生物电子等排原理在药物先导化合物优化中的应用

先导化合物的优化是新药研究和开发的重要环节。由于先导化合物只提供一种具有特定药理作用的新结构类型,往往由于在药理、药效学、药代动力学等方面的缺点或不足而不能直接用于临床。因此,需要对先导化合物进行进一步化学结构改造或修饰,以期优化上述特性。“生物电子等排取代(bioisostericreplacement)”即为对先导化合物进行合理优化的有效策略之一。本文简要综述了生物电子等排原理在药物先导化合物优化中的应用。     

NMR techniques for characterization of ligand binding: utility for lead generation and optimization in drug discovery.

Over the last ten years, nmr spectroscopy has evolved into an important discipline in drug discovery. Initially, nmr was most useful as a technique to provide structural information regarding protein drug targets and target-ligand interactions. More recently, it has been shown that nmr may be used as an alternative method for identification of small molecule ligands that bind to protein drug targets. High throughput implementation of these experiments to screen small molecule libraries may lead to identification of potent and novel lead compounds. In this review, we will use examples from our own research to illustrate how nmr experiments to characterize ligand binding may be used to both screen for novel compounds during the process of lead generation, as well as provide structural information useful for lead optimization during the latter stages of a discovery program.     

A medicinal chemists’ guide to the unique difficulties of lead optimization for tuberculosis

Tuberculosis is a bacterial disease that predominantly affects the lungs and results in extensive tissue pathology. This pathology contributes to the complexity of drug development as it presents discrete microenvironments within which the bacterium resides, often under conditions where replication is limited and intrinsic drug susceptibility is low. This consolidated pathology also results in impaired vascularization that limits access of potential lead molecules to the site of infection. Translating these considerations into a target-product profile to guide lead optimization programs involves implementing unique in vitro and in vivo assays to maximize the likelihood of developing clinically meaningful candidates.     

胰升血糖素样肽-1及其受体与 2 型糖尿病的治疗

胰岛素对治疗 2 型糖尿病有一定效果,但长期使用会引起低血糖反应;双胍类药物降糖疗效显著,但会引起消化道不良反应 . 因此,寻找一种安全有效的药物是 2 型糖尿病治疗的当务之急 . 胰升血糖素样肽-1 作为一种胰岛素分泌促进剂和胰岛素增敏剂越来越受人们的关注,将它用于治疗糖尿病不会产生低血糖,对 1 型和 2 型糖尿病都有疗效 . 讨论胰升血糖素样肽-1及其受体的最新研究状况 .     

一级吸收药物的生物利用度估计的两点法

本文应用系统分析方法,建立了一种一级吸收药物的生物利用度的简便估计的两点法。这种方法,只需测量血管内和血管外给药后的两个相同时点的血药浓度值。不论该药的处置系统是多少室,均能得到较好的结果。这种方法不仅比目前常用的点一点法和点一面法简单,而且结果更精确。     

The molecular mechanism behind resistance of the kinase FLT3 to the inhibitor quizartinib

Fms‐like tyrosine kinase 3 (FLT3) is a receptor tyrosine kinase that is a drug target for leukemias. Several potent inhibitors of FLT3 exist, and bind to the inactive form of the enzyme. Unfortunately, resistance due to mutations in the kinase domain of FLT3 limits the therapeutic effects of these inhibitors. As in many other cases, it is not straightforward to explain why certain mutations lead to drug resistance. Extensive fully atomistic molecular dynamics (MD) simulations of FLT3 were carried out with an inhibited form (FLT‐quizartinib complex), a free (apo) form, and an active conformation. In all cases, both the wild type (wt) proteins and two resistant mutants (D835F and Y842H) were studied. Analysis of the simulations revealed that impairment of protein‐drug interactions cannot explain the resistance mutations in question. Rather, it appears that the active state of the mutant forms is perturbed by the mutations. It is therefore likely that perturbation of deactivation of the protein (which is necessary for drug binding) is responsible for the reduced affinity of the drug to the mutants. Importantly, this study suggests that it is possible to explain the source of resistance by mutations in FLT3 by an analysis of unbiased MD simulations.     

Gene amplification in amphotericin B-resistant Leishmania tarentolae

Two Leishmania tarentolae cells were selected step by step for resistance to the polyene antibiotic amphotericin B, a second-line drug against the parasite Leishmania. One of the mutants was cross-resistant to ketoconazole. DNA amplification was observed in both mutants. The amplicons were extrachromosomal circles and were derived from different chromosomes. In one mutant the circle was unusually stable as it remained within the cell despite numerous passages in the absence of the drug. A circumstantial link between the copy number of amplicons and the resistance levels was established. Gene transfection experiments indicated that the link between the locus amplified and the resistance levels was not straightforward and possibly several mutations act together to lead to amphotericin B resistance.     

Identification of dengue viral RNA-dependent RNA polymerase inhibitor using computational fragment-based approaches and molecular dynamics study

Dengue is a major public health concern in tropical and subtropical countries of the world. There are no specific drugs available to treat dengue. Even though several candidates targeted both viral and host proteins to overcome dengue infection, they have not yet entered into the later stages of clinical trials. In order to design a drug for dengue fever, newly emerged fragment-based drug designing technique was applied. RNA-dependent RNA polymerase, which is essential for dengue viral replication is chosen as a drug target for dengue drug discovery. A cascade of methods, fragment screening, fragment growing, and fragment linking revealed the compound [2-(4-carbamoylpiperidin-1-yl)-2-oxoethyl]8-(1,3-benzothiazol-2-yl)naphthalene-1-carboxylate as a potent dengue viral polymerase inhibitor. Both strain energy and binding free energy calculations predicted that this could be a better inhibitor than the existing ones. Molecular dynamics simulation studies showed that the dengue polymerase–lead complex is stable and their interactions are consistent throughout the simulation. The hydrogen-bonded interactions formed by the residues Arg792, Thr794, Ser796, and Asn405 are the primary contributors for the stability and the rigidity of the polymerase–lead complex. This might keep the polymerase in closed conformation and thus inhibits viral replication. Hence, this might be a promising lead molecule for dengue drug designing. Further optimization of this lead molecule would result in a potent drug for dengue.     

Machine learning and ligand binding predictions: A review of data,methods, and obstacles

Computational predictions of ligand binding is a difficult problem, with more accurate methods being extremely computationally expensive. The use of machine learning for drug binding predictions could possibly leverage the use of biomedical big data in exchange for time-intensive simulations. This paper reviews current trends in the use of machine learning for drug binding predictions, data sources to develop machine learning algorithms, and potential problems that may lead to overfitting and ungeneralizable models. A few popular datasets that can be used to develop virtual high-throughput screening models are characterized using spatial statistics to quantify potential biases. We can see from evaluating some common benchmarks that good performance correlates with models with high-predicted bias scores and models with low bias scores do not have much predictive power. A better understanding of the limits of available data sources and how to fix them will lead to more generalizable models that will lead to novel drug discovery.     

A vinblastine fluorescent probe for pregnane X receptor in a time-resolved fluorescence resonance energy transfer assay

The pregnane X receptor (PXR) regulates the metabolism and excretion of xenobiotics and endobiotics by regulating the expression of drug-metabolizing enzymes and transporters. The unique structure of PXR allows the binding of many drugs and drug leads to it, possibly causing undesired drug–drug interactions. Therefore, it is crucial to evaluate whether lead compounds bind to PXR. Fluorescence-based assays are preferred because of their sensitivity and nonradioactive nature. One fluorescent PXR probe is currently commercially available; however, because its chemical structure is not publicly disclosed, it is not optimal for studying ligand–PXR interactions. Here we report the characterization of BODIPY FL–vinblastine, generated by labeling vinblastine with the fluorophore 4,4-difluoro-5,7-dimethyl-4-bora-3a,4a-diaza-s-indacene (BODIPY FL), as a high-affinity ligand for human PXR with a K_d value of 673 nM. We provide evidence that BODIPY FL–vinblastine is a unique chemical entity different from either vinblastine or the fluorophore BODIPY FL in its function as a high-affinity human PXR ligand. We describe a BODIPY FL–vinblastine-based human PXR time-resolved fluorescence resonance energy transfer assay, which was used to successfully test a panel of human PXR ligands. The BODIPY FL–vinblastine-based biochemical assay is suitable for high-throughput screening to evaluate whether lead compounds bind to PXR.     

Identification and characterization of folding inhibitors of hen egg lysozyme: an example of a new paradigm of drug design

Studies of protein folding indicate the presence of native contacts in the denatured state, giving rise to folding elements which contribute to the accomplishment of the native state. The possibility of finding molecules which can interact with specific folding elements of a target protein preventing it from reaching its native state, and hence from becoming biologically active, is particularly attractive. The notion that folding elements not only provide molecular recognition directing the folding process, but also have conserved sequence, implies that targeting such elements will make protein folding inhibitors less susceptible to mutations which, in many cases, abrogate drug effects. The folding-inhibition strategy can lead to a truly novel and rational approach to drug design, aside from providing new insight into folding. This is illustrated in the case of hen egg lysozyme.     

Characterization of [3H]-Valinomycin binding to red blood cell membrane

Valinomycin was tritiated by exchange and its biological activity found to be similar to that of nonlabeled drug. [³H]-valinomycin binds to red blood cell membranes following a biphasic pattern. High concentrations of the drug lead to an irreversible binding while low concentrations lead to a completely reversible binding. Maximum binding was obtained at acidic pH (pH 4.2) and physiological temperature (37°C). We demonstrate that valinomycin binds strongly to the lipidic phase of the membrane. When binding to erythrocytes and reticulocytes was compared, it was found that the mature red blood cells had less binding capacity than the reticulocytes.     

生物膜耐药机制研究进展

生物膜形成是微生物耐药的重要原因之一,也是许多慢性感染性疾病反复发作和难以治疗的主要原因,微生物生物膜可以通过渗透限制,改变生物膜内外微环境,形成特殊的基因型等多种方式导致耐药。生物膜耐药机制的研究已成为医学、药学、微生物学等众多领域关注的课题。就生物膜耐药机制的最新进展进行综述。     

Drugs,leads, and drug-likeness: an analysis of some recently launched drugs

An analysis of the origins of recently launched drugs reveals that most were derived by modification of known drug structures or from lead structures obtained from the scientific literature. High-throughput screening did not have a significant impact on the derivation of these drugs. The drug structures are very closely related to their leads.     

圣乔治教堂诺卡菌引起的肺部感染1例

诺卡菌肺部感染可引起肺诺卡菌病,因其无特异性的临床表现,容易误诊、漏诊。因此,临床实验室的培养鉴定能力非常重要,若不能及时诊治,则会导致病死率较高。诺卡菌病临床较为少见,为引起临床实验室对诺卡菌的鉴定和药敏试验的重视,本文报道了上海市嘉定区中心医院2019年2月收治的1例由圣乔治教堂诺卡菌(Nocardia cyriacigeorgica)感染引起的肺诺卡菌病病例,针对其临床特征、实验室检测及治疗等进行分析,期望对临床诊治诺卡菌病有所帮助。     

Sensitive cell viability assay for use in drug screens and for studying the mechanism of action of drugs in Dictyostelium discoideum

In order to increase the effectiveness of Dictyostelium discoideum as a lead genetic model for drug discovery, a luminescence-based assay has been adapted and standardized for sensitive and rapid cell viability measurements. The applicability of the assay was demonstrated by measuring the cytotoxicity of several drugs in wild-type and mutant cells. The robustness and ease of the assay demonstrate that it can be used in high-throughput applications such as drug or mutant screens. Conclusions from these studies are applicable to evaluating cell viability assays in other systems as well.     

The SARS-CoV-2 main protease as drug target

The unprecedented pandemic of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is threatening global health. The virus emerged in late 2019 and can cause a severe disease associated with significant mortality. Several vaccine development and drug discovery campaigns are underway. The SARS-CoV-2 main protease is considered a promising drug target, as it is dissimilar to human proteases. Sequence and structure of the main protease are closely related to those from other betacoronaviruses, facilitating drug discovery attempts based on previous lead compounds. Covalently binding peptidomimetics and small molecules are investigated. Various compounds show antiviral activity in infected human cells.