## 3 Results and Discussion
### Stochastic Simulation and Knockout Based Analysis
Clinical research has recognized oxidative stress as a significant element that contributes to the advancement and progression of atherosclerosis [65; 66; 67]. To analyze the combination of anti-oxidant treatments together with HMGCR inhibition being a key player in cholesterol synthesis, we excluded from the studied model the following transitions: \(t_{39}\) (HMGCR activation), \(t_{46}\) (reaction catalyzed by HMGCR phosphatase), \(t_{4}\) (increasing activity by SREBP-2), and \(t_{117}\) (oxidation). As a result, we could observe the atherosclerosis restraint (see Figure 6C). At the same time, the processes mediated by HDL remained unaffected (see Figure 7C). **Scenario 1C**. _Modulating the activity of phosphoprotein phosphatase inhibitor-1 (PPI-1)._  
When phosphorylated by PKA, PPI-1 (phosphoprotein phosphatase inhibitor-1) can act as an inhibitor for various phosphatases. In the context of HMGCR regulation, it inhibits PP-2A (also known as HMGCR phosphatase), which removes phosphates from AMPK and HMGCR, and thus maintains HMGCR in the inactive state [68; 69]. To examine the effect of PPI-1 inhibition, the transitions \(t_{34}\) (dephosphorylation), \(t_{44}\) (PPI 1 OH activation), and \(t_{62}\) (processes increasing PPI activity) were removed from the analyzed model. Upon analyzing the results obtained, we observed that the level of foamy cell formation was only slightly affected (see Figure 6D). In contrast, the level of HDL-3 remained unchanged (see Figure 7D). Therefore, the anti-oxidation treatment was combined with PPI-1 inhibition through additionally blocking transition \(t_{117}\) (oxidation), which led to complete atherosclerosis development attenuation (see Figure 6E). At the same time, HDL-mediated processes stayed unaffected (see Figure 7E). **Scenario 2**. _Targeting microsomal triglyceride transfer protein (MTTP)._  
Figure 7: The outcomes of the in silico knockout analysis performed under Scenario 1, for place \(p_{53}\) (HDL-3 cholesterol CE in blood). **(A)** The model has been simulated without anything knocked out. **(B)** The effect of excluding the following transitions: \(t_{39}\), \(t_{46}\), and \(t_{4}\) (Scenario 1A). **(C)** The effect of excluding the following transitions: \(t_{39}\), \(t_{46}\), \(t_{4}\), and \(t_{117}\) (Scenario 1B). **(D)** The effect of excluding the following transitions: \(t_{34}\), \(t_{45}\), and \(t_{62}\) (Scenario 1C). **(E)** The effect of excluding the following transitions: \(t_{34}\), \(t_{45}\), \(t_{62}\), and \(t_{117}\) (Scenario 1C). Microsomal triglyceride transfer protein (MTTP) is a crucial protein involved in the formation and release of apolipoprotein B lipoproteins. It is responsible for the transfer of lipids from the site of their synthesis into the lumen during the assembly of VLDLs. Its inhibition is associated with decreased TAG and LDL-C and can be used as a plasma lipid-lowering drug [70; 71]. In order to assess the impact of MTTP knockout on the progression and development of atherosclerosis, transition \(t_{110}\) (MTTP synthesis) was excluded from the studied system. As depicted in Figure 8B, the foamy cell formation process was not influenced in a significant way, and as in previous scenarios, the HDL-3 levels stayed intact (see Figure 9B). The endogenous biosynthesis of cholesterol also remained unaltered (see Figure 10B). Thus, the anti-oxidation treatment was combined with MTTP inhibition by additionally blocking transition \(t_{117}\) (oxidation). It resulted in complete atherosclerosis development attenuation (see Figure 8C), while endogenous cholesterol biosynthesis (see Figure 10C and HDL-mediated processes remained unaffected (see Figure 9C).