Influence of molecular parameters on the degradation of chitosan by a commercial enzyme

The degradative activities of neutral protease against chitosan samples with different molecular parameters were characterized. The effects of the degree of deacetylation (DD) and molecular weight (MW) of chitosan on its susceptibility to degradation were investigated. The DD and MW of the chitosans were determined using potentiometric titration and viscometry, respectively. The molecular weight distribution of initial and degraded commercial chitosan was investigated by gel permeation chromatography. Initial degradation rates (r) were determined from the plots of viscosity decrease against time of degradation. The time courses of degradation of chitosans with neutral protease were non-linear and the enzymatic hydrolysis was an endo-action. Classical Michaelis-Menten kinetic parameters were measured by analyzing the amount of reducing sugars and Eadie-Hofstee plots established that hydrolysis of chitosan by neutral protease obeyed Michaelis-Menten kinetics. Michaelis-Menten parameters and initial degradation rates were calculated and compared to determine the influences of DD and MW on hydrolysis. The results showed that higher DD and higher MW chitosans possessed a lower affinity for the enzyme and a slower degradation rate. Those samples with a lower DD and lower MW were more susceptible substrates.     

Computational Simulation of HIV Protease Inhibitors to the Main Protease (Mpro) of SARS-CoV-2: Implications for COVID-19 Drugs Design

SARS-CoV-2 is highly homologous to SARS-CoV. To date, the main protease (Mpro) of SARS-CoV-2 is regarded as an important drug target for the treatment of Coronavirus Disease 2019 (COVID-19). Some experiments confirmed that several HIV protease inhibitors present the inhibitory effects on the replication of SARS-CoV-2 by inhibiting Mpro. However, the mechanism of action has still not been studied very clearly. In this work, the interaction mechanism of four HIV protease inhibitors Darunavir (DRV), Lopinavir (LPV), Nelfinavir (NFV), and Ritonavire (RTV) targeting SARS-CoV-2 Mpro was explored by applying docking, molecular dynamics (MD) simulations, and MM–GBSA methods using the broad-spectrum antiviral drug Ribavirin (RBV) as the negative and nonspecific control. Our results revealed that LPV, RTV, and NFV have higher binding affinities with Mpro, and they all interact with catalytic residues His41 and the other two key amino acids Met49 and Met165. Pharmacophore model analysis further revealed that the aromatic ring, hydrogen bond donor, and hydrophobic group are the essential infrastructure of Mpro inhibitors. Overall, this study applied computational simulation methods to study the interaction mechanism of HIV-1 protease inhibitors with SARS-CoV-2 Mpro, and the findings provide useful insights for the development of novel anti-SARS-CoV-2 agents for the treatment of COVID-19.     

Jusanin,a New Flavonoid from Artemisia commutata with an In Silico Inhibitory Potential against the SARS-CoV-2 Main Protease

A new flavonoid, Jusanin, (1) has been isolated from the aerial parts of Artemisia commutata. The chemical structure of Jusanin has been elucidated using 1D, 2D NMR, and HR-Ms spectroscopic methods to be 5,2′,4′-trihydroxy-6,7,5′-trimethoxyflavone. Being new in nature, the inhibition potential of 1 has been estimated against SARS-CoV-2 using different in silico techniques. Firstly, molecular similarity and fingerprint studies have been conducted for Jusanin against co-crystallized ligands of eight different SARS-CoV-2 essential proteins. The studies indicated the similarity between 1 and X77, the co-crystallized ligand SARS-CoV-2 main protease (PDB ID: 6W63). To confirm the obtained results, a DFT study was carried out and indicated the similarity of (total energy, HOMO, LUMO, gap energy, and dipole moment) between 1 and X77. Accordingly, molecular docking studies of 1 against the target enzyme have been achieved and showed that 1 bonded correctly in the protein’s active site with a binding energy of −19.54 Kcal/mol. Additionally, in silico ADMET in addition to the toxicity evaluation of Jusanin against seven models have been preceded and indicated the general safety and the likeness of Jusanin to be a drug. Finally, molecular dynamics simulation studies were applied to investigate the dynamic behavior of the M^pro-Jusanin complex and confirmed the correct binding at 100 ns. In addition to 1, three other metabolites have been isolated and identified to be сapillartemisin A (2), methyl-3-[S-hydroxyprenyl]-cumarate (3), and β-sitosterol (4).     

虚拟活性化合物的自动生成

虚拟活性化合物的自动生成是从药效团和预先设定的结构碎片出发,通过碎片选择、碎片组装和柔性构象搜索来获得虚拟活性结构。经过对HIV-1蛋白酶抑制剂药效团进行虚拟活性化合物生成,得到了16个虚拟活性化合物,通过构象分析发现生成的化合物满足药效团的限制条件。说明这一方法能够有效的生成虚拟活性结构,与药效团检索结果对比发现生成的虚拟活性结构新颖易于合成。     

分子动力学研究抑制剂APV与HIV-1蛋白酶的作用机制

采用分子动力学模拟和结合自由能计算研究了抑制剂APV与HIV-1蛋白酶的作用机制. 研究结果表明范德瓦尔斯作用主控了APV与HIV-1蛋白酶的结合. 采用基于残基的自由能分解方法计算了抑制剂-残基相互作用,结果表明9个残基Gly27、Ile32、Val47、Ile50、Ile84、Ala28′、Gly49′、Ile50′和Arg87′与APV产生了大于1.0 kcal/mol的强相互作用,而且证明CH-π,CH-O相互作用和极性作用是其结合的主要形式. 期待该结果可以为以HIV-1蛋白酶为靶标的抗艾滋病药物设计提供理论上的指导.     

宇佐美曲霉 L336酸性蛋白酶 发酵过程动力学研究

宇佐美曲霉栗色变种 L336是一株高产酸性蛋白酶的生产菌 ,采用转置培养法 ,对其发酵过程的 一些动力学特点进行了研究 ,结果表明 ,酸性蛋白酶是细胞利用内源营养从头合成的 ,属于非生长关联 型; 腺嘌呤是菌体生长的生长因子 ,代谢类似物对酶合成产生较大的抑制 ;而蛋白胨是酶合成的诱导因 子 ,发酵液溶氧水平较大地影响酶合成能力 . 本研究为其工业发酵工艺的构建提供了理论依据 .     

Enzymatic regioselective symthesis of vinthesis of vinyl lactose ester and its chemical polymerization

Transesterification reaction of lactose with divinyladipate in pyridine catalyzed by an alkaline protease from Bacillus subtilis at 50(C for 3 days gave 6(-O-vinyladipoyl-lactose (yield 35%). Poly(6(-O-vinyladipoyl-lactose) with Mn = 21,200, Mw = 32,900, Mw/Mn = 1.56 could be obtained by chemical polymerization. Poly(vinyl alcohol) containing lactose branch was biodegradable. After 6 days in aqueous buffer (PH 7), this alkaline protease could degrade the polymer to an Mn of ca. 2100, Mw/Mn = 2.56.