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Statins are 3-hydroxy-3-methylglutaryl-CoA reductase inhibitors broadly used for the control of hypercholesterolemia. Recently, they are reported to have beneficial effects on certain cancers. In this study, we show that statins inhibited the histone deacetylase (HDAC) activity and increased the accumulation of acetylated histone-H3 and the expression of p21WAF/CIP in human cancer cells. Computational modeling showed the direct interaction of the carboxylic acid moiety of statins with the catalytic site of HDAC2. In the subsequent enzymatic assay, it was shown that lovastatin inhibited HDAC2 activity competitively with a Ki value of 31.6 μmol/L. Sp1 but not p53 sites were found to be the statins-responsive element shown by p21 luciferase-promoter assays. DNA affinity protein binding assay and chromatin immunoprecipitation assay showed the dissociation of HDAC1/2 and association of CBP, leading to the histone-H3 acetylation on the Sp1 sites of p21 promoter. In vitro cell proliferation and in vivo tumor growth were both inhibited by statins. These results suggest a novel mechanism for statins through abrogation of the HDAC activity and promoter histone-H3 acetylation to regulate p21 expression. Therefore, statins might serve as novel HDAC inhibitors for cancer therapy and chemoprevention. [Cancer Res 2008;68(7):2375–83]

Supplementary Figures 1-2 from Statins Increase p21 through Inhibition of Histone Deacetylase Activity and Release of Promoter-Associated HDAC1/2

Intrinsically disordered proteins (IDP) are at the center of numerous biological processes, and attract consequently extreme interest in structural biology. Numerous approaches have been developed for generating sets of IDP conformations verifying a given set of experimental measurements. We propose here to perform a systematic enumeration of protein conformations, carried out using the TAiBP approach based on distance geometry. This enumeration was performed on two proteins, Sic1 and pSic1, corresponding to unphosphorylated and phosphorylated states of an IDP. The relative populations of the obtained conformations were then obtained by fitting SAXS curves as well as Ramachandran probability maps, the original finite mixture approach RamaMix being developed for this second task. The similarity between profiles of local gyration radii provides to a certain extent a converged view of the Sic1 and pSic1 conformational space. Profiles and populations are thus proposed for describing IDP conformations. Different variations of the resulting gyration radius between phosphorylated and unphosphorylated states are observed, depending on the set of enumerated conformations as well as on the methods used for obtaining the populations., The project ANR-19-CE45-0019 (multiBioStruct) is acknowledged for funding, as well as Institut Pasteur, CNRS, Ecole Polytechnique and Université de Rennes.

Objective: The objective of this experiment was to investigate the effects of different colors produced by light emitting diode (LED) on Brown Tsaiya ducks.Methods: A total of 144 female Brown Tsaiya ducks were randomly allocated into three individual cage rearing chambers with different LED illumination colors as treatments. Three different treatments were: i) white color, ii) blue color, and iii) red color. The experiment periods were from ducks 21 to 49 weeks of age, determined traits included i) egg laying performance, ii) feed intake, iii) egg shell breaking strength, iv) egg shell thickness, v) egg Haugh unit, vi) egg weight, vii) serum Estradiol and Progesterone concentration, and viii) behavior pattern.Results: The results indicated that when compared with white and blue color, red color could stimulate ducks sexual maturation and raised the egg laying performance. The red light group was also observed to have the highest feed intake among three treatments. The blue treatment had the lowest egg shell breaking strength and the highest egg weight among three treatments, nevertheless, no significant difference was observed among three treatments on egg shell thickness and egg Haugh unit. The red light group had higher serum estradiol concentration than the white and blue groups, but no significant difference among treatments on the serum Progesterone concentration was found. The results of behavior pattern indicated that red light group showed more feeding and less resting behavior compared to the blue light group.Conclusion: We found a potential of applying red light illumination in the indoor laying duck raising system with positive results on egg laying performance and acceptable egg weight, equivalent egg qualities compared to white and blue light.

Limited therapeutic options are available for advanced-stage hepatocellular carcinoma owing to its poor diagnosis. Drug resistance to sorafenib, the only available targeted agent, is commonly reported. The comprehensive elucidation of the mechanisms underlying sorafenib resistance may thus aid in the development of more efficacious therapeutic agents. To clarify the signaling changes contributing to resistance, we applied quantitative phosphoproteomics to analyze the differential phosphorylation changes between parental and sorafenib-resistant HuH-7 cells. Consequently, an average of ~1500 differential phosphoproteins were identified and quantified, among which 533 were significantly upregulated in resistant cells. Further bioinformatic integration via functional categorization annotation, pathway enrichment and interaction linkage analysis led to the discovery of alterations in pathways associated with cell adhesion and motility, cell survival and cell growth and the identification of a novel target, EphA2, in resistant HuH-7R cells. In vitro functional analysis indicated that the suppression of EphA2 function impairs cell proliferation and motility and, most importantly, overcomes sorafenib resistance. The attenuation of sorafenib resistance may be achieved prior to its development through the modulation of EphA2 and the subsequent inhibition of Akt activity. Binding analyses and in silico modeling revealed a ligand mimic lead compound, prazosin, that could abate the ligand-independent oncogenic activity of EphA2. Finally, data obtained from in vivo animal models verified that the simultaneous inhibition of EphA2 with sorafenib treatment can effectively overcome sorafenib resistance and extend the projected survival of resistant tumor-bearing mice. Thus our findings regarding the targeting of EphA2 may provide an effective approach for overcoming sorafenib resistance and may contribute to the management of advanced hepatocellular carcinoma., Liver cancer: A new route to fighting drug resistance Inhibiting the activity of a protein known as EphA2 may help overcome the development of drug resistance during treatment of hepatocellular carcinoma, the most common form of liver cancer. Resistance often develops to sorafenib, the main drug treatment option for the advanced disease. Researchers in Taiwan led by Lu-Ping Chow at the National Taiwan University in Taipei investigated the role of around 1500 phosphoproteins, which are regulated by the attachment and removal of small chemical groups containing phosphorus and oxygen. The activity of the phosphoprotein EphA2 was identified as a major contributor to drug resistance. This was linked to the ability of EphA2 to interfere with a molecular signaling pathway previously implicated in sorafenib activity. Suppressing EphA2 activity suppressed the development of sorafenib resistance in cultured cells and in mice with liver cancer, suggesting therapeutic possibilities.

Objectives The immunomodulatory effects of statins may reduce the immune response induced by influenza vaccines. However, evidence regarding the effect of statin use on the effectiveness of seasonal influenza vaccines against medically attended acute respiratory illness (MAARI) in the elderly remains scarce. Methods We conducted a retrospective cohort study using data from Taiwan’s National Health Insurance Research Database. Elderly adults aged ≧ 66 years who were vaccinated with seasonal influenza vaccines during the 2007–2008 to 2012–2013 influenza seasons were enrolled for this analysis. We compared the risk of MAARI between statin and non-statin users. Propensity score matching and conditional logistic regression models were used to analyze the data. Results A total of 440,180 elderly were included in this study. In general, the risk of MAARI was higher in statin users than non-statin users (odds ratio [OR]: 1.03, 95% confidence interval [CI]: 1.02–1.05). Statin exposure after vaccination was associated with a higher risk of MAARI (OR: 1.05, 95% CI: 1.02–1.07). Among different statin agents, simvastatin and lovastatin use was associated with a significant increase in the risk of MAARI (ORsimvastatin: 1.14, 95% CI: 1.10–1.18; ORlovastatin: 1.18, 95% CI: 1.12–1.25). Conclusions Statin exposure, especially simvastatin and lovastatin, was associated with a higher risk of MAARI in the seasonal influenza vaccinated elderly. Future studies exploring the differences between individual statins and mechanisms of their immunomodulatory effects are necessary.

Background and Objective This study aimed to develop pH-responsive polylactide-glycolic acid co-polymer and chitosan (PLGA/chitosan) nanosphere as an inflammation-responsive vehicle and evaluate the potential of the nanosphere encapsulating metronidazole, an antibiotic, and N-phenacylthiazolium bromide (PTB), a host modulator, for treating periodontitis. Material and Methods PLGA/chitosan nanospheres were fabricated using oil-in-water emulsion method. Experimental periodontitis was induced on the rat maxillae, and the sites were randomly allocated to four treatment categories, including periodontitis alone (PR), periodontitis with nanospheres alone, nanospheres encapsulating metronidazole (MT) and nanospheres encapsulating PTB (PB). The ligature was retained until the animals were killed, and the treatment outcome was evaluated by the progression of periodontal bone loss (PPBL), inflammatory cell infiltration and collagen deposition. Results The encapsulated drug was released rapidly from the nanospheres without significant initial burst release at pH 5.5. Compared with group PR, PPBL was significantly reduced in groups MT and PB on day 4 (P

The protein-protein interaction energetics can be obtained by calculating the potential of mean force (PMF) from umbrella sampling (US) simulations, in which samplings are often enhanced along a predefined vector as the reaction coordinate. However, any slight change in the vector may significantly vary the calculated PMF, and therefore the energetics using a random choice of vector may mislead. A non-predefined curve path-based sampling enhancement approach is a natural alternative, but was relatively less explored for protein-protein systems. In this work, dissociation of the barnase-barstar complex is simulated by implementing non-predefined curvilinear pathways in US simulations. A simple variational principle is applied to determine the lower bound PMF, which could be used to derive the standard free energy of binding. Two major dissociation pathways, which include interactions with the RNA-binding loop and the Val 36 to Gly 40 loop, are observed. Further, the proposed approach was used to discriminate the decoys from protein-protein docking studies. © 2019 Wiley Periodicals, Inc.

Complement activation plays a major role in many acute and chronic inflammatory conditions. C3d, a terminal product of complement activation, remains covalently attached to cells and is an excellent biomarker of complement-mediated inflammation. We employed a virtual high-throughput screening protocol to identify molecules with predicted binding to complement C3d and with intrinsic fluorescence properties to enable detection. Pharmacophore models were developed based on known C3d-ligand interactions and information from computational analysis of structural and molecular dynamics data. Iterative pharmacophore-based virtual screening was performed to identify druglike molecules with physicochemical similarity to the natural C3d ligand CR2. Hits from the pharmacophore screens were docked to C3d and ranked based on predicted binding free energies. Top-ranked molecules were selected for experimental validation of binding affinity to C3d, using microscale thermophoresis, and for their suitability to become molecular imaging agents, using fluorescence spectroscopy. This work serves as a foundation for identifying additional fluorescent molecules with high-affinity for C3d that will subsequently be explored as noninvasive in vivo diagnostics of complement-mediated inflammation, for spatiotemporal monitoring of disease progression, and for targeting therapeutics to sites of inflammation.

Cancer is a class of highly complex diseases involving multiple genes and multiple cross-talks between signaling networks. Cancer cells may be developed from inherited defects or acquired damages of DNA. However, many cancers are resistant to treatment, and metastasis of cancers makes the disease even more intractable. Secondary malignancies are frequently observed after cancer chemotherapy. The call for more effective cancer therapy is obligatory. Using drug-cocktails that combine multiple anti-cancer agents working in different mechanisms has been a standard treatment of cancers to overcome the drug resistance problem. More recently, design of multiple ligands (may be more easily understood as "multiple target ligands"), i.e., single agents that target multiple biomolecules in a rational manner, receives increasing attention. For those who work on computational drug design, such tasks serve as new opportunities for achieving drugs with more effective pharmacological actions, in addition to designing compounds with better binding affinity, better selectivity, or to discovering compounds that can exert their actions allosterically. Some recent methodological developments on computational drug design are reviewed, and a few recent drug design efforts on a selected set of targets (topoisomerases, Ras proteins, protein kinases, and histone deacetylases) toward cancer treatment and cancer prevention are summarized.

Type II topoisomerases resolve topological problems of DNA double helices by passing one duplex through the reversible double-stranded break they generated on another duplex. Despite the wealth of information in the cleaving operation, molecular understanding of the enzymatic DNA ligation remains elusive. Topoisomerase poisons are widely used in anti-cancer and anti-bacterial therapy and have been employed to entrap the intermediates of topoisomerase IIβ with religatable DNA substrate. We removed drug molecules from the structure and conducted molecular dynamics simulations to investigate the enzyme-mediated DNA religation. The drug-unbound intermediate displayed transitions toward the resealing-compliant configuration: closing distance between the cleaved DNA termini, B-to-A transformation of the double helix, and restoration of the metal-binding motif. By mapping the contact configurations and the correlated motions between enzyme and DNA, we identified the indispensable role of the linker preceding winged helix domain (WHD) in coordinating the movements of TOPRIM, the nucleotide-binding motifs, and the bound DNA substrate during gate closure. We observed a nearly vectorial transition in the recovery of the enzyme and identified the previously uncharacterized roles of Asn508 and Arg677 in DNA rejoining. Our findings delineate the dynamic mechanism of the DNA religation conducted by type II topoisomerases.

Alzheimer's disease is a neurodegenerative disorder characterized by deposition of β-amyloid (Aβ) fibrils accompanied with progressive neurite loss. None of the clinically approved anti-Alzheimer's agents target both pathological processes. We hypothesized that conjugation of a metal chelator to destabilize Aβ fibrils (fAβs) and a long-chain fatty alcohol to induce neurite outgrowth may generate a novel molecular scaffold that targets both pathologies. The hydroxyalkylquinoline J2326 was designed and synthesized by joining an 11-carbon alcohol to 5-chloro-8-methoxyquinoline at the 2-position and its anti-neurodegenerative potentials in vitro and in vivo were characterized. It attenuated fAβ formation and disaggregated the existing fAβ zinc-dependently as well as zinc-independently. It also triggered extracellular signal-regulated kinase-dependent neurite outgrowth and increased synaptic activity in neuronal cells. In fAβ-driven neurodegeneration in vitro, J2326 reversed neurite collapse and neurotoxicity. These roles of J2326 were also demonstrated in vivo and were pivotal to the observed improvement in memory of mice with hippocampal fAβ lesions. These results show that the effectiveness of J2326 on fAβ-driven neurodegeneration is ascribed to its novel scaffold. This might give clues to evolving attractive therapy for future clinical trials.

Seven new diarylheptanoids (1-7) were isolated from the n-BuOH-soluble fraction of the rhizome of Hedychium coronarium. Hedycoropyrans A-C (1-3) contain a tetrahydropyran moiety, while hedycorofurans A-D (4-7) contain a tetrahydrofuran moiety, belonging to a rare structural class of diarylheptanoids. Their structures including stereochemistry were elucidated on the basis of 1D and 2D NMR and ECD spectroscopic analyses and HRESIMS data of the parent compounds and the isopropylidene derivatives of 4 and 7.

International audience; G-quadruplex DNA ligands attract much attention because of their potential use in biology. Indeed they may interfere with G-quadrulex nucleic acid function in cells. Most of the G-quadruplex ligands so far reported (including also metal complexes) are large planar aromatic compounds that interact by π–π stacking with an external G-quartet of quadruplex. Porphyrins are well-known G-quadruplex ligands. We report herein a new porphyrin scaffold (meso-tetrakis(4-(N-methyl-pyridinium-2-yl)phenyl)porphyrin) able to strongly and selectively bind to G-quadruplex DNA. We show that even when this porphyrin is metallated with cobalt(III), i.e. it carries two water molecules as axial ligands on the cobalt ion, on each face of the porphyrin, the interaction occurs by a π-stacking-like mode with an external G-quartet of quadruplex DNA.

// Chiou-Tsun Tsai 1 , Pei-Ming Yang 1 , Ting-Rong Chern 3 , Shu-Hui Chuang 1 , Jung-Hsin Lin 2,3,4 , Lars Klemm 5 , Markus Muschen 5 and Ching-Chow Chen 1 1 Department of Pharmacology, College of Medicine, National Taiwan University, Taipei, Taiwan 2 School of Pharmacy, College of Medicine, National Taiwan University, Taipei, Taiwan 3 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan 4 Institute of Biomedical Science, Academia Sinica, Taipei, Taiwan 5 Department of Laboratory Medicine, University of California San Francisco, San Francisco, California Correspondence: Ching-Chow Chen, email: // Keywords : AID, 5-aza-CdR, Zebularine, DNMT1 Received : August 23, 2013 Accepted : November 23, 2013 Published : November 25, 2013 Abstract Activation-induced cytidine deaminase (AID) was originally identified as an inducer of somatic hypermutation (SHM) and class switch recombination (CSR) in immunoglobulin genes. However, AID can also cause mutations in host genes and contribute to cancer progression and drug resistance. In this study, molecular docking showed the interaction of free 5-aza-CdR and Zebularine (Zeb) with AID. However, only 5-aza-CdR-incorporated ssDNA bound to the active site of AID and inhibited AID expression through proteasomal degradation. 5-aza-CdR demonstrated cytotoxicity against AID-positive and -negative hematopoietic cancer cells. In contrast, Zeb exhibited a cytotoxic effect only in AID-negative cells due to its inability to inhibit AID expression. This differential effect might be due to the DNMT1 stabilization induced by AID, thus restricting the ability of Zeb to deplete DNMT1 and induce tumor suppressor genes (TSGs), such as p21, in AID-positive cells. Moreover, the in vivo anticancer effect of 5-aza-CdR but not Zeb in AID-positive hematopoietic cancer cells was demonstrated. The study not only displays the association of AID and DNMT1 and identifies a novel biological function of AID, but also provides novel information regarding the use of DNMT inhibitors to treat AID-positive hematopoietic cancers.

G Protein-Coupled Receptors (GPCRs) are the most common therapeutic targets for drug discovery by the pharmaceutical industries. Since 2007, several three-dimensional X-ray crystallographic structures of ligand-activated GPCRs have been determined in their agonist-bound or inverse agonist-bound states, providing a wealth of fundamental resources for the investigation of the atomic-level mechanism of receptor activation and deactivation. A number of computational methods, such as conventional and enhanced sampling Molecular Dynamic (MD) simulations have been applied to investigate the receptor dynamics bound with ligands of different functional types (i.e., agonist and inverse agonist). In this article, we reviewed recent efforts in characterizing the dynamical activation and deactivation mechanisms of GPCRs induced by different functional types of ligands.

The knowledge about to which biomolecules a small molecule binds is highly valuable in the drug development process. Although analytical methods to dissect ligand-binding proteome have made substantial progress in the past decades, it is generally too costly, if not infeasible, to know where a small molecule binds at very high resolution. Computational prediction of binding partners of small chemical molecules has become a useful approach to evaluate their potential therapeutic applications or adverse effects. In this article two computational approaches that were adopted to perform target identification, namely, molecular docking and pharmacophore fitting, are reviewed. Both approaches enable the identification of key interactions between the biomolecules and the small molecules. Databases that can be used to further improve the implementation and the computational methods and to benchmark their performances are also included.

Therapeutics that have been used by large populations and showed limited or little adverse effects can be good candidates for cancer chemo-prevention. As an example of such therapeutics, statins, i.e., HMG-CA reductase inhibitors, have been widely prescribed for lowering the blood cholesterol level and for treating cardiovascular diseases. In 2008, we discovered that statins are moderate inhibitors of histone deacetylases (HDACs), which provides an epigenetic mechanism for their efficacy in cancer prevention. HDACs have been long recognized for as an important class of therapeutic targets, and these enzymes utilize a Zn2+ ion at its active site for catalysis. Subsequently, in our 2013 J. Med. Chem. article, we showed that we are able to strengthen this epigenetic mechanism and designed more potent and effective therapeutic agents for cancer prevention and treatment, including cancer metastasis, and published in Clin. Cancer Res. in 2016. To investigate the structure-activity relationships of a broad class of HDAC inhibitors with distinct chemical moieties, we have conducted QM/MM molecular dynamics simulations of several systems of HDAC isoforms bound with various ligands. In contrast to molecular dynamics simulations with classical force fields, which always rendered over-coordinated configurations of the Zn2+ at the active site, with the coordination numbers (CN) to be either 6 or 7, in our QM/MM molecular dynamics simulations, the CNs of Zn2+ remain 4 or 5. With the structural and energetics analysis from these QM/MM molecular dynamics simulations, we are able to delineate the origins of isoform-selectivity of different HDAC inhibitors, including the aforementioned HMGR-HDAC dual-action inhibitors that we recently developed. Citation Format: Jung-Hsin Lin. Unraveling isoform selectivities of a broad class of HDAC inhibitors with QM/MM molecular dynamics simulations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1660.

Methotrexate (MTX) is a dihydrofolate reductase (DHFR) inhibitor widely used for treating human cancers, and overexpression of histone deacetylase (HDAC) is usually found in tumors. HDAC inhibitors (HDACi) can reactivate tumor suppressor genes and serve as potential anti-cancer drugs. In this study, we found that MTX shared structural similarity with some HDACi and molecular modeling showed that MTX indeed docks into the active site of HDLP, a bacterial homologue of HDAC. Subsequent in vitro assay demonstrated MTX's inhibition on HDAC activity in human cancer cells. The global acetylation of histone H3 was also induced by MTX. Moreover, MTX inhibited immunoprecipitated HDAC1/2 activity but not their protein levels. This study provides evidence that MTX inhibits HDAC activity.

Many proteins use a long channel to guide the substrate or ligand molecules into the well-defined active sites for catalytic reactions or for switching molecular states. In addition, substrates of membrane transporters can migrate to another side of cellular compartment by means of certain selective mechanisms. SLITHER (http://bioinfo.mc.ntu.edu.tw/slither/or http://slither.rcas.sinica.edu.tw/) is a web server that can generate contiguous conformations of a molecule along a curved tunnel inside a protein, and the binding free energy profile along the predicted channel pathway. SLITHER adopts an iterative docking scheme, which combines with a puddle-skimming procedure, i.e. repeatedly elevating the potential energies of the identified global minima, thereby determines the contiguous binding modes of substrates inside the protein. In contrast to some programs that are widely used to determine the geometric dimensions in the ion channels, SLITHER can be applied to predict whether a substrate molecule can crawl through an inner channel or a half-channel of proteins across surmountable energy barriers. Besides, SLITHER also provides the list of the pore-facing residues, which can be directly compared with many genetic diseases. Finally, the adjacent binding poses determined by SLITHER can also be used for fragment-based drug design.