Molecular dynamics simulation study of PTP1B with allosteric inhibitor and its application in receptor based pharmacophore modeling

Allosteric inhibition of protein tyrosine phosphatase 1B (PTP1B), has paved a new path to design specific inhibitors for PTP1B, which is an important drug target for the treatment of type II diabetes and obesity. The PTP1B_1–282-allosteric inhibitor complex crystal structure lacks α7 (287–298) and moreover there is no available 3D structure of PTP1B_1–298 in open form. As the interaction between α7 and α6–α3 helices plays a crucial role in allosteric inhibition, α7 was modeled to the PTP1B_1–282 in open form complexed with an allosteric inhibitor (compound-2) and a 5 ns MD simulation was performed to investigate the relative orientation of the α7–α6–α3 helices. The simulation conformational space was statistically sampled by clustering analyses. This approach was helpful to reveal certain clues on PTP1B allosteric inhibition. The simulation was also utilized in the generation of receptor based pharmacophore models to include the conformational flexibility of the protein-inhibitor complex. Three cluster representative structures of the highly populated clusters were selected for pharmacophore model generation. The three pharmacophore models were subsequently utilized for screening databases to retrieve molecules containing the features that complement the allosteric site. The retrieved hits were filtered based on certain drug-like properties and molecular docking simulations were performed in two different conformations of protein. Thus, performing MD simulation with α7 to investigate the changes at the allosteric site, then developing receptor based pharmacophore models and finally docking the retrieved hits into two distinct conformations will be a reliable methodology in identifying PTP1B allosteric inhibitors. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

N-(2-吡啶甲基)-L-丝氨酸铜配合物的合成、晶体结构及抑制蛋白酪氨酸磷酸酶活性

在甲醇溶液中, 还原希夫碱HL[N-(2-吡啶甲基)-L-丝氨酸]与CuCl₂·2H₂O以摩尔比1∶1反应, 得到1个新的中性单核铜配合物[CuLCl(H₂O)](Ⅰ). 通过X射线单晶衍射、 元素分析、 红外光谱、 电喷雾质谱和粉末X射线衍射分析等对其进行了表征. 晶体结构分析表明, 在该配合物中还原希夫碱以三齿双螯合环配位到中心铜离子, 同时氯离子和溶剂水分子也参与配位, 形成1个具有四方锥构型的五配位铜(Ⅱ)配合物, 该配合物通过分子间弱相互作用连接成二维超分子结构. 生物活性测试结果表明, 配合物Ⅰ能有效抑制蛋白酪氨酸磷酸酶1B(PTP1B)和T细胞蛋白酪氨酸磷酸酶(TCPTP), IC₅₀值分别为0.32和0.45 μmol/L.     

V型对称三唑并噻二唑衍生物的合成与生物活性

为构筑V型对称结构的三唑并噻二唑类衍生物, 将间苯二甲酸和5-氨基间苯二甲酸分别与3-脂肪基-1,2,4-三唑(1)缩合, 在POCl₃催化下, 合成了14个V型对称结构三唑并噻二唑稠环衍生物(2a~2g和3a~3g), 其中13个化合物为首次合成.通过红外光谱、 核磁共振波谱和高分辨质谱等对目标产物的结构进行了表征. 研究了目标产物对细胞周期分裂蛋白25B(Cdc25B)和蛋白酪氨酸磷酸酶1B(PTP1B)的抑制性能, 结果发现, 部分目标产物对Cdc25B表现出良好的抑制活性, 其中化合物3b和3f的抑制活性IC₅₀值分别为(1.34±0.39)和(0.61±0.09) μg/mL, 有望作为治疗癌症的潜在Cdc25B抑制剂; 化合物3b~3g对PTP1B均表现出良好的抑制活性, 其中化合物3b和3e的IC₅₀值分别为(0.36±0.05)和(0.97±0.08) μg/mL, 有望作为治糖尿病的潜在PTP1B抑制剂.     

PTP1B Inhibitory Secondary Metabolites from an Antarctic Fungal Strain Acremonium sp. SF-7394

Chemical investigation of the Antarctic lichen-derived fungal strain Acremonium sp. SF-7394 yielded a new amphilectane-type diterpene, acrepseudoterin (1), and a new acorane-type sesquiterpene glycoside, isocordycepoloside A (2). In addition, three known fungal metabolites, (−)-ternatin (3), [D-Leu]-ternatin (4), and pseurotin A (5), were isolated from the EtOAc extract of the fungal strain. Their structures were mainly elucidated by analyzing their NMR and MS data. The absolute configuration of 1 was proposed by electronic circular dichroism calculations, and the absolute configuration of the sugar unit in 2 was determined by a chemical method. The inhibitory effects of the isolated compounds on protein tyrosine phosphatase 1B (PTP1B) were evaluated by enzymatic assays; results indicated that acrepseudoterin (1) and [D-Leu]-ternatin (4) dose-dependently inhibited the enzyme activity with IC₅₀ values of 22.8 ± 1.1 μM and 14.8 ± 0.3 μM, respectively. Moreover, compound 1 was identified as a competitive inhibitor of PTP1B.     

Phytochemical identification of Lithocarpus polystachyus extracts by ultra-high-performance liquid chromatography–quadrupole time-of-flight–MS and their protein tyrosine phosphatase 1B and α-glucosidase activities

Lithocarpus polystachyus leaves exhibit antidiabetic activity and is consumed as a herbal tea in China. In this study, phytochemical profiles of L. polystachyus leaves were identified and characterized by ultra-high-performance liquid chromatography–quadrupole time-of-flight–MS in both positive and negative ion modes. A total of 17 compounds were tentatively characterized and identified by accurate mass and characteristic fragment ions. The total phenolic contents in the leaf extracts ranged from 9.0 to 13.4 g gallic acid equivalents/100 g of dry weight (DW). In addition, the effect of these extracts on inhibiting the activities of α-glucosidase and protein tyrosine phosphatase 1B (PTP1B) were evaluated. L. polystachyus extracts demonstrated significant inhibition of α-glucosidase (more than 88.1% at a concentration of 1.25 mg/mL) and acarbose (93.6% at a concentration of 5 mg/mL) while the PTP1B inhibition rate was over 84.3%. The antioxidant capacities of the leaf extracts were determined using 2,2-diphenyl-1-picrylhydrazyl, ABTS, and ferric reducing ability of plasma methods and ranged from 50.5 to 72.5 g trolox, from 43.2 to 77.7 g trolox, and from 5.0 to 10.6 g butylated hydroxytoluene (BHT; equaling trolox or BHT per 100 g of DW), respectively. Based on these results, L. polystachyus can be considered as a functional food owing to its antidiabetic and antioxidative activities, which are attributed to its rich phenolic and dihydrochalcone contents.     

A Novel Sarsolenane Diterpene as a PTP1B Inhibitor from Hainan Soft Coral Sarcophyton trocheliophorum Marenzeller

A novel sarsolenane diterpene, named secodihydrosarsolenone ( 1 ), as a minor component was obtained from the South China Sea soft coral Sarcophyton trocheliophorum Marenzeller. Its structure was elucidated by detailed spectroscopic analysis. Compound 1 exhibited moderate inhibitory activity (IC₅₀ =13.7 µmol•L⁻¹) against protein tyrosine phosphatase 1B (PTP1B ), a key target for the treatment of type 2 diabetes, representing the first report of PTP1B inhibitory activity for sarsolenane diterpenes. This discovery promotes computational prediction of binding mode between the enzyme and the metabolite, suggesting a crucial role of the residues Tyr46, Ser216 and Arg221 in the binding action.     

Insight into Gentisic Acid Antidiabetic Potential Using In Vitro and In Silico Approaches

Numerous scientific studies have confirmed the beneficial therapeutic effects of phenolic acids. Among them gentisic acid (GA), a phenolic acid extensively found in many fruit and vegetables has been associated with an enormous confirmed health benefit. The present study aims to evaluate the antidiabetic potential of gentisic acid and highlight its mechanisms of action following in silico and in vitro approaches. The in silico study was intended to predict the interaction of GA with eight different receptors highly involved in the management and complications of diabetes (dipeptidyl-peptidase 4 (DPP4), protein tyrosine phosphatase 1B (PTP1B), free fatty acid receptor 1 (FFAR1), aldose reductase (AldR), glycogen phosphorylase (GP), α-amylase, peroxisome proliferator-activated receptor gamma (PPAR-γ) and α-glucosidase), while the in vitro study studied the potential inhibitory effect of GA against α-amylase and α-glucosidase. The results indicate that GA interacted moderately with most of the receptors and had a moderate inhibitory activity during the in vitro tests. The study therefore encourages further in vivo studies to confirm the given results.     

Synthesis of Triazole‐Linked Amino Acid‐Aryl C‐Glycoside Hybrids via Click Chemistry as Novel PTP1B Inhibitors

Triazolyl phenylalanine and tyrosine‐aryl C‐glycoside hybrids were readily synthesized via microwave‐assisted Cu(I)‐catalyzed azide‐alkyne 1,3‐dipolar cycloaddition in high yields. Successive enzymatic assay identified the synthesized glycoconjugates as novel PTP1B inhibitors with low micromole‐ranged inhibitory activity and at least several‐fold selectivity over other homologous PTPs tested. In addition, the benzyl groups on glucosyl moiety were found crucial toward PTP1B inhibition.     

Synthesis and biological evaluation of novel N-(alkyoxyphenyl)- aminocarbonylbenzoic acid derivatives as PTP1B inhibitors

Based on the fact that petroselinic acid showed good inhibitory activity (IC50=6.99 µmol/L) against protein tyrosine phophatase 1B(PTP1B) in vitro，a series of novel N-(alkoxyphenyl)-aminocarbonyl benzoic acid derivatives were designed and synthesised. The results indicated that most of the derivatives showed more potent activities against PTP1B. Especially, compound 13 had obvious activity with an IC50 of 106 nmol/L in vitro.     

多管藻中具有PTP1B酶抑制活性的新化合物

应用正相硅胶、凝胶SephadexLH20柱色谱和反相HPLC等方法,从多管藻(Polysiphoniaurceolata)中分离得到6个溴酚类化合物,通过IR、MS、1D和2DNMR等波谱技术分析鉴定,发现一个有明显的PTP1B抑制活性(IC50=4·9μg/mL)的新化合物:3-溴-4-[3-溴-4,5-二羟基苯基]甲基-5-羟甲基-1,2-二苯酚(1)。另5个已知化合物分别为3-溴-4,5-二羟基苄基乙基醚(2)、3-溴-4,5-二羟基苯甲醇(3)、3-溴-4,5-二羟基苯甲醛(4)、3,5-二溴-4-羟基苯甲醛(5)、3,5-二溴-4-羟基苯甲醇(6)。