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Call For Paper
Bentham Science Publishers would like to invite you to submit your research paper for publishing in the Journal of
Current Computer Aided-Drug Design
Wednesday, November 2, 2016
Highlighted Article: Mathematical Nanotoxicoproteomics: Quantitative Characterization of Effects of Multi-walled Carbon Nanotubes (MWCNT) and TiO2 Nanobelts (TiO2-NB) on Protein Expression Patterns in Human Intestinal Cells
Mathematical Nanotoxicoproteomics: Quantitative Characterization of Effects of Multi-walled Carbon Nanotubes (MWCNT) and TiO2 Nanobelts (TiO2-NB) on Protein Expression Patterns in Human Intestinal Cells
Author(s):
Subhash C. Basak, Marjan Vracko and Frank A. Witzmann Pages 259 - 264 (6)
Abstract:
Background: Various applications of nanosubstances in industrial and consumer goods sectors are growing rapidly because of their useful chemical and physical properties.
Objectives: Assessment of hazard posed by exposure to nanosubstances is essential for the protection of human and ecological health.
Methods: We analyzed the proteomics patterns of Caco-2/HT29-MTX cells in co-culture exposed for three and twenty four hours to two kinds of nanoparticles: multi-walled carbon nanotubes (MWCNT) and TiO2 nanobelts (TiO2-NB). For each nanosubstance cells were exposed to two concentrations of the material before carrying out proteomics analyses: 10 μg and 100 μg. In each case over 3000 proteins were identified. A mathematically based similarity index, which measures the changes in abundances of cellular proteins that are highly affected by exposure to the nanosubstances, was used to characterize toxic effects of the nanomaterials.
Results: We identified 8 and 25 proteins, which are most highly affected by MWCNT and TiO2-NB, respectively. These proteins may be responsible for specific response of cells to the nanoparticles. Further 14 reported proteins are affected by either of the two nanoparticles and they are probably related to nonspecific toxic response of the cells.
Conclusion: The similarity methods proposed in this paper may be useful in the management and visualization of the large amount of data generated by proteomics technologies.
Keywords:
Aspect ratio, big data, Caco cell, multi-walled carbon nanotubes (MWCNT), optical devices, photocatalyst, proteomics, superconductor materials, TiO2 nanobelts (TiO2-NB).
Affiliation:
Natural Resources Research Institute and University of Minnesota Duluth, Duluth, MN 55811, USA.
For More Information Please Visit Our website Current Computer-Aided Drug Design
Tuesday, October 25, 2016
Most Accessed Article: Characterizing the Zika Virus Genome – A Bioinformatics Study
Characterizing the Zika Virus Genome – A Bioinformatics Study
Author(s):
Ashesh Nandy, Sumanta Dey, Subhash C. Basak, Dorota Bielinska-Waz and Piotr WazPages 87-97 (11)
Abstract:
Background: The recent epidemic of Zika virus infections in South and Latin America have raised serious concern on its ramifications for the population in the Americas and spread of the virus worldwide. The Zika virus disease is a relatively new phenomenon for which sufficient and comprehensive data and investigative reports have not been available to date.
Objective: To carry out a bioinformatics study of the available Zika virus genomic sequences to characterize the virus.
Method: 2D graphical representation method is used for visual rendering and compute sequence parameters and descriptors of the African and Asian-American groups of the Zika viruses to characterize the sequences. We also used MEGA5.2 and other software to compute various biological properties of interest like phylogenetic relationships, transition-transversion ratios, amino acid usage, codon usage bias and hydropathy index of the Zika genomes and virions.
Results: The phylogenetic relationships show that the African and Asian-American Zika virus genomes are grouped in two clades. The 2D plots of typical genomes of these types also show dramatic differences indicating that the gene sequences at the 5’-end coding regions for the structural proteins are rather strongly conserved. Among other characteristics, the transition/transversion ratio matrices for the sequences in each of the two clades show that analogous to the dengue virus, the transition rates are about 10 to 15 times the transversion rates.
Conclusion: These findings are important for computer-assisted approaches towards surveillance of emerging Zika virus strains as well as in the design of drugs and vaccines to combat the growth and spread of the Zika virus.
Keywords:
Zika virus, Zika virus phylogeny, Zika virus characterization, African and Asian-American clades, 2D graphical representation, amino acid changes, cladewise transition-transversion ratios, Zika sequence descriptors.
Affiliation:
Centre for Interdisciplinary Research and Education, 404B Jodhpur Park, Kolkata 700068, India.
Graphical Abstract:
For More Information Please Visit Our Website Current Computer Aided-Drug Design
Wednesday, October 19, 2016
Podcast on Lemont B. Kier: A Bibliometric Exploration of his Scientific Production and its Use
Podcast on Lemont B. Kier: A Bibliometric Exploration of his Scientific Production and its Use
Wednesday, October 5, 2016
Podcast on Introduction to Molecular Topology Basic Concepts and Application to Drug Design'
Podcast on Introduction to Molecular Topology Basic Concepts and Application to Drug Design'
Current Computer Aided-Drug Design
Current Computer-Aided Drug Design aims to publish all the latest developments in drug design based on computational techniques. The field of computer-aided drug design has had extensive impact in the area of drug design.
Current Computer-Aided Drug Design is an essential journal for all medicinal chemists who wish to be kept informed and up-to-date with all the latest and important developments in computer-aided methodologies and their applications in drug discovery. Each issue contains a series of timely, in-depth reviews, original research articles and letter articles written by leaders in the field, covering a range of computational techniques for drug design, screening, ADME studies, etc., providing excellent rationales for drug development.
Articles from the journal Current Computer Aided-Drug Design,
12 Issue 1:
12 Issue 1:
- Editorial: Computer-Assisted Approaches as Decision Support Systems in the Overall Strategy of Combating Emerging Diseases: Some Comments Regarding Drug Design, Vaccinomics, and Genomic Surveillance of the Zika Virus
- Using Deep Learning for Compound Selectivity Prediction
- Applications of Receptor- and Ligand-based Models in Inverse Docking Experiments: Recognition of Dihydrofolate Reductase Using 7,8-Dialkyl- 1,3-Diaminopyrrolo[3,2-f]Quinazolines
- 1-R-2-([1,2,4]Triazolo[1,5-c]quinazoline-2-ylthio)etanon(ol)s: Synthesis, Bioluminescence Inhibition, Molecular Docking Studies, Antibacterial and Antifungal Activities
- 3D-QSAR Studies on the Biological Activity of Imidazolidinylpiperidinylbenzoic Acids as Chemokine Receptor Antagonists
- Artificial Neural Network Analysis of Pharmacokinetic and Toxicity Properties of Lead Molecules for Dengue Fever, Tuberculosis and Malaria
- Metabolic Electron Attachment as a Primary Mechanism For Toxicity Potentials of Halocarbons
- Identification of Novel BACE1 Inhibitors by Combination of Pharmacophore Modeling, Structure-Based Design and In Vitro Assay
Courtesy by : Bentham Insight
Current Computer Aided-Drug Design
Current Computer-Aided Drug Design aims to publish all the latest developments in drug design based on computational techniques. The field of computer-aided drug design has had extensive impact in the area of drug design.
Current Computer-Aided Drug Design is an essential journal for all medicinal chemists who wish to be kept informed and up-to-date with all the latest and important developments in computer-aided methodologies and their applications in drug discovery. Each issue contains a series of timely, in-depth reviews, original research articles and letter articles written by leaders in the field, covering a range of computational techniques for drug design, screening, ADME studies, etc., providing excellent rationales for drug development.
Articles from the journal Current Computer Aided-Drug Design, 12 Issue 1:
- Editorial: Computer-Assisted Approaches as Decision Support Systems in the Overall Strategy of Combating Emerging Diseases: Some Comments Regarding Drug Design, Vaccinomics, and Genomic Surveillance of the Zika Virus
- Using Deep Learning for Compound Selectivity Prediction
- Applications of Receptor- and Ligand-based Models in Inverse Docking Experiments: Recognition of Dihydrofolate Reductase Using 7,8-Dialkyl- 1,3-Diaminopyrrolo[3,2-f]Quinazolines
- 1-R-2-([1,2,4]Triazolo[1,5-c]quinazoline-2-ylthio)etanon(ol)s: Synthesis, Bioluminescence Inhibition, Molecular Docking Studies, Antibacterial and Antifungal Activities
- 3D-QSAR Studies on the Biological Activity of Imidazolidinylpiperidinylbenzoic Acids as Chemokine Receptor Antagonists
- Artificial Neural Network Analysis of Pharmacokinetic and Toxicity Properties of Lead Molecules for Dengue Fever, Tuberculosis and Malaria
- Metabolic Electron Attachment as a Primary Mechanism For Toxicity Potentials of Halocarbons
- Identification of Novel BACE1 Inhibitors by Combination of Pharmacophore Modeling, Structure-Based Design and In Vitro Assay
Courtesy by : Bentham Insight
Highlighted Article Flyer for the journal “Current Computer-Aided Drug Design” Volume 11, Number 4
courtesy by : https://benthamsciencepublishers.wordpress.com/2016/07/15/highlighted-article-flyer-for-the-journal-current-computer-aided-drug-design/
Recently Published Issue of the Journal Current Computer-Aided Drug Design
Current Computer-Aided Drug Design aims to publish all the latest developments in drug design based on computational techniques. The field of computer-aided drug design has had extensive impact in the area of drug design. It is an essential journal for all medicinal chemists who wish to be kept informed and up-to-date with all the latest and important developments in computer-aided methodologies and their applications in drug discovery. Each issue contains a series of timely, in-depth reviews, original research articles and letter articles written by leaders in the field, covering a range of computational techniques for drug design, screening, ADME studies, etc., providing excellent rationales for drug development.
Following are the articles from the Journal of Current Computer Aided-Drug Design, 10 Issue 4
Article: Characteristics of Influenza HA-NA Interdependence Determined Through a Graphical Technique
Author(s): Ashesh Nandy, Tapati Sarkar, Subhash C. Basak, Papiya Nandy and Sukhen Das
Article: Theoretical Modeling of HPV: QSAR and Novodesign with Fragment Approach
Author(s): Girinath G. Pillai, Lauri Sikk, Tarmo Tamm, Mati Karelson, Peeter Burk and Kaido Tamm
Article: Docking Modes of BB-3497 into the PDF Active Site – A Comparison of the Pure MM and QM/MM Based Docking Strategies
Author(s): Tripti Kumari, Upasana Issar and Rita Kakkar
Article: 3D-QSAR Analysis on ATR Protein Kinase Inhibitors Using CoMFA and CoMSIA
Author(s): Xiurong Li, Mao Shu, Yuanqiang Wang, Rui Yu, Shuang Yao and Zhihua Lin
Article: Pharmacophore Based 3DQSAR of Phenothiazines as Specific Human Butyrylcholinesterase Inhibitors for Treatment of Alzheimer’s Disease;
Author(s): Harish S. Kundaikar, Neha P. Agre and Mariam S. Degani
Article: A Combined Cheminformatics and Computational Approach for the Prediction of Anti-HIV Small Molecules
Author(s): Naghmeh Poorinmohammad and Hassan Mohabatkar
Article: A Structural Feature of the Non-Peptide Ligand Interactions with Mice Mu-Opioid Receptors
Author(s): Hamid R. Noori, Christian Mucksch and Herbert M. Urbassek
Article: 3D Modeling of Dengue Virus NS4B and Chikungunya Virus nsP4: Identification of a Common Drug Target and Designing a Single Antiviral Inhibitor
Author(s): Garisekurthi Satheesh, Nagu P. Prabhu and Musturi Venkataramana
Article: Development of a Two-Step Indirect Method for Modeling Ecom50
Author(s): Lowell H. Hall, L. Mark Hall, Dennis W. Hill, Douglas M. Hawkins, Ming-Hui Chen and David F. Grant
Article: Virtual Screening and Synthesis of Novel Antitubercular Agents Through Interaction-Based Pharmacophore and Molecular Docking Studies
Author(s): Deepak Bhattarai, Muhammad Muddassar, Jae Wan Jang, Seung Kon Hong, Eunice Eunkyeong Kim, Taegwon Oh, Sang-Nae Cho, Ae Nim Pae and Gyochang Keum
Courtesy by Bentham Insight
Current Computer Aided-Drug Design, 12 Issue 2
Current Computer-Aided Drug Design aims to publish all the latest developments in drug design based on computational techniques. The field of computer-aided drug design has had extensive impact in the area of drug design.
Current Computer-Aided Drug Design is an essential journal for all medicinal chemists who wish to be kept informed and up-to-date with all the latest and important developments in computer-aided methodologies and their applications in drug discovery. Each issue contains a series of timely, in-depth reviews, original research articles and letter articles written by leaders in the field, covering a range of computational techniques for drug design, screening, ADME studies, etc., providing excellent rationales for drug development.
Articles from the journal Current Computer Aided-Drug Design, 12 Issue 2
- EDITORIAL: Chemodescriptor Based QSARs of Structurally Homogeneous Versus Heterogeneous Chemical Data Sets: Some Comments on the Congenericity Principle vis-à-vis Diversity Begets Diversity Principle
- Characterizing the Zika Virus Genome – A Bioinformatics Study
- Clarification of Interaction Mechanism of Mouse Hepatitis Virus (MHV) N and nsp3 Protein with Homology Modeling and Protein-Protein Docking Analysis
- Molecular Dynamics Simulation Reveal the Mechanism of Resistance of Mutant Actins to Latrunculin A – Insight into Specific Modifications to Design Novel Drugs to Overcome Resistance
- Rhodomyrtone Target Exploration: Computer Aided Search on Staphylococcus aureus Key Proteins as a Potential Therapeutic Target
- Discovery of Novel HIV-1 Integrase Inhibitors Using QSAR-Based Virtual Screening of the NCI Open Database
- Design of Broad-Spectrum Inhibitors of Influenza A Virus M2 Proton Channels: A Molecular Modeling Approach
- Current Status of Computer-Aided Drug Design for Type 2 Diabetes
For details on the articles, please visit this link :: http://bit.ly/2aNd20q
courtesy by : https://benthamsciencepublishers.wordpress.com/2016/08/26/new-issue-current-computer-aided-drug-design-12-issue-2/
Monday, July 25, 2016
Structure-Activity Relationships and Rational Design Strategies for Radical- Scavenging Antioxidants
Author(s):
Hong-Yu ZhangPages 257-273 (17)
Abstract:
In the past two decades, there has been growing interest in finding novel and non-toxic antioxidants to meet the requirements in chemical, food and pharmaceutical industries. To accelerate the antioxidant discovery process, various theoretical methods have been employed to investigate the structure-activity relationships of antioxidants. Accordingly, some rational-design strategies for antioxidants have been proposed and applied in practice. This review summarizes the current knowledge on this topic, which will be helpful to direct the practice in related fields.
Keywords:
antioxidant, radical, structure-activity relationship, rational design
Affiliation:
Shandong Provincial Research Center for Bioinformatic Engineering and Technique, Center forAdvanced Study, Shandong University of Technology, Zibo 255049, P. R. China.
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Discovery of Potent Anti-SARS-CoV MPro Inhibitors
Author(s):
Suzanne Sirois, Rui Zhang, Weina Gao, Hui Gao, Yun Li, Huiqin Zheng and Dong-Qing WeiPages 191-200 (10)
Abstract:
SARS is a viral respiratory illness caused by a previously unrecognized coronavirus, called SARS-associated coronavirus (SARS-CoV). Because of the potential for a rapid spread of the disease, it is vitally important to identify drugs that effectively inhibit a known target of the SARS coronavirus. Because of its essential role in proteolytic processing, the main protease MPro, a cysteine protease, is considered an attractive target for antiviral drugs against SARS and other coronavirus infections. In this review, we will present both peptidic and non-peptidic inhibitors that have been designed against SARS MPro. The most challenging requirement in designing cysteine inhibitors is to obtain a selective non-covalent electrophilic isostere that can react with the catalytic nucleophile. Emphasis will be put on our recent results, both experimental and theoretical, in the search for potent wide-spectrum inhibitors. The antiviral activity of the octopeptide AVLQSGFR against SARS-associated coronavirus will be presented as well as the recent hits obtained from virtual high throughput screening (vHTS) based on the identification of six hydrogen bond pharmacophore points from KZ7088 docked into the active site of SARS MPro.
Keywords:
SARS, severe acute respiratory syndrome, coronavirus main proteinase, KZ7088, pharmacophore search, binding pocket, computer-assisted drug design, docking, virtual screening
Affiliation:
College of Life Science and Technology, Shanghai Jiaotong University, 800 Dongchuan Road,Minhang District, Shanghai, 200240, China.
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Structure-Guided Design of Antibodies
Author(s):
Justin A. Caravella, Deping Wang, Scott M. Glaser and Alexey LugovskoyPages 128-138 (11)
Abstract:
Monoclonal antibodies capable of recognizing antigens with high affinity and specificity represent a wellestablished class of biological agents. Since the development of hybridoma technology in 1975, advances in recombinant DNA technologies and computational and biophysical methods have allowed us to develop a better understanding of the relationships between antibody sequence, structure, and function. These advances enable us to manipulate antibody sequences with the goal of improving upon, or creating new biological or biophysical properties. In this review we will focus on recent successes in using structure-guided computational methods to design antibodies and antibody-like molecules with optimized affinity and specificity to antigen and for enhancing protein stability.
Keywords:
Antibody engineering, structure-based design, affinity maturation, effector function, protein stability
Affiliation:
Physical Biochemistry, Drug Discovery, Biogen Idec Inc., 14 Cambridge Center, Cambridge, MA 02142, USA.
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Antiprotozoal Nitazoxanide Derivatives: Synthesis, Bioassays and QSAR Study Combined with Docking for Mechanistic Insight
Author(s):
Thomas Scior, Jorge Lozano-Aponte, Subhash Ajmani, Eduardo Hernández-Montero, Fabiola Chávez-Silva, Emanuel Hernández-Núñez, Rosa Moo-Puc, Andres Fraguela-Collar and Gabriel Navarrete-VázquezPages 21-31 (11)
Abstract:
In view of the serious health problems concerning infectious diseases in heavily populated areas, we followed the strategy of lead compound diversification to evaluate the near-by chemical space for new organic compounds. To this end, twenty derivatives of nitazoxanide (NTZ) were synthesized and tested for activity against Entamoeba histolytica parasites. To ensure drug-likeliness and activity relatedness of the new compounds, the synthetic work was assisted by a quantitative structure-activity relationships study (QSAR). Many of the inherent downsides – well-known to QSAR practitioners – we circumvented thanks to workarounds which we proposed in prior QSAR publication. To gain further mechanistic insight on a molecular level, ligand-enzyme docking simulations were carried out since NTZ is known to inhibit the protozoal pyruvate ferredoxin oxidoreductase (PFOR) enzyme as its biomolecular target.
Keywords:
3D-QSAR, 4D-QSAR, 5D-QSAR, mathematical regularization, nitrothiazole, PFOR, QSAR pitfalls, tizoxanide.
Affiliation:
Department of Pharmacy, Facultad de Ciencias Químicas, Benemérita Universidad Autónoma de Puebla, Ciudad Universitaria, Edificio 105 C/106, C.P. 72570 Puebla, PUE., Mexico
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Current Status of Computer-Aided Drug Design for Type 2 Diabetes
Author(s):
Shabana Bibi and Katsumi SakataPages 167-177 (11)
Abstract:
Background: Diabetes is a metabolic disorder that requires multiple therapeutic approaches. The pancreas loses its functionality to properly produce the insulin hormone in patients with diabetes mellitus. In 2012, more than one million people worldwide died as a result of diabetes, which was the eighth leading cause of death.
Objective: Most drugs currently available and approved by the U.S. Food and Drug Administration cannot reach an adequate level of glycemic control in diabetic patients, and have many side effects; thus, new classes of compounds are required. Efforts based on computer-aided drug design (CADD) can mine a large number of databases to produce new and potent hits and minimize the requirement of time and dollars for new discoveries.
Methods: Pharmaceutical sciences have made progress with advances in drug design concepts. Virtual screening of large databases is most compatible with different computational methods such as molecular docking, pharmacophore, quantitative structure-activity relationship, and molecular dynamic simulation. Contribution of these methods in selection of antidiabetic compounds has been discussed.
Results: The Computer-Aided Drug Design (CADD) approach has contributed to successful discovery of novel antidiabetic agents. This mini-review focuses on CADD approach on currently approved drugs and new therapeutic agents-indevelopment that may achieve suitable glucose levels and decrease the risk of hypoglycemia, which is a major obstacle to glucose control and a special concern for therapies that increase insulin levels.
Conclusion: Drug design and development for type 2 diabetes have been actively studied. However, a large number of antidiabetic drugs are still in early stages of development. The conventional target- and structure-based approaches can be regarded as part of the efforts toward therapeutic mechanism-based drug design for treatment of type 2 diabetes. It is expected that further improvement in CADD approach will enhance the new discoveries.
Keywords:
Computer-aided drug design, diabetes mellitus, FDA-approved therapeutic options, glucose level, hypoglycemia, therapeutic mechanism-based drug design.
Affiliation:
Department of Environment and Life Engineering, Graduate School of Engineering, Maebashi Institute of Technology, Maebashi, Gunma 371-0816, Japan.
Graphical Abstract:
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