Complementarity Principle in Terms of Electron Density for the Study of EGFR Complexes

Kandagalla, Shivananda; Rimac, Hrvoje; Потемкин, В. А.; Grishina, Maria

doi:10.4155/fmc-2020-0265

Cited by 18 publications

(14 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This limitation characterizes the boundary of the atom in Bader’s theory. The electron density was calculated in the cubic grid with the distance between nearest junctions 0.1 Å (each junction is the m th point) [ 29 , 33 , 34 ].…”

Section: Methodsmentioning

confidence: 99%

Electron Density Analysis of SARS-CoV-2 RNA-Dependent RNA Polymerase Complexes

2021

Self Cite

View full text Add to dashboard Cite

The work is devoted to the study of the complementarity of the electronic structures of the ligands and SARS-CoV-2 RNA-dependent RNA polymerase. The research methodology was based on determining of 3D maps of electron densities of complexes using an original quantum free-orbital AlteQ approach. We observed a positive relationship between the parameters of the electronic structure of the enzyme and ligands. A complementarity factor of the enzyme-ligand complexes has been proposed. The console applications of the AlteQ complementarity assessment for Windows and Linux (alteq_map_enzyme_ligand_4_win.exe and alteq_map_enzyme_ligand_4_linux) are available for free at the ChemoSophia webpage.

show abstract

Section: Methodsmentioning

confidence: 99%

Electron Density Analysis of SARS-CoV-2 RNA-Dependent RNA Polymerase Complexes

2021

Self Cite

View full text Add to dashboard Cite

show abstract

“…These are 1boz, 1hfp, 1kms, 3ghc, 3gi2, 3ntz, 3nu0, 4kfj, 4qhv [23][24][25][26][27][28][29]. We evaluated the enzyme-ligand complementarity for human DHFR complexes without hydrogen atoms in the same way as it was performed in [7][8][9] for complexes of other enzymes.…”

Section: Considered Complexesmentioning

confidence: 99%

“…Second, 3D maps of electron density were evaluated in the zones of the maximum enzyme-ligand overlap, namely in the space where the electron densities of the enzyme and the ligand are greater than 0.001 au (namely, at m points of molecular space with ρ E > 0.001 au and ρ L > 0.001 au) in the same way as it was performed in [7][8][9] for other complexes. Let us call these zones the zones of intermolecular contacts.…”

Section: Maps Of Electron Densitymentioning

confidence: 99%

“…Three-dimensional maps of electron density were constructed for the complexes using the AlteQ method [12][13][14][15][16]. We found the complementarity factor which describes enzyme-ligand complementarity of the complexes without hydrogens very well [7][8][9]. It was shown that this method can be used for the search for the most correct binding poses of ligands during docking procedures [9].…”

Section: Introductionmentioning

confidence: 98%

“…We tried to develop the idea of complementarity in chemical systems to present it in the form of a mathematical expression relating the electron densities of a receptor and a ligand in their complexes. Recently, we investigated [7][8][9] different enzyme-ligand complexes (namely, complexes of cyclin-dependent protein kinases, mouse acetylcholinesterase, HIV-1 protease, EGFR) taken from the Protein Data Bank [10,11]. Three-dimensional maps of electron density were constructed for the complexes using the AlteQ method [12][13][14][15][16].…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

The Complementarity Principle—One More Step towards Analytical Docking on the Example of Dihydrofolate Reductase Complexes

Потемкин

Grishina

2021

Life

Self Cite

View full text Add to dashboard Cite

New approaches to assessing the “enzyme–ligand” complementarity, taking into account hydrogens, have been proposed. The approaches are based on the calculation of three-dimensional maps of the electron density of the receptor–ligand complexes. The action of complementarity factors, first proposed in this article, has been demonstrated on complexes of human dihydrofolate reductase (DHFR) with ligands. We found that high complementarity is ensured by the formation of the most effective intermolecular contacts, which are provided due to predominantly paired atomic–atomic interactions, while interactions of the bifurcate and more disoriented type are minimized. An analytical docking algorithm based on the proposed receptor–ligand complementarity factors is proposed.

show abstract

Cucumis melo var. momordica as a Potent Antidiabetic, Antioxidant and Possible Anticovid Alternative: Investigation through Experimental and Computational Methods

Yadav¹,

Grishina

Shahbaaz

et al. 2022

Chemistry & Biodiversity

View full text Add to dashboard Cite

Diabetes mellitus is a typical life threatening of disease, which generate due to the dysfunction of β cells of pancreas. In 2014, WHO stated that 422 million people were infected with DM. The current pattern of management of diabetes included synthetic or plant based oral hypoglycemic drugs and insulin but drug resentence is become a very big issues in antidiabetic therapy. Thus, it's very earnest to discover now medication for this disease. Now the days, it is well acknowledged that diabetic patients are more prone towards covid and related complications. Thus, medical practitioners reformed the methodology of prescribing medication for covid infected antidiabetic therapy and encouraging the medication contains dual pharmacological properties. It is also well know that polyphenols specifically hold a significant role in oxidative stress and reduced the severity of many inflammatory diseases. Cucumis melo has rich history as ethano-pharmacological use in Indian subcontinent. The fruit and seed are well-known for the treatment of various diseases due to the presence of phenolics. Therefore, in this study, the combined mixture of flower and seeds were used for the extraction of polyphenolic rich extract and tested for antidiabetic activity through the antioxidant and in vivo experiments. The antioxidant potential measurement exhibited that the selected plant extract has the significant competence to down-regulate oxidative stress (DPPH scavenging IC 50 at 60.7 � 1.05 μg/mL, ABTS IC 50 at 62.15 � 0.50 μg/mL). Furthermore, the major polyphenolic phyto-compounds derived from the Cucumis melo were used for in silico anticovid activity, docking, and complementarity studies. The anticovid activity prognosis reflected that selected phyto-compounds amentoflavone and vanillic acid have optimal possibility to interact with 3C-like protease and through this moderate anticovid activity can be exhibit. The docking experiments established that the selected compounds have propensity to interact with protein tyrosine phosphatase 1B, 11β-Hydroxysteroid dehydrogenase, superoxide dismutase, glutathione peroxidase, and catalase β-glucuronidase receptor. In vivo experiments showed that 500 mg/kg, Cucumis melo extract ominously amplified body weight, plasma insulin, high-density lipoprotein levels, and biochemical markers. Furthermore, extract significantly downregulate the blood glucose, total cholesterol, triglycerides, low-density lipoprotein, and very low-density lipoprotein.

show abstract

Complementarity Principle in Terms of Electron Density for the Study of EGFR Complexes

Cited by 18 publications

References 28 publications

Electron Density Analysis of SARS-CoV-2 RNA-Dependent RNA Polymerase Complexes

Electron Density Analysis of SARS-CoV-2 RNA-Dependent RNA Polymerase Complexes

The Complementarity Principle—One More Step towards Analytical Docking on the Example of Dihydrofolate Reductase Complexes

Cucumis melo var. momordica as a Potent Antidiabetic, Antioxidant and Possible Anticovid Alternative: Investigation through Experimental and Computational Methods

Contact Info

Product

Resources

About