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Molecular docking

Neha Maurya, Mehraj Ud Din Parray, Jitendra Kumar Maurya, Amit Kumar, Rajan Patel
The binding nature of amphiphilic drugs viz. promethazine hydrochloride (PMT) and adiphenine hydrochloride (ADP), with human hemoglobin (Hb) was unraveled by fluorescence, absorbance, time resolved fluorescence, fluorescence resonance energy transfer (FRET) and circular dichroism (CD) spectral techniques in combination with molecular docking and molecular dynamic simulation methods. The steady state fluorescence spectra indicated that both PMT and ADP quenches the fluorescence of Hb through static quenching mechanism which was further confirmed by time resolved fluorescence spectra...
March 11, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
Luciana Romão, Vanessa P do Canto, Paulo A Netz, Vivaldo Moura-Neto, Ângelo C Pinto, Cristian Follmer
Glioblastoma multiform (GBM) is the most common and devastating type of primary brain tumor, being considered the deadliest of human cancers. In this context, extensive efforts have been undertaken to develop new drugs that exhibit both antiproliferation and antimetastasis effects on GBM. 1,4-Naphthoquinone (1,4-NQ) scaffold has been found in compounds able to inhibit important biological targets associated with cancer, which includes DNA topoisomerase, Hsp90 and monoamine oxidase. Among potential antineoplastic 1,4-NQs is the plant-derived lapachol (2-hydroxy-3-prenyl-1,4-naphthoquinone) that was found to be active against the Walker-256 carcinoma and Yoshida sarcoma...
March 20, 2018: Anti-cancer Drugs
Mahtab Alam, Abul Kalam Najmi, Iqbal Ahmad, Farhan Jalees Ahmad, Md Jawaid Akhtar, Syed Sarim Imam, Mohd Akhtar
The study performed molecular docking, formulated, characterized thymoquinone (TQ) loaded solid lipid nano particles (TQSLN) and exhibited comparative antidepressant activity. TQ loaded nano lipid formulations were prepared by solvent injection methods and characterize for different in-vitro parameters. The optimized formulation was evaluated for depression using unpredictable chronic mild stress (UCMS) model for a period of six weeks. TQSLN was assessed in modified forced swim test (MFST), tail suspension test (TST), locomotor activity followed by biochemical parameters such as monoaminesand brain derived neurotrophic factor (BDNF)...
March 21, 2018: Artificial Cells, Nanomedicine, and Biotechnology
Widodo, Nadya Veronica Margarecaesha Anyndita, Nurul Dluha, Muhaimin Rifa'i, Karimatul Himmah, Mulya Dwi Wahyuningsih
Background: Epstein-Barr virus (EBV) can cause cancer in people from around the world. There is no EBV vaccine available for use on a global scale. However, emerging evidence suggests that the epitope on the gp350/220 capsid protein may be developed into an EBV vaccine. Nevertheless, the production of small, single epitope is challenging of stability issues and possible alteration of peptide structure. In this study, a tandem epitope was developed consisting of three single epitopes, aimed to improve stability, antigenicity and preserve epitope structure...
March 2018: Heliyon
Kuhu Sharma, Dilip Sharma, Monika Sharma, Nishant Sharma, Pankaj Bidve, Namrata Prajapati, Kiran Kalia, Vinod Tiwari
Despite considerable advances in understanding mechanisms involved in chronic pain, effective treatment remains limited. Astaxanthin, a marine natural drug, having potent anti-oxidant and anti-inflammatory activities is known to possess neuroprotective effects. However, effects of astaxanthin against nerve injury induce chronic pain remains unknown. Overactivity of glutamatergic NMDARs results in excitotoxicity which may participate in astrocytic and microglial activation during pathology which further contribute to the development of neuropathic pain...
March 17, 2018: Neuroscience Letters
Hailong Li, Zhongyuan Tang, Peng Chu, Yanlin Song, Ying Yang, Bin Sun, Mengyue Niu, Eskandar Qaed, Abdullah Shopit, Guozhu Han, Xiaodong Ma, Jinyong Peng, Min Hu, Zeyao Tang
Methylglyoxal (MGO), an active metabolite of glucose, is observed in high levels in the tissues and blood of diabetic patients. Phosphocreatine (PCr), a high-energy phosphate compound, exhibits a range of pharmacological actions but little is well known of its neuroprotective action. The aim of the present study was to investigate the neuroprotective effects and the possible mechanisms of PCr. Diabetes is closely associated with neurodegenerative diseases, leading not only to the peripheral nervous system (PNS) and but also to central nervous system (CNS) damage...
March 17, 2018: Free Radical Biology & Medicine
Yuxin Gu, Yu Yang, Bin Wan, Minjie Li, Liang-Hong Guo
Organophosphate flame retardants (OPFRs), as alternatives of brominated flame retardants, can cause neurodevelopmental effects similar to organophosphate pesticides. However, the molecular mechanisms underlying the toxicity remain elusive. O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) regulates numerous neural processes through the O-GlcNAcylation modification of nuclear and cytoplasmic proteins. In this study, we aimed to investigate the molecular mechanisms accounting for the developmental neurotoxicity of OPFRs by identifying potential targets of OPFRs and the attendant effects...
March 17, 2018: Biochemical Pharmacology
Kazuhiro J Fujimoto, Daiki Nema, Masayuki Ninomiya, Mamoru Koketsu, Hidetaka Sadanari, Masaya Takemoto, Tohru Daikoku, Tsugiya Murayama
A novel type of antiviral agent for human cytomegalovirus (HCMV) is required, because the appearance of ganciclovir (GCV) resistant viruses has been reported. Tricin (4',5,7-trihydroxy-3',5'-dimethoxyflavone) has been shown to suppress significantly HCMV replication in human embryonic lung (HEL) fibroblast cells. Recently, we revealed that the action of tricin is different from that of GCV and cyclin-dependent kinase 9 (CDK9) is one of the target proteins of tricin. These results suggested that tricin is considered as a novel type of anti-HCMV agent...
March 17, 2018: Antiviral Research
Aftab Ahmad, Mohammed F Abuzinadah, Huda M Alkreathy, Babajan Banaganapalli, Mohd Mujeeb
BACKGROUND: Ursolic acid (UA) is a promising molecule with anti-inflammatory, analgesic and potential anti-arthritic activity. METHODS: This study was undertaken to make formulation and evaluation of Ocimum sanctum L. leaf extract (OLE) loaded nano-structured lipid carriers (OLE-NLCs) for improved transdermal delivery of UA. Different surfactants, solid lipids and liquid lipids were used for the preparation of NLCs. The NLCs were developed using emulsion solvent diffusion and evaporation method...
2018: PloS One
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
Talia Serseg, Khedidja Benarous
Side effects of some drugs may be useful in certain cases. In this work, we studied the inhibitory effects of some medications as: Folic Acid which is taken by pregnant women, Colchicine and Febuxostat which is used as treatment of gout disease. These cases are linked to obesity, where women (BMI ≥ 30) have twice higher odds of having an NTD-affected pregnancy than the normal weight women, and the Gout disease frequently occurs in combination of a Metabolic syndrome. The risk of gout increases with the increase of the mass index...
March 18, 2018: Endocrine, Metabolic & Immune Disorders Drug Targets
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
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
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
Seyed Zachariah Moradi, Amin Nowroozi, Komail Sadrjavadi, Sajad Moradi, Kamran Mansouri, Leila Hosseinzadeh, Mohsen Shahlaei
It has been reported that the antiestrogen Tamoxifen induces liver tumors in rats and genotoxic effects in vitro through DNA interaction. So, it can be proposed that its structural analogue, Clomifene, also can bind to DNA. To test this hypothesis, the DNA binding properties of Clomifene have been studied by absorption spectroscopy, fluorescence spectroscopy, cellular uptake, cell viability, cell proliferation and molecular modeling techniques. Evidences are provided that Clomifene could interact with DNA via minor groove interaction mode...
March 16, 2018: International Journal of Biological Macromolecules
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
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