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protein docking

Beena Negi, Prija Poonan, Mohammad Fawad Ansari, Deepak Kumar, Sakshi Aggarwal, Ramandeep Singh, Amir Azam, Diwan S Rawat
A series of 22 novel metronidazole-triazole-styryl hybrids were synthesized and evaluated for their in vitro antiamoebic activity against HM1: IMSS strain of Entamoeba histolytica. Some of the hybrids were found to be more active (IC50  = 0.12-0.35 μM) than the reference drug metronidazole (IC50  = 1.79 μM). The most active compounds were found to be non-toxic (up to 50 μM) against the Vero cells showing a good safety profile of these hybrids. The docking and ADMET studies were also conducted to investigate the probable mode of action...
March 13, 2018: European Journal of Medicinal Chemistry
Jin Liu, Yu Chen, Jing-Ya Li, Cheng Luo, Jia Li, Kai-Xian Chen, Xu-Wen Li, Yue-Wei Guo
Phidianidines A and B are two novel marine indole alkaloids bearing an uncommon 1,2,4-oxadiazole ring and exhibiting various biological activities. Our previous research showed that the synthesized phidianidine analogs had the potential to inhibit the activity of protein tyrosine phosphatase 1B (PTP1B), a validated target for Type II diabetes, which indicates that these analogs are worth further structural modification. Therefore, in this paper, a series of phidianidine derivatives were designed and rapidly synthesized with a function-oriented synthesis (FOS) strategy...
March 20, 2018: Marine Drugs
Tanuj Sharma, Mohammad Imran Siddiqi
Unique intrinsic properties of peptides like low toxicity, high biological activity and specificity make them attractive therapeutic agents. PDZ binding peptide inhibitors have been demonstrated for curing of Alzheimer, Parkinson, Dementia and other central nervous system ailments. In this article, we report the successful use of an integrated computational protocol to analyze the structural basis of how peptides bind to the shallow groove of the third PDZ domain (PDZ3) from the Post Synaptic Density (PSD-95) protein...
March 20, 2018: Journal of Biomolecular Structure & Dynamics
Kolla Rajasekhar, Kapilkumar Mehta, Thimmaiah Govindaraju
Amyloid beta (Aβ) aggregation is the key trait responsible for the pathological devastation caused by Alzheimer's disease (AD). Among the various pathways of multifaceted toxicity exhibited by Aβ aggregates in neuronal cells, generation of reactive oxygen species (ROS) by Aβ-CuII complex and mitochondrial damage are prominent. Aβ interferes with mitochondrial transport channels, causing mitochondrial dysfunction. Herein, we present nontoxic hybrid multifunctional modulators (HMMs, TGR86-88) developed by integrating the structural and functional features of the metal chelating aggregation modulator, clioquinol (Clq) and the antioxidant epigallocatechin gallate (EGCG)...
March 20, 2018: ACS Chemical Neuroscience
Geetha Rani Yuvaraj, Baddrireddi Subhadra Lakshmi
Estrogen receptor α (ER α) is an important therapeutic target in the regulation of ligand dependent signaling in breast cancer. The current study investigates the anti-estrogenic potential of the Diarylheptanoid, 5-hydroxy-7-(4-hydroxy-3 methoxyphenyl)-1-phenyl-3-heptanone (DAH) in silico. Rigid Docking analysis of DAH at the ligand binding domain (LBD) of ER α showed hydrogen bond interactions with Arg394 and Glu353 at the active site, similar to the positive controls 4 - Hydroxy Tamoxifen (4-OHT) and Fulvestrant (FUL)...
March 20, 2018: Journal of Biomolecular Structure & Dynamics
Irene Maffucci, Xiao Hu, Valentina Fumagalli, Alessandro Contini
Nwat-MMGBSA is a variant of MM-PB/GBSA based on the inclusion of a number of explicit water molecules that are the closest to the ligand in each frame of a molecular dynamics trajectory. This method demonstrated improved correlations between calculated and experimental binding energies in both protein-protein interactions and ligand-receptor complexes, in comparison to the standard MM-GBSA. A protocol optimization, aimed to maximize efficacy and efficiency, is discussed here considering penicillopepsin, HIV1-protease, and BCL-XL as test cases...
2018: Frontiers in Chemistry
Tanzeel Ur Rehman, Arif-Ullah Khan, Azar Abbas, Javid Hussain, Farman Ullah Khan, Kimberly Stieglitz, Shamsher Ali
In the present study, we describe various pharmacological effects and computational analysis of nepetolide, a tricyclic clerodane-type diterpene, isolated from Nepeta suavis . Nepetolide concentration-dependently (1.0-1000 µg/mL) exhibited 1,1-diphenyl,2-picrylhydrazyl free radical scavenging activity with maximum effect of 87.01 ± 1.85%, indicating its antioxidant potential, as shown by standard drug, ascorbic acid. It was moderately active against bacterial strain of Staphylococcus aureus . In brine shrimp's lethality model, nepetolide potently showed cytotoxic effect, with LC50 value of 8...
March 2018: Saudi Pharmaceutical Journal: SPJ: the Official Publication of the Saudi Pharmaceutical Society
Dharmendra K Yadav, Surendra Kumar, Saloni, Sanjeev Misra, Lalit Yadav, Mahesh Teli, Praveen Sharma, Sandeep Chaudhary, Naresh Kumar, Eun Ha Choi, Hyung Sik Kim, Mi-Hyun Kim
SIRT6 and COX-2 are oncogenes target that promote the expression of proinflammatory and pro-survival proteins through a signaling pathway, which leads to increased survival and proliferation of tumor cells. However, COX-2 also suppresses skin tumorigenesis and their relationship with SIRT6, making it an interesting target for the discovery of drugs with anti-inflammatory and anti-cancer properties. Herein, we studied the interaction of thieno[3,2-c]pyran analogs and RONS species with SIRT6 and COX-2 through the use of molecular docking and molecular dynamic simulations...
March 19, 2018: Scientific Reports
Mohamed Salla, Rodrigo Aguayo-Ortiz, Danmaliki Gaddafi Ibrahim, Alaa Zare, Ahmed Said, Jack Moore, Vrajeshkumar Pandya, Robin Manaloor, Sunny Fong, Anna R Blankstein, Spencer Gibson, Laura Ramos Garcia, Pascal Meier, Khushwant S Bhullar, Basil P Hubbard, Yahya Fiteh, Harissios Vliagoftis, Ing Swie Goping, Dion Brocks, Peter Hwang, Jose Carlos A Martinez Velazquez, Shairaz Baksh
Receptor interacting protein kinase 2 (RIP2 or RICK herein referred to as RIPK2) is linked to the pathogen pathway that activates NFkB and autophagic activation. Using molecular modeling (docking) and chemoinformatics analyses we utilized the RIPK2/ponatinib crystal structure and searched in chemical databases for small molecules exerting binding interactions similar to those exerted by ponatinib. The identified RIPK2 inhibitors potently inhibited the proliferation of cancer cells by > 70% as well as inhibition of NFkB activity...
March 19, 2018: Journal of Pharmacology and Experimental Therapeutics
Xiangyi Wen, Matthew J Van Hook, Justin J Grassmeyer, Alex I Wiesman, Grace M Rich, Karlene M Cork, Wallace B Thoreson
Endocytosis is an essential process at sites of synaptic release. Not only are synaptic vesicles recycled by endocytosis, but the removal of proteins and lipids by endocytosis is needed to restore release site function at active zones after vesicle fusion. Synaptic exocytosis from vertebrate photoreceptors involves synaptic ribbons that serve to cluster vesicles near the presynaptic membrane. In this study, we hypothesize that this clustering increases the likelihood that exocytosis at one ribbon release site may disrupt release at an adjacent site and therefore that endocytosis may be particularly important for restoring release site competence at photoreceptor ribbon synapses...
March 19, 2018: Journal of General Physiology
Nagraj Mani, Andrew G Cole, Janet R Phelps, Andrzej Ardzinski, Kyle D Cobarrubias, Andrea Cuconati, Bruce D Dorsey, Ellen Evangelista, Kristi Fan, Fang Guo, Haitao Guo, Ju-Tao Guo, Troy O Harasym, Salam Kadhim, Steven G Kultgen, Amy C H Lee, Alice H L Li, Quanxin Long, Sara A Majeski, Richeng Mao, Kevin D McClintock, Stephen P Reid, Rene Rijnbrand, Nicholas M Snead, Holly M Micolochick Steuer, Kim Stever, Sunny Tang, Xiaohe Wang, Qiong Zhao, Michael J Sofia
AB-423 is a sulfamoylbenzamide (SBA) class of HBV capsid inhibitor in Phase 1 clinical trials. In cell culture models AB-423 showed potent inhibition of HBV replication (EC50 /EC90 = 0.08-0.27 μM/0.33-1.32 μM) with no significant cytotoxicity (CC50 >10 μM). Addition of 40% human serum resulted in a 5-fold increase in the EC50 values. AB-423 inhibited HBV genotypes A through D and nucleos/tide-resistant variants in vitro Treatment of HepDES19 cells with AB-423 resulted in capsid particles devoid of encapsidated pgRNA and rcDNA indicating it is a class II capsid inhibitor...
March 19, 2018: Antimicrobial Agents and Chemotherapy
Zacharenia Nikitaki, Marcela Holá, Mattia Donà, Athanasia Pavlopoulou, Ioannis Michalopoulos, Karel J Angelis, Alexandros G Georgakilas, Anca Macovei, Alma Balestrazzi
Eukaryotic genome surveillance is dependent on the multiple, highly coordinated network functions of the DNA damage response (DDR). Highlighted conserved features of DDR in plants and animals represent a challenging opportunity to develop novel interdisciplinary investigations aimed at expanding the sets of DNA damage biomarkers currently available for radiation exposure monitoring (REM) in environmental and biomedical applications. In this review, common and divergent features of the most relevant DDR players in animals and plants are described, including the intriguing example of the plant and animal kingdom-specific master regulators SOG1 (suppressor of gamma response) and p53...
January 2018: Mutation Research
Haofeng Gao, Chanjuan Li, Ramesh Bandikari, Ziduo Liu, Nan Hu, Qiang Yong
BACKGROUND: In industries lipolytic reactions occur in insensitive conditions such as high temperature thus novel stout esterases with unique properties are attracts to the industrial application. Protein engineering is the tool to obtain desirable characters of enzymes. A novel esterase gene was isolated from South China Sea and subjected to a random mutagenesis and site directed mutagenesis for higher activity and thermo-stability compared to wild type. RESULTS: A novel esterase showed the highest hydrolytic activity against p-nitrophenyl acetate (pNPA, C2) and the optimal activity at 40 °C and pH 8...
March 19, 2018: Microbial Cell Factories
Dandan Xiang, Tianyi Chu, Meng Li, Qiangwei Wang, Guonian Zhu
Mounting evidence suggests there is a link between exposure to synthetic pyrethroids (SPs) and the development of obesity. The information presented in this study suggests that cis-bifenthrin (cis-BF) could activate pregnane X receptor (PXR) mediated pathway and lead to the lipid accumulation of human hepatoma (HepG2) cells. Cells were incubated in the control or different concentrations of cis-BF for 24 h. The 1 × 10-7  M and 1 × 10-6  M cis-BF exposure were found to induce cellular triglyceride (TG) accumulation significantly...
March 3, 2018: Chemosphere
Qingyi Tong, Huijuan You, Xintao Chen, Kongchao Wang, Weiguang Sun, Yufeng Pei, Xiaodan Zhao, Ming Yuan, Hucheng Zhu, Zengwei Luo, Yonghui Zhang
Despite All-trans retinoic acid (ATRA) has transformed acute promyelocytic leukemia (APL) from the most fatal to the most curable hematological cancer, there remains a clinical challenge that many high-risk APL patients who fail to achieve a complete molecular remission or relapse and become resistant to ATRA. Herein, we report that 5-(4-methoxyphenethyl)-[1, 3] dioxolo [4, 5-j] phenanthridin-6(5H)-one (ZYH005) exhibits specific anticancer effects on APL and ATRA-resistant APL in vitro and vivo, while shows negligible cytotoxic effect on non-cancerous cell lines and peripheral blood mononuclear cells from healthy donors...
March 15, 2018: Nucleic Acids Research
Huai Guan, Maoying Wang, Chenghong Liao, Jing Liang, Prajwalini Mehere, Meiling Tian, Hairong Liu, Howard Robinson, Jianyong Li, Qian Han
Mosquitoes transmit a number of diseases in animals and humans, including Dengue, Chikungunya and Zika viruses that affect millions of people each year. Controlling the disease-transmitting mosquitoes has proven to be a successful strategy to reduce the viruses transmission. Polyamines are required for the life cycle of the RNA viruses, Chikungunya virus and Zika virus, and a depletion of spermidine and spermine in the host via induction of spermine N-acetyltransferase restricts their replication. Spermine N-acetyltransferase is a key catabolic enzyme in the polyamine pathway, however there is no information of the enzyme identification in any insects...
2018: PloS One
Marta Sánchez-Soto, Verònica Casadó-Anguera, Hideaki Yano, Brian Joseph Bender, Ning-Sheng Cai, Estefanía Moreno, Enric I Canela, Antoni Cortés, Jens Meiler, Vicent Casadó, Sergi Ferré
The poor norepinephrine innervation and high density of Gi/o-coupled α2A - and α2C -adrenoceptors in the striatum and the dense striatal dopamine innervation have prompted the possibility that dopamine could be an effective adrenoceptor ligand. Nevertheless, the reported adrenoceptor agonistic properties of dopamine are still inconclusive. In this study, we analyzed the binding of norepinephrine, dopamine, and several compounds reported as selective dopamine D2 -like receptor ligands, such as the D3 receptor agonist 7-OH-PIPAT and the D4 receptor agonist RO-105824, to α2 -adrenoceptors in cortical and striatal tissue, which express α2A -adrenoceptors and both α2A - and α2C -adrenoceptors, respectively...
March 18, 2018: Molecular Neurobiology
Ying Han, Yangmin Zheng, Jingpu Zhang, Changqin Hu
Most third- and fourth-generation cephalosporins, such as cefotaxime, cefmenoxime, cefepime, and cefpirome, contain an aminothiazoyl ring at the C-7 position. Drug impurity, which may be produced either during synthesis or upon degradation, can induce adverse effects. Various reports have indicated that neurotoxicity is a side effect of cephalosporin. In this study, we developed methods for assessing the free-swimming activities and behaviors in zebrafish larvae in response to continuous darkness and stimulation of light-to-dark photoperiod transition by chemical treatments...
2018: Frontiers in Pharmacology
Travis R Helgren, Elif S Seven, Congling Chen, Thomas E Edwards, Bart L Staker, Jan Abendroth, Peter J Myler, James R Horn, Timothy J Hagen
Methionine aminopeptidase (MetAP) is a dinuclear metalloprotease responsible for the cleavage of methionine initiator residues from nascent proteins. MetAP activity is necessary for bacterial proliferation and is therefore a projected novel antibacterial target. A compound library consisting of 294 members containing metal-binding functional groups was screened against Rickettsia prowazekii MetAP to determine potential inhibitory motifs. The compounds were first screened against the target at a concentration of 10 µM and potential hits were determined to be those exhibiting greater than 50% inhibition of enzymatic activity...
March 15, 2018: Bioorganic & Medicinal Chemistry Letters
Keppanan Ravindran, Sivaperumal Sivaramakrishnan, Mubasher Hussain, Chandra Kanta Dash, Bamisope Steve Bamisile, Muhammad Qasim, Wang Liande
Entomopathogenic fungi are rich sources of bioactive secondary metabolites that possess insecticidal properties. The present study reported a novel approach for the identification of insecticidal compounds produced by Lecanicillium lecanii 09 and to assess their toxicity against the diamondback moth Plutella xylostella L. The cyclic peptides groups of toxic substances were separated from L. lecanii 09 through submerged liquid state fermentation. The most abundant toxic metabolite, Bassianolide was purified by high-performance liquid chromatography (HPLC) and its molecular weight and purity were determined by Liquid chromatography - mass spectroscopy (LC-MS), Fourier transformed infrared spectroscopy (FT-IR), and H1 nuclear magnetic resonance (NMR) respectively...
March 15, 2018: Comparative Biochemistry and Physiology. Toxicology & Pharmacology: CBP
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