π-Hole Tetrel Bonds—Lewis Acid Properties of Metallylenes

The MP2/aug-cc-pVTZ calculations were performed on the dihalometallylenes to indicate their Lewis acid and Lewis base sites. The results of the Cambridge Structural Database search show corresponding and related crystal structures where the tetrel center often possesses the configuration of a trigonal bipyramid or octahedron. The calculations were also carried out on dimers of dichlorogermylene and dibromogermylene and on complexes of these germylenes with one and two 1,4-dioxide molecules. The Ge⋯Cl, Ge⋯Br, and Ge⋯O interactions are analyzed. The Ge⋯O interactions in the above mentioned germylene complexes may be classified as the π-hole tetrel bonds. The MP2 calculations are supported by the results of the Quantum Theory of Atoms in Molecules (QTAIM) and the Natural Bond Orbital (NBO) approaches.

Syntheses and crystal structures of 2-(p-tolyl)-1H-perimidine hemihydrate and 1-methyl-2-(p-tolyl)-1H-perimidine

The title compounds, 2-(4-methylphenyl)-1H-perimidine hemihydrate (1, C18H14N2·0.5H2O) and 1-methyl-2-(4-methylphenyl)-1H-perimidine (2, C19H16N2), were prepared and characterized by 1H NMR and single-crystal X-ray diffraction. The organic molecule of the hemihydrate lies on a twofold rotation axis while the water molecule lies on the intersection of three twofold rotation axes (point group symmetry 222). As a consequence, the hydrogen atoms that are part of the N—H group and the water molecule as well as the CH3 group of the p-tolyl ring are disordered over two positions. In compound 1, the perimidine and the 2-aryl rings are slightly twisted while its N-methylated derivative 2 has a more distorted conformation because of the steric repulsion between the N-methyl group and the 2-aryl ring. In the crystal structures, molecules of perimidine 2 are held together only by C—H...π contacts while the parent perimidine 1 does not exhibit this type of interaction. Its crystal packing is established by intermolecular N—H...O hydrogen bonds with the solvent water molecules and additionally stabilized by π–π stacking.

Crystal structures of three N,N,N′-trisubstituted thioureas for reactivity-controlled nanocrystal synthesis

The synthesis and single-crystal X-ray structures of three N,N,N′-trisubstituted thioureas are reported, namely N,N,N′-tribenzylthiourea, C22H22N2S (1), N-methyl-N,N′-diphenylthiourea, C14H14N2S (2), and N,N-di-n-butyl-N′-phenylthiourea, C15H24N2S (3). The influence of the different substituents on the thioureas is clear from the delocalization of the thiourea C—N and C=S bonds, while the crystal structures show infinite chains of N,N,N′-tribenzylthiourea (1), hydrogen-bonded pairs of N-methyl-N,N′-diphenylthiourea (2) and hexamer ring assemblies of N,N-di-n-butyl-N′-phenylthiourea (3) molecules. The above-mentioned compounds were synthesized via a mild, general procedure, readily accessible precursors and with a high yield, providing straightforward access to a whole library of thioureas.

Key interactions in the trimolecular complex consisting of the rheumatoid arthritis-associated DRB1*04:01 molecule, the major glycosylated collagen II peptide and the T-cell receptor

ObjectivesRheumatoid arthritis (RA) is an autoimmune disease strongly associated with the major histocompatibility complex (MHC) class II allele DRB1*04:01, which encodes a protein that binds self-peptides for presentation to T cells. This study characterises the autoantigen-presenting function of DRB1*04:01 (HLA-DRA*01:01/HLA-DRB1*04:01) at a molecular level for prototypic T-cell determinants, focusing on a post-translationally modified collagen type II (Col2)-derived peptide.MethodsThe crystal structures of DRB1*04:01 molecules in complex with the peptides HSP70289-306, citrullinated CILP982-996 and galactosylated Col2259-273 were determined on cocrystallisation. T cells specific for Col2259-273 were investigated in peripheral blood mononuclear cells from patients with DRB1*04:01-positive RA by cytofluorometric detection of the activation marker CD154 on peptide stimulation and binding of fluorescent DRB1*0401/Col2259-273 tetramer complexes. The cDNAs encoding the T-cell receptor (TCR) α-chains and β-chains were cloned from single-cell sorted tetramer-positive T cells and transferred via a lentiviral vector into TCR-deficient Jurkat 76 cells.ResultsThe crystal structures identified peptide binding to DRB1*04:01 and potential side chain exposure to T cells. The main TCR recognition sites in Col2259-273 were lysine residues that can be galactosylated. RA T-cell responses to DRB1*04:01-presented Col2259-273 were dependent on peptide galactosylation at lysine 264. Dynamic molecular modelling of a functionally characterised Col2259-273-specific TCR complexed with DRB1*04:01/Col2259-273 provided evidence for differential allosteric T-cell recognition of glycosylated lysine 264.ConclusionsThe MHC-peptide-TCR interactions elucidated in our study provide new molecular insights into recognition of a post-translationally modified RA T-cell determinant with a known dominant role in arthritogenic and tolerogenic responses in murine Col2-induced arthritis.

Synthesis and Columnar Organization of Partially Fluorinated Dehydrobenz[18]annulenes

Two diamond-shaped and partially fluorinated dehydrobenz[18]annulene macrocycles have been synthesized through a one-pot synthesis relying on fourfold Sonogashira coupling. Single crystal structures of the prepared macrocycles show continuous columnar stacks of these molecules that are mediated by the fluoroarene–alkyne, arene–alkyne, fluoroarene–fluoroarene, and alkyne–alkyne [π···π] interactions instead of the expected fluoroarene–arene [π···π] interaction.

Structural insights into the potency and selectivity of covalent pan-FGFR inhibitors

FIIN-2, TAS-120 (Futibatinib) and PRN1371 are highly potent pan-FGFR covalent inhibitors targeting the p-loop cysteine of FGFR proteins, of which TAS-120 and PRN1371 are currently in clinical trials. It is critical to analyze their target selectivity and their abilities to overcome gatekeeper mutations. In this study, we demonstrate that FIIN-2 and TAS-120 form covalent adducts with SRC, while PRN1371 does not. FIIN-2 and TAS-120 inhibit SRC and YES activities, while PRN1371 does not. Moreover, FIIN-2, TAS-120 and PRN1371 exhibit different potencies against different FGFR gatekeeper mutants. In addition, the co-crystal structures of SRC/FIIN-2, SRC/TAS-120 and FGFR4/PRN1371 complexes reveal structural basis for kinase targeting and gatekeeper mutations. Taken together, our study not only provides insight into the potency and selectivity of covalent pan-FGFR inhibitors, but also sheds light on the development of next-generation FGFR covalent inhibitors with high potency, high selectivity, and stronger ability to overcome gatekeeper mutations.