Up-Goer Five challenge: Patient specific protein-drug binding affinity calculations

Authorea ◽  
2017 ◽  
Author(s):  
David Wright
2020 ◽  
Author(s):  
Mallikarjuna Nimgampalle ◽  
Vasudharani Devanthan ◽  
Ambrish Saxena

Recently Chloroquine and its derivative Hydroxychloroquine have garnered enormous interest amongst the clinicians and health authorities’ world over as a potential treatment to contain COVID-19 pandemic. The present research aims at investigating the therapeutic potential of Chloroquine and its potent derivative Hydroxychloroquine against SARS-CoV-2 viral proteins. At the same time we have screened some chemically synthesized derivatives of Chloroquine and compared their binding efficacy with chemically synthesized Chloroquine derivatives through <i>in silico</i>approaches. For the purpose of the study, we have selected some essential viral proteins and enzymes implicated in SARS-CoV-2 replication and multiplication as putative drug targets.<br>


Molecules ◽  
2020 ◽  
Vol 25 (8) ◽  
pp. 1945 ◽  
Author(s):  
Marta Ziegler-Borowska ◽  
Kinga Mylkie ◽  
Pawel Nowak ◽  
Patryk Rybczynski ◽  
Adam Sikora ◽  
...  

Binding and transport of ligands is one of the most important functions of human blood serum proteins. Human serum albumin is found in plasma at the highest concentration. Because of this, it is important to study protein–drug interactions for this albumin. Since there is no single model describing this interaction, it is necessary to measure it for each active substance. Drug binding should also be studied in conditions that simulate pathological conditions of the body, i.e., after oxidative stress. Due to this, it is expected that the methods for testing these interactions need to be easy and fast. In this study, albumin immobilized on magnetic nanoparticles was successfully applied in the study of protein–drug binding. Ketoprofen was selected as a model drug and interactions were tested under normal conditions and artificially induced oxidative stress. The quality of obtained results for immobilized protein was confirmed with those for free albumin and literature data. It was shown that the type of magnetic core coverage does not affect the quality of the obtained results. In summary, a new, fast, effective, and universal method for testing protein–drug interactions was proposed, which can be performed in most laboratories.


2015 ◽  
Vol 55 (9) ◽  
pp. 1936-1943 ◽  
Author(s):  
Hung Nguyen ◽  
Tien Tran ◽  
Yoshifumi Fukunishi ◽  
Junichi Higo ◽  
Haruki Nakamura ◽  
...  

PROTEOMICS ◽  
2012 ◽  
Vol 12 (23-24) ◽  
pp. 3598-3609 ◽  
Author(s):  
Sarah Feldkirchner ◽  
Joachim Schessl ◽  
Stefan Müller ◽  
Benedikt Schoser ◽  
Franz-Georg Hanisch

2013 ◽  
Vol 102 (8) ◽  
pp. 2679-2688
Author(s):  
Raja Ghosh ◽  
Si Pan ◽  
Lijuan Wang ◽  
Simon Lu

2021 ◽  
Author(s):  
Konstantinos Konstantinidis ◽  
Ioannis Karakasiliοtis ◽  
Kostas Anagnostopoulos ◽  
Georgios Boulougouris

<p> In this work, a novel approach is proposed based on the accurate computation of a protein’s inaccessible volume as regards to a ligand, plus the corresponding surface area, where the ligand can be placed in order to “touch” the protein without any overlaps. The proposed approach can be thought as an extension of the widely used concept of the Solvent-Accessible Surface Area (SASA), evaluating the surface generated by the ligand while being rolled over all the atoms of the protein without penetrating them. Identification of the inaccessible volume of each candidate protein-ligand pair is also provided in the context of this study, along with the boundary surface where the ligand can be placed so as to be in “contact” with the protein, which is expected to significantly enhance the ability to investigate specific protein drug interactions.</p>


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