Machine learning modeling to identify affinity improved biobetter anticancer drug trastuzumab and the insight of molecular recognition of trastuzumab towards its antigen HER2

Author(s):  
Nataraj Balakrishnan ◽  
Gurunathan Baskar ◽  
Sathyanarayan Balaji ◽  
Malathi Kullappan ◽  
Surapaneni Krishna Mohan
2019 ◽  
Author(s):  
Anthony Tabet ◽  
Thomas Gebhart ◽  
Guanglu Wu ◽  
Charlie Readman ◽  
Merrick Pierson Smela ◽  
...  

DFT, NMR, ITC, and cell confluence data are used to generate predictive algorithms of supramolecular binding to cucurbit[7]uril and experimentally validate these predictions.


Author(s):  
Thomas Linden ◽  
Frank Hanses ◽  
Daniel Domingo-Fernández ◽  
Lauren Nicole DeLong ◽  
Alpha Tom Kodamullil ◽  
...  

2020 ◽  
Vol 20 (21) ◽  
pp. 1858-1867
Author(s):  
Xian Tan ◽  
Yang Yu ◽  
Kaiwen Duan ◽  
Jingbo Zhang ◽  
Pingping Sun ◽  
...  

Anticancer drug screening can accelerate drug discovery to save the lives of cancer patients, but cancer heterogeneity makes this screening challenging. The prediction of anticancer drug sensitivity is useful for anticancer drug development and the identification of biomarkers of drug sensitivity. Deep learning, as a branch of machine learning, is an important aspect of in silico research. Its outstanding computational performance means that it has been used for many biomedical purposes, such as medical image interpretation, biological sequence analysis, and drug discovery. Several studies have predicted anticancer drug sensitivity based on deep learning algorithms. The field of deep learning has made progress regarding model performance and multi-omics data integration. However, deep learning is limited by the number of studies performed and data sources available, so it is not perfect as a pre-clinical approach for use in the anticancer drug screening process. Improving the performance of deep learning models is a pressing issue for researchers. In this review, we introduce the research of anticancer drug sensitivity prediction and the use of deep learning in this research area. To provide a reference for future research, we also review some common data sources and machine learning methods. Lastly, we discuss the advantages and disadvantages of deep learning, as well as the limitations and future perspectives regarding this approach.


2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Kohulan Rajan ◽  
Jan-Mathis Hein ◽  
Christoph Steinbeck ◽  
Achim Zielesny

AbstractThe open rich-client Molecule Set Comparator (MSC) application enables a versatile and fast comparison of large molecule sets with a unique inter-set molecule-to-molecule mapping obtained e.g. by molecular-recognition-oriented machine learning approaches. The molecule-to-molecule comparison is based on chemical descriptors obtained with the Chemistry Development Kit (CDK), such as Tanimoto similarities, atom/bond/ring counts or physicochemical properties like logP. The results are summarized and presented graphically by interactive histogram charts that can be examined in detail and exported in publication quality.


2019 ◽  
Author(s):  
Anthony Tabet ◽  
Thomas Gebhart ◽  
Guanglu Wu ◽  
Charlie Readman ◽  
Merrick Pierson Smela ◽  
...  

DFT, NMR, ITC, and cell confluence data are used to generate predictive algorithms of supramolecular binding to cucurbit[7]uril and experimentally validate these predictions.


2020 ◽  
Vol 22 (10) ◽  
pp. 500-508
Author(s):  
Alexander T. Taguchi ◽  
James Boyd ◽  
Chris W. Diehnelt ◽  
Joseph B. Legutki ◽  
Zhan-Gong Zhao ◽  
...  

Author(s):  
SANJAY GOSWAMI ◽  
KSHAMA DHOBALE ◽  
RAVINDRA WAVHALE ◽  
BARNALI GOSWAMI ◽  
SHASHWAT BANERJEE

Purpose: The field of cancer nanomedicine has made significant progress, but its clinical translation is impeded by many challenges, such as the difficulty in analysing intracellular anticancer drug release by the nanocarriers due to the lack of suitable tools. Here, we propose the development of a combinatorial imaging and analysis technique to evaluate anticancer drug such as doxorubicin HCl (DOX) released by a nanocarrier inside the HCT116 colon cancer cells and its subsequent intracellular accumulation. Procedure: Fluorescent cell images were captured and subjected to combined image analysis and machine learning based procedures to assess and quantify the delivery and retention rate of DOX inside the cancer cells by multifunctional CNT-DOX-Fe3O4nanocarrier. Results: We show that DOX in HCT116 cells was higher for multifunctional CNT-DOX-Fe3O4nanocarrierthan free DOX, indicating efficient and steady release of DOX as well as superior retentive property of the nanocarrier. Initially (1 h and 4 h) the luminance intensity of DOX in the cell cytoplasm delivered by CNT-DOX-Fe3O4nanocarrier was ~0.34 times and ~0.42 times lesser than that of free DOX delivered normally. However, at 24 h and 48 h post treatment the luminance intensity of DOX for CNT-DOX-Fe3O4nanocarrier was ~1.98 times and 1.92 times higher than that of free DOX. Furthermore, the luminance intensity of DOX for CNT-DOX-Fe3O4in the whole cell was ~1.35 times and ~1.62 times higher than that of free DOX at 24h and 48 h, respectively. Conclusions: The high-throughput nature of our image analysis workflow allowed us to automate the process of DOX retention analysis, and enabled us to devise machine learning-based modeling to predict the percentage of anticancer drug retention in cells. The development of models to automatically quantify and predict intra-cellular drug release in cancer cells could benefit personalized treatments by optimizing the design of nanocarriers.


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