Evolution of camel CYP2E1 and its associated power of binding toxic industrial chemicals and drugs

Camels are raised in harsh desert environment for hundreds of years ago. By modernization of live and the growing industrial revolution in camels rearing areas, camels are exposed to considerable amount of chemicals, industrial waste, environmental pollutions and drugs. Furthermore, camels have unique gene evolution of some genes to withstand living in harsh environments. In this work, the camel cytochrome P450 2E1 (CYP2E1) is compromised to detect its evolution rate and its power to bind with various chemicals, protoxins, procarcinogens, industrial toxins and drugs. In comparison with human CYP2E1, camel CYP2E1 more efficiently binds to small toxins as aniline, benzene, catechol, amides, butadiene, toluene and acrylamide. Larger compounds were more preferentially bound to the human CYP2E1 in comparison with camel CYP2E1. The binding of inhalant anesthetics was almost similar in both camel and human CYP2E1 coinciding with similar anesthetic effect as well as toxicity profiles. Furthermore, evolutionary analysis indicated the high evolution rate of camel CYP2E1 in comparison with human, farm and companion animals. The evolution rate of camel CYP2E1 was among the highest evolution rate in a subset of 57 different organisms. These results indicate rapid evolution and potent toxin binding power of camel CYP2E1.     

人类谷胱甘肽硫转移酶家族等位基因蛋白B与抑制剂作用模型的理论研究

采用分子动力学模拟方法系统地研究了谷胱甘肽硫转移酶家族(Glutathione S-transferases,GSTs)的等位基因蛋白B(GSTP1*B)与抑制剂利尿酸(EA)以及EA的谷胱甘肽(GSH)共轭物EAG(I),EAG(O)的具体结合方式.抑制剂及其谷胱甘肽共轭物与蛋白的相互作用能计算结果及分子动力学轨迹的统计分析结果表明,GSTP1*B与EA的谷胱甘肽共轭物的结合能力优于其与EA的结合能力,Phe8,Arg13,Trp38和Tyr108是作用过程中的关键残基,对稳定抑制剂及其谷胱甘肽共轭物在GSTP1*B的G和H位点的构象具有重要的作用.通过对构象的统计分析发现,残基Phe8和Tyr108与GSTP1*B酶对抑制剂的选择性密切相关.     

GSH对两种谷胱甘肽过氧化物酶模拟物活性影响的研究

设计并合成了谷胱甘肽过氧化物酶(GPX)模拟物6A,6A’-二苯胺-6B,6B’-二硒桥联-β-环糊精(6-AnSeCD). 采用双酶偶联法测定GPX的活力结果显示, 6A,6A’-二环己胺-6B,6B’-二硒桥联-β-环糊精(6-CySeCD)催化谷胱甘肽还原H2O2和枯烯H2O2的活力均比6-AnSeCD的高. 为了进一步考察6-CySeCD和6-AnSeCD与GSH之间的相互作用, 进行了分子动力学(MD)模拟和分子对接研究. 结果表明, 与GSH的结合使GPX模拟物的构象发生变化, 这种改变可能是影响桥连GPX模拟物催化活性的关键因素.     

Insights into the Functions of M-T Hook Structure in HIV Fusion Inhibitor Using Molecular Modeling

HIV-1 membrane fusion plays an important role in the process that HIV-1 entries host cells. As a treatment strategy targeting HIV-1 entry process, fusion inhibitors have been proposed. Nevertheless, development of a short peptide possessing high anti-HIV potency is considered a daunting challenge. He et al. found that two residues, Met626 and Thr627, located the upstream of the C-terminal heptad repeat of the gp41, formed a unique hook-like structure (M-T hook) that can dramatically improve the binding stability and anti-HIV activity of the inhibitors. In this work, we explored the molecular mechanism why M-T hook structure could improve the anti-HIV activity of inhibitors. Firstly, molecular dynamic simulation was used to obtain information on the time evolution between gp41 and ligands. Secondly, based on the simulations, molecular mechanics Poisson–Boltzmann surface area (MM-PBSA) and molecular mechanics Generalized Born surface area (MM-GBSA) methods were used to calculate the binding free energies. The binding free energy of the ligand with M-T hook was considerably higher than the other without M-T. Further studies showed that the hydrophobic interactions made the dominant contribution to the binding free energy. The numbers of Hydrogen bonds between gp41 and the ligand with M-T hook structure were more than the other. These findings should provide insights into the inhibition mechanism of the short peptide fusion inhibitors and be useful for the rational design of novel fusion inhibitors in the future.     

Interaction Between 1,2,3-Trichloropropane and Haloalkane Dehalogenase LinB

The haloalkane dehalogenase LinB from Sphingomonas paucimobills UT26 was found to transform the 1,2,3-trichloropropane(TCP) into inorganic halide ions and 2,3-dichloro-1-propanol although the catalytic activity is very low(Kcat=0.005 s-1).In this study,molecular dynamics simulation and docking studies were performed to investigate the binding of TCP to LinB.The docking results indicate that LinB does not restrict TCP to be bound productively in the active site and the water-mediated inhibition occurs in the...     

Molecular Dynamics Study of Interaction between Acrylamide Copolymers and Alumina Crystal

Four acrylamide polymer flocculants, anionic polyacrylamide P(AA-co-AM), cationic poly-acrylamide P(DMB-co-AM), nonionic polyacrylamide P(AM), and hydrophobical polyacry-lamide P(OA-co-AM) have been prepared by copolymerizing with acrylic acid, cationic monomer dimethylethyl (acryloxyethyl) ammonium bromide (DMB) and hydrophobical monomer octadecyl acrylate with acrylamide. The interactions between the flocculants withthe (012) surface of alumina crystal (Al₂O₃) have been simulated by molecular dynamics method. All the polymers can bind tightly with Al₂O₃ crystal, the interaction between the O of polymers and Al of the (012) surface of Al₂O₃ is significantly strong. The order of binding energy is as follows: P(DMB-co-AM)>P(OA-co-AM)>P(AA-co-AM)>P(AM), implying a better flocculation performance of P(DMB-co-AM) than the others. Analy-sis indicates that binding energy is mainly determined by Coulomb interaction. Bonds are found between the O atoms of the polymers and the Al atoms of Al₂O₃. The poly-mers' structures deform when they combine with Al₂O₃ crystal, but the deformation en-ergies are low and far less than non-bonding energies. Flocculation experiments in sus-pension medium of 1%Kaolin show a transmittancy of 90.8% for 6 mg/L P(DMB-co-AM) and 73.0% for P(AM). The sequence of flocculation performance of four polymers is P(DMB-co-AM)>P(OA-co-AM)>P(AA-co-AM)>P(AM), which is in excellent agreement with the simulation results of binding energy.     

Structure-based design and evaluation of novel N-phenyl-1H-indol-2-amine derivatives for fat mass and obesity-associated (FTO) protein inhibition

Fat mass and obesity-associated (FTO) protein contributes to non-syndromic human obesity which refers to excessive fat accumulation in human body and results in health risk. FTO protein has become a promising target for anti-obesity medicines as there is an immense need for the rational design of potent inhibitors to treat obesity. In our study, a new scaffold N-phenyl-1H-indol-2-amine was selected as a base for FTO protein inhibitors by applying scaffold hopping approach. Using this novel scaffold, different derivatives were designed by extending scaffold structure with potential functional groups. Molecular docking simulations were carried out by using two different docking algorithm implemented in CDOCKER (flexible docking) and AutoDock programs (rigid docking). Analyzing results of rigid and flexible docking, compound MU06 was selected based on different properties and predicted binding affinities for further analysis. Molecular dynamics simulation of FTO/MU06 complex was performed to characterize structure rationale and binding stability. Certainly, Arg96 and His231 residue of FTO protein showed stable interaction with inhibitor MU06 throughout the production dynamics phase. Three residues of FTO protein (Arg96, Asp233, and His231) were found common in making H-bond interactions with MU06 during molecular dynamics simulation and CDOCKER docking.     

Evaluation of binding performance of bioactive compounds against main protease and mutant model spike receptor binding domain of SARS-CoV-2: Docking,ADMET properties and molecular dynamics simulation study

Phytochemicals present in medicinal plants have a variety of biological activities that help to combat against diseases. As part of efforts to study the binding performance of different phytochemicals derived from different plants like Zingiber officinale, Citrus limon, Syzygiumaromaticum, Ocimum tenuiflorum and Curcumin. We have screened 424 molecules. The binding affinity as well as physicochemical properties of the thebaine, acacetin, indomethacin, crinamineacetate, (S)-1-Piperideine-6-carboxylate, levamisole, melatonin, nicotinicacid, curcumin, methotrimeprazine, omeprazole, and methaqualone phytocompounds were analyzed through computational study. From the molecular docking study we found that, LEU50, ASN72, PRO96, TYR154, GLY170, ALA193, ARG222, and MET274 residues of main protease play a crucial role in binding with ligands. The present study revealed a noticeable interaction of GLY446, SER477, GLY482, THR500 and LEU518 residues with mutant of spike receptor binding domain SARS-CoV-2 protein were observed. Finally, 100 ns molecular dynamics simulation were used to study their dynamic properties as well as conformational flexibility. Free energy landscape analysis was performed of the 6LU7- acacetin and 6Y2E-acacetin systems and spike RBD-acacetin system. From molecular docking study and molecular dynamics study revealed that, the compound acacetin shows promising inhibitor towards both main protease as well as mutant spike RBD of SARS-CoV-2 protein.     

SARS冠状病毒3CL蛋白酶及其抑制剂的理论研究

应用AutoDock程序将SARS冠状病毒3CL蛋白酶及其抑制剂配体和受体进行了对接,并用InsightⅡ中的Discover 3模块进行了分子动力学模拟,分析了蛋白酶活性口袋的形状,讨论了其亚基的氢键、静电、疏水等相互作用,为进一步设计药物提供了重要的参考信息.     

盐酸拓扑替康与人血清白蛋白的相互作用及分子模拟

用荧光光谱法、分光光度法研究了盐酸拓扑替康(topotecan hydrochloride, 简记为THC)与人血清白蛋白(human serum albumins, HSA)的相互结合反应. 计算了反应的结合常数、结合位点数和热力学常数. 盐酸拓扑替康在人血清白蛋白上的结合位置与色氨酸残基间的距离为3.63 nm. 分子模型研究表明, 盐酸拓扑替康与人血清白蛋白的亚结构域IIA结合, 二者间的作用力主要为疏水作用, 此外, 蛋白质的丙氨酸(Ala-291)残基和天冬氨酸(Asp-256)残基与盐酸拓扑替康之间还存在氢键作用力.     

Study on the Binding of Chloride Ion to Hemoglobin Using Electromotive Force Method

The electromotive force of the concentration cell, in which both half‐cells contain the same concentration of sodium chloride, and one of which also contains hemoglobin (Hb), was measured on the isoelectric point of Hb (pH = 6.70). On the basis of Scatchard equation, a stepwise binding model and an improved calculation method were presented. Using the new calculation method, the number of the chloride‐binding sites on Hb molecule and the corresponding binding constants were calculated. The results show that there are three classes of binding groups on a Hb molecule, the number of the binding sites and the corresponding binding constants are n₁ = 1, K⁰₁ = 245; n₂ = 8, K⁰₂ = 3.50; n₃ = 8, K⁰₃ = 1.91, respectively. The factors of influencing the interaction between Cl^? and Hb molecule were clarified, and that the differences between our results and the results of computer modeling, as well as the results of molecular dynamics simulation were also discussed.     

Binding site and elution behavior of DNA and other large biomolecules in monolithic anion-exchange chromatography

Our previous study has shown that there is a good correlation between the number of charges of DNA (from trimer to 50-mer) and the number of binding sites B in electrostatic interaction chromatography (ion-exchange chromatography, IEC). It was also found that high salt (NaCl) concentration is needed to elute large DNAs (>0.6 M). In this paper we further performed experiments with large DNAs (up to 95-mer polyT and polyA) and charged liposome particles of different sizes (ca. 30, 50 and 100 nm) with a monolithic anion-exchange disk in order to understand the binding and elution mechanism of very large charged biomolecules or particles. The peak salt (NaCl) concentration increased with increasing DNA length. However, above 50-mer DNAs the value did not increase significantly with DNA length (ca. 0.65–0.70 M). For liposome particles of different sizes the peak salt concentration (ca. 0.62 M) was similar and slightly lower than that for large DNAs (ca. 0.65–0.70 M). The binding site values (ca. 25–30) are smaller than those for large DNAs. When arginine was used as a mobile phase modulator, the elution position of polyA and polyT became very close whereas in NaCl gradient elution polyT appeared after polyA eluted. This was mainly due to suppression of hydrophobic interaction by arginine.