# _In Silico_ Development of SARS-CoV-2 Non-Covalent Mpro Inhibitors: A Review
## 2 Mpro Inhibitors for SARS-CoV-2
### Molecular Dynamics (MD) in Drug Development
However, while the simulation duration and methodological rigour here are notable, these studies still fall short of validating pharmacokinetic or toxicological profiles, leaving a gap between computational promise and clinical relevance. Figure 12: (**a**) The structure of the most stable compound of Withacoagulin H with the lowest binding energy complex with a coagulin H (W30). (**b**) Values during molecular dynamics simulation of W30 with Mpro, Root mean square deviation (RMSD), radius of gyration (rGyr), intramolecular hydrogen bonds (intraHB), molecular surface area (MoISA), solvent accessible surface area (SASA), polar surface area (PSA). Colour coding: hydrogen bond (green), hydrophobic contacts (purple) and water-bridge (blue). (**c**) Root mean square deviation (RMSD) plot of W30 as a function of time and (**d**) Root mean square fluctuations (RMSF) plot for W30 [66]. Exploring marine-derived natural products has also yielded promising candidates in the search for Mpro inhibitors. Screening 227 terpen, six compounds, including explosides B, stood out for their significant inhibitory potential [73]. MD simulations over 100 ns confirmed the stability of the explosides B-Mpro complex, which demonstrated a binding affinity of \(-51.9\) kcal/mol, far superior to the reference inhibitor, Lopinavir (Figure 13). This comparison adds context to the potency of natural products. Yet, despite robust MD validation over 100 ns, there remains a lack of biological characterisation--no data on cytotoxicity, metabolic stability, or viral inhibition--which limits their utility beyond theoretical models. Similar critiques apply to studies on natural flavonoids, which have emerged as strong contenders in Mpro inhibition. In docking studies and MD simulations, rutin, a flavonoid derivative, demonstrated the lowest predicted binding energy of \(-8.67\) kcal/mol, aligning perfectly with the Mpro binding site (6 LU7) [88]. While this robust simulation stability supports its potential as a therapeutic candidate, real-world factors such as solubility and pharmacokinetics may significantly impact its therapeutic potential. Therefore, including experimental validation, such as cell-based assays or animal models, is essential for bridging the gap between _in silico_ predictions and therapeutic efficacy. Most of these natural compounds suffer from issues like poor bioavailability or low stability, which complicates their transition from computational models to viable ther  
Figure 13: Calculated MM/GBSA binding energy per frame for explosides B (black) and lopinavir (red) with Mpro over 100 ns MD simulations [73]. Licenced under the CC-BY 4.0 licence. \begin{table}
\begin{tabular}{c c c c c c} \hline \hline
**Complexes** & \(\Delta E_{\text{ele}}\)**a** & \(\Delta E_{\text{vdw}}\)**b** & \(\Delta G_{\text{pol}}\)**c** & \(\Delta G_{\text{nonpol}}\)**d** & \(\Delta G_{\text{calc}}\)**e** \\ \hline Z1244904919-Mpro & & & & & & \\ \hline \hline \end{tabular} Note. * Electrostatic (\(\Delta E_{\text{ele}}\)) energy in the gas phase. * Van der Waals (\(\Delta E_{\text{vdw}}\)) energy terms in the gas phase. * Polar (\(\Delta E_{\text{pol}}\)) solvent energies by solving the GB equation. * Calculated binding free energy (\(\Delta G_{\text{calc}}\)), \(\Delta G_{\text{calc}}=\Delta E_{\text{ele}}+\Delta E_{\text{vdw}}+\Delta E_{ \text{pol}}+\Delta E_{\text{nonpol}}\).  
\end{table} 
Table 5: The binding free energies (kcal/mol) components of Z1244904919 and Z1759961356 [88]. peutics. Other chemical scaffolds, such as benzimidazolzoles and benzothiazoles, have also demonstrated promising inhibitory capacities. For example, one benzimidazole-Mpro complex (Comp 1) exhibited a binding free energy of \(-7.3\) kcal/mol [89]. Trajectories for key properties like RMSD, molecular surface area (MolSA), radius of gyration (rGyr), polar surface area (PSA), and solvent-accessible surface area (SASA) confirmed the stability and favourable dynamics of the complex over 100 ns simulations (Figure 14).