Virtual screening and rational drug design method using structure generation system based on 3D-QSAR and docking

An efficient virtual and rational drug design method is presented. It combines virtual bioactive compound generation with 3D-QSAR model and docking. Using this method, it is possible to generate a lot of highly diverse molecules and find virtual active lead compounds. The method was validated by the study of a set of anti-tumor drugs. With the constraints of pharmacophore obtained by DISCO implemented in SYBYL 6.8, 97 virtual bioactive compounds were generated, and their anti-tumor activities were predicted by CoMFA. Eight structures with high activity were selected and screened by the 3D-QSAR model. The most active generated structure was further investigated by modifying its structure in order to increase the activity. A comparative docking study with telomeric receptor was carried out, and the results showed that the generated structures could form more stable complexes with receptor than the reference compound selected from experimental data. This investigation showed that the proposed method was a feasible way for rational drug design with high screening efficiency.     

Virtual screening and rational drug design method using structure generation system based on 3D-QSAR and docking

An efficient virtual and rational drug design method is presented. It combines virtual bioactive compound generation with 3D-QSAR model and docking. Using this method, it is possible to generate a lot of highly diverse molecules and find virtual active lead compounds. The method was validated by the study of a set of anti-tumor drugs. With the constraints of pharmacophore obtained by DISCO implemented in SYBYL 6.8, 97 virtual bioactive compounds were generated, and their anti-tumor activities were predicted by CoMFA. Eight structures with high activity were selected and screened by the 3D-QSAR model. The most active generated structure was further investigated by modifying its structure in order to increase the activity. A comparative docking study with telomeric receptor was carried out, and the results showed that the generated structures could form more stable complexes with receptor than the reference compound selected from experimental data. This investigation showed that the proposed method was a feasible way for rational drug design with high screening efficiency.     

Identifying conformational changes of the β2 adrenoceptor that enable accurate prediction of ligand/receptor interactions and screening for GPCR modulators

The new β₂ Adrenoceptor (β₂AR) crystal structures provide a high-resolution snapshot of receptor interactions with two particular partial inverse agonists, (−)-carazolol and timolol. However, both experimental and computational studies of GPCR structure are significantly complicated by the existence of multiple conformational states coupled to ligand type and receptor activity. Agonists and antagonists induce or stabilize distinct changes in receptor structure that mediate a range of pharmacological activities. In this work, we (1) established that the existing β₂AR crystallographic conformers can be extended to describe ligand/receptor interactions for additional antagonist types, (2) generated agonist-bound receptor conformations, and (3) validated these models for agonist and antagonist virtual ligand screening (VLS). Using a ligand directed refinement protocol, we derived a single agonist-bound receptor conformation that selectively retrieved a diverse set of full and partial β₂AR agonists in VLS trials. Additionally, the impact of extracellular loop two conformation on VLS was assessed by docking studies with rhodopsin-based β₂AR homology models, and loop-deleted receptor models. A general strategy for constructing and selecting agonist-bound receptor pocket conformations is presented, which may prove broadly useful in creating agonist and antagonist bound models for other GPCRs. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Homology modelling of the human adenosine A2B receptor based on X-ray structures of bovine rhodopsin, the β2-adrenergic receptor and the human adenosine A2A receptor

A three-dimensional model of the human adenosine A_2B receptor was generated by means of homology modelling, using the crystal structures of bovine rhodopsin, the β₂-adrenergic receptor, and the human adenosine A_2A receptor as templates. In order to compare the three resulting models, the binding modes of the adenosine A_2B receptor antagonists theophylline, ZM241385, MRS1706, and PSB601 were investigated. The A_2A-based model was much better able to stabilize the ligands in the binding site than the other models reflecting the high degree of similarity between A_2A and A_2B receptors: while the A_2B receptor shares about 21% of the residues with rhodopsin, and 31% with the β₂-adrenergic receptor, it is 56% identical to the adenosine A_2A receptor. The A_2A-based model was used for further studies. The model included the transmembrane domains, the extracellular and the intracellular hydrophilic loops as well as the terminal domains. In order to validate the usefulness of this model, a docking analysis of several selective and nonselective agonists and antagonists was carried out including a study of binding affinities and selectivities of these ligands with respect to the adenosine A_2A and A_2B receptors. A common binding site is proposed for antagonists and agonists based on homology modelling combined with site-directed mutagenesis and a comparison between experimental and calculated affinity data. The new, validated A_2B receptor model may serve as a basis for developing more potent and selective drugs.     

Receptor-based 3D QSAR analysis of estrogen receptor ligands – merging the accuracy of receptor-based alignments with the computational efficiency of ligand-based methods

One of the major challenges in computational approaches to drug design is the accurate prediction of binding affinity of biomolecules. In the present study several prediction methods for a published set of estrogen receptor ligands are investigated and compared. The binding modes of 30 ligands were determined using the docking program AutoDock and were compared with available X-ray structures of estrogen receptor-ligand complexes. On the basis of the docking results an interaction energy-based model, which uses the information of the whole ligand-receptor complex, was generated. Several parameters were modified in order to analyze their influence onto the correlation between binding affinities and calculated ligand-receptor interaction energies. The highest correlation coefficient (r ² = 0.617, q ² _LOO = 0.570) was obtained considering protein flexibility during the interaction energy evaluation. The second prediction method uses a combination of receptor-based and 3D quantitative structure-activity relationships (3D QSAR) methods. The ligand alignment obtained from the docking simulations was taken as basis for a comparative field analysis applying the GRID/GOLPE program. Using the interaction field derived with a water probe and applying the smart region definition (SRD) variable selection, a significant and robust model was obtained (r ² = 0.991, q ² _LOO = 0.921). The predictive ability of the established model was further evaluated by using a test set of six additional compounds. The comparison with the generated interaction energy-based model and with a traditional CoMFA model obtained using a ligand-based alignment (r ² = 0.951, q ² _LOO = 0.796) indicates that the combination of receptor-based and 3D QSAR methods is able to improve the quality of the underlying model.     

中药活性成分对血栓素A2受体抑制作用的分子模拟

中药中黄酮类化合物和白藜芦醇等活性成分对血栓素A2受体具有抑制作用,但具体机理不详.本研究通过同源模建方法,以墨鱼视紫红质蛋白为模板,构建血栓素A2受体的蛋白质结构模型.并使用分子对接方法研究中药活性成分白藜芦醇和芹菜苷元与血栓素A2受体模型的作用方式,据此建立药效团模型,筛选其他潜在的血栓素A2受体抑制剂.结果表明:白藜芦醇等中药活性成分能与血栓素A2受体活性口袋中的残基发生氢键作用,结合方式与血栓素相似.血栓素与Ser201、Leu198、Arg295和Thr298发生氢键作用,白藜芦醇等活性成分与Ser201、Leu198和Arg295发生氢键作用.建立的药效团模型由7个药效元素以及排斥性空间元素组成,经测试对高活性的血栓素A2受体抑制剂有比较好的选择性.使用该药效团模型对中药天然产物数据库进行筛选,命中了一批可能具有血栓素A2受体抑制作用的活性化合物.其中一些已经报道有抑制血小板凝聚活性.本研究表明血栓素A2受体可能是活血化瘀类中药的一个潜在的靶点.     

Novel neoclerodane diterpene derivatives from the smoke of salvinorin A

Salvinorin A is a naturally occurring potent and selective kappa opioid receptor agonist, and smoking salvinorin A produces the most intense hallucinogenic effects in human. Eight neoclerodane diterpene derivatives were isolated from the smoke of salvinorin A, and their structures were identified by spectroscopic methods. The major structural changes include epimerizations, eliminations, and rearrangements.     

Exploring the molecular basis of selectivity in A1 adenosine receptors agonists: a case study

Adenosine is a naturally occurring purine nucleoside that has a wide variety of well-documented regulatory functions and physiological roles. Selective activation of the adenosine A₁ receptor has drawn attention in drug discovery for the therapeutic effects on neural and cardiovascular disorders. We have developed a model of the human A₁ adenosine receptor using bovine rhodopsin as a template. A flexible docking approach has been subsequently carried out for evaluating the molecular interactions of twenty-one selective A₁ agonists with the receptor model. The results of these studies are consistent with mutational and biochemical data. In particular, they highlight a wide hydrogen-bonding network between the nucleoside portion of the ligands and the A₁ receptor as well as key amino acids for hydrophobic interactions with the different N⁶-groups of the agonists. The models presented here provide a detailed molecular map for the selective stimulation of the adenosine A₁ receptor subtype and a steady basis for the rational design of new A₁ selective ligands.     

Forensic analysis of <Emphasis Type="Italic">Salvia divinorum</Emphasis> using multivariate statistical procedures. Part II: association of adulterated samples to <Emphasis Type="Italic">S. divinorum</Emphasis>

Salvia divinorum is a plant material that is of forensic interest due to the hallucinogenic nature of the active ingredient, salvinorin A. In this study, S. divinorum was extracted and spiked onto four different plant materials (S. divinorum, Salvia officinalis, Cannabis sativa, and Nicotiana tabacum) to simulate an adulterated sample that might be encountered in a forensic laboratory. The adulterated samples were extracted and analyzed by gas chromatography–mass spectrometry, and the resulting total ion chromatograms were subjected to a series of pretreatment procedures that were used to minimize non-chemical sources of variance in the data set. The data were then analyzed using principal components analysis (PCA) to investigate association of the adulterated extracts to unadulterated S. divinorum. While association was possible based on visual assessment of the PCA scores plot, additional procedures including Euclidean distance measurement, hierarchical cluster analysis, Student’s t tests, Wilcoxon rank-sum tests, and Pearson product moment correlation were also applied to the PCA scores to provide a statistical evaluation of the association observed. The advantages and limitations of each statistical procedure in a forensic context were compared and are presented herein.     

The Antagonist pGlu-βGlu-Pro-NH2 Binds to an Allosteric Site of the Thyrotropin-Releasing Hormone Receptor

After we identified pGlu-βGlu-Pro-NH₂ as the first functional antagonist of the cholinergic central actions of the thyrotropin-releasing hormone (TRH, pGlu-His-Pro-NH₂), we became interested in finding the receptor-associated mechanism responsible for this antagonism. By utilizing a human TRH receptor (hTRH-R) homology model, we first refined the active binding site within the transmembrane bundle of this receptor to enhance TRH’s binding affinity. However, this binding site did not accommodate the TRH antagonist. This directed us to consider a potential allosteric binding site in the extracellular domain (ECD). Searches for ECD binding pockets prompted the remodeling of the extracellular loops and the N-terminus. We found that different trajectories of ECDs produced novel binding cavities that were then systematically probed with TRH, as well as its antagonist. This led us to establish not only a surface-recognition binding site for TRH, but also an allosteric site that exhibited a selective and high-affinity binding for pGlu-βGlu-Pro-NH₂. The allosteric binding of this TRH antagonist is more robust than TRH’s binding to its own active site. The findings reported here may shed light on the mechanisms and the multimodal roles by which the ECD of a TRH receptor is involved in agonist and/or antagonist actions.     

Hierarchical virtual screening: identification of potential high-affinity and selective β(3)-adrenergic receptor agonists

The hierarchical virtual screening (HVS) study, consisting of pharmacophore modelling, docking and VS of the generated focussed virtual library, has been carried out to identify novel high-affinity and selective β(3)-adrenergic receptor (β-AR) agonists. The best pharmacophore model, comprising one H-bond donor, two hydrophobes, one positive ionizable and one negative ionizable feature, was developed based on a training set of 51 β(3)-AR agonists using the pharmacophore generation protocol implemented in Discovery Studio. The model was further validated with the test set, external set and ability of the pharmacophoric features to complement the active site amino acids of the homology modelled β(3)-AR developed using MODELLER software. The focussed virtual library was generated using the structure-based insights gained from our earlier reported comprehensive study focussing on the structural basis of β-AR subtype selectivity of representative agonists and antagonists. The HVS with the sequential use of the best pharmacophore model and homology modelled β(3)-AR in the screening of the generated focussed library has led to the identification of potential virtual leads as novel high-affinity and selective β(3)-AR agonists.     

Structure characterization and spectroscopic investigation of ciprofloxacin drug

Ciprofloxacin (CPF, C₁₇H₁₈FN₃O₃) drug is used in the treatment of some bacterial infectious diseases. The drug was investigated using thermal analysis (TA) measurements (TG/DTG) and electron impact mass spectral (EI-MS) fragmentation at 70 eV techniques. Furthermore, the drug was characterized and investigated by other spectroscopic tools as IR, UV–Vis, ¹H-, and ¹³C-NMR. Semi-empirical MO calculation using PM3 procedure has been carried out on neutral molecule and positively charged species. The calculations included, bond length, bond order, bond strain, partial charge distribution, ionization energy, and heat of formation (ΔH _f). The PM3 procedure provides a basis for fine distinction among sites of initial bond cleavage, which is crucial to the rationalization of subsequent fragmentation of the molecule. The mass spectra and thermal analysis fragmentation pathways were proposed and compared to each other to select the most suitable scheme representing the correct fragmentation of this drug. From EI-MS, the main primary cleavage site of the charged molecule is that due to C–COOH bond cleavage with H-rearrangement to skeleton and CO₂ loss which can further decompose by piperazine loss. Thermal analysis of the neutral form of the drug reveals the high response of the drug to the temperature variation with very fast rate. Thermal decomposition has carried out in several sequential steps in the temperature range 40–650 °C. The initial thermal decomposition is similar to that obtained by mass spectrometric fragmentation (C–COOH fragment) but differ in that a rearrangement occurs by OH and CO loss. Therefore, comparison between MS and TA helps in selection the proper pathway representing the fragmentation of this drug. This comparison successfully confirmed by MO calculation. Finally, the effect of fluorine atom on the stability of the drug was discussed.     

Pharmacophore modelling,molecular docking and virtual screening for EGFR (HER 1) tyrosine kinase inhibitors

A pharmacophore model has been developed using diverse classes of epidermal growth factor receptor (EGFR) tyrosine kinase (TK) inhibitors useful in the treatment of human tumours. Among the top 10 generated hypotheses, the second hypothesis, with one hydrogen bond acceptor, one ring aromatic and three hydrophobic features, was found to be the best on the basis of Cat Scramble validation as well as test set prediction (r _training?=?0.89, r _test?=?0.82). The model also maps well to the external test set molecules as well as clinically active molecules and corroborates the docking studies. Finally, 10 hits were identified as potential leads after virtual screening of ZINC database for EGFR TK inhibition. The study may facilitate the designing and discovery of novel EGFR TK inhibitors.     

A homology-based model of the human 5-HT2A receptor derived from an in silico activated G-protein coupled receptor

A homology-based model of the 5-HT_2A receptor was produced utilizing an activated form of the bovine rhodopsin (Rh) crystal structure [1,2]. In silico activation of the Rh structure was accomplished by isomerization of the 11-cis-retinal (1) chromophore, followed by constrained molecular dynamics to relax the resultant high energy structure. The activated form of Rh was then used as a structural template for development of a human 5-HT_2A receptor model. Both the 5-HT_2A receptor and Rh are members of the G-protein coupled receptor (GPCR) super-family. The resulting homology model of the receptor was then used for docking studies of compounds representing a cross-section of structural classes that activate the 5-HT_2A receptor, including ergolines, tryptamines, and amphetamines. The ligand/receptor complexes that ensued were refined and the final binding orientations were observed to be compatible with much of the data acquired through both diversified ligand design and site directed mutagenesis.     

Design of new secreted phospholipase A<Subscript>2</Subscript> inhibitors based on docking calculations by modifying the pharmacophore segments of the FPL67047XX inhibitor

Docking calculations that allow the estimation of the binding energy of small ligands in the GIIA sPLA₂ active site were used in a structure-based design protocol. Four GIIA sPLA₂ inhibitors co-crystallised with the enzyme, were used for examining the enzyme active site and for testing the FlexX in SYBYL 6.8 molecular docking program to reproduce the crystallographic experimental data. The FPL67047XX inhibitor was chosen as a prototype structure for applying free energy perturbation (FEP) studies. Structural modifications of the initial structure of the FPL67047XX inhibitor (IC₅₀ 0.013 μM) were performed in an effort to optimise the interactions in the GIIA sPLA₂ active site. The structural modifications were based on: (1) the exploration of absolute configuration (i.e. comparison of the binding score of (R)- and (S)-enantiomers); (2) bioisosterism (i.e. replacement of the carboxylate group with the bioisosteric sulphonate and phosphonate groups); (3) insertion of substituents that fit better in the active site. The generated new structures exhibited higher binding energy. Such structures may spark off the interest of medicinal chemists for synthesizing potentially more active GIIA sPLA₂ inhibitors.     

3D-QSAR and docking studies of estrogen compounds based on estrogen receptor β

Close attention has been paid to estrogen compounds because these chemicals may pose a serious threat to the health of humans and wildlife. Estrogen receptor (ER) exists as two subtypes, ERα and ERβ. The difference in amino acids sequence of the binding sites of ERα and ERβ might lead to a result that some synthetic estrogens and naturally occurring steroidal ligands have different relative affinities and binding modes for ERα and ERβ. In this investigation, comparative molecular similarity indices analysis...