Systemic evolutionary chemical space exploration for drug discovery.

Chemical space exploration is a major task of the hit-finding process during the pursuit of novel chemical entities. Compared with other screening technologies, computational de novo design has become a popular approach to overcome the limitation of current chemical libraries. Here, we reported a de novo design platform named systemic evolutionary chemical space explorer (SECSE). The platform was conceptually inspired by fragment-based drug design, that miniaturized a "lego-building" process within the pocket of a certain target. The key to virtual hits generation was then turned into a computational search problem. To enhance search and optimization, human intelligence and deep learning were integrated. Application of SECSE against phosphoglycerate dehydrogenase (PHGDH), proved its potential in finding novel and diverse small molecules that are attractive starting points for further validation. This platform is open-sourced and the code is available at http://github.com/KeenThera/SECSE.

Differences Among Sexes in Blood Pressure: A Combinatorial Consequence of the Differences between RAAS Components, Sex Hormones, and Time Course.

For all lives regardless of sex, the longitudinal increase in blood pressure (BP) with age is attributed to lifestyle, internal environments like systemic brain-derived neurotrophic factor (BDNF) signaling, and external environments, allowing the individuals to better adapt to the developmental and environmental changes. Basic levels of renin-angiotensin-aldosterone system (RAAS) components in males and females define the fundamental sex difference in BP, which may be set by prenatal programming and the profound influence of BP after birth. The innate sex difference in BP is magnified during puberty growth and later on, affected and modified by menopause in women. At the age of 70 and older, blood pressure has been found to be similar for men and women. Understanding the prenatal setup and development of sexual dimorphism in BP may provide preventative therapeutic strategies, including timing and choice of drugs, for individuals with abnormal BP.

Resting-State Functional Magnetic Resonance Imaging Reveals Overactivation of the Habitual Control Brain System in Tobacco Dependence.

INTRODUCTION: We studied the regulatory mechanism of the habitual brain network in tobacco dependence to provide a theoretical basis for the regulation and cessation of tobacco dependence. METHODS: We used resting-state functional magnetic resonance imaging (rs-fMRI) to explore the Fractional amplitude of low-frequency fluctuations (fALFF) and functional connectivity (FC) of the habitual brain network in tobacco-dependent subjects and to evaluate the relationship between the FC level and tobacco selection preference behavior. In total, 29 male tobacco-dependent participants and 28 male nonsmoking participants were recruited. rs-fMRI was used to collect blood oxygen level-dependent signals of the participants in the resting and awake states. After rs-fMRI, all subjects completed cigarette/coin selection tasks (task 1 and task 2). RESULTS: Compared with the control group, the tobacco dependence group showed increased fractional amplitude values of fALFF in the left posterior cingulate cortex and right parahippocampus. FC in the tobacco-dependent group was increased in the right inferior temporal gyrus, left middle frontal gyrus, left cingulated gyrus, and bilateral superior frontal gyrus, compared with that in the control group. Moreover, the preference selection behavior was associated with the enhancement of FC about parts of the brain regions in the habitual brain network of the tobacco-dependent participants. Thus, habitual network activity was significantly enhanced in tobacco-dependent participants in the resting state. Moreover, a positive correlation was found between the cigarette selection preference of the smokers and certain brain regions related to the habitual network. DISCUSSION: This suggests that increased activity of the habitual brain network may be essential in the development of tobacco-dependent behavior.

DNA Compatible Intermolecular Wittig Olefination for the Construction of α, ß-Unsaturated Carbonyl Compounds.

A robust DNA-compatible Wittig reaction mediated by PPh2CH3 has been validated for DNA-conjugated α-chloroacetamides with aldehydes and, alternatively, DNA-conjugated aldehydes with α-halo acetamides or ketones. Further, 2-aminopyridines were acylated with α-chloroacetyl chloride and then reacted with DNA-conjugated aldehydes. Lastly, a pilot library employing our optimized Wittig reaction protocol was synthesized. The ability to generate α,ß-unsaturated carbonyl compounds may be particularly useful for the design of DNA-encoded libraries capable of covalently interacting with protein targets.

Magnetic resonance imaging and photothermal conversion properties of Gd-C nanocomposites for interstitial lymphography.

Dual-functional agents for magnetic resonance imaging (MRI) guided photothermal therapy (PTT) of lymph cancer are highly desired. Signal enhancement, selectivity between lymphatic nodes/vessels and blood vessels, and photothermal conversion property are the criteria for such dual-functional agent. In the current work, we demonstrated the potential of Gd-C nanocomposites as dual-functional agents for the MRI and PTT of lymph node cancer. Gd-C nanocomposites were synthesized via a hydrothermal carbonization approach with gadolinium chloride as Gd source and citric acid (CA) as C source. The particle size of the nanocomposites ranges from 40 to 100 nm which is smaller than the intercellular space of lymphatic vessels but much larger than that of the blood vessels. The nanocomposites were successfully applied to the MRI of cervical lymph nodes of rabbits. The signal enhancement of the lymph nodes reached the maximum value of 434% at 10 min after injection, without displaying any blood vessel. The Gd-C nanocomposites also exhibited strong photothermal conversion effect. Under the illumination of an 808 nm laser, the aqueous suspension containing 1.0 wt % Gd-C nanocomposites gave a maximum temperature rise of 28.2 °C and a light utilization efficiency of 30.4%. The results indicate that Gd-C nanocomposites have significant potential in MRI guided PTT of lymph cancer.

Thymine DNA glycosylase recognizes the geometry alteration of minor grooves induced by 5-formylcytosine and 5-carboxylcytosine.

The dynamic DNA methylation-demethylation process plays critical roles in gene expression control and cell development. The oxidation derivatives of 5-methylcytosine (5mC) generated by Tet dioxygenases in the demethylation pathway, namely 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC), could impact biological functions by altering DNA properties or recognition by potential reader proteins. Hence, in addition to the fifth base 5mC, 5hmC, 5fC, and 5caC have been considered as the sixth, seventh, and eighth bases of the genome. How these modifications would alter DNA and be specifically recognized remain unclear, however. Here we report that formyl- and carboxyl-modifications on cytosine induce the geometry alteration of the DNA minor groove by solving two high-resolution structures of a dsDNA decamer containing fully symmetric 5fC and 5caC. The alterations are recognized distinctively by thymine DNA glycosylase TDG via its finger residue R275, followed by subsequent preferential base excision and DNA repair. These observations suggest a mechanism by which reader proteins distinguish highly similar cytosine modifications for potential differential demethylation in order to achieve downstream biological functions.

Evaluation of quantitative parameters of dynamic contrast-enhanced magnetic resonance imaging in qualitative diagnosis of hepatic masses.

BACKGROUND: To explore the value of parameters of multiphase dynamic contrast-enhanced magnetic resonance imaging (MDCE-MRI) in the qualitative diagnosis of hepatic masses. METHODS: Eighty patients with hepatic masses were retrospectively analyzed. All the patients underwent MDCE-MRI at 3.0 T MR before treatment. Mean enhancement time (MET), positive enhancement integral (PEI), a maximum slope of increase (MSI), and a maximum slope of decrease (MSD) were measured. RESULTS: There were significant differences between benign and malignant hepatic masses with respect to MET, PEI, and MSI values. The PEI and MSI values between hemangiomas, hepatocellular carcinomas (HCCs), cholangiocarcinomas, and metastatic tumors had significant differences. The MSD value between metastatic tumors, HCCs, and hemangiomas were significantly different. The area under the curve (AUC) values of the receiver operator characteristic curves for MET, PEI, and MSI were 0.70, 0.72, and 0.80, respectively. The specificity of MET, PEI, and MSI were all 77%, and the sensitivities of MSI was the highest, of which was 82.40%. Logistic regression analysis showed the regression equation to be P = 1/[1 + e0.008 × 1 + 0.007 × 2-6.707], and taking the Youden index maximum points as a diagnostic point was 0.2946. CONCLUSION: Some parameters of MDCE-MRI have significant roles in differentiating hepatic masses.

Identification of novel inhibitors of histone acetyltransferase hMOF through high throughput screening.

The histone acetyltransferases (HATs) in mammals include GCN5 N-acetyltransferases, the MOZ, YBF2, SAS2, and TIP60 proteins, and the orphan HATs. The males absent on the first (MOF) is mainly related to acetylation of histone H4 Lys16 and has influence on downstream genes expression. However, the only inhibitor MG149 presented low activity against MOF. Besides, there was no high throughput screening platform on MOF, which limited the inhibitor discovery and functional study. In our study, we set up a high throughput screening platform based on amplified luminescent proximity homogeneous assay (ALPHA), which led us to a moderate inhibitor DC_M01. By chemical modification, we found DC_M01_7, which was the analog of DC_M01 with an IC50 value of 6 µM. DC_M01_7 significantly inhibited HCT116 cells proliferation and could also inhibit histone 4 lysine 16 acetylation in HCT116 cells. To sum up, our work will probably assist the further development of more potent MOF inhibitors and the functional study of hMOF.

Conformation and dynamics of the C-terminal region in human phosphoglycerate mutase 1.

Phosphoglycerate mutase 1 (PGAM1), an important enzyme in glycolysis, is overexpressed in a number of human cancers, thus has been proposed as a promising metabolic target for cancer treatments. The C-terminal portion of the available crystal structures of PGAM1 and its homologous proteins is partially disordered, as evidenced by weak electron density. In this study, we identified the conformational behavior of the C-terminal region of PGAM1 as well as its role during the catalytic cycle. Using the PONDR-FIT server, we demonstrated that the C-terminal region was intrinsically disordered. We applied the Monte Carlo (MC) method to explore the conformational space of the C-terminus and conducted a series of explicit-solvent molecular dynamics (MD) simulations, and revealed that the C-terminal region is inherently dynamic; large-scale conformational changes in the C-terminal segment led to the structural transition of PGAM1 from the closed state to the open state. Furthermore, the C-terminal segment influenced 2,3-bisphosphoglycerate (2,3-BPG) binding. The proposed swing model illustrated a critical role of the C-terminus in the catalytic cycle through the conformational changes. In conclusion, the C-terminal region induces large movements of PGAM1 from the closed state to the open state and influences cofactor binding during the catalytic cycle. This report describes the dynamic features of the C-terminal region in detail and should aid in design of novel and efficient inhibitors of PGAM1. A swing mechanism of the C-terminal region is proposed, to facilitate further studies of the catalytic mechanism and the physiological functions of its homologues.

Discovery of novel trimethoxy-ring BRD4 bromodomain inhibitors: AlphaScreen assay, crystallography and cell-based assay.

As a member of the bromodomain and extra terminal domain (BET) protein family, BRD4 is closely related to cancers and other diseases. Small-molecule BRD4 inhibitors have already demonstrated promising potential for the therapy of BRD4-related cancers. In this study, we report the discovery and evaluation of a novel category of BRD4 inhibitors, which share a trimethoxy ring and target the first bromodomain of the human BRD4 protein. The IC50 value of the most potent compound, DC-BD-03, is 2.01 µM. In addition, a high-resolution crystal structure of the compound DC-BD-29 with the first bromodomain of BRD4 was determined, which revealed the binding mode and facilitated further structure-based optimization. These compounds exhibited anti-proliferation activity, caused cell cycle arrest, and induced apoptosis in human leukemia MV4-11 cells. Thus, the results presented in this study indicated the potential of this series of compounds as drug candidates for the therapy of BRD4-related cancers.

Discovery of novel DNA methyltransferase 3A inhibitors via structure-based virtual screening and biological assays.

DNA methyltransferases are involved in diverse biological processes and abnormal methylation patterns play essential roles in cancer initiation and progression. DNA methyltransferase 3A (DNMT3A) acting as a de novo DNA methyltransferase, has gained widespread attention especially in haematological diseases. To date, large numbers of DNMTs inhibitors have been discovered, however, the small molecular inhibitors targeting DNMT3A are still in its infancy. In this study, structure-based virtual screening in combination with biological assays was performed to discovery potent novel DNMT3A inhibitors. Compound 40 and 40_3 displayed comparable in vitro inhibitory activity against DNMT3A with IC50 values of 46.5µM and 41µM, respectively. Further binding mode analysis suggested these molecules inhibit DNMT3A activity through binding the S-adenosyl-l-methionine (SAM) pocket. Overall, 40 and 40_3 may serve as novel scaffolds for further optimization and small molecular probes for investigating DNMT3A function.

Discovery and Optimization of Novel, Selective Histone Methyltransferase SET7 Inhibitors by Pharmacophore- and Docking-Based Virtual Screening.

Histone methyltransferases are involved in various biological functions, and these methylation regulating enzymes' abnormal expression or activity has been noted in several human cancers. Within this context, SET domain-containing (lysine methyltransferase) 7 (SET7, also called KMT7, SETD7, SET9) is of increasing significance due to its diverse roles in biological functions and diseases, such as diabetes, cancers, alopecia areata, atherosclerotic vascular disease, HIV, and HCV. In this study, DC-S100, which was discovered by pharmacophore- and docking-based virtual screening, was identified as the hit compound of SET7 inhibitor. Structure-activity relationship (SAR) analysis was performed on analogs of DC-S100 and according to the putative binding mode of DC-S100, structure modifications were made to improve its activity. Of note, compounds DC-S238 and DC-S239, with IC50 values of 4.88 and 4.59 µM, respectively, displayed selectivity for DNMT1, DOT1L, EZH2, NSD1, SETD8, and G9a. Taken together, DC-S238 and DC-S239 can serve as leads for further investigation as SET7 inhibitors and the chemical toolkits for functional biology studies of SET7.

[Relationship between episodic memory and resting-state brain functional connectivity network in patients with Alzheimer's disease and mild cognition impairment].

OBJECTIVE: To explore the relationship between the scores of episodic memory (EM) encoding and retrieving and the resting-state changes of brain functional connectivity (FC) network of Alzheimer's disease (AD) and mild cognition impairment (MCI) patients. METHODS: All subjects were recruited from special care clinic and ward and health physical examination center, Qingdao Huanxiu Community and Affiliated Hospital, Medical College of Qingdao university from January 2009 to July 2012.They were divided into AD group (n = 16), MCI group (n = 24) and normal control (NC) group (n = 24). The resting-state fMRI scans were performed with GE3.0T to acquire the blood oxygenation level dependent signals for EM encoding and retrieving. The two-sample t test was conducted between the groups and linear correlation analysis performed between EM and FC. RESULTS: Compared to the NC group, the AD and MCI groups exhibited decreased FC to posterior cingulated cortex (PCC) mainly in bilateral lateral temporal lobe, medial prefrontal cortex and right insula.Increased regions existed in posterior cerebellar lobe. Compared with the MCI group, the AD group showed decreased FC to PCC in medial prefrontal cortex, bilateral insulas, right inferior temporal gyrus and right fusiform gyrus.And increased regions lied in posterior cerebellar lobe, right occipital lobe and left superior parietal lobule. Compared with the NC group, the MCI group exhibited decreased FC to PCC in left lingualis gyrus, left frontal lobe, right middle temporal gyrus and corpus callosum.And increased regions lied in posterior cerebellar lobe.EM encoding scores (%) (AD group 34 ± 20, MCI group 47 ± 17, NC group 69 ± 15) were significantly different among three groups (P < 0.05).And retrieving scores (%) (AD group 31 ± 18, MCI group 57 ± 22, NC group 81 ± 16) were significantly different among three groups (P < 0.05). Altered functional connectivity regions of left triangle orbital-inferior frontal gyrus (r = 0.642 98), left cuneus (r = 0.642 98) and left caudate nucleus (r = 0.642 68) showed positive correlations with the EM encoding scores in AD group (all P < 0.005). Other groups were not statistically significant. CONCLUSION: The resting-state FC networks of AD and MCI groups show significant differences. The MCI and AD patients have progressively decreased scores of episodic memory encoding and retrieving.And the declines of episodic memory encoding and partial regions of resting-state FC network are positively correlated in the AD group.

Brain areas activated by uncertain reward-based decision-making in healthy volunteers.

Reward-based decision-making has been found to activate several brain areas, including the ventrolateral prefrontal lobe, orbitofrontal cortex, anterior cingulate cortex, ventral striatum, and mesolimbic dopaminergic system. In this study, we observed brain areas activated under three degrees of uncertainty in a reward-based decision-making task (certain, risky, and ambiguous). The tasks were presented using a brain function audiovisual stimulation system. We conducted brain scans of 15 healthy volunteers using a 3.0T magnetic resonance scanner. We used SPM8 to analyze the location and intensity of activation during the reward-based decision-making task, with respect to the three conditions. We found that the orbitofrontal cortex was activated in the certain reward condition, while the prefrontal cortex, precentral gyrus, occipital visual cortex, inferior parietal lobe, cerebellar posterior lobe, middle temporal gyrus, inferior temporal gyrus, limbic lobe, and midbrain were activated during the 'risk' condition. The prefrontal cortex, temporal pole, inferior temporal gyrus, occipital visual cortex, and cerebellar posterior lobe were activated during ambiguous decision-making. The ventrolateral prefrontal lobe, frontal pole of the prefrontal lobe, orbitofrontal cortex, precentral gyrus, inferior temporal gyrus, fusiform gyrus, supramarginal gyrus, inferior parietal lobule, and cerebellar posterior lobe exhibited greater activation in the 'risk' than in the 'certain' condition (P < 0.05). The frontal pole and dorsolateral region of the prefrontal lobe, as well as the cerebellar posterior lobe, showed significantly greater activation in the 'ambiguous' condition compared to the 'risk' condition (P < 0.05). The prefrontal lobe, occipital lobe, parietal lobe, temporal lobe, limbic lobe, midbrain, and posterior lobe of the cerebellum were activated during decision-making about uncertain rewards. Thus, we observed different levels and regions of activation for different types of reward processing during decision-making. Specifically, when the degree of reward uncertainty increased, the number of activated brain areas increased, including greater activation of brain areas associated with loss.

[An experimental study of the cervical lymphatic imaging in interstitial magnetic resonance lymphography of tongue using Dextran-DTPA-Gd].

PURPOSE: To explore the application value of the cervical lymphatic imaging in interstitial magnetic resonance lymphography using submucosal injection of Dextran-DTPA-Gd. METHODS: 0.2 mL Dextran-DTPA-Gd (3.96 mmol/L) was injected into the submucosa of the bilateral lingual margins in 12 New Zealand rabbits,and then massaged the injection site for 30 seconds. MR images were obtained before injection and 10, 15, 20, 25, 30, 35, 40, 50, 90 minutes after injection by 3D TOF CE-MRA sequence.The signal intensities of cervical lymph node were measured, the enhancing rates(E%) were calculated and the signal enhancing rates -time curve was drawn. The data was analysed using SPSS11.5 software package. RESULTS: The cervical lymph nodes,the first and second lymphatics were strengthened significantly after injecting Dextran-DTPA-Gd, but the blood vessels were not enhanced at the same time. The enhancing rates of cervical lymph node reached the peak(344%) at 30-min,and the best strengthening effect was achieved between 20-min and 50-min. CONCLUSIONS: As IMRLG contrast agent,the Dextran-DTPA-Gd could image lymphatic drainage lines of the neck and the cervical lymph nodes efficiently.

Development of a novel class of B-Raf(V600E)-selective inhibitors through virtual screening and hierarchical hit optimization.

Oncogenic mutations in critical nodes of cellular signaling pathways have been associated with tumorigenesis and progression. The B-Raf protein kinase, a key hub in the canonical MAPK signaling cascade, is mutated in a broad range of human cancers and especially in malignant melanoma. The most prevalent B-Raf(V600E) mutant exhibits elevated kinase activity and results in constitutive activation of the MAPK pathway, thus making it a promising drug target for cancer therapy. Herein, we describe the development of novel B-Raf(V600E) selective inhibitors via multi-step virtual screening and hierarchical hit optimization. Nine hit compounds with low micromolar IC(50) values were identified as B-Raf(V600E) inhibitors through virtual screening. Subsequent scaffold-based analogue searching and medicinal chemistry efforts significantly improved both the inhibitor potency and oncogene selectivity. In particular, compounds 22f and 22q possess nanomolar IC(50) values with selectivity for B-Raf(V600E)in vitro and exclusive cytotoxicity against B-Raf(V600E) harboring cancer cells.

[Radiological diagnosis of primary malignant fibrous histiocytoma of bone].

OBJECTIVE: To explore the radiological diagnosis of primary malignant fibrous histiocytoma (MFH) of bone. METHODS: Sixteen patients with biopsy-or surgery-confirmed MFH received both plain X-ray and CT examinations, among whom six patients simultaneously received MRI. The imaging features were analyzed and the differential diagnoses were assessed. RESULTS: (1) Plain X-ray findings: All these lesions showed irregularly osteolytic, accompanied by cortical destruction. Five patients had varied degrees of cortical expansion, 12 had large soft tissue masses adjacent to the lesions, and only 2 had periosteal reaction. (2) CT findings: All lesions were osteolytic areas but had no evidences that its internal architecture had been replaced by soft tissue mass, and the cortical adjacent to the lesions were permeative osteolysis. Four patients had internal or marginal crest within the lesions and marginal inconsecutive osteosclerosis. Twelve had large soft tissue masses but without any calcification and residual architecture adjacent to the lesions, among which 3 patients had solitary or multiple cystic attenuation areas within the masses. No clear periosteal reaction was observed on CT. (3) MRI findings: All of lesions in 6 patients who received MRI showed inhomogeneous long T1 and long T2 abnormal signal intensity with soft tissue masses adjacent to the osteo-destructions. CONCLUSIONS: The imaging manifestations of MFH were specific to some extent. Combined utilization of plain X-ray, CT, and MRI is helpful for the diagnosis and differential diagnosis of MFH.