Chemistry/structural biology of psychedelic drugs and their receptor(s).

This brief review highlights some of the structure-activity relationships of classic serotonergic psychedelics. In particular, we discuss structural features of three chemotypes: phenethylamines, ergolines and certain tryptamines, which possess psychedelic activity in humans. Where they are known, we point out the underlying molecular mechanisms utilized by each of the three chemotypes of psychedelic molecules. With a focus on the 5-HT2A receptor subtype, a G-protein coupled receptor known to be the primary target of psychedelics, we refer to several X-ray and cryoEM structures, with a variety of ligands bound, to illustrate the underlying atomistic basis for some of the known pharmacological observations of psychedelic drug actions.

Long Dynamic ß1-ß2 Loops in M. tb MazF Toxins Affect the Interaction Modes and Strengths of the Toxin-Antitoxin Pairs.

Tuberculosis is a worldwide plague caused by the pathogen Mycobacterium tuberculosis (M. tb). Toxin-antitoxin (TA) systems are genetic elements abundantly present in prokaryotic organisms and regulate important cellular processes. MazEF is a TA system implicated in the formation of "persisters cells" of M. tb, which contain more than 10 such members. However, the exact function and inhibition mode of each MazF are not fully understood. Here we report crystal structures of MazF-mt3 in its apo form and in complex with the C-terminal half of MazE-mt3. Structural analysis suggested that two long but disordered ß1-ß2 loops would interfere with the binding of the cognate MazE-mt3 antitoxin. Similar loops are also present in the MazF-mt1 and -mt9 but are sustainably shortened in other M. tb MazF members, and these TA pairs behave distinctly in terms of their binding modes and their RNase activities. Systematic crystallographic and biochemical studies further revealed that the biochemical activities of M. tb toxins were combined results between the interferences from the characteristic loops and the electrostatic interactions between the cognate TA pairs. This study provides structural insight into the binding mode and the inhibition mechanism of the MazE/F TA pairs, which facilitate the structure-based peptide designs.

Structure of MltG from Mycobacterium abscessus reveals structural plasticity between composed domains.

MltG, a membrane-bound lytic transglycosylase, has roles in terminating glycan polymerization in peptidoglycan and incorporating glycan chains into the cell wall, making it significant in bacterial cell-wall biosynthesis and remodeling. This study provides the first reported MltG structure from Mycobacterium abscessus (maMltG), a superbug that has high antibiotic resistance. Our structural and biochemical analyses revealed that MltG has a flexible peptidoglycan-binding domain and exists as a monomer in solution. Further, the putative active site of maMltG was disclosed using structural analysis and sequence comparison. Overall, this study contributes to our understanding of the transglycosylation reaction of the MltG family, aiding the design of next-generation antibiotics targeting M. abscessus.

Difluoroboron complexes as versatile precursors for steroid modification. Lumiestrone-based steroid derivatives: synthesis and structural studies.

A preparation method for steroid-based difluoroboron complexes has been developed using lumiestrone as a steroid example. Previously inaccessible lumiestrone-based difluoroboron complexes annulated at positions 16 and 17 of the D ring have been prepared. Such difluoroboron complexes may have large synthetic potential for heterofunctionalization of steroids at the D ring. An application of a borylation mixture Ac2O-BF3•OEt2 significantly simplify the preparation of steroid "dimers" bearing two estrone moieties connected at positions 2 and 2' via a linker. Crystal structures of key representatives have been determined by X­ray diffraction.

N2H4 derived Sulfonic Acids: Hydrazine Disulfonate, [(SO3)HNNH(SO3)]2-, and Hydrazine Iso-disulfonate, [H2NN(SO3)2]2.

The reaction of hydrazinium sulfate and chlorosulfonic acid in pyridine leads to the pyridinium salt of the hydrazine disulfonate anion, [(SO3)HNNH(SO3)]2-. The salt is the starting material for the preparation of further hydrazine disulfonates, for example of alkaline metals and barium. In all compounds, the [(SO3)HNNH(SO3)]2- anion adopts the gauche conformation. The conformer is chiral but all of the investigated compounds crystallize as racemates. The disulfonate anion can occur in another constitution with the two sulfonate groups attached to only one nitrogen atom. This so-called hydrazine iso-disulfonate, [H2NN(SO3)2]2-, has been prepared through a substitution reaction between potassium imidodisulfonate, K[HN(SO3)2], and hydroxylamine-O-sulfonic acid, H2NOSO3H. The hydrazine iso-disulfonate anion has been crystallized as potassium and barium compound, respectively. The compounds were characterized by XRD, vibrational spectroscopy, DFT calculations and thermal analyses.

Solid State and Solution Structures of Lanthanide Nitrate Complexes of Tris-(1-napthylphosphine oxide).

Coordination complexes of lanthanide metals with tris-1-naphthylphosphine oxide (Nap3PO, L) have not been previously reported in the literature. We describe here the formation of lanthanide(III) nitrate complexes Ln(NO3)3L4 (Ln = Eu to Lu) and the structures of [Ln(NO3)3L2]·2L (Ln = Eu, Dy, Ho, Er) and L. The core structure of the complexes is an eight-coordinate [Ln(NO3)3L2] with the third and fourth ligands H-bonded via their oxygen atoms to one of the naphthyl rings. The structures are compared with those of the analogous complexes of triphenylphosphine oxide and show that the Ln-O(P) bond in the Nap3PO complexes is slightly longer than expected on the basis of differences in coordination numbers. The reaction solutions, investigated by 31P and 13C NMR spectroscopy in CD3CN, show that coordination of L occurs across the lanthanide series, even though complexes can only be isolated from Eu onwards. Analysis of the 31P NMR paramagnetic shifts shows that there is a break in the solution structures with a difference between the lighter lanthanides (La-Eu) and heavier metals (Tb-Lu) which implies a minor difference in structures. The isolated complexes are very poorly soluble, but in CDCl3, NMR measurements show dissociation into [Ln(NO3)3L2] and 2L occurs.

Transforming crystal structures of cobalt molybdate to generate electron-rich sites for electrochemical detection of Pb(II).

BACKGROUND: Most of the investigations on distinct crystal structures of catalysts are individually focused on the difference of surface functional groups or adsorption properties, but rarely explore the changes of active sites to affect the electrocatalytic performance. Catalysts with diverse crystal structures had been applied to modified electrodes in different electrocatalytic reactions. However, there is currently a lack of an essential understanding for the role of real active sites in catalysts with crystalline structures in electroanalysis, which is crucial for designing highly sensitive sensing interfaces. RESULTS: Herein, cobalt molybdate with divergent crystal structures (α-CoMoO4 and ß-CoMoO4) were synthesized by adjusting the calcination temperature, indicating that α-CoMoO4 (800 °C) (60.00 µA µM-1) had the highest catalytic ability than ß-CoMoO4 (700 °C) (38.68 µA µM-1) and α-CoMoO4 (900 °C) (29.55 µA µM-1) for the catalysis of Pb(II). It was proved that the proportion of Co(II) and Mo(IV) as electron-rich sites in α-CoMoO4 (800 °C) were higher than ß-CoMoO4 (700 °C) and α-CoMoO4 (900 °C), possessing more electrons to participate in the valence cycles of Co(II)/Co(III) and Mo(IV)/Mo(VI) to boost the catalytic reduction of Pb(II). Specifically, Co(II) transferred a part of electrons to Mo(VI), promoting the formation of Mo(IV). Co(II) and Mo(IV), as the electron-rich sites, providing electrons to Pb(II), further accelerating the conversion of Pb(II) into Pb(0). SIGNIFICANCE: In the process of detecting Pb(II), the CoMoO4 structures under different temperatures have distinct content of electron-rich sites Co(II) and Mo(IV). α-CoMoO4 (800 °C), with the highest content are benefited to detect Pb(II). This work is conducive to understanding the effect of the changes of active sites resulting from crystal transformation on the electrocatalytic performance, and provides a way to construct sensitive electrochemical interfaces of distinct active sites.

Understanding mechanisms of terpene synthases using substrate analogs.

Terpene synthases (TS) transform achiral prenyl substrates into elaborate hydrocarbon scaffolds with multiple stereocenters through a series of cyclization reactions and carbon skeleton rearrangements. The reactions involve high-energy carbocation intermediates that must be stabilized by the enzyme along the pathway to the desired products. A variety of substrate analogs have been used to investigate TS mechanism. This article will focus on a class of analogs which strategically replace hydrogen atoms with fluorine to inhibit the generation of specific carbocation intermediates. We will explore the synthesis and use of the analogs to study TS mechanism.

Solid-State Reaction of Alkylamines with CO2 in Ambient Air.

This paper explores possible procedures to accelerate CO2 capture from ambient air by a crystalline alkylamine surfactant (octadecylamine), leading to the corresponding crystalline ammonium-carbamate. Conversion of the amine to the carbamate, in different conditions, is studied by four different techniques: WAXD, FTIR, TGA, and DSC. The WAXD study also gives relevant information on the crystal structures of both amine and derived carbamate. Kinetics of reactions of the crystalline amine are mainly studied by DSC scans, by evaluating melting enthalpies of residual amine. The kinetics of conversion of the amine in ambient CO2 is strongly accelerated by ball milling with full conversion achieved after only 4 h, while the reaction kinetics of amine powder simply exposed to ambient CO2 is complete only after nearly 103 h. A substantial increase in kinetics of the solid-state amine reaction with ambient CO2 can be also achieved by increasing the temperature up to 50 °C, i. e. at a temperature slightly lower than amine melting. However, the time for full conversion remains much higher than for room-temperature ball-milled amine (roughly 102 h vs 4 h). Hence, suitable ball-milling procedures can lead to complete and relatively fast conversion of the crystalline amine to the crystalline ammonium-carbamate, even with ambient CO2.

A solid solution to computational challenges presented by crystal structures exhibiting disorder.

Crystal structues exhibiting disorder still present a barrier for many computational methods. Dittrich et al. [(2024). IUCrJ, 11, 347-358] showcase a unified approach, tackling solid solutions, near symmetry and more.

Novel C3-Methylene-Bridged Indole Derivatives with and without Substituents at N1: The Influence of Substituents on Their Hemolytic, Cytoprotective, and Antimicrobial Activity.

Alkaloids are natural compounds useful as scaffolds for discovering new bioactive molecules. This study utilized alkaloid gramine to synthesize two groups of C3-substituted indole derivatives, which were either functionalized at N1 or not. The compounds were characterized by spectroscopic methods. The protective effects of the new compounds against in vitro oxidative hemolysis induced by standard oxidant 2,2'-azobis(2-amidinopropane dihydro chloride (AAPH) on human erythrocytes as a cell model were investigated. Additionally, the compounds were screened for antimicrobial activity. The results indicated that most of the indole derivatives devoid of the N1 substitution exhibited strong cytoprotective properties. The docking studies supported the affinities of selected indole-based ligands as potential antioxidants. Furthermore, the derivatives obtained exhibited potent fungicidal properties. The structures of the eight derivatives possessing indole moiety bridged to the imidazole-, benzimidazole-, thiazole-, benzothiazole-, and 5-methylbenzothiazoline-2-thiones were determined by X-ray diffraction. The C=S bond lengths in the thioamide fragment pointed to the involvement of zwitterionic structures of varying contribution. The predominance of zwitterionic mesomers may explain the lack of cytoprotective properties, while steric effects, which limit multiple the hydrogen-bond acceptor properties of a thione sulfur, seem to be responsible for the high hemolytic activity.

Synthesis, Structural Characterisation, and Electrochemical Properties of Copper(II) Complexes with Functionalized Thiosemicarbazones Derived from 5-Acetylbarbituric Acid.

The reaction between 5-acetylbarbituric acid and 4-dimethylthiosemicarbazide or 4-hexamethyleneiminyl thiosemicarbazide produces 5-acetylbarbituric-4-dimethylthiosemicarbazone (H2AcbDM) and 5-acetylbarbituric-4N-hexamethyleneiminyl thiosemicarbazone (H2Acbhexim). Eight new complexes with different copper(II) salts have been prepared and characterized using elemental analysis, molar conductance, UV-Vis, ESI-HRMS, FT-IR, magnetic moment, EPR, and cyclic voltammetry. In addition, three-dimensional molecular structures of [Cu(HAcbDM)(H2O)2](NO3)·H2O (3a), [Cu(HAcbDM)(H2O)2]ClO4 (4), and [Cu(HAcbHexim)Cl] (6) were determined by single crystal X-ray crystallography, and an analysis of their supramolecular structure was carried out. The H-bonded assemblies were further studied energetically using DFT calculations and MEP surface and QTAIM analyses. In these complexes, the thiosemicarbazone coordinates to the metal ion in an ONS-tridentate manner, in the O-enolate/S-thione form. The electrochemical behavior of the thiosemicarbazones and their copper(II) complexes has been investigated at room temperature using the cyclic voltammetry technique in DMFA. The Cu(II)/Cu(I) redox system was found to be consistent with the quasi-reversible diffusion-controlled process.

Synthesis under high pressure: crystal structure and properties of cubic Dy36O11F50[AsO3]12 ∙ H2O.

The multi-anionic compound with the composition Dy36O11F50[AsO3]12 ∙ H2O, which can be described in the non-centrosymmetric cubic space group F 4¯3 c, already shows an unusually large unit cell with an axis of a = 2587.59(14) pm. Its crystal structure exhibits isolated ψ1-tetrahedral [AsO3]3- anions, but both the coordination numbers and the linking schemes of the Dy3+-centered polyhedra differ significantly from the mostly layered structures described so far in literature. (Dy1)3+ is sevenfold coordinated by oxygen atoms and F- anions, forming a capped trigonal prism [(Dy1)O4.333F2.667]8.333-, and the remaining two cations (Dy2)3+ and (Dy3)3+ both reside in an eightfold coordination of anions. In both cases they form slightly distorted square antiprisms, which have the compositions of [(Dy2)O3.667F4.333]8.667- and [(Dy3)O4.667F3.333]9.667-, respectively. Some of the oxygen atoms are not part of ψ1-[AsO3]3- tetrahedra, but occur as O2- anions and one of these even shares a common crystallographic position with fluoride (F-). It is also worth mentioning that the single crystals were obtained as comparatively large cubes with an edge length of several 100 µm providing very good data with regard to single-crystal X-ray diffraction. To verify the simultaneous presence of oxygen and fluorine, electron-beam microprobe analysis was carried out, and a single-crystal Raman spectrum ruled out the presence of hydroxide anions or protonated [AsO3]3- groups, but proved the interstitial crystal-water molecules, which could not be determined precisely by the crystal-structure refinement.

Linking solid-state phenomena via energy differences in `archetype crystal structures'.

Categorization underlies understanding. Conceptualizing solid-state structures of organic molecules with `archetype crystal structures' bridges established categories of disorder, polymorphism and solid solutions and is herein extended to special position and high-Z' structures. The concept was developed in the context of disorder modelling [Dittrich, B. (2021). IUCrJ, 8, 305-318] and relies on adding quantum chemical energy differences between disorder components to other criteria as an explanation as to why disorder - and disappearing disorder - occurs in an average structure. Part of the concept is that disorder, as probed by diffraction, affects entire molecules, rather than just the parts of a molecule with differing conformations, and the finding that an R·T energy difference between disorder archetypes is usually not exceeded. An illustrative example combining disorder and special positions is the crystal structure of oestradiol hemihydrate analysed here, where its space-group/subgroup relationship is required to explain its disorder of hydrogen-bonded hydrogen atoms. In addition, we show how high-Z' structures can also be analysed energetically and understood via archetypes: high-Z' structures occur when an energy gain from combining different rather than overall alike conformations in a crystal significantly exceeds R·T, and this finding is discussed in the context of earlier explanations in the literature. Twinning is not related to archetype structures since it involves macroscopic domains of the same crystal structure. Archetype crystal structures are distinguished from crystal structure prediction trial structures in that an experimental reference structure is required for them. Categorization into archetype structures also has practical relevance, leading to a new practice of disorder modelling in experimental least-squares refinement alluded to in the above-mentioned publication.

Mirk/Dyrk1B Kinase Inhibitors in Targeted Cancer Therapy.

During the last years, there has been an increased effort in the discovery of selective and potent kinase inhibitors for targeted cancer therapy. Kinase inhibitors exhibit less toxicity compared to conventional chemotherapy, and several have entered the market. Mirk/Dyrk1B kinase is a promising pharmacological target in cancer since it is overexpressed in many tumors, and its overexpression is correlated with patients' poor prognosis. Mirk/Dyrk1B acts as a negative cell cycle regulator, maintaining the survival of quiescent cancer cells and conferring their resistance to chemotherapies. Many studies have demonstrated the valuable therapeutic effect of Mirk/Dyrk1B inhibitors in cancer cell lines, mouse xenografts, and patient-derived 3D-organoids, providing a perspective for entering clinical trials. Since the majority of Mirk/Dyrk1B inhibitors target the highly conserved ATP-binding site, they exhibit off-target effects with other kinases, especially with the highly similar Dyrk1A. In this review, apart from summarizing the data establishing Dyrk1B as a therapeutic target in cancer, we highlight the most potent Mirk/Dyrk1B inhibitors recently reported. We also discuss the limitations and perspectives for the structure-based design of Mirk/Dyrk1B potent and highly selective inhibitors based on the accumulated structural data of Dyrk1A and the recent crystal structure of Dyrk1B with AZ191 inhibitor.

Chiral Heterometallic Cu8Ln4 Complexes with Enantiopure Schiff Base Ligands: Synthesis, Structural, Spectroscopic and Magnetic Studies.

The enantiomerically pure Schiff base ligands H2L-S and H2L-R yield chiral heterometallic dodecanuclear complexes of the form [Cu8Ln4(OH)8(OMe)4(O2CBut)8(L-S or L-R)4(H2O)4] where LnIII=Gd (1S), Tb (2S), Dy (3S, 3R), Ho (4S, 4R), Er (5S) or Y (6S, 6R) and H2L=(S or R)-2-{[(1-hydroxypropan-2-yl)imino]methyl}-6-methoxyphenol. The complexes are isomorphous and crystallize in the non-centrosymmetric polar space group C2 in enantiomeric conformation. The chirality of the Schiff base ligands originates from the respective S- or R- enantiomer of 2-aminopropan-1-ol, is imparted to the complexes and to the crystals that belong to non-centrosymmetric space group. The chirality and enantiomeric conformation of all complexes are retained in dmso solutions as confirmed by Circular Dichroism spectra which consist of mirror images, expected for enantiomeric pairs. All complexes consist of four distorted cubane-like subunits [Cu2Ln2(µ3-OH)2(µ3-OMe)(µ3-OR)], which share the LnIII ions and result in a cyclic distorted tetragonal arrangement; each edge of the {LnIII 4} quadrilateral is occupied by two µ-OH- ions that further bridge to a CuII ion. Magnetic susceptibility measurements revealed ferromagnetic interactions for 3S with LnIII=Dy and antiferromagnetic interactions for all other complexes. AC susceptibility data of 3S under 1 kOe external dc field indicate slow magnetic relaxation phenomena below 2 K.

The Phase Control of Transition Metallic Elements via Facile Chemical and Physical Syntheses.

The crystal phases of metals are important factors to tune the properties of metals, and therefore received extensive attention. Traditionally, phase control is performed within limited numbers of elements by harsh conditions, such as face-centered cubic Fe by high temperature. This review summarizes most reports in metal phase control area, including elements of Fe, Co, Ni, Cu, Ru, Pd, Rh, Os and Au. For every metallic element, the facile phase control methods are systematically introduced, such as epitaxial growth, ball milling, chemical reduction, etc. Their corresponding applications and the mechanisms for phase control are thoroughly discussed.

Insights from structure-activity relationships and the binding mode of peptidic α-ketoamide inhibitors of the malaria drug target subtilisin-like SUB1.

Plasmodium multi-resistance, including against artemisinin, seriously threatens malaria treatment and control. Hence, new drugs are urgently needed, ideally targeting different parasitic stages, which are not yet targeted by current drugs. The SUB1 protease is involved in both hepatic and blood stages due to its essential role in the egress of parasites from host cells, and, as potential new target, it would meet the above criteria. We report here the synthesis as well as the biological and structural evaluation of substrate-based α-ketoamide SUB1 pseudopeptidic inhibitors encompassing positions P4-P2'. By individually substituting each position of the reference compound 1 (MAM-117, Ac-Ile-Thr-Ala-AlaCO-Asp-Glu (Oall)-NH2), we better characterized the structural determinants for SUB1 binding. We first identified compound 8 with IC50 values of 50 and 570 nM against Pv- and PfSUB1, respectively (about 3.5-fold higher potency compared to 1). Compound 8 inhibited P. falciparum merozoite egress in culture by 37% at 100 µM. By increasing the overall hydrophobicity of the compounds, we could improve the PfSUB1 inhibition level and antiparasitic activity, as shown with compound 40 (IC50 values of 12 and 10 nM against Pv- and PfSUB1, respectively, IC50 value of 23 µM on P. falciparum merozoite egress). We also found that 8 was highly selective towards SUB1 over three mammalian serine peptidases, supporting the promising value of this compound. Finally, several crystal 3D-structures of SUB1-inhibitor complexes, including with 8, were solved at high resolution to decipher the binding mode of these compounds.

Homo- and hetero-oligomeric protein-protein associations explain autocrine and heterologous pheromone-cell interactions in Euplotes.

In Euplotes, protein pheromones regulate cell reproduction and mating by binding cells in autocrine or heterologous fashion, respectively. Pheromone binding sites (receptors) are identified with membrane-bound pheromone isoforms determined by the same genes specifying the soluble forms, establishing a structural equivalence in each cell type between the two twin proteins. Based on this equivalence, autocrine and heterologous pheromone/receptor interactions were investigated analyzing how native molecules of pheromones Er-1 and Er-13, distinctive of mating compatible E. raikovi cell types, associate into crystals. Er-1 and Er-13 crystals are equally formed by molecules that associate cooperatively into oligomeric chains rigorously taking a mutually opposite orientation, and each burying two interfaces. A minor interface is pheromone-specific, while a major one is common in Er-1 and Er-13 crystals. A close structural inspection of this interface suggests that it may be used by Er-1 and Er-13 to associate into heterodimers, yet inapt to further associate into higher complexes. Pheromone-molecule homo-oligomerization into chains accounts for clustering and internalization of autocrine pheromone/receptor complexes in growing cells, while the heterodimer unsuitability to oligomerize may explain why heterologous pheromone/receptor complexes fail clustering and internalization. Remaining on the cell surface, they are credited with a key role in cell-cell mating adhesion.

Structures of 3-acetylpyridine adenine dinucleotide and ADP-ribose bound to the electron input module of respiratory complex I.

Energy-converting NADH:ubiquinone oxidoreductase, respiratory complex I, is a major enzyme of energy metabolism that couples NADH oxidation and ubiquinone reduction with proton translocation. The NADH oxidation site features different enzymatic activities with various nucleotides. While the kinetics of these reactions are well described, only binding of NAD+ and NADH have been structurally characterized. Here, we report the structures of the electron input module of Aquifex aeolicus complex I with bound ADP-ribose and 3-acetylpyridine adenine dinucleotides at resolutions better than 2.0 Å. ADP-ribose acts as inhibitor by blocking the "ADP-handle" motif essential for nucleotide binding. The pyridine group of APADH is minimally offset from flavin, which could contribute to its poorer suitability as substrate. A comparison with other nucleotide co-structures surprisingly shows that the adenine ribose and the pyrophosphate moiety contribute most to nucleotide binding, thus all adenine dinucleotides share core binding modes to the unique Rossmann-fold in complex I.