Two-domain GH30 xylanase from human gut microbiota as a tool for enzymatic production of xylooligosaccharides: Crystallographic structure and a synergy with GH11 xylosidase

Production of value-added compounds and sustainable materials from agro-industrial residues is essential for better waste management and building of circular economy. This includes valorization of hemicellulosic fraction of plant biomass, the second most abundant biopolymer from plant cell walls, aiming to produce prebiotic oligosaccharides, widely explored in food and feed industries. In this work, we conducted biochemical and biophysical characterization of a prokaryotic two-domain R. champanellensis xylanase from glycoside hydrolase (GH) family 30 (RcXyn30A), and evaluated its applicability for XOS production from glucuronoxylan in combination with two endo-xylanases from GH10 and GH11 families and a GH11 xylobiohydrolase. RcXyn30A liberates mainly long monoglucuronylated xylooligosaccharides and is inefficient in cleaving unbranched oligosaccharides. Crystallographic structure of RcXyn30A catalytic domain was solved and refined to 1.37 Å resolution. Structural analysis of the catalytic domain releveled that its high affinity for glucuronic acid substituted xylan is due to the coordination of the substrate decoration by several hydrogen bonds and ionic interactions in the subsite -2. Furthermore, the protein has a larger β5-α5 loop as compared to other GH30 xylanases, which might be crucial for creating an additional aglycone subsite (+3) of the catalytic site. Finally, RcXyn30A activity is synergic to that of GH11 xylobiohydrolase.

An auristatin-based antibody-drug conjugate targeting EphA2 in pancreatic cancer treatment

Pancreatic adenocarcinoma, a highly aggressive form of cancer with a poor prognosis, necessitates the development of innovative treatment strategies. Our prior research showcased the growth-inhibiting effects of the anti-EphA2 antibody drug hSD5 on pancreatic cancer tumors. This antibody targets and induces the degradation of the EphA2 receptor while also prompting the antibody's internalization. A deeper dive into the hSD5 Fab crystallographic structure and docking studies revealed that hSD5's CDRH3 drives the primary interaction between hSD5 and the EphA2 active site. In this study, we developed a novel antibody-drug conjugate (ADC)-the auristatin-based hSD5-vedotin specifically targeting EphA2 in pancreatic cancer cells. This ADC aims at the tumor-specific antigen EphA2, triggering endocytosis and releasing the conjugated payload molecule Monomethyl auristatin E (MMAE), amplifying the tumor-killing effect. Upon cellular entry, hSD5-vedotin demonstrated an impressive tumor-killing response, inhibiting tumor cell growth and promoting apoptosis even at lower antibody concentrations. In a pancreatic cancer xenograft animal model, hSD5-vedotin showcased the potential to suppress tumor growth entirely. Notably, potential immune resistance responses were also observed in recurrent pancreatic cancer tumors. Our empirical results underscore the possibility of developing hSD5-vedotin further, which we anticipate will have a broader and more potent therapeutic impact on pancreatic cancer and other EphA2-related cancers.

Design, synthesis, biological evaluation and structural characterization of novel GEBR library PDE4D inhibitors

Memory and cognitive functions depend on the cerebral levels of cyclic adenosine monophosphate (cAMP), which are regulated by the phosphodiesterase 4 (PDE4) family of enzymes. Selected rolipram-related PDE4 inhibitors, members of the GEBR library, have been shown to increase hippocampal cAMP levels, providing pro-cognitive benefits with a safe pharmacological profile. In a recent SAR investigation involving a subset of GEBR library compounds, we have demonstrated that, depending on length and flexibility, ligands can either adopt a twisted, an extended or a protruding conformation, the latter allowing the ligand to form stabilizing contacts with the regulatory domain of the enzyme. Here, based on those findings, we describe further chemical modifications of the protruding subset of GEBR library inhibitors and their effects on ligand conformation and potency. In particular, we demonstrate that the insertion of a methyl group in the flexible linker region connecting the catechol portion and the basic end of the molecules enhances the ability of the ligand to interact with both the catalytic and the regulatory domains of the enzyme.

Structural and molecular dynamics investigations of ligand stabilization via secondary binding site interactions in Paenibacillus xylanivorans GH11 xylanase

Glycoside hydrolases (GHs) are essential for plant biomass deconstruction. GH11 family consist of endo-β-1,4-xylanases which hydrolyze xylan, the second most abundant cell wall biopolymer after cellulose, into small bioavailable oligomers. Structural requirements for enzymatic mechanism of xylan hydrolysis is well described for GH11 members. However, over the last years, it has been discovered that some enzymes from GH11 family have a secondary binding sites (SBS), which modulate the enzymes activities, but mechanistic details of the molecular communication between the active site and SBS of the enzymes remain a conundrum. In the present work we structurally characterized GH11 xylanase from Paenibacillus xylanivorans A57 (PxXyn11B), a microorganism of agricultural importance, using protein crystallography and molecular dynamics simulations. The PxXyn11B structure was solved to 2.5 Å resolution and different substrates (xylo-oligosaccharides from X3 to X6), were modelled in its active and SBS sites. Molecular Dynamics (MD) simulations revealed an important role of SBS in the activity and conformational mobility of PxXyn11B, demonstrating that binding of the reaction products to the SBS of the enzyme stabilizes the N-terminal region and, consequently, the active site. Furthermore, MD simulations showed that the longer the ligand, the better is the stabilization within active site, and the positive subsites contribute less to the stabilization of the substrates than the negative ones. These findings provide rationale for the observed enzyme kinetics, shedding light on the conformational modulation of the GH11 enzymes via their SBS mediated by the positive molecular feedback loop which involve the products of the enzymatic reaction.

Synthesis and matched molecular pair analysis of covalent reversible inhibitors of the cysteine protease CPB

Cysteine protease B (CPB) can be targeted by reversible covalent inhibitors that could serve as antileishmanial compounds. Here, sixteen dipeptidyl nitrile derivatives were synthesized, tested against CPB, and analyzed using matched molecular pairs to determine the effects of stereochemistry and p-phenyl substitution on enzyme inhibition. The compound (S)-2-(((S)-1-(4-bromophenyl)-2,2,2-trifluoroethyl)amino)-N-(1-cyanocyclopropyl)-3-phenylpropanamide (5) was the most potent CPB inhibitor (pKi = 6.82), which was also selective for human cathepsin B (pKi < 5). The inversion of the stereochemistry from S to R was more detrimental to potency when placed at the P2 position than at P3. The p-Br derivatives were more potent than the p-CH₃ and p-OCH₃ derivatives, probably due to intermolecular interactions with the S3 subsite.

Structural differences in enamel and dentin in human, bovine, porcine, and ovine teeth

BACKGROUND

The aim was to study differences between crystalline nanostructures from the enamel and dentin of human, bovine, porcine, and ovine species.

METHODS

Dentine and enamel fragments extracted from sound human, bovine, porcine and ovine incisors and molars were mechanically ground up to a final particle size of <100μm. Samples were analyzed using X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), and differential scanning calorimetry (DSC).

RESULTS

Human enamel (HE) and dentin (HD) showed a-axis and c-axis lengths of the carbonate apatite (CAP) crystal lattice nearer to synthetic hydroxyapatite (SHA), which had the smallest size. Enamel crystal sizes were always higher than those of dentin for all species. HE and HD had the largest crystal, followed by bovine samples. Hydroxyapatites (HAs) in enamel had a higher crystallinity index (CI), CI_Rietveld and CI_FTIR, than the corresponding dentin of the same species. HE and HD had the highest CIs, followed by ovine enamel (OE). The changes in heat capacity that were nearest to values in human teeth during the glass transition (ΔCp) were in porcine specimens. There was a significant direct correlation between the size of the a-axis and the substitution by both type A and B carbonates. The size of the nanocrystals and the crystallinity (CI_Rietveld y CI_FTIR) were significantly and negatively correlated with the proteic phase of all the substrates. There was a strongly positive correlation between the caloric capacity, the CIs and the crystal size and a strongly negative correlation between carbonates type A and B and proteins.

CONCLUSIONS

There are differences in the organic and inorganic content of human, bovine, porcine and ovine enamels and dentins which should be taken into account when interpreting the results of studies using animal substrates as substitutes for human material.

Diagenesis-inspired reaction of magnesium ions with surface enamel mineral modifies properties of human teeth

Mineralized tissues such as teeth and bones consist primarily of highly organized apatitic calcium-phosphate crystallites within a complex organic matrix. The dimensions and organization of these apatite crystallites at the nanoscale level determine in part the physical properties of mineralized tissues. After death, geological processes such as diagenesis and dolomitization can alter the crystallographic properties of mineralized tissues through cycles of dissolution and re-precipitation occurring in highly saline environments. Inspired by these natural exchange phenomena, we investigated the effect of hypersalinity on tooth enamel. We discovered that magnesium ions reacted with human tooth enamel through a process of dissolution and re-precipitation, reducing enamel crystal size at the surface of the tooth. This change in crystallographic structure made the teeth harder and whiter. Salt-water rinses have been used for centuries to ameliorate oral infections; however, our discovery suggests that this ancient practice could have additional unexpected benefits.

STATEMENT OF SIGNIFICANCE

Here we describe an approach inspired by natural geological processes to modify the properties of a biomineral - human tooth enamel. In this study we showed that treatment of human tooth enamel with solutions saturated with magnesium induced changes in the nanocrystals at the outer surface of the protective enamel layer. As a consequence, the physical properties of the tooth were modified; tooth microhardness increased and the color shade became whiter, thus suggesting that this method could be used as a clinical treatment to improve dental mechanical properties and esthetics. Such an approach is simple and straightforward, and could also be used to develop new strategies to synthesize and modify biominerals for biomedical and industrial applications.

Total structure determination of surface doping [Ag46Au24(SR)32](BPh4)2 nanocluster and its structure-related catalytic property

The structure effect is widely present in the catalysis of alloy systems. However, the surface structure of this system is still ambiguous because of the limitations of the current surface characterization tools. We reported the x-ray crystallographic structure of the first and the largest AgAu alloy nanocluster with a doping shell formulated as [Ag46Au24(SR)32](BPh4)2. This nanocluster consists of an achiral bimetallic Ag2@Au18@Ag20 core protected by a chiral Ag24Au6(SR)32 shell. The catalysis experiments further revealed that the surface structure affects the selectivity of products significantly. This is the first case to find the structure effect in atomically precise alloy nanoclusters. Our work will benefit the basic understanding of bimetal distribution, as well as the structure-related catalytic property of alloy nanoclusters at the atomic level.

Molecular dynamics and density functional studies on the metabolic selectivity of antipsychotic thioridazine by cytochrome P450 2D6: Connection with crystallographic and metabolic results

CYP2D6, a cytochrome P450 isoform, significantly contributes to the metabolism of many clinically important drugs. Thioridazine (THD) is one of the phenothiazine-type antipsychotics, which exhibit dopamine D2 antagonistic activity. THD shows characteristic metabolic profiles compared to other phenothiazine-type antipsychotics such as chlorpromazine. The sulfur atom attached to the phenothiazine ring is preferentially oxidized mainly by CYP2D6, that is, the 2-sulfoxide is a major metabolite, and interestingly this metabolite shows more potent activity against dopamine D2 receptors than THD. On the other hand, the formation of this metabolite causes many serious problems for its clinical use. Wójcikowski et al. (Drug Metab. Dispos. 2006, 34, 471) reported a kinetic study of THD formed by CYP2D6. Recently, Wang et al. (J. Biol. Chem. 2012, 287, 10834 and J. Biol. Chem. 2015, 290, 5092) revealed the crystallographic structure of THD with CYP2D6. In the current study, the binding and reaction mechanisms at the atomic and electronic levels were computationally examined based on the assumption as to whether or not the different crystallographic binding poses correspond to the different metabolites. The binding and oxidative reaction steps in the whole metabolic process were investigated using molecular dynamics and density functional theory calculations, respectively. The current study demonstrated the essential importance of the orientation of the substrate in the reaction center of CYP2D6 for the metabolic reaction.