Designing Anti-Cancer Drugs and Directing Anti-Cancer Drug Therapy (original) (raw)
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Designing anti-cancer drugs and directing anti-cancer therapy
2014
A prototype for a web application was designed and implemented as a guide to be used by clinicians when designing the best drug therapy for a specific cancer patient, given biological data derived from the patients tumor tissue biopsy. A representation of the patients metabolic pathways is displayed as a graph in the application, with nodes as substrates and products and edges as enzymes. The top metabolically active subpaths in the pathway, ranked using an algorithm based on both the patients biological data and the graph topology, are also displayed and can be individually highlighted to examine potential enzymatic sites to be disrupted by a drug these sites serve as a guide for designing the patients specific drug therapy. Displayed next to each sub-path is the sub-path score used to decide its rank, as well as the predicted patient survival time to indicate how effective that specific drug will be in alleviating that patient's cancer. Future work includes an animation component to track the patients progress and re-design the drug therapy as needed. Corresponding author's academic email: elinor@soe.ucsc.edu.
Designing of a New Anticancer Agent: An Internet Based Drug Design Approach
International Journal of Drug Design and Discovery
With the development of computational chemistry and molecular docking studies SAR and pharmacophore based drug design have been modified to target based drug discovery using sophisticated computational tools which is not very much user friendly and has got many incompatibility issues with many operating systems(OS) and other system configurations. In this paper SAR (Structure Activity Relationship) and pharmacophore based drug design approaches have been described by the used of free internet based tools which are very much user friendly and can almost compatible with any platform. In this paper some doxorubicin analogues have been designed using pharmacophore study as potent anticancer agents and their drug like properties, toxicity, metabolic sites and other parameters are predicted by the free internet based tools.
Automated synthesis and visualization of a chemotherapy treatment regimen network
Studies in health technology and informatics, 2013
Cytotoxic treatments for cancer remain highly toxic, expensive, and variably efficacious. Many chemotherapy regimens are never directly compared in randomized clinical trials (RCTs); as a result, the vast majority of guideline recommendations are ultimately derived from human expert opinion. We introduce an automated network meta-analytic approach to this clinical problem, with nodes representing regimens and edges direct comparison via RCT(s). A chemotherapy regimen network is visualized for the primary treatment of chronic myelogenous leukemia (CML). Node and edge color, size, and opacity are all utilized to provide additional information about the quality and strength of the depicted evidence. Historical versions of the network are also created. With this approach, we were able to compactly compare the results of 17 CML regimens involving RCTs of 9700 patients, representing the accumulation of 45 years of evidence. Our results closely parallel the recommendations issued by a prof...
2022
Within the next twenty years, the number of cancer patients is expected to rise by 70%. Current cancer treatments still face several limitations, such as severe side effects and a high incidence of disease recurrence. Drug combination therapies are a promising strategy to achieve higher therapeutic effects while reducing side effects. This new direction in cancer drug research has led to data-driven medicine. To predict whether certain drugs would have a synergistic effect when combined, the DREAM Challenge coordinators released data for thousands of experimentally tested drug combinations. The DREAM Challenge served as inspiration for selecting drug combinations that have the potential to be synergistic. We here describe an approach using biological pathway knowledge and applying this to the selected combinations with a previously described mathematical model, the Loewe-Additivity approach. The calculated interaction index (II) served to distinguish between synergistic (II < 1),...
Using Web Technologies for Integrative Drug Discovery
2010
Abstract Recent years have seen a huge increase in the amount of publicly-available information relevant to drug discovery, including online databases of compound and bioassay information; scholarly publications linking compounds with genes, targets and diseases; and predictive models that can suggest new links between compounds, genes, targets and diseases.
A Web Tool for Generating High Quality Machine-readable Biological Pathways
Journal of Visualized Experiments, 2017
PathWhiz is a web server built to facilitate the creation of colorful, interactive, visually pleasing pathway diagrams that are rich in biological information. The pathways generated by this online application are machine-readable and fully compatible with essentially all web-browsers and computer operating systems. It uses a specially developed, web-enabled pathway drawing interface that permits the selection and placement of different combinations of pre-drawn biological or biochemical entities to depict reactions, interactions, transport processes and binding events. This palette of entities consists of chemical compounds, proteins, nucleic acids, cellular membranes, subcellular structures, tissues, and organs. All of the visual elements in it can be interactively adjusted and customized. Furthermore, because this tool is a web server, all pathways and pathway elements are publicly accessible. This kind of pathway "crowd sourcing" means that PathWhiz already contains a large and rapidly growing collection of previously drawn pathways and pathway elements. Here we describe a protocol for the quick and easy creation of new pathways and the alteration of existing pathways. To further facilitate pathway editing and creation, the tool contains replication and propagation functions. The replication function allows existing pathways to be used as templates to create or edit new pathways. The propagation function allows one to take an existing pathway and automatically propagate it across different species. Pathways created with this tool can be "re-styled" into different formats (KEGG-like or textbook like), colored with different backgrounds, exported to BioPAX, SBGN-ML, SBML, or PWML data exchange formats, and downloaded as PNG or SVG images. The pathways can easily be incorporated into online databases, integrated into presentations, posters or publications, or used exclusively for online visualization and exploration. This protocol has been successfully applied to generate over 2,000 pathway diagrams, which are now found in many online databases including HMDB, DrugBank, SMPDB, and ECMDB.