Topological analysis of electron density in large biomolecular systems

Current Drug Discovery Technologies
Maria A Grishina, Vladimir A Potemkin

Abstract

AlteQ approach was applied to the tolopogical analysis of electron density for "substrate - cytochrome" complexes. The approach is based on the use of Slater's type atomic contributions. Parameters of the atomic contributions were found using high resolution X-ray diffraction data for organic and inorganic molecules. Relationships of the parameters with atomic number, ionization potentials and electronegativities were determined. The sufficient quality of the molecular electron structure representation was shown under comparison of AlteQ predicted and observed electron densities. AlteQ algorithm was applied for evaluation of electron structure of "CYP3A4 - substrate" complexes modeled using BiS/MC restricted docking procedure. Topological analysis (similar to Atoms In Molecules (AIM) theory suggested by Richard F.W. Bader) of the AlteQ molecular electron density was carried out for each complex. The determination of (3,-1) bond, (3,+1) ring, (3,+3) cage critical points of electron density in the intermolecular "CYP3A4 - substrate" space was performed. Different characteristics such as electron density, Laplacian eigen values, etc. at the critical points were computed. It was shown that significant number of (3,-1) bond critical...Continue Reading

References

May 21, 1999·British Journal of Clinical Pharmacology·T S TracyI W Wainer
Dec 11, 1999·Nucleic Acids Research·H M BermanP E Bourne
Feb 5, 2000·Xenobiotica; the Fate of Foreign Compounds in Biological Systems·N IshiguroT Igarashi
Dec 18, 2001·Drug Metabolism and Disposition : the Biological Fate of Chemicals·Espen MoldenHege Christensen
Jun 22, 2002·Chemico-biological Interactions·Guangyu Zhao, John W Allis
May 21, 2003·Drug Metabolism and Disposition : the Biological Fate of Chemicals·Wenjiang ZhangEdward M Sellers
Aug 12, 2004·The Journal of Chemical Physics·Wenhua Jiang, Yongmei Wang
Aug 30, 2005·Biophysical Journal·Shelly Tzlil, Avinoam Ben-Shaul
Sep 7, 2006·Proceedings of the National Academy of Sciences of the United States of America·Marika Ekroos, Tove Sjögren
Nov 9, 2006·Journal of the American Chemical Society·Elizabeth A ZhurovaA Alan Pinkerton
Jan 20, 2007·Acta Crystallographica. Section B, Structural Science·Vladimir G TsirelsonVladimir A Potemkin
Mar 22, 2008·Journal of Computer-aided Molecular Design·Vladimir A Potemkin, Maria A Grishina
Aug 30, 2008·Drug Discovery Today·Vladimir Potemkin, Maria Grishina
May 29, 2009·Journal of Chemical Information and Modeling·Vladimir A PotemkinMaria A Grishina
Oct 7, 2009·Biophysical Journal·Jesse Ziebarth, Yongmei Wang
Dec 14, 2011·Journal of Computational Chemistry·Tian Lu, Feiwu Chen
Oct 1, 2013·Journal of Computer-aided Molecular Design·Elena SalminaVladimir A Potemkin
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus
Mar 10, 2018·Current Medicinal Chemistry·Vladimir Potemkin, Maria Grishina
Jan 3, 2017·Annals of Internal Medicine·Faisal G BakaeenBlase A Carabello

❮ Previous
Next ❯

Citations

Jul 22, 2020·Future Medicinal Chemistry·Hrvoje RimacVladimir A Potemkin
Dec 22, 2020·Journal of Biomolecular Structure & Dynamics·Vladislav NaumovichMagda H Abdellattif
Apr 3, 2021·Journal of Chemical Information and Modeling·Hrvoje RimacVladimir Potemkin
Apr 14, 2021·Future Medicinal Chemistry·Shivananda KandagallaMaria A Grishina
Jul 3, 2021·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Nadezhda PalkoVladimir Potemkin

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.

© 2022 Meta ULC. All rights reserved