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https://www.readbyqxmd.com/read/28734205/identification-of-mycobacterium-tuberculosis-enoyl-acyl-carrier-protein-reductase-inhibitors-a-combined-in-silico-and-in-vitro-analysis
#1
Mohsin Y Lone, Mohd Athar, Vivek K Gupta, Prakash C Jha
Mycobacterium tuberculosis (Mtb), had developed evolutionary changes in its genome to adapt for survival and thereby generated multi-drug resistant strains. However, novel drug targets that remained unchanged for their biochemical role has impressed the research community to target such proteins. The comprehensive analysis of multiple protein targets has influenced us to make a consensus structural rule exploited by pharmacophore and other allied techniques from a large repository of protein structures. In this pursuit, we made a retrospective analysis of pharmacophores mapped from the tuberculosis structural proteome and identified unique patterns that can be employed for the novel molecules design...
July 14, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28732283/deciphering-the-mechanism-of-interaction-of-edifenphos-with-calf-thymus-dna
#2
Ajaz Ahmad, Masood Ahmad
Edifenphos is an important organophosphate pesticide with many antifungal and anti-insecticidal properties but it may cause potential hazards to human health. In this work, we have tried to explore the binding mode of action and mechanism of edifenphos to calf thymus DNA (CT-DNA). Several experiments such as ultraviolet-visible absorption spectra and emission spectroscopy showed complex formation between edifenphos and CT-DNA and low binding constant values supporting groove binding mode. These results were further confirmed by circular dichroism (CD), CT-DNA melting studies, viscosity measurements, density functional theory and molecular docking...
July 13, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28732041/understanding-russell-s-viper-venom-factor-v-activator-s-substrate-specificity-by-surface-plasmon-resonance-and-in-silico-studies
#3
Pradeep K Yadav, Christian B Antonyraj, Syed Ibrahim Basheer Ahamed, Sistla Srinivas
Blood coagulation factor V (FV) is activated either by Factor X or thrombin, cleaving at three different sites viz., Site I (Arg709-Ser710), site II (Arg1018-Thr1019), and site III (Arg1545-Ser1546). Russell's viper venom factor V activator (RVV-V) is a thrombin-like serine proteinase that activates FV with selective, single cleavage at site III. A long lasting effort is being pending in understanding the 'selective' binding specificity of the RVV-V towards site III. Here, we present the binding kinetic study of RVV-V with two designed peptides corresponding to the regions from site I (Gln699-Asn713) and site II (1008Lys-Pro1022), respectively, that include 15 amino acids...
2017: PloS One
https://www.readbyqxmd.com/read/28731684/the-binding-mode-of-n-hydroxyamidines-to-indoleamine-2-3-dioxygenase-1-ido1
#4
Ute Friederike Röhrig, Vincent Zoete, Olivier Michielin
Indoleamine 2,3-dioxygenase 1 (IDO1) is an important target in cancer immunotherapy. The most advanced clinical compound, epacadostat (INCB024360), binds to the heme cofactor of IDO1 through a N-hydroxyamidine function. Conflicting binding modes have recently been proposed, reporting iron binding either through the hydroxyamidine oxygen or nitrogen atoms. Here, we use quantum chemical calculations, docking, and QM/MM calculations based on available X-ray data to resolve this issue and to propose a physically meaningful binding mode...
July 21, 2017: Biochemistry
https://www.readbyqxmd.com/read/28730429/a-new-method-to-predict-ion-effects-in-rna-folding
#5
Li-Zhen Sun, Shi-Jie Chen
The strong interaction between metal ions in solution and highly charged RNA molecules is critical for RNA structure formation and stabilization. Metal ions binding to RNA can induce RNA structural changes that are important for RNA cellular functions. Therefore, quantitative modeling of the ion effects is essential for RNA structure prediction and RNA-based molecular design. Recently, inspired by the increasing experimental evidence that supports the importance of ion correlation and fluctuation in ion-RNA interactions, we developed a new computational model, Monte Carlo Tightly Bound Ion (MCTBI) model...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28729760/structural-insight-into-the-binding-of-c60-derivatives-with-enoyl-pyruvate-transferase-from-helicobacter-pylori
#6
Mohammad Teimouri, Muhammad Junaid, Abbas Khan, Houjin Zhang
Helicobacter pylori (H. pylori) is a human pathogen associated with acute gastritis and peptic ulcer. The MurA enzyme is an important drug target for the identification of ligands with improved efficacy and acceptable pharmaco-kinetic properties. We developed a homology model of H. Pylori MurA followed by refinement and molecular dynamics (MD) simulations. A total of 16 C60-derivatives were docked and its docking score were compared. Some of the known inhibitors were also similarly characterized and compared...
2017: Bioinformation
https://www.readbyqxmd.com/read/28729722/structure-based-discovery-of-small-molecule-inhibitors-of-cariogenic-virulence
#7
Qiong Zhang, Bhavitavya Nijampatnam, Zhang Hua, Thao Nguyen, Jing Zou, Xia Cai, Suzanne M Michalek, Sadanandan E Velu, Hui Wu
Streptococcus mutans employs a key virulence factor, three glucosyltransferase (GtfBCD) enzymes to establish cariogenic biofilms. Therefore, the inhibition of GtfBCD would provide anti-virulence therapeutics. Here a small molecule library of 500,000 small molecule compounds was screened in silico against the available crystal structure of the GtfC catalytic domain. Based on the predicted binding affinities and drug-like properties, small molecules were selected and evaluated for their ability to reduce S. mutans biofilms, as well as inhibit the activity of Gtfs...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729627/a-mechanism-based-qstr-model-for-acute-to-chronic-toxicity-extrapolation-a-case-study-of-antibiotics-on-luminous-bacteria
#8
Dali Wang, Yue Gu, Min Zheng, Wei Zhang, Zhifen Lin, Ying Liu
The determination of the chronic toxicity is time-consumed and costly, so it's of great interest to predict the chronic toxicity based on acute data. Current methods include the acute to chronic ratios (ACRs) and the QSTR models, both of which have some usage limitations. In this paper, the acute and chronic mixture toxicity of three types of antibiotics, namely sulfonamides, sulfonamide potentiators and tetracyclines, were determined by a bioluminescence inhibition test. A novel QSTR model was developed for predicting the chronic mixture toxicity using the acute data and docking-based descriptors...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729623/3d-qsar-studies-on-maslinic-acid-analogs-for-anticancer-activity-against-breast-cancer-cell-line-mcf-7
#9
Sarfaraz Alam, Feroz Khan
Global prevalence of breast cancer and its rising frequency makes it a key area of research in drug discovery programs. The research article describes the development of field based 3D-QSAR model based on human breast cancer cell line MCF7 in vitro anticancer activity, which defines the molecular level understanding and regions of structure-activity relationship for triterpene maslinic acid and its analogs. The key features such as average shape, hydrophobic regions and electrostatic patterns of active compounds were mined and mapped to virtually screen potential analogs...
July 20, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28729227/computational-and-experimental-prediction-of-molecules-involved-in-the-anti-melanoma-action-of-berberine
#10
Bin Liu, Xiu-Qiong Fu, Ting Li, Tao Su, Hui Guo, Pei-Li Zhu, Anfernee Kai-Wing Tse, Shi-Ming Liu, Zhi-Ling Yu
ETHNOPHARMACOLOGIC RELEVANCE: Berberine (BBR) is a naturally occurring alkaloid compound that can be found in Chinese medicinal herbs such as Rhizoma Coptidis and Phellodendri Cortex. These BBR containing herbs are commonly used by Chinese medicine doctors to treat cancers including melanoma. In this study, we explored proteins potentially involved in the anti-melanoma effects of BBR using an integrative computational and experimental approach. MATERIALS AND METHODS: Target proteins of BBR were predicted using the reverse pharmacophore screening, molecular docking and molecular dynamics...
July 17, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28729056/discovery-and-structure-activity-relationship-of-auriculatone-a-potent-hepatoprotective-agent-against-acetaminophen-induced-liver-injury
#11
Meng Zhou, Min Wang, Rui-Feng Zhong, Xiang-Ming Liao, Lian-Li Deng, Guo-Bo Xu, Xun He, Jing Li, Yong-Jun Li, Ting Liu, Yong-Lin Wang, Shang-Gao Liao
Acetaminophen (APAP, paracetamol) overdose has been the most frequent cause of drug-induced liver failure. APAP-induced liver toxicity can be fatal in many cases even with treatment of the clinically used N-acetylcysteine (NAC), and the need for novel therapeutic agents is apparent. Through evaluating the hepatoprotective effects of the co-occurring substances present in oleanolic acid tablets which have been used in China for decades as an adjuvant therapy for acute and chronic hepatitis, auriculatone was found to protect HL-7702 cells from APAP-induced liver injury comparable to NAC at the concentration of 10μM...
July 10, 2017: Bioorganic & Medicinal Chemistry Letters
https://www.readbyqxmd.com/read/28728898/kbe009-an-antimalarial-bestatin-like-inhibitor-of-the-plasmodium-falciparum-m1-aminopeptidase-discovered-in-an-ugi-multicomponent-reaction-derived-peptidomimetic-library
#12
Jorge González-Bacerio, Sarah El Chamy Maluf, Yanira Méndez, Isel Pascual, Isabelle Florent, Pollyana M S Melo, Alexandre Budu, Juliana C Ferreira, Ernesto Moreno, Adriana K Carmona, Daniel G Rivera, Maday Alonso Del Rivero, Marcos L Gazarini
Malaria is a global human parasitic disease mainly caused by the protozoon Plasmodium falciparum. Increased parasite resistance to current drugs determines the relevance of finding new treatments against new targets. A novel target is the M1 alanyl-aminopeptidase from P. falciparum (PfA-M1), which is essential for parasite development in human erythrocytes and is inhibited by the pseudo-peptide bestatin. In this work, we used a combinatorial multicomponent approach to produce a library of peptidomimetics and screened it for the inhibition of recombinant PfA-M1 (rPfA-M1) and the in vitro growth of P...
July 4, 2017: Bioorganic & Medicinal Chemistry
https://www.readbyqxmd.com/read/28728523/structural-insights-into-the-binding-of-small-ligand-molecules-to-a-g-quadruplex-dna-located-in-the-hiv-1-promoter
#13
Petar M Mitrasinovic
Targeting guanine (G)-rich DNA sequences, folded into non-canonical G-quadruplex (G4) structures, by small ligand molecules is a promising strategy for gene therapy of various diseases. There is experimental proposal that, among eight studied ligands, nitidine chloride - NC and a benzo phenanthridine derivative - BPD have the highest binding affinities for such a sequence (5'-T(1)G(2)G(3)C(4)C(5)T(6)G(7)G(8)G(9)C(10)G(11)G(12)G(13)A(14)C(15)T(16)G(17)G(18)G(19)-3') in the HIV-1 promoter, indicating that an anti-HIV-1 prodrug may regulate the expression of the promoter...
July 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28728517/using-molecular-dynamics-for-the-refinement-of-atomistic-models-of-gpcrs-by-homology-modeling
#14
Cecylia S Lupala, Bahareh Rasaeifar, Patricia Gomez-Gutierrez, Juan J Perez
Despite GPCRs share a common seven helix bundle, analysis of the diverse crystallographic structures available reveal specific features that might be relevant for ligand design. Despite the number of crystallographic structures of GPCRs is steadily increasing, there are still challenges that hamper the availability of new structures. In the absence of a crystallographic structure, homology modelling remains one of the important techniques for constructing 3D models of proteins. In the present study we investigated the use of molecular dynamics simulations for the refinement of GPCRs models constructed by homology modeling...
July 20, 2017: Journal of Biomolecular Structure & Dynamics
https://www.readbyqxmd.com/read/28728106/multipotent-ache-and-bace-1-inhibitors-for-the-treatment-of-alzheimer-s-disease-design-synthesis-and-bio-analysis-of-7-amino-1-4-dihydro-2h-isoquilin-3-one-derivates
#15
Xiong-Jie Zhao, Da-Min Gong, Yu-Ren Jiang, Dong Guo, Yao Zhu, You-Chao Deng
In this paper, the preparation of a new class of multi-target-directed ligands (MTDLs) based on a 7-amino-1,4-dihydro-2H-isoquilin-3-one, whose lead (compound I) showed promising properties in acetylcholinesterase (AChE) inhibitory activity [1], is described. The results of in vitro activities and molecular docking demonstrated that the target molecule (compounds 10a-n) with three parts of aromatic moieties and appropriate structural length can interact with aromatic residues in catalytic active site (CAS), peripheral anionic site (PAS) and the channel of AChE...
July 5, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28728105/discovery-of-imidazopyridines-containing-isoindoline-1-3-dione-framework-as-a-new-class-of-bace1-inhibitors-design-synthesis-and-sar-analysis
#16
Sara Azimi, Afsaneh Zonouzi, Omidreza Firuzi, Aida Iraji, Mina Saeedi, Mohammad Mahdavi, Najmeh Edraki
Alzheimer's disease is characterized by chronic neurodegeneration leading to dementia. The main cause of neurodegeneration is considered to be the accumulation of amyloid-β. Inhibiting BACE1 is a well-studied approach to lower the burden of amyloid-β aggregates. We designed a series of imidazopyridines-based compounds bearing phthalimide moieties as inhibitors of BACE1. The compounds 8a-o were synthesized by the Groebke-Blackburn-Bienaymé three-component reaction of heteroaromatic amidines, aldehydes and isocyanides...
June 24, 2017: European Journal of Medicinal Chemistry
https://www.readbyqxmd.com/read/28728041/multi-structure-docking-analysis-of-bace1-crystal-structures-and-non-peptidic-ligands
#17
Zahra Haghighijoo, Bahram Hemmateenejad, Najmeh Edraki, Ramin Miri, Saeed Emami
In order to design novel non-peptidic inhibitors of BACE1, many research groups have attempted using computational studies including docking analyses. Since there are too many 3D structures for BACE1 in the protein database, the selection of suitable crystal structures is a key prerequisite for the successful application of molecular docking. We employed a multi-structure docking protocol. In which 615 ligands' structures were docked into 150 BACE1 structures. The large number of the resultant docking scores were post-processed by different data analysis methods including exploratory data analysis, regression analysis and discriminant analysis...
June 28, 2017: Journal of Molecular Graphics & Modelling
https://www.readbyqxmd.com/read/28727189/inversion-of-cpadh5-enantiopreference-and-altered-chain-length-specificity-for-methyl-3-hydroxyalkanoates
#18
Yunus Ensari, Gaurao V Dhoke, Mehdi D Davari, Marco Bocola, Anna Joelle Ruff, Ulrich Schwaneberg
Expanding the substrate scope of enzymes opens up new routes for synthesis of valuable chemicals. Ketone-functionalized fatty acid derivatives and corresponding chiral alcohols are valuable building blocks for the synthesis of a variety of chemicals including pharmaceuticals. The alcohol dehydrogenase from Candida parapsilosis (cpADH5) catalyzes the reversible oxidations of chiral alcohols and has a broad substrate range; a challenge for cpADH5 is to convert alcohols with small substituents (methyl or ethyl) next to the oxidized alcohol moiety...
July 20, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28726760/synthesis-antitumor-evaluation-and-molecular-docking-of-new-morpholine-based-heterocycles
#19
Zeinab A Muhammad, Mastoura M Edrees, Rasha A M Faty, Sobhi M Gomha, Seham S Alterary, Yahia N Mabkhot
A series of new morpholinylchalcones was prepared and then used as building blocks for constructing a series of 7-morpholino-2-thioxo-2,3-dihydropyrido[2,3-d]pyrimidin-4(1H)-ones via their reaction with 6-aminothiouracil. The latter thiones reacted with the appropriate hydrazonoyl chloride to give the corresponding pyrido[2,3-d][1,2,4]triazolo[4,3-a]pyrimidin-5(1H)-ones. The assigned structures for all the newly synthesized compounds were confirmed on the basis of elemental analyses and spectral data and the mechanisms of their formation were also discussed...
July 20, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28726402/opioid-receptor-modulators-with-a-cinnamyl-group
#20
Lokesh Ravilla, N Venkata Subba Naidu, Shalini Dogra, Deepmala Umrao, Prem N Yadav, Ansuman Biswas, Daliah Michael, Kanagaraj Sekar, Kuppuswamy Nagarajan
To obtain selective and potent opioid receptor ligands, we synthesized dehydro derivatives of alvimopan and found compound (28f), a selective but modest affinity MOR antagonist, weaker than alvimopan (1). We replaced the aryl piperidine unit by an aryl piperazine to obtain the 1-(α-carboxycinnamyl)-4-arylpiperazines like (13h), which to our surprise had no MOR or DOR activity but was a KOR agonist with moderate affinity. In contrast, literature examples of aryl piperazines (4) and (5) were reported to be pan opioid receptor antagonists, while (6) was a MOR agonist...
July 20, 2017: Journal of Medicinal Chemistry
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