## 3 Results
### Molecular Dynamics Simulations  
Based on the docking results and confirmation of favorable ADME properties, we selected compounds L1 and L2 for further in-depth analysis through molecular dynamics simulations. We began by calculating the variation in the overall stability of the three systems' backbone atoms using the RMSD (nm) measurements. The root mean square deviation values of the created systems were compared with the reference complex (HSP90_MEY) \begin{table}
\begin{tabular}{c c c c c c c} \hline \hline
**Comp.** & **L1** & **L2** & **L3** & **L4** & **L5** & **MEY** \\ \hline \multicolumn{8}{c}{Absorption} \\ \hline Caco-2 Permeability & \(-5.108\) & \(-5.030\) & \(-4.849\) & \(-4.989\) & \(-4.815\) & \(-5.856\) \\ \hline MDCK Permeability & \(1.8\times 10^{-5}\) & \(2.3\times 10^{-5}\) & \(1.2\times 10^{-5}\) & \(9.2\times 10^{-6}\) & \(2.7\times 10^{-5}\) & \(1.3\times 10^{-5}\) \\ \hline Pgp-inhibitor & poor & excellent & excellent & medium & excellent & medium \\ \hline HIA & excellent & excellent & excellent & excellent & excellent & medium \\ \hline F20\% & poor & poor & excellent & excellent & poor & excellent \\ \hline \multicolumn{8}{c}{Distribution} \\ \hline PPB & 97.989\% & 98.221\% & 95.037\% & 98.178\% & 95.329\% & 98.622\% \\ \hline VD L/Kg & 0.501 & 0.196 & 0.781 & 4.954 & 0.424 & 0.429 \\ \hline BBB Penetration & excellent & excellent & medium & excellent & excellent & excellent \\ \hline \textless{}0.3; excellent, 0.3-0.7; medium, 0.7–1.0; poor. & & & & & \\ \hline \hline \end{tabular}
\end{table} 
Table 3: In silico prediction of absorption and distribution of the top lead compounds. over 300 ns of simulation. Figure 4 depicts the RMSD profile for each investigated system. The RMSD description of the HSP90_L1 complex was substantially more stable, with an average RMSD of 0.1219 nm, compared to the reference complex (with an average RMSD of 0.413 nm). At the molecular level, compound L1 established a very stable complex with the HSP90 receptor, allowing it to selectively inhibit the protein's essential and biological functions. In addition, the average RMSD value of the HSP90_L1 complex was 0.288 nm. This measurement demonstrates that compound L2 forms a less stable complex with the active site of HSP90 than compound L1, although it is more stable than the reference drug (MEY). Moreover, The RMSD measures how a protein's backbone changes from its initial to its final structural state. Multiple studies have consistently found RMSD values ranging between 0 and 0.3 nm in their analyses of molecular dynamics simulations. Ultimately, the findings suggest that compounds L1 and L2 can be promising selective drugs in oncology. The average values of the various features acquired over a 300 ns period by molecular dynamics simulation are shown in Table 4. Furthermore, when comparing the reference system to the detected compounds (L1 and L2) during binding, the average RMSF values of all residues were almost the same. Each system's RMSF profile showed variations from its original structures, pointing to minor dynamic alterations, as can be seen in Figure 5. Moreover, all of the systems' variations matched those of the MEY medication, demonstrating the structural stability of the systems being investigated. These suggested chemicals hold promise as possible candidates for the development of targeted and efficient treatments for incurable diseases, given the consistent results of RMSF and RMSD investigations. \begin{table}
\begin{tabular}{c c c c} \hline
**System** & **HSP90\_L1** & **HSP90\_L1** & **HSP90\_MEY** \\ \hline RMSD (nm) & 0.219 & 0.288 & 0.413 \\ \hline RMSF (nm) & 0.164 & 0.175 & 0.164 \\ \hline Rg (nm) & 1.724 & 1.739 & 1.707 \\ \hline SASA (nm\({}^{2}\)) & 112.311 & 113.561 & 111.869 \\ \hline \end{tabular}
\end{table} 
Table 4: Mean values of various features from 300 ns MD simulations. Figure 4: Analysis of root mean square deviation for the backbone atoms and complexes of HSP90. HSP90's structural compactness was assessed using Rg.