A facile strategy for the construction of a phage display cyclic peptide library for the selection of functional macrocycles.

Cyclic peptides represent invaluable scaffolds in biological affinity, providing diverse collections for discovering functional molecules targeting challenging biological entities and protein-protein interactions. The field increasingly focuses on developing cyclization strategies and chemically modified combinatorial libraries in conjunction with M13 phage display, to identify macrocyclic peptide inhibitors for traditionally challenging targets. Here, we introduce a cyclization strategy utilizing ortho-phthalaldehyde (OPA) for the discovery of active macrocycles characterized by asymmetric scaffolds with side-chain cyclization. Through this approach, aldehyde groups attached to free molecules sequentially attack the ε-amine of lysine and the thiol of cysteine, facilitating the rapid cyclization of genetically encoded linear precursor libraries displayed on phage particles. The construction of a 109-member library and subsequent screening successfully identified cyclic peptide binders targeting three therapeutically relevant proteins: PTP1B, NEK7, and hKeap1. The results confirm the efficacy in rapidly obtaining active ligands with micromolar potency. This work provides a fast and efficient operable high-throughput platform for screening functional peptide macrocycles, which hold promise for broad application in therapeutics, chemically biological probes, and disease diagnosis.

Nucleoside modification-based flexizymes with versatile activity for tRNA aminoacylation.

Extensive research has focused on genetic code reprogramming using flexizymes (Fxs), ribozymes enabling diverse tRNA acylation. Here we describe a nucleoside-modification strategy for the preparation of flexizyme variants derived from 2'-OMe, 2'-F, and 2'-MOE modifications with unique and versatile activities, enabling the charging of tRNAs with a broad range of substrates. This innovative strategy holds promise for synthetic biology applications, offering a robust pathway to expand the genetic code for diverse substrate incorporation.

Polyarylisocyanides Derived from an Alkyne-Pd(II) Catalyst as Robust Alignment Media with Excellent Enantiodiscimination.

The development of chiral alignment media for measuring anisotropic NMR parameters provides an opportunity to determine the absolute configuration of chiral molecules without the need for derivatization. However, chiral alignment media with a high and robust enantiodiscriminating property for a wide range of chiral molecules are still scarce. In this study, we synthesized cholesterol-end-functionalized helical polyisocyanides from a chiral monomer using a cholesterol-based alkyne-Pd(II) initiator. These stereoregular polyisocyanides form stable and weak anisotropic lyotropic liquid crystals (LLCs) in dichloromethane systems, exhibiting highly optical activities in both single left- and right-handed helices. The preparation process of the media was straightforward, and the aligning property of the LLCs could be controlled by adjusting the concentration and temperature. Using the chiral polyisocyanides, we extracted the residual dipolar coupling for an enantiomeric pair of isopinocampheol (IPC), as well as a number of pharmaceutical molecules, demonstrating excellent enantiodiscriminating properties for a broad range of chiral compounds.

Programming Peptide Liquid Crystal Media to Acquire Independent Sets of Residual Dipolar Couplings and Enantiodiscrimination in Multiple Solvent Systems.

Multiple independent sets of residual dipolar couplings (RDCs) acquired by relying on different alignment media show the great potential for de novo structure determination of organic compounds. However, this methodology is severely compromised by the limited availability of multialignment media. In this work, an engineering strategy was developed to program the oligopeptide amphiphiles (OPAs) to create different peptide liquid crystal (LC) media for the acquisition of independent sets of RDCs. With no need for de novo design on peptide sequences, the molecular alignment can be simply modulated by varying the length of the hydrophobic tails within OPAs. Relying on these programmed peptide LC media, five independent sets of RDCs were extracted in a highly efficient and accurate manner. Because of the similar bulk composition of OPAs, this approach offers the significant advantage in circumventing the possible incompatibilities of analytes with one or several different alignment media, therefore avoiding the analysis complication. Notably, these peptide LC media show enantiodifferentiating properties, and the enantiodiscriminating capabilities could also be optimized through the programmed strategy. Furthermore, we show that these media are compatible with different polar solvents, allowing the possible de novo structure elucidation of organic compounds with varied polarities and solubilities.

Garbractin A, a Polycyclic Polyprenylated Acylphloroglucinol with a 4,11-dioxatricyclo[4.4.2.01,5]Dodecane Skeleton from Garcinia bracteata Fruits.

Garbractin A (1), a structurally complicated polycyclic polyprenylated acylphloroglucinol (PPAP) with an unprecedented 4,11-dioxatricyclo[4.4.2.01,5] dodecane skeleton, was isolated from the fruits of Garcinia bracteata, along with five new biosynthetic analogues named garcibracteatones A-E (2-6). Their structures containing absolute configurations were revealed using spectroscopic data, the residual dipolar coupling-enhanced NMR approach, and quantum chemical calculations. The antihyperglycemic effect of these PPAPs (1-6) was evaluated using insulin-resistant HepG2 cells (IR-HepG2 cells) induced through palmitic acid (PA). Compounds 1, 3, and 4 were found to significantly promote glucose consumption in the IR-HepG2 cells and, therefore, may hold potential as candidates for treating hyperglycemia.

Weakly aligned Ti3C2Tx MXene liquid crystals: measuring residual dipolar coupling in multiple co-solvent systems.

Residual Dipolar Coupling (RDC), acquired relying on weakly alignment media, is highly valuable for the structural elucidation of organic molecules. Arising from the striking features of no background signals and low critical concentrations, two-dimensional (2D) liquid crystals (LCs) show the clear advantages of acting as alignment media to measure RDCs. So far, creating multisolvent compatible 2D LC media through a simple and versatile method is still formidably challenging. Herein, we report the rapid creation of aligned media based on the Ti3C2Tx MXene, which self-aligned in multiple co-solvents including CH3OH-H2O, DMSO-H2O, DMF-H2O, and acetone-H2O. We demonstrated the applicability of these aligned media for the RDC measurement of small organic molecules with different polarities and solubilities. Notably, Ti3C2Tx MXene LCs without chemical modification enabled RDC measurements on aromatic molecules. The straightforward preparation of Ti3C2Tx media and its compatibility with multiple solvents will push RDC measurement as a routine methodology for structural elucidation. It may also facilitate the investigation of solvation effects on conformational dynamics.

Tricrilactones A-H, Potent Antiosteoporosis Macrolides with Distinctive Ring Skeletons from Trichocladium crispatum, an Alpine Moss-Associated Fungus.

Tricrilactones A-H (1-8), a new family of oligomeric 10-membered macrolides featuring collectively five unique ring skeletons, were isolated from a hitherto unexplored fungus, Trichocladium crispatum. Compounds 1 and 7 contain two unconventional bridged (aza)tricyclic core skeletons, 2, 3, 5, and 6 share an undescribed tetracyclic 9/5/6/6 ring system, 4 bears an uncommon 9/5/6/10/3-fused pentacyclic architecture, and 8 is a dimer bridged by an unexpected C-C linkage. Their structures, including absolute configurations, were elucidated by spectroscopic analysis, quantum chemical calculations, and X-ray diffraction analysis. Importantly, the absolute configuration of the highly flexible side chain of 1 was resolved by the asymmetric synthesis of its four stereoisomers. The intermediate-trapping and isotope labeling experiments facilitated the proposal of the biosynthetic pathway for these macrolides. In addition, their antiosteoporosis effects were evaluated in vivo (zebrafish).

Paecilins F-P, new dimeric chromanones isolated from the endophytic fungus Xylaria curta E10, and structural revision of paecilin A.

A total of eleven new dimeric chromanones, paecilins F-P (2-12), were isolated from the endophytic fungus Xylaria curta E10, along with four known analogs (1, 13-15). Their structures and absolute configurations were determined by extensive experimental spectroscopic methods, single-crystal X-ray diffraction, and equivalent circulating density (ECD) calculations. In addition, the structure of paecilin A, which was reported to be a symmetric C8-C8' dimeric pattern, was revised by analysis of the nuclear magnetic resonance (NMR) data, and single-crystal X-ray diffraction. Compound 1 showed antifungal activity against the human pathogenic fungus Candida albicans with a minimum inhibitory concentration of 16 µg/mL, and Compounds 8 and 10 showed antibacterial activity against the gram-negative bacterium Escherichia coli with the same minimum inhibitory concentration of 16 µg/mL.

Programmable alignment media from self-assembled oligopeptide amphiphiles for the measurement of independent sets of residual dipolar couplings in organic solvents.

NMR spectroscopy in anisotropic media has emerged as a powerful technique for the structural elucidation of organic molecules. Its application requires weak alignment of analytes by means of suitable alignment media. Although a number of alignment media, that are compatible with organic solvents, have been introduced in the last 20 years, acquiring a number of independent, non-linearly related sets of anisotropic NMR data from the same organic solvent system remains a formidable challenge, which is however crucial for the alignment simulations and deriving dynamic and structural information of organic molecules unambiguously. Herein, we introduce a programmable strategy to construct several distinct peptide-based alignment media by adjusting the amino acid sequence, which allows us to measure independent sets of residual dipolar couplings (RDCs) in a highly efficient and accurate manner. This study opens a new avenue for de novo structure determination of organic compounds without requiring prior structural information.

Ti3C2Tx MXene Liquid Crystal: Access to Create Background-Free and Easy-Made Alignment Medium.

The formation of lyotropic liquid crystals (LCs) in two-dimensional (2D) colloidal dispersions enables the production of mesoscopic/macroscopic ordered materials from nanoscale building blocks. In contrast to graphene oxide (GO) LCs, the practical applications of MXene LCs are less exploited. This study bridges the gap by utilizing a simple and versatile fabrication method to prepare Ti3C2Tx MXene LC that can be applied as a background-free alignment medium for the residual dipolar coupling (RDC) measurement of organic molecules. Ti3C2Tx LC displays the size- and concentration-dependent alignment degree. Ti3C2Tx nanoflakes with an average size of around 600 nm can provide the quadrupolar 2H splitting of 71 Hz at a concentration of 50 mg/mL and show excellent fluidity at such a high concentration. Compared with other alignment media, Ti3C2Tx LC exhibits the features of no-background and narrow line broadening, which actualizes the acquirement of clean and high-quality NMR spectra for the accurate RDC extraction. Notably, the alignment of LCs is determined to be maintainable in the redispersed solution after freeze-drying, providing the great convenience for the preparation of alignment Ti3C2Tx media, long-term sample preservation, and quantitative evaluation of alignment degree. Meanwhile, the alignment LC media for RDC measurement can be established in other MXenes such as Ti2CTx and Ti3CNTx. Collectively, our findings demonstrate the potential of creating various alignment media from the fascinating MXene family.

Three new pyrrole alkaloids from the endophytic fungus Albifimbria viridis.

Three new pyrrole alkaloids albifipyrrols A-C (1-3), were isolated from the endophytic fungus Albifimbria viridis collected from the Chinese medicinal plant. Their structures were elucidated by extensive NMR and HRESIMS spectrometric analyses. All compounds were evaluated for immunosuppressive activity. Fortunately, compound 2 exhibits certain inhibition specifically against the LPS-induced proliferation of B lymphocyte cells with IC50 value 16.16 µM.

Self-Assembly of Helical Polymers and Oligomers to Create Liquid Crystalline Alignment for Anisotropic NMR Parameters.

The measurement of anisotropic residual dipolar couplings (RDCs) parameters for the structure elucidation of organic molecules relies on suitable alignment media. Employment of self-assembled liquid crystalline systems to create anisotropic alignment can be an effective way to realize aligned samples and acquire RDCs. This Mini-review highlights the recent advances on amino acid-based helical polymers and supramolecular oligomers forming rigid, rod-like structures that aggregate into ordered liquid crystalline phases, including amino acid-based helical polyisocyanides, polyacetylenes, polypeptides, and oligopeptides assembled alignment media. The methodology for the determination of anisotropic liquid crystals is briefly discussed, and a summary of recent research progress in the enantiodifferentiation of helical polymers aligned media is followed. In addition, the self-assembled mechanism of oligopeptides and their RDCs structural analysis are also described.

Solvent-tailored ordered self-assembly of oligopeptide amphiphiles to create an anisotropic meso-matrix.

Herein, we have developed a solvent-tailored ordered self-assembly strategy to create anisotropic nanomaterials. A trace amount of water has been found to be a predominant factor to direct peptide self-assembly into an anisotropic meso-matrix in DMSO. The obtained meso-matrix was applied to measure the anisotropic RDC parameter of organic molecules for structural elucidation.

Structural Elucidation of Garcipaucinones A and B From Garcinia paucinervis Using Quantum Chemical Calculations.

Two tocotrienol derivatives, garcipaucinones A (1) and B (2), and a biosynthetically related known analogue (3) were isolated from the fruit of Garcinia paucinervis. Their structures including absolute configurations were unequivocally determined by spectroscopic methods complemented with electronic circular dichroism (ECD) calculations and gauge-independent atomic orbital (GIAO) NMR calculations. Compounds 1 and 2 are the first naturally occurring tocotrienol derivatives with a 3,10-dioxatricyclo-[7.3.1.02,7]tridecane skeleton incorporating an unusual γ-pyrone motif. A reasonable biosynthetic pathway for formation of the two compounds is proposed. The antiproliferative and anti-inflammatory activities of compounds 1 and 2 were also evaluated.

Evaluation of different boosting ensemble machine learning models and novel deep learning and boosting framework for head-cut gully erosion susceptibility.

The objective of this study is to assess the gully head-cut erosion susceptibility and identify gully erosion prone areas in the Meimand watershed, Iran. In recent years, this study area has been greatly influenced by several head-cut gullies due to unusual climatic factors and human induced activity. The present study is therefore intended to address this issue by developing head-cut gully erosion prediction maps using boosting ensemble machine learning algorithms, namely Boosted Tree (BT), Boosted Generalized Linear Models (BGLM), Boosted Regression Tree (BRT), Extreme Gradient Boosting (XGB), and Deep Boost (DB). Initially, we produced a gully erosion inventory map using a variety of resources, including published reports, Google Earth images, and field records of the Global Positioning System (GPS). Subsequently, we distributed this information randomly and choose 70% (102) of the test gullies and the remaining 30% (43) for validation. The methodology was designed using morphometric and thematic determinants, including 14 head-cut gully erosion conditioning features. We have also investigated the following: (a) Multi-collinearity analysis to determine the linearity of the independent variables, (b) Predictive capability of piping models using train and test dataset and (c) Variables importance affecting head-cut gully erosion. The study reveals that altitude, land use, distances from road and soil characteristics influenced the method with the greatest impact on head-cut gully erosion susceptibility. We presented five head-cut gully erosion susceptibility maps and investigated their predictive accuracy through area under curve (AUC). The AUC test reveals that the DB machine learning method demonstrated significantly higher accuracy (AUC = 0.95) than the BT (AUC = 0.93), BGLM (AUC = 0.91), BRT (AUC = 0.94) and XGB (AUC = 0.92) approaches. The predicted head-cut gully erosion susceptibility maps can be used by policy makers and local authorities for soil conservation and to prevent threats to human activities.

Chaetolactam A, an Azaphilone Derivative from the Endophytic Fungus Chaetomium sp. g1.

Chaetolactam A (1), an unprecedented azaphilone derivative bearing a unique 9-oxa-7-azabicyclo[4.2.1]octan-8-onering system, together with two new compounds, 11-epi-chaetomugilide B (2) and chaetomugilide D (3) was isolated from an endophytic fungus, Chaetomium sp. g1. Notably, extensive NMR data analyses, NMR calculations with DP4 and DP4+ analyses, ECD calculations, and the RDC method were employed to establish the structure of 1. Furthermore, 2 exhibited potent apoptosis induction activity by mediating caspase-3 activation and PARP degradation at 3 µM in HL-60.

Measurement of Residual Dipolar Couplings of Organic Molecules in Multiple Solvent Systems Using a Liquid-Crystalline-Based Medium.

Residual dipolar coupling (RDC), a robust anisotropic NMR parameter for structural elucidation of organic molecules, is only accessible in an anisotropic environment. Herein, we introduce a novel alignment medium based on the molecular self-assembly of oligopeptide amphiphile (OPA). This medium is compatible with different intermediate and polar solvent systems, such as CD3 OD, [D6 ]DMSO, and D2 O. The preparation of the OPA-based medium is simple and rapid, while only very weak background signals were observed from OPAs. Furthermore, we show that the purity of OPA has only a minor influence on the quality of the RDC data. These advantages allow RDC measurements of organic molecules with different polarities and solubilities with high efficiency and accuracy.

Efficient Enantiodifferentiation of Carboxylic Acids Using BINOL-Based Amino Alcohol as a Chiral NMR Solvating Agent.

A new optically active BINOL-amino alcohol has been designed and synthesized in a good yield and applied as chiral nuclear magnetic resonance (NMR) solvating agent for enantioselective recognition. Analysis by 1H NMR spectroscopy demonstrated that it has excellent enantiodifferentiation properties toward carboxylic acids and non-steroidal anti-inflammatory drugs (14 examples). The non-equivalent chemical shifts (up to 0.641 ppm) of various mandelic acids were evaluated by the reliable peak of well-resolved 1H NMR signals. In addition, enantiomeric excesses of the ortho-chloro-mandelic acid with different enantiomeric ratio were calculated based on integration of proton well-separated splitting signals.

Practical aspects of oligopeptide AAKLVFF as an alignment medium for the measurements of residual dipolar coupling of organic molecules.

Practical aspects of the oligopeptide AAKLVFF as an alignment medium are discussed, including large-scale synthesis of the oligopeptide, detailed description of preparation of the alignment medium, and acquisition of the RDCs. The resulting orienting medium is stable and highly homogeneous with tunable alignment strength in methanol.

Stereochemical Elucidation of Natural Products from Residual Chemical Shift Anisotropies in a Liquid Crystalline Phase.

Determination of the stereochemistry of organic molecules still represents one of the major obstacles in the structure elucidation procedure in drug discovery. Although the application of residual dipolar couplings (RDCs) has revolutionized this field, residual chemical shift anisotropies (RCSAs) which contain valuable structural information for nonprotonated carbons have only been scarcely employed so far. In this study, we present a simple but highly effective solution to extract RCSAs of the analytes in a liquid crystalline phase formed by AAKLVFF oligopeptides. This method does not require any special instruments, devices, or correction during postacquisition data analysis and thus can be easily applied in any chemistry laboratory. To illustrate the potential of this method, the relative configurations of four known natural products (1-4) belonging to different structural classes were confirmed. Moreover, we unambiguously elucidated the stereochemistry of spiroepicoccin A (5), a rare thiodiketopiperazine marine natural product whose configuration could not be assigned based on conventional NMR methods.