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The influence of small inhibitors on protein interactions

The correlations were performed on real solutions in a biochemical laboratory.
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Examples of joint analysis of preliminary calculated and experimental data

Price list for Line Product

Main categories of molecular complexes with small inhibitors or atoms, and a list of prices for calculating each molecular complex.
Features
Set one
Set two
Set Three
Set Four
[Monomer+Inhibitor] or Atom
up to 10 mutations
up to 40 mutations
up to 150 mutations
up to 250 mutations
[3-4weeks]
up to TWO inhibitors
[Dimer+Inhib.1+Inhib.2] or Atoms
up to 30 mutations
up to 100 mutations
up to 150 mutations
[3-5 weeks]
up to 4 inhibitors
[Tetramer+Several Inh-s]
[Trimer+Several Inhib-s]
up to 10 mutations
up to 50 mutations
[6-8 weeks]
[pentamer+Several Inh-s]
[any protein complex +Inh.]
up to 10 mutations
50 Euro
130 Euro
249 Euro
349 Euro
EGFR kinase+Afatinib
The effect of the L858M/L861Q mutations on drug sensitivity was examined in vitro. Stable EGFR L858M/L861Q Ba/F3 cells were generated, and cell viability/proliferation after treatment with EGFR TKIs was measured by MTS assay. The response to afatinib was similar for both cell lines (1.5 nM for L858R IC50 versus 1.8 nM for L858M/L861Q IC50).
[EGFR L858M/L861Q cis Mutations Confer Selective Sensitivity to Afatinib]
Example N1




The top graph is the experimental plot of the interactions of EGFR kinase and Afatinib, taking into account oncogenic mutations in the kinase.



The graph below is the calculated plot of the interactions of EGFR kinase and Afatinib, taking into account oncogenic mutations in the kinase.

The calculations of resistance for various mutations were given both in the absence of Afatinide (gray bars) and with the addition of Afatinib (blue bars)
EGFR kinase+Gefitinib
Enzyme kinetic parameters and inhibitor dissociation constants of the wild-type and mutant EGFR kinases.
The G719S/T790M mutant binds gefitinib with increased affinity, as compared with the wild type and the G719S mutant.
The equilibrium fluorescence quenching method was used to obtain the gefitinib binding constant, as described (Yun et al., 2007).
Example N2
The graph shows the calculated data lg(cond(W)) on the effect of oncogenic mutations on the binding of EGFR to Afatinib.
The stability lg(cond(W)) value indicates an increase in the binding of Afatinib to EGFR (G719S/T790M) compared to wtEGFR.
A direct correlation is observed between the calculated lg(cond(W)) and experimental data IC50.


Inhibition of the wild-type and mutant EGFRs by increasing concentrations of gefitinib.
NIH3T3 cells retro-virally transferred with EGFRs were pre-treated with the indicated concentrations of gefitinib for 4 h. Activation of EGFRs, as monitored by auto-phosphorylation (Tyr1173). IC50s were measured by quantifying the phosphorylation signals.
Therefore, the T790M mutation effectively enhances the drug resistance of the G719S mutant. The acquired drug resistance of the G719S/T790M double mutant is not attributed to the reduced binding of gefitinib, because the G719S/T790M double mutant bound gefitinib with a Kd=5.6 nM, which is tighter than G719S (Kd=31.9 nM) and the wild type (Kd=14.2 nM).
[Structural basis for the altered drug sensitivities of non-small cell lung cancer-associated mutants of human epidermal growth factor receptor]


Joint analysis of the effect of key mutations in the EGFR protein on binding to JBJ-04-125-02 and AMP:
[EGFR+JBJ+AMP]-[EGFR+JBJ+AMP]

A mutant-selective EGFR allosteric inhibitor, JBJ-04-125-02, which as a single agent, can inhibit cell proliferation and EGFR L858R/T790M/C797S signaling in vitro and in vivo. However, increased EGFR dimer formation limits treatment efficacy and leads to drug resistance. Remarkably, osimertinib, an ATP-competitive covalent EGFR inhibitor, uniquely and significantly enhances the binding of JBJ-04-125-02 for mutant EGFR.
Example N3
Calculated Data
Experiment data IC50
[EGFR-AMP]-[EGFR-AMP]
[EGFR-AMP-JBJ]-[EGFR-AMP-JBJ]
Calculated Data for next following cases:
Description of the experiment, EGFR kinase and small molecules
The small inhibitor displaces ATP molecules from the EGFR-binding pocket, thereby inhibiting the kinase activity.
[EGFR-JBJ-04-125-02]-[EGFR-JBJ-04-125-02]
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PPAR +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.
Example N4
The structure of imatinib-bound PPAR° R288A mutant, indicating the key amino acid residues.

PDB 6KTN PPAR+Imatinib structure (a)




Results of experimental (b) and numerical (c) measurements of affinity changes upon R288A substitution in PPARgamma upon binding to imatinib.


Surface plasmon resonance (SPR) analyses of the binding affinities for imatinib of PPAR° WT in the ligand-binding domain and PPAR° R288A mutant in the ligand-binding domain (b) and dependence of lg(cond(W)) value on amino acid residue replacement of R288A binding with imatinib c)

Thus, our developed numerical method makes it possible to determine the range of stability changes of dimeric complexes involving a small chemical molecule and a protein molecule in the presence of a three-dimensional structure of the dimeric complex.

Applying our method will make it possible to identify mutations that lead to the decreased/increased affinity of components.

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

metastatic breast cancer, breast cancer, colon cancer, what is colon cancer,
Calculation of additional physical parameters of the small chemical molecule Imatinib
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