Hadean Bioscience

名城大学 / 金沢大学医薬保健研究域薬学系当該年度では、まず一部の残基がD-アミノ酸となった場合の[GADV]-タンパク質の立体構造について、MDシミュレーションによって推定した。D-アミノ酸の出現確率が50%の場合に加え、確率が25%、12.5%の場合についても計算を行った。これらの検討の結果、D-アミノ酸の含まれる割合が高くなればなるほどアミノ酸鎖が二次構造を形成する頻度が下がる傾向にあることが示された。この結果は、「アミノ酸がラセミ体で存在する環境」と「アミノ酸の一方の光学異性体が多い環境」では後者のほうが何らかの構造をもったタンパク質を構築しやすいことを示唆しており、この立体構造形成能の違いが一種の淘汰圧として働いて、生体におけるホモキラリティの起源となった可能性が考えられる。また、タンパク質中におけるアミノ酸の立体反転機構について、量子化学計算を用いて明らかにした。どのような環境下でアミノ酸の立体反転が起こるのか、その立体障壁はどのくらいかを量子化学計算によって求めた。その結果、水分子やリン酸イオンなどが立体反転の触媒となり得ることや、反転することがよく知られているアスパラギン酸のみならずグルタミン酸も反転する可能性があることなどが示唆された。さらに[GADV]-タンパク質以外にも、バリンの代わりにセリン (S) を含めた[GADS]-ペプチドの立体構造についてもMDシミュレーションを用いた解析を行っている。疎水性残基が多いペプチドほど二次構造をとる傾向が高いことは事前に想定できたため、溶媒接触可能表面積や極性表面積を用いて、水溶性と立体構造とのバランスを評価した。これらについてはおおむね加えた残基の性質に応じて立体構造形成能や表面積が増加・減少する傾向にあった。また、既知タンパク質（酵素）の一部のアミノ酸を変異させる研究も行っており、おおむね実験的に得られた酵素活性を再現する結果が得られた。研究課題/領域番号:15H01064, 研究期間(年度):2015-04-01 – 2017-03-3

Triethylated chromones with substituted naphthalenes as tubulin inhibitors

Previously synthesized 2-(benzo[]thiophene-3′-yl)-6,8,8-triethyldesmosdumotin B (, TEDB-TB) and 2-(naphth-1′-yl)-6,8,8-triethyldesmosdumotin B () showed potent activity against multiple human tumor cell lines, including a multidrug-resistant (MDR) subline, by targeting spindle formation and/or the microtubule network. Consequently, ester analogues of hydroxylated naphthyl substituted TEBDs (–) were prepared and evaluated for their effects on tumor cell proliferation and on tubulin assembly. Among all new compounds, compound , a 4′-acetoxynaphthalen-1′-yl derivative, displayed the most potent antiproliferative activity (IC 0.2–5.7 μM). Selected analogues were confirmed to be tubulin assembly inhibitors in cell-free and cell-based assays using MDR tumor cells. The new analogues partially inhibited colchicine binding to tubulin, suggesting their binding mode would be different from that of colchicine. This observation was supported by computational docking model analyses. Thus, the newly synthesized triethylated chromones with esterified naphthalene groups have good potential for development as a new class of mitotic inhibitors that target tubulin

明示的に水を取り扱った分子動力学シュミレーションの変異体の計算に対する有用性の検討.Bovine Pancreatic Trypsin Inhibitorを用いた試験

Computational simulations can reproduce or predict structural changes of proteins upon various mutations in a short time.In this study,molecular dynamics simulations of the wild type and mutants of bovine pancreatic trypsin inhibitor with explicit solvent were carried out to evaluate reliability of molecular dynamics simulation.We used two force fields,ff03 and ff99SB,and compared the results.Effects of the amino acid mutations on structural stability were largely reproduced by the simulations

ウリジン二リン酸グルクロン酸転移酵素1A1の立体構造予測

In this study,we construct the three dimensional structure of Uridine Diphosphate Glucuronosyltransferate (UGT) 1A1 by using for template homology/analyogy recognition engine (phyre) server.Ten PDB entries including UGT2B7 were used for template of the model,and both UDP-glucuronic acid binding domain and substrate binding domain were obtained. By using the modeled structure,structural refinement was carried out by molecular dynamics (MD) simulations.In order to investigate the role of cysteine,MD simulations of both UGT1A1 models with and without the Cys127-Cys156 disulfide bond were performed.As the results of the simulations,structural features of UGT1A1 can be investigated, and refined structure of it was obtained

FADおよびFADH2存在下におけるD-アスパラギン酸酸化酵素とD-アスパラギン酸のドッキングシュミレーション

recently, D-amino acids have been found to exist in the human body both as free amino acids and as residues in proteins. The free D-Asp is degraded by d-aspartate oxidase(DDO). DDO with cofactor FAD catalyzes the oxidative deamination of D-Asp and oxaloacetic acid is generated. On the other hand, it is reported that DDO with cofactor FADH2 can also form a complex with D-Asp. in this study, computational docking between D-Asp and DDO was carried out with FAD or FADH2 as the cofactor. The results of docking studies indicate that D-Asp can be recognized both by DDO with FAD and DDO with FADH2, and the difference in binding affinity between the oxidative and reductive states is caused by difference of hydrogen bonding patterns

ブラウン動力学法によるタンパク質-リガンド複合体予測構造の評価.インフルエンザノイラミニターゼと阻害剤の複合体のシュミレーション

The prediction of protein-ligand complex structures plays an important role in structures based drug design.In this study,evaluations of predicted protein-ligand structures by using Brownian dynamics simulations were carried out.The complex strycture were generated by computational docking trials,which were frequently used in actual drug design.From the obtained complex structures,"correct answer"which reproduced the experimental structure and"incorrent answers"which were different from crystal structure were selected,and simulations of them were carried out.The complex between influenza A virus neuraminidase and its inhibitor was used as test set for the test calculations. For"incorret answers",the 3D structures were broken by the simulations,and the results seem to be caused by instabilities of the predicted structures

The habu genome reveals accelerated evolution of venom protein genes

Evolution of novel traits is a challenging subject in biological research. Several snake lineages developed elaborate venom systems to deliver complex protein mixtures for prey capture. To understand mechanisms involved in snake venom evolution, we decoded here the ~1.4-Gb genome of a habu, Protobothrops flavoviridis. We identified 60 snake venom protein genes (SV) and 224 non-venom paralogs (NV), belonging to 18 gene families. Molecular phylogeny reveals early divergence of SV and NV genes, suggesting that one of the four copies generated through two rounds of whole-genome duplication was modified for use as a toxin. Among them, both SV and NV genes in four major components were extensively duplicated after their diversification, but accelerated evolution is evident exclusively in the SV genes. Both venom-related SV and NV genes are significantly enriched in microchromosomes. The present study thus provides a genetic background for evolution of snake venom composition