Academic Journal
Inverse Mixed-Solvent Molecular Dynamics for Visualization of the Residue Interaction Profile of Molecular Probes
| العنوان: | Inverse Mixed-Solvent Molecular Dynamics for Visualization of the Residue Interaction Profile of Molecular Probes |
|---|---|
| المؤلفون: | Keisuke Yanagisawa, Ryunosuke Yoshino, Genki Kudo, Takatsugu Hirokawa |
| المصدر: | International Journal of Molecular Sciences; Volume 23; Issue 9; Pages: 4749 |
| بيانات النشر: | Multidisciplinary Digital Publishing Institute |
| سنة النشر: | 2022 |
| المجموعة: | MDPI Open Access Publishing |
| مصطلحات موضوعية: | mixed-solvent molecular dynamics, interaction pattern analysis, residue interaction profile, visualization |
| جغرافية الموضوع: | agris |
| الوصف: | To ensure efficiency in discovery and development, the application of computational technology is essential. Although virtual screening techniques are widely applied in the early stages of drug discovery research, the computational methods used in lead optimization to improve activity and reduce the toxicity of compounds are still evolving. In this study, we propose a method to construct the residue interaction profile of the chemical structure used in the lead optimization by performing “inverse” mixed-solvent molecular dynamics (MSMD) simulation. Contrary to constructing a protein-based, atom interaction profile, we constructed a probe-based, protein residue interaction profile using MSMD trajectories. It provides us the profile of the preferred protein environments of probes without co-crystallized structures. We assessed the method using three probes: benzamidine, catechol, and benzene. As a result, the residue interaction profile of each probe obtained by MSMD was a reasonable physicochemical description of the general non-covalent interaction. Moreover, comparison with the X-ray structure containing each probe as a ligand shows that the map of the interaction profile matches the arrangement of amino acid residues in the X-ray structure. |
| نوع الوثيقة: | text |
| وصف الملف: | application/pdf |
| اللغة: | English |
| Relation: | Molecular Informatics; https://dx.doi.org/10.3390/ijms23094749 |
| DOI: | 10.3390/ijms23094749 |
| الاتاحة: | https://doi.org/10.3390/ijms23094749 |
| Rights: | https://creativecommons.org/licenses/by/4.0/ |
| رقم الانضمام: | edsbas.E62FEBC0 |
| قاعدة البيانات: | BASE |
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