1
|
González-Paz L, Lossada C, Hurtado-León ML, Vera-Villalobos J, Paz JL, Marrero-Ponce Y, Martinez-Rios F, Alvarado Y. Biophysical Analysis of Potential Inhibitors of SARS-CoV-2 Cell Recognition and Their Effect on Viral Dynamics in Different Cell Types: A Computational Prediction from In Vitro Experimental Data. ACS OMEGA 2024; 9:8923-8939. [PMID: 38434903 PMCID: PMC10905729 DOI: 10.1021/acsomega.3c06968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 01/20/2024] [Accepted: 02/05/2024] [Indexed: 03/05/2024]
Abstract
Recent reports have suggested that the susceptibility of cells to SARS-CoV-2 infection can be influenced by various proteins that potentially act as receptors for the virus. To investigate this further, we conducted simulations of viral dynamics using different cellular systems (Vero E6, HeLa, HEK293, and CaLu3) in the presence and absence of drugs (anthelmintic, ARBs, anticoagulant, serine protease inhibitor, antimalarials, and NSAID) that have been shown to impact cellular recognition by the spike protein based on experimental data. Our simulations revealed that the susceptibility of the simulated cell systems to SARS-CoV-2 infection was similar across all tested systems. Notably, CaLu3 cells exhibited the highest susceptibility to SARS-CoV-2 infection, potentially due to the presence of receptors other than ACE2, which may account for a significant portion of the observed susceptibility. Throughout the study, all tested compounds showed thermodynamically favorable and stable binding to the spike protein. Among the tested compounds, the anticoagulant nafamostat demonstrated the most favorable characteristics in terms of thermodynamics, kinetics, theoretical antiviral activity, and potential safety (toxicity) in relation to SARS-CoV-2 spike protein-mediated infections in the tested cell lines. This study provides mathematical and bioinformatic models that can aid in the identification of optimal cell lines for compound evaluation and detection, particularly in studies focused on repurposed drugs and their mechanisms of action. It is important to note that these observations should be experimentally validated, and this research is expected to inspire future quantitative experiments.
Collapse
Affiliation(s)
- Lenin González-Paz
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB),Instituto Venezolano de Investigaciones
Científicas (IVIC),Maracaibo, Zulia 4001, República Bolivariana de Venezuela
| | - Carla Lossada
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Biocomputación
(LB),Instituto Venezolano de Investigaciones
Científicas (IVIC),Maracaibo, Zulia 4001, República Bolivariana de Venezuela
| | - María Laura Hurtado-León
- Facultad
Experimental de Ciencias (FEC). Departamento de Biología. Laboratorio
de Genética y Biología Molecular (LGBM),Universidad del Zulia (LUZ),Maracaibo 4001, República Bolivariana de Venezuela
| | - Joan Vera-Villalobos
- Facultad
de Ciencias Naturales y Matemáticas, Departamento de Química
y Ciencias Ambientales, Laboratorio de Análisis Químico
Instrumental (LAQUINS), Escuela Superior
Politécnica del Litoral, Guayaquil EC090112, Ecuador
| | - José L. Paz
- Departamento
Académico de Química Inorgánica, Facultad de
Química e Ingeniería Química, Universidad Nacional Mayor de San Marcos. Cercado de Lima, Lima 15081, Perú
| | - Yovani Marrero-Ponce
- Grupo
de Medicina Molecular y Traslacional (MeM&T), Colegio de Ciencias
de la Salud (COCSA), Escuela de Medicina, Edificio de Especialidades
Médicas; e Instituto de Simulación Computacional (ISC-USFQ),
Diego de Robles y vía Interoceánica, Universidad San Francisco de Quito (USFQ), Quito, Pichincha 170157, Ecuador
| | - Felix Martinez-Rios
- Universidad
Panamericana. Facultad de Ingeniería. Augusto Rodin 498, Ciudad de México 03920, México
| | - Ysaías.
J. Alvarado
- Centro
de Biomedicina Molecular (CBM). Laboratorio de Química Biofísica
Teórica y Experimental (LQBTE),Instituto
Venezolano de Investigaciones Científicas (IVIC),Maracaibo, Zulia 4001, República Bolivariana
de Venezuela
| |
Collapse
|
2
|
Lin Y, Enyoh CE, Wang Q, Lu S, Zhang W, Xiao K, Zhou S, Kaneko T, Seguchi A, Wang W, Guo Y. Novel Approaches for Inhibiting the Indoor Allergen Der f 2 Excreted from House Dust Mites by Todomatsu Oil Produced from Woodland Residues. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:10881. [PMID: 36078598 PMCID: PMC9517791 DOI: 10.3390/ijerph191710881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/20/2022] [Accepted: 08/28/2022] [Indexed: 06/15/2023]
Abstract
House dust mite (HDM) is a globally ubiquitous domestic cause of allergic diseases. There is a pressing demand to discover efficient, harmless, and eco-friendly natural extracts to inhibit HDM allergens that are more likely to trigger allergies and challenging to be prevented entirely. This study, therefore, is aimed at assessing the inhibition of the allergenicity of major HDM allergen Der f 2 by todomatsu oil extracted from residues of Abies Sachalinensis. The inhibition was investigated experimentally (using enzyme-linked immunosorbent assay (ELISA), surface plasmon resonance (SPR), and sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE)) and in silico using molecular docking. The results showed that todomatsu oil inhibits the allergenicity of Der f 2 by reducing its amount instead of the IgG binding capacity of a single protein. Moreover, the compounds in todomatsu oil bind to Der f 2 via alkyl hydrophobic interactions. Notably, most compounds interact with the hydrophobic amino acids of Der f 2, and seven substances interact with CYS27. Contrarily, the principal compounds fail to attach to the amino acids forming the IgG epitope in Der f 2. Interestingly, chemical components with the lowest relative percentages in todomatsu oil show high-affinity values on Der f 2, especially β-maaliene (-8.0 kcal/mol). In conclusion, todomatsu oil has been proven in vitro as a potential effective public health strategy to inhibit the allergenicity of Der f 2.
Collapse
Affiliation(s)
- Yichun Lin
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Christian Ebere Enyoh
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Qingyue Wang
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Senlin Lu
- School of Environmental and Chemical Engineering, Shanghai University, 99 Shangdalu, Baoshan District, Shanghai 200444, China
| | - Wei Zhang
- School of Life Sciences, Shanghai University, 99 Shangdalu, Baoshan District, Shanghai 200444, China
| | - Kai Xiao
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Shumin Zhou
- School of Life Sciences, Shanghai University, 99 Shangdalu, Baoshan District, Shanghai 200444, China
| | - Toshihiko Kaneko
- Japan Aroma Laboratory Co., Ltd. (S. T. Corporation), Tokyo 161-8540, Japan
| | - Akifumi Seguchi
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Weiqian Wang
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Yue Guo
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| |
Collapse
|
3
|
Abdel-Mageed W, Al-Wahaibi L, Rehman M, M. Al-Saleem M, Basudan O, El-Gamal A, AlAjmi M, Backheet E, Khalifa A. Phenolics from the heartwood of Tecoma mollis as potential inhibitors of COVID-19 virus main protease and spike proteins: An In silico study. Pharmacogn Mag 2021. [DOI: 10.4103/pm.pm_35_21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|