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.     

Computer modelling of the conformational equilibrium of 2-and 2,5,5-substituted 1,3,2-dioxaborinanes

Empirical, semiempirical, and nonempirical quantum-chemical methods were used to study the conformational equilibrium of 2,5,5-substituted 1,3,2-dioxaborinanes. The sofa invertomers were found to correspond to the local and global minima on the potential energy surface. The position of the equilibrium between these forms is a function of the substituents at C₍₅₎ of the heterocycle. __________ Translated from Khimiya Geterotsiklicheskikh Soedinenii, No. 12, pp. 1860–1865, December, 2007.     

Conductometric study of cationic and anionic complexes in propylene carbonate

Conductivity data are used to determine thermodynamic complex formation constants for cases in which both the initial electrolyte and the complexed electrolyte form ion pairs. Using the method described in the text, the complex formation constants of Li⁺, Na⁺ and K⁺ with the crown ether 18-crown-6 and of Li⁺ with the ligand triphenylphosphine oxide in propylene carbonate have been evaluated from conductance data. The complexation of AgBr in propylene carbonate solutions of n-etrabutylammonium bromide has also been studied by the measurement of molar conductivities. The results of these studies indicate that ion pairing should not be neglected, even in high permittivity solvents such as propylene carbonate, and that the ion pair association constants correlate well with structural studies on cation-crown ether molecular conformations.     

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.     

Coulombic Basis for Relative Hydrogen-Bonding Basicities and Conformational Energies of Tertiary Amine Oxides and Phosphine Oxides

The structures, energies, and natural atomic charges of 2-dimethylaminophenol oxide, 2-Me₂N-(O)C₆H₄OH, and 2-dimethylphosphinylphenol, 2-Me₂P(O)C₆H₄OH, in three different conformations were computed at the ab initio MP2/6-31G* level. Computed natural charges indicate distributions of electron density in amine oxides and phosphine oxides that are quite different from what is normally assumed on the basis of the formal charges in the usual representations of these compounds. The charges on nitrogen and phosphorus in these compounds are typically computed to be approximately zero on nitrogen and +2 on phosphorus, and the oxygen is considerably more negative in the phosphine oxide than in the amino oxide. Electronegativity differences thus play a larger role and formal charges a smaller one in determining atomic charges in these compounds than is generally believed. Despite the more negative oxygen in phosphine oxides, amine oxides are computed to be considerably more basic when participating in hydrogen bonding. Calculations treating the computed natural charges on these six conformations as point charges for classical approximations of the coulombic energies support the idea that the quantum mechanically computed relative energies are largely determined by coulombic interactions.     

Possible conformations and relative stability of the 7-membered ring in 1α,5β,6,7α(H)-and 1β,5α,6,7α(H)-guai-11(13)-en-6,12-olides

Stereoisomers of 1,5,6,7(H)- and 1,5,6,7(H)-guai-11(13)-en-6,12-olides are calculated using molecular mechanics. The possibility of forming various conformations in the 7-membered ring is examined as a function of the fusion to the 5-membered C-ring. The effect of the methyl orientation on the conformation of the 7-membered ring and the relative stability of the conformers are discussed.Insitute of Phytochemistry, Karaganda, fax (3212)-43-37-73. Translated from Khimiya Prirodnykh Soedinenii, No. 1, pp. 54–56, January–February, 2000.     

Intramolecular co-operative hydrogen bond in calix[<Emphasis Type="Italic">n</Emphasis>]arenes (<Emphasis Type="Italic">n</Emphasis> = 4, 6, 8) bearing bulky substituents

Based on the Fourier transform IR spectroscopy together with the published NMR and X-ray data, it was shown that cyclic co-operative intramolecular hydrogen bond in calix[n]arene (n = 4, 6, 8) molecules is mainly responsible for their conformational state irrespective of the presence or absence of bulky substituents at the upper rim of the molecules. In accordance with the size of a macrocycle (n = 4, 6, 8), the stable conformation, secured by such a hydrogen bond, constitutes a cone, a pinched cone, and a pleated loop, respectively. The new, potentially competing system of hydrogen bonds in calix[6]arenes with 3-carboxymethyl-1-adamantyl substituents does not affect the conformational state of the macrocycle and its H-bonding. Six carboxy groups at the upper rim form in pairs three cyclic dimers, which does not disturb the hydrogen bonds of the hydroxy groups and the conformation of the macrocycle. In addition, the cavity of the molecule is considerably enlarged. The removal or rearrangement of the guest molecules in the solid calixarene by heating up to 180 °C only slightly affects the conformational state of macrocycles bearing bulky substituents, whereas in calixarenes devoid of such substituents, the similar procedure leads to somewhat of a distortion of the macrocycles (judging from the IR spectral indications of hydrogen bonding). Published in Russian in Izvestiya Akademii Nauk. Seriya Khimicheskaya, No. 6, pp. 1062–1068, June, 2007.     

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.