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Current Computer-aided Drug Design

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https://www.readbyqxmd.com/read/29380703/structural-basis-of-antisickling-effects-of-selected-fda-approved-drugs-a-drug-repurposing-study
#1
Olujide O Olubiyi, Maryam O Olagunju, James O Oni, Abidemi O Olubiyi
Sickle cell disease is characterized by a point mutation involving substitution of glutamic acid at position 6 to valine. Encoded in this hydrophobic mutation is both an intrinsic capacity for the beta globin molecules to assemble into thermodynamically favoured polymeric states as well as a rational way of interrupting the aggregation. In this work, starting with a theoretical model that employs occlusive binding onto the beta globin aggregation surface and using a range of computational methods and an effective energy for screening, a number of FDA approved drugs with computed aggregation inhibitory activities were identified...
January 29, 2018: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/29359676/computational-exploration-of-natural-compounds-to-target-cytosolic-phospholipase-a-2-protein-a-novel-therapeutic-target-for-spinal-cord-injury
#2
Hongwu Fan, Shengqun Wang, Qiheng Zhao, Zhigang Qin
BACKGROUND: Cytosolic phospholipase A2 (cPLA2), an important isoform of PLA2 that mediates the release of arachidonic acid, plays a role in the pathogenesis of spinal cord injury (SCI). The expression and activation of Cpla2is significantly higher in SCI, leading to neuronal death in spinal cord tissue. Novel strategies are needed to substantially reverse the effect of cPLA2 activation; one such strategy is inhibiting cPLA2 by jamming its lipid binding C2 domain. OBJECTIVE: To develop a much needed strategy to treat SCI we used a computer aided drug design (CADD) method to discover novel cPLA2 inhibitors...
January 22, 2018: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/29332601/quantitative-structure-activity-relationship-study-of-betulinic-acid-derivatives-against-hiv-using-smiles-based-descriptors
#3
Apilak Worachartcheewan, Alla P Toropova, Andrey A Toropov, Suphakit Siriwong, Jatupat Prapojanasomboon, Virapong Prachayasittikul, Chanin Nanatasenamat
BACKGROUND: Human immunodeficiency virus (HIV) is the causative agent of acquired immunodeficiency syndrome (AIDS) that imposes a global health burden. Therefore, HIV therapeutic agents have been discovery and development. OBJECTIVE: To construct quantitative-structure activity relationship (QSAR) models of betulinic acid derivatives with anti-HIV activity using simplified molecular-input line-entry system (SMILES)-based descriptors Methods: A data set of 107 betulinic acid derivatives and their anti-HIV activity was used to develop QSAR models...
January 11, 2018: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/29332600/finding-novel-anti-carcinomas-compounds-by-targeting-sfrp4-through-molecular-modeling-docking-and-dynamic-simulation-studies
#4
M Hassan, M Azhar, Q Abbas, H Reza, A A Moustafa, S Shahzadi, Z Ashraf, S Y Seo
BACKGROUND: Secreted frizzled-related protein 4 (SFRP4) is a glycoprotein that act as a competitor of both canonical and non-canonical Wnt pathways. SFRP4 is mostly expressed in ovary and played a significant role as a target molecule to cure ovarian carcinoma. OBJECTIVE: Multiple chemical agonists are being used to cure ovary melanoma. We are interested to theoretically analyze the compounds through computational approaches for their inhibitory effects against SFRP4...
January 11, 2018: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/29189115/editorial-computer-assisted-vaccine-design-cavd-approach-can-help-in-the-management-of-the-emerging-h7n9-influenza-virus
#5
EDITORIAL
Ashesh Nandy, Subhash C Basak
No abstract text is available yet for this article.
November 10, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/29189114/meet-our-associate-editor
#6
Shahul H Nilar
No abstract text is available yet for this article.
November 10, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28969532/binding-site-and-potency-prediction-of-teixobactin-and-other-lipid-ii-ligands-by-statistical-base-scoring-of-conformational-space-maps
#7
Claudiu N Lungu, Mircea V Diudea
A receptor binding pocket may be occupied by a ligand in various plausible conformations, among which only few ones are energetically related to a biological activity in the physiological efficiency domain. This paper reports the mapping of the conformational space of Lipid II in its interaction with Teixobactin and other Lipid II ligands. Statistical analysis of the resulted data enabled the selection of most favorable ligands and receptor conformations; a score was generated for ordering the ligand-receptor complexes, according to the their lowest energy and in correlation with the efficiency of their biological function...
September 26, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28699497/quantitative-structure-activity-relationships-of-aquatic-narcosis-a-review
#8
Chandana Adhikari, Bijay Kumar Mishra
BACKGROUND: Prior estimation of toxicity of each and every, existing and yet to be synthesized chemicals is a must to elude their adverse effect on the environment. Experimental determination of such parameters is time consuming, cost effective and above all it demands the sacrifice of many vertebrates. At this end the REACH regulations advocate for the use of non-testing predictive methods such as read-across, weight-of-evidence and QSAR (quantitative structure-activity relationship) techniques...
July 11, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28606047/design-synthesis-and-biological-evaluation-of-vanillin-hydroxamic-acid-derivatives-as-novel-peptide-deformylase-inhibitors
#9
Jian Gao, Shengzhi Qiu, Li Liang, Zhixiang Hao, Qianqian Zhou, Fanfan Wang, Jie Mou, Qisi Lin
BACKGROUND: Infectious disease is increasingly hampering human health, which challenge the discovery of new antibacterial target. Peptide deformylase (PDF), a metalloenzyme responsible for catalyzing the remove of the N-formyl group from nascent proteins, was considered as an important target in antibacterial drug discovery. OBJECTIVE: Reported here are the design, synthesis and biological evaluation of vanillin hydroxamic acid derivatives. METHOD AND RESULTS: Analysis of the structure-activity relationships lead to the discovery of compound 8, which exhibits promising antibacterial activity against Escherichia coli, Staphylococcus aureus, Aspergillus oryzae, and Aspergillus foetidus with the MIC value of 0...
June 12, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28595521/a-comparative-study-on-selective-ppar-modulators-through-quantitative-structure-activity-relationship-pharmacophore-and-docking-analyses
#10
Ashis Nandy, Kunal Roy, Achintya Saha
BACKGROUND: Metabolic syndrome is a matrix of different metabolic disorders which are the leading cause of death in human beings. Peroxysome proliferated activated receptor (PPAR) is a nuclear receptor involvedin metabolism of fats and glucose. OBJECTIVE: In order to explore structural requirements for selective PPAR modulators to control lipid and carbohydrate metabolism, the multi-cheminformatics studies have been performed. METHOD: Insilico modeling studies have been performed on a diverse set of PPAR modulators through quantitative structural-activity relationship (QSAR), pharmacophore mapping and docking studies...
June 8, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28554315/pharmacophore-modelling-and-4d-qsar-study-of-ruthenium-ii-arene-complexes-as-anticancer-agents-inhibitors-by-electron-conformational-genetic-algorithm-method
#11
Sevtap Çağlar Yavuz, Nazmiye Sabancı, Emin Sarıpınar
OBJECTIVE: The EC-GA method was employed in this study as a 4D-QSAR method, for the identification of the pharmacophore (Pha) of ruthenium(II) arene complex derivatives and quantitative prediction of activity. METHOD: The arrangement of the computed geometric and electronic parameters for atoms and bonds of each compound occurring in a matrix is known as the electron-conformational matrix of congruity (ECMC). It contains the data from HF/3-21G level calculations...
May 28, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28523999/molecular-docking-studies-applied-to-a-dataset-of-cruzain-inhibitors
#12
Edeildo Ferreira da Silva-Júnior, Paulo Henrique Barcellos França, Frederico Fávaro Ribeiro, Francisco Jaime Bezerra Mendonça-Júnior, Luciana Scotti, Marcus Tullius Scotti, Thiago Mendonça de Aquino, João Xavier de Araújo-Júnior
BACKGROUND: Chagas' disease is one of the main causes of heart failure in developing countries. The disadvantages of current therapy include the undesirable side-effects, resistance, and therapeutic adhesion. The development of new efficient and safe drugs is, therefore, an issue of extreme importance. OBJECTIVES: In order to gain a better understanding of how the compounds interact with the target, computational methods are essential. METHOD: In this theoretical study, we report a docking protocol applied to a dataset of 173 cruzain inhibitors with IC50 values of less than 10 μM, belonging 16 different chemical classes...
May 18, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28462697/insight-mechanism-of-the-selective-lanosterol-synthase-inhibitor-molecular-modeling-docking-and-density-functional-theory-approaches
#13
Suramanian Karunagaran, Chandrasekaran Meganathan, Rengarajan Kavitha, Muthu Vadivelu, Kuen Woo Lee
BACKGROUND: Lanosterol synthase (Oxidosqualene cyclase) is an enzyme, plays a central role in cholesterol and sterols biosynthesis. Lanosterol synthase drugs used to lower the level of cholesterol in the blood and treat wide variety of diseases like atherosclerosis, coronary heart diseases etc. OBJECTIVE: There is a great interest in the identification of drugs that target this enzyme for anticholesteraemic agent using insilico tools. METHODS: Ligand based pharmacophore model was developed using Discovery Studio 2...
April 26, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28462696/hybrid-docking-qsar-studies-of-1-4-dihydropyridine-3-5-dicarboxamides-as-potential-antitubercular-agents
#14
Yasaman Rasouli, Asghar Davood
BACKGROUND: Tuberculosis is one of the main medical problems that some people are suffering still from this infectious disease. 1, 4-dihydropyridines are a multi-target ligands that recently are recognized as an anti-tubercular agents. METHOD: In the current research we did computational studies of some synthesized 1, 4-dihydropyridine-3, 5-dicarboxamides in non-hydrolyzed and hydrolyzed forms to find the drug-receptor interactions profile. RESULTS: Among equations that obtained for non-hydrolyzed compounds, the model with better statistical parameters such as R2= 0...
April 26, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28413992/screening-and-elucidation-of-selected-natural-compounds-for-anti-alzheimer-s-potential-targeting-bace-1-enzyme-a-case-computational-study
#15
Syed Sayeed Ahmad, Salman Akhtar, Syed Mohd Danish Rizvi, Mohammad A Kamal, Usman Sayeed, Mohd Kalim A Khan, Mohd Haris Siddiqui, Jamal M Arif
BACKGROUND: The present study clarifies the molecular interactions of human BACE1 with novel natural ligands and also with the well-known ligand 2, 2, 4-trihydroxychalcone and Galangin for comparison. OBJECTIVE: The study of enzyme- ligands interaction is interest, description of ligands binding to the active site of target molecule could be beneficial to better understanding the mechanism of the ligand on the target molecule. METHOD: Lipinski rule of five, and docking study was performed between ligands and enzyme using 'Autodock4...
April 14, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28382867/an-integrated-computational-approach-for-plant-based-protein-tyrosine-phosphatase-non-receptor-type-1-inhibitors
#16
Shabana Bibi, Katsumi Sakata
BACKGROUND: Protein tyrosine phosphatase non-receptor type 1 is a therapeutic target for the type 2 diabetes mellitus. According to the International Diabetes Federation 2015 report, one out of 11 adults suffer from diabetes mellitus globally. OBJECTIVE: Current anti-diabetic drugs can cause life-threatening side-effects. The present study proposes a pipeline for the development of effective and plant-derived anti-diabetic drugs that may be safer and better tolerated...
April 6, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28382866/dynamic-simulation-docking-and-dft-studies-applied-to-a-set-of-anti-acetylcholinesterase-inhibitors-in-the-enzyme-%C3%AE-secretase-bace-1-an-important-therapeutic-target-in-alzheimer-s-disease
#17
Edeildo F Silva-Júnior, Paulo H Barcellos França, Lucindo José Quintas-Júnior, Francisco J B Mendonça-Junior, Luciana Scotti, Marcus T Scotti, Thiago Mendonça de Aquino, João Xavier Araújo-Júnior
BACKGROUND: Alzheimer's disease (AD) affects mainly elderly people over 60 years of age. Currently, there are more than 35 million people with this disease worldwide. The enzyme β-secretase is involved in the processing of the amyloid precursor protein and plays a key role in the physiopathology of AD. The action of some acetylcholinesterase inhibitors (AChEI) as β-secretase inhibitors has been reported. OBJECTIVE: The aim of this study was to highlight the modes of the binding of acetylcholinesterase ligands onto the active site of the β-secretase enzyme...
April 6, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28382865/multitargeted-molecular-docking-study-of-natural-derived-alkaloids-on-breast-cancer-pathway-components
#18
Ramit Singla, Vikas Jaitak
BACKGROUND: Targeting of multiple sites is a pharmacologically, pharmacokinetic and dynamically more acceptable approach for complex diseases such as BC. It is recommended that the women who are at high risk of developing BC might be given foods enhanced by indole alkaloids from vegetables like cabbage and broccoli. Administration of indole-3-carbinol is associated with decreased incidence of hormone-responsive BC (HRBC) which is implicated due to the induction of cytochrome P450 and glutathione-S-transferase which metabolizes chemical mutagens and by altering estrogen metabolism...
April 6, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28294050/an-integrated-multi-qsar-modeling-approach-for-designing-knoevenagel-type-indoles-with-enhancing-cytotoxic-profiles
#19
Sk Abdul Amin, Nilanjan Adhikari, Tarun Jha, Shovanlal Gayen
BACKGROUND: Unconventional Knoevenagel-type indoles have been the topic of interest of many synthetic chemists because of its promising efficacy in different diseases including in cancer. OBJECTIVE: To explore the structural requirements of Knoevenagel-type cytotoxic indoles for higher efficacy. METHODS: Multi-QSAR modeling (MLR, ANN, SVM, Bayesian classification, HQSAR and Topomer CoMFA) was performed on these analogs. RESULTS: All these modeling techniques were validated individually and interpreted with the experimental SAR observations...
March 9, 2017: Current Computer-aided Drug Design
https://www.readbyqxmd.com/read/28294049/in-silico-analysis-of-amp-activated-protein-kinase-and-ligand-based-virtual-screening-for-identification-of-novel-ampk-activators
#20
Ammarah Ghaffar, Sidra Batool, Gohar Mushtaq, Muhammad Amjad Kamal
BACKGROUND: Adenosine-Monophosphate-Activated protein kinase (AMPK) is a conserved kinase that plays an important role in maintaining the homeostasis of cells. AMPK activation has a positive impact on treatment of diseases such as diabetes, obesity and cancer as well. This observation led to the development of AMPK activators. Certain naturally occurring compounds have also been known to activate AMPK. METHOD: In this study, we retrieved the AMPK activators that includes chemical drugs, xenobiotics and natural compounds and analyzed their interactions with AMPK via docking studies...
March 9, 2017: Current Computer-aided Drug Design
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