function, enabling pathogens to neutralize hydrogen peroxide during infection. We discovered the presence of indole nitrogen-linked hydroperoxyl adduct (MYW-OOH) in Mycobacterium tuberculosis KatG in the solution state under ambient conditions, suggesting its natural occurrence. By isolating predominantly MYW-OOH-containing KatG protein, we investigated the chemical stability and functional impact of MYW-OOH. We discovered that MYW-OOH inhibits catalase activity, presenting a unique temporary lock. Exposure to peroxide or increased temperature removes the hydroperoxyl adduct from the protein cofactor, converting MYW-OOH to MYW and restoring the detoxifying ability of the enzyme against hydrogen peroxide. Thus, the N-linked hydroperoxyl group is releasable. KatG with MYW-OOH represents a catalase dormant, but primed, state of the enzyme. These findings provide insight into chemical strategies targeting the bifunctional enzyme KatG in pathogens, highlighting the role of N-linked hydroperoxyl modifications in enzymatic function.

AbstractResearch was conducted using a functional malachite green colorimetric assay to evaluate acetyl-coenzyme A carboxylase (ACCase) activity previously identified as resistant to sethoxydim and select aryloxyphenoxypropionate (FOPs) herbicides, fenoxaprop, and fluazifop. Two resistant southern crabgrass [Digitaria ciliaris (Retz.) Koeler] biotypes, R1 and R2, containing an Ile-1781-Leu amino acid substitution and previously identified as resistant to sethoxydim, pinoxaden, and fluazifop but not clethodim was utilized as the resistant chloroplastic ACCase source compared with known susceptible (S) ACCase. Dose-response studies with sethoxydim, clethodim, fluazifop-p-butyl, and pinoxaden (0.6 to 40 µM) were conducted to compare the ACCase–herbicide interactions of R1, R2, and S using the malachite green functional assay. Assay results indicated that R biotypes required more ACCase-targeting herbicides to inhibit ACCase activity compared with S. IC50 values of all four herbicides for R biotypes were consistently an order of magnitude greater than those of S. No sequencing differences in the carboxyltransferase domain was observed for R1 and R2; however, R2 IC50 values were greater across all herbicides. These results indicate the malachite green functional assay is effective in evaluating ACCase activity of R and S biotypes in the presence of ACCase-targeting herbicides, which can be used as a replacement for the 14C-based radiometric functional assays.

KatG is produced by a broad range of pathogenic fungi and bacteria, including Mycobacterium tuberculosis. Rapid disproportionation of H2O2 prevents its use by host defensive responses for production of far more bactericidal/fungicidal compounds (e.g, HOCl). KatG’s robust catalase activity depends on a unique post‐translationally generated protein‐based cofactor that arises from covalent links between the side chains of Met255, Tyr229, and Trp107 (MYW). In this study, we addressed the early stages of formation of this unique adduct and how its absence impacts the structure and function of KatG. We have capitalized on our protocols for first expressing/purifying KatG lacking heme (i.e., apoKatG or aKatG) and reconstituting it with heme during purification (i.e., rKatG). We have shown that our rWT KatG contains heme but has yet to form the MYW cofactor; the MYW structure is formed upon reaction with peroxide to generate the mature form of the enzyme (mWT KatG). We have also generated MYW‐disruptive variants in their reconstituted forms (i.e., rM255I, rY229F, rW107F). All rKatGs showed spectral features as well as catalase and/or peroxidase activities consistent the forms expressed and purified already containing the heme cofactor. Analysis of tryptic peptides of rKatG and mKatG in LC/MS/MS revealed the presence of MYW‐related ions, though to a much lesser extent in the rKatG as compared to the mKatG, suggesting that the MYW adduct has yet to be generated in rKatG upon reacting with peroxides. In our observation, MYW lacking variants are partially or completely devoid of MYW‐related ions regardless of their treatment with peroxides indicating that the rM255I variant was only able to form the partial YW adduct whereas adduct formation was completely abrogated in the rY229F and rW107F KatG variants. The resulting mechanistic changes in these mutants are probed in our study using stopped‐flow and rapid freeze‐quench experiments. Stopped‐flow spectroscopy captured [FeIV=O]‐like intermediate (compound II), followed by FeIII‐O2•– species (compound III) in rM255I and rY229F variants, consistent with the observation of rWT, although the ferric state has never emerged with the variants. In contrast, compound II has not been detected, but compound III has been the very first intermediate detected in the matured enzymes even when they reacted with the very low equivalences of H2O2. These early intermediates, observed only with the reconstituted enzymes, demonstrate the feasibility of KatG’s novel MYW cofactor elucidation and characterization, the step essential for exhibiting catalase activity. However, the variant W107F showed identical absorption features of heme‐based intermediates in reconstituted and matured form. This mutation leads to a damage in the hydrogen bonding network, therefore inhibiting the formation of early intermediates. Further investigation of the radical intermediates by EPR will provide valuable insight on the preferred site of crosslink initiation.

Isoniazid (INH) is one of the two most effective first-line antitubercular drugs and is still used at the present time as a scaffold for developing new compounds to fight TB. In a previous study, we have observed that an INH derivative, an hydrazide N'-substituted with a C10acyl chain, was able to counterbalance its smaller reactivity with a higher membrane permeability. This resulted in an improved performance against the most prevalent Mycobacterium tuberculosis (Mtb) resistant strain (S315T), compared to INH. In this work, we have designed two new series of INH derivatives (alkyl hydrazides and hydrazones) with promising in silico properties, namely membrane permeabilities and spontaneous IN* radical formation. The kinetics, cytotoxicity, and biological activity evaluations confirmed the in silico predictions regarding the very high reactivity of the alkyl hydrazides. The hydrazones, on the other hand, showed very similar behavior compared to INH, particularly in biological tests that take longer to complete, indicating that these compounds are being hydrolyzed back to INH. Despite their improved membrane permeabilities, the reactivities of these two series are too high, impairing their overall performance. Nevertheless, the systematic data gathered about these compounds have showed us the need to find a balance between lipophilicity and reactivity, which is paramount to devise better INH-based derivatives aimed at circumventing Mtb resistance.

Catalase‐peroxidases (KatG) has been engineered by nature to exhibit dual functionalism of catalase and peroxidase mechanisms, serving to protect the organisms that carry it against peroxide‐dependent oxidative damage. Despite bearing no resemblance to monofunctional (i.e., typical) catalases, KatGs have robust catalase activity due at least in part to a novel covalent linkage between three side chains (by Mycobacterium tuberculosis KatG [MtKatG] numbering, Met‐255, Tyr‐229, and Trp‐107) (MYW). This MYW cofactor redox cycles between its radical (MYW•+) and fully covalent states, enabling KatG to leverage heme intermediates for catalatic O2 production. However, the molecular mechanism by which the adduct is formed and how this unique structure contributes to overall catalytic mechanism of KatG is yet to be explored. Here, optical stopped‐flow spectrophotometry, rapid freeze‐quench EPR spectroscopy and mutagenesis have been used to investigate the mechanism of MYW adduct formation. We have expressed and purified MtKatG lacking heme and reconstituted with the cofactor after purification. This produces KatG lacking the MYW crosslink, allowing us to monitor its formation upon reaction with peroxides. Under multiple‐turnover conditions using H2O2, optical stopped‐flow experiments showed an initial appearance of a high‐valent ferryl‐like (FeIV=O) intermediate instead of the typical FeIII‐O2•‐ ‐like steady‐state intermediate of KatG's catalase activity. Nevertheless, in contrast to catalase‐negative canonical heme peroxidases, full catalase H2O2 decomposition did emerge, returning the enzyme to its FeIII state. EPR experiments revealed that an admixture of radical species appeared before MYW cofactor radical intermediate, suggestive of the preferred site of crosslink initiation. In addition to that, KatG variants lacking the MYW adduct (M255I, Y229F and W107F) were also constructed, expressed, purified, and reconstituted with heme. Stopped flow and UV‐vis analysis of these variants showed disrupted catalase activities and incomplete catalatic turnover. These observations strongly suggest that, these distal side residues actively participate in intramolecular electron transfer, thereby fulfilling a mechanistic role in KatG catalase mechanism. Our reconstituted KatG proteins may permit investigation of radical transfer reactions leading to formation of KatG's novel MYW cofactor as well as the influence of other protein radical transfer reactions on that process.

MRP.py is a Python-based parametrization program for covalently modified amino acid residues for molecular dynamics simulations. Charge derivation is performed via an RESP charge fit, and force constants are obtained through rewriting of either protein or GAFF database parameters. This allows for the description of interfacial interactions between the modifed residue and protein. MRP.py is capable of working with a variety of protein databases. MRP.py's highly general and systematic method of obtaining parameters allows the user to circumvent the process of parametrizing the modified residue-protein interface. Two examples, a covalently bound inhibitor and covalent adduct consisting of modified residues, are provided in the Supporting Information.

Ilimaquinone (IQ), a marine sponge metabolite, has been considered as a potential therapeutic agent for various diseases due to its broad range of biological activities. We show that IQ irreversibly inactivates Mycobacterium tuberculosis shikimate kinase (MtSK) through covalent modification of the protein. Inactivation occurred with an apparent second-order rate constant of about 60 M-1 s(-1). Following reaction with IQ, LC-MS analyses of intact MtSK revealed covalent modification of MtSK by IQ, with the concomitant loss of a methoxy group, suggesting a Michael addition mechanism. Evaluation of cryptic fragments of IQ derivatized MtSK by MS/MS demonstrated that Ser and Thr residues were most frequently modified with lesser involvement of Lys and Tyr. In or near the MtSK active site, three residues of the P-loop (K15, S16, and T17) as well as S77, T111, and S44 showed evidence of IQ-dependent derivatization. Accordingly, inclusion of ATP in IQ reactions with MtSK partially protected the enzyme from inactivation and limited IQ-based derivatization of K15 and S16. Additionally, molecular docking models for MtSK IQ were generated for IQ-derivatized S77 and T111. In the latter, ATP was observed to sterically clash with the IQ moiety. Out of three other enzymes evaluated, lactate dehydrogenase was derivatized and inactivated by IQ, but pyruvate kinase and catalase-peroxidase (KatG) were unaffected. Together, these data suggest that IQ is promiscuous (though not entirely indiscriminant) in its reactivity. As such, the potential of IQ as a lead in the development of antitubercular agents directed against MtSK or other targets is questionable.

Tuberculosis represents a significant public health crisis. There is an urgent need for novel molecular scaffolds against this pathogen. We screened a small library of marine-derived compounds against shikimate kinase from Mycobacterium tuberculosis (MtSK), a promising target for antitubercular drug development. Six manzamines previously shown to be active against M. tuberculosis were characterized as MtSK inhibitors: manzamine A (1), 8-hydroxymanzamine A (2), manzamine E (3), manzamine F (4), 6-deoxymanzamine X (5), and 6-cyclohexamidomanzamine A (6). All six showed mixed noncompetitive inhibition of MtSK. The lowest K-1 values were obtained for 6 across all MtSK substrate complexes. Time dependent analyses revealed two-step, slow-binding inhibition. The behavior of 1 was typical; initial formation of an enzyme inhibitor complex (EI) obeyed an apparent K-1 of similar to 30 mu M with forward (k(5)) and reverse (k(6)) rate constants for isomerization to an EI* complex of 0.18 and 0.08 min(-1), respectively. In contrast, 6 showed a lower K-1 for the initial encounter complex (similar to 1.5 mu M), substantially faster isomerization to EI* (k(5) = 0.91 min(-1)), and slower back conversion of EI* to EI (k(6) = 0.04 min(-1)). Thus, the overall inhibition constants, K-1*, for 1 and 6 were 10 and 0.06 mu M, respectively. These findings were consistent with docking predictions of a favorable binding mode and a second, less tightly bound pose for 6 at MtSK. Our results suggest that manzamines, in particular 6, constitute a new scaffold from which drug candidates with novel mechanisms of action could be designed for the treatment of tuberculosis by targeting MtSK.

Single dose high-throughput screening (HTS) followed by dose-response evaluations is a common strategy for the identification of initial hits for further development. Early identification and exclusion of false positives is a cost-saving and essential step in early drug discovery. One of the mechanisms of false positive compounds is the formation of aggregates in assays. This study evaluates the mechanism(s) of inhibition of a set of 14 compounds identified previously as actives in Mycobacterium tuberculosis (Mt) cell culture screening and in vitro actives in Mt shikimate kinase (MtSK) assay. Aggregation of hit compounds was characterized using multiple experimental methods, LC-MS, 1HNMR, dynamic light scattering (DLS), transmission electron microscopy (TEM), and visual inspection after centrifugation for orthogonal confirmation. Our results suggest that the investigated compounds containing oxadiazole-amide and aminobenzothiazole moieties are false positive hits and non-specific inhibitors of MtSK through aggregate formation.

KatG is a bifunctional, heme-dependent enzyme in the front-line defense of numerous bacterial and fungal pathogens against H2O2-induced oxidative damage from host immune responses. Contrary to the expectation that catalase and peroxidase activities should be mutually antagonistic, peroxidatic electron donors (PxEDs) enhance KatG catalase activity. Here, we establish the mechanism of synergistic cooperation between these activities. We show that at low pH values KatG can fully convert H2O2 to O2 and H2O only if a PxED is present in the reaction mixture. Stopped-flow spectroscopy results indicated rapid initial rates of H2O2 disproportionation slowing concomitantly with the accumulation of ferryl-like heme states. These states very slowly returned to resting (i.e. ferric) enzyme, indicating that they represented catalase-inactive intermediates. We also show that an active-site tryptophan, Trp-321, participates in off-pathway electron transfer. A W321F variant in which the proximal tryptophan was replaced with a non-oxidizable phenylalanine exhibited higher catalase activity and less accumulation of off-pathway heme intermediates. Finally, rapid freeze-quench EPR experiments indicated that both WT and W321F KatG produce the same methionine-tyrosine-tryptophan (MYW) cofactor radical intermediate at the earliest reaction time points and that Trp-321 is the preferred site of off-catalase protein oxidation in the native enzyme. Of note, PxEDs did not affect the formation of the MYW cofactor radical but could reduce non-productive protein-based radical species that accumulate during reaction with H2O2 Our results suggest that catalase-inactive intermediates accumulate because of off-mechanism oxidation, primarily of Trp-321, and PxEDs stimulate KatG catalase activity by preventing the accumulation of inactive intermediates.

Catalase-peroxidase (KatG) is an enzyme capable of utilizing both catalase and peroxidase activity to break down hydrogen peroxide. Catalase activity by the enzyme generally dominates, but peroxidatic electron donors have been shown to stimulate catalase activity, likely by rescuing catalase-inactive intermediates resulting from off-pathway electron transfer. To investigate tryptophan 438 as a potential conduit for this misdirected transfer, a variant form of the enzyme (W438F), which contained a phenylalanine in place of the tryptophan, was produced by site-directed mutagenesis, expressed, and purified. Catalase a n d p e r o x i d a s e a c t i v i t i e s were measured v ia UV-Vis spectrophotometry, and catalase activity was also monitored by oxygen production. We observed a threefold increase in catalase activity by the variant as compared to wild-type KatG. Additionally, W438F displayed a threefold decrease in peroxidase activity. These results are consistent with the possibility that off-pathway electron transfer could occur by this route, as the phenylalanine substitution would obstruct this oxidizable passage and cause a diminished requirement for the peroxidatic rescue event. However, oxygen production data also revealed stimulation of catalase activity by peroxidatic electron donors at pH 5, and further investigation is needed to understand this pathway.

The growing resistance to current antimalarial drugs is a major concern for global public health. The pressing need for new antimalarials has led to an increase in research focused on the Plasmodium parasites that cause human malaria. Thioredoxin reductase (TrxR), an enzyme needed to maintain redox equilibrium in Plasmodium species, is a promising target for new antimalarials. This review paper provides an overview of the structure and function of TrxR, discusses similarities and differences between the thioredoxin reductases (TrxRs) of different Plasmodium species and the human forms of the enzyme, gives an overview of modeling Plasmodium infections in animals, and suggests the role of Trx functions in antimalarial drug resistance. TrxR of Plasmodium falciparum is a central focus of this paper since it is the only Plasmodium TrxR that has been crystallized and P. falciparum is the species that causes most malaria cases. It is anticipated that the information summarized here will give insight and stimulate new directions in which research might be most beneficial.

Catalase-peroxidases (KatGs), the only catalase-active members of their superfamily, all possess a 35-residue interhelical loop called large loop 2 (LL2). It is essential for catalase activity, but little is known about its contribution to KatG function. LL2 shows weak sequence conservation; however, its length is nearly identical across KatGs, and its apex invariably makes contact with the KatG-unique C-terminal domain. We used site-directed and deletion mutagenesis to interrogate the role of LL2 and its interaction with the C-terminal domain in KatG structure and catalysis. Single and double substitutions of the LL2 apex had little impact on the active site heme [by magnetic circular dichroism or electron paramagnetic resonance (EPR)] and activity (catalase or peroxidase). Conversely, deletion of a single amino acid from the LL2 apex reduced catalase activity by 80%. Deletion of two or more apex amino acids or all of LL2 diminished catalase activity by 300-fold. Peroxide-dependent but not electron donor-dependent kcat/KM values for deletion variant peroxidase activity were reduced 20-200-fold, and kon for cyanide binding diminished by 3 orders of magnitude. EPR spectra for deletion variants were all consistent with an increase in the level of pentacoordinate high-spin heme at the expense of hexacoordinate high-spin states. Together, these data suggest a shift in the distribution of active site waters, altering the reactivity of the ferric state, toward, among other things, compound I formation. These results identify the importance of LL2 length conservation for maintaining an intersubunit interaction that is essential for an active site water distribution that facilitates KatG catalytic activity.

Owing to the persistence of tuberculosis (TB) as well as the emergence of multidrug-resistant and extensively drug-resistant (XDR) forms of the disease, the development of new antitubercular drugs is crucial. Developing inhibitors of shikimate kinase (SK) in the shikimate pathway will provide a selective target for antitubercular agents. Many studies have used in silico technology to identify compounds that are anticipated to interact with and inhibit SK. To a much more limited extent, SK inhibition has been evaluated by in vitro methods with purified enzyme. Currently, there are no data on in vivo activity of Mycobacterium tuberculosis shikimate kinase (MtSK) inhibitors available in the literature. In this review, we present a summary of the progress of SK inhibitor discovery and evaluation with particular attention toward development of new antitubercular agents.

A simple and reliable liquid chromatographymass spectrometry (LC-MS) assay has been developed and validated for the kinetic characterization and evaluation of inhibitors of shikimate kinase from Mycobacterium tuberculosis (MtSK), a potential target for the development of novel antitubercular drugs. This assay is based on the direct determination of the reaction product shikimate-3-phosphate (S3P) using electrospray ionization (ESI) and a quadrupole time-of-flight (Q-TOF) detector. A comparative analysis of the kinetic parameters of MtSK obtained by the LC-MS assay with those obtained by a conventional UV-assay was performed. Kinetic parameters determined by LC-MS were in excellent agreement with those obtained from the UV assay, demonstrating the accuracy, and reliability of this method. The validated assay was successfully applied to the kinetic characterization of a known inhibitor of shikimate kinase; inhibition constants and mode of inhibition were accurately delineated with LC-MS.

Catalase-peroxidase (KatG) is found in eubacteria, archaea, and lower eukaryotae. The enzyme from Mycobacterium tuberculosis has received the greatest attention because of its role in activation of the antitubercular pro-drug isoniazid, and the high frequency with which drug resistance stems from mutations to the katG gene. Generally, the catalase activity of KatGs is striking. It rivals that of typical catalases, enzymes with which KatGs share no structural similarity. Instead, catalatic turnover is accomplished with an active site that bears a strong resemblance to a typical peroxidase (e.g., cytochrome c peroxidase). Yet, KatG is the only member of its superfamily with such capability. It does so using two mutually dependent cofactors: a heme and an entirely unique Met-Tyr-Trp (MYW) covalent adduct. Heme is required to generate the MYW cofactor. The MYW cofactor allows KatG to leverage heme intermediates toward a unique mechanism for H2O2 oxidation. This review evaluates the range of intermediates identified and their connection to the diverse catalytic processes KatG facilitates, including mechanisms of isoniazid activation.