Novel Antimycobacterial Compounds Suppress NAD Biogenesis by Targeting a Unique Pocket of NaMN Adenylyltransferase.

Conventional treatments to combat the tuberculosis (TB) epidemic are falling short, thus encouraging the search for novel antitubercular drugs acting on unexplored molecular targets. Several whole-cell phenotypic screenings have delivered bioactive compounds with potent antitubercular activity. However, their cellular target and mechanism of action remain largely unknown. Further evaluation of these compounds may include their screening in search for known antitubercular drug targets hits. Here, a collection of nearly 1400 mycobactericidal compounds was screened against Mycobacterium tuberculosis NaMN adenylyltransferase ( MtNadD), a key enzyme in the biogenesis of NAD cofactor that was recently validated as a new drug target for dormant and active tuberculosis. We found three chemotypes that efficiently inhibit MtNadD in the low micromolar range in vitro. SAR and cheminformatics studies of commercially available analogues point to a series of benzimidazolium derivatives, here named N2, with bactericidal activity on different mycobacteria, including M. abscessus, multidrug-resistant M. tuberculosis, and dormant M. smegmatis. The on-target activity was supported by the increased resistance of an M. smegmatis strain overexpressing the target and by a rapid decline in NAD(H) levels. A cocrystal structure of MtNadD with N2-8 inhibitor reveals that the binding of the inhibitor induced the formation of a new quaternary structure, a dimer-of-dimers where two copies of the inhibitor occupy symmetrical positions in the dimer interface, thus paving the way for the development of a new generation of selective MtNadD bioactive inhibitors. All these results strongly suggest that pharmacological inhibition of MtNadD is an effective strategy to combat dormant and resistant Mtb strains.

Structural analysis of mycobacterial homoserine transacetylases central to methionine biosynthesis reveals druggable active site.

Mycobacterium tuberculosis is the cause of the world's most deadly infectious disease. Efforts are underway to target the methionine biosynthesis pathway, as it is not part of the host metabolism. The homoserine transacetylase MetX converts L-homoserine to O-acetyl-L-homoserine at the committed step of this pathway. In order to facilitate structure-based drug design, we determined the high-resolution crystal structures of three MetX proteins, including M. tuberculosis (MtMetX), Mycolicibacterium abscessus (MaMetX), and Mycolicibacterium hassiacum (MhMetX). A comparison of homoserine transacetylases from other bacterial and fungal species reveals a high degree of structural conservation amongst the enzymes. Utilizing homologous structures with bound cofactors, we analyzed the potential ligandability of MetX. The deep active-site tunnel surrounding the catalytic serine yielded many consensus clusters during mapping, suggesting that MtMetX is highly druggable.

Structural Variability of EspG Chaperones from Mycobacterial ESX-1, ESX-3, and ESX-5 Type VII Secretion Systems.

Type VII secretion systems (ESX) are responsible for transport of multiple proteins in mycobacteria. How different ESX systems achieve specific secretion of cognate substrates remains elusive. In the ESX systems, the cytoplasmic chaperone EspG forms complexes with heterodimeric PE-PPE substrates that are secreted from the cells or remain associated with the cell surface. Here we report the crystal structure of the EspG1 chaperone from the ESX-1 system determined using a fusion strategy with T4 lysozyme. EspG1 adopts a quasi 2-fold symmetric structure that consists of a central ß-sheet and two α-helical bundles. In addition, we describe the structures of EspG3 chaperones from four different crystal forms. Alternate conformations of the putative PE-PPE binding site are revealed by comparison of the available EspG3 structures. Analysis of EspG1, EspG3, and EspG5 chaperones using small-angle X-ray scattering reveals that EspG1 and EspG3 chaperones form dimers in solution, which we observed in several of our crystal forms. Finally, we propose a model of the ESX-3 specific EspG3-PE5-PPE4 complex based on the small-angle X-ray scattering analysis.

Peptide Inhibitors Targeting the Neisseria gonorrhoeae Pivotal Anaerobic Respiration Factor AniA.

Neisseria gonorrhoeae causes the sexually transmitted infection gonorrhea, which is highly prevalent worldwide and has a major impact on reproductive and neonatal health. The superbug status of N. gonorrhoeae necessitates the development of drugs with different mechanisms of action. Here, we focused on targeting the nitrite reductase AniA, which is a pivotal component of N. gonorrhoeae anaerobic respiration and biofilm formation. Our studies showed that gonococci expressing AniA containing the altered catalytic residues D137A and H280A failed to grow under anaerobic conditions, demonstrating that the nitrite reductase function is essential. To facilitate the pharmacological targeting of AniA, new crystal structures of AniA were refined to 1.90-Å and 2.35-Å resolutions, and a phage display approach with libraries expressing randomized linear dodecameric peptides or heptameric peptides flanked by a pair of cysteine residues was utilized. Biopanning experiments led to the identification of 29 unique peptides, with 1 of them, C7-3, being identified multiple times. Evaluation of their ability to interact with AniA using enzyme-linked immunosorbent assay and computational docking studies revealed that C7-3 was the most promising inhibitor, binding near the type 2 copper site of the enzyme, which is responsible for interaction with nitrite. Subsequent enzymatic assays and biolayer interferometry with a synthetic C7-3 and its derivatives, C7-3m1 and C7-3m2, demonstrated potent inhibition of AniA. Finally, the MIC50 value of C7-3 and C7-3m2 against anaerobically grown N. gonorrhoeae was 0.6 mM. We present the first peptide inhibitors of AniA, an enzyme that should be further exploited for antigonococcal drug development.

Transcription of the Streptococcus pyogenes hyaluronic acid capsule biosynthesis operon is regulated by previously unknown upstream elements.

The important human pathogen Streptococcus pyogenes (group A Streptococcus [GAS]) produces a hyaluronic acid (HA) capsule that plays critical roles in immune evasion. Previous studies showed that the hasABC operon encoding the capsule biosynthesis enzymes is under the control of a single promoter, P1, which is negatively regulated by the two-component regulatory system CovR/S. In this work, we characterize the sequence upstream of P1 and identify a novel regulatory region controlling transcription of the capsule biosynthesis operon in the M1 serotype strain MGAS2221. This region consists of a promoter, P2, which initiates transcription of a novel small RNA, HasS, an intrinsic transcriptional terminator that inefficiently terminates HasS, permitting read-through transcription of hasABC, and a putative promoter which lies upstream of P2. Electrophoretic mobility shift assays, quantitative reverse transcription-PCR, and transcriptional reporter data identified CovR as a negative regulator of P2. We found that the P1 and P2 promoters are completely repressed by CovR, and capsule expression is regulated by the putative promoter upstream of P2. Deletion of hasS or of the terminator eliminates CovR-binding sequences, relieving repression and increasing read-through, hasA transcription, and capsule production. Sequence analysis of 44 GAS genomes revealed a high level of polymorphism in the HasS sequence region. Most of the HasS variations were located in the terminator sequences, suggesting that this region is under strong selective pressure. We discovered that the terminator deletion mutant is highly resistant to neutrophil-mediated killing and is significantly more virulent in a mouse model of GAS invasive disease than the wild-type strain. Together, these results are consistent with the naturally occurring mutations in this region modulating GAS virulence.

Pentapeptide boronic acid inhibitors of Mycobacterium tuberculosis MycP1 protease.

Mycosin protease-1 (MycP1) cleaves ESX secretion-associated protein B (EspB) that is a virulence factor of Mycobacterium tuberculosis, and accommodates an octapeptide, AVKAASLG, as a short peptide substrate. Because peptidoboronic acids are known inhibitors of serine proteases, the synthesis and binding of a boronic acid analog of the pentapeptide cleavage product, AVKAA, was studied using MycP1 variants from Mycobacterium thermoresistible (MycP1mth), Mycobacterium smegmatis (MycP1msm) and M. tuberculosis (MycP1mtu). We synthesized the boropentapeptide, HAlaValLysAlaAlaB(OH)2 (1) and the analogous pinanediol PD-protected HAlaValLysAlaAlaBO2(PD) (2) using an Fmoc/Boc peptide strategy. The pinanediol boropentapeptide 2 displayed IC50 values 121.6±25.3 µM for MycP1mth, 93.2±37.3 µM for MycP1msm and 37.9±5.2 µM for MycP1mtu. Such relatively strong binding creates a chance for crystalizing the complex with 2 and finding the structure of the unknown MycP1 catalytic site that would potentially facilitate the development of new anti-tuberculosis drugs.

1-Phenyl-3-(pyrid-2-yl)benzo[e][1,2,4]triazinyl: the first "Blatter radical" for coordination chemistry.

A neutral air- and moisture-stable N,N'-chelating radical ligand, 1-phenyl-3-(pyrid-2-yl)benzo[e][1,2,4]triazinyl (1) was synthesized and characterized by electron paramagnetic resonance spectroscopy, X-ray crystallography, and magnetic measurements. Subsequent reaction of 1 with Cu(hfac)2·2H2O (hfac = hexafluoroacetylacetonate) under ambient conditions afforded the coordination complex Cu(1)(hfac)2 in which the radical binds to the metal in a bidentate fashion. Magnetic susceptibility data collected from 1.8 to 300 K indicate a strong ferromagnetic metal-radical interaction in the complex and weak antiferromagnetic radical···radical interactions between the Cu(1)(hfac)2 units. Detailed computational investigations support this assignment. Radical 1 is a new addition to the growing library of 1,2,4-triazinyl radicals and the first member of this family of paramagnetic species synthesized specifically for coordination purposes.

Ferromagnetic ordering in bisthiaselenazolyl radicals: variations on a tetragonal theme.

A series of five isostructural bisthiaselenazolyl radicals 2 have been prepared and characterized by X-ray crystallography. The crystal structures, all belonging to the tetragonal space group P42(1)m, consist of slipped pi-stack arrays of undimerized radicals packed about 4 centers running along the z-direction, an arrangement which gives rise to a complex lattice-wide network of close intermolecular Se---Se' contacts. Variations in R1 (Et, Pr, CH2CF3) with R2 = Cl lead to significant changes in the degree of slippage of the pi-stacks and hence the proximity of the Se---Se' interactions. By contrast, variations in R2 (Cl, Br, Me) with R1 = Et induce very little change in either the degree of slippage or the intermolecular contacts. Variable-temperature conductivity (sigma) measurements show relatively constant values for the conductivity sigma(300 K) (10(-5)-10(-4) S cm(-1)) and thermal activation energy E(act) (0.27-0.31 eV). Variable-temperature magnetic susceptibility measurements indicate that radicals 2b and 2c (R1 = Pr, CH2CF3; R2 = Cl) behave as weakly antiferromagnetically coupled Curie-Weiss paramagnets, but in 2a, 2d and 2e (R1 = Et; R2 = Cl, Me, Br) ferromagnetic ordering is observed, with T(c) values of 12.8 (R2 = Cl), 13.6 (R2 = Me), and 14.1 K (R2 = Br). The origin of the dramatically different magnetic behavior across the series has been explored in terms of a direct through-space mechanism by means of DFT calculations on individual pairwise exchange energies. These indicate that antiferromagnetic exchange between radicals along the pi-stacks increases with pi-stack slippage.

Self-association of the N-methyl benzotellurodiazolylium cation: implications for the generation of super-heavy atom radicals.

The N-methyl benzotellurodiazolylium cation self-associates in the solid state via short (2.471(3) A) 4-center TeN' intermolecular contacts; electrochemical data and the results of DFT calculations suggest that the dimers persist in solution.

Enhanced conductivity and magnetic ordering in isostructural heavy atom radicals.

Synthetic methods have been developed to generate the complete series of resonance-stabilized heterocyclic thia/selenazyl radicals 1a-4a. X-ray crystallographic studies confirm that all four radicals are isostructural, belonging to the tetragonal space group P42(1)m. The crystal structures consist of slipped pi-stack arrays of undimerized radicals packed about 4 centers running along the z direction, an arrangement which gives rise to a complex lattice-wide network of close intermolecular E2---E2' contacts. Variable temperature conductivity (sigma) measurements reveal an increase in conductivity with increasing selenium content, particularly so when selenium occupies the E2 position, with sigma(300 K) reaching a maximum (for E1 = E2 = Se) of 3.0 x 10(-4) S cm(-1). Thermal activation energies E(act) follow a similar profile, decreasing with increasing selenium content along the series 1a (0.43 eV), 3a (0.31 eV), 2a (0.27 eV), 4a (0.19 eV). Variable temperature magnetic susceptibility measurements indicate that all four radicals exhibit S = 1/2 Curie-Weiss behavior over the temperature range 20-300 K. At lower temperatures, the three selenium-based radicals display magnetic ordering. Radical 3a, with selenium positioned at the E1 site, undergoes a phase transition at 14 K to a weakly spin-canted (phi = 0.010 degrees) antiferromagnetic state. By contrast, radicals 2a and 4a, which both possess selenium in the E2 position, order ferromagnetically, with Curie temperatures of T(c) = 12.8 and 17.0 K, respectively. The coercive fields H(c) at 2 K of 2a (250 Oe) and 4a (1370 Oe) are much larger than those seen in conventional light atom organic ferromagnets. The transport properties of the entire series 1a-4a are discussed in the light of Extended Hückel Theory band structure calculations.

Tetrathiophenalenyl radical and its disulfide-bridged dimer.

The presence of two disulfide groups in the tetrathiophenalenyl radical TTPLY leads to a highly delocalized spin distribution and the lowest cell potential ever observed for a monofunctional phenalenyl derivative. While the heteroatom substituents successfully block C-C bond formation, TTPLY nonetheless associates in the solid state to afford the hypervalent S-S-bonded dimer (TTPLY)2.

Trisphenalenyl-based neutral radical molecular conductor.

We report the preparation, crystallization, and solid-state characterization of the first member of a new family of tris(1,9-disubstituted phenalenyl)silicon neutral radicals. In the solid state, the radical packs as weak partial pi-dimers with intermolecular carbon...carbon contacts that fall at the van der Waals atomic separation. Magnetic susceptibility measurements indicate approximately 0.7 Curie spins per molecule from room temperature down to 50 K, below which antiferromagnetic coupling becomes apparent; the compound has a room-temperature single-crystal conductivity of sigmaRT = 2.4 x 10(-6) S cm(-1).

Spin-canting in heavy atom heterocyclic radicals.

A pair of isostructural bis-selenathiazolyl and bis-diselenazolyl radical conductors display weak (spin-canted) ferromagnetism with Tc values of 18 K and 27 K respectively.

Characterization of the diradical *NSNSC-CNSSN* and [NSNSC-CNSSN][MF6]n (n=1, 2). The first observation of an excited triplet state in dimers of 7pi -CNSSN* radicals.

Preparation and full characterization of the main-group diradical *NSNSC-CNSSN*, 8, the MF6- salt (As, Sb) of radical cation +NSNSC-CNSSN*, 8*+, and the AsF6- salt of the dication +NSNSC-CNSSN+, 82+, are presented. 8, a=6.717 (4), b=11.701(2), c=8.269(3) A, alpha=gamma=90, beta=106.69(3) degrees, monoclinic, space group P21/n, Z=4, T=203 K; 8SbF6, a=6.523(2), b=7.780(2), c=12.012(4) A, alpha=91.994(4), beta=96.716(4), gamma=09.177(4) degrees, triclinic, space group P, Z=2, T=198 K; 8[AsF6]2, a=12.7919(14), b=9.5760(11), c=18.532(2) A, alpha=gamma=90, beta=104.034(2) degrees, monoclinic, space group Pn, Z=6, T=198 K. Preparation of 8MF6 was carried out via a reduction of [CNSNS]2[MF6]2 (M=As, Sb) with either ferrocene or a SbPh3-NBu4Cl mixture. In the solid state, diamagnetic 8SbF6 contains centrosymmetric dimers [8*+]2 linked via two-electron four-centered pi*-pi* interactions with a thermally excited triplet state as detected by electron paramagnetic resonance (EPR). This is the first observation of a triplet excited state for a 7pi 1,2,3,5-dithiadiazolyl radical dimer. The singlet-triplet gap of the [-CNSSN*]2 radical pair was -1800+/-100 cm(-1) (-22+/-1 kJ/mol) with the ZFS components |D|=0.0267(6) cm(-1) and |E|=0.0012(1) cm(-1), corresponding to an in situ dimerization energy of ca. -11 kJ/mol. Cyclic voltammetry measurements of 8[AsF6]2 showed two reversible waves associated with a stepwise reduction of the two isomeric rings [E1/2 (+2/+1)=1.03 V; E1/2 (+1/0)=0.47 V, respectively]. 8MF6 (M=As, Sb) was further reduced to afford the mixed main-group diradical 8, containing two isomeric radical rings. In solution, 8 is thermodynamically unstable with respect to *NSSNC-CNSSN*, but is isolable in the solid state because of its low solubility in SO2. Likewise, 8SbF6, 8 is dimeric, with pi*-pi* interactions between different isomeric rings, and consequently diamagnetic; however, a slight increase in paramagnetism was observed upon grinding [from C=6.5(3)x10(-4) emu.K/mol and temperature-independent paramagnetism (TIP)=1.3(1)x10(-4) emu/mol to C=3.2(1)x10(-3) emu.K/mol and TIP=9.0(1)x10(-4) emu/mol], accompanied by an increase in the lattice-defect S=1/2 sites [from 0.087(1) to 0.43(1)%]. Computational analysis using the multiconfigurational approach [CASSCF(6,6)/6-31G*] indicated that the two-electron multicentered pi*-pi* bonds in [8*+]2 and [8]2 have substantial diradical characters, implying that their ground states are diradicaloid in nature. Our results suggest that the electronic structure of organic-radical ion pairs, for example, [TTF*+]2, [TCNE*-]2, [TCNQ*-]2, [DDQ*-]2, and related pi dimers, can be described in a similar way.

Electronic and magnetic interactions in pi-stacked bisthiadiazinyl radicals.

The preparation of two bisthiadiazinyls (7, R1 = Me, Et; R2 = Cl, R3 = Ph), the first examples of a new class of resonance-stabilized heterocyclic thiazyl radical, are reported. Both radicals have been characterized in solution by EPR spectroscopy and cyclic voltammetry, which confirm highly delocalized spin distributions and low electrochemical cell potentials, features which augur well for the use of these materials as building blocks for neutral radical conductors. In the solid state, the radicals are undimerized, crystallizing in slipped pi-stack arrays which ensure the availability of electrons as potential charge carriers. However, despite these favorable electrochemical and structural properties, both materials exhibit low conductivities, with sigma(300K) < 10-7 S cm-1, a result which can be rationalized in terms of their EHT band electronic structures, which indicate that intermolecular interactions lateral to the pi-stacks are limited. The materials are thus very 1-D with low bandwidths, so that a Mott insulating state prevails. When R1 = Me, the intermolecular overlap along the pi-stacks is weak and the material is essentially paramagnetic. When R1 = Et, intermolecular pi-overlap is greater and variable-temperature magnetic susceptibility measurements indicate a strongly antiferromagnetically coupled system, the behavior of which has been modeled in terms of a molecular-field modified 1-D Heisenberg chain of S = 1/2 centers. Broken-symmetry DFT methods have been used to estimate the magnitude of individual exchange interactions within both structures.

An alternating pi-stacked bisdithiazolyl radical conductor.

A general synthetic route to the resonance-stabilized pyrazine-bridged bisdithiazolyl framework, involving the reductive deprotection of 2,6-diaminopyrazine-bisthiocyanate and cyclization with thionyl chloride, has been developed. An N-methyl bisdithiazolyl radical, 4-methyl-4H-bis[1,2,3]dithiazolo[4,5-b:5',4'-e]pyrazin-3-yl, has been prepared and characterized in solution by electron paramagnetic resonance spectroscopy and cyclic voltammetry. Its crystal structure has been determined at several temperatures. At 295 K, the structure belongs to the space group Cmca and consists of evenly spaced radicals pi-stacked in an alternating ABABAB fashion along the x-direction. At 123 K, the space group symmetry is lowered by loss of C-centering to Pccn, so that the radicals are no longer evenly spaced along the pi-stack. At 88 K, a further lowering of space group symmetry to P21/c is observed. Extended Hückel Theory band structure calculations indicate a progressive opening of a band gap at the Fermi level in the low-temperature structures. Magnetic susceptibility measurements over the range 4-300 K reveal essentially diamagnetic behavior below 120 K. Variable-temperature single-crystal conductivity (sigma) measurements indicate that the conductivity is activated, even at room temperature, with a room-temperature value sigma RT=0.001 S cm-1 and a thermal activation energy Eact=0.19 eV. Under an applied pressure of 5 GPa, sigma RT is increased by 3 orders of magnitude, but the conductivity remains activated, with Eact being lowered to 0.11 eV at 5.5 GPa.

Phenalenyl-based neutral radical molecular conductors: substituent effects on solid-state structures and properties.

We report the preparation, crystallization, and solid-state characterization of cycloheptyl and cyclooctyl-substituted spirobiphenalenyl radicals and the corresponding sigma-dimer of the cyclooctyl derivative. The crystal structure shows that the cycloheptyl radical (9) is monomeric in the solid state, with the molecules packed in an unusual one-dimensional (1-D) fashion that we refer to as a pi-chain structure, whereas the cyclooctyl variant exists both as pi-dimer 10 and sigma-dimer 10d. The neutral radical 9 shows the temperature-independent Pauli paramagnetism characteristic of a metal with a magnetic susceptibility, chip approximately 4.5x10(-4) emu/mol and is assigned a resonating valence bond (RVB) ground state. We highlight the relationship between the magnetic properties of the Heisenberg antiferromagnet and the RVB ground state in 1-D and further elucidate the electronic structure of this new class of compounds. Magnetic susceptibility measurements show that 10 is a diamagnetic pi-dimer, whereas 10d is a diamagnetic sigma-dimer. Extended Hückel calculations for 9 indicate that the solid is a one-dimensional organic metal with a bandwidth of about 0.4 eV. Pressed pellet conductivity measurements indicate values of sigmaRT=1.5x10(-3) S/cm for compound 9 and sigmaRT=1.0x10(-6) S/cm for compound 10. The structural results and transport properties are discussed in the light of extended Hückel theory band structure calculations and DFT investigations of the electronic structure of related compounds.

Isostructural bisdithiazolyl and bisthiaselenazolyl radicals: trends in bandwidth and conductivity.

Reaction of N-alkylated pyridine-bridged bisdithiazolylium cations [1]+ (R1 =Me, Et; R2 =Ph) with selenium dioxide in acetic acid provides a one-step high-yield synthetic route to bisthiaselenazolylium cations [2]+ (R1 = Me, Et; R2 = Ph). The corresponding radicals 1 and 2 can be prepared by chemical or electrochemical reduction of the cations. Structural analysis of the radicals has been achieved by a combination of single-crystal and powder X-ray diffraction methods. While the two sulfur radicals 1 adopt different space groups (P3(1)21 for R1 = Me and P(-)1 for R1 = Et), the two selenium radicals 2 (space groups P3(1)21 for R1 = Me and P3(2)21 for R1 =Et) are isostructural with each other and also with 1 (R1 = Me, R2 = Ph). Variable-temperature magnetic measurements on all four compounds confirm that they are undimerized S = 1/2 systems, with varying degrees of weak intermolecular antiferromagnetic coupling. Variable-temperature electrical conductivity measurements on the two selenium radicals provide conductivities sigma(300 K) = 7.4 x 10-6 (R1 = Et) and 3.3 x 10-5 S cm-1 (R1 = Me), with activation energies, E(act), of 0.32 (R1 = Et) and 0.29 eV (R1 = Me). The differences in conductivity within the isostructural series is interpreted in terms of their relative solid-state bandwidths, as estimated from Extended Hückel band-structure calculations.

Resonance stabilized bisdiselenazolyls as neutral radical conductors.

An efficient and versatile synthetic route to resonance stabilized bisselenathiazolyl and bisdiselenazolyl radicals 3 and 4 is described. Structural analysis of 3 and 4 confirm that lattice and pi-delocalization energies are sufficient to offset solid-state dimerization of the radicals and that the two selenium-containing radicals are isostructural with the all-sulfur based system 1. Variable temperature conductivity measurements indicate that sequential replacement of sulfur by selenium leads to a progressive increase in conductivity and reduction in thermal activation energy.