Applying ultra-accelerated quantum chemical molecular dynamics technique for the evaluation of ligand protein interactions

Kamlesh Kumar Sahu, Mohamed Ismael, Shah Md Abdur Rauf, Ai Suzuki, Riadh Sahnoun, Michihisa Koyama, Hideyuki Tsuboi, Nozomu Hatakeyama, Akira Endou, Hiromitsu Takaba, Ramesh Chandra Deka, Carlos A. Del Carpio, Momoji Kubo, Akira Miyamoto

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Ligand-protein interactions have been studied using several chemical information techniques including quantum chemical methods that are applied to truncated systems composed of the ligand molecule and the surrounding amino acids of the receptor. Fragmented quantum molecular chemical studies are also a choice to study the enzyme-ligand system holistically, however there are still restrictions on the number of water molecules that can be included in a study of this nature. In this work we adopt a completely different approach to study ligand-protein interactions accounting explicitly for as many solvent molecules as possible and without the need for a fragmented calculation. Furthermore, we embed our quantum chemical calculations within a molecular dynamics framework that enables a fundamentally fast system for quantum chemical molecular dynamic simulations (QCMD). Central to this new system for QCMD is the tight binding QC system, newly developed in our laboratories, which combined with the MD paradigm results in an ultra-accelerated QCMD method for protein-ligand interaction evaluations. We have applied our newly developed system to the dihydrofolate reductase (DHFR)-methotrexate (MTX) system. We show how the proposed method leads us to new insights into the main interactions that bind MTX to the enzyme, mainly the interaction between the amino group of MTX and Asp27 of DHFR, as well as MTX amino group with Thr113 of DHFR, which have been only elucidated experimentally to date.

Original languageEnglish
Pages (from-to)1-10
Number of pages10
JournalMedicinal Chemistry Research
Volume19
Issue number1
DOIs
Publication statusPublished - Feb 1 2010

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Molecular Dynamics Simulation
Molecular dynamics
Methotrexate
Tetrahydrofolate Dehydrogenase
Ligands
Proteins
Amino Acid Receptors
Molecules
Computer simulation
Enzymes
Water

All Science Journal Classification (ASJC) codes

  • Pharmacology, Toxicology and Pharmaceutics(all)
  • Organic Chemistry

Cite this

Applying ultra-accelerated quantum chemical molecular dynamics technique for the evaluation of ligand protein interactions. / Sahu, Kamlesh Kumar; Ismael, Mohamed; Rauf, Shah Md Abdur; Suzuki, Ai; Sahnoun, Riadh; Koyama, Michihisa; Tsuboi, Hideyuki; Hatakeyama, Nozomu; Endou, Akira; Takaba, Hiromitsu; Deka, Ramesh Chandra; Del Carpio, Carlos A.; Kubo, Momoji; Miyamoto, Akira.

In: Medicinal Chemistry Research, Vol. 19, No. 1, 01.02.2010, p. 1-10.

Research output: Contribution to journalArticle

Sahu, KK, Ismael, M, Rauf, SMA, Suzuki, A, Sahnoun, R, Koyama, M, Tsuboi, H, Hatakeyama, N, Endou, A, Takaba, H, Deka, RC, Del Carpio, CA, Kubo, M & Miyamoto, A 2010, 'Applying ultra-accelerated quantum chemical molecular dynamics technique for the evaluation of ligand protein interactions', Medicinal Chemistry Research, vol. 19, no. 1, pp. 1-10. https://doi.org/10.1007/s00044-009-9167-y
Sahu, Kamlesh Kumar ; Ismael, Mohamed ; Rauf, Shah Md Abdur ; Suzuki, Ai ; Sahnoun, Riadh ; Koyama, Michihisa ; Tsuboi, Hideyuki ; Hatakeyama, Nozomu ; Endou, Akira ; Takaba, Hiromitsu ; Deka, Ramesh Chandra ; Del Carpio, Carlos A. ; Kubo, Momoji ; Miyamoto, Akira. / Applying ultra-accelerated quantum chemical molecular dynamics technique for the evaluation of ligand protein interactions. In: Medicinal Chemistry Research. 2010 ; Vol. 19, No. 1. pp. 1-10.
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