The discovery of novel HDAC3 inhibitors via virtual screening and in vitro bioassay

Histone deacetylase 3 (HDAC3) is a potential target for the treatment of human diseases such as cancers, diabetes, chronic inflammation and neurodegenerative diseases. Previously, we proposed a virtual screening (VS) pipeline named “Hypo1_FRED_SAHA-3” for the discovery of HDAC3 inhibitors (HDAC3Is) and had thoroughly validated it by theoretical calculations. In this study, we attempted to explore its practical utility in a large-scale VS campaign. To this end, we used the VS pipeline to hierarchically screen the Specs chemical library. In order to facilitate compound cherry-picking, we then developed a knowledge-based pose filter (PF) by using our in-house quantitative structure activity relationship- (QSAR-) modelling approach and coupled it with FRED and Autodock Vina. Afterward, we purchased and tested 11 diverse compounds for their HDAC3 inhibitory activity in vitro. The bioassay has identified compound 2 (Specs ID: AN-979/41971160) as a HDAC3I (IC₅₀?=?6.1?μM), which proved the efficacy of our workflow. As a medicinal chemistry study, we performed a follow-up substructure search and identified two more hit compounds of the same chemical type, i.e. 2–1 (AQ-390/42122119, IC₅₀?=?1.3?μM) and 2–2 (AN-329/43450111, IC₅₀?=?12.5?μM). Based on the chemical structures and activities, we have demonstrated the essential role of the capping group in maintaining the activity for this class of HDAC3Is. In addition, we tested the hit compounds for their in vitro activities on other HDACs, including HDAC1, HDAC2, HDAC8, HDAC4 and HDAC6. We have identified these compounds are HDAC1/2/3 selective inhibitors, of which compound 2 show the best selectivity profile. Taken together, the present study is an experimental validation and an update to our earlier VS strategy. The identified hits could be used as starting structures for the development of highly potent and selective HDAC3Is.     

Detector location selection based on VIP analysis in near-infrared detection of dural hematoma

Detection of dural hematoma based on multi-channel near-infrared differential absorbance has the advantages of rapid and non-invasive detection. The location and number of detectors around the light source are critical for reducing the pathological characteristics of the prediction model on dural hematoma degree. Therefore, rational selection of detector numbers and their distances from the light source is very important. In this paper, a detector position screening method based on Variable Importance in the Projection (VIP) analysis is proposed. A preliminary modeling based on Partial Least Squares method (PLS) for the prediction of dural position μ_a was established using light absorbance information from 30 detectors located 2.0–5.0?cm from the light source with a 0.1?cm interval. The mean relative error (MRE) of the dural position μ_a prediction model was 4.08%. After VIP analysis, the number of detectors was reduced from 30 to 4 and the MRE of the dural position μ_a prediction was reduced from 4.08% to 2.06% after the reduction in detector numbers. The prediction model after VIP detector screening still showed good prediction of the epidural position μ_a. This study provided a new approach and important reference on the selection of detector location in near-infrared dural hematoma detection.     

Towards automated cancer screening: Label‐free classification of fixed cell samples using wavelength modulated Raman spectroscopy

The ability to provide quantitative, objective and automated pathological analysis would provide enormous benefits for national cancer screening programmes, in terms of both resource reduction and improved patient wellbeing. The move towards molecular pathology through spectroscopic methods shows great promise, but has been restricted by spectral quality, acquisition times and lack of direct clinical application. In this paper, we present the application of wavelength modulated Raman spectroscopy for the automated label‐ and fluorescence‐free classification of fixed squamous epithelial cells in suspension, such as those produced during a cervical smear test. Direct comparison with standard Raman spectroscopy shows marked improvement of sensitivity and specificity when considering both human papillomavirus (sensitivity +12.0%, specificity +5.3%) and transformation status (sensitivity +10.3%, specificity +11.1%). Studies on the impact of intracellular sampling location and storage effects suggest that wavelength modulated Raman spectroscopy is sufficiently robust to be used in fixed cell classification, but requires further investigations of potential sources of molecular variation in order to improve current clinical tools.      

Steroids from Ganoderma sinense as new natural inhibitors of cancer-associated mutant IDH1

Isocitrate dehydrogenase (IDH) is one of the key enzymes in the tricarboxylic acid cycle, and IDH mutations have been associated with many cancers, including glioblastoma, sarcoma, acute myeloid leukemia, etc. Three natural steroids 1–3 from Ganoderma sinense, a unique and rare edible-medicinal fungi in China, were found as potential IDH1 inhibitors by virtual ligand screening method. Among the three compounds, 3 showed the highest binding affinity to IDH1 with significant calculated binding free energy. Enzymatic kinetics demonstrated that 3 inhibited mutant enzyme in a noncompetitive manner. The half effective concentration of 3 for reducing the concentration of D-2HG in HT1080 cells was 35.97 μM. The levels of histone H3K9me3 methylation in HT1080 cells were reduced by treating with 3. Furthermore, knockdown of mutant IDH1 in HT1080 cells decreased the anti-proliferative sensitivity to 3. In short, our findings highlight that compound 3 may have clinical potential in tumor therapies as an effective inhibitor of mutant IDH1.     

Who's In and Who's Out—Compositional Control of Biomolecular Condensates

Biomolecular condensates are two- and three-dimensional compartments in eukaryotic cells that concentrate specific collections of molecules without an encapsulating membrane. Many condensates behave as dynamic liquids and appear to form through liquid–liquid phase separation driven by weak, multivalent interactions between macromolecules. In this review, we discuss current models and data regarding the control of condensate composition, and we describe our current understanding of the composition of representative condensates including PML nuclear bodies, P-bodies, stress granules, the nucleolus, and two-dimensional membrane localized LAT and nephrin clusters. Specific interactions, such as interactions between modular binding domains, weaker interactions between intrinsically disorder regions and nucleic acid base pairing, and nonspecific interactions, such as electrostatic interactions and hydrophobic interactions, influence condensate composition. Understanding how specific condensate composition is determined is essential to understanding condensates as biochemical entities and ultimately discerning their cellular and organismic functions.     

浑善达克沙地生物土壤结皮及其下层土壤中好氧不产氧光营养细菌群落结构及多样性

【目的】揭示浑善达克沙地不同类型生物土壤结皮(Biological soil crusts,BSCs)及其下层土壤好氧不产氧光营养细菌(Aerobic anoxygenic phototrophic bacteria,AAPB)群落结构及多样性。【方法】利用Illumina Mi Seq二代高通量测序平台对puf M基因进行测序,使用生物信息学分析方法对序列进行比对分析AAPB的群落结构和多样性。【结果】生物土壤结皮及其下层土壤中,Proteobacteria和Alpha-Proteobacteria是优势门和纲,主要有6个属Bradyrhizobium(9.69%–90.02%)、Brevundimonas(0.83%–16.04%)、Methylobacterium(1.74%–12.56%)、Rhodospirillum(0.91%–32.87%)、Roseiflexus(0.02%–1.79%)和Sphingomonas(0.13%–11.23%);结皮层样品间及下层土壤样品间AAPB种类相似,但丰度有差异;随结皮的发育,结皮层及其下层土壤中AAPB群落多样性升高。【结论】浑善达克沙地BSCs中AAPB群落结构相对复杂,与水体和一般土壤环境中的组成区别明显;AAPB多样性高,且多样性随发育阶段升高而升高,预示着AAPB在荒漠生态系统稳定中有重要的作用。     

肠道中乳酸杆菌属特异性定量引物的筛选及验证

【目的】乳酸杆菌与人和动物的健康有密切关系,它的存在及含量变化可以作为评价宿主健康的指标之一。在乳酸杆菌定量研究中,特异性引物往往是定量成功的关键。然而,已有引物质量参差不齐,难以保证其特异性。本文旨在通过理论与试验的方法快速筛选出用于定量的乳酸杆菌属特异性引物,同时为今后引物筛选和设计提供理论基础。【方法】查阅文献、挑选出12对基于16S rRNA基因序列设计的乳酸杆菌属引物,通过MEGA 6.0软件确定引物相对位置,计算引物匹配率,以引物相对位置和匹配率为依据重新组合引物,获得理论特异性乳酸杆菌属引物,再通过琼脂糖凝胶电泳和QX200Droplet Digital PCR系统对新组合引物的特异性进行检验。【结果】通过理论与试验相结合的方法确定了一对特异性较好的乳酸杆菌属定量引物Lab1,它的扩增产物大小约300 bp。ddPCR系统检验结果发现其特异性和灵敏性较好,还可以有效定量粪便中的乳酸杆菌。【结论】引物设计理论结合特异性试验这种方法可以快速有效地筛选出特异性较好的引物,同时为今后引物筛选和设计提供理论基础。     

不同因素对六盘山地区甘肃鼢鼠肠道细菌多样性的影响

【目的】研究甘肃鼢鼠肠道细菌的群落结构和多样性,探讨不同环境因素对六盘山地区甘肃鼢鼠肠道细菌多样性的影响。【方法】通过Illumina高通量测序技术,对甘肃鼢鼠的36个盲肠样品进行16S rRNA V3–V4区的高通量测序,分析了肠道细菌多样性、丰度和群落结构,探讨地域、性别和季节等因素对甘肃鼢鼠肠道细菌多样性的影响。【结果】甘肃鼢鼠肠道细菌群落主要包括3个门,其中Firmicutes门占主导地位,其次是Bacteroidetes和Proteobacteri。在属水平,优势菌属分别为Oscillospira、Ruminococcus、Coprococcus和Desulfovibrio等。不同县(区)样品中,彭阳县、隆德县和泾源县三个县的甘肃鼢鼠肠道细菌菌群结构相似度较高,海原县甘肃鼢鼠肠道细菌群落结构在组内相似度高,与其他县(区)相似度低;雌性甘肃鼢鼠肠道细菌群落结构相似性高,而雄性细菌群落结构在样品间差异较大;甘肃鼢鼠肠道细菌菌群多样性秋季显著高于春季,细菌群落结构相似度秋季高于春季。【结论】不同地域、性别和季节因素对甘肃鼢鼠肠道细菌群落结构产生显著的影响,甘肃鼢鼠肠道细菌群落结构和多样性的变化对基于食源的季节性变化具有积极的响应。     

Joker: An algorithm to insert patterns into sequences for designing antimicrobial peptides

Innovative alternatives to control bacterial infections are need due to bacterial resistance rise. Antimicrobial peptides (AMPs) have been considered as the new generation of antimicrobial agents. Based on the fact that AMPs are sequence-dependent, a linguistic model for designing AMPs was previously developed, considering AMPs as a formal language with a grammar (patterns or motifs) and a vocabulary (amino acids). Albeit promising, that model has been poorly exploited mainly because thousands of sequences need to be generated, and the outcome has high similarity to already known AMPs. Here we present Joker, an innovative algorithm that improves the application of the linguistic model for rational design of antimicrobial peptides. We modelled the AMPs as a card game, where Joker combines the cards in the hand (patterns) with the cards in the table (sequence templates), generating a few variants. Our algorithm is capable of improving existing AMPs or even creating new AMPs from inactive peptides. A standalone version of Joker is available for download at <http://github.com/williamfp7/Joker> and requires a Linux 32-bit machine.