Chapter 3: Small Molecules and Disease

“Big” molecules such as proteins and genes still continue to capture the imagination of most biologists, biochemists and bioinformaticians. “Small” molecules, on the other hand, are the molecules that most biologists, biochemists and bioinformaticians prefer to ignore. However, it is becoming increasingly apparent that small molecules such as amino acids, lipids and sugars play a far more important role in all aspects of disease etiology and disease treatment than we realized. This particular chapter focuses on an emerging field of bioinformatics called “chemical bioinformatics” – a discipline that has evolved to help address the blended chemical and molecular biological needs of toxicogenomics, pharmacogenomics, metabolomics and systems biology. In the following pages we will cover several topics related to chemical bioinformatics. First, a brief overview of some of the most important or useful chemical bioinformatic resources will be given. Second, a more detailed overview will be given on those particular resources that allow researchers to connect small molecules to diseases. This section will focus on describing a number of recently developed databases or knowledgebases that explicitly relate small molecules – either as the treatment, symptom or cause – to disease. Finally a short discussion will be provided on newly emerging software tools that exploit these databases as a means to discover new biomarkers or even new treatments for disease.

What to Learn in This Chapter

• The meaning of chemical bioinformatics
• Strengths and limitations of existing chemical bioinformatic databases
• Using databases to learn about the cause and treatment of diseases
• The Small Molecule Pathway Database (SMPDB)
• The Human Metabolome Database (HMDB)
• DrugBank
• The Toxin and Toxin-Target Database (T3DB)
• PolySearch and Metabolite Set Enrichment Analysis

This article is part of the “Translational Bioinformatics” collection for PLOS Computational Biology.

     

小分子有机化合物与DC-SIGN相互作用的荧光光谱分析

采用实验和理论化学研究相结合的方法研究分子间相互作用,这种在计算机上进行“模拟实验”与传统“有机化学实验”相辅相成的研究策略,正在成为有机化学研究的重要手段.本论文利用荧光光谱分析法来研究小分子有机化合物与蛋白底物之间的相互作用机制.利用先进的分子模拟软件,结合分子力学、量子力学和神经网络等方法与分子对接等理论化学手段,建立和优化相互作用的分子间形成复合物的空间构象,并且预测分子间相互作用的稳定性.用荧光光谱分析法对12种小分子有机化合物与DC-SIGN(DC-specific ICAM-3 grabbing nonintegrin)之间的相互作用进行了研究,结果与理论分子模型计算十分吻合.在这12种化合物中,1-脲基氨基甘露糖与DC-SIGN络合的效果最好.这一发现可能对研究新一代抗艾滋病药物有重要意义.     

靶向小分子创新药物

寻找药物新靶点是全球创新药物研究激烈竞争的焦点."组学"、生物信息学、系统生物学、药物筛选现代检测技术等新理论、新技术的发展使新的筛选模型和评价技术不断取得突破.靶向抗肿瘤药物的开发是靶向小分子创新药物的重点任务,多靶点的抗肿瘤药物开发及新靶点的发现是抗肿瘤药物研发的新趋势.     

Block of Nav1.8 by Small Molecules

Sodium channels are key proteins in regulating neuronal excitability and accumulating data suggest that specific subtypes of voltage-dependent sodium channels are important in signaling various types of pain. Consistent with this theme, Jarvis et al (2007) recently reported the identification of a subtype-selective Nav1.8 blocker that was active in several pre-clinical models of pain. During the course of these studies compounds were also identified that showed large differences in potency when tested on Nav1.8 channels from different species. This Addendum illustrates one of these compounds along with the potency correlation between recombinant and native tetrodotoxin-resistant sodium channels for additional examples. These data show that significant differences can be observed for sodium channel blockers across species and highlight the importance of considering this possibility when searching for new compounds and research tools to probe sodium channel function.     

Effects of Small Molecules on Chaperone-Mediated Autophagy

Autophagy, including macroautophagy (MA), chaperone-mediated autophagy (CMA), crinophagy, pexophagy and microautophagy, are processes by which cells select internal components such as proteins, secretory vesicles, organelles, or foreign bodies, and deliver them to lysosomes for degradation. MA and CMA are activated during conditions of serum withdrawal in cell culture and during short-term (MA) and prolonged (CMA) starvation in organisms. Although MA and CMA are activated under similar conditions, they are regulated by different mechanisms. We used pulse/chase analysis under conditions in which most intracellular proteolysis is due to CMA to test a variety of compounds for effects on CMA. We show that inhibitors of MA such as 3-methyladenine, wortmannin, and LY294002 have no effect on CMA. Protein degradation by MA is sensitive to microtubule inhibitors such as colcemide and vinblastine, but protein degradation by CMA is not. Activators of MA such as rapamycin also have no effect on CMA. We demonstrate that CMA, like MA, is inhibited by protein synthesis inhibitors anisomycin and cycloheximide. CMA is also partially inhibited when the P38 mitogen activated protein kinase is blocked. Finally we demonstrate that the glucose-6-phophate dehydrogenase inhibitor, 6-aminonicotinamide, and heat shock protein of 90 kilodaltons inhibitor, geldanamycin, have the ability to activate CMA.     

Elucidating Turnover Pathways of Bioactive Small Molecules by Isotopomer Analysis: The Persistent Organic Pollutant DDT

The persistent organic pollutant DDT (1,1,1-trichloro-2,2-bis(4-chlorophenyl)ethane) is still indispensable in the fight against malaria, although DDT and related compounds pose toxicological hazards. Technical DDT contains the dichloro congener DDD (1-chloro-4-[2,2-dichloro-1-(4-chlorophenyl)ethyl]benzene) as by-product, but DDD is also formed by reductive degradation of DDT in the environment. To differentiate between DDD formation pathways, we applied deuterium NMR spectroscopy to measure intramolecular deuterium distributions (²H isotopomer abundances) of DDT and DDD. DDD formed in the technical DDT synthesis was strongly deuterium-enriched at one intramolecular position, which we traced back to ²H/¹H fractionation of a chlorination step in the technical synthesis. In contrast, DDD formed by reductive degradation was strongly depleted at the same position, which was due to the incorporation of ²H-depleted hydride equivalents during reductive degradation. Thus, intramolecular isotope distributions give mechanistic information on reaction pathways, and explain a puzzling difference in the whole-molecule ²H/¹H ratio between DDT and DDD. In general, our results highlight that intramolecular isotope distributions are essential to interpret whole-molecule isotope ratios. Intramolecular isotope information allows distinguishing pathways of DDD formation, which is important to identify polluters or to assess DDT turnover in the environment. Because intramolecular isotope data directly reflect isotope fractionation of individual chemical reactions, they are broadly applicable to elucidate transformation pathways of small bioactive molecules in chemistry, physiology and environmental science.     

Molecular Dynamics Simulations of some Small Organic Molecules

Abstract

Free energy differences between different conformers of D-ribofuranose, L-malic acid and meso-tartaric acid in solution were calculated using Molecular Dynamics simulations. In case of ribose the α → β transition was studied. For the acids attention was focussed on the transitions between the three possible staggered conformers with respect to the central C-C bond. In all cases a thermodynamic integration method was employed to evaluate the free energy difference. The use of an alternative technique, umbrella sampling, for ribose did not give promising results.

It was shown that one needs a fairly accurate picture of the accessible conformational space in case of flexible molecules like the ones considered here before one can determine meaningful free energy differences. Large hysteresis effects between forward and reverse simulated transitions were observed, but contrary to the general belief they are no direct measure of the accuracy of the calculated ΔG values. In all cases the ΔG values resulting from the simulations and from NMR experiments agree within the, considerable, error limits and for the different forms of D-ribose, L-malic acid and L-tartaric acid the relative order of their populations is also correctly reproduced.     

Modulating Molecular Functions of p53 with Small Molecules

Association of the p53 with many human cancers makes it a valuable therapeutic target. Stress-induced molecular interactions of p53 with other effector proteins are immensely intertwined with regulation of its functions in orchestrating a wide array of cellular responses, thereby defying analysis of the underlying molecular mechanisms with conventional molecular and cellular biology methods. Recent discoveries of small molecules that can selectively modulate the molecular interactions of p53 offer promising opportunities to address the challenge of dissecting these complex mechanisms and increase the hope for pharmacological control of p53 for clinical benefits of cancer patients.     

MDM2-P53蛋白质相互作用的小分子抑制物

p53作为重要的抑癌基因已经成为一个治疗癌症重点的突破目标之一。直接调节p53基因或调节P53和MDM2蛋白质相互作用是再激活p53基因的两种重要机制。对于表达野生型P53的癌症设计小分子阻断剂阻断MDM2与P53蛋白相互作用是一个很有前景的治疗癌症的方向。文章主要总结了作为治疗癌症的新方法-MDM2-P53蛋白相互作用小分子抑制物的最新研究进展,其中最新的是人工合成化合物Nutlin-3和MI-219。     

Dynamics of Small Molecules in a Dense Polymer Matrix: Molecular Dynamics Studies

Abstract

The anomalous diffusion regime appearing in the self-diffusion of small molecules in bulk amorphous polymers has been extensively studied by molecular dynamics simulations. A rather long simulation of duration ～ 10 ^?8 s is performed on a polyethylene-like simple polymer model containing either oxygen molecules or helium atoms as a diffusant. Dynamic properties evaluated for these diffusants are the mean-square displacement, the van Hove self correlation function, and the self part of the density autocorrelation. It is first confirmed that the anomalous diffusion regime appears in a few hundred picoseconds for oxygen molecule, while the Einstein relation adopted beyond this regime results in the self-diffusion coefficient of the order of ～ 10^?5 cm²/s. This anomaly is still observed for helium that diffuses much faster than oxygen. In the anomalous diffusion regime, it is found that the correlation functions for the two diffusants show characteristic features and become essentially the same as time is scaled appropriately. These features allow the estimation of the two characteristic spatial scales which are probably dominated by the microstructure of the polymer matrix, namely, the cage size and the distance between adjacent cages. The time dependence of the mean-square displacements of the two diffusants can be well interpreted by these characteristic spatial scales as time is scaled with the self-diffusion coefficients. It is shown that the anomalous diffusion regime arises from the inhomogeneous microstructure of the polymer matrix.     

Analysis of Group Randomized Trials with Multiple Binary Endpoints and Small Number of Groups

The group randomized trial (GRT) is a common study design to assess the effect of an intervention program aimed at health promotion or disease prevention. In GRTs, groups rather than individuals are randomized into intervention or control arms. Then, responses are measured on individuals within those groups. A number of analytical problems beset GRT designs. The major problem emerges from the likely positive intraclass correlation among observations of individuals within a group. This paper provides an overview of the analytical method for GRT data and applies this method to a randomized cancer prevention trial, where multiple binary primary endpoints were obtained. We develop an index of extra variability to investigate group-specific effects on response. The purpose of the index is to understand the influence of individual groups on evaluating the intervention effect, especially, when a GRT study involves a small number of groups. The multiple endpoints from the GRT design are analyzed using a generalized linear mixed model and the stepdown Bonferroni method of Holm.     

Construction of DNA Hemicatenanes from Two Small Circular DNA Molecules

DNA hemicatenanes, one of the simplest possible junctions between two double stranded DNA molecules, have frequently been mentioned in the literature for their possible function in DNA replication, recombination, repair, and organization in chromosomes. They have been little studied experimentally, however, due to the lack of an appropriate method for their preparation. Here we have designed a method to build hemicatenanes from two small circular DNA molecules. The method involves, first, the assembly of two linear single strands and their circularization to form a catenane of two single stranded circles, and, second, the addition and base-pairing of the two single stranded circles complementary to the first ones, followed by their annealing using DNA topoisomerase I. The product was purified by gel electrophoresis and characterized. The arrangement of strands was as expected for a hemicatenane and clearly distinct from a full catenane. In addition, each circle was unwound by an average of half a double helical turn, also in excellent agreement with the structure of a hemicatenane. It was also observed that hemicatenanes are quickly destabilized by a single cut on either of the two strands passing inside the junction, strongly suggesting that DNA strands are able to slide easily inside the hemicatenane. This method should make it possible to study the biochemical properties of hemicatenanes and to test some of the hypotheses that have been proposed about their function, including a possible role for this structure in the organization of complex genomes in loops and chromosomal domains.     

Amyloid-Precursor-Protein-Lowering Small Molecules for Disease Modifying Therapy of Alzheimer's Disease

Alzheimer''s disease (AD) is the most common form of dementia in the elderly with progressive cognitive decline and memory loss. According to the amyloid-hypothesis, AD is caused by generation and subsequent cerebral deposition of β-amyloid (Aβ). Aβ is generated through sequential cleavage of the transmembrane Amyloid-Precursor-Protein (APP) by two endoproteinases termed beta- and gamma-secretase. Increased APP-expression caused by APP gene dosage effects is a risk factor for the development of AD. Here we carried out a large scale screen for novel compounds aimed at decreasing APP-expression. For this we developed a screening system employing a cell culture model of AD. A total of 10,000 substances selected for their ability of drug-likeness and chemical diversity were tested for their potential to decrease APP-expression resulting in reduced Aβ-levels. Positive compounds were further evaluated for their effect at lower concentrations, absence of cytotoxicity and specificity. The six most promising compounds were characterized and structure function relationships were established. The novel compounds presented here provide valuable information for the development of causal therapies for AD.