Structural Motifs Research Articles

Structural Insights into the Mechanism of a Polyketide Synthase Thiocysteine Lyase Domain.

Polyketide synthases (PKSs) are renowned for the structural diversity of the polyketide natural products they produce, but sulfur-containing functionalities are rarely installed by PKSs. We previously characterized thiocysteine lyase (SH) domains involved in the biosynthesis of the leinamycin (LNM) family of natural products, exemplified by LnmJ-SH and guangnanmycin (GnmT-SH). Here we report a detailed investigation into the PLP-dependent reaction catalyzed by the SH domains, guided by a 1.8 Å resolution crystal structure of GnmT-SH. A series of elaborate substrate mimics were synthesized to answer specific questions garnered from the crystal structure and from the biosynthetic logic of the LNM family of natural products. Through a combination of bioinformatics, molecular modeling, in vitro assays, and mutagenesis, we have developed a detailed model of acyl carrier protein (ACP)-tethered substrate-SH, and interdomain interactions, that contribute to the observed substrate specificity. Comparison of the GnmT-SH structure with archetypical PLP-dependent enzyme structures revealed how Nature, via evolution, has modified a common protein structural motif to accommodate an ACP-tethered substrate, which is significantly larger than any of those previously characterized. Overall, this study demonstrates how PLP-dependent chemistry can be incorporated into the context of PKS assembly lines and sets the stage for engineering PKSs to produce sulfur-containing polyketides.

The Photocleavable Protein PhoCl-Based Dynamic Hydrogels.

Dynamic protein hydrogels have attracted increasing attention owing to their tunable physiochemical and mechanical properties, customized functionality, and biocompatibility. Among the different types of dynamic hydrogels, photoresponsive hydrogels are of particular interest. Here, we report the engineering of a photoresponsive protein hydrogel by using the photocleavable protein PhoCl. We employed the well-developed SpyTag and SpyCatcher chemistry to engineer PhoCl-containing covalently cross-linked hydrogels. In the hydrogel network, PhoCl, which can be cleaved into two fragments upon violet irradiation, is employed as a dynamic structural motif to regulate the cross-linking density of the hydrogel network. The resultant PhoCl-containing hydrogels showed photoresponsive viscoelastic properties. Upon violet irradiation, the PhoCl hydrogels soften, leading to an irreversible reduction in the storage moduli. However, no gel-sol transition was observed. Leveraging this light-induced stiffness change, we employed this hydrogel as a cell culture substrate to investigate the mechanobiological response of NIH-3T3 fibroblast cells. Our results showed that 3T3 cells can change their morphologies in response to the stiffness change of the PhoCl hydrogel substrate dynamically, rendering PhoCl-based hydrogels a useful substrate for other mechanobiological studies.

Why is binding of a divalent metal cation to a structural motif containing four carboxylate residues not accompanied by a conformational change?

We earlier showed that Torpedo californica acetylcholinesterase (AChE) contains a cluster of four conserved aspartates that can strongly bind divalent cations, which we named the 4D motif. Binding of the divalent metal cations greatly increases its thermal stability. Here we systematically examined all available crystallographic structures of T. californica AChE. Two additional metal-binding sites were identified, both composed of acidic and histidine residues. Relative binding to the 4D and additional sites was studied using metadynamics simulations. It was observed that in crystal structures devoid of metal ions in the 4D site, the conformation of T. californica AChE is almost identical to that in structures in which it is occupied by a divalent metal ion. Closer examination of the 4D motif reveals that three of the four acidic residues form ion pairs with conserved basic residues surrounding them. We named this new motif the 4A/3B motif. Molecular dynamics with quantum potential simulations was used to quantify the 4D motif's binding strength compared with that of the metal-binding site in the protein fXIIIa, which consists of four aspartates, but is devoid of adjacent cationic residues. Whereas fXIIIa's 4D site, in the absence of a metal cation, expanded significantly in the simulation, that of Torpedo AChE displayed only minor periodic changes in size. Furthermore, the energy of metal ion unbinding from the two sites differs by ca. 10 kcal/mol. We identified several other proteins in the PDB that contain the 4A/3B motif, whose conformations are identical in the presence or absence of a metal ion. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at https://proteopedia.org/w/Journal:Protein_Science:4.

Advancements in transition metal-catalyzed 1,2,3-triazole synthesis via azide–alkyne cycloaddition

Abstract 1,2,3-triazoles have emerged as important structural motifs in chemical biology, attracting increasing focus in recent years because of their wide range of uses. These compounds can be efficiently synthesized using click reactions. Its versatility makes it valuable in drug discovery and materials science. Significant advancements have been made in recent years in the process of making 1,2,3-triazoles, reflecting the growing curiosity and investment in the area of research. The catalytic performance of transition metals Cu, Ir, Rh, Ru, Ni, Pd, Au, Ag, and Zn, which were used as ligands and salts in the azide–alkyne cycloaddition method of 1,2,3-triazole synthesis, has been covered in this review. Cu-complexes and salts were found to be more effective for selective synthesis among all transition metals. Furthermore, it is determined that some azide–alkyne reactions are entirely catalytic in nature and cannot be carried out as such by switching transition metals.

Targeting Vascular Endothelial Growth Factor Receptor 2 (VEGFR-2): Latest Insights on Synthetic Strategies

Vascular endothelial growth factor receptor 2 (VEGFR-2) is a crucial mediator of angiogenesis, playing a pivotal role in both normal physiological processes and cancer progression. Tumors harness VEGFR-2 signaling to promote abnormal blood vessel growth, which is a key step in the metastasis process, making it a valuable target for anticancer drug development. While there are VEGFR-2 inhibitors approved for therapeutic use, they face challenges like drug resistance, off-target effects, and adverse side effects, limiting their effectiveness. The quest for new drug candidates with VEGFR-2 inhibitory activity often starts with the selection of key structural motifs present in molecules currently used in clinical practice, expanding the chemical space by generating novel derivatives bearing one or more of these moieties. This review provides an overview of recent advances in the development of novel VEGFR-2 inhibitors, focusing on the synthesis of new drug candidates with promising antiproliferative and VEGFR-2 inhibition activities, organizing them by relevant structural features.

Two groups and three classes of the conserved structural organization of nucleophile and non-canonical ElbowFlankOxy networks in different superfamily proteins

The nucleophile elbow is a well-known structural motif, which exists in proteins with catalytic triads and contains a catalytic nucleophile and the first node of an oxyanion hole. Here, we show that structural similarities of proteins with the nucleophile elbow extend beyond simple nucleophile elbow motifs. The motifs are incorporated into larger conserved structural organizations, the ElbowFlankOxy networks, incorporating motifs and flanking residues and networks of conserved interactions. A detailed structural analysis shows two major types of ElbowFlankOxy networks, depending on the formation of the oxyanion hole. Additionally, the ElbowFlankOxy networks show three classes: Class 1-2-3, 3-1-2, and 2-3-1, defined by the order in which the catalytic nucleophile and key interacting residues are located in the amino acid sequence, giving rise to six ElbowFlankOxy network variations. This makes it possible to properly position homologous non-catalytic, non-standard, and unusual catalytic triad active sites of proteins with the nucleophile elbow within the fold classification.

Multisample motif discovery and visualization for tandem repeats.

Tandem Repeats (TR) occupy a significant portion of the human genome and are the source of polymorphism due to variations in sizes and motif compositions. Some of these variations have been associated with various neuropathological disorders, highlighting the clinical importance of assessing the motif structure of TRs. Moreover, assessing the TR motif variation can offer valuable insights into evolutionary dynamics and population structure. Previously, characterizations of TRs have been limited by short-read sequencing technology, which lacks the ability to accurately capture the full TR sequences. As long-read sequencing becomes more accessible and can capture the full complexity of TRs, there is now also a need for tools to characterize and analyze TRs using long-read data across multiple samples. In this study, we present MotifScope, a novel algorithm for characterization and visualization of TRs based on a de novo k-mer approach for motif discovery. Comparative analysis against established tools reveals that MotifScope can identify a greater number of motifs and more accurately represent the underlying repeat sequence. Moreover, MotifScope has been specifically designed to enable motif composition comparisons across assemblies of different individuals, as well as across long-read sequencing reads within an individual, through combined motif discovery and sequence alignment. We showcase potential applications of MotifScope in diverse fields, including population genetics, clinical settings, and forensic analyses.

Facile Synthesis of New Antiviral Fluoro-Quinazolines Enabled by Merging Domino Reactions

AbstractQuinazolines, particularly fluoro-quinazolines, represent important structural motifs in bioactive molecules and pharmaceuticals. Despite several known synthetic routes, the efficient synthesis of fluorine-containing quinazolines remains a challenge. Herein, the straightforward and sustainable synthesis of fluorine-substituted quinazolines using domino sequences is reported. The obtained novel fluoro-quinazoline compounds exhibit significant in vitro activity against human cytomegalovirus (HCMV), expanding the library of potential antiviral drug compounds. Our finding outlays the synthetic toolkit for fluoro-quinazolines and introduces new agents for HCMV therapy.

Intermolecular Oxidopyrylium (5 + 2) Cycloaddition/Reductive Ring-Opening Strategy for the Synthesis of α-Methoxytropones.

α-Methoxytropone is a structural motif found in various natural products and other compounds of interest to the scientific community but remains a synthetic challenge. The present Note describes the synthesis of variously substituted α-methoxytropones and related compounds through an intermolecular 3-hydroxy-4-pyrone-based oxidopyrylium (5 + 2) cycloaddition followed by a samarium iodide-mediated reductive ring-opening. The strategy is highlighted in the synthesis of a novel AC-ring analogue of colchicine to compare it to existing methods.

A New Class of Oxyhalide Solid Electrolytes NaNbCl6‐2xOx for Solid‐state Sodium Batteries

AbstractSodium‐based batteries are gaining momentum due to the abundance and lower cost of sodium compared to lithium. Solid‐state sodium batteries can also provide further safety advantages. However, sodium‐based solid‐state electrolytes (SSEs) that meet all the rigorous requirements, such as high ionic conductivity, oxidative stability with the cathode, and ease of processability, are lacking. We present here a new class of sodium‐based oxyhalide electrolytes NaNbCl6‐2xOx with a facile mechanochemical synthesis. The oxyhalide NaNbCl4O exhibits close to two orders of magnitude higher ambient‐temperature sodium‐ion conductivity (1.03×10−4 S cm−1) compared to the halide counterpart NaNbCl6 (3×10−6 S cm−1). Structural motifs unique to the oxygen content in NaNbCl6‐2xOx are identified with 23Na and 93Nb magic angle spinning nuclear magnetic resonance (MAS NMR) spectroscopy and x‐ray diffraction (XRD). Solid‐state sodium batteries assembled with NaNbCl4O electrolyte and the cobalt‐ and nickel‐free layered Na0.70Fe0.3Mn0.65Al0.05O2 cathode exhibit a maximum discharge capacity of 155 mAh g−1 with good cycle life at ambient temperature.

Small Molecule Modulator of the mTORC2 Pathway Discovered from a DEL Library Designed to Bind to Pleckstrin Homology Domains.

Pleckstrin homology (PH) domains are structural motifs critical for cellular processes, such as signal transduction and cytoskeletal organization. Due to their involvement in various diseases, PH domains are promising therapeutic targets, yet their highly charged and hydrophobic binding sites are not ideal for traditional small drugs. In this study, we designed a DNA-encoded library (DEL) mimicking phospholipids to identify novel modulators targeting PH domains with uncharted chemical properties. Screening against several PH domains led to the discovery of 2DII, a small molecule that selectively binds to mSin1PH. This compound can modulate mTORC2 activity by impairing mTORC2's membrane interactions, resulting in reduced AKT1 phosphorylation. A micromapping via Dexter energy transfer based on 2DII bearing an iridium catalyst (2DII-Ir), along with a biotin-diazirine small molecule was used for target identification by proteomics, which confirmed mSin1 as the primary intracellular target of 2DII, demonstrating its potential for selective mTORC2 pathway modulation. These findings introduce a novel strategy for targeting PH domains and provide a foundation for the development of therapeutic interventions that modulate PH-domain-dependent signaling pathways.

Organic Room Temperature Phosphorescence from BN‐Substituted Xanthene Derivatives

AbstractEmissive organic materials are predominantly fluorescent and there is significant interest in realizing and understanding examples that defy this paradigm and exhibit phosphorescence under ambient conditions. Organic room temperature phosphorescence (ORTP) offers the long‐lived excited states and bathochromically‐shifted emission maxima of phosphorescence without the use of potentially toxic and expensive transition metals. Most ORTP materials rely on well‐studied structural motifs that include aryl carbonyls, sulfones, and heavy main group elements. We report the unexpected ORTP of a series of heavy atom‐free BN‐substituted xanthene derivatives. The creation of heteroatom‐rich scaffolds, combined with stabilizing C−H⋅⋅⋅F interactions in the solid‐state, resulted in oxygen‐tolerant heavy atom‐free organic phosphorescence without relying on the use of cryogenic temperatures, polymer matrices, or host–guest interactions. The observation of ORTP in these simple systems sets a blueprint for the further development of heavy atom‐free organic phosphors.

Inhibition of Kornblum Reaction with Lithium Salts in SN2 Reactions of Sulfonates and a Nucleophile Containing a Pyridine N-Oxide Moiety: Convergent and Selective Synthesis of an MRGPRX2 Antagonist.

A critical step in the development of a convergent synthesis of an MRGPRX2 antagonist (1) was the SN2 reaction with a highly functionalized lactamide electrophile and a unique difluoropiperidine nucleophile containing a pyridine N-oxide moiety. Initial reactions with sulfonate leaving groups exhibited superb stereoselectivity, but yields were very low due to side reactions originated from competitive Kornblum reactions of the pyridine N-oxide and the sulfonates. Markedly improved reaction profiles were achieved by including stoichiometric lithium triflate. NMR data provided insights into how the lithium cation impacted the pyridine N-oxide through coordination and attenuating its nucleophilicity, leading to the inhibition of the undesired Kornblum reactions. Our approach is highly relevant to preservation of the N-oxide, a structural motif known to several marketed products and emerging as an important class in drug discovery in nucleophilic substitutions. Application of this method enabled the production of the target (1 and its HCl salt 1a) up to multikilogram scale with high selectivity and in much improved yield.

Organocatalytic Electrophilic Arene Amination: Rapid Synthesis of 2-Quinolones.

For decades, the synthesis of 2-quinolones, a crucial structural motif in pharmaceuticals and agrochemicals, has relied heavily on costly noble metal complexes and structurally complex ligands. Despite considerable efforts from synthetic chemists, a mild, metal-free, environmentally friendly, and cost-effective approach has remained elusive. This study introduces a robust, metal-free synthetic platform that leverages an innovative organoiodine-catalyzed electrophilic arene C(sp2)-H amination strategy to efficiently produce a wide range of new and modifiable 2-quinolones. Moreover, this study allows ready synthetic access to novel 8-aryl-substituted 2-quinolones, uncovering new chemical spaces with significant potential for medicinal applications.

Decarboxylative click cycloaddition: an emerging strategy towards substituted 1,2,3-triazole derivatives.

1,2,3-triazole is a vital structural motif of various drugs and therapeutic leads, as well as a linker for bioconjugation and molecular recognition. Cu-catalysed click cycloaddition of azides with terminal alkynes (CuAAc) is an important reaction to construct the triazole core. In recent years, various decarboxylative click strategies utilizing alkynoic acids as stable surrogates for low boiling or gaseous alkynes have been developed. For instance, propiolic acid, which is easy to transport, is a safe alternative for flammable gaseous acetylene. In this review article, we have covered the recent development in the decarboxylative click cycloaddition of alkynoic acids with azides leading to the synthesis of diversely substituted triazoles, including monosubstituted, 1,4-disubstituted and fully substituted 1,2,3-triazoles. Various aspects such as mechanistic insights and optimization conditions/role of catalyst are highlighted.

Photo-induced hydroxypentafluorosulfanylation of alkenes with SF5Cl and oxygen gas and their further derivatization

Fluorinated or fluoroalkylated alcohols are common structural motifs in biologically active molecules, natural products, and pharmaceuticals. However, pentafluorosulfanyl (SF5) alcohols, a unique class of SF5 compounds that serve as synthetically valuable building blocks, are difficult to prepare with current methodologies. In this article, we present a single-step, metal-free, and photo-induced hydroxypentafluorosulfanylation of styrenes or α,β-unsaturated esters/amide, producing a series of structurally diverse pentafluorosulfanyl alcohols with up to 89% yields. This reaction is mild and operationally simple, using molecular oxygen as the hydroxy source. The protocol is suitable for a wide range of alkenes, including natural products and drug molecule derivatives. The formed SF5 alcohol units can be readily converted into diverse functionalized SF5 compounds, such as α-SF5 ketones, SF5 diols, and SF5 cyclic carbonates. The potential applications of these SF5 compounds in pharmaceutical and material sciences are vast, making this research a step forward in the field.

Pt-Driven Stable and Metastable Ternary Compounds with Tunable Partial Flat Bands in Immiscible Si-Sn System.

A combined machine learning approach and first-principles calculations are employed to efficiently explore energetically favorable ternary compounds involving Pt and an immiscible Si-Sn pair of elements. We predict two stable Pt-Si-Sn ternary compounds (Pt2Si2Sn and Pt8SiSn2) and reproduce the experimentally synthesized Pt5SiSn. The crystal structures of Pt5SiSn and Pt8SiSn2 are composed of a SiPt8 cube and SnPt12 cuboctahedron. Based on these structural motifs, we design a series of Pt-Si-Sn ternary compounds that contain SiPt8 and SnPt12 units and discover some stable and metastable compounds. Partial flat bands near the Fermi level appear in these compounds, and the positions of partial flat bands move upward with increasing the Pt content. The partial flat bands are dominated by Pt atoms. These Pt-Si-Sn ternary compounds provide a platform to study flat band-related properties. Our results open a way to design new compounds in the ternary system.

Genome-wide identification and functional analysis of CYP450 genes in eggplant (Solanum melongena L.) with a focus on anthocyanin accumlation

BackgroundIn plants, Cytochrome P450 (CYP450) constitutes the largest family of metabolic enzymes and plays a crucial role in various physiological processes, including plant growth and development. Eggplants are well-known for their peel’s high concentration of anthocyanin compounds that provide significant health benefits to humans. The accumulation of anthocyanins in eggplant peels is an important process during growth and development. Therefore, it is essential to identify the CYP450 genes in eggplant (SmCYPs) and analyze their expression profiles during the period of anthocyanin accumulation in the peel.ResultsA total of 180 SmCYPs were identified in the eggplant genome and classified into eight subfamilies based on phylogenetic analysis. These SmCYPs exhibited highly conserved gene structure (exon/intron) and protein motifs, especially within their respective subgroup. Sixteen pairs of genes with collinearity were identified through gene duplication analysis. Promoter cis-acting element analysis revealed that SmCYPs are involved in various responses, including growth and development, stress responsiveness, and light responsiveness. Transcriptome data analysis revealed that all SmCYPs were expressed in various eggplant tissues, such as roots, stems, leaves, flowers, and fruits; with diverse expression patterns among members. The expression patterns of SmCYPs in eggplant peel also exhibited diversity during different stages of anthocyanin accumulation. qRT-PCR analysis demonstrated similar expression patterns for 15 selected SmCYPs as observed in the transcriptome data. Metabolomics analysis further suggested that SmCYPs are involved in the biosynthesis of secondary metabolites and metabolic pathways related to flavonoid and flavone/flavonol biosynthesis. Notably, three specific SmCYPs (SmCYP73A1/75A/98A1) play a significant role in flavonoid biosynthesis, particularly in anthocyanin synthesis in eggplant.ConclusionGenome-wide identification, phylogenetic analysis, expression profile analysis, and exploration of metabolic pathways related to SmCYPs provide valuable insights into the roles of these genes in anthocyanin accumulation in various tissues and organs, including eggplant peel. The findings from this study lay a foundation for the functional analysis of SmCYPs involvement in anthocyanin accumulation in eggplant peel, providing a molecular basis for breeders to cultivate novel varieties of eggplants with high levels of anthocyanin content.

Dual effects of mefenamic acid on the IKs molecular complex.

Mutations in both KCNQ1 and KCNE1, which together form the cardiac IKs current, are associated with inherited conditions such as long and short QT syndromes. Mefenamic acid, a non-steroidal anti-inflammatory drug, is an IKs potentiator and may be utilised as an archetype to design therapeutically useful IKs agonists. However, here we show that mefenamic acid can also act as an IKs inhibitor, and our data reveal its dual effects on KCNQ1/KCNE1 channels. Effects of mefenamic acid on wild type (WT) and mutant KCNQ1/KCNE1 channels expressed in tsA201 cells were studied using whole cell patch clamp. Molecular dynamics simulations were used to determine trajectory clustering. Mefenamic acid inhibits WT IKs at high concentrations while preserving some attributes of current potentiation. Inhibitory actions of mefenamic acid are unmasked at lower drug concentrations by KCNE1 and KCNQ1 mutations in the mefenamic acid binding pocket, at the extracellular end of KCNE1 and in the KCNQ1 S6 helix. Mefenamic acid does not inhibit KCNQ1 in the absence of KCNE1 but inhibits IKs current in a concentration-dependent manner in the mutant channels. Inhibition involves modulation of pore kinetics and/or voltage sensor domain-pore coupling in WT and in the KCNE1 E43C mutant. This work highlights the importance of structural motifs at the extracellular inter-subunit interface of KCNQ1 and KCNE1 channels, and their interactions, in determining the nature of drug effects on the IKs channel complex and has important implications for treating patients with specific long QT mutations.

Self-assembled properties of water cuboids

Although liquid water and ice are characterised by predominantly tetrahedral coordination, small water clusters often exhibit a cubic structural motif. In this article, the stability of hydrogen-bonded water nanostructures in the form of n 1×n 2×n 3 cuboids is investigated. The requirement for complete hydrogen bonding imposes a strong constraint on their structure. The equations of the donor–acceptor balance are derived, from which all possible forms of completely hydrogen-bonded cuboids are deduced. The flexible non-additive AMOEBA potential is used for geometric optimisation of the set of configurations with different directions of hydrogen (H-) bonds. It has been established that the majority of completely hydrogen-bonded structures are formed by one layer of fused cubes. The lowest energy configurations of the, in fact, bilayer structures are formed by trans-configurations of transverse pairs of molecules, although some H-bonds are broken in this case. It is noted that the structure of the cuboids may result from the assembly of short nanotubes and smaller cuboids. On the other hand, unrealised H-bonds at the corners of the cuboids make it possible to assemble larger bilayer structures.