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Nathiya Ranganathan, Gayathri Mahalingam
Endophytic fungi, especially from mangrove plants, are rich source of secondary metabolites, which plays a major role in various pharmacological actions preferably in cancer and bacterial infections. To perceive its role in antidiabetic activity we isolated and tested the metabolites derived from a novel strain Alternaria longipes strain VITN14G obtained from mangrove plant Avicennia officinalis. The crude extract was analyzed for antidiabetic activity and subjected to column chromatography. The isolated fractions were screened in vitro for α-glucosidase and α-amylase inhibitory activities...
October 15, 2018: Journal of Cellular Biochemistry
Pham Ngoc Khanh, Tran Thu Huong, Ottavia Spiga, Alfonso Trezza, Ninh The Son, To Dao Cuong, Vu Thi Ha, Nguyen Manh Cuong
OBJECTIVE: Prismatomeris memecyloides Craib (Rubiaceae) is a medicinal plant traditionally used by ethnic minorities in Vietnam for the treatment of erectile dysfunction (ED). The aim of this study was to investigate the chemical compositions and screen in silico its possible inhibitory effect against PDE-5 which reduced cyclic guanosine-3',5'-monophosphate (cGMP) levels and indirectly caused the male ED. METHODS: Separation of natural compounds were carried out on chromatographic column with silica gel or reversed phase materials, eluting with different solvent gradients...
October 2018: Revista Internacional de Andrología
S Priyanka, M Jayashree, R Shivani, S Anwesha, K V Bhaskara Rao, Arnold E I
OBJECTIVE: The present study was focused on the characterization and in silico analysis of antibacterial compound derived from marine actinobacteria isolated from the sediments of salterns of Ongole, Andhra Pradesh, India. METHODS: The sediment sample was serially diluted and marine actinobacteria were isolated in actinomycetes isolation agar. A total of 9 colonies were recovered and among them, 5 morphologically distinct isolates were selected for further processing...
September 27, 2018: Journal of Infection and Public Health
Mahmoud A A Ibrahim, Alaa M A Hassan
Leukotriene B4 (LTB4) exerts its biological effects through stimulation of specific G protein-coupled receptors (GPCRs)-namely BLT1 and BLT2. Due to the absence of human BLT1 and BLT2 crystal structures, the current study was set to predict the 3D structures of these two receptors for structure-based anti-inflammatory drug discovery. Homology modeling of the BLT1 receptor was first constructed, based on various X-ray and NMR GPCR templates, followed by molecular dynamics (MD) refinement. Using a single-template approach, nine well-established alignment methods and ten secondary structure prediction methods during the backbone generation were implemented and assessed...
September 28, 2018: Protein Journal
Mohankrishna Ghanta, Elango Panchanathan, Bhaskar Venkata Kameswara Subrahmanya Lakkakula, Anbumani Narayanaswamy, P A Abhinand, Stalin Antony
Soluble guanylate cyclase (sGC) is a type of lyase enzyme with profoundly increasing importance in treatments of cardiovascular and neurodegenerative disorders. Modulation of sGC activity demonstrated beneficial effects against Parkinson's disease by reducing glutamate excitotoxicity. It is of interest to evaluate the pharmacological activity of Momordica charantia phytoconstituent (DGalacturonic acid) and ODQ with catalytic domain of sGC enzyme, using Autodock version 4.2 programs. Docking results revealed the binding ability of ODQ at the allosteric sites of sGC...
2018: Bioinformation
K Srikanth Kumar, A Lakshmana Rao, M V Basaveswara Rao
Various thiazolidine-2,4-dione derivatives 3a-l possessing indole moiety were designed, synthesized using appropriate conventional heating as well as microwave irradiation methods. All the synthesized compounds were characterized physically and spectrally. The compounds were evaluated for in vitro antibacterial activity, in vitro antioxidant activity and in vivo hypoglycemic activity in relation to the standard drugs. Most of the new compounds exhibited moderate activity and some showed considerable activity...
September 2018: Heliyon
Lei Yuan, Lei Sheng, Wenhui He, Chunyang Zou, Baichun Hu, Jun Liu, Wentao Ge, Yang Liu, Jian Wang, Enlong Ma
It is still challenging to determine the potential targets of natural products, which is essential for further drug research and development. Due to its novel mechanism of action of inducing autophagy effects in breast cancer cells, asperphenamate has received our considerable attention. However, its unknown target inevitably impedes further study. In our previous work, the target enzyme of asperphenamate was predicted as cathepsin by the natural product consensus pharmacophore strategy. Then, asperphenamate and its three derivatives were chosen to study in detail by molecular docking calculations with AutoDock 4 suite...
September 20, 2018: Bioorganic Chemistry
Lalehan Ozalp, Safiye Sağ Erdem, Başak Yüce-Dursun, Özal Mutlu, Mehmet Özbil
Phthalocyanines are considered as good DNA binders, which makes them promising anti-tumor drug leads. The purpose of this study is to investigate the interactions between DNA and quaternary metallophthalocyanine derivatives (Q-MPc) possessing varying metals (M = Zn, Ni, Cu, Fe, Mg and Ca) by molecular docking since there seems to be a lack of information in the literature regarding this issue. In this direction, Autodock Vina and Molegro Virtual Docker programs were employed. Autodock Vina results reveal that each Q-MPc derivative binds to DNA strongly with similar binding energies and almost identical binding modes...
September 13, 2018: Computational Biology and Chemistry
Bashir A Yousef, Amina I Dirar, Mohamed Ahmed A Elbadawi, Mohamed K Awadalla, Magdi A Mohamed
Background: Plants of the Amaryllidaceae family have been under intense scrutiny for the presence of a couple of alkaloidal secondary metabolites with endued cytotoxic activity, such as pancratistatin ( 1 ), 7-deoxypancratistatin ( 2 ), narciclasine ( 3 ), 7-deoxynarciclasine ( 4 ), trans -dihydronarciclasine ( 5 ), and 7-deoxy- trans -dihydronarciclasine ( 6 ). Nevertheless, preclinical evaluation of these alkaloids has been put on hold because of the limited quantity of materials available from isolation...
July 2018: Journal of Pharmacy & Bioallied Sciences
Xibing He, Viet H Man, Beihong Ji, Xiang-Qun Xie, Junmei Wang
We participated in the Cathepsin S (CatS) sub-challenge of the Drug Design Data Resource (D3R) Grand Challenge 3 (GC3) in 2017 to blindly predict the binding poses of 24 CatS-bound ligands, the binding affinity ranking of 136 ligands, and the binding free energies of a subset of 33 ligands in Stage 1A and Stage 2. Our submitted predictions ranked relatively well compared to the submissions from other participants. Here we present our methodologies used in the challenge. For the binding pose prediction, we employed the Glide module in the Schrodinger Suite 2017 and AutoDock Vina...
September 14, 2018: Journal of Computer-aided Molecular Design
Mayura A Kale, Gajanan M Sonwane
The computational studies on 2-phenazinamines with their protein targets have been carried out to design compounds with potential anticancer activity. This strategy of designing compounds possessing selectivity over specific tyrosine kinase has been achieved through G-QSAR and molecular docking studies. The objective of this research has been to design newer 2-phenazinamine derivatives as Bcr-Abl tyrosine kinase inhibitors by G-QSAR, molecular docking studies followed by wet lab studies along with evaluation of their anticancer potential...
September 13, 2018: Current Drug Discovery Technologies
Benarous Khedidja, Benguechoua Madjeda, Ghibeche Abderrahmane
BACKGROUND: Inhibition activity of 8 synthetic molecules known as anti-allergy drugs on lipases have been investigated. The enzymatic inhibition produced by these molecules is described here for the first time. OBJECTIVE: The used anti-allergy drugs are: loratidine, primalan, zyrtec, histagan, periactin, ketotifene, rifex and bilastine. METHODS: lipase inhibition is studied using spectrophotometric method. Molecular docking has been achieved for the first time for these drugs using AutoDock Vina program to discuss the nature of interactions, structure activity relationship and the mechanism of inhibition...
September 10, 2018: Anti-inflammatory & Anti-allergy Agents in Medicinal Chemistry
Vitor Won-Held Rabelo, Daiane de Jesus Viegas, Erline Machado Neves Tucci, Nelilma Correia Romeiro, Paula Alvarez Abreu
Candidiasis is the most common fungal infection in immunocompromised patients, and Candida albicans is the fourth leading agent of nosocomial infections. Mortality from this infection is significant; however, the therapeutic treatment is limited, which demands the search for new drugs and new targets. In this context, oxidosqualene cyclase (OSC) catalyzes the cyclization of the 2,3-oxidosqualene to form lanosterol, an intermediate of ergosterol biosynthesis. Therefore, this enzyme constitutes an attractive therapeutic target...
September 4, 2018: Journal of Steroid Biochemistry and Molecular Biology
Shilu Mathew, Asmaa A Al Thani, Hadi M Yassine
BACKGROUND: With the emergence of new influenza virus strains that are resistant to current inhibitors such as oseltamivir (anti-neuraminidase (NA)) and amantadine (anti-M2 proton channel), influenza A viruses continue to be a serious threat to the public health worldwide. With this in view, there is a persistent need for the development of broader and more effective vaccines and therapeutics. Identification of broadly neutralizing antibodies (bNAbs) that recognize relatively invariant structures ‎on influenza haemagglutinin (HA) stem has invigorated efforts to develop universal influenza vaccines...
2018: PloS One
Michael Zhenin, Malkeet Singh Bahia, Gilles Marcou, Alexandre Varnek, Hanoch Senderowitz, Dragos Horvath
Ligand affinity prediction from docking simulations is usually performed by means of highly empirical and diverse protocols. These protocols often involve the re-scoring of poses generated by a force field (FF) based Hamiltonian to provide either estimated binding affinities-or alternatively, some empirical goodness score. Re-scoring is performed by so-called scoring functions-typically, a reweighted sum of FF terms augmented by additional terms (e.g., desolvation/entropic penalty, hydrophobicity, aromatic interactions etc...
September 2018: Journal of Computer-aided Molecular Design
Yi Fu, Zhiguo Chen, Jun Sun
Molecular docking has emerged as an important tool in drug design and development. Currently, there is a relatively large and ever-increasing number of molecular docking programs. However, despite the great advances in the docking technique over the last decade, most methods cannot be used to dock highly flexible ligands successfully. In this study, based on the Autodock software, a new search algorithm, hybrid algorithm of Random Drift Particle Swarm Optimisation and local search (LRDPSO), that focuses on protein-ligand applications was presented...
November 14, 2018: Journal of Theoretical Biology
Asifa Majeed, Amir Rashid, Birgit Helm
The high-affinity IgE receptor complex plays an essential part in allergic responses and involved in downstream signaling, released inflammatory mediators that cause allergic responses. The transmembrane region of the high-affinity IgE has a conserved motif (LFAVDTGL) where a polar aspartate (D194) is important for the ligand binding. This modeling study proposes novel potential binding sites between high affinity immunoglobulin E receptor α subunit (FcεRIα) and FcRγ and as a consequence, we propose a new model of FcεRIα and FcRγ interaction (T194) which can mediate downstream signaling in allergic response...
September 2018: Pakistan Journal of Pharmaceutical Sciences
D Sam Paul, N Gautham
We have earlier reported the iMOLSDOCK technique to perform 'induced-fit' peptide-protein docking. iMOLSDOCK uses the mutually orthogonal Latin squares (MOLSs) technique to sample the conformation and the docking pose of the small molecule ligand and also the flexible residues of the receptor protein, and arrive at the optimum pose and conformation. In this paper we report the extension carried out in iMOLSDOCK to dock nonpeptide small molecule ligands to receptor proteins. We have benchmarked and validated iMOLSDOCK with a dataset of 34 protein-ligand complexes as well as with Astex Diverse dataset, with nonpeptide small molecules as ligands...
September 2018: Journal of Computer-aided Molecular Design
Kerry A Ramsbottom, Daniel F Carr, Andrew R Jones, Daniel J Rigden
Adverse drug reactions have been linked with genetic polymorphisms in HLA genes in numerous different studies. HLA proteins have an essential role in the presentation of self and non-self peptides, as part of the adaptive immune response. Amongst the associated drugs-allele combinations, anti-HIV drug Abacavir has been shown to be associated with the HLA-B*57:01 allele, and anti-epilepsy drug Carbamazepine with B*15:02, in both cases likely following the altered peptide repertoire model of interaction. Under this model, the drug binds directly to the antigen presentation region, causing different self peptides to be presented, which trigger an unwanted immune response...
September 2018: Molecular Immunology
George Oche Ambrose, Olanrewaju John Afees, Nwufoh Chika Nwamaka, Nzikahyel Simon, Adebo Adeola Oluwaseun, Tosin Soyinka, Alakanse Suleiman Oluwaseun, Seyi Bankole
The life-threatening sides effect of the current EGFR mutant inhibitors (drugs) such as the eruption of rash which can be seen on the face, chest, back and even the trunk, diarrhea, nausea, vomiting, anorexia and stomatitis, necessitates the discovery of new potent and safe compounds as a chemo-therapeutic measure against lung cancer. Approximately about 10% of patients with Non-small cell lung cancer (NSCLC) in the US and about 35% in East Asia have tumor associated EGFR. These mutations occur within EGFR exon 18-21, which encodes a portion of the EGFR kinase domain and enables researchers to identify compounds that only recognizes and binds to the cancer cells...
2018: Bioinformation
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