Solution cis-Proline Conformation of IPCs Inhibitor Aureobasidin A Elucidated via NMR-Based Conformational Analysis

Heterophyllin B: Combining Isotropic and Anisotropic NMR for the Conformational Analysis of a Natural Occurring Cyclic Peptide

Heterophyllin B is a natural occurring cyclic peptide with diverse attributed bioactivities. NMR-based conformational analysis of cyclic peptides often poses a challenge due to limited isotropic solution-state NMR data. In this study, we combined isotropic and anisotropic NMR observables including J-coupling, NOEs, amide proton temperature coefficients, and residual dipolar couplings (RDCs), which enabled the determination of a minimal conformational ensemble of heterophyllin B in methanol at density functional theory (DFT) accuracy. For conformational sampling of a cyclic peptide with a high degree of conformational freedom, we proposed a computational strategy that combines the Conformer-Rotamer Ensemble Sampling Tool (CREST) with the Commandline Energetic SOrting (CENSO). This combined computational and NMR-based approach offers a robust framework for the conformational analysis of cyclic peptides.

A comprehensive solute-medium interaction model for anisotropic NMR data prediction

Prediction of order parameters and hence anisotropic NMR data of a molecule dissolved in a dilute alignment medium can provide a unique means of solving certain challenging structural elucidation problems. Here, a comprehensive prediction model based on solute-medium interactions is developed featuring the use of medium-specific parameters as only fitting variables to depict intermolecular interactions in an alignment system, including repulsive, dispersive, and electrostatic interactions between the solute and the medium polymer, as well as their interactions with implicit solvent. This model is implemented on the framework of a surface decomposition method previously designed to formalize medium-induced solute alignment without a priori knowledge of the medium structure. Having descriptors for all interactions, the new model performs significantly better than the original hard-body model when the medium and solute exhibit strong electrostatic and dispersion interactions. This model offers a general method to extract the physical properties of a medium polymer by combining the experimental NMR data of different model compounds and then use these properties to predict the NMR data of other molecules of interest.

Discovery of potent antiosteoporotic cyclic depsipeptides with an unusual nitrile hydroxy acid from Microascus croci

Two cyclic octadepsipeptides, microascusins A and B (1 and 2), were identified from the marine sponge-associated Microascus croci IMB19-064 co-cultivated with Escherichia coli. Their structures and conformations in solution were determined by comprehensive spectroscopic data analysis. The absolute configurations of amino and hydroxy acids were determined by the advanced Marfey's and O-Marfey's methods, respectively, as well as chiral-phase HPLC analysis. Microascusins A (1) and B (2) represent a new type of cyclic octadepsipeptides characterized by the presence of the unique hydroxy acid l-2-hydroxy-4-cyanobutyric acid. Compound 1 exhibited potent in vitro antiosteoporotic activity with dual regulation effects of promoting the osteoblast-mediated bone formation as well as inhibiting the RANKL-induced osteoclast differentiation at the concentrations of 0.1-10 nM. Further in vivo study showed that compound 1 could improve bone mineralization after dexamethasone-induced bone damage in zebrafish through up-regulating the expression of the osteoblast-specific genes Bmp2 and Oc.

Talaromides A-C, Bioactive Cyclic Heptapeptides from Talaromyces siglerae Isolated from a Marine Sponge

Three new cyclic heptapeptides, talaromides A-C (1-3), were isolated from cultures produced by the fungus Talaromyces siglerae (Ascomycota), isolated from an unidentified sponge. The structures, featuring an unusual proline-anthranilic moiety, were elucidated by analysis of spectroscopic data and chemical transformations, including the advanced Marfey's method and GITC derivatization. Talaromides A and B inhibited migration activity against PANC-1 human pancreatic cancer cells without significant cytotoxicity.

Ultra-clean pure shift NMR with optimal water suppression for analysis of aqueous pharmaceutical samples

Pure shift NMR experiments greatly enhance spectral resolution by collapsing multiplet structures into singlets and, with water suppression, can be used for aqueous samples. Here, we combine ultra-clean pure-shift NMR (SAPPHIRE) with two different internally encoded water suppression schemes to achieve optimal performance for small molecule and macrocyclic peptide pharmaceuticals in water and acetonitrile-water mixtures.

Update on fungal lipid biosynthesis inhibitors as antifungal agents

Fungal diseases today represent a world-wide problem. Poor hygiene and decreased immunity are the main reasons behind the manifestation of this disease. After COVID-19, an increase in the rate of fungal infection has been observed in different countries. Different classes of antifungal agents, such as polyenes, azoles, echinocandins, and anti-metabolites, as well as their combinations, are currently employed to treat fungal diseases; these drugs are effective but can cause some side effects and toxicities. Therefore, the identification and development of newer antifungal agents is a current need. The fungal cell comprises many lipids, such as ergosterol, phospholipids, and sphingolipids. Ergosterol is a sterol lipid that is only found in fungal cells. Various pathways synthesize all these lipids, and the activities of multiple enzymes govern these pathways. Inhibiting these enzymes will ultimately impede the lipid synthesis pathway, and this phenomenon could be a potential antifungal therapy. This review will discuss various lipid synthesis pathways and multiple antifungal agents identified as having fungal lipid synthesis inhibition activity. This review will identify novel compounds that can inhibit fungal lipid synthesis, permitting researchers to direct further deep pharmacological investigation and help develop drug delivery systems for such compounds.

Understanding fluconazole tolerance in Candida albicans: implications for effective treatment of candidiasis and combating invasive fungal infections

OBJECTIVES

Fluconazole (FLC) tolerant phenotypes in Candida species contribute to persistent candidemia and the emergence of FLC resistance. Therefore, making FLC fungicidal and eliminating FLC tolerance are important for treating invasive fungal diseases (IFDs) caused by Candida species. However, the mechanisms of FLC tolerance in Candida species remain to be fully explored.

METHODS

This review discusses the high incidence of FLC tolerance in Candida species and the importance of successfully clearing FLC tolerance in treating candidiasis. We further define and characterize FLC tolerance in C. albicans.

RESULTS

This review identifies global factors affecting FLC tolerance and suggest that FLC tolerance is a strategy of C. albicans response to FLC damage whose mechanism differs from FLC resistance.

CONCLUSIONS

This review highlights the significance of the cell membrane and cell wall integrity in FLC tolerance, guiding approaches to combat IFDs caused by Candida species..

Complex peptide macrocycle optimization: combining NMR restraints with conformational analysis to guide structure-based and ligand-based design

Systematic optimization of large macrocyclic peptide ligands is a serious challenge. Here, we describe an approach for lead-optimization using the PD-1/PD-L1 system as a retrospective example of moving from initial lead compound to clinical candidate. We show how conformational restraints can be derived by exploiting NMR data to identify low-energy solution ensembles of a lead compound. Such restraints can be used to focus conformational search for analogs in order to accurately predict bound ligand poses through molecular docking and thereby estimate ligand strain and protein-ligand intermolecular binding energy. We also describe an analogous ligand-based approach that employs molecular similarity optimization to predict bound poses. Both approaches are shown to be effective for prioritizing lead-compound analogs. Surprisingly, relatively small ligand modifications, which may have minimal effects on predicted bound pose or intermolecular interactions, often lead to large changes in estimated strain that have dominating effects on overall binding energy estimates. Effective macrocyclic conformational search is crucial, whether in the context of NMR-based restraints, X-ray ligand refinement, partial torsional restraint for docking/ligand-similarity calculations or agnostic search for nominal global minima. Lead optimization for peptidic macrocycles can be made more productive using a multi-disciplinary approach that combines biophysical data with practical and efficient computational methods.