Binding free energies and energy components of protein-CAP complexes calculated using the MM/PBSA approach.
| Complex | Average binding energy (kcal/mol) | ||||
|---|---|---|---|---|---|
| ΔEvdw | ΔEele | ΔGpol | ΔGnonpol | aΔGbind | |
| ESR1 | –48.69 | –6.57 | 20.32 | –4.00 | –38.94 ± 3.38 |
| HMOX1 | –33.73 | –14.06 | 25.47 | –4.50 | –26.83 ± 4.99 |
| NGF | –36.58 | –8.60 | 22.82 | –4.10 | –26.45 ± 3.93 |
| SIRT1 | –38.77 | –7.80 | 24.68 | –4.65 | –26.54 ± 7.76 |
aΔGbind represents the total binding free energy calculated as the sum of all individual energy components (ΔGbind = ΔEvdw + ΔEele + ΔGpol + ΔGnonpol), and expressed as mean ± standard deviation. CAP: capsaicin; MM/PBSA: Molecular Mechanics Poisson-Boltzmann Surface Area; ESR1: estrogen receptor 1; HMOX1: heme oxygenase 1; NGF: nerve growth factor; SIRT1: sirtuin 1.
The supplementary tables for this article are available at: https://www.explorationpub.com/uploads/Article/file/1004132_sup_1.pdf.
Luis Antonio Ramirez-Contreras (CVU: 1319432), Luis Alfonso Hernández-Villaseñor (CVU: 629990), and Salvador Hernández-Estrada (CVU: 1319414) gratefully acknowledge the financial support for the scholarship from SECIHTI-México for Doctoral studies in the Biociencias program from the Centro Universitario de Los Altos (CUALTOS) of the University of Guadalajara. Andrés Frausto de Alba (CVU: 1272002) gratefully acknowledges the financial support for the scholarship from SECIHTI-México for Doctoral studies in the Ciencia y Tecnología program from the Centro Universitario de Los Lagos (CULAGOS) of the University of Guadalajara. Thanks to the Instituto de Investigación en Ciencias Médicas from CUALTOS for the infrastructure support, the Molecular Modelling and Materials area from Centro Universitario de Los Lagos (CULAGOS), and the University of Guadalajara’s Data Analysis and Supercomputing Centre (CADS) for the computational and technical support provided through the Leo Atrox supercomputer.
LARC: Conceptualization, Methodology, Software, Formal analysis, Investigation, Data curation, Writing—original draft, Writing—review & editing, Visualization. LMAE: Conceptualization, Validation, Investigation, Resources, Writing—original draft, Writing—review & editing, Visualization, Supervision. SHE: Validation, Investigation, Writing—review & editing, Visualization. LAHV: Validation, Investigation, Writing—review & editing, Visualization. JMSJ: Validation, Writing—original draft, Writing—review & editing, Visualization, Supervision. LHH: Validation, Investigation, Resources, Visualization, Supervision. GCH: Validation, Investigation, Resources, Visualization, Supervision. AFdA: Methodology, Software, Validation, Formal analysis, Investigation, Data curation, Writing—original draft, Writing—review & editing, Visualization. All authors have read and agreed to the published version of the manuscript.
The authors declare that they have no conflicts of interest.
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Data related to capsaicin targets, Parkinson’s disease targets, and Alzheimer’s disease targets, among other data, supporting the findings of this study are available from the corresponding author upon reasonable request.
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