Crystal structure of Bordetella pertussis BugD solute receptor unveils the basis of ligand binding in a new family of periplasmic binding proteins

Periplasmic binding proteins of a new family particularly well represented in Bordetella pertussis have been called Bug receptors. One B.pertussis Bug protein is part of a tripartite tricarboxylate transporter while the functions of the other 77 are unknown. We report the first structure of a Bug receptor, BugD. It adopts the characteristic Venus flytrap motif observed in other periplasmic binding proteins, with two globular domains bisected by a deep cleft. BugD displays a closed conformation resulting from the fortuitous capture of a ligand, identified from the electron density as an aspartate. The structure reveals a distinctive alpha carboxylate-binding motif, involving two water molecules that bridge the carboxylate oxygen atoms to the protein. Both water molecules are hydrogen bonded to a common carbonyl group from Ala14, and each forms a hydrogen bond with one carboxylate oxygen atom of the ligand. Additional hydrogen bonds are found between the ligand alpha carboxylate oxygen atoms and protein backbone amide groups and with a threonine hydroxyl group. This specific ligand-binding motif is highly conserved in Bug proteins, indicating that they may all be receptors of amino acids or other carboxylated solutes, with a similar binding mode. The present structure thus unveils the bases of ligand binding in this large family of periplasmic binding proteins, several hundred members of which have been identified in various bacterial species.     

Synthesis, crystal structures, electrochemical and magnetic properties of polynuclear {Fe4} and {Fe8Na4} carboxylate/picolinate clusters

Reaction of sodium picolinate with Fe^III oxo-centered carboxylate triangles in MeCN in the presence of PPh₄Cl yields (PPh₄)[Fe₄O₂(O₂CR)₇(pic)₂] (R = Ph (1), Bu^t (2)). Omitting the phosphonium cation produces [Fe₈Na₄O₄(O₂CPh)₁₆(pic)₄(H₂O)₄] (3), which contains two Fe₄Na₂ units bridged by two picolinate ligands. X-ray crystal structures of 1 and 3 are reported.Voltammetric profiles in MeCN show four one-electron reduction steps for complexes 1 and 2. Variable-temperature magnetic susceptibility measurements in polycrystalline samples of 1 and 3 reveal strong antiferromagnetic couplings leading to S = 0 ground states.     

Zinc complexes with tricarballylic acid and Lewis bases with zero- and two-dimensional structures

Three ternary zinc complexes of the open chain polycarboxylic acid, tricarballylic (1,2,3-propane-tricarboxylic) acid (PTCH₃) have been isolated and characterized with crystallographic and physicochemical techniques. [Zn(PTCH)(phen)(H₂O)]₂ · 4H₂O (1) (where phen = 1,10-phenanthroline) has a unique dinuclear structure, while [Zn(PTCH)(bpy)]_n · 3nH₂O (2) and [Zn(PTCH)(epy)]_n · 4nH₂O (3) (where bpy = 4,4′-bipyridine and epy = 1,2-bis(4-pyridine)ethane) have 2D polymeric structures. The bis-deprotonated ligand, in all three complexes, uses for coordination only two oxygen atoms, which belong to the same carboxylate in 1, and to two different carboxylates in 2 and 3.     

A triazole‐based fluorescence probe for detecting Hg2+ ions and its biological application

A new compound, ethyl 5‐phenyl‐2‐(p‐tolyl)‐2H‐1,2,3‐triazole‐4‐carboxylate was successfully introduced and synthesized as a novel rhodamine B derivative named REPPC, and characterized by ¹H nuclear magnetic resonance (NMR), ¹³C NMR, and high resolution mass spectrometry (HRMS). It showed an obvious fluorescence and UV–visible light absorption enhancement towards Hg²⁺ ion without interference from common metal ions in N,N‐dimethylformamide–H₂O (pH 7.4). The spirolactam ring moiety of rhodamine in REPPC was converted to the open‐ring form generating a 1:1 complex with the intervention of a mercury ion, verified by electrospray ionization‐mass spectroscopy testing and density functional theory calculation. REPPC was used to visualize the level of mercury ions in living HeLa cells with encouraging results.     

On the appearance of carboxylates in electrostatic potential maps

Electron microscopy can provide accurate, high‐resolution images of the distribution of electrostatic potential (ESP) in biological macromolecules. Careful examination of ESP maps that have been published for peptides and proteins at resolution ranging from 1.0 Å to 2.9 Å reveals that the negative charges of carboxylate groups have a profound effect on their appearance. It is clear that investigators must take the negative features in their experimental ESP maps into account when modeling the conformations of Asp and Glu side chains and those of the residues that surround them.     

Synthesis and pharmacological characterization of novel xanthine carboxylate amides as A2A adenosine receptor ligands exhibiting bronchospasmolytic activity

The carboxylate amides of 8-phenyl-1,3-dimethylxanthine described herein represent a new series of selective ligands of the adenosine A_2A receptors exhibiting bronchospasmolytic activity. The effects of location of 8-phenyl substitutions on the adenosine receptor (AR) binding affinities of the newly synthesized xanthines have also been studied. The compounds displayed moderate to potent binding affinities toward various adenosine receptor subtypes when evaluated through radioligand binding studies. However, most of the compounds showed the maximum affinity for the A_2A subtype, some with high selectivity versus all other subtypes. Xanthine carboxylate amide 13b with a diethylaminoethylamino moiety at the para-position of the 8-phenylxanthine scaffold was identified as the most potent A_2A adenosine receptor ligand with K_i = 0.06 μM. Similarly potent and highly A_2A-selective are the isovanillin derivatives 16a and 16d. In addition, the newly synthesized xanthine derivatives showed good in vivo bronchospasmolytic activity when tested in guinea pigs.     

Synthesis, characterization and in vitro antitumor activity of three organotin(IV) complexes with carbazole ligand

Three novel organotin(IV) complexes with 2-(9H-carbazol-9-yl) acetic acid (HL), of the formulae {[nBu₂SnOL]₂O}₂ (1), [nBuSn(O)OL]₆ (2) and [nBu₃SnOL]₆ (3) were prepared. All compounds were characterized by X-ray crystallography, confirming that complex (1) is tetranuclear one with ladder framework, complex (2) is a hexanuclear organotin(IV) complex with drum structure and complex (3) is a macrocycle with 24-membered stannoxane ring. Furthermore, all complexes were tested in vitro for their cytotoxic activity, using human hepatocellular carcinoma cell line (BEL-7402) and human hepatocellular liver carcinoma cell line (HepG2). Complex (1) displayed the best cytotoxicity and can be pointed out as a promising substrate to be subject of further investigations.     

Ironing out siderophore biosynthesis: a review of non-ribosomal peptide synthetase (NRPS)-independent siderophore synthetases

Iron is required for microbial growth and proliferation. To survive in low-iron environments, some microorganisms secrete ferric iron chelators called siderophores. Siderophore biosynthesis occurs via two pathways: the non-ribosomal peptide synthetase (NRPS) pathway and the NRPS-independent siderophore (NIS) synthetase pathway. NIS enzymes function by adenylating a carboxylic acid substrate, typically citrate, or a derivative, followed by nucleophilic capture of an amine or alcohol and displacement of a citryl intermediate. In this review, we summarize recent advances in NIS biochemistry with a particular focus on structural biology and confirm the classification of NIS enzymes into Types A, A’, B, and C based on substrate specificity. Based on a phylogenetic analysis, we also propose a new subclass of NIS enzymes, Type C’, responsible for dimerization and macrocyclization of complex and substituted amine or amide intermediates. Finally, we describe the role of NIS enzymes in virulence of pathogenic microbes and discuss NIS inhibitors as potential anti-microbial agents.