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.     

Structural Bases for Hesperetin Derivatives: Inhibition of Protein Tyrosine Phosphatase 1B,Kinetics Mechanism and Molecular Docking Study

In the present study, we investigated the structure-activity relationship of naturally occurring hesperetin derivatives, as well as the effects of their glycosylation on the inhibition of diabetes-related enzyme systems, protein tyrosine phosphatase 1B (PTP1B) and α-glycosidase. Among the tested hesperetin derivatives, hesperetin 5-O-glucoside, a single-glucose-containing flavanone glycoside, significantly inhibited PTP1B with an IC₅₀ value of 37.14 ± 0.07 µM. Hesperetin, which lacks a sugar molecule, was the weakest inhibitor compared to the reference compound, ursolic acid (IC₅₀ = 9.65 ± 0.01 µM). The most active flavanone hesperetin 5-O-glucoside suggested that the position of a sugar moiety at the C-5-position influences the PTP1B inhibition. It was observed that the ability to inhibit PTP1B is dependent on the nature, position, and number of sugar moieties in the flavonoid structure, as well as conjugation. In the kinetic study of PTP1B enzyme inhibition, hesperetin 5-O-glucoside led to mixed-type inhibition. Molecular docking studies revealed that hesperetin 5-O-glucoside had a higher binding affinity with key amino residues, suggesting that this molecule best fits the PTP1B allosteric site cavity. The data reported here support hesperetin 5-O-glucoside as a hit for the design of more potent and selective inhibitors against PTP1B in the search for a new anti-diabetic treatment.     

Valeriaquinone A,a unique anthraquinone–coumarin hybrid with selective inhibition of PTP1B from Knoxia valerianoides

Valeriaquinone A（1）, an unprecedented anthraquinone–coumarin hybrid, was isolated from the roots of Knoxia valerianoides. Its structure was determined by extensive spectroscopic analyses and X-ray diffraction. The plausible biosynthetic pathways for 1 were proposed. Compound 1 exhibited strong protein tyrosine phosphatase 1 B（PTP1 B） inhibition with high selectivity（> 30 fold） over homologous T cell protein tyrosine phosphatase（TCPTP） potentially by binding to an allosteric site predicted by ...     

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。     

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.     

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.     

酪氨酸蛋白磷酸酯酶1B抑制剂的分子对接和三维定量构效关系研究

用一种柔性分子对接方法(FlexX)将12个2-草酰胺苯甲酸类抑制剂和酪氨酸蛋白磷酸酯酶(PTP1B)活性口袋进行分子对接,对接程序预测的抑制剂和酶之间的相互作用能与抑制活性之间有很好的相关性(非线性相关系数R²达0.859),这说明对接结果可以比较准确地预测抑制剂和PTP1B之间的结合模式.然后,将33个同类抑制剂的骨架叠合在分子对接预测的结合构象上,用比较分子力场分析方法(CoMFA)对其进行三维定量活性构效关系研究,得到的CoMFA模型具有很好的统计相关性(交互验证回归系数q²为0.650),并可以准确地预测测试集6个化合物的活性(平均标准偏差为0.177).同时,由CoMFA模型得出的抑制剂改造信息与用FlexX预测的结合模式是一致的,进一步证明我们预测的结合模式是正确的.为研究这类抑制剂和PTP1B的结合模式及对抑制剂进行结构改造提供了信息.     

Druggability Assessment of Allosteric Proteins by Dynamics Simulations in the Presence of Probe Molecules

Druggability assessment of a target protein has emerged in recent years as an important concept in hit-to-lead optimization. A reliable and physically relevant measure of druggability would allow informed decisions on the risk of investing in a particular target. Here, we define "druggability" as a quantitative estimate of binding sites and affinities for a potential drug acting on a specific protein target. In the present study, we describe a new methodology that successfully predicts the druggability and maximal binding affinity for a series of challenging targets, including those that function through allosteric mechanisms. Two distinguishing features of the methodology are (i) simulation of the binding dynamics of a diversity of probe molecules selected on the basis of an analysis of approved drugs and (ii) identification of druggable sites and estimation of corresponding binding affinities on the basis of an evaluation of the geometry and energetics of bound probe clusters. The use of the methodology for a variety of targets such as murine double mutant-2, protein tyrosine phosphatase 1B (PTP1B), lymphocyte function-associated antigen 1, vertebrate kinesin-5 (Eg5), and p38 mitogen-activated protein kinase provides examples for which the method correctly captures the location and binding affinities of known drugs. It also provides insights into novel druggable sites and the target's structural changes that would accommodate, if not promote and stabilize, drug binding. Notably, the ability to identify high affinity spots even in challenging cases such as PTP1B or Eg5 shows promise as a rational tool for assessing the druggability of protein targets and identifying allosteric or novel sites for drug binding.     

Studies of the mechanism of selectivity of protein tyrosine phosphatase 1B (PTP1B) bidentate inhibitors using molecular dynamics simulations and free energy calculations

Bidentate inhibitors of protein tyrosine phosphatase 1B (PTP1B) are considered as a group of ideal inhibitors with high binding potential and high selectivity in treating type II diabetes. In this paper, the binding models of five bidentate inhibitors to PTP1B, TCPTP, and SHP-2 were investigated and compared by using molecular dynamics (MD) simulations and free energy calculations. The binding free energies were computed using the Molecular Mechanics/Poisson-Boltzmann Surface Area (MM/PBSA) methodology. The calculation results show that the predicted free energies of the complexes are well consistent with the experimental data. The Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) free energy decomposition analysis indicates that the residues ARG24, ARG254, and GLN262 in the second binding site of PTP1B are essential for the high selectivity of inhibitors. Furthermore, the residue PHE182 close to the active site is also important for the selectivity and the binding affinity of the inhibitors. According to our analysis, it can be concluded that in most cases the polarity of the portion of the inhibitor that binds to the second binding site of the protein is positive to the affinity of the inhibitors while negative to the selectivity of the inhibitors. We expect that the information we obtained here can help to develop potential PTP1B inhibitors with more promising specificity.     

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.     

新型二氟甲基磷酸类酪氨酸蛋白磷酸酯酶1B抑制剂的分子动力学模拟和结合自由能计算

通过分子对接建立了一系列含二氟甲基磷酸基团(DFMP)或二氟甲基硫酸基团(DFMS)的抑制剂与酪氨酸蛋白磷酸酯酶1B(PTP1B)的相互作用模式, 并通过1 ns的分子动力学模拟和molecular mechanics/generalized Born surface area (MM/GBSA)方法计算了其结合自由能. 计算获得的结合自由能排序和抑制剂与靶酶间结合能力排序一致; 通过基于主方程的自由能计算方法, 获得了抑制剂与靶酶残基间相互作用的信息, 这些信息显示DFMP/DFMS基团的负电荷中心与PTP1B的221位精氨酸正电荷中心之间的静电相互作用强弱决定了此类抑制剂的活性, 进一步的分析还显示位于DFMP/DFMS基团中的氟原子或其他具有适当原子半径的氢键供体原子会增进此类抑制剂与PTP1B活性位点的结合能力.     

Structure-based prediction of free energy changes of binding of PTP1B inhibitors

The goals were (1) to understand the driving forces in the binding of small molecule inhibitors to the active site of PTP1B and (2) to develop a molecular mechanics-based empirical free energy function for compound potency prediction. A set of compounds with known activities was docked onto the active site. The related energy components and molecular surface areas were calculated. The bridging water molecules were identified and their contributions were considered. Linear relationships were explored between the above terms and the binding free energies of compounds derived based on experimental inhibition constants. We found that minimally three terms are required to give rise to a good correlation (0.86) with predictive power in five-group cross-validation test (q2 = 0.70). The dominant terms are the electrostatic energy and non-electrostatic energy stemming from the intra- and intermolecular interactions of solutes and from those of bridging water molecules in complexes.     

Characterization of hydroxycinnamic acid derivatives binding to bovine serum albumin

Hydroxycinnamic acid derivatives (HCAs) are a group of naturally occurring polyphenolic compounds which possess various pharmacological activities. In this work, the interactions of bovine serum albumin (BSA) with six HCA derivatives, including chlorogenic acid (CHA), caffeic acid (CFA), m-coumaric acid (m-CA), p-coumaric acid (p-CA), ferulic acid (FA) and sinapic acid (SA) have been investigated by NMR spectroscopic techniques in combination with fluorescence and molecular modeling methods. Competitive STD NMR experiments using warfarin sodium and L-tryptophan as site-selective probes indicated that HCAs bind to site I in the subdomain IIA of BSA. From the analysis of the STD NMR-derived binding epitopes and molecular docking models, it was deduced that CHA, CFA, m-CA and p-CA show similar binding modes and orientation, in which the phenyl ring is in close contact with protein surface, whereas carboxyl group points out of the protein. However, FA and SA showed slightly different binding modes, due to the steric hindrance of methoxy-substituents on the phenyl ring. Relaxation experiments provided detailed information about the relationship between the affinity and structure of HCAs. The binding affinity was the strongest for CHA and ranked in the order CHA > CFA > m-CA ≥ p-CA > FA > SA, which agreed well with the results from fluorescence experiments. Based on our experimental results, we also conclude that HCAs bind to BSA mainly by hydrophobic interaction and hydrogen bonding. This study therefore provides valuable information for elucidating the mechanisms of BSA-HCAs interaction.     

A Formylglycine-Peptide for the Site-Directed Identification of Phosphotyrosine-Mimetic Fragments**

Discovery of protein-binding fragments for precisely defined binding sites is an unmet challenge to date. Herein, formylglycine is investigated as a molecular probe for the sensitive detection of fragments binding to a spatially defined protein site . Formylglycine peptide 3 was derived from a phosphotyrosine-containing peptide substrate of protein tyrosine phosphatase PTP1B by replacing the phosphorylated amino acid with the reactive electrophile. Fragment ligation with formylglycine occurred in situ in aqueous physiological buffer. Structures and kinetics were validated by NMR spectroscopy. Screening and hit validation revealed fluorinated and non-fluorinated hit fragments being able to replace the native phosphotyrosine residue. The formylglycine probe identified low-affinity fragments with high spatial resolution as substantiated by molecular modelling. The best fragment hit, 4-amino-phenyl-acetic acid, was converted into a cellularly active, nanomolar inhibitor of the protein tyrosine phosphatase SHP2.     

Mononuclear copper(II) complexes with 3,5-substituted-4-salicylidene-amino-3,5-dimethyl-1,2,4-triazole: synthesis, structure and potent inhibition of protein tyrosine phosphatases

Six copper complexes of Schiff base ligands containing 3,5-substituted-4-salicylideneamino-3,5-dimethyl-1,2,4-triazole have been synthesized and well characterized. The structures of complexes 1 and 2 were determined by X-ray crystal analysis. Fluorescence and potentiometric study indicated that in the physiological pH range, one ligand was dissociated from the complexes to form 1:1 mononucleus copper complexes. The complexes potently inhibit protein tyrosine phosphatase 1B (PTP1B), T-cell protein tyrosine phosphatase (TCPTP), megakaryocyte protein tyrosine phosphatase 2 (PTP-MEG2) and Src homology phosphatase 1 (SHP-1) with 3-4 fold selectivity against PTP1B over TCPTP and PTP-MEG2, and 3-9 fold over SHP-1, but display almost no inhibition against Src homology phosphatase 2 (SHP-2). Complex 1 inhibits PTP1B with a competitive model with K(i) of 30 nM. Substitution with small groups at the phenyl of the ligand does not obviously influence the inhibitory ability of the complexes.     

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.     

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.     

新型细胞分裂周期25磷酸酯酶B和蛋白酪氨酸磷酸酶1B抑制剂三唑并噻二唑-均三嗪的合成

以苯亚氨基为桥,设计合成了18个含有三唑并噻二唑和均三嗪双杂环的新型分子(4a~4i和5a~5i),并利用红外光谱、核磁共振谱和高分辨质谱等技术手段对其进行了结构表征。将吗啉和四氢吡咯分别与三聚氯氰发生双取代反应合成三嗪衍生物(1A和1B),然后将1A和1B分别与对氨基苯甲酸反应,合成重要中间体(2A和2B)。通过熔融法将8种脂肪酸与二氨基硫脲缩合得1,2,4-三唑衍生物3a~3h,最后将2A和2B在三氯氧磷和四丁基溴化铵催化下分别与3a~3h反应得目标产物。为了进一步比较3-脂肪基和3-苯基对药效活性的影响,利用相同方法设计合成了目标产物4i和5i。评价了目标产物对细胞分裂周期25磷酸酯酶B(Cdc25B)和蛋白酪氨酸磷酸酶1B(PTP1B)抑制活性。结果发现:所有目标分子对Cdc25B均表现出良好的抑制活性,半抑制浓度(IC_(50)值)在2.40~0.31 mg/L之间,目标分子4a~4f和5a~5i的IC_(50)值均低于阳性参照物Na_3VO_4[(1.25±0.14)mg/L],有望成为潜在的Cdc25B抑制剂;在PTP1B测试中,14个目标分子具有优良的抑制活性,IC_(50)值在0.98~0.37 mg/L之间,低于阳性参照物齐墩果酸[(1.19±0.27)mg/L],有望成为潜在的PTP1B抑制剂。     

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.     

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.