Molecular design based on 3D-pharmacophore. Application to 5-HT subtypes receptors

A first definition of a pharmacophore for the serotonin reuptake inhibitors was carried out by considering a three-dimensional model which correlates the chemical structures of series of reuptake inhibitors with their biological affinities. A molecular design was described by analyzing two different 3D serotonin pharmacophores. This successful approach enabled us to consider the design of new serotonin ligands by the same method.     

Molecular design based on 3D-pharmacophore. Application to 5-HT4 receptor

A definition of a pharmacophore for the 5-HT4 antagonist was carried out by considering a three-dimensional model which correlates the chemical structures of series of antagonists with their biological affinities. A molecular design is described by analyzing the differences between two 3D serotonin pharmacophores. This successful structural modification demonstrates the efficiency of this approach to design new serotonin ligands.     

Molecular modeling studies focused on 5-HT7 versus 5-HT1A selectivity. Discovery of novel phenylpyrrole derivatives with high affinity for 5-HT7 receptors

The present study discusses the well-known 5-HT7/5-HT1A selectivity issue through a new series of phenylpyrrole derivatives. The first hits emerged from a virtual screening performed on a chemolibrary. Further study led to an optimization of a preliminary 5-HT7 pharmacophore model. The importance of each pharmacophoric feature is confirmed, but these characteristics have to be coupled to geometric constraints in order to achieve a 5-HT7 selectivity. Indeed, 5-HT1A affinity probably arises from extended conformations, whereas a bent one appears to be best suited for 5-HT7 selectivity.     

Molecular dynamics of 5-HT1A and 5-HT2A serotonin receptors with methylated buspirone analogues

In the present study experimentally determined ligand selectivity of three methylated buspirone analogues (denoted as MM2, MM5 and P55) towards 5-HT_1A and 5-HT_2A serotonin receptors was theoretically investigated on a molecular level. The relationships between the ligand structure and 5-HT_1A and 5-HT_2A receptor affinities were studied and the results were found to be in agreement with the available site-directed mutagenesis and binding affinity data. Molecular dynamics (MD) simulations of ligand-receptor complexes were performed for each investigated analogue, docked twice into the central cavity of 5-HT_1A/5-HT_2A, each time in a different orientation. Present results were compared with our previous theoretical results, obtained for buspirone and its non-methylated analogues. It was found that due to the presence of the methyl group in the piperazine ring the ligand position alters and the structure of the ligand-receptor complex is modified. Further, the positions of derivatives with pyrimidinyl aromatic moiety and quinolinyl moiety are significantly different at the 5-HT_2A receptor. Thus, methylation of such derivatives alters the 3D structures of ligand-receptor complexes in different ways. The ligand-induced changes of the receptor structures were also analysed. The obtained results suggest, that helical domains of both receptors have different dynamical behaviour. Moreover, both location and topography of putative binding sites for buspirone analogues are different at 5-HT_1A and 5-HT_2A receptors.     

Definition of a pharmacophore for partial agonists of serotonin 5-HT3 receptors

A definition of a partial agonists serotonin 5-HT3 pharmacophore was carried out by considering a three-dimensional model which correlates the chemical structures of series of piperazinopyrrolothienopyrazines, piperazinopyridopyrrolopyrazines, piperazinopyrroloquinolaxines, piperazinopyridopyrroloquinoxalines, aminoalkyloximinopyrroloindoles, aminoalkyloximinothienopyrrolizines, and aminoalkyloximinopyrrolizines with the biological affinities. The model is formed by five features corresponding to two hydrogen bond acceptors, one aromatic ring, one hydrophobic group, and one positive ionizable site (quaternary ammonium ions). The nature of the features and the distances between them explain the partial agonist activities of these compounds.     

Predicted structures and dynamics for agonists and antagonists bound to serotonin 5-HT2B and 5-HT2C receptors

Subtype 2 serotonin (5-hydroxytryptamine, 5-HT) receptors are major drug targets for schizophrenia, feeding disorders, perception, depression, migraines, hypertension, anxiety, hallucinogens, and gastrointestinal dysfunctions. (1) We report here the predicted structure of 5-HT2B and 5-HT2C receptors bound to highly potent and selective 5-HT2B antagonist PRX-08066 3, (pKi: 30 nM), including the key binding residues [V103 (2.53), L132 (3.29), V190 (4.60), and L347 (6.58)] determining the selectivity of binding to 5-HT2B over 5-HT2A. We also report structures of the endogenous agonist (5-HT) and a HT2B selective antagonist 2 (1-methyl-1-1,6,7,8-tetrahydro-pyrrolo[2,3-g]quinoline-5-carboxylic acid pyridine-3-ylamide). We examine the dynamics for the agonist- and antagonist-bound HT2B receptors in explicit membrane and water finding dramatically different patterns of water migration into the NPxxY motif and the binding site that correlates with the stability of ionic locks in the D(E)RY region.     

New hexahydrocarbazoles and spiro indoles, and their affinity for D2 dopamine and 5-HT2A serotonin receptors.

In a search for novel atypical antipsychotics, the synthesis of new hexahydrocarbazoles and spiro indoles N-substituted with a 3-(dimethylamino)propyl chain is described, together with the results of an in vitro evaluation of their affinities for D2 and 5-HT2A receptors.     

Molecular recognition of oxoanions based on guanidinium receptors

Guanidinium is a versatile functional group with unique properties. In biological systems, hydrogen-bonding and electrostatic interactions involving the arginine side chains of proteins are critical to stabilise complexes between proteins and nucleic acids, carbohydrates or other proteins. Leading examples of artificial receptors for carboxylates, phosphates and other oxoanions, such as sulfate or nitrate are highlighted in this tutorial review, addressed to readers interested in biology, chemistry and supramolecular chemistry.     

Modulation of Serotonin Receptors in Neurodevelopmental Disorders: Focus on 5-HT7 Receptor

Since neurodevelopmental disorders (NDDs) influence more than 3% of children worldwide, there has been intense investigation to understand the etiology of disorders and develop treatments. Although there are drugs such as aripiprazole, risperidone, and lurasidone, these medications are not cures for the disorders and can only help people feel better or alleviate their symptoms. Thus, it is required to discover therapeutic targets in order to find the ultimate treatments of neurodevelopmental disorders. It is suggested that abnormal neuronal morphology in the neurodevelopment process is a main cause of NDDs, in which the serotonergic system is emerging as playing a crucial role. From this point of view, we noticed the correlation between serotonin receptor subtype 7 (5-HT₇R) and NDDs including autism spectrum disorder (ASD), fragile X syndrome (FXS), and Rett syndrome (RTT). 5-HT₇R modulators improved altered behaviors in animal models and also affected neuronal morphology via the 5-HT₇R/G₁₂ signaling pathway. Through the investigation of recent studies, it is suggested that 5-HT₇R could be a potential therapeutic target for the treatment of NDDs.     

Molecular Structure and Affinity to 5-HT1A Receptor of Chlorophenyl(Piperazinylalkyl)Phthalimides

Abstract

X-ray crystallography, quantum-chemical calculations and conformational analysis have been employed to study chlorophenyl(piperazinylalkyl)phthalimides, potential ligands of 5-HT_1A receptor. The molecular recognition of investigated compounds by 5-HT_1Aserotonin receptor has been estimated according to their ability to inhibit the [³H8]-DPAT binding. The model for 5-HT_1A pharmacophore has been proposed based on crystal structures of N-(aryl)piperazinyl — alkylphthalimides.     

多巴胺在其第三受体蛋白结构中的分子通道上传输动力学

本文基于多巴胺与其第三受体复合蛋白(D_3R)结构,采用分子动力学技术Gromacs 4.5程序中的伞形样本方法,研究多巴胺在多巴胺第三受体蛋白结构中的运动轨迹及其过程中自由能变化,探讨多巴胺在其分子通道上传输运动机制动力学。分子模拟表明,处在发挥神经递质作用部位的多巴胺,通过D_3R结构中的功能分子通道沿着y+轴朝细胞外方向传输运动的自由能变化数值为134.6 kJ?mol~(-1),沿着y-轴朝细胞内传输运动的自由能变化为211.5 kJ?mol~(-1)。在D_3R结构中,多巴胺沿着x+、x-、z+、z-轴朝细胞双层膜方向传输运动的自由能变化分别为65.8、245.0、551.4、172.8 kJ?mol~(-1),数值说明DOP更容易沿着x+轴方向从TM5(第五跨膜螺旋)与TM6(第六跨膜螺旋)缝隙之间离开D_3R内部结构。处在细胞间隙空间的自由多巴胺,在等温等压条件下沿着逆y+轴方向通过多巴胺第三受体内功能分子通道,到达发挥神经递质作用的部位是一个自发过程,因为在该轨迹上多巴胺分子与受体相互作用是一个负自由能变化(-134.6 kJ?mol~(-1))。所以,多巴胺与多巴胺受体很容易相互结合,发挥神经递质作用。发挥了神经递质功能作用的多巴胺分子,沿着x+轴方向的保护分子通道从TM5与TM6缝隙之间离开D_3R内部结构,避免过度发挥多巴胺神经递质功能作用。根据多巴胺功能和保护分子通道观点,我们提出帕金森病新病理和精神分裂症新病理。论文还探讨多巴胺分子通道理论及其新病理应用于治疗控制这两种病症及其相关药物研究开发。     

eSHAFTS: Integrated and graphical drug design software based on 3D molecular similarity

With the development of computer technology, computer-aided drug design (CADD) has become an important means for drug research and development, and its representative method is virtual screening. Various virtual screening platforms have emerged in an endless stream and play great roles in the field of drug discovery. With the increasing number of compound molecules, virtual screening platforms face two challenges: low fluency and low visibility of software operations. In this article, we present an integrated and graphical drug design software eSHAFTS based on three-dimensional (3D) molecular similarity to overcome these shortcomings. Compared with other software, eSHAFTS has four main advantages, which are integrated molecular editing and drawing, interactive loading and analysis of proteins, multithread and multimode 3D molecular similarity calculation, and multidimensional information visualization. Experiments have verified its convenience, usability, and reliability. By using eSHAFTS, various tasks can be submitted and visualized in one desktop software without locally installing any dependent plug-ins or software. The software installation package can be downloaded for free at http://lilab.ecust.edu.cn/home/resource.html . © 2019 Wiley Periodicals, Inc.     

Starting point to molecular design: efficient automated 3D model builder Key3D

Obtaining three-dimensional (3D) structures from structural formulae is a crucial process in molecular design. We have developed a new 3D model builder, Key3D, in which the simplified distance geometry technique and structure optimization based on the MMFF force field are combined. In an evaluation study using 598 crystal structures, the high performance and accuracy of Key3D were demonstrated. In the "flexible-fitting" test, which is focused on practical usefulness in the molecular design process, 88% of the Key3D structures acceptably reproduced the reference crystal structures (root-mean-square deviation <0.6 A) upon rotation of acyclic bonds. These results indicate that Key3D will be very effective in providing starting points for practical molecular design.     

左苯丙胺在多巴胺第三受体分子通道中传输分子动力学模拟

左旋苯丙胺(又称左苯丙胺, RAT)在临床上被用于治疗多种病症,作用在中枢神经细胞多巴胺受体上,同时它具有依赖性和成瘾性。为了探讨RAT被用作药物的药理和成瘾机制,本文用分子模拟获得RAT与多巴胺第三受体(D₃R)复合蛋白优化结构,并且采用伞形样本平均力势(PMF)方法和卵磷脂脂质分子模拟生物膜,采用分子动力学模拟获得RAT在D₃R结构中分子通道运动轨迹和自由能变化。RAT通过D₃R结构中的功能分子通道,朝细胞外方向传输运动的自由能变化为91.4 kJ·mol^-1。RAT通过D₃R结构中的保护分子通道,朝细胞双层膜方向传输运动的自由能变化为117.7 kJ·mol^-1。自由能数值表明RAT分子更容易通过D₃R结构中的功能分子通道,发挥其功能作用,增大功能多巴胺分子的释放,导致包括依赖性和成瘾性多种功能效果。研究结果证明RAT被用作药物的药理和成瘾机制与它在多巴胺受体中的分子通道上传输动力学和机制有密切关联。     

Haloacetylated enol ethers. 7 . Synthesis of 3-aryl-5-trihalomethylisoxazoles and 3-aryl-5-hydroxy-5-trihalomethyl-4,5-dihydroisoxazoles

β-Aryl-β-methoxyvinyl trihalomethyl ketones 1a-g, 2a-g [aryl = p-YC₆H₄ where Y= H, Me, OMe, F, Cl, Br, NO₂] are cyclocondensed with hydroxylamine hydrochloride to afford the 3-aryl-5-hydroxy-5-trihalomethyl-4,5-dihydroisoxazoles 3a-g, 4a-f in good yield. The dehydratation of compounds 3a-g with concentrated sulfuric acid, led the corresponding 3-aryl-5-trichloromethylisoxazoles 5a-g . An alternative one-pot procedure yields 3-aryl-5-trihalomethylisoxazoles 5,6a-g directly by cyclocondesation of 1,2a-g with hydroxylamine hydrochloride in the presence of an excess of concentrated hydrochloric acid.     

TOPS-MODE based QSARs derived from heterogeneous series of compounds. Applications to the design of new herbicides

A new application of TOPological Sub-structural MOlecular DEsign (TOPS-MODE) was carried out in herbicides using computer-aided molecular design. Two series of compounds, one containing herbicide and the other containing nonherbicide compounds, were processed by a k-Means Cluster Analysis in order to design the training and prediction sets. A linear classification function to discriminate the herbicides from the nonherbicide compounds was developed. The model correctly and clearly classified 88% of active and 94% of inactive compounds in the training set. More specifically, the model showed a good global classification of 91%, i.e., (168 cases out of 185). While in the prediction set, they showed an overall predictability of 91% and 92% for active and inactive compounds, being the global percentage of good classification of 92%. To assess the range of model applicability, a virtual screening of structurally heterogeneous series of herbicidal compounds was carried out. Two hundred eighty-four out of 332 were correctly classified (86%). Furthermore this paper describes a fragment analysis in order to determine the contribution of several fragments toward herbicidal property; also the present of halogens in the selected fragments were analyzed. It seems that the present TOPS-MODE based QSAR is the first alternate general "in silico" technique to experimentation in herbicides discovery.     

Crystal and Molecular Structure of Bis(η5-methylcyclopentadienyl)titana(IV)-cyclohexasulfane Ti(η5-C5H4CH3)2S5

The crystal and molecular structure of Ti(n⁵-C₅H₄CH₃)₂S₅has been determined by X-ray diffraction studies. The substance crystallizes in the monoclinic crystal system [a = 6.8642(5), b = 16.507(1), c = 13.074(1) Å, β = 82.407(3)°, space group P2₁/n, Z = 4]. The geometry about the titanium atom is a distorted tetrahedron, with a (centroid)-Ti-(centroid) angle of 131.29° and a S? Ti? S angle of 93.38°. The six-membered ring TiS₅ has a cyclohexane-like chair configuration. The structural results are compared to those for similar type titanium complexes.