三维定量构效关系和同源分子模拟在细胞色素P450研究中的应用

细胞色素P4 5 0 (CYP4 5 0 )是参与各种外源物和内源物代谢的重要酶系 ,研究该酶与底物或抑制剂的相互作用对于阐明药物作用机制及疾病预防、治疗具有重要意义。CYP4 5 0对药物代谢的选择性不仅与底物本身密切相关 ,还与酶活性位点血红蛋白中的特殊氨基酸残基排列分布对底物的特异性识别有关。在人CYP4 5 0的晶体结构未知的情况下 ,三维定量构效关系。

Insights into the discovery of new 5-HT1A receptor ligands:receptor based pharmacophore

5-HT1A receptor is a crucial therapeutic target for the treatment of anxiety, depression, pain, etc. Design and preparation of potent 5-HT1A receptor ligands for drug discovery has attracted extensive attention in the past few years. In this paper, a three dimensional model of human 5-HT1A receptor was constructed by means of homology modeling. And the docking of MP349 to the receptor suggested a reliable binding mode for 5-HT1A receptor ligand. Based on this ligand-receptor binding mode, an elaborate receptor structure based pharmacophore model was established, which revealed many important features responsible for ligand and 5-HT1A receptor interactions. A virtual screening experiment verified the ability of this pharmacophore model to discover true 5-HT1A receptor ligand. The results of this research would provide important information for further optimizations of 5-HT1A receptor ligands and guide related new lead discoveries.

Molecular models of different states of the human multidrug resistance protein 4(MRP4/ABCC4)

ATP-binding cassette（ABC） transporter multidrug resistance protein 4（MRP4, ABCC4） is involved in multidrug resistance（MDR）, which is an increasing challenge to the treatment of cancers and infections. MRP4 is overexpressed in several types of cancers, and MRP4 inhibition shows striking effects against cancer progression and drug resistance. However, the structural knowledge of this protein remains unclear due to lack of an MRP4 X-ray structure, and homology modeling approach is an effective way to obtain three-dimensional structure of MRP4. We constructed three molecular models of human MRP4 mainly based on the inward facing Caenorhabditis elegans P-glycoprotein（P-gp）, the Thermotoga maritima heterodimeric ABC transporter TM287-TM288（TM287/288） and the outward facing Staphylococcus aureus Sav1866 crystal structures, which represented substrate uptake, transport and release state, respectively. The structures were further energy minimized and optimized by molecular dynamic simulations（MDS）. All the models were validated by various tools and servers, and the results showed that the quality of the models was reasonable and acceptable. These MRP4 models could be used as working tools for experimental studies on the structure and functions of MRP4 and designing more specific membrane transport modulating agents（MTMA）.

Predicting hiCE inhibitors based upon pharmacophore models derived from the receptor and its ligands

Human intestinal carboxyl esterase （hiCE） is a drug target for ameliorating irinotecan-induced diarrhea. By reducing irinotecan- induced diarrhea, hiCE inhibitors can improve the anti-cancer efficacy of irinotecan. To find effective hiCE inhibitors, a new virtual screening protocol that combines pharmacophore models derived from the hiCE structure and its ligands has been pro- posed. The hiCE structure has been constructed through homology techniques using hCESI＇s crystal structure. The hiCE structure was optimized via molecular dynamics simulations with the most known active hiCE inhibitors docked into the structure. An optimized pharmacophore, derived from the receptor, was then generated. A ligand-based pharmacophore was also generated from a larger set of known hiCE inhibitors. The final hiCE inhibitor predictions were based upon the virtual screening hits from both ligand-based and receptor-based pharmacophore models. The hit rates from the ligand-based and receptor-based pharmacophore models are 88% and 86%, respectively. The final hit rate is 94%. The two models are highly consistent with one another （85%）. This proves that both models are reliable.

Molecular dynamics simulation of the interactions between EHD1 EH domain and multiple peptides

Objective： To provide essential information for peptide inhibitor design, the interactions of Eps15 homology domain of Eps15 homology domain-containing protein 1 （EHD1 EH domain） with three peptides containing NPF （asparagine-proline-phenylalanine）, DPF （aspartic acid-proline-phenylalanine）, and GPF （glycine-proline-phenylalanine） motifs were deciphered at the atomic level. The binding affinities and the underlying structure basis were investigated. Methods： Molecular dynamics （MD） simulations were performed on EHD1 EH domain/peptide complexes for 60 ns using the GROMACS package. The binding free energies were calculated and decomposed by molecular mechanics/ generalized Born surface area （MM/GBSA） method using the AMBER package. The alanine scanning was performed to evaluate the binding hot spot residues using FoldX software. Results： The different binding affinities for the three peptides were affected dominantly by van der Waals interactions. Intermolecular hydrogen bonds provide the struc- tural basis of contributions of van der Waals interactions of the flanking residues to the binding. Conclusions： van der Waals interactions should be the main consideration when we design peptide inhibitors of EHD1 EH domain with high affinities. The ability to form intermolecular hydrogen bonds with protein residues can be used as the factor for choosing the flanking residues.