Molecular electrostatic potentials as input for the alignment of HIV-1 integrase inhibitors in 3D QSAR

Comparative molecular similarity indices analysis (CoMSIA), a three-dimensional quantitative structure activity relationship (3D QSAR) paradigm, was used to examine the correlations between the calculated physicochemical properties and the in vitro activities (3'-processing and 3'-strand transfer inhibition) of a series of human immunodeficiency virus type 1 (HIV-1) integrase inhibitors. The training set consisted of 34 molecules from five structurally diverse classes: salicylpyrazolinones, dioxepinones, coumarins, quinones, and benzoic hydrazides. The data set was aligned using extrema of molecular electrostatic potentials (MEPs). The predictive ability of the resultant model was evaluated using a test set comprised of 7 molecules belonging to a different structural class of thiazepinediones. A CoMSIA model using an MEP-based alignment showed considerable internal as well external predictive ability (r2(cv) = 0.821, r2(pred) = 0.608 for 3'-processing; and r2(cv) = 0.759, r2(pred.) = 0.660 for 3'-strand transfer).     

In silico virtual screening of potent inhibitor to hamper the interaction between HIV-1 integrase and LEDGF/p75 interaction using E-pharmacophore modeling,molecular docking,and dynamics simulations

The rapid increase of HIV-1 infection throughout the globe has a high demand for a superior drug with lesser side effects. LEDGF/p75, the human Lens Epithelium-Derived Growth Factor is identified as a promising cellular cofactor with integrase in facilitating the viral replication in an early stage by acting as a tethering factor in the pre-integration to the chromatin. Therefore, the present study was designed to identify a potent inhibitor by applying an E-pharmacophore based virtual screening, molecular docking, and dynamics simulation approaches. Finally, ZINC22077550 and ZINC32124441 were best identified potent molecules with the efficient binding affinity, strong hydrogen bonding, and acceptable pharmacological properties to hamper the interaction between integrase and LEDGF/p75. Further, the DFT and MDS studies were also analyzed, and shown a favorable energetic state and dynamic stability then reference compound. In conclusion, we suggest that these findings could be novel therapeutics in the future and may increase the lifespan of individuals suffering from viral infection.     

Molecular Dynamics Simulation of HIV-1 Integrase Dimer Complexed with Viral DNA

The biological function of HIV‐1 integrase (IN) is to integrate viral DNA into the host cell chromosome, and the specific binding of IN with viral DNA is a precondition for IN to function correctly. Beforehand, the binding mode of IN dimer (IN₂) with the 27 bp segment of viral DNA before 3′ processing (3′‐P) was obtained via a molecular docking method. Based on the binding mode, the aim of this article was to explore the changes of motive mode and correlative motion for the IN₂ and DNA systems after their binding through dynamical cross‐correlation map (DCCM) and principal component analysis (PCA). Finally, solvent effect during the association was analyzed briefly. The results show that there is a significantly increased positive correlation in the interface region between IN₂ and viral DNA, and some obvious motive mode changes of the two systems (IN₂ and DNA) were also observed after their binding. It was found that water molecules played an important role in the recognition between IN₂ and viral DNA through analyzing the water‐mediated hydrogen bonds.     

Synthesis of potential HIV integrase inhibitors inspired by natural polyphenol structures

Drawing inspiration from the structural features of some natural polyphenols, the synthesis of two different model compounds as potential inhibitors of HIV integrase (IN) has been described. The former was characterised by a diketo acid (DKA) bioisostere, such as a β-hydroxycarbonyl moiety, between two fragments containing aromatic groups, while in the latter an epoxide linked two polyoxygenated aromatic residues. The moieties present in the structures are thought to function by chelating divalent metal ions on the enzyme catalytic site. Overall, 10 compounds were prepared and some of that submitted to molecular modelling studies (to investigate their interactions with the active site of IN), to metal titration studies (to detect their chelating capability) and to biological assays.     

A structure-based design approach to advance the allyltyrosine-based series of HIV integrase inhibitors

As of mid-2017, only one structure of the human immunodeficiency virus (HIV) integrase core domain co-crystallised with an active site inhibitor was reported. In this structure (1QS4), integrase is complexed with a diketo-acid based strand-transfer inhibitor (INSTI). This structure has been a preferred platform for the structure-based design of INSTIs despite concerns relating to structural irregularities arising from crystallographic packing effects. A survey of the current pool of 297 reported integrase catalytic core structures indicated that the anatomy of the active site in the complex structure 1QS4 exhibits subtle variations relative to all other structures examined. Consequently, the 1QS4 structure was employed for docking studies. From the docking of twenty-seven allyltyrosine analogues, a 3-point inhibitor binding motif required for activity was established and successfully utilised in the development of a tripeptide displaying an EC₅₀ value of 10 ± 5 μM in HIV infected human T-cells. Additional docking of “in-house” compound libraries unearthed a methyl ester based nitrile derivative displaying an IC₅₀ value of 0.5 μM in a combined 3′-processing and strand-transfer assay.     

HIV-1整合酶与抑制剂金精三羧酸复合物的分子动力学模拟

用分子对接程序(Autodock)将含有一个Mg²⁺的HIV-1整合酶核心区(以下简称IN-A)与抑制剂小分子金精三羧酸(简称Aurin)进行对接,预测其未知的复合物结构,然后用分子动力学(MD)方法对IN-A与Aurin的对接结果进行了950 ps的模拟.MD模拟结果发现,IN-A与Aurin形成了两个稳定的氢键,Mg²⁺也与Aurin上的氧原子形成了稳定的配键,IN-A与Aurin之间的静电相互作用能和范德华相互作用能的平均值分别为-205.8和-162.7 kJ/mol.根据MD模拟得到的IN-A与Aurin相互作用后的构象变化信息,我们对对接复合物结构进行了修正,给出了更加合理和稳定的复合物预测结构.本工作得到的HIV-1整合酶与抑制剂Aurin的结合模式信息将有助于设计和改造出效果更好的抗HIV-1整合酶的先导化合物.     

用分子对接方法预测HIV-1整合酶与金精三羧酸抑制剂的相互作用

用分子对接方法(Docking)研究了HIV-1整合酶与其抑制剂金精三羧酸的结合过程.为弄清金属离子在结合中所起的作用,选择含有一个Mg+2或不含Mg+2的两种不同的整合酶受体分别与金精三羧酸对接.结果表明, Mg+2对稳定配体与受体的结合起了重要作用. 金精三羧酸配体与含有一个金属Mg+2的整合酶受体对接,最优结合自由能为-45.19 kJ/mol. 当Mg+2失去后,整合酶的活性中心构象将发生变化,使金精三羧酸抑制剂与整合酶的结合自由能(-24.35 kJ/mol)明显增加. 预测了未知的HIV-1整合酶与其抑制剂金精三羧酸的复合物结构, 并可对基于结构的抗HIV-1整合酶的药物设计提供重要信息.