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.     

The search for a new model structure of β-Factor XIIa

We present the search for a new model of -factor XIIa, a blood coagulation enzyme, with an unknown experimental 3D-structure. We decided to build not one but three different models using different homologous proteins as well as different techniques and different modellers. Additional studies, including extensive molecular dynamics simulations on the solvated state, allowed us to draw several conclusions concerning homology modelling, in general, and -factor XIIa, in particular.     

The Self-catalytic Esterification Reaction of O-Phosphoryl Serine Derivative

O-Phosphoryl serine derivative can perform serf-catalytic esterification reaction in the mixture of CH3OH and CHCl3 at the room temperature. The phosphoryl group participation was the key step of the esterification. This type of reactions were proposed through an intermediate of mixed phosphoric-carboxylic anhydride that might provide a clue to the function of the phosphoryl group in the phosphorylated enzymes and in the prebiotic synthesis of protein.     

O-二异丙氧磷酰基丝氨酸(或苏氨酸或酪氨酸)的合成

介绍一种简单方便地合成O-二异丙氧磷酰基丝氨酸(或苏氨酸或酪氨酸)的方法.其中O-二异丙氧磷酰基-L-丝氨酸(或苏氨酸)可从对应的N-磷酰化-L-丝氨酸(或苏氨酸)利用磷酰基N→0迁移的性质并在超声辅助下合成,而N-二异丙氧磷酰基-L-丝氨酸(或苏氨酸)的合成由L-丝氨酸(或苏氨酸)在次氯酸钠的水溶液中高收率地获得.O-二异丙氧磷酰基酪氨酸的合成可通过铜盐同时保护氨基和羧基,使用二异丙基磷酰氯为磷酰化试剂磷酰化,用硫化氢脱铜保护制备.     

Nucleophilic proteolytic antibodies

Proteolytic antibodies appear to utilizecatalytic mechanisms akin to nonantibody serine proteases, assessed from mutagenesis and protease-inhibitor studies. The catalytic efficiency derives substantially from the ability to recognize the ground state with high affinity. Because the proteolytic activity is germline-encoded, catalysts with specificity for virtually any target polypeptide could potentially be developed by applying appropriate immunogens and selection strategies. Analysis of transition-state stabilizing interactions suggests that chemical reactivity ofactive-site serine residues is an important contributor to catalysis. A prototype antigen analog capable of reacting covalently with nucleophilic serine residues permitted enrichment of the catalysts from a phage-displayed lupus light-chain library. Further mechanistic developments in understanding proteolytic antibodies may lead to the isolation of catalysts suitable for passive immunotherapy of major diseases, and elicitation of catalytic immunity as a component of prophylactic vaccination.     

Toward direct determination of conformations of protein building units from multidimensional NMR experiments. V. NMR chemical shielding analysis of N-formyl-serinamide,a model for polar side-chain containing peptides

Knowledge of chemical shift-structure relationships could greatly facilitate the NMR chemical shift assignment and structure refinement processes that occur during peptide/protein structure determination via NMR spectroscopy. To determine whether such correlations exist for polar side chain containing amino acid residues the serine dipeptide model, For-L-Ser-NH(2), was studied. Using the GIAO-RHF/6-31+G(d) and GIAO-RHF/TZ2P levels of theory the NMR chemical shifts of all hydrogen ((1)H(N), (1)H(alpha), (1)H(beta1), (1)H(beta2)), carbon ((13)C(alpha), (13)C(beta), (13)C') and nitrogen ((15)N) atoms have been computed for all 44 stable conformers of For-L-Ser-NH(2). An attempt was made to establish correlation between chemical shift of each nucleus and the major conformational variables (omega(0), phi, psi, omega(1), chi,(1) and chi(2)). At both levels of theory a linear correlation can be observed between (1)H(alpha)/phi, (13)C(alpha)/phi, and (13)C(alpha)/psi. These results indicate that the backbone and side-chain structures of For-L-Ser-NH(2) have a strong influence on its chemical shifts.     

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.     

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.

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.