分子对接在药物虚拟筛选中的应用进展

虚拟筛选是药物设计的重要手段之一,利用小分子化合物与药物靶标间的分子对接运算,研究人员可以准确地获取两者之间的相互作用情况,从候选化合物库中快速筛选出潜在的药物或药物前体,从而加速药物开发过程。介绍了虚拟筛选与分子对接的相关原理与流程,主要综述了对药物进行虚拟筛选时所涉及的分子对接技术类型、常见的分子对接软件以及分子对接典型样例。分子对接对提高虚拟筛选的效率、降低药物开发的成本具有重要的现实意义。     

化学基元组学与药物创新

化学基元组学(chemomics)是与化学信息学、生物信息学、合成化学等学科相关的交叉学科.生物系统从内源性小分子(天然砌块)出发,通过酶催化的化学反应序列制造天然产物.生物系统通过化学反应和天然砌块向目标天然产物"砌入"一组原子,这样的一组原子称为化学基元(chemoyl).化学基元组(chemome)是生物组织中所含有的化学基元的全体.化学基元组学研究各种化学基元的结构、组装与演化的基本规律.在生存压力和繁衍需求的驱动下,生物系统已经进化出有效手段来合成天然产物以应付环境的变化,并产生了丰富多彩的生物和化学多样性.近年来,人们意识到药物创新的瓶颈之一是药物筛选资源的日益枯竭.化学基元组学可以解决这个瓶颈问题,它通过揭示生物系统制备化学多样性的规律,发展仿生合成方法制备类天然化合物库(quasi natural product libraries)以供药物筛选.本文综述了化学基元组学的主要研究内容及其在药物创新各领域中的潜在应用.     

第九届全国计算（机）化学学术会议（第一轮通知）

主办单位:中国化学会计算机化学专业委员会协办单位:化学生物传感与计量学国家重点实验室(湖南大学)承办单位:四川大学国际计算机化学包括化学信息学研究的发展方兴未艾,近几年来伴随着理论与计算化学、分子模拟与设计、数据挖掘技术,因特网资源综合利用以及化学计量学等领域的发展,取得了令世人瞩目的重要进展.我国的计算(机)化学包括化学信息学研究也伴随着这些学科的飞速进步得到快速发展,通过学科相互交叉、相互渗透,目前发展快速、成效显著,在某些研究方面接近或达到国际先进水平.为更好地总结、交流我国在计算(机)化学包括化学信息学…     

化学信息学的涵义及教育

化学信息学是近年来发展起来的新学科 ,它的产生与发展是基于化学信息量指数般增长 ,特别是组合化学及高通量筛选的迅速发展。组合化学方法能像搭积木块一样快速合成及制备大量的化合物。一个组合化学库包括数百个至数十万个化合物 ,为药物开发提供丰富的化合物源。高通量筛选能达到 1× 1 0 4～ 1× 1 0 5 个化合物 /天。组合化学及高通量筛选为药物研制提供新的技术支柱 ,同时也为化学信息学的产生与发展提供良好的机遇。　　人类基因组计划为药物开发与疾病的治疗提供众多的新靶标。据 1 996年统计用于药物研制的靶标有 483个分子靶 (其…     

分子点群虚拟仿真实验的建设与实践*

结合结构化学课程中分子对称性知识点的教学,自主设计和开发了分子点群虚拟仿真实验(PGVL)平台,帮助学生深入认识理解分子对称性知识的重点和难点。该仿真实验采用Web技术构建,支持分子模型的显示和互动,使学生可以完成分子的各种对称操作、指出分子结构中的对称元素、推导分子点群及认识分子结构和性质之间的关系。PGVL在分子对称性教学中的应用,不仅完善了结构化学分子模型实践教学体系,而且提升了学生对结构化学课程的学习兴趣,丰富了结构化学实践教学内容,取得了良好的教学效果。     

PPAR激动剂的定向设计、虚拟筛选及合成

过氧化物酶体增殖因子活化受体(PPAR)是核受体超家族的一员.基于受体结构的药物分子设计与组合化学策略相结合,构建了过氧化物酶体增殖因子活化受体(PPAR)激动剂的虚拟化合物库.将已知小分子配体(GW409544)与PPAR晶体复合物进行剥离,得到受体的活性构象,并利用此活性受体分子与虚拟库中小分子进行对接和虚拟筛选,得到理论上结合较强的化合物,并对这些化合物进行合成,共合成9个新化合物.活性筛选结果显示化合物对PPAR具有一定的亲和力,其中有三个化合物显示出对PPARα,PPARγ的双重激动作用,从而指导新活性化合物的设计和合成.     

蛋白质中总巯基的测定及标记

生物硫醇的检测与蛋白质荧光标记是当今科学研究的热门领域。本实验使用传统的Ellman法及Naph-EA-Mal荧光探针标记法对牛血清白蛋白(Bovine Serum Albumin, BSA)的巯基进行检测,并利用该探针实现了细胞内巯基的原位标记,使学生对传统方法和前沿热点均有较好的掌握和了解。通过本实验的开展,学生不仅可以清楚了解蛋白三维结构对其所含基团的反应活性的影响,而且可以从化学层面理解硫醇类探针的工作原理及活细胞中生物硫醇的原位成像。实验内容涵盖蛋白质还原、变性、生物大分子与小分子的分离、生物大分子的化学修饰以及活细胞荧光成像等,综合性强且容易操作。教学内容可以实现模块化,便于不同学校根据条件选取相应的教学内容。教学实践不仅可以让学生复习巩固化学生物学知识,也帮助学生了解前沿交叉学科热点,同时在虚拟实验平台开设了补充实验,使得教学更加立体化。     

基于MOE软件的虚拟仿真实验*——多奈哌齐与乙酰胆碱酯酶的分子对接

基于MOE软件设计了多奈哌齐与乙酰胆碱酯酶的分子对接虚拟仿真实验。通过分子结构预处理、分子对接以及数据分析等内容,帮助学生掌握分子对接的基本技能,深入理解立体化学结构对药物-靶分子相互作用的影响。本实验可以作为药物化学、生物化学等基础课的扩展内容,提高学生研究式学习的兴趣和能力。     

基于3D-药效团的P糖蛋白和细胞色素P4503A4的协同作用机理研究

P糖蛋白(P-glycoprotein,Pgp)和细胞色素P4503A4(CYP3A4)是决定药物ADME性质的两个重要蛋白,目前还无法通过实验方法,从分子水平清晰阐明这两个蛋白采取怎样的互补作用机理来降低外来药物的生物利用度.通过3D-药效团模建方法,提取Pgp和CYP3A4的共同底物的特征阐明这两个蛋白可能的协同作用模式.所得的药效团有助于理解药物分子同这两个蛋白的作用模式,同时该模型可以指导新药设计和改造,从而提高药物的生物利用度.     

人工智能发现活性分子背景下天然药物化学教学的转型与发展*

人工智能(AI)在活性分子发现及药物筛选方面的应用日趋深入,革新了传统发现天然药物的方式,重构了药物发现及设计的格局。这就要求天然药物化学人才熟练掌握天然药物化学基础知识、具备多学科交叉分析问题能力以及培养和树立与时俱进的逻辑思维。为顺应人工智能时代发展要求,天然药物化学教学需要构建AI参与天然药物发现教学体系、提供AI参与天然药物发现的直观教学、筛选优秀网络教学资源引导学生自主学习,同时培养学生在AI参与天然药物发现中的思考能力。     

Nonadiabatic effects in the nuclear probability and flux densities through the fractional Schrödinger equation

Nonadiabatic effects in the nuclear dynamics of the H₂⁺ molecular ion, initiated by ionization of the H₂ molecule, is studied by means of the probability and flux distribution functions arising from the space fractional Schrödinger equation. In order to solve the fractional Schrödinger eigenvalue equation, it is shown that the quantum Riesz fractional derivative operator fulfills the usual properties of the quantum momentum operator acting on the bra and ket vectors of the abstract Hilbert space. Then, the fractional Fourier grid Hamiltonian method is implemented and applied to molecular vibrations. The eigenenergies and eigenfunctions of the fractional Schrödinger equation describing the vibrational motion of the H₂⁺ and D₂⁺ molecules are analyzed. In particular, it is shown that the position-momentum Heisenberg's uncertainty relationship holds independently of the fractional Schrödinger equation. Finally, the probability and flux distributions are presented, demonstrating the applicability of the fractional Schrödinger equation for taking into account nonadiabatic effects.     

Some simple remarks on variational bounds in Faddeev-type formalisms

A bound on the energy obtained from the differential equation forms of Faddeev-type equations is derived. The procedure is based on the standard variation principle for the Schrödinger equation plus the observation that the ordinary Schrödinger wavefunction |ψ(i)> equals the sum of the Faddeev-type “channel wavefunctions” |ψ_λ(i)>.     

An effective quasirelativistic hamiltonian

Several ways of introducing effective relativistic potentials into the Schrödinger equation are discussed. A detailed study of a potential, which leads to the radial electron density exhibiting the same asymptotic behaviour as the Dirac density is performed. This potential, which is a j-dependent correction to the radial Schrödinger equation and which retains exactly the analytical form of the equation, may be easily implemented in atomic and molecular calculations.     

Local energy calculations employing importance sampling: Positronium hydride wavefunctions as severe tests of the method

Ground-state positronium hydride wavefunctions are generated by least squares solutions of the Schrödinger equation and compared with variational results. Effects on wavefunction quality of configuration space sampling and of low-lying virtual excited states are detailed.     

Unique continuation for the magnetic Schrödinger equation

The unique-continuation property from sets of positive measure is here proven for the many-body magnetic Schrödinger equation. This property guarantees that if a solution of the Schrödinger equation vanishes on a set of positive measure, then it is identically zero. We explicitly consider potentials written as sums of either one-body or two-body functions, typical for Hamiltonians in many-body quantum mechanics. As a special case, we are able to treat atomic and molecular Hamiltonians. The unique-continuation property plays an important role in density-functional theories, which underpins its relevance in quantum chemistry.     

Exact solution of multidimensional hyper‐radial Schrödinger equation for many‐electron quantum systems

In quantum theory, solving Schrödinger equation analytically for larger atomic and molecular systems with cluster of electrons and nuclei persists to be a tortuous challenge. Here, we consider, Schrödinger equation in arbitrary N‐dimensional space corresponding to inverse‐power law potential function originating from a multitude of interactions participating in a many‐electron quantum system for exact solution within the framework of Frobenius method via the formulation of an ansatz to the hyper‐radial wave function. Analytical expressions for energy spectra, and hyper‐radial wave functions in terms of known coefficients of inverse‐power potential function, and wave function parameters have been obtained. A generalized two‐term recurrence relation for power series expansion coefficients has been established. © 2016 Wiley Periodicals, Inc.     

Solutions of N-dimensional Schrödinger equation with Morse potential via Laplace transforms

A study is undertaken to investigate an analytical solution for the N-dimensional Schrödinger equation with the Morse potential based on the Laplace transformation method. The results show that in the Pekeris approximation, the radial part of the Schrödinger equation reduces to the corresponding equation in one dimension. In addition, a comparison is made between the energy spectrum resulted from this method and the spectra that are obtained from the two-point quasi-rational approximation method and the Nikiforov–Uvarov approach.     

Optimization of complex slater‐type functions with analytic derivative methods for describing photoionization differential cross sections

The complex basis function (CBF) method applied to various atomic and molecular photoionization problems can be interpreted as an method to solve the driven‐type (inhomogeneous) Schrödinger equation, whose driven term being dipole operator times the initial state wave function. However, efficient basis functions for representing the solution have not fully been studied. Moreover, the relation between their solution and that of the ordinary Schrödinger equation has been unclear. For these reasons, most previous applications have been limited to total cross sections. To examine the applicability of the CBF method to differential cross sections and asymmetry parameters, we show that the complex valued solution to the driven‐type Schrödinger equation can be variationally obtained by optimizing the complex trial functions for the frequency dependent polarizability. In the test calculations made for the hydrogen photoionization problem with five or six complex Slater‐type orbitals (cSTOs), their complex valued expansion coefficients and the orbital exponents have been optimized with the analytic derivative method. Both the real and imaginary parts of the solution have been obtained accurately in a wide region covering typical molecular regions. Their phase shifts and asymmetry parameters are successfully obtained by extrapolating the CBF solution from the inner matching region to the asymptotic region using WKB method. The distribution of the optimized orbital exponents in the complex plane is explained based on the close connection between the CBF method and the driven‐type equation method. The obtained information is essential to constructing the appropriate basis sets in future molecular applications. © 2017 Wiley Periodicals, Inc.     

A two-step method with vanished phase-lag and its first two derivatives for the numerical solution of the Schrödinger equation

In this paper we introduce a new explicit hybrid Numerov-type method. This method is of fourth algebraic order and has phase-lag and its first two derivatives equal to zero. We present a stability analysis and an error analysis based on the radial Schrödinger equation. Finally we apply the new proposed method to the resonance problem of the radial Schrödinger equation and we present the final conclusion based on the theoretical analysis and numerical results.