X-ray Crystallography Research Articles

Tuning Excited State Character in Iridium(III) Photosensitizers and Its Influence on TTA-UC.

A series of mixed ligand, photoluminescent organometallic Ir(III) complexes have been synthesized to incorporate substituted 2-phenyl-1H-naphtho[2,3-d]imidazole cyclometalating ligands. The structures of three example complexes were categorically confirmed using X-ray crystallography each sharing very similar structural traits including evidence of interligand hydrogen bond contacts that account for the shielding effects observed in the 1H NMR spectra. The structural iterations of the cyclometalated ligand provide tuning of the principal electronic transitions that determine the visible absorption and emission properties of the complexes: emission can be tuned in the visible region between 550 and 610 nm and with triplet lifetimes up to 10 μs. The nature of the emitting state varies across the series of complexes, with different admixtures of ligand-centered and metal-to-ligand charge transfer triplet levels evident. Finally, the use of the complexes as photosensitizers in triplet-triplet annihilation energy upconversion (TTA-UC) was investigated in the solution state. The study showed that the complexes possessing the longest triplet lifetimes showed good viability as photosensitizers in TTA-UC. Therefore, the use of an electron-withdrawing group on the 2-phenyl-1H-naphtho[2,3-d]imidazole ligand framework can be used to rationally promote TTA-UC using this class of complex.

Coinage Metal Complexes of a Sterically Encumbered Anionic Pyridylborate.

Sterically loaded, anionic pyridine has been synthesized and utilized successfully in the stabilization of a homoleptic series of coinage metal complexes. The treatment of [4-(Ph3B)-2,6-Trip2Py]K (Trip =2,4,6-iPr3C6H2) with CuBr(PPh3), AgCl(PPh3) or AuCl(PPh3) (Py = pyridine) afforded the corresponding [4-(Ph3B)-2,6-Trip2Py]M(PPh3) (M = Au, Ag, Cu) complexes, via salt metathesis, as isolable, crystalline solids. Notably, these reactions avoid the facile single electron transfer chemistry reported with the less bulky ligand systems. The X-ray structures revealed that they are two-coordinate metal adducts. The M-N and M-P bond distances are longest in the silver and shortest in the copper adduct among the three group 11 family members. Computational analysis revealed an interesting stability dependence on steric bulk of the anionic pyridine (i.e., pyridyl borate) ligand. A comparison of structures and bonding of [4-(Ph3B)-2,6-Trip2Py]Au(PPh3) to pyridine and m-terphenyl complexes, {[2,6-Trip2Py]Au(PPh3)}[SbF6] and [2,6-Trip2Ph]Au(PPh3) are also provided. The Au(I) isocyanide complex, [4-(Ph3B)-2,6-Trip2Py]Au(CNBut) has been stabilized using the same anionic pyridylborate illustrating that it can support other gold-ligand moieties as well.

Direct Interaction of Minocycline to p47phox Contributes to its Attenuation of TNF-α-Mediated Neuronal PC12 Cell Death: Experimental and Simulation Validation.

Kaempferol illustrates an example of attempting to discover new treatments for neurodegeneration by investigating the potential efficacy of natural products. Despite the identification of several molecular targets for this bio-active compound, the precise underlying pathways are not well elucidated yet. Recently, it has been shown through pulldown assay that kaemferol directly interacts with p47phox, the organizer subunit of NADPH oxidase-2 (NOX2) complex. Hence, in this study, we used homology modelling, computational docking, mutation analysis, molecular dynamics simulations and free energy calculations to determine how kaempferol interacts with p47phox. Firstly, 3D structure of p47phox was generated using x-ray structures of its domains. Then, it was docked with kaempferol, and finally 100-ns molecular dynamics (MD) simulations were performed and the global properties like root-mean square deviation (RMSD) and root-mean square fluctuations (RMSF) were calculated. Literature survey and computational analysis of key interacting amino acid residues of p47phox provided insights into a possible binding site for kaempferol, approximately around Trp193 and Cys196 located within the N-terminal SH3 domain of p47phox. Moreover, free energy calculations indicated that in silico substitution of Trp193 and Cys196 with arginine and alanine, respectively, results in less favorable interaction corroborating their importance in binding with kaempferol. Taken together, these findings suggest that kaempferol directly attaches to N-SH3 domain p47 phox, with a subsequent diminution of p47phox protein-protein interaction and possibly attenuation of NOX2 complex assembly, which reduces reactive oxygen species (ROS) generation. These observations will be beneficial for researchers exploring neuroprotection and for the development of p47phox inhibitors.

Coordination Compounds of Nickel(II) with 3,5–Dibromo–Salicylaldehyde: Structure and Interaction with Biomolecules

Three neutral nickel(II) complexes of 3,5–dibromo–salicylaldehyde (3,5–diBr–saloH) were synthesized in the presence or absence of 1,10–phenanthroline (phen) or its derivative 2,9–dimethyl–1,10–phenanthroline (neoc) as co–ligands, namely [Ni(3,5–diBr–salo)2(neoc)] (complex 1), [Ni(3,5–diBr–salo)2(phen)] (complex 2) and [Ni(3,5–diBr–salo)2(H2O)2] (complex 3), and were characterized by various techniques. The crystal structure of [Ni(3,5–diBr–salo)2(neoc)] was determined by single-crystal X-ray crystallography. According to employed studying techniques, the complexes interact tightly with calf-thymus DNA by an intercalative fashion. Furthermore, compounds 1–3 bind tightly and reversibly to human and bovine serum albumin.

Structural and Computational Insights into Dynamics and Intermediate States of Orexin 2 Receptor Signaling.

Orexin 2 receptor (OX2R) is a G protein-coupled receptor (GPCR) whose activation is crucial to regulation of the sleep-wake cycle. Recently, inactive and active state structures were determined from X-ray crystallography and cryo-electron microscopy single particle analysis, and the activation mechanisms have been discussed based on these static data. GPCRs have multiscale intermediate states during activation, and insights into these dynamics and intermediate states may aid the precise control of intracellular signaling by ligands in drug discovery. Molecular dynamics (MD) simulations are used to investigate dynamics induced in response to thermal perturbations, such as structural fluctuations of main and side chains. In this study, we proposed collective motions of the TM domain during activation by performing 30 independent microsecond-scale MD simulations for various OX2R systems and applying relaxation mode analysis. The analysis results suggested that TM3 had a vertical structural movement relative to the membrane surface during activation. In addition, we extracted three characteristic amino acid residues on TM3, i.e., Q1343.32, V1423.40, and R1523.50, which exhibited large conformational fluctuations. We quantitatively evaluated the changes in their equilibrium during activation in relation to the movement of TM3. We also discuss the regulation of ligand binding recognition and intracellular signal selectivity by changes in the equilibrium of Q1343.32 and R1523.50, respectively, according to MD simulations and GPCR database. Additionally, the OX2R-Gi signaling complex is stabilized in the conformation resembling a non-canonical (NC) state, which was previously proposed as an intermediate state during activation of neurotensin 1 receptor. Insights into the dynamics and intermediate states during activation gained from this study may be useful for developing biased agonists for OX2R.

Impact of protein conformations on binding free energy calculations in the beta-secretase 1 system.

In binding free energy calculations, simulations must sample all relevant conformations of the system in order to obtain unbiased results. For instance, different ligands can bind to different metastable states of a protein, and if these protein conformational changes are not sampled in relative binding free energy calculations, the contribution of these states to binding is not accounted for and thus calculated binding free energies are inaccurate. In this work, we investigate the impact of different beta-sectretase 1 (BACE1) protein conformations obtained from x-ray crystallography on the binding of BACE1 inhibitors. We highlight how these conformational changes are not adequately sampled in typical molecular dynamics simulations. Furthermore, we show that insufficient sampling of relevant conformations induces substantial error in relative binding free energy calculations, as judged by a variation in calculated relative binding free energies up to 2kcal/mol depending on the starting protein conformation. These results emphasize the importance of protein conformational sampling and pose this BACE1 system as a challenge case for further method development in the area of enhanced protein conformational sampling, either in combination with binding calculations or as an endpoint correction.

ARIP: A Tool for Precise Interatomic Contact Area and Volume Calculation in Proteins

The interplay patterns of amino acid residues are pivotal in determining the tertiary structure and flexibility of proteins, which in turn are intricately linked to their functionality and interactions with other molecules. Here, we introduce ARIP, a novel tool designed to identify contact residues within proteins. ARIP employs a modified version of the dr_sasa algorithm and an atomic overlap weighted algorithm to directly calculate the contact area and volume between atoms based on their van der Waals radius. It also allows for the selection of solvent radii, recognizing that not every atom in proteins can interact with water molecules. The solvent parameters were derived from the analysis of approximately 5000 protein and nucleic acid structures with water molecules determined using X-ray crystallography. One advantage of the modified algorithm is its capability to analyze multiple models within a single PDB file, making it suitable for molecular dynamic capture. The contact volume is symmetrically distributed between the interacting atoms, providing more informative results than contact area for the analysis of intra- and intermolecular interactions and the development of scoring functions. Furthermore, ARIP has been applied to four distinct cases: capturing key residue–residue contacts in NMR structures of P4HB, protein–drug binding of CYP17A1, protein–DNA binding of SPI1, and molecular dynamic simulations of BRD4.

Synthesis, characterization and stability of phosphonium phenolate zwitterions derived from a (diphenylphosphino)phenol derivative and oxiranes

AbstractPhosphonium phenolate zwitterions have been synthesized from 2,4-di-tert-butyl-6-(diphenylphosphino)phenol and five different oxirane derivatives. The reaction does not proceed at a detectable rate when the two reactants are combined in dichloromethane at room temperature. Despite the substantial ring strain, the reaction proceeds only with the addition of methanol, which acts as a hydrogen transfer shuttle, allowing a slow conversion to the desired zwitterions. The compounds have been fully characterized and single crystal X-ray crystallography has been performed on the methyloxirane and the phenyl glycidyl ether-derived zwitterion. The phosphonium phenolate units exhibit an ylidic bonding situation as evidenced by spectroscopic and crystallographic analysis. Glycidyl ethers were found to react faster than alkyl and aryloxiranes. Decomposition studies of the zwitterions showed high thermal stability in solution under ambient conditions. Under forced conditions (150 °C, 6 h), decomposition to the corresponding phosphine oxide and secondary aliphatic alcohols, the formally hydrogenated oxirane derivative, was observed. Graphical abstract

Structural basis and synergism of ATP and Na+ activation in bacterial K+ uptake system KtrAB

The K+ uptake system KtrAB is essential for bacterial survival in low K+ environments. The activity of KtrAB is regulated by nucleotides and Na+. Previous studies proposed a putative gating mechanism of KtrB regulated by KtrA upon binding to ATP or ADP. However, how Na+ activates KtrAB and the Na+ binding site remain unknown. Here we present the cryo-EM structures of ATP- and ADP-bound KtrAB from Bacillus subtilis (BsKtrAB) both solved at 2.8 Å. A cryo-EM density at the intra-dimer interface of ATP-KtrA was identified as Na+, as supported by X-ray crystallography and ICP-MS. Thermostability assays and functional studies demonstrated that Na+ binding stabilizes the ATP-bound BsKtrAB complex and enhances its K+ flux activity. Comparing ATP- and ADP-BsKtrAB structures suggests that BsKtrB Arg417 and Phe91 serve as a channel gate. The synergism of ATP and Na+ in activating BsKtrAB is likely applicable to Na+-activated K+ channels in central nervous system.

Boron catalysis in a designer enzyme.

Enzymes play an increasingly important role in improving the benignity and efficiency of chemical production, yet the diversity of their applications lags heavily behind chemical catalysts as a result of the relatively narrow range of reaction mechanisms of enzymes. The creation of enzymes containing non-biological functionalities facilitates reaction mechanisms outside nature's canon and paves the way towards fully programmable biocatalysis1-3. Here we present a completely genetically encoded boronic-acid-containing designer enzyme with organocatalytic reactivity not achievable with natural or engineered biocatalysts4,5. This boron enzyme catalyses the kinetic resolution of hydroxyketones by oxime formation, in which crucial interactions with the protein scaffold assist in the catalysis. A directed evolution campaign led to a variant with natural-enzyme-like enantioselectivities for several different substrates. The unique activation mode of the boron enzyme was confirmed using X-ray crystallography, high-resolution mass spectrometry (HRMS) and 11B NMR spectroscopy. Our study demonstrates that genetic-code expansion can be used to create evolvable enantioselective enzymes that rely on xenobiotic catalytic moieties such as boronic acids and access reaction mechanisms not reachable through catalytic promiscuity of natural or engineered enzymes.

Biomimetic Hydrogen-Bonded G ⋅ C ⋅ G ⋅ C Quadruplex within a Tetraphenylethene-Based Octacationic Spirobicycle in Water.

In biological systems, nucleotide quadruplexes (such as G-quadruplexes) in DNA and RNA that are held together by multiple hydrogen bonds play a crucial functional role. The biomimetic formation of these hydrogen-bonded quadruplexes captured by artificial systems in water poses a significant challenge but can offer valuable insights into these complex functional structures. Herein, we report the formation of biomimetic hydrogen-bonded G ⋅ C ⋅ G ⋅ C quadruplex captured by a tetraphenylethene (TPE) based octacationic spirobicycle (1). The spirobicyclic compound possesses a three-dimensional (3D) crossing dual-cavity structure, which enables the encapsulation of four d(GpC) dinucleotide molecules, thereby realizing 1 : 4 host-guest complexation in water. The X-ray structure reveals that four d(GpC) molecules further form a two-layer G ⋅ C ⋅ G ⋅ C quadruplex with Watson-Crick hydrogen bonds, which are stabilized within the dual hydrophobic cavities of 1 through the cooperative non-covalent interactions of hydrogen bonds, CH⋅⋅⋅π interactions, and hydrophobic effect. Due to the dynamically-rotational propeller chirality of TPE units, 1 with adaptive chirality can further serve as a chiroptical sensor to exhibit opposite Cotton effects with mirror-image CD spectra for the pH-dependent hydrogen-bonded assemblies of d(GpC) including the Watson-Crick G ⋅ C ⋅ G ⋅ C (pH 9.22) and Hoogsteen G ⋅ C+ ⋅ G ⋅ C+ (pH 5.74) quartets through the host-guest chirality transfer in water.

Convenient Preparation, Thermal Properties and X-ray Structure Determination of 2,3-Dihydro-5,6,7,8-tetranitro-1,4-benzodioxine (TNBD): A Promising High-Energy-Density Material

2,3-dihydro-5,6,7,8-tetranitro-1,4-benzodioxine (TNBD), molecular formula = C8H4N4O10, is a completely nitrated aromatic ring 1,4-benzodioxane derivative. The convenient method of TNBD synthesis was developed (yield = 81%). The detailed structure of this compound was investigated by X-ray crystallography. The results of the thermal analysis (TG) obtained with twice re-crystallized material revealed the onset at 240 °C (partial sublimation started) and melting at 286 °C. The investigated material degraded completely at 290–329 °C. The experimental density of 1.85 g/cm3 of TNBD was determined by X-ray crystallography. The spectral properties of TNBD (NMR, FT-IR and Raman) were explored. The detonation properties of TNBD calculated by the EXPLO 5 code were slightly superior in comparison to standard high-energy material—tetryl (detonation velocity of TNBD—7727 m/s; detonation pressure—278 kbar; and tetryl—7570 m/s and 226.4 kbar at 1.614 g/cm3, or 260 kbar at higher density at 1.71 g/cm3. The obtained preliminary results might suggest TNBD can be a potential thermostable high-energy and -density material (HEDM).

Magnetic Anisotropy and Relaxation in Four-Coordinate Cobalt(II) Single-Ion Magnets with a [CoIIO4] Core.

A mononuclear four-coordinate Co(II) complex with a [CoIIO4] core, namely, PPN[Li(MeOH)4][Co(L)2] (1) (PPN = bis(phosphoranediyl)iminium; H2L = perfluoropinacol), has been studied by X-ray crystallography, magnetic characterization, and theoretical calculations. This complex presents a severely distorted coordination geometry. The O-Co-O bite angle is 83.42°/83.65°, and the dihedral twist angle between the O-Co-O chelate planes is 55.6°. The structural distortion results in a large easy-axis magnetic anisotropy with D = -104(1) cm-1 and a transverse component with |E| = +4(2) cm-1. Alternating current (ac) susceptibility measurements demonstrate that 1 exhibits slow relaxation of magnetization at zero static field. However, the frequency-dependent out-of-phase (χ"M) susceptibilities of 1 at 0 Oe do not show a characteristic maximum. Upon the application of a dc field or the dilution with a diamagnetic Zn matrix, the quantum tunneling of magnetization (QTM) process can be successfully suppressed. Notably, after dilution with the Zn matrix, the obtained sample exhibits a structure different from that of the pristine complex. In this altered sample, the asymmetric unit does not contain the Li(MeOH)4+ cation, resulting in an O-Co-O bite angle of 86.05° and a dihedral twist angle of 75.84°, thereby leading to an approximate D2d symmetry. Although such differences are not desirable for magnetic studies, this study still gives some insights. Theoretical calculations reveal that the D parameter is governed by the O-Co-O bite angle, in line with our previous report for other tetrahedral Co(II) complex with a [CoIIN4] core. On the other hand, the rhombic component is found to increase as the dihedral angle deviates from 90°. These findings provide valuable guidelines for fine-tuning the magnetic properties of Co(II) complexes.

A Fluorinated Chaperone Gives X-ray Crystal Structures of Acyclic Natural Product Derivatives up to 338 Molecular Weight.

Crystallizing molecules with long flexible chains is a challenge, making it difficult to perform X-ray crystallography. Chaperones can assist in the crystallization of compounds that do not crystallize by themselves by producing solvate crystals that contain the analyte in their three-dimensional lattices. Among the most versatile chaperones for liquid analytes are tetraaryladamantanes (TAAs), but the size of the compounds that can be encapsulated is limited, and attempts to surpass this limit with known TAAs were unsuccessful. Here we report that 1,3,5,7-tetrakis(2-fluoro-4-methoxyphenyl)adamantane (TFM) is a crystallization chaperone for acyclic molecules up to the molecular weight of phytyl acetate (338 g/mol). Encapsulation of such a large acyclic compound was achieved when the analyte was esterified and when a two-step temperature protocol was used for crystallization. Exploratory work indicates that a drop to -20 °C allows for encapsulation of squalene (Mr 411 g/mol), albeit with positional disorder of the analyte. Our X-ray crystal structures of solvates with flexible analytes shed light on how crystalline order can be imposed on large acyclic analytes. The new, fluorinated TAA gives access to crystal structures that were inaccessible thus far.

Deciphering DED assembly mechanisms in FADD-procaspase-8-cFLIP complexes regulating apoptosis

Fas-associated protein with death domain (FADD), procaspase-8, and cellular FLICE-inhibitory proteins (cFLIP) assemble through death-effector domains (DEDs), directing death receptor signaling towards cell survival or apoptosis. Understanding their three-dimensional regulatory mechanism has been limited by the absence of atomic coordinates for their ternary DED complex. By employing X-ray crystallography and cryogenic electron microscopy (cryo-EM), we present the atomic coordinates of human FADD-procaspase-8-cFLIP complexes, revealing structural insights into these critical interactions. These structures illustrate how FADD and cFLIP orchestrate the assembly of caspase-8-containing complexes and offer mechanistic explanations for their role in promoting or inhibiting apoptotic and necroptotic signaling. A helical procaspase-8-cFLIP hetero-double layer in the complex appears to promote limited caspase-8 activation for cell survival. Our structure-guided mutagenesis supports the role of the triple-FADD complex in caspase-8 activation and in regulating receptor-interacting protein kinase 1 (RIPK1). These results propose a unified mechanism for DED assembly and procaspase-8 activation in the regulation of apoptotic and necroptotic signaling across various cellular pathways involved in development, innate immunity, and disease.

Bioinspired Water Preorganization in Confined Space for Efficient Water Oxidation Catalysis in Metallosupramolecular Ruthenium Architectures.

ConspectusNature has established a sustainable way to maintain aerobic life on earth by inventing one of the most sophisticated biological processes, namely, natural photosynthesis, which delivers us with organic matter and molecular oxygen derived from the two abundant resources sunlight and water. The thermodynamically demanding photosynthetic water splitting is catalyzed by the oxygen-evolving complex in photosystem II (OEC-PSII), which comprises a distorted tetramanganese-calcium cluster (CaMn4O5) as catalytic core. As an ubiquitous concept for fine-tuning and regulating the reactivity of the active site of metalloenzymes, the surrounding protein domain creates a sophisticated environment that promotes substrate preorganization through secondary, noncovalent interactions such as hydrogen bonding or electrostatic interactions. Based on the high-resolution X-ray structure of PSII, several water channels were identified near the active site, which are filled with extensive hydrogen-bonding networks of preorganized water molecules, connecting the OEC with the protein surface. As an integral part of the outer coordination sphere of natural metalloenzymes, these channels control the substrate and product delivery, carefully regulate the proton flow by promoting pivotal proton-coupled electron transfer processes, and simultaneously stabilize short-lived oxidized intermediates, thus highlighting the importance of an ordered water network for the remarkable efficiency of the natural OEC.Transferring this concept from nature to the engineering of artificial metal catalysts for fuel production has fostered the fascinating field of metallosupramolecular chemistry by generating defined cavities that conceptually mimic enzymatic pockets. However, the application of supramolecular approaches to generate artificial water oxidation catalysts remained scarce prior to our initial reports, since such molecular design strategies for efficient activation of substrate water molecules in confined nanoenvironments were lacking. In this Account, we describe our research efforts on combining the state-of-the art Ru(bda) catalytic framework with structurally programmed ditopic ligands to guide the water oxidation process in defined metallosupramolecular assemblies in spatial proximity. We will elucidate the governing factors that control the quality of hydrogen-bonding water networks in multinuclear cavities of varying sizes and geometries to obtain high-performance, state-of-the-art water oxidation catalysts. Pushing the boundaries of artificial catalyst design, embedding a single catalytic Ru center into a well-defined molecular pocket enabled sophisticated water preorganization in front of the active site through an encoded basic recognition site, resulting in high catalytic rates comparable to those of the natural counterpart OEC-PSII.To fully explore their potential for solar fuel devices, the suitability of our metallosupramolecular assemblies was demonstrated under (electro)chemical and photocatalytic water oxidation conditions. In addition, testing the limits of structural diversity allowed the fabrication of self-assembled linear coordination oligomers as novel photocatalytic materials and long-range ordered covalent organic framework (COF) materials as recyclable and long-term stable solid-state materials for future applications.

Synthesis and characterization of Cu(II) complexes supported by a pyridylamide ligand

In our effort to understand the impact of ligand platforms on the structure diversity and chemical properties of copper clusters, a tripod pyridylamide ligand H3tpmbc was used in this work. Two one-dimensional polymeric Cu(II) complexes [Cu(H3tpmbc)Cl2]n (1) and [Cu2(H3tpmbc)Cl4]n (2) were isolated and characterized. X-ray crystallography analysis showed that both structures have a similar one-dimensional backbone. The main structure difference of the two complexes is the presence of a second Cu(II) site in complex 2. Hirshfeld analysis revealed the presence of interesting C–H⋅⋅⋅π and π⋅⋅⋅π interaction networks in both complexes. Spectroscopic characterization of both complexes and [CuPyCl2] suggests the source of the color difference between the two polymers at the solid state. Computational studies based on the X-ray crystal structures were performed and the results provided a deeper understanding of the electronic structures of the Cu(II) site(s) in both complexes. Thermal gravimetric analysis (TGA) demonstrated that the two complexes have the similar thermal behavior, and this could be attributed to the similar one-dimensional backbone structure.

Phosphorus–nitrogen compounds: part 75—design, synthesis, stereogenic and conformational properties of chiral dispiro(N/N)cyclotriphosphazenes: structural analysis and photophysical and bioactivity studies

AbstractMultiheterocyclic inorganic–organic hybrid phosphazenes have robust inorganic ring systems with the stabilities of the phosphorus nitrogen skeleton and many different substituents bonded to the P atoms. In present study, unsymmetrical dispirocyclotriphosphazenes were prepared due to their potential to depict steric hindrance and electronic rearrangement in creating permanent chirality for certain conformational and configurational isomers. These isomers may have an effect on DNA bindings and activitiy against selected fungi and bacteria, remarkably. Herein, tetrachlorocyclotriphosphazenes (1 and 2) were reacted with 9-ethyl-N-methyl-3-carbazolyl-1,2-diaminoethane (3), 9-ethyl-N-ethyl-3-carbazolyl-1,2-diaminoethane (4) and 9-ethyl-N-methyl-3-carbazolyl-1,3-diaminopropane (5) to give the new unsymmetrical cis/trans-dispirocyclotriphosphazenes, [(ClBz/BzSpiro-6)R1(N3P3)(CzSpiro-n)R2]Cl2 (Cz: Carbazolyl; R1:Me R2:Me or Et; n = 5 or 6; trans 6a–11a and cis 6b–11b). Characterizations, chiralities, and photophysical and biological properties of the new compounds were examined. The molecular and crystal structures of cis-6b, cis-7b, trans-9a, cis-9b, trans-10a and cis-10b were determined by single crystal X-ray crystallography. The chiralities of these compounds with unsymmetrical spiro-architectures were confirmed by X-ray crystallography. These results were further proven by 31P NMR data recorded with the addition of a chiral solvent (CSA). Additionally, circular dichroism (CD) spectra also supported the results. Photophysical measurements indicate that these compounds show emission with lifetimes of approximately 5.6–5.9 ns. In addition, the bioactivities of some isomers were found to be different and quite high against some bacterial and yeast strains. Trans-8a was very active against B. cereus (MBC = 78.1 µM), while cis-6b, trans-9a and cis-9b were very active against the pathogenic yeast C. albicans (MFC = 156.3 µM). Graphical abstract

Structural Analysis of the Macrocyclic Inhibitor BI-4020 Binding to EGFR Kinase.

A novel macrocyclic inhibitor of mutant EGFR (BI-4020) has shown promise in pre-clinical studies of T790M and C797S drug-resistant non-small cell lung cancer. To better understand the molecular basis for BI-4020 selectivity and potency, we have carried out biochemical activity assays and structural analysis with X-ray crystallography. Biochemical potencies agree with previous studies indicating that BI-4020 is uniquely potent against drug-resistant L858R/T790M and L858R/T790M/C797S variants. X-ray structures with wild-type (2.4 Å) and T790M/V948R (3.1 Å) EGFR kinase domains show that BI-4020 is likely rendered selective due to interactions with the kinase domain hinge region as well as T790M, akin to Osimertinib. Additionally, BI-4020 is also rendered more potent due to its constrained macrocycle geometry as well as additional H-bonds to conserved K745 and T845 residues in both active and inactive conformations. These findings taken together show how this novel macrocyclic inhibitor is both highly potent and selective for mutant EGFR in a reversible mechanism and motivate structure-inspired approaches to developing targeted therapies in medicinal oncology.

Unexpected One-Pot Synthesis of 3-Cinnamoyl-3-hydroxyphthalide Derivatives

AbstractA new and simple method to prepare 3-cinnamoyl-3-hydroxyphthalide derivatives from 2-hydroxy-3-methyl-1,4-naphthoquinone and substituted benzaldehydes was unexpectedly uncovered. The reaction was conveniently performed in DMSO at 100 °C with K3PO4 as a base and AlCl3 as a catalyst. We propose that the reaction proceeds by a cascade process involving nucleophilic addition followed by demethylation and rearrangement. The products were typically obtained in moderate to good yields. The highest yield (95%) was obtained when the reaction of 2-bromobenzaldehyde was performed for 24 hours. X-ray crystallography of the product derived from 2-fluorobenzaldehyde unequivocally confirmed the structure of the hydroxyphthalide derivatives.