NMR and X-ray crystallography, complementary tools in structural proteomics of small proteins

NMR spectroscopy and X-ray crystallography, the two primary experimental methods for protein structure determination at high resolution, have different advantages and disadvantages in terms of sample preparation and data collection and analysis. It is therefore of interest to assess their complementarity when applied to small proteins. Structural genomics/proteomics projects provide an ideal opportunity to make such comparisons as they generate data in a systematic manner for large enough numbers of proteins to allow firm conclusions to be drawn. Here we report a comparison for 263 unique proteins screened by both NMR spectroscopy and X-ray crystallography in our structural proteomics pipeline. Only 21 targets (8%) were deemed amenable to both methods based on an initial 2D 15N-HSQC NMR spectrum and optimized crystallization trials. However, the use of both methods in the pipeline increased the total number of targets amenable to structure determination to 107, with 43 amenable to NMR only and 43 amenable to X-ray crystallographic methods only. We did not observe a correlation between 15N-HSQC spectral quality and the success of the same protein in crystallization screens. Similar results were found for an independent set of 159 proteins as reported in the accompanying paper by Snyder et al. Thus, we conclude that both methods are highly complementary, and in order to increase the number of proteins suited for structure determination, we suggest that both methods be used in parallel in screening of all small proteins for structure determination.     

Binding Modes of Thioflavin T on the Surface of Amyloid Fibrils Studied by NMR

The mechanism for the interaction of thioflavin T (ThT) with amyloid fibrils at the molecular level is not known. Here, we used ¹H NMR spectroscopy to determine the binding mode of ThT on the surface of fibrils from lysozyme and insulin. Relayed rotating‐frame Overhauser enhancements in ThT were observed, indicating that the orientation of ThT is orthogonal to the fibril surface. Importantly, the assembly state of ThT on both surfaces is different. On the surface of insulin fibrils, ThT is oligomeric, as indicated by rapid ¹H spin‐lattice relaxation rate in the rotating frame (R_1ρ), presumably due to intermolecular dipole–dipole interactions between ThT molecules. In contrast, ThT on the surface of lysozyme fibrils is a monomer, as indicated by slower ¹H R_1ρ. These results shed new light into the mechanism for the enhancement of ThT fluorescence and may lead to more efficient detectors of amyloid assemblies, which have escaped detection by ThT in monomer form.     

Synthesis of [Ni(η-CH2C6H4R-4){PPh(CH2CH2PPh2)2}] (R = H, Me or MeO) and protonation reactions with HCl

The complexes [Ni(η²-CH₂C₆H₄R-4)(triphos)]BPh₄ {R = H, Me or MeO; triphos = PhP(CH₂CH₂PPh₂)₂} have been prepared and characterised by spectroscopy and X-ray crystallography. In all cases the coordination geometry of the nickel is best described as square-planar with an η²-benzyl ligand occupying one of the positions. The orientation of the η²-benzyl ligand is dictated by the steric restrictions imposed by the phenyl groups on the triphos ligand, so that the phenyl group on the unique secondary phosphorus and the aromatic group of the benzyl ligand (which are trans to one another) are oriented in the same direction. [Ni(η²-CH₂C₆H₄R-4)(triphos)]⁺ react with an excess of anhydrous HCl in MeCN to form [NiCl(triphos)]⁺ (characterised as the [BPh₄]⁻ salt by X-ray crystallography) and the corresponding substituted toluene. The kinetics of the reaction of all [Ni(η²-CH₂C₆H₄R-4)(triphos)]⁺ and HCl in the presence of Cl⁻ have been determined using stopped-flow spectrophotometry. All reactions exhibit a first-order dependence on the concentration of complex and a first-order dependence on the ratio [HCl]/[Cl⁻]. Varying the 4-R-substituent on the benzyl ligand shows that electron-withdrawing substituents facilitate the rate of the reaction. It is proposed that the mechanism involves initial rapid protonation at the nickel to form [NiH(η²-CH₂C₆H₄R-4)(triphos)]²⁺, followed by intramolecular proton migration from nickel to carbon to yield the products.     

Anti-Inflammatory Dysidazirine Carboxylic Acid from the Marine Cyanobacterium Caldora sp. Collected from the Reefs of Fort Lauderdale,Florida

Dysidazirine carboxylic acid (1) was isolated from the lipophilic extract of a collection of the benthic marine cyanobacterium Caldora sp. from reefs near Fort Lauderdale, Florida. The planar structure of this new compound was determined by spectroscopic methods and comparisons between HRMS and NMR data with its reported methyl ester. The absolute configuration of the single chiral center was determined by the conversion of 1 to the methyl ester and the comparison of its specific rotation data with the two known methyl ester isomers, 2 and 3. Molecular sequencing with 16S rDNA indicated that this cyanobacterium differs from Caldora penicillata (Oscillatoriales) and represents a previously undocumented and novel Caldora species. Dysidazirine (2) showed weak cytotoxicity against HCT116 colorectal cancer cells (IC₅₀ 9.1 µM), while dysidazirine carboxylic acid (1) was non-cytotoxic. Similar cell viability patterns were observed in RAW264.7 cells with dysidazirine only (2), displaying cytotoxicity at the highest concentration tested (50 µM). The non-cytotoxic dysidazirine carboxylic acid (1) demonstrated anti-inflammatory activity in RAW264.7 cells stimulated with LPS. After 24 h, 1 inhibited the production of NO by almost 50% at 50 µM, without inducing cytotoxicity. Compound 1 rapidly decreased gene expression of the pro-inflammatory gene iNOS after 3 h post-LPS treatment and in a dose-dependent manner (IC₅₀ ~1 µM); the downregulation of iNOS persisted at least until 12 h.     

Structure determination and infrared spectroscopy of K(UO2)(SO4)(OH)(H2O) and K(UO2)(SO4)(OH)

Two potassium uranyl sulfate compounds were synthesized, and their crystal structures were determined by single-crystal X-ray diffraction. K(UO2)(SO4)(OH)(H2O) (KUS1) crystallizes in space group P21/c, a = 8.0521(4) A, b = 7.9354(4) A, c = 11.3177(6) A, beta = 107.6780(10) degrees , V = 689.01(6) A3, and Z = 4. K(UO2)(SO4)(OH) (KUS2) is orthorhombic Pbca, a = 8.4451(2) A, b = 10.8058(4) A, c = 13.5406(5)A, V = 1235.66(7)A3, and Z = 8. Both structures were refined on the basis of F2 for all unique data collected with Mo Kalpha radiation and a CCD-based detector to agreement indices R1 = 0.0251 and 0.0206 calculated for 2856 and 2616 reflections for KUS1 and KUS2, respectively. The structures contain vertex-sharing uranyl pentagonal bipyramids and sulfate tetrahedra linked into new chains and sheet topologies. Infrared spectroscopy provides additional information about the linkages between the sulfate and uranyl polyhedra, as well as the hydrogen bonding present in the structures. The U-O-S connectivity is examined in detail, and the local bond angle is impacted by the steric constraints of the crystal structure.     

2-Mercaptomethyl-thiazolidines use conserved aromatic–S interactions to achieve broad-range inhibition of metallo-β-lactamases

Infections caused by multidrug resistant (MDR) bacteria are a major public health threat. Carbapenems are among the most potent antimicrobial agents that are commercially available to treat MDR bacteria. Bacterial production of carbapenem-hydrolysing metallo-β-lactamases (MBLs) challenges their safety and efficacy, with subclass B1 MBLs hydrolysing almost all β-lactam antibiotics. MBL inhibitors would fulfil an urgent clinical need by prolonging the lifetime of these life-saving drugs. Here we report the synthesis and activity of a series of 2-mercaptomethyl-thiazolidines (MMTZs), designed to replicate MBL interactions with reaction intermediates or hydrolysis products. MMTZs are potent competitive inhibitors of B1 MBLs in vitro (e.g., K_i = 0.44 μM vs. NDM-1). Crystal structures of MMTZ complexes reveal similar binding patterns to the most clinically important B1 MBLs (NDM-1, VIM-2 and IMP-1), contrasting with previously studied thiol-based MBL inhibitors, such as bisthiazolidines (BTZs) or captopril stereoisomers, which exhibit lower, more variable potencies and multiple binding modes. MMTZ binding involves thiol coordination to the Zn(ii) site and extensive hydrophobic interactions, burying the inhibitor more deeply within the active site than d/l-captopril. Unexpectedly, MMTZ binding features a thioether–π interaction with a conserved active-site aromatic residue, consistent with their equipotent inhibition and similar binding to multiple MBLs. MMTZs penetrate multiple Enterobacterales, inhibit NDM-1 in situ, and restore carbapenem potency against clinical isolates expressing B1 MBLs. Based on their inhibitory profile and lack of eukaryotic cell toxicity, MMTZs represent a promising scaffold for MBL inhibitor development. These results also suggest sulphur–π interactions can be exploited for general ligand design in medicinal chemistry.

Metallo-β-lactamases (MBLs) are major culprits of resistance to carbapenems in bacteria. A series of thiazolidines are potent MBL inhibitors, restoring the activity of carbapenems. Metal binding and sulphur–π interactions are key to inhibition.     

Competing Effects of Chlorination on the Strength of Te⋅⋅⋅O Chalcogen Bonds Select the Structure of Mixed Supramolecular Macrocyclic Aggregates of Iso-Tellurazole N-Oxides

Chlorination of 3-methyl-5-phenyl-1,2-tellurazole-2-oxide yielded the λ⁴Te dichloro derivative. Its crystal structure demonstrates that the heterocycle retains its ability to autoassociate by chalcogen bonding (ChB) forming macrocyclic tetramers. The corresponding Te⋅⋅⋅O ChB distances are 2.062 Å, the shortest observed to date in aggregates of this type. DFT−D3 calculations indicate that while the halogenated molecule is stronger as a ChB donor it also is a weaker ChB acceptor; the overall effect is that the ChBs in the chlorinated homotetramer are not significantly stronger. However, partial halogenation or scrambling selectively yield the 2 : 2 heterotetramer with alternating λ⁴Te and λ²Te centers, which calculations identified as the thermodynamically preferred arrangement.     

The isolation of new norcycloartene triterpenoids from the tropical marine alga Tydemaniaexpeditionitis (chlorophyta)

Three new Δ³-norcycloartene triterpenoids, with differing side chain functionalities, have been isolated from the tropical green alga $\text{Tydemania}$$\text{expeditionitis}$ collected in Guam. The structures of these new compounds were secured by x-ray crystallography and by chemical interconversion.     

Chemical Validation of Mycobacterium tuberculosis Phosphopantetheine Adenylyltransferase Using Fragment Linking and CRISPR Interference**

The coenzyme A (CoA) biosynthesis pathway has attracted attention as a potential target for much-needed novel antimicrobial drugs, including for the treatment of tuberculosis (TB), the lethal disease caused by Mycobacterium tuberculosis (Mtb). Seeking to identify inhibitors of Mtb phosphopantetheine adenylyltransferase (MtbPPAT), the enzyme that catalyses the penultimate step in CoA biosynthesis, we performed a fragment screen. In doing so, we discovered three series of fragments that occupy distinct regions of the MtbPPAT active site, presenting a unique opportunity for fragment linking. Here we show how, guided by X-ray crystal structures, we could link weakly-binding fragments to produce an active site binder with a K_D <20 μM and on-target anti-Mtb activity, as demonstrated using CRISPR interference. This study represents a big step toward validating MtbPPAT as a potential drug target and designing a MtbPPAT-targeting anti-TB drug.     

Ionization of carbonic acid in sodium chloride solutions at 25°C

The stoichiometric pK ₁ ^* and pK ₂ ^* for the ionization of carbonic acid has been determined from emf measurements in NaCl soluions to 6.0m at 25°C. Our results at low concentrations are in good agreement with the results of Harned and Bonner, of Dyrssen and Hansson and of Roy et al. The calculated values of pK ₁ ^* using Pitzer's equations agree with the measured values to ±0.01 pK units provided higher order terms are used. It was necessary to use a triplet interaction parameter () and higher order electrostatic terms (^E) to calculate reliable values of pK ₂ ^* (±0.03 pK units) over the entire concentration range. These results demonstrate the reliability of the Pitzer equations to estimate activity coefficients in concentrated salt solutions.