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.     

Synthesis of mangiferin derivates and study their potent PTP1B inhibitory activity

Protein tyrosine phosphatase 1B (PTP1B) has received considerable attention from the drug industry as a potential treatment for diabetes mellitus.Mangiferin has been reported to possess significant antidiabetic activity.Based on the previous study,eight new mangiferin derivates were synthesized and evaluated for their PTP1B inhibitory activity.Some of them displayed good inhibitory activity on PTP1B.     

Chemical constituents from Sambucus adnata and their protein-tyrosine phosphatase 1B inhibitory activities

The MeOH extract from the whole plants of Sambucus adnata has shown significant protein-tyrosine phosphatase 1B (PTP1B) inhibitory activity. Chemical study on the extract resulted in the isolation of thirteen compounds, including a novel triterpene (1). The structure of 1 was determined to be 1α,3β-dihydroxy-urs-12-en-11-one-3-yl palmitate on the basis of extensive spectroscopic analyses. Among the isolated compounds, ursolic acid, oleanolic acid and (±)-boehmenan showed the most potent PTP1B inhibitory activity in vitro with the IC(50) values of 4.1, 14.4 and 43.5 μm, respectively. The kinetic analysis indicated that (±)-boehmenan inhibits PTP1B activity in a competitive manner.     

3,6-二取代三唑并噻二唑衍生物的合成及其对细胞分裂周期25B磷酸酶和蛋白酪氨酸磷酸酶1B抑制活性评价

合成出了一系列含苯并咪唑/芳氧甲基骨架的3,6-二取代三唑并噻二唑衍生物3a~3l,其结构经傅里叶变换红外光谱仪(FT-IR)、核磁共振波谱仪(NMR)和元素分析得以确认。 评价了它们对细胞分裂周期25B磷酸酶(Cdc25B)/蛋白酪氨酸磷酸酶1B(PTP1B)的抑制活性,讨论了构效关系。 生物活性测试结果显示,化合物3a对Cdc25B和PTP1B的抑制活性最高,其半数抑制浓度(IC₅₀)值分别为(0.46±0.02) μg/mL和(1.77±0.40) μg/mL。 所得研究结果为开发新型Cdc25B/PTP1B抑制剂提供了参考依据。     

基于咔唑的单-/双-硫代碳酰腙衍生物的合成及Cdc25B/PTP1B抑制活性评价

合成了一系列新型的基于咔唑的单-/双-硫代碳酰腙衍生物.利用IR、1H NMR、13C NMR和元素分析对其进行了结构表征.评价了目标化合物对Cdc25B和PTP1B的抑制活性,讨论了其结构与活性的关系.实验结果显示,大部分目标化合物对Cdc25B和PTP1B表现出良好的抑制活性.其中,1,5-双[(9-戊基-3-咔唑基)亚甲基]硫代碳酰腙(4d)对Cdc25B的抑制活性最高,IC50为(0.23±0.02)μg/m L.1,5-双[(9-乙基-3-咔唑基)亚甲基]硫代碳酰腙(4a)对PTP1B的抑制活性最高, IC50为(1.00±0.16)μg/m L.对目标化合物4a和4d进行分子对接研究和密度泛函理论(DFT)计算,结果表明,目标化合物4d和4a分别进入到了Cdc25B和PTP1B酶的活性位点区域,有活性作用的主要是硫代碳酰腙和咔唑基团.     

基于咔唑的新型碳酰腙衍生物的合成及蛋白酪氨酸磷酸酶1B(PTP1B)抑制活性评价

合成出了一系列新型基于咔唑的单-/双-碳酰腙衍生物3和4.利用1H NMR、13C NMR、IR和元素分析对其进行了结构表征.评价了目标化合物对蛋白酪氨酸磷酸酶1B(PTP1B)的抑制活性,讨论了结构与活性的关系.实验结果显示,大部分化合物对PTP1B具有良好的抑制活性,其中1,5-双[(9-丁基-3-咔唑基)亚甲基]碳酰腙(4c)的抑制活性最高,IC50=(4.81±0.41)mmol/L,且活性高于对照药物齐墩果酸.对目标化合物1-[(9-庚基-3-咔唑基)亚甲基]碳酰腙(3f)和4c进行分子对接研究和密度泛函理论(DFT)计算.分子对接结果表明,化合物3f和4c结合到PTP1B酶由螺旋α3和α6形成的活性位点,与PTP1B酶通过氢键、极性、疏水和p-p等相互作用形成了稳定的复合物.     

Inhibition of protein tyrosine phosphatase 1beta by hispidin derivatives isolated from the fruiting body of Phellinus linteus

Protein tyrosine phosphatase 1beta (PTP1beta) acts as a negative regulator of insulin signaling. Selective inhibition of PTP1beta has served as a potential drug target for the treatment of type 2 diabetes mellitus. We evaluated the inhibitory effect of Phellinus linteus against PTP1beta as part of our ongoing search for natural therapeutic and preventive agents for diabetes mellitus. Fractions of the P. linteus extract were found to exhibit significant inhibitory activities against PTP1beta. In an attempt to identify bioactive components, we isolated, from the most active ethyl acetate fraction, five hispidin derivatives (phelligridimer A, davallialactone, hypholomine B, interfungins A, and inoscavin A) and four phenolic compounds (protocatechuic acid, protocatechualdehyde, caffeic acid, and ellagic acid). The chemical structures of these compounds were elucidated from spectroscopic evidence and by comparison with published data. All the compounds strongly inhibited PTP1beta activity in an in vitro assay; their IC50 values ranged from 9.0 +/- 0.01 to 58.2 +/- 0.3 microM. Our results indicated that the hispidin skeleton may be an important moiety for inhibitory activity of the above compounds against PTP1beta. Thus, hispidin derivatives could be a potent new class of natural PTP1beta inhibitors.     

Total synthesis of bis-（2,3-dibromo-4,5-dihydroxyphenyl）-methane as potent PTP1B inhibitor

Protein tyrosine phosphatase 1B （PTP1B） plays an important role as a negative regulator and has been proved to be an effective target for the treatment of type 2 diabetes mellitus. Bis-（2,3-dibromo-4,5-dihydroxyphenyl）-methane 7 was first reported as a natural bromophenol with significant inhibition against PTP1B which was isolated from red algae Rhodomela conrervoides. Intrigued by its astonishing activity （IC50 = 2.4 μmol/L）, compound 7 was synthesized with the overall yield of 24% and evaluated for its PTPIB inhibitory activity compared with natural compound.     

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.     

Indole- and Pyrazole-Glycyrrhetinic Acid Derivatives as PTP1B Inhibitors: Synthesis,In Vitro and In Silico Studies

Regulating insulin and leptin levels using a protein tyrosine phosphatase 1B (PTP1B) inhibitor is an attractive strategy to treat diabetes and obesity. Glycyrrhetinic acid (GA), a triterpenoid, may weakly inhibit this enzyme. Nonetheless, semisynthetic derivatives of GA have not been developed as PTP1B inhibitors to date. Herein we describe the synthesis and evaluation of two series of indole- and N-phenylpyrazole-GA derivatives (4a–f and 5a–f). We measured their inhibitory activity and enzyme kinetics against PTP1B using p-nitrophenylphosphate (pNPP) assay. GA derivatives bearing substituted indoles or N-phenylpyrazoles fused to their A-ring showed a 50% inhibitory concentration for PTP1B in a range from 2.5 to 10.1 µM. The trifluoromethyl derivative of indole-GA (4f) exhibited non-competitive inhibition of PTP1B as well as higher potency (IC₅₀ = 2.5 µM) than that of positive controls ursolic acid (IC₅₀ = 5.6 µM), claramine (IC₅₀ = 13.7 µM) and suramin (IC₅₀ = 4.1 µM). Finally, docking and molecular dynamics simulations provided the theoretical basis for the favorable activity of the designed compounds.     

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.     

含氮杂环氧钒配合物对PTP1B和ALP的抑制活性研究

蛋白酪氨酸磷酸酶1B (protein tyrosine phosphatase 1B, PTP1B)是当前开发治疗糖尿病药物的优秀靶标, 也是钒配合物抗糖尿病作用相关的重要靶蛋白. 研究了三种含氮平面杂环螯合配体2,2’-联咪唑(L1), 2,2’-联吡啶(L2), 1,10-邻菲咯啉(L3)的氧钒配合物对PTP1B以及碱性磷酸酶(alkaline phosphatase, ALP)的体外抑制作用. 结果表明, 1∶1和2∶1型配位的氧钒化合物均表现出对PTP1B较强的抑制活性, IC50值在120～260 nmol/L间, 抑制能力接近双麦芽酚氧钒配合物(BMOV). 抑制动力学实验表明这些氧钒配合物对PTP1B的抑制模式均为竞争性抑制, 抑制常数在20～160 nmol/L. 其对PTP1B抑制活性较ALP高103倍, 表明氧钒配合物对两种磷酸酶的抑制具有一定的选择性.     

Protein tyrosine phosphatase 1B inhibitors from a marine-derived fungal strain aspergillus sp. SF-5929

Abstract

In the course of our continuing investigation of bioactive secondary metabolites from marine-derived fungal strains, a racemate of a novel diphenolic derivative named (±)-tylopilusin D (1) along with ten previously known secondary metabolites (2–11) were isolated from a marine-derived fungal strain Aspergillus sp. SF-5929. Their structures were elucidated mainly by analysis of NMR and MS data. In addition, the inhibitory effects of the isolated compounds against protein tyrosine phosphatase 1B (PTP1B) activity were evaluated, and compounds 1, 2, and 5–7 inhibited PTP1B activity with IC₅₀ values ranging from 3.3 to 8.1?µM. Kinetics studies suggested that compounds 1, 2, and 5 had noncompetitive inhibitory effects against PTP1B.     

1,4-双[3-脂肪基/苯基-1,2,4-三唑并[3,4-b]-1,3,4-噻二唑-6-基]芳基衍生物的合成与生物活性

在三氯氧磷催化下, 6种3-脂肪基-1,2,4-三唑(1a~1f)和3-苯基-1,2,4-三唑(1g)分别与对苯二甲酸和2-氨基-1,4-对苯二甲酸发生环化反应, 高产率合成了14种双枝三唑并噻二唑稠环衍生物(2和3), 并对其进行了结构表征及药物活性测试. 目标化合物对Cdc25B和PTP1B抑制活性筛选结果表明, 化合物2f, 3a和3g对Cdc25B有较高的抑制活性, IC₅₀值分别为(3.45±0.60), (0.69±0.10)和(1.52±0.19) μg/mL; 化合物3a和3b对PTP1B表现出较高的抑制活性, IC₅₀值分别为(0.98±0.13)和(2.00±0.16) μg/mL.     

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.     

4-苯基-1,3-硒唑衍生物的合成及其对蛋白酪氨酸磷酸酯酶-1B抑制活性

蛋白酪氨酸磷酸酯酶-1B(PTP1B)是抗糖尿病治疗的重要靶点,因此创制活性优良的PTP1B抑制剂具有重要意义。 本文设计并合成了11个含1,3-硒唑和1,2,4-三唑活性组块新型结构目标分子(ZLXZ1-ZLXZ11),并利用傅里叶变换红外光谱仪(FTIR)、核磁共振波谱仪(NMR)和高分辨质谱(HRMS)等对其进行了结构表征。 首先选择ZLXZ1和ZLXZ11在MOE 2015.10程序上,与PTP1B进行分子对接模拟,结果表明,在ZLXZ1分子中硒唑环上的硒原子与PTP1B中副催化位点Tyr46、Ala217、Lys120和Asp 48分别形成了π-H作用和氢键作用。 在ZLXZ11分子中硒唑上的硒原子与PTP1B中Asp181、Arg221和Asp48形成了氢键作用。 在分子对接模拟的基础上,测试了11个目标分子的抑制活性,结果表明,所有目标分子的抑制率均在87.02%以上,其中3个目标分子PTP1B抑制活性高于阳性参照物齐墩果酸,抑制活性优良,有望成为潜在的PTP1B抑制剂。     

新型1-(1,3,5-三嗪-6-基)-3-甲基-4-(5-苯基-1,3,4-噁二唑-2-基)吡唑的合成及活性评价

设计合成了18个以吡唑桥连1,3,4-噁二唑和1,3,5-三嗪的新型多杂环分子[7A(a~f),7B(a~f)和7C(a~f)];通过红外光谱(IR)、核磁共振波谱(NMR)和高分辨质谱(HRMS)等对目标分子进行了结构表征;评价了目标分子对蛋白酪氨酸磷酸酯酶1B(PTP1B)和细胞分裂周期25磷酸酯酶B(Cdc25B)的抑制活性.结果表明,所有目标分子对PTP1B和Cdc25B均有较好的抑制活性,其中,9个目标分子表现出优异的PTP1B和Cdc25B抑制效果,IC50值低于齐墩果酸(PTP1B抑制活性测试参照物)和正钒酸钠(Cdc25B抑制活性测试阳性参照物),有望成为潜在的PTP1B和Cdc25B抑制剂.     

Molecular Dynamics Approach to Probe the Allosteric Inhibition of PTP1B by Chlorogenic and Cichoric Acid

Protein tyrosine phosphatase 1B (PTP1B), a major negative regulator of the insulin and leptin signaling pathway, is a potential target for therapeutic intervention against diabetes and obesity. The recent discovery of an allosteric site in PTP1B has created an alternate strategy in the development of PTP1B targeted therapy. The current study investigates the molecular interactions between the allosteric site of PTP1B with two caffeoyl derivatives, chlorogenic acid (CGA) and cichoric acid (CHA), using computational strategies. Molecular docking analysis with CGA and CHA at the allosteric site of PTP1B were performed and the resulting protein-ligand complexes used for molecular dynamics simulation studies for a time scale of 10 ns. Results show stable binding of CGA and CHA at the allosteric site of PTP1B. The flexibility of the WPD loop was observed to be constrained by CGA and CHA in the open (inactive), providing molecular mechanism of allosteric inhibition. The allosteric inhibition of CGA and CHA of PTP1B was shown to be favorable due to no restriction by the α-7 helix in the binding of CGA and CHA at the allosteric binding site. In conclusion, our results exhibit an inhibitory pattern of CGA and CHA against PTP1B through potent binding at the allosteric site.     

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.