A review on molecular topology: applying graph theory to drug discovery and design

Molecular topology is an application of graph theory and statistics in fields like chemistry, biology, and pharmacology, in which the molecular structure matters. Its scope is the topological characterization of molecules by means of numerical invariants, called topological indices, which are the main ingredients of the molecular topological models. These are statistical models that are instrumental in the discovery of new applications of naturally occurring molecules, as well as in the design of synthetic molecules with specific chemical, biological, or pharmacological properties. In this review, we focus on pharmacology, which is a novel field of application of molecular topology. Besides summarizing some recent developments, we also seek to bring closer this interesting biomedical application of mathematics to an interdisciplinary readership.

Effects of N2 and CO2 on the flammability of 2,3,3,3-tetrafluoropropene at elevated temperatures

The flammability characteristics of refrigerants are affected by environmental factors, making them prone to flammability and explosion accidents in cooling systems. In this paper, the flammability characteristics of R1234yf–air mixtures with N₂ and CO₂ were investigated comparatively at temperatures between 20 and 50 °C at 80% relative humidity. The lower and upper flammability limits of R1234yf were measured. The limiting oxygen concentration (LOC), critical flammable ratio (CFR), and critical flammable concentration (CFC) of the R1234yf–air mixtures with inert gases were investigated. The paper developed a linear formula between the flammability limit of R1234yf and the temperature. The changes in CFC with different temperatures were negligible for R1234yf. Furthermore, the mixed refrigerant had both non-flammability and the lowest vapor pressure when the CFR of the R1234yf/CO₂ mixture was 2.9. The experimental results were used to propose a new prediction model to estimate the flammability limits of R1234yf. Finally, molecular simulation explained the effect of inert gases on the flammability of R1234yf from a microscopic point of view. The research aimed to provide valid evidence and data for preventing flammable and explosive refrigerant incidents.     

Alpha-male paternity in elephant seals

The aim of this study was to assess paternity of males that dominated mating in harems at northern (Mirounga angustirostris) and southern (M. leonina) elephant seal rookeries using DNA fingerprinting and microsatellite DNA analysis. Southern alpha males had greater reproductive success than most northern alphas at similar-sized harems. Comparison of the relatedness between pups within harems also suggested that fewer males achieved matings in the southern elephant seal population. This was consistent with behavioral observations that suggest greater competition for mates in northern elephant seal harems. Reproductive success was consistent with estimates of mating success in some cases, but lower than expected for some northern elephant seal alpha males. A lower reproductive success than predicted from mating behavior may arise from a variety of factors including sperm competition, male sperm depletion from frequent mating, or reduced fertility. The alternatives are discussed in the context of environmental and historical factors. Received: 17 August 1998 / Received in revised form: 28 March 1999 / Accepted: 30 May 1999     

造纸中段废水的混凝-臭氧氧化深度处理研究

就混凝-臭氧氧化组合工艺对造纸中段废水生物处理出水的净化效果进行了研究.结果表明,Ca(OH)2对废水色度、TOC、COD和254 nm的紫外吸收值(UV254)的去除效果均优于聚合氯化铝/聚丙烯酰胺(PAC/PAM);Ca(OH)2-O3组合工艺的处理效果也优于PAC/PAM-O3工艺.当Ca(OH)2投加量为1 g/L、臭氧投加量为50 mg/L时,废水色度降低至10倍以下,COD小于150 mg/L.经Ca(OH)2混凝处理后,相对分子量在0.5～1.0 ku和10.0 ku以上的有机物显著减少;进一步臭氧氧化处理后,除0.5 ～1.0 ku范围的有机物大幅度增加外,其余分子量有机物显著减少.由于对色度贡献很大的大分子量物质的去除,废水的色度显著下降直至无色.     

2-巯基噻唑啉与过氧化氢酶的相互作用机理研究

2-巯基噻唑啉是一种被广泛应用的抗腐蚀剂和光亮剂,然而它的一些残留物会对环境造成损坏,为探究2-巯基噻唑啉的毒性作用,采用光谱学技术和分子对接技术来考察2-巯基噻唑啉和过氧化氢酶的相互作用影响,其中酶活性实验表明2-巯基噻唑啉会抑制过氧化氢酶的活性,分子对接结果显示2-巯基噻唑啉会结合在过氧化氢酶的活性位点处,并最终导致过氧化氢酶空间结构和微环境的变化,根据荧光测试结果,表明2-巯基噻唑啉和过氧化氢酶之间的猝灭方式为静态猝灭。通过测量不同温度下的结合位点数、结合常数以及热力学常数,显示2-巯基噻唑啉与过氧化氢酶主要通过氢键和范德华力相结合。该研究从分子水平上考察了2-巯基噻唑啉对蛋白质的毒性作用,对于阐明污染物的毒性机理具有重要意义。     

Insights into the structural and conformational requirements of polybrominated diphenyl ethers and metabolites as potential estrogens based on molecular docking

PBDEs and their metabolites are of concern due to their increasing concentrations in the environment and their toxic effects. Knowledge about the toxicological mechanisms of PBDEs and metabolites is urgently needed for further screening. The objective of the present study was to explore the structural and conformational requirements of PBDE compounds as human estrogen receptor alpha (hERα) agonists, and further screened out hERα agonists from PBDE compounds. Molecular docking and postdocking analysis were adopted to attain the aim. The obtained results revealed that PBDEs can be primarily screened for their estrogenicity using score values, hydrogen bonds interaction with amino acid residues Glu353 and/or Arg394 might be important for HO-PBDEs’ estrogenicity. For most MeO-PBDEs, hydrophobic interaction might be the key factor affecting their estrogenic activity. The current study suggested that molecular docking and postdocking analysis can serve as an efficient pre-screening technique for identifying potential estrogens.     

Interaction of diuron to human serum albumin: Insights from spectroscopic and molecular docking studies

This investigation was undertaken to determine the interaction of diuron with human serum albumin (HSA) was studied by monitoring the spectral behavior of diuron-HSA system. The fluorescence of HSA at 340 nm excited at 230 nm was obviously quenched by diuron due to dynamic collision and the quenching constant was of the order of 10⁴ L mol^?1 at 310 K. However, no fluorescence quenching was observed when excited at 280 nm. Thermodynamic investigations revealed that the combination between diuron and HSA was entropy driven by predominantly hydrophobic interactions. The binding of diuron induced the drastic reduction in α-helix conformation and the significant enhancement in β-turn conformation of HSA. In addition, both sites marker competition study and molecular modeling simulation evidenced the binding of diuron to HSA primarily took place in subdomain IIIA (Sudlow's site II).     

Production of anti-amoxicillin ScFv antibody and simulation studying its molecular recognition mechanism for penicillins

The molecular recognition mechanism of an antibody for its hapten is very interesting. The objective of this research was to study the intermolecular interactions of an anti-amoxicillin antibody with penicillin drugs. The single chain variable fragment (ScFv) antibody was generated from a hybridoma cell strain excreting the monoclonal antibody for amoxicillin. The recombinant ScFv antibody showed similar recognition ability for penicillins to its parental monoclonal antibody: simultaneous recognizing 11 penicillins with cross-reactivities of 18–107%. The three-dimensional structure of the ScFv antibody was simulated by using homology modeling, and its intermolecular interactions with 11 penicillins were studied by using molecular docking. Results showed that three CDRs are involved in antibody recognition; CDR L3 Arg 100, CDR H3 Tyr226, and CDR H3 Arg 228 were the key contact amino acid residues; hydrogen bonding was the main antibody–drug intermolecular force; and the core structure of penicillin drugs was the main antibody binding position. These results could explain the recognition mechanism of anti-amoxicillin antibody for amoxicillin and its analogs. This is the first study reporting the production of ScFv antibody for penicillins and stimulation studying its recognition mechanism.     

基于农校对接的高校食品安全管理研究

从高校食品工作的特点出发,总结了高校食品安全的特点,提出了＂农校对接＂的解决途径,并分析了开展农校对接的意义,从高校食品安全管理者、食品供应者、物流等角度阐述了开展农校对接的具体措施。