Testing and Validation of a mathematical model of Sildenafil metabolic pathways

Abstract

Biomedical research is multidisciplinary and uses integrated approaches, making use of different experimental models. The experimental models are divided into biological methods, in vivo and in vitro models, and in “silico” methods, based on the use of computers to create the models necessary for carrying out biological studies.

The purpose of this thesis work is to carry out the quantitative validation of a model of metabolic pathways, developed by a student of the University of Pisa in collaboration with Teoresi, for the study of the action of drugs, in the specific case of the active ingredient Sildenafil contained in the drug Viagra. The developed model allows to model the NO/cGMP metabolic pathway leading to smooth muscle relaxation. Following the validation of the model, the second objective of the thesis work is to carry out a molecular docking study in order to verify the possible compatibility of the use of Sildenafil for further clinical applications other than those already approved by the various government bodies. The study of molecular docking is a computational method used to predict the possible interaction between a macromolecule, the receptor, and a small molecule, the ligand, starting from information on their three-dimensional structure. In this thesis work we want to evaluate the possible application of Sildenafil to renal smooth muscle for the treatment of renal ischemia and reperfusion injuries. The model is a model developed in Python, an object-oriented high-level programming language. For the study of molecular docking it was decided to use the Autodock Vina software, an open-source program. The real data used to validate the model were obtained from an analysis of clinical trials, which involved the use of the active ingredient Sildenafil for the treatment of various pathologies, such as erectile dysfunction or pulmonary arterial hypertension.

Objective

The aim of this thesis work is the quantitative validation of the metabolic pathways model previously developed by a collaboration between Teoresi and the University of Pisa, testing the model using data obtained from clinical trials carried out using the active ingredient Sildenafil on patients suffering from various pathologies. Furthermore, through a molecular docking study the possible application of Sildenafil on renal smooth muscle for the treatment of a previously identified pathology, ie renal ischemia/reperfusion injury, will be evaluated.

Research Methodology

Model validation through four experimental tests in Python and molecular docking simulations.

Conclusions

Limitation of the model: at low doses (1.5, 20 mg) it underestimates the concentration trend of the active ingredient Sildenafil, while the concentration trend of cGMP approaches what is reported in the literature, for high doses (50, 60, 100 mg) there is an overestimation of the residual concentration of cGMP, while the model approaches the literature regarding the concentration of Sildenafil. The molecular docking study highlighted Calpaine, but not Caspase-3, as a possible new target molecule of Sildenafil for the treatment of renal disease. Sildenafil fits into the hydrophobic pocket of Calpain as does its chemical inhibitor PD150606. The molecular docking study would seem to confirm what has been reported in the literature: that the activation of Calpains is upstream of the activation of Caspase-3 in apoptosis and that an inhibition of Caspase-3 activity following the intake of Sildenafil is due to an inhibition of Calpaine.

Future developments

In the future, optimization of the model is expected to allow simulation even in pathological conditions and quantitatively validate the model, re-evaluating, for example, the hypotheses and simplifications adopted for the development of the model or implementing further functions to allow the description of the entire metabolism . Furthermore, the identification of additional target molecules for the treatment of renal disease using Sildenafil and a molecular docking study to verify the possible interaction with these molecules are expected.