Computational Design of Novel Allosteric Inhibitors for Plasmodium falciparum DegP

The serine protease, DegP exhibits proteolytic and chaperone activities, essential for cellular protein quality control and normal cell development in eukaryotes. The P. falciparum DegP is essential for the parasite survival and required to combat the oscillating thermal stress conditions during the infection, protein quality checks and protein homeostasis in the extra-cytoplasmic compartments, thereby establishing it as a potential target for drug development against malaria. Previous studies have shown that diisopropyl fluorophosphate (DFP) and the peptide SPMFKGV inhibit E. coli DegP protease activity. To identify novel potential inhibitors specific to PfDegP allosteric and the catalytic binding sites, we performed a high throughput in silico screening using Malaria Box, Pathogen Box, Maybridge library, ChEMBL library and the library of FDA approved compounds. The screening helped identify five best binders that showed high affinity to PfDegP allosteric (T0873, T2823, T2801, {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, CD00811) and the catalytic binding site (T0078L, T1524, T2328, BTB11534 and 552691). Further, molecular dynamics simulation analysis revealed {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, BTB11534 as the best hits forming a stable complex. WaterMap and electrostatic complementarity were used to evaluate the novel bio-isosteric chemotypes of {"type":"entrez-protein","attrs":{"text":"RJC02337","term_id":"1480409465","term_text":"RJC02337"}}RJC02337, that led to the identification of 231 chemotypes that exhibited better binding affinity. Further analysis of the top 5 chemotypes, based on better binding affinity, revealed that the addition of electron donors like nitrogen and sulphur to the side chains of butanoate group are more favoured than the backbone of butanoate group. In a nutshell, the present study helps identify novel, potent and Plasmodium specific inhibitors, using high throughput in silico screening and bio-isosteric replacement, which may be experimentally validated.     

Phosphono Bisbenzguanidines as Irreversible Dipeptidomimetic Inhibitors and Activity‐Based Probes of Matriptase‐2

Matriptase‐2, a type II transmembrane serine protease, plays a key role in human iron homeostasis. Inhibition of matriptase‐2 is considered as an attractive strategy for the treatment of iron‐overload diseases, such as hemochromatosis and β‐thalassemia. In the present study, synthetic routes to nine dipeptidomimetic inactivators were developed. Five active compounds ( 41 – 45 ) were identified and characterized kinetically as irreversible inhibitors of matriptase‐2. In addition to a phosphonate warhead, these dipeptides possess two benzguanidine moieties as arginine mimetics to provide affinity for matriptase‐2 by binding to the S1 and S3/S4 subpockets, respectively. This binding mode was strongly supported by covalent docking analysis. Compounds 41 – 45 were obtained as mixtures of two diastereomers and were therefore separated into the single epimers. Compound 45 A , with S configuration at the N‐terminal amino acid and R configuration at the phosphonate carbon atom, was the most potent matriptase‐2 inactivator with a rate constant of inactivation of 2790 m ^?1 s^?1 and abolished the activity of membrane‐bound matriptase‐2 on the surface of intact cells. Based on the chemotyp of phosphono bisbenzguanidines, the design and synthesis of a fluorescent probe ( 51 A ) by insertion of a coumarin label is described. The in‐gel fluorescence detection of matriptase‐2 was demonstrated by applying 51 A as the first activity‐based probe for this enzyme.     

Limiting the Number of Potential Binding Modes by Introducing Symmetry into Ligands: Structure‐Based Design of Inhibitors for Trypsin‐Like Serine Proteases

In the absence of X‐ray data, the exploration of compound binding modes continues to be a challenging task. For structure‐based design, specific features of active sites in different targets play a major role in rationalizing ligand binding characteristics. For example, dibasic compounds have been reported as potent inhibitors of various trypsin‐like serine proteases, the active sites of which contain several binding pockets that can be targeted by cationic moieties. This results in several possible orientations within the active site, complicating the binding mode prediction of such compounds by docking tools. Therefore, we introduced symmetry in bi‐ and tribasic compounds to reduce conformational space in docking calculations and to simplify binding mode selection by limiting the number of possible pocket occupations. Asymmetric bisbenzamidines were used as starting points for a multistage and structure‐guided optimization. A series of 24 final compounds with either two or three benzamidine substructures was ultimately synthesized and evaluated as inhibitors of five serine proteases, leading to potent symmetric inhibitors for the pharmaceutical drug targets matriptase, matriptase‐2, thrombin and factor Xa. This study underlines the relevance of ligand symmetry for chemical biology.     

Serine‐Selective Aerobic Cleavage of Peptides and a Protein Using a Water‐Soluble Copper–Organoradical Conjugate

The site‐specific cleavage of peptide bonds is an important chemical modification of biologically relevant macromolecules. The reaction is not only used for routine structural determination of peptides, but is also a potential artificial modulator of protein function. Realizing the substrate scope beyond the conventional chemical or enzymatic cleavage of peptide bonds is, however, a formidable challenge. Here we report a serine‐selective peptide‐cleavage protocol that proceeds at room temperature and near neutral pH value, through mild aerobic oxidation promoted by a water‐soluble copper–organoradical conjugate. The method is applicable to the site‐selective cleavage of polypeptides that possess various functional groups. Peptides comprising D ‐amino acids or sensitive disulfide pairs are competent substrates. The system is extendable to the site‐selective cleavage of a native protein, ubiquitin, which comprises more than 70 amino acid residues.     

Access to the Aeruginosin Serine Protease Inhibitors through the Nucleophilic Opening of an Oxabicyclo[2.2.1]heptane: Total Synthesis of Microcin SF608

Serine proteases play key roles in many biological processes and are associated with several human diseases such as thrombosis or cancer. During the search for selective inhibitors of serine proteases, a family of linear peptides named the aeruginosins was discovered in marine cyanobacteria. We herein report an entry route into the synthetically challenging core fragment of these natural products. Starting from the common oxabicyclic building block 11 , we accessed the octahydroindole core of the aeruginosins, exemplified by the total synthesis of microcin SF608 ( 2 ). Key to the synthetic strategy is a highly efficient nucleophilic opening of an oxabicyclo[2.2.1]heptane producing the hydroindole motif of microcin SF608. Moreover, during the synthetic efforts we have observed an unusual regioselective epoxide reduction. Detailed experimental studies of this reaction led us to propose a mechanistic rationale involving intramolecular hydrogen atom delivery by a carbamate NH group to control the regioselectivity of the homolytic epoxide cleavage.     

Interaction mechanism between serine functional groups and single‐walled carbon nanotubes

The adsorption of serine (Ser) on the (8, 8) and (10, 0) single‐walled carbon nanotubes (CNTs) was studied by density‐functional tight‐binding calculations. For Ser, the two most stable configurations were chosen to research the interactions with the CNT. It found that the most stable Ser/(8, 8) and Ser/(10, 0) complexes have similar structures, in which the amino group, carboxyl, and side chain of serine directly interact with the CNT. The binding energies, charge transfer properties, the shortest distance (d₁) between the H atom and the corresponding benzene ring, distance (d₂) between the H atom and the center of benzene ring (HCB), and the angle (α) between the HCB line and the corresponding benzene ring plane were analyzed to explain the interactions. Because of the interaction, the ?CH of the main chain runs away from the surface of CNT, and the angles between the ?C?H bond of the main chain and the carboxyl, the amino group, and the side chain of the Ser become small. The strain energies and changes of angles and dihedral angles of the serine after adsorption were analyzed to illustrate the deformation. The interactions of Ser with the CNT were further illustrated by calculating the molecular orbitals and the partial density of states of the stable complexes. We further compared the binding energies of armchair (n, n) and zigzag (n, 0) CNTs to investigate the diameter dependence of binding energies. Copyright © 2015 John Wiley & Sons, Ltd.     

Recyclable Siloxy Serine Organocatalyst for the Direct Asymmetric Mannich Reactions in Ionic Liquids

A recyclable siloxy-L-serine organocatalyst has been developed to catalyze the asymmetric direct three-component Mannich reactions in ionic liquid hmim[PF₆], furnishing the β-amino carbonyl scaffold in high enantio- and diastereoselectivities. The direct Mannich reaction between a selection of aromatic aldehydes and ketones resulted in good yields and high enantioselectivities.

Synthesis of Sulfonylurea Derivatives Used as Oral Antidiabetics by the Selenium-Assisted Carbonylation Using Carbon Monoxide with Sulfur

Sulfonylurea derivatives including useful antidiabetics (Tolbutamide, Chlorpropamide) were synthesized in good yields from benzene-sulfonamides with thiocarbamates in the presence of DBU. Thiocarbamates were prepared by the selenium-assisted carbonylation of primary amines with carbon monoxide, sulfur, and methyl iodide under mild conditions.