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Janakiraman V, Sudhan M, Ahmad SF, Attia SM, Emran TB, Ahmed SSSJ. Molecular Docking, Quantum Mechanics and Molecular Dynamics Simulation of Anti-CAD Drugs Against High-Risk Xanthine Dehydrogenase Variants Associated with Oxidative Stress Pathways. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2024; 23:1109-1128. [DOI: 10.1142/s2737416524500315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2025]
Abstract
Xanthine dehydrogenase (XDH) contributes significantly to generating reactive oxygen species in coronary artery disease (CAD). XDH has been proposed as a therapeutic target, but its genetic variants could affect protein structure and drug response. We aimed to assess protein structure modification occur due to genetic variants and to screen 215 CAD drugs for their utility in personalized CAD treatment against the XDH variants. A series of computational methods were implemented to identify pathogenic variants that cause XDH structure instability localized at the con served regions contributing to functional significance. Then, the XDH structures with the pathogenic variants were modeled using two different approaches to select the best models for docking with the CAD drugs. Finally, the stability of the docked complexes and their ability to transfer electrons were evaluated using molecular dynamics (MD) simulations and quantum mechanics/molecular mechanics (QM/MM) calculation. Among 751 variants examined; R149C and Q919R showed high pathogenicity, localized in conserved regions could alter protein structure and function. Further, docking of CAD drugs against XDH (native, R149C and Q919R) showed vericiguat with higher affinity, ranging from −7.95 kcal/mol to −10.41 kcal/mol, than the well-known XDH inhibitor (febuxostat, −5.73 kcal/mol to −8.35 kcal/mol). This indicates that vericiguat will be effective in CAD treatment, regardless of the XDH variants. Additionally, MD simulation and QM/MM confirmed vericiguat stability and electron transfer ability to form hydrogen bonds with the XDH protein. In conclusion, vericiguat will be beneficial for the personalized treatment of CAD by inhibiting XDH variants. Additional clinical studies are necessary to confirm our findings.
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Affiliation(s)
- V. Janakiraman
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam 603103, Tamil Nadu, India
| | - M. Sudhan
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam 603103, Tamil Nadu, India
| | - Sheikh F. Ahmad
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Sabry M. Attia
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Talha Bin Emran
- Department of Pathology and Laboratory Medicine, Warren Alpert Medical School, Brown University, Providence, RI 02912, USA
- Legorreta Cancer Center, Brown University, Providence, RI 02912, USA
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka 1207, Bangladesh
| | - Shiek S. S. J. Ahmed
- Drug Discovery and Multi-omics Laboratory, Faculty of Allied Health Sciences, Chettinad Academy of Research and Education, Chettinad Hospital and Research Institute, Kelambakkam 603103, Tamil Nadu, India
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Campos-López B, Meza-Meza MR, Pesqueda-Cendejas K, Ruiz-Ballesteros AI, Rivera-Escoto M, Vargas-Morales JM, Parra-Rojas I, Mora-García PE, Vizmanos B, Montoya-Buelna M, Cerpa-Cruz S, De la Cruz-Mosso U. Nutritional, biochemical, and clinical determinants of hyperuricemia in systemic lupus erythematosus patients: Relationship with clinical and renal disease activity. Lupus 2023; 32:270-283. [PMID: 36562214 DOI: 10.1177/09612033221146923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Systemic lupus erythematosus (SLE) is the prototypical autoimmune disease considered as an independent risk factor for mortality by cardiovascular disease. Currently, uric acid is described as a novel biomarker associated with cardiometabolic risk. However, nutritional and serum determinants that influence hyperuricemia development in autoimmune diseases have not been fully elucidated. This study aimed to assess the nutritional, biochemical, and cardiometabolic determinants of hyperuricemia and its relationship with clinical variables in SLE patients. A cross-sectional study was conducted in 167 SLE patients and 195 control subjects (CS). Nutrient intake, anthropometry, biochemical, and cardiometabolic indexes were evaluated. In SLE patients, adequate protein (OR = 0.4; p = 0.04) and carbohydrate (OR = 0.2; p = 0.01) intakes were associated with a lower risk of hyperuricemia. SLE patients with hyperuricemia presented a higher risk of clinical (OR = 2.2; p = 0.03) and renal activity (OR = 3.4; p < 0.01), as well as triglycerides ≥150 mg/dL (OR = 3.6; p < 0.01), hs-CRP ≥1 mg/L (OR = 3.1; p < 0.01), Kannel score ≥3 (OR = 2.5; p = 0.02), and BMI ≥25 kg/m2 (OR = 2.2; p = 0.02). Oppositely, serum levels of HDL-C ≥40 mg/dL (OR = 0.2; p < 0.01) were associated with a lower risk of hyperuricemia. According to the pharmacotherapy administered, prednisone treatment was associated with a high risk of hyperuricemia (OR = 4.7; p < 0.001). In contrast, the hydroxychloroquine treatment was associated with a lower risk of hyperuricemia (OR = 0.4; p = 0.02). In conclusion, SLE patients with hyperuricemia presented a high risk of clinical and renal activity as well as worse cardiometabolic status. Notably, an adequate intake of protein, carbohydrates, healthy HDL-C serum levels, and hydroxychloroquine treatment could be determinants of lower risk of hyperuricemia.
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Affiliation(s)
- Bertha Campos-López
- Red de Inmunonutrición y Genómica Nutricional en las Enfermedades Autoinmunes, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico.,Instituto de Neurociencias Traslacionales, Departamento de Neurociencias, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico
| | - Mónica R Meza-Meza
- Red de Inmunonutrición y Genómica Nutricional en las Enfermedades Autoinmunes, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico.,Instituto de Neurociencias Traslacionales, Departamento de Neurociencias, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico
| | - Karen Pesqueda-Cendejas
- Red de Inmunonutrición y Genómica Nutricional en las Enfermedades Autoinmunes, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico.,Instituto de Neurociencias Traslacionales, Departamento de Neurociencias, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico
| | - Adolfo I Ruiz-Ballesteros
- Red de Inmunonutrición y Genómica Nutricional en las Enfermedades Autoinmunes, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico.,Instituto de Neurociencias Traslacionales, Departamento de Neurociencias, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico
| | - Melissa Rivera-Escoto
- Red de Inmunonutrición y Genómica Nutricional en las Enfermedades Autoinmunes, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico.,Instituto de Neurociencias Traslacionales, Departamento de Neurociencias, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico
| | - Juan M Vargas-Morales
- Red de Inmunonutrición y Genómica Nutricional en las Enfermedades Autoinmunes, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico.,Facultad de Ciencias Químicas, Universidad Autónoma de San Luis Potosí, San Luis Potosí, Mexico
| | - Isela Parra-Rojas
- Red de Inmunonutrición y Genómica Nutricional en las Enfermedades Autoinmunes, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico.,Laboratorio de Investigación en Obesidad y Diabetes, Facultad de Ciencias Químico-Biológicas, Universidad Autónoma de Guerrero, Chilpancingo de los Bravo, Mexico
| | - Paulina E Mora-García
- Red de Inmunonutrición y Genómica Nutricional en las Enfermedades Autoinmunes, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico.,Instituto de Neurociencias Traslacionales, Departamento de Neurociencias, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico
| | - Barbara Vizmanos
- Red de Inmunonutrición y Genómica Nutricional en las Enfermedades Autoinmunes, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico
| | - Margarita Montoya-Buelna
- Red de Inmunonutrición y Genómica Nutricional en las Enfermedades Autoinmunes, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico.,Laboratorio de Inmunología, Departamento de Fisiología, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico
| | - Sergio Cerpa-Cruz
- Departamento de Reumatología, O. P. D. Hospital Civil de Guadalajara Fray Antonio Alcalde, Guadalajara, Mexico
| | - Ulises De la Cruz-Mosso
- Red de Inmunonutrición y Genómica Nutricional en las Enfermedades Autoinmunes, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico.,Instituto de Neurociencias Traslacionales, Departamento de Neurociencias, Centro Universitario de Ciencias de la Salud, 27802Universidad de Guadalajara, Guadalajara, Mexico
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