دورية أكاديمية
Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution.
| العنوان: | Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution. |
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| المؤلفون: | Nguyen HL; Life Science Lab, Institute for Computational Science and Technology, QuangTrung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 729110, Vietnam.; Ho Chi Minh City University of Technology (HCMUT), Ho Chi Minh City 740500, Vietnam.; Vietnam National University, Ho Chi Minh City 71300, Vietnam., Thai NQ; Life Science Lab, Institute for Computational Science and Technology, QuangTrung Software City, Tan Chanh Hiep Ward, District 12, Ho Chi Minh City 729110, Vietnam.; Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap 81100, Vietnam., Li MS; Institute of Physics, Polish Academy of Sciences, Al. Lotnikow 32/46, Warsaw 02-668, Poland. |
| المصدر: | Journal of chemical theory and computation [J Chem Theory Comput] 2022 Jun 14; Vol. 18 (6), pp. 3860-3872. Date of Electronic Publication: 2022 May 05. |
| نوع المنشور: | Journal Article |
| اللغة: | English |
| بيانات الدورية: | Publisher: American Chemical Society Country of Publication: United States NLM ID: 101232704 Publication Model: Print-Electronic Cited Medium: Internet ISSN: 1549-9626 (Electronic) Linking ISSN: 15499618 NLM ISO Abbreviation: J Chem Theory Comput Subsets: MEDLINE |
| أسماء مطبوعة: | Original Publication: Washington, D.C. : American Chemical Society, c2005- |
| مواضيع طبية MeSH: | Acetylcholinesterase*/chemistry , Camphor 5-Monooxygenase*/chemistry, Binding Sites ; Ligands ; Molecular Dynamics Simulation ; Protein Binding |
| مستخلص: | Steered molecular dynamics (SMD) simulation is a powerful method in computer-aided drug design as it can be used to access the relative binding affinity with high precision but with low computational cost. The success of SMD depends on the choice of the direction along which the ligand is pulled from the receptor-binding site. In most simulations, the unidirectional pathway was used, but in some cases, this choice resulted in the ligand colliding with the complex surface of the exit tunnel. To overcome this difficulty, several variants of SMD with multidirectional pulling have been proposed, but they are not completely devoid of disadvantages. Here, we have proposed to determine the direction of pulling with a simple scoring function that minimizes the receptor-ligand interaction, and an optimization algorithm called differential evolution is used for energy minimization. The effectiveness of our protocol was demonstrated by finding expulsion pathways of Huperzine A and camphor from the binding site of Torpedo California acetylcholinesterase and P450cam proteins, respectively, and comparing them with the previous results obtained using memetic sampling and random acceleration molecular dynamics. In addition, by applying this protocol to a set of ligands bound with LSD1 (lysine specific demethylase 1), we obtained a much higher correlation between the work of pulling force and experimental data on the inhibition constant IC50 compared to that obtained using the unidirectional approach based on minimal steric hindrance. |
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| المشرفين على المادة: | 0 (Ligands) EC 1.14.15.1 (Camphor 5-Monooxygenase) EC 3.1.1.7 (Acetylcholinesterase) |
| تواريخ الأحداث: | Date Created: 20220505 Date Completed: 20220615 Latest Revision: 20220716 |
| رمز التحديث: | 20240628 |
| مُعرف محوري في PubMed: | PMC9202309 |
| DOI: | 10.1021/acs.jctc.1c01158 |
| PMID: | 35512104 |
| قاعدة البيانات: | MEDLINE |
Find this issue from the American Chemical Society | تدمد: | 1549-9626 |
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| DOI: | 10.1021/acs.jctc.1c01158 |