Synthesis of N-hydroxy peptides: chemical ligation of O-acyl hydroxamic acids

[process--see text] A novel chemical ligation process is described that results in the construction of N-hydroxy peptides.     

Diverse catalytic systems for nitrogen-heterocycle formation from O-acyl ketoximes

O-Acyl ketoximes has been proven to be versatile building blocks for practical construction of N-heterocycles. In the last few years, diverse catalytic systems have been discovered to enable efficient transformations of O-acyl ketoximes to a range of nitrogen-heterocycles. Herein, we summarized our recent examples of novel nitrogen-heterocycle formation with new function findings of O-acyl ketoximes through facile aerobic copper catalysis, metal-free NO bond activation, multi-component assembly, and bis-annulations. From the green chemistry perspective, these works represent efficient methods with high atom economy, high selectivity, and minimized chemical waste. These findings also complement well to the previous mainly copper-based catalytic systems and more importantly enrich the oxime chemistry in organic synthesis.     

Traceless solid-phase synthesis of 3-substituted isoxazoles from polystyrene-supported vinyl selenide

A novel facile procedure for traceless solid-phase synthesis of 3-substituted isoxazoles in good yields and with excellent purities using polymer-supported vinyl selenide has been developed.     

Multiple isomers and protonation sites of the phenylalanine/serine dimer

Our investigation of the phenylalanine/serine (Phe/Ser) protonated dimer suggests that the intermolecular interaction between the two amino acids is more complex than could have been anticipated from previous studies of similar systems. Isomer-specific infrared (IR) spectra, recorded at an internal temperature of ~10 K, demonstrate the presence of at least five isomers with nonzwitterionic structures. Moreover, isotopic substitution experiments provide evidence for different protonation sites among these isomers.     

Spatial localization of ligand binding sites from electron current density surfaces calculated from NMR chemical shift perturbations

Rapid, accurate structure determination of protein-ligand complexes is an essential component in structure-based drug design. We have developed a method that uses NMR protein chemical shift perturbations to spatially localize a ligand when it is complexed with a protein. Chemical shift perturbations on the protein arise primarily from the close proximity of electron current density from the ligand. In our approach the location of the center of the electron current density for a ligand aromatic ring was approximated by a point-dipole, and dot densities were used to represent ligand positions that are allowed by the experimental data. The dot density is increased in the region of space that is consistent for the most data. A surface can be formed in regions of the highest dot density that correlates to the center of the ligand aromatic ring. These surfaces allow for the rapid evaluation of ligand binding, which is demonstrated on a model system and on real data from HCV NS3 protease and HCV NS3 helicase, where the location of ligand binding can be compared to that obtained from difference electron density from X-ray crystallography.     

Quantum chemical treatment of active sites in zeolites

A short review on the quantum chemical study of the Bronsted and Lewis acid sites (BAS and LAS) is presented. Various factors that strongly influence the power of BAS in zeolites are considered. Different possible ways of LAS formation in zeolites are dicussed. The probable mechanism of selective oxidation in FeHZSM-5 is considered and the resulting active site structure is calculatedab initio. The initial step of hydrogen peroxide activation in Ti-silicalite is studied and the scale of the energy of structural deformation to proceed during the reaction is evaluated.     

Synthesis of Schiff bases from 1-naphthylamine and vanillin, vanillal, and their O-acyl derivatives

Previously unknown Schiff bases were synthesized by the condensation of 1-naphthylamine with vanillin, vanillal, and their O-acyl derivatives in ethanol.     

Gaussian mapping of chemical fragments in ligand binding sites

We present a new approach to automatically define a quasi-optimal minimal set of pharmacophoric points mapping the interaction properties of a user-defined ligand binding site. The method is based on a fitting algorithm where a grid of sampled interaction energies of the target protein with small chemical fragments in the binding site is approximated by a linear expansion of Gaussian functions. A heuristic approximation selects from this expansion the smallest possible set of Gaussians required to describe the interaction properties of the binding site within a prespecified accuracy. We have evaluated the performance of the approach by comparing the computed Gaussians with the positions of aromatic sites found in experimental protein-ligand complexes. For a set of 53 complexes, good correspondence is found in general. At a 95% significance level, approximately 65% of the predicted interaction points have an aromatic binding site within 1.5 A. We then studied the utility of these points in docking using the program DOCK. Short docking times, with an average of approximately 0.18 s per conformer, are obtained, while retaining, both for rigid and flexible docking, the ability to sample native-like binding modes for the ligand. An average 4-5-fold speed-up in docking times and a similar success rate is estimated with respect to the standard DOCK protocol.     

Recognizing five molecular ligand-binding sites with similar chemical structure

Accurate identification of ligand-binding sites and discovering the protein–ligand interaction mechanism are important for understanding proteins' functions and designing new drugs. Meanwhile, accurate computational prediction and mechanism research are two grand challenges in proteomics. In this article, ligand-binding residues of five ligands (ATP, ADP, GTP, GDP, and NAD) are predicted as a group, due to their similar chemical structures and close biological function relations. The data set of binding sites by five ligands (ATP, ADP, GTP, GDP, and NAD) are collated from Biolip database. Then, five features, containing increment of diversity value, matrix scoring value, auto-covariance, secondary structure information, and surface accessibility information are used in binding site predictions. The support vector machine (SVM) model is used with the five features to predict ligand-binding sites. Finally, prediction results are tested by fivefold cross validation. Accuracy (Acc) of five ligands (ATP, ADP, GTP, GDP, and NAD) achieves 77.4%, 71.2%, 82.1%, 82.9%, and 85.3%, respectively; and Matthew correlation coefficient (MCC) of the above five ligands achieves 0.549, 0.424, 0.643, 0.659, and 0.702, respectively. The research result shows that for ligands with similar chemical structures, microenvironment of their binding sites and their sensitivities to features are similar, while, differences of their ligand-binding properties exist at the same time. © 2019 Wiley Periodicals, Inc.     

Identification of the estrogen receptor Cd-binding sites by chemical modification

The widely reported interactions of the estrogen receptor (ER) with endocrine disrupting chemicals (EDCs) present in the environment gave raise to public concern and led to a number of screening and testing initiatives on the international level. Recent studies indicated that certain heavy metals, including cadmium, can mimic the effects of the endogenous estrogen receptor agonist 17beta-estradiol, and lead to estrogen receptor activation. Previous studies of the chimeric proteins, which incorporate the ligand-binding domain of the human ER, identified Cys 381, Cys 447, Glu 523, His 524 and Asp 538 as possible sites of interactions with cadmium. In the present study we utilized the rainbow trout ER ligand-binding domain fused to glutathione-S-transferase, and used Cd-shielding against various types of chemical modification of the fusion protein to study non-covalent interactions between the ER and Cd. The distribution of exposed and shielded residues allowed to identify amino acid residues involved in the interaction. Our data indicated preferential protection of Cys groups by cadmium, suggesting their involvement in the interaction. This supports data found in the literature on the strong binding affinity of the thiol group towards metals. However, not all Cys in the fusion protein sequence were protected against chemical modification, illustrating the importance of their chemical environment. In general, the location of rtER-LBD Cys residues implicated in Cd interactions did not confirm assignments made by alanine-scanning mutagenesis for the hER, probably due to differences in experimental setup and fusion proteins used. The involvement of other functional groups such as carboxylic acids in the Cd interactions, though not confirmed, can not be completely ruled out due to the general limitations of the chemical modification approach discussed in detail. Suggestions for an improved experimental setup were made.     

Quantum chemical modeling of enzyme active sites and reaction mechanisms

Density functional methods, in particular the B3LYP functional, together with the explosive enhancement of computational power, have in the last 5 years or so made it possible to model enzyme active sites and reaction mechanisms in a quite realistic way. Many mechanistic problems have indeed been addressed and solved. This review gives a brief account of the methods and models used to study enzyme active sites and their reaction mechanisms using quantum chemical methods. Examples are given from our recent work in this field. Future perspectives of the field are discussed.     

Qualitative analysis of the fluorophosphonate-based chemical probes using the serine hydrolases from mouse liver and poly-3-hydroxybutyrate depolymerase (PhaZ) from Bacillus thuringiensis

The serine hydrolase family consists of more than 200 members and is one of the largest enzyme families in the human genome. Although up to 50?% of this family remains unannotated, there are increasing evidences that activities of certain serine hydrolases are associated with diseases like cancer neoplasia, invasiveness, etc. By now, several activity-based chemical probes have been developed and are applied to profile the global activity of serine hydrolases in diverse proteomes. In this study, two fluorophosphonate (FP)-based chemical probes were synthesized. Further examination of their abilities to label and pull down serine hydrolases was conducted. In addition, the poly-3-hydroxybutyrate depolymerase (PhaZ) from Bacillus thuringiensis was demonstrated as an appropriate standard serine hydrolase, which can be applied to measure the labeling ability and pull-down efficiency of FP-based probes. Furthermore, mass spectrometry (MS) was used to identify the serine residue that covalently bonded to the active probes. Finally, these FP-based probes were shown capable of establishing the serine hydrolase profiles in diverse mouse tissues; the serine hydrolases pulled down from mouse liver organ were further identified by MS. In summary, our study provides an adequate method to evaluate the reactivity of FP-based probes targeting serine hydrolases.

Asymmetric synthesis of the carbapenam core from serine

The stereospecific synthesis of the functionalized carbapenam core 16 from the serine-derived trisubstituted pyrrolidine 9 is reported. The synthetic strategy relies on synthesizing an appropriately functionalized pyrrolidine, followed by an intramolecular azetidone formation utilizing a modified Mukiyama reagent. The efficient one-pot conversion of the benzenesulfonamide-protected pyrrolidine 9 to the Cbz-protected pyrrolidine 10 is also reported.     

Relaxation-assisted separation of chemical sites in NMR spectroscopy of static solids

We discuss the potential use of relaxation times toward the resolution of inequivalent chemical sites in the NMR spectroscopy of powdered or disordered samples. This proposal is motivated by the significant differences that can often be detected in the relaxation behavior of sites in solids, particularly when focusing on NMR observations of quadrupolar nuclei possessing different coordination and/or dynamic environments. It is shown that in these cases the implementation of a non-negative least-squares analysis on relaxation data sets enables the bidimensional resolution of overlapping powder line shapes, even when dealing with static samples. In combination with signal-enhancement methodologies such as the quadrupolar Carr-Purcell Meiboom-Gill train, such relaxation-assisted separations open up valuable routes toward the high-resolution characterization of systems involving insensitive (e.g., low-gamma) nuclei. The principles and limitations of the 2D NMR approach resulting from these considerations are discussed, and their potential is exemplified with a variety of static and spinning investigations. Their extension to other nuclear systems where spectral resolution is problematic, such as protons in organic solids, is also briefly considered.     

EUDOC: a computer program for identification of drug interaction sites in macromolecules and drug leads from chemical databases

The completion of the Human Genome Project, the growing effort on proteomics, and the Structural Genomics Initiative have recently intensified the attention being paid to reliable computer docking programs able to identify molecules that can affect the function of a macromolecule through molecular complexation. We report herein an automated computer docking program, EUDOC, for prediction of ligand-receptor complexes from 3D receptor structures, including metalloproteins, and for identification of a subset enriched in drug leads from chemical databases. This program was evaluated from the standpoints of force field and sampling issues using 154 experimentally determined ligand-receptor complexes and four "real-life" applications of the EUDOC program. The results provide evidence for the reliability and accuracy of the EUDOC program. In addition, key principles underlying molecular recognition, and the effects of structural water molecules in the active site and different atomic charge models on docking results are discussed. Copyright 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1750-1771, 2001     

Reinvestigation of a polymer-supported chiral auxiliary derived from serine

Due to concerns over the reliability of the reported synthesis and application of a polymer-supported chiral auxiliary by our group, we have reinvestigated the preparation of the polymer. Analysis of the resin has now been carried out by MAS ¹³C NMR spectroscopy, and as a result we now withdraw our previous claim of success.