Examples of calculated data obtained for Imatinib

Biochemical software

Imatinib

Imatinib is used to treat certain types of leukemia (cancer that begins in the white blood cells) and other cancers and disorders of the blood cells. Imatinib is also used to treat certain types of gastrointestinal stromal tumors.
Imatinib is in a class of medications called kinase inhibitors. It works by blocking the action of the abnormal protein that signals cancer cells to multiply. This helps stop the spread of cancer cells.
Imatinib also inhibits the receptor tyrosine kinases for platelet-derived growth factor (PDGF) and stem cell factor (SCF)/c-kit; the SCF/c-kit receptor tyrosine kinase is activated in gastrointestinal stromal tumor (GIST). This agent inhibits proliferation and induces apoptosis in cells that overexpress these oncoproteins.[2]
The results of applying our technique can be of good help for the pre-experimental determination of such quantities as the affinity expressed by the dissociation constant or the half maximal inhibitory concentration (IC50).
Peroxisome proliferator-activated receptor (PPAR ) belongs to the thyroid hormone receptor-like nuclear receptor subfamily 1, which is one of the ligand-activated transcription factors. PPAR forms a heterodimer with retinoid X receptors (RXRs), recruits coactivators, and then binds to the cognate peroxisome proliferative response elements on target genes. PPAR is a good therapeutic target for type 2 diabetes mellitus, as well as other metabolic diseases including obesity and atherosclerosis [1]
Direction of affinity change
A value lg(cond(W)) that shows the stability of a biological complex and shows the direction of change in the affinity of a dimer under various mutations.

Chemical structure of Imatinib-PPAR dimer with indication of key amino acid residues

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Useful application of the obtained numerical results.
The results of our studies can be applied in predicting:
- Inhibitory potency and binding ability of small molecules
- Inhibitor dissociation constants for the WT and mutant
kinases
- Enzyme kinetic parameters
- Explain the enhanced drug sensitivity of different mutants
- Changing in the binding site caused by
the mutation on the enzyme's binding affinity for TKIs
- Enzyme kinetic assays and IC50 determinations
- Inhibitor binding constants, the drug resistance
Provide important information for the development of more potent and selective drugs for use in resistant individuals.
[1] Structural Basis for the Regulation of PPAR Activity by Imatinib
[2] National Library of Medicine
National Center for Biotechnology Information

Chemical structure of Imatinib

In the process of obtaining the calculated parameters, we use the method of quantum mechanical calculations. We get the distribution of charges, as well as calculate the conformational mobility of a small chemical molecule.
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Calculation of additional physical parameters of the small chemical molecule Imatinib

Examples using small molecules are given below

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