Simulation Analysis of Occupancy Rates of Baicalein， Quercetin and Galangin on Target Sites of Xanthine Oxidase / 中国实验方剂学杂志

Objective:To simulate the occupancy rates of baicalein， quercetin and galangin on the target sites of xanthine oxidase <italic>in vivo</italic>. Method:In this experiment， the half inhibitory concentration （IC₅₀） of febuxostat， baicalein， quercetin and galangin against xanthine oxidase were determined by <italic>in vitro</italic> enzymatic reaction. Binding free energy was predicted by molecular docking technology and their association rate constant （k_on） and dissociation rate constant （k_off） were determined by surface plasmon resonance technology. Based on measured binding kinetic parameters （k_on and k_off） and extracted pharmacokinetic data， the target occupancy model <italic>in vivo</italic> was established. Result:The IC₅₀values of febuxostat， baicalein， quercetin and galangin were 0.002 7， 1.63， 0.38， 1.59 µmol·L^-1， respectively. The IC₅₀ of febuxostat was very close to that reported in the literature. The predicted curve of target occupancy rate <italic>in vivo</italic> of febuxostat was consistent with its duration of clinical efficacy. When single intragastric administration of long-circulating liposomes of quercetin with dose of 100 mg·kg^-1 in rats， the time of target occupancy rate >70% <italic>in vivo</italic> lasted for about 3.9 h. When rats were orally administered baicalein and galangin with dose of 200 mg·kg^-1， the time of target occupancy rate >50% <italic>in vivo </italic>lasted for about 10 h and 1.7 h， respectively. Conclusion:The prediction model of xanthine oxidase target occupancy constructed by drug target binding kinetics and <italic>in vivo</italic> pharmacokinetic curves can effectively evaluate the <italic>in vivo</italic> inhibitory activity of compounds against the target.

Study on drug-target binding kinetics profiles of flavonoids in Chrysanthemum morifolium and xanthine oxidase / 中国中药杂志

Based on the target occupancy mathematical model, the binding kinetic process of potential active ingredients of lowering uric acid in Chrysanthemum morifolium with xanthine oxidase(XOD) was evaluated. The potential active ingredients of lowering uric acid in Ch. morifolium were screened by UPLC-Q-Exactivems MS technology, reference substance identification and in vitro enzymatic kinetics experiments. The binding kinetic parameters of xanthine oxidase and potential inhibitor in Ch. morifolium were determined by surface plasma resonance(SPR). The verified mathematical model of the XOD target occupancy evaluated the kinetic binding process of inhibitors and xanthine oxidase in vivo. According to UPLC-Q-Exactive MS and reference substance identification, 39 potential uric acid-lowering active ingredients in Ch. morifolium extracts were identified and the inhibitory activities of 23 compounds were determined. Three potential xanthine oxidase inhibitors were screened, namely genistein, luteolin, and apigenin. whose IC_(50 )were 1.23, 1.47 and 1.59 μmol·L~(-1), respectively. And the binding rate constants(K_(on)) were 1.26×10~6, 5.23×10~5 and 6.36×10~5 mol·L~(-1)·s~(-1), respectively. The dissociation rate constants(K_(off)) were 10.93×10~(-2), 1.59×10~(-2), and 5.3×10~(-2 )s~(-1), respectively. After evaluation by different administration methods, the three selected compounds can perform rapid and sustained inhibition of xanthine oxidase in vivo under combined administration. This study comprehensively evaluated the target occupancy process of three effective components in different ways of administration in vivo by UPLC-MS, concentration-response method, SPR technology and xanthine oxidase target occupancy model, which would provide a new research idea and method for screening active ingredients in traditional Chinese medicine.

On the molecular drug design from viewpoint of precision medicine / 药学学报

Precision medicine (PM) involves the application of "omics" analysis and system biology to analyze the cause of disease at the molecular level for targeted treatments of individual patient. Based on the targeted treatment PM is closely related to pharmaceuticals, which, as a therapeutic means and supply front, mainly embody the two aspects:drug discovery/development, and clinical administration. Innovation of new molecular entities with safety and specific efficacy is the prerequisite and guarantee for the PM practice; on the other hand, the outcome and clues in clinical PM feedback to new drug research. PM and drug research/application are interdependent and promote each other. Aimed at precision medicine, drug discovery and development involve well-known contents:the discovery and validation of targets, the association between target functions and indications (proof of concept), lead discovery and optimization, the association between preclinical investigations and clinical trials, the lean of industrialization and pharmacoeconomics. At the molecular level the therapeutic efficacy originates from the interactive binding between specific atoms or groups of the drug molecule and the complementary atoms or groups of the macromolecular target in three-dimensional space. The strict arrangement of such critical atoms, groups, or fragments reflect specific features for a precise binding to the corresponding target. An alteration of amino acid residues in mutational targets leads to the change in conformation of the target protein, and an accurate structure of drug is necessary for binding to the mutant species and avoiding off-targeting effect. For the tailoring of clinical treatment to the individual patient design and development of various new molecular entities are critical for treatment choice according to the molecular features of biological markers of patients. This article provides some examples and methods of drug design and development in the new period.

New perspectives on the computational characterization of the kinetics of binding-unbinding in drug design: implications for novel therapies / Nuevas perspectivas sobre la caracterización computacional de la cinética de unión-desunión en el diseño de fármacos: implicaciones para terapias de vanguardia

Abstract: The efficiency and the propensity of a drug to be bound to its target protein have been inseparable concepts for decades now. The correlation between the pharmacological activity and the binding affinity has been the first rule to design and optimize a new drug rationally. However, this argument does not prove to be infallible when the results of in vivo assays have to be confronted. Only recently, we understand that other magnitudes as the kinetic rates of binding and unbinding, or the mean residence time of the complex drug-protein, are equally relevant to draw a more accurate model of the mechanism of action of a drug. It is in this scenario where new computational techniques to simulate the all-atom dynamics of the biomolecular system find its valuable place on the challenge of designing new molecules for more effective and less toxic therapies.

Resumen: La eficiencia de un fármaco se ha relacionado habitualmente con su constante de afinidad, magnitud que puede ser medida experimentalmente in vitro y que cuantifica la propensión mostrada por la molécula ligando para interaccionar con su proteína diana. Este modo de entender el mecanismo de acción ha guiado durante años el desarrollo de nuevas moléculas con potencial farmacológico. Sin embargo, dicho modelo o criterio no es infalible cuando se confronta con los resultados de ensayos in vivo. Otras magnitudes, como las constantes cinéticas de asociación o disociación o el tiempo de residencia del ligando acoplado a su proteína diana, demuestran ser igualmente necesarias para comprender y predecir la capacidad farmacológica del compuesto químico. En este nuevo escenario, con ayuda de las técnicas computacionales de simulación molecular, la correcta caracterización del proceso dinámico de unión y desunión del ligando y receptor resulta imprescindible para poder diseñar racionalmente nuevas moléculas que permitan terapias más eficaces y menos tóxicas.

Antibacterial Mechanisms of Berberine and Reasons for Little Resistance of Bacteria / 中草药·英文版

Objective To study the antibacterial mechanisms of berberine and try to understand the reasons why bacteria cells difficultly resisted to it. Methods Detecting the minimal inhibitory concentration (MIC) of bacterial cultures incubated under sub-MIC concentration of berberine, Huanglian, and Neomycin for more than 200 generations, in order to analyze the bacteria resistance. Detecting the binding kinetics of berberine to DNA, RNA, and proteins. Observing the changes in bacterial cell surface structure with scanning electron microscopy. Detecting the Ca2+ and K.+ released from berberine-treated bacterial cells with atomic absorption spectrum. Detection the absorption of methyl-3H-thymine (3H-dT), 3H-uridine (3H-U), and 3H-tyrosine (3H-Tyr) into berberine-treated bacterial cells. Results MICs of bacterial cultures, growing more than 200 generations in MH medium with 1/2 MIC of berberine (BA200) or Huanglian (HA200), did not increase compared to the control, while remarkably increased in MH medium with 1/2 MIC of Neomycin (NA200). In addition, from the culture NA200 it was easy to isolate resistant mutant strains which could grow in MH medium with more than four times MIC Neomycin, but from the culture BA200 and HA200 it was difficult to isolate berberine or Huanglian mutant strains could grow in MH medium with more than four times MIC berberine or Huanglian. The binding kinetics of berberine to DNA, RNA, and proteins illustrated that berberine could easily and tightly bind to DNA and RNA, and hardly dis-bind from DNA- and RNA-berberine complexes. Berberine could easily bind to protein too, but also easily dis-bind from berberine-protein complex. The bacterial cells treated with berberine sharply decreased the absorption of 3H-dT, 3H-U, and 3H-Tyr, as the radioactive precursors of DNA, RNA, and protein biosynthesis. Berberine could damage bacterial cell surface structure, especially for Gram-negative bacteria. Ca2+ and K+ released from berberine-treated cells increased significantly compared to the control. Conclusion All of above results indicate that bacterial cells could not easily become resistant mutants to berberine. The mechanisms for the bactericidal effect of berberine include: inhibiting DNA duplication, RNA transcription, and protein biosynthesis; influencing or inhibiting enzyme activities; destructing the bacterial cell surface structure and resulting in Ca2+ and K+ released from cells. All of the berberine bactericidal mechanisms are the most essential physiological functions for a live cell, if influenced any one such function, the mutation would be lethal mutation, so that it is difficult to get berberine resistant cells. The results in this paper also prefigure that berberine and its related Chinese medicines would provide a feasible way to control antibiotic resistance problem.