SARS-Cov-2 RNA- dependent polymerase binding studies
The 14 drug compounds tested on nsp12 protein via molecular docking studies. In Fig. 1 we can see the crystal structure of the protein together with three drug molecules (chloroquine, remdesivir and saquinavir). SARS-Cov-2 RNA depended polymerase consisted by four chains A, B, C and D. All the tested compounds interacted on A chain but in different sides of the protein. For example, chloroquine seems to prefer the outer structure of the protein, while remdesivir binds in the inner pocket of the protein. At the same figure we can also see the amino acid residues of the A chain that interacting with the three molecules. Remdesivir, interacts via hydrogen bonding with TRP-617, TYR-619, ASP 760, ASP 761, amino acids while interacts with van der Waals forces with the amino acids TYR 455, ARG 553, ASP 618, TYR 619, LYS 621 and ASP 760. Hydrogen bonding interactions are considered hydrophilic interactions while van der Waals forces are considered hydrophobic interactions. Saquinavir interacts with the protein with only two hydrogen bonds with SER 318 and PHE 321. Regarding van der Waals forces, Saquinavir interacts with TYR 265, PHE 321, PRO322, PRO 323, ARG 349 and PRO 461. The amino acids residue is on less than 5 Angstrom distance of the molecules. We are explaining the interactions of Remdesivir and Saquinavir, because they gave the lowest energy values in molecular interactions with the protein, which means that these molecules can form stable complexes with the specific protein and have better binding affinity. Our docking results agree with the predicted pharmacological properties that we are going to see later in this article. Remdesivir is more hydrophilic than hydrophobic molecule while Saquinavir have less solubility in polar environments. The data of the amino acid residues energies of the rest 12 molecules can be found in a table in supplementary material. Additionally, in Table 1 we can find the binding scores (binding energies in kcal/mol) of the 14 drugs that presented in this study. In Table 2 we can observe how this energy distributes in hydrogen bonds, van der Waals forces and electrostatic interactions. Interestingly only Benidipine and Famotidine interacting electrostatically with this protein and the structural activity of molecules that interact electrostatically with the specific protein could be evaluated in another study. Except of the binding energies of the molecules, in Table 1 we can find information on the current uses of the drugs and their current status regarding Covid-19 disease. It seems that our findings are valid as Remdesivir continues with Phase (III) clinical trials. On the other hand, to the best of our knowledge Saquinavir is not participating in any clinical trial and our opinion based on our findings is that it is a promising candidate.
Remdesivir and Saquinavir Computational Studies
Based on the molecular docking results, we wanted to study further the structures of Remdesivir and Saquinavir in order to try to find a correlation between structure and binding activity for these two molecules. For that reason, we employ computational chemistry studies. DFT reveals the values of the energy difference between HOMO and LUMO as well as the highest occupied molecular orbital (EHOMO) and lowest unoccupied molecular orbital (ELUMO) energies which plays a very important role in stability and reactivity of molecules. The EHOMO energies of molecules show the molecule’s ability to give electrons. On the other hand, ELUMO characterizes the ability of the compound to accept electrons. The energy gap (Δgap of Remdesivir and Saquinavir are close but Remdesivir has a value of 20.903 ev while Saquinavir a value of 18.037 ev. The electronic correlation effects play an essential role in the stability of these type of systems, and therefore, it will affect the equilibrium distances and the interaction energies. Electronegativity (χ) is a measure of the power of an atom to attract a bonding pair of electrons. According to this theorem is expressed as follows. Based on equation:
larger Δgap always indicates lower chemical reactivity and higher kinetic stability of the investigated species. The chemical reactivity of molecules is caused by the simultaneous effect of different parameters. So, we can say that Saquinavir is a little bit more chemical reactive and has lower kinetic stability than Remdesivir. In Table 3 we can see the calculated values based on DFT studies. Detailed calculated values can be found in supplementary material.
The predicted pharmacological properties of these two candidate molecules are depicted in Table 4. Solubility results of the molecules agreed with docking studies saying that Saquinavir is less polar molecule than Remdesivir. The interesting fact here though is that based on Cramer rules both the molecules are categorised as class (III) toxic which means that their side effects should not overpass. Thus, a more detailed evaluation on the toxicity of Remdesivir and Saquinavir should be done. These two drugs are FDA approved for other conditions but nobody could guaranty the interactions and safety use for that disease (Covid-19) without further studies.