Three-dimensional structure of Escherichia coli dihydrodipicolinate reductase in complex with NADH and the inhibitor 2,6-pyridinedicarboxylate

Inhibitors of lysine biosynthesis enzymes as potential new herbicides

Lysine is an amino acid that is essential for the growth and development of all organisms owing to its role in a plethora of critical biological functions and reactions. In plants, lysine is synthesised via five sequential enzyme-catalysed reactions collectively known as the diaminopimelate (DAP) pathway, whereas animals are reliant on their plant dietary intake to obtain lysine. Given that lysine is one of the most nutritionally limiting amino acids, several studies have focused on developing strategies to modulate the activity of DAP pathway enzymes to improve the nutritional value of crops. More recently, research has emerged on the potential of inhibiting DAP pathway enzymes for the development of herbicides with a novel mode of action. Over reliance on a small number of modes of action has led to a herbicide resistance crisis, necessitating the development of new modes of action to which no resistance exists. As such, the first herbicidal inhibitors of the DAP pathway have been developed, which target the first three enzymes in lysine biosynthesis. This review explores the structure, function, and inhibition of these enzymes, as well as highlighting promising avenues for the future development of new plant lysine biosynthesis inhibitors.

Computational Exploration of Limonin as a Potential Inhibitor of DapB in Klebsiella pneumoniae

Klebsiella pneumoniae has emerged as a significant multidrug-resistant pathogen, classified as a critical priority by the World Health Organization. The rising rates of antibiotic resistance have led to increased therapeutic failures, diminishing the effectiveness of existing antibiotics. Consequently, there is an urgent need for alternative treatments to effectively inhibit the growth of K. pneumoniae and mitigate associated diseases. Phytochemicals have demonstrated potential advantages over traditional antibiotics, prompting their exploration as innovative therapeutic agents. This study aimed to identify phytochemicals that can inhibit dapB, a vital enzyme in the lysine biosynthesis pathway of K. pneumoniae, which is essential for protein synthesis and the cross-linking of the bacterial peptidoglycan cell wall. We screened 17,934 phytochemicals based on Lipinski's Rule of Five, along with their Absorption, Distribution, Metabolism, Excretion properties and toxicological parameters. Next, we conducted triplicate docking studies against dapB to evaluate the library further. The most promising molecules then underwent 100 ns Molecular Dynamics simulations in triplicate, followed by MM/PBSA based binding free energy calculations to identify potential dapB inhibitors. This in silico analysis highlighted limonin as a promising inhibitor of dapB in K. pneumoniae. Further experimental validation is crucial to enhance limonin's potential as a novel therapeutic agent against K. pneumoniae-associated diseases.

Characterization of lignin-degrading enzyme PmdC, which catalyzes a key step in the synthesis of polymer precursor 2-pyrone-4,6-dicarboxylic acid

Pyrone-2,4-dicarboxylic acid (PDC) is a valuable polymer precursor that can be derived from the microbial degradation of lignin. The key enzyme in the microbial production of PDC is 4-carboxy-2-hydroxymuconate-6-semialdehyde (CHMS) dehydrogenase, which acts on the substrate CHMS. We present the crystal structure of CHMS dehydrogenase (PmdC from Comamonas testosteroni) bound to the cofactor NADP, shedding light on its three-dimensional architecture, and revealing residues responsible for binding NADP. Using a combination of structural homology, molecular docking, and quantum chemistry calculations, we have predicted the binding site of CHMS. Key histidine residues in a conserved sequence are identified as crucial for binding the hydroxyl group of CHMS and facilitating dehydrogenation with NADP. Mutating these histidine residues results in a loss of enzyme activity, leading to a proposed model for the enzyme's mechanism. These findings are expected to help guide efforts in protein and metabolic engineering to enhance PDC yields in biological routes to polymer feedstock synthesis.

Repurposed inhibitor of bacterial dihydrodipicolinate reductase exhibits effective herbicidal activity

Herbicide resistance represents one of the biggest threats to our natural environment and agricultural sector. Thus, new herbicides are urgently needed to tackle the rise in herbicide-resistant weeds. Here, we employed a novel strategy to repurpose a 'failed' antibiotic into a new and target-specific herbicidal compound. Specifically, we identified an inhibitor of bacterial dihydrodipicolinate reductase (DHDPR), an enzyme involved in lysine biosynthesis in plants and bacteria, that exhibited no antibacterial activity but severely attenuated germination of the plant Arabidopsis thaliana. We confirmed that the inhibitor targets plant DHDPR orthologues in vitro, and exhibits no toxic effects against human cell lines. A series of analogues were then synthesised with improved efficacy in germination assays and against soil-grown A. thaliana. We also showed that our lead compound is the first lysine biosynthesis inhibitor with activity against both monocotyledonous and dicotyledonous weed species, by demonstrating its effectiveness at reducing the germination and growth of Lolium rigidum (rigid ryegrass) and Raphanus raphanistrum (wild radish). These results provide proof-of-concept that DHDPR inhibition may represent a much-needed new herbicide mode of action. Furthermore, this study exemplifies the untapped potential of repurposing 'failed' antibiotic scaffolds to fast-track the development of herbicide candidates targeting the respective plant enzymes.

The coordinated action of the enzymes in the L-lysine biosynthetic pathway and how to inhibit it for antibiotic targets

BACKGROUND

Antimicrobial resistance is a global health issue that requires immediate attention in terms of new antibiotics and new antibiotic targets. The l-lysine biosynthesis pathway (LBP) is a promising avenue for drug discovery as it is essential for bacterial growth and survival and is not required by human beings.

SCOPE OF REVIEW

The LBP involves a coordinated action of fourteen different enzymes distributed over four distinct sub-pathways. The enzymes involved in this pathway belong to different classes, such as aspartokinase, dehydrogenase, aminotransferase, epimerase, etc. This review provides a comprehensive account of the secondary and tertiary structure, conformational dynamics, active site architecture, mechanism of catalytic action, and inhibitors of all enzymes involved in LBP of different bacterial species.

MAJOR CONCLUSIONS

LBP offers a wide scope for novel antibiotic targets. The enzymology of a majority of the LBP enzymes is well understood, although these enzymes are less widely studied in the critical pathogens (according to the 2017 WHO report) that require immediate attention. In particular, the enzymes in the acetylase pathway, DapAT, DapDH, and Aspartokinase in critical pathogens have received little attention. High throughput screening for inhibitor design against the enzymes of lysine biosynthetic pathway is rather limited, both in number and in the extent of success.

GENERAL SIGNIFICANCE

This review can serve as a guide for the enzymology of LBP and help in identifying new drug targets and designing potential inhibitors.

Complete Genome Sequence Analysis of Kribbella sp. CA-293567 and Identification of the Kribbellichelins A & B and Sandramycin Biosynthetic Gene Clusters

Minor genera actinomycetes are considered a promising source of new secondary metabolites. The strain Kribbella sp. CA-293567 produces sandramycin and kribbellichelins A & B In this work, we describe the complete genome sequencing of this strain and the in silico identification of biosynthetic gene clusters (BGCs), focusing on the pathways encoding sandramycin and kribbellichelins A-B. We also present a comparative analysis of the biosynthetic potential of 38 publicly available genomes from Kribbella strains.

A dual-target herbicidal inhibitor of lysine biosynthesis

Herbicides with novel modes of action are urgently needed to safeguard global agricultural industries against the damaging effects of herbicide-resistant weeds. We recently developed the first herbicidal inhibitors of lysine biosynthesis, which provided proof-of-concept for a promising novel herbicide target. In this study, we expanded upon our understanding of the mode of action of herbicidal lysine biosynthesis inhibitors. We previously postulated that these inhibitors may act as proherbicides. Here, we show this is not the case. We report an additional mode of action of these inhibitors, through their inhibition of a second lysine biosynthesis enzyme, and investigate the molecular determinants of inhibition. Furthermore, we extend our herbicidal activity analyses to include a weed species of global significance.

Comparative structural and mechanistic studies of 4-hydroxy-tetrahydrodipicolinate reductases from Mycobacterium tuberculosis and Vibrio vulnificus

BACKGROUND

The products of the lysine biosynthesis pathway, meso-diaminopimelate and lysine, are essential for bacterial survival. This paper focuses on the structural and mechanistic characterization of 4-hydroxy-tetrahydrodipicolinate reductase (DapB), which is one of the enzymes from the lysine biosynthesis pathway. DapB catalyzes the conversion of (2S, 4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate (HTPA) to 2,3,4,5-tetrahydrodipicolinate in an NADH/NADPH dependent reaction. Genes coding for DapBs were identified as essential for many pathogenic bacteria, and therefore DapB is an interesting new target for the development of antibiotics.

METHODS

We have combined experimental and computational approaches to provide novel insights into mechanism of the DapB catalyzed reaction.

RESULTS

Structures of DapBs originating from Mycobacterium tuberculosis and Vibrio vulnificus in complexes with NAD⁺, NADP⁺, as well as with inhibitors, were determined and described. The structures determined by us, as well as currently available structures of DapBs from other bacterial species, were compared and used to elucidate a mechanism of reaction catalyzed by this group of enzymes. Several different computational methods were used to provide a detailed description of a plausible reaction mechanism.

CONCLUSIONS

This is the first report presenting the detailed mechanism of reaction catalyzed by DapB.

GENERAL SIGNIFICANCE

Structural data in combination with information on the reaction mechanism provide a background for development of DapB inhibitors, including transition-state analogues.

A Comparative Genomics Approach for Shortlisting Broad-Spectrum Drug Targets in Nontuberculous Mycobacteria

Many members of nontuberculous mycobacteria (NTM) are opportunistic pathogens causing several infections in animals. The incidence of NTM infections and emergence of drug-resistant NTM strains are rising worldwide, emphasizing the need to develop novel anti-NTM drugs. The present study is aimed to identify broad-spectrum drug targets in NTM using a comparative genomics approach. The study identified 537 core proteins in NTM of which 45 were pathogen specific and essential for the survival of pathogens. Furthermore, druggability analysis indicated that 15 were druggable among those 45 proteins. These 15 proteins, which were core proteins, pathogen-specific, essential, and druggable, were considered as potential broad-spectrum candidates. Based on their locations in cytoplasm and membrane, targets were classified as drug and vaccine targets. The identified 15 targets were different enzymes, carrier proteins, transcriptional regulator, two-component system protein, ribosomal, and binding proteins. The identified targets could further be utilized by researchers to design inhibitors for the discovery of antimicrobial agents.

4-Hydroxy-tetrahydrodipicolinate reductase from Neisseria gonorrhoeae - structure and interactions with coenzymes and substrate analog

Neisseria gonorrhoeae, an obligate human pathogen, is a leading cause of communicable diseases globally. Due to rapid development of drug resistance, the rate of successfully curing gonococcal infections is rapidly decreasing. Hence, research is being directed toward finding alternative drugs or drug targets to help eradicate these infections. 4-Hydroxy-tetrahydrodipicolinate reductase (DapB), an important enzyme in the meso-diaminopimelate pathway, is a promising target for the development of new antibiotics. This manuscript describes the first structure of DapB from N. gonorrhoeae determined at 1.85 Å. This enzyme uses NAD(P)H as cofactor. Details of the interactions of the enzyme with its cofactors and a substrate analog/inhibitor are discussed. A large scale bioinformatics analysis of DapBs' sequences is also described.

Crystal structure of dihydrodipicolinate reductase (PaDHDPR) from Paenisporosarcina sp. TG-14: structural basis for NADPH preference as a cofactor

Dihydrodipicolinate reductase (DHDPR) is a key enzyme in the diaminopimelate- and lysine-synthesis pathways that reduces DHDP to tetrahydrodipicolinate. Although DHDPR uses both NADPH and NADH as a cofactor, the structural basis for cofactor specificity and preference remains unclear. Here, we report that Paenisporosarcina sp. TG-14 PaDHDPR has a strong preference for NADPH over NADH, as determined by isothermal titration calorimetry and enzymatic activity assays. We determined the crystal structures of PaDHDPR alone, with its competitive inhibitor (dipicolinate), and the ternary complex of the enzyme with dipicolinate and NADPH, with results showing that only the ternary complex had a fully closed conformation and suggesting that binding of both substrate and nucleotide cofactor is required for enzymatic activity. Moreover, NADPH binding induced local conformational changes in the N-terminal long loop (residues 34–59) of PaDHDPR, as the His35 and Lys36 residues in this loop interacted with the 2′-phosphate group of NADPH, possibly accounting for the strong preference of PaDHDPR for NADPH. Mutation of these residues revealed reduced NADPH binding and enzymatic activity, confirming their importance in NADPH binding. These findings provide insight into the mechanism of action and cofactor selectivity of this important bacterial enzyme.

Rational modification of Corynebacterium glutamicum dihydrodipicolinate reductase to switch the nucleotide-cofactor specificity for increasing l-lysine production

l-lysine is an important amino acid in animals and humans and NADPH is a vital cofactor for maximizing the efficiency of l-lysine fermentation. Dihydrodipicolinate reductase (DHDPR), an NAD(P)H-dependent enzyme, shows a variance in nucleotide-cofactor affinity in bacteria. In this study, we rationally engineered Corynebacterium glutamicum DHDPR (CgDHDPR) to switch its nucleotide-cofactor specificity resulting in an increase in final titer (from 82.6 to 117.3 g L^-1 ), carbon yield (from 0.35 to 0.44 g [g glucose]^-1 ) and productivity (from 2.07 to 2.93 g L^-1  hr^-1 ) of l-lysine in JL-6 ΔdapB::Ec-dapB^C115G,G116C in fed-batch fermentation. To do this, we comparatively analyzed the characteristics of CgDHDPR and Escherichia coli DHDPR (EcDHDPR), indicating that hetero-expression of NADH-dependent EcDHDPR increased l-lysine production. Subsequently, we rationally modified the conserved structure of cofactor-binding motif, and results indicated that introducing the mutation K11A or R13A in CgDHDPR and introducing the mutation R16A or R39A in EcDHDPR modifies the nucleotide-cofactor affinity of DHDPR. Lastly, the effects of these mutated DHDPRs on l-lysine production were investigated. The highest increase (26.2%) in l-lysine production was observed for JL-6 ΔdapB::Ec-dapB^C115G,G116C , followed by JL-6 Cg-dapB^C37G,G38C (21.4%) and JL-6 ΔdapB::Ec-dapB^C46G,G47C (15.2%). This is the first report of a rational modification of DHDPR that enhances the l-lysine production and yield through the modulation of nucleotide-cofactor specificity.

Plant DHDPR forms a dimer with unique secondary structure features that preclude higher-order assembly

Dihydrodipicolinate reductase (DHDPR) catalyses the second reaction in the diaminopimelate pathway of lysine biosynthesis in bacteria and plants. In contrast with the tetrameric bacterial DHDPR enzymes, we show that DHDPR from Vitis vinifera (grape) and Selaginella moellendorffii are dimeric in solution. In the present study, we have also determined the crystal structures of DHDPR enzymes from the plants Arabidopsis thaliana and S. moellendorffii, which are the first dimeric DHDPR structures. The analysis of these models demonstrates that the dimer forms through the intra-strand interface, and that unique secondary features in the plant enzymes block tetramer assembly. In addition, we have also solved the structure of tetrameric DHDPR from the pathogenic bacteria Neisseria meningitidis Measuring the activity of plant DHDPR enzymes showed that they are much more prone to substrate inhibition than the bacterial enzymes, which appears to be a consequence of increased flexibility of the substrate-binding loop and higher affinity for the nucleotide substrate. This higher propensity to substrate inhibition may have consequences for ongoing efforts to increase lysine biosynthesis in plants.

New complexes of Cu(II) with dipicolinate and pyridyl-based ligands: An experimental and DFT approach

The three novel mononuclear copper(II) complexes with dipicolinate and pyridyl-based ligands [Cu(dipic)(L)(OH₂)] (L=4-picoline, vinylpyridine, 4-styrylpyridine; dipic^2-=dipicolinate) were afforded and structurally characterized. X-ray diffraction studies accounted for slight distorted square-pyramidal structures in which the dianion dipic^2- acts as a tridentate ligand in a mer-fashion, the N-donor species occupy an in-plane position, and a water molecule was detected apically coordinated. To assess the effect of the nature of the pyridyl-substituent (para position) on electronic properties, other complexes were also synthesized: [Cu(dipic)(py)(OH₂)], [{Cu(dipic)(OH₂)}₂(μ-pyz)] and [{Cu(dipic)(OH₂)}(μ-pypy){Cu(dipic)}] (py=pyridine, pyz=pyrazine, pypy=(E)-1,2-bis(pyridine-4-yl)ethane). Absorptive behavior in the UV-VIS region was studied in solution and in the solid state (reflectance measurements). Additionally, geometry and population analyses were conducted by means of DFT calculations. Electronic UV-VIS spectra were simulated for both dinuclear complexes in the framework of the TD-DFT methodology to assign the origin of the absorption bands.

Design, Synthesis, and Biological Activities of Novel Pyrazole Oxime Compounds Containing a Substituted Pyridyl Moiety

In this paper, in order to find novel biologically active pyrazole oximes, a series of pyrazole oxime compounds bearing a substituted pyridyl unit were prepared. Bioassays showed that some target compounds were found to have good acaricidal activity against Tetranychus cinnabarinus at a concentration of 500 μg/mL, compound 9q especially displayed potent acaricidal activity against T. cinnabarinus when the concentration was reduced to 100 μg/mL. Interestingly, most target compounds possessed excellent insecticidal activities against Oriental armyworm at 500 μg/mL. Moreover, some compounds were active against Aphis medicaginis and Nilaparvata lugens at 500 μg/mL. Additionally, compounds 9b, 9g, 9l, 9p, 9q, 9r, 9s, 9t, 9u, and 9v displayed significant antiproliferative activities against HepG2 cells with IC₅₀ values of 1.53-17.27 μM, better than that of the control 5-fluorouracil (IC₅₀ = 35.67 μM).

The crystal structure of dihydrodipicolinate reductase from the human-pathogenic bacterium Bartonella henselae strain Houston-1 at 2.3 Å resolution

In bacteria, the second committed step in the diaminopimelate/lysine anabolic pathways is catalyzed by the enzyme dihydrodipicolinate reductase (DapB). DapB catalyzes the reduction of dihydrodipicolinate to yield tetrahydrodipicolinate. Here, the cloning, expression, purification, crystallization and X-ray diffraction analysis of DapB from the human-pathogenic bacterium Bartonella henselae, the causative bacterium of cat-scratch disease, are reported. Protein crystals were grown in conditions consisting of 5%(w/v) PEG 4000, 200 mM sodium acetate, 100 mM sodium citrate tribasic pH 5.5 and were shown to diffract to ∼2.3 Å resolution. They belonged to space group P4322, with unit-cell parameters a = 109.38, b = 109.38, c = 176.95 Å. Rr.i.m. was 0.11, Rwork was 0.177 and Rfree was 0.208. The three-dimensional structural features of the enzymes show that DapB from B. henselae is a tetramer consisting of four identical polypeptides. In addition, the substrate NADP+ was found to be bound to one monomer, which resulted in a closed conformational change in the N-terminal domain.

Molecular replacement then and now

The `phase problem' in crystallography results from the inability to directly measure the phases of individual diffracted X-ray waves. While intensities are directly measured during data collection, phases must be obtained by other means. Several phasing methods are available (MIR, SAR, MAD, SAD and MR) and they all rely on the premise that phase information can be obtained if the positions of marker atoms in the unknown crystal structure are known. This paper is dedicated to the most popular phasing method, molecular replacement (MR), and represents a personal overview of the development, use and requirements of the methodology. The first description of noncrystallographic symmetry as a tool for structure determination was explained by Rossmann and Blow [Rossmann & Blow (1962), Acta Cryst. 15, 24-31]. The term `molecular replacement' was introduced as the name of a book in which the early papers were collected and briefly reviewed [Rossmann (1972), The Molecular Replacement Method. New York: Gordon & Breach]. Several programs have evolved from the original concept to allow faster and more sophisticated searches, including six-dimensional searches and brute-force approaches. While careful selection of the resolution range for the search and the quality of the data will greatly influence the outcome, the correct choice of the search model is probably still the main criterion to guarantee success in solving a structure using MR. Two of the main parameters used to define the `best' search model are sequence identity (25% or more) and structural similarity. Another parameter that may often be undervalued is the quality of the probe: there is clearly a relationship between the quality and the correctness of the chosen probe and its usefulness as a search model. Efforts should be made by all structural biologists to ensure that their deposited structures, which are potential search probes for future systems, are of the best possible quality.

Characterisation of the first enzymes committed to lysine biosynthesis in Arabidopsis thaliana

In plants, the lysine biosynthetic pathway is an attractive target for both the development of herbicides and increasing the nutritional value of crops given that lysine is a limiting amino acid in cereals. Dihydrodipicolinate synthase (DHDPS) and dihydrodipicolinate reductase (DHDPR) catalyse the first two committed steps of lysine biosynthesis. Here, we carry out for the first time a comprehensive characterisation of the structure and activity of both DHDPS and DHDPR from Arabidopsis thaliana. The A. thaliana DHDPS enzyme (At-DHDPS2) has similar activity to the bacterial form of the enzyme, but is more strongly allosterically inhibited by (S)-lysine. Structural studies of At-DHDPS2 show (S)-lysine bound at a cleft between two monomers, highlighting the allosteric site; however, unlike previous studies, binding is not accompanied by conformational changes, suggesting that binding may cause changes in protein dynamics rather than large conformation changes. DHDPR from A. thaliana (At-DHDPR2) has similar specificity for both NADH and NADPH during catalysis, and has tighter binding of substrate than has previously been reported. While all known bacterial DHDPR enzymes have a tetrameric structure, analytical ultracentrifugation, and scattering data unequivocally show that At-DHDPR2 exists as a dimer in solution. The exact arrangement of the dimeric protein is as yet unknown, but ab initio modelling of x-ray scattering data is consistent with an elongated structure in solution, which does not correspond to any of the possible dimeric pairings observed in the X-ray crystal structure of DHDPR from other organisms. This increased knowledge of the structure and function of plant lysine biosynthetic enzymes will aid future work aimed at improving primary production.

Structure and nucleotide specificity of Staphylococcus aureus dihydrodipicolinate reductase (DapB)

Lysine biosynthesis proceeds by the nucleotide-dependent reduction of dihydrodipicolinate (DHDP) to tetrahydrodipicolinate (THDP) by dihydrodipicolinate reductase (DHDPR). The S. aureus DHDPR structure reveals different conformational states of this enzyme even in the absence of a substrate or nucleotide-cofactor. Despite lacking a conserved basic residue essential for NADPH interaction, S. aureus DHDPR differs from other homologues as NADPH is a more preferred co-factor than NADH. The structure provides a rationale-Lys35 compensates for the co-factor site mutation. These observations are significant for bi-ligand inhibitor design that relies on ligand-induced conformational changes as well as co-factor specificity for this important drug target.

Catalytic mechanism and cofactor preference of dihydrodipicolinate reductase from methicillin-resistant Staphylococcus aureus

Given the rapid rise in antibiotic resistance, including methicillin resistance in Staphylococcus aureus (MRSA), there is an urgent need to characterize novel drug targets. Enzymes of the lysine biosynthesis pathway in bacteria are examples of such targets, including dihydrodipicolinate reductase (DHDPR, E.C. 1.3.1.26), which is the product of an essential bacterial gene. DHDPR catalyzes the NAD(P)H-dependent reduction of dihydrodipicolinate (DHDP) to tetrahydrodipicolinate (THDP) in the lysine biosynthesis pathway. We show that MRSA-DHDPR exhibits a unique nucleotide specificity utilizing NADPH (K(m)=12μM) as a cofactor more effectively than NADH (K(m)=26μM). However, the enzyme is inhibited by high concentrations of DHDP when using NADPH as a cofactor, but not with NADH. Isothermal titration calorimetry (ITC) studies reveal that MRSA-DHDPR has ∼20-fold greater binding affinity for NADPH (K(d)=1.5μM) relative to NADH (K(d)=29μM). Kinetic investigations in tandem with ITC studies show that the enzyme follows a compulsory-order ternary complex mechanism; with inhibition by DHDP through the formation of a nonproductive ternary complex with NADP(+). This work describes, for the first time, the catalytic mechanism and cofactor preference of MRSA-DHDPR, and provides insight into rational approaches to inhibiting this valid antimicrobial target.

NMR studies uncover alternate substrates for dihydrodipicolinate synthase and suggest that dihydrodipicolinate reductase is also a dehydratase

Despite extensive effort, the drug target dihydrodipicolinate synthase (DHDPS) continues to evade effective inhibition. We used NMR spectroscopy to examine the substrate specificity of this enzyme and found that two pyruvate analogues previously classified as weak competitive inhibitors were turned over productively by DHDPS. Four other analogues were confirmed not to be substrates. Finally, our examination of the natural product of DHDPS and its degradation revealed that dihydrodipicolinate reductase (DHDPR) possesses previously unrecognized dehydratase activity.

Cloning, expression and crystallization of dihydrodipicolinate reductase from methicillin-resistant Staphylococcus aureus

Dihydrodipicolinate reductase (DHDPR; EC 1.3.1.26) catalyzes the nucleotide (NADH/NADPH) dependent second step of the lysine-biosynthesis pathway in bacteria and plants. Here, the cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DHDPR from methicillin-resistant Staphylococcus aureus (MRSA-DHDPR) are presented. The enzyme was crystallized in a number of forms, predominantly with ammonium sulfate as a precipitant, with the best crystal form diffracting to beyond 3.65 A resolution. Crystal structures of the apo form as well as of cofactor (NADPH) bound and inhibitor (2,6-pyridinedicarboxylate) bound forms of MRSA-DHDPR will provide insight into the structure and function of this essential enzyme and valid drug target.

The structure of dihydrodipicolinate reductase (DapB) from Mycobacterium tuberculosis in three crystal forms

Dihydrodipicolinate reductase (DHDPR, DapB) is an enzyme that belongs to the L-lysine biosynthetic pathway. DHDPR reduces the alpha,beta-unsaturated cyclic imine 2,3-dihydrodipicolinic acid to yield the compound 2,3,4,5-tetrahydrodipicolinic acid in a pyridine nucleotide-dependent reaction. The substrate of this reaction is the unstable product of the preceding enzyme dihydrodipicolinate synthase (DHDPS, DapA). Here, the structure of apo-DHDPR from Mycobacterium tuberculosis is reported in two orthorhombic crystal forms, as well as the structure of DHDPR from M. tuberculosis in complex with NADH in a monoclinic crystal form. A comparison of the results with previously solved structures of this enzyme shows that DHDPR undergoes a major conformational change upon binding of its cofactor. This conformational change can be interpreted as one of the low-frequency normal modes of the structure.

catena-Poly[[[diacrylato-κO,O'-neodymium(III)]-di-μ-acrylato-κO,O':O';κO:O,O'-[triaqua-neodymium(III)]-di-μ-acrylato-κO,O':O';κO:O,O'] trihydrate]

The title compound, {[Nd₂(CH₂CHCOO)₆(H₂O)₃]·3H₂O}_n, was synthesized by hydro­thermal methods. The structure contains one-dimensional coordination polymers in which two distinct Nd^III atoms show different coordination modes. One is coordinated by four bidentate acrylate ligands, two of which bridge Nd^III atoms, and by two O atoms from a further two bridging acrylate ligands. The other Nd^III atom is coordinated by two bidentate acrylate ligands, two O atoms from bridging acrylate ligands, and three water mol­ecules. Extensive hydrogen bonding between the coordinated and uncoordin­ated water mol­ecules and the O atoms of the acrylate ligands link the coordination polymers into a three-dimensional network.

Bis(ethano-lato-κO)(5,10,15,20-tetra-phenyl-calix[4]pyrrole)manganese(III) hexa-fluoro-phosphate

The title compound, [Mn(C₂H₅O)₂(C₄₄H₂₈N₄)]PF₆, was synthesized from manganese(III) 2,4-penta­nedionate and 5,10,15,20-tetra­phenyl­calix[4]pyrrole by a hydro­thermal reaction. The Mn^III atom is located on an inversion centre and the asymmetric unit comprises one half-formula unit. The Mn^III ion is hexa­coordinated by four N atoms from one 5,10,15,20-tetra­phenyl­calix[4]pyrrole ligand and two O atoms from two deprotonated ethanol mol­ecules. The equatorially located atoms (the Mn and four N atoms) are planar. The dihedral angles between the planes of the phenyl rings and the equatorial plane are 53.3 (2) and 81.8 (2)°. One hexa­fluoro­phosphate anion balances the charge.

Binding synergy and cooperativity in dihydrodipicolinate reductase: implications for mechanism and the design of biligand inhibitors

Dihydrodipicolinate reductase (DHPR) is a homotetramer that catalyzes reduction of dihydrodipicolinate (DHP). We recently reported a biligand inhibitor ( K i = 100 nM) of DHPR, comprised of fragments that bind in the NADH (CRAA = catechol rhodanine acetic acid) and DHP (PDC = pyridine dicarboxylate) binding sites. Herein, we characterize binding synergy and cooperativity for ligand binding to Escherichia coli DHPR: NADH or CRAA and PDC (stable analog of DHP). While K d values indicate little synergy between NADH and PDC, (1)H- (15)N HSQC chemical shift perturbation and saturation transfer difference (STD) titrations indicate that PDC induces a more dramatic conformational change than NADH, consistent with a role in domain closure. PDC binds cooperatively (Hill coefficient = 2), while NADH does not, based on STD titrations that monitor only fast exchange processes. However, HSQC titrations monitoring Trp253 (located between monomers) indicate that NADH binds in two steps, with high affinity binding to only one of the monomers. Therefore, DHPR binds cofactor via a sequential model, with negative cooperativity. These results, interpreted in light of steady-state data, suggest that DHPR activity requires NADH binding at only one of the four monomers. Implications of our results for fragment assembly are discussed, using CRAA tethering to PDC as a model biligand: (a) if one fragment (ex. PDC) must induce a large structural change before the other fragment is brought proximal, this must be screened for upfront, and (b) cooperative or synergistic interactions between binding sites can lead to unexpected and misleading effects in NMR-based screening.

Tetra-μ-2,5-difluoro-benzoato-bis-[(2,2'-bipyridine)(2,5-difluoro-benzoato)gadolinium(III)]

In the centrosymmetric title compound, [Gd₂(C₇H₃F₂O₂)₆(C₁₀H₈N₂)₂], the asymmetric unit comprises one cation chelated by two 2,5-difluoro­benzoate and one 2,2′-bipyridine. Two cations are linked into dimers via three bridging carboxyl­ate groups from three 2,5-difluoro­benzoic acid units. The Gd^III ion is nine-coord­inated by seven O atoms and two N atoms.

Diazido-bis{2-[3-(dimethyl-amino)propyl-imino-meth-yl]phenol}manganese(III) perchlorate

The title compound, [Mn(N₃)₂(C₁₂H₁₈N₂O)₂]ClO₄, was synthesized from manganese(III) acetate, sodium azide and 2-[3-(dimethyl­amino)propyl­imino­meth­yl]phenol by a hydro­thermal reaction. The Mn^III ion is hexa­coordinated by two N and two O atoms from two phenolate ligands and two N atoms from two azide ligands. The Mn^III cation lies on an inversion centre and, as a result, the asymmetric unit comprises one half-mol­ecule.

Tricyclo-hexyl(piperidine-1-dithio-carboxyl-ato-κS)tin(IV)

In the title compound, [Sn(C₆H₁₁)₃(C₆H₁₀NS₂)], the Sn^IV atom is tetra­coordinated by three C atoms from cyclo­hexyl groups and one S atom from a piperidine­dithio­carboxyl­ate anion. The coordination geometry is distorted tetra­hedral, with Sn—C bond lengths in the range 2.133 (6)–2.188 (6) Å and with an Sn—S bond length of 2.4516 (19) Å. The nonbonded S atom of the piperidine­dithio­carboxyl­ate anion makes an Sn⋯S contact of 3.174 (3) Å.

Chemical proteomics-based drug design: target and antitarget fishing with a catechol-rhodanine privileged scaffold for NAD(P)(H) binding proteins

Drugs typically exert their desired and undesired biological effects by virtue of binding interactions with protein target(s) and antitarget(s), respectively. Strategies are therefore needed to efficiently manipulate and monitor cross-target binding profiles (e.g., imatinib and isoniazid) as an integrated part of the drug design process. Herein we present such a strategy, which reverses the target --> lead rational drug design paradigm. Enabling this approach is a catechol-rhodanine privileged scaffold for dehydrogenases, which is easily tuned for affinity and specificity toward desired targets. This scaffold crosses bacterial (E. coli) cell walls, and proteome-wide studies demonstrate it does indeed bind to and identify NAD(P)(H)-binding proteins that are potential drug targets in Mycobacterium tuberculosis and antitargets (or targets) in human liver. This approach to drug discovery addresses key difficulties earlier in the process by only pursuing targets for which a chemical lead and optimization strategy are available, to permit rapid tuning of target/antitarget binding profiles.

catena-Poly[[aqua-{4-[N'-(2,4-dioxo-3-pentyl-idene)-hydrazino]-benzoato}-copper(II)]-μ-acetato]

In the title compound, [Cu(CH(3)CO(2))(C(12)H(11)N(2)O(4))(H(2)O)](n), the Cu(II) cation is tetra-coordinated by three carboxyl-ate O atoms from one 4-[N'-(2,4-dioxo-3-pentyl-idene)-hydrazino]-benzoate ligand and two acetate bridges, and by one water mol-ecule. The acetate bridges link adjacent Cu(II) cations, forming a chain. The crystal structure involves O-H⋯O hydrogen bonds.

Tetra-aqua-bis[(1-carboxyl-atomethyl-1,3-benzimidazol-3-ium-3-yl)acetato-κO]palladium(II) dihydrate

In the title compound, [Pd(C₁₁H₉N₂O₄)₂(H₂O)₄]·2H₂O, the palladium(II) cation lies on an inversion centre and is hexa­coordinated by two carboxyl­ate O atoms from two (1-carboxyl­atomethyl-1,3-benzimidazol-3-ium-3-yl)acetate ligands and four water mol­ecules, with a slightly distorted octa­hedral geometry. O—H⋯O hydrogen bonds link the mol­ecules together.

Tris[2-(propyl-imino-meth-yl)phenolato-κN,O]cobalt(III)

The title compound, [Co(C(10)H(12)NO)(3)], was synthesized from cobalt(III) fluoride and 2-(propyl-imino-meth-yl)phenol in refluxing methanol. The Co(III) ion is hexa-coordinated by three N and three O atoms from three bidentate Schiff base ligands in an octa-hedral geometry.

Tetra-kis(μ-2,4-difluoro-benzoato)bis-[(2,4-difluoro-benzoato)(1,10-phenanthroline)gadolinium(III)]

In the title compound, [Gd(2)(C(7)H(3)F(2)O(2))(6)(C(12)H(8)N(2))(2)], the asymmetric unit comprises one Gd(3+) cation chelated by two 2,4-difluoro-benzoate and one 1,10-phenanthroline ligands. Two cations are linked into a centrosymmetric dimer via three bridging carboxyl-ate groups of 2,4-difluoro-benzoate ligands. Each Gd(3+) ion is nine-coordinated by seven O atoms and two N atoms.

μ-Oxido-bis-{chlorido[tris-(2-pyridylmethyl)amine]manganese(III)} bis-(hexa-fluorido-phosphate)

In the title compound, [Mn₂O(C₁₈H₁₈ClN₄)₂](PF₆)₂, the Mn atom is chelated by a tetra­dentate ligand via four N atoms, and further bonded to one chloride ion and one bridging oxide, to give a centrosymmetric cation and distorted octa­hedral coordination geometry.

Oxalatobis(propane-1,3-diamine)manganese(II) chloride monohydrate

In the asymmetric unit of the title compound, [Mn(C(2)O(4))(C(3)H(10)N(2))(2)]Cl·H(2)O, there are two independent Mn(III) complexes, two Cl(-) anions and two uncoordinated water mol-ecules. Each Mn(III) atom is hexa-coordinated by four N atoms from two propane-1,3-diamine ligands and two O atoms from one oxalate ligand, resulting in a slightly distorted octa-hedral MnO(2)N(4) geometry. Mn-O and Mn-N bond lengths are in the ranges 1.969 (2)-2.020 (3) and 2.068 (3)-2.113 (4) Å, respectively. There are weak inter-molecular O-H⋯O, O-H⋯Cl, N-H⋯O and N-H⋯Cl hydrogen bonds with D⋯A distances in the range 2.831 (4)-3.423 (3) Å.

Cloning, expression, purification, crystallization and preliminary X-ray diffraction analysis of DapB (Rv2773c) from Mycobacterium tuberculosis

Dihydrodipicolinate reductase from Mycobacterium tuberculosis (DapB, DHDPR, Rv2773c) has been cloned and heterologously expressed in Escherichia coli, purified using standard chromatographic techniques and crystallized in three different crystal forms. Preliminary diffraction data analysis suggests the presence of two tetramers in the asymmetric unit of one crystal form and half a tetramer in the other two crystal forms.