In the current study, four nucleotide inhibitors are tested against both host-cell (Inosine monophosphate dehydrogenase) and pathogen's proteins (RNA-dependent RNA polymerase). These proteins proved their effectiveness as drug targets (6, 13, 35, 36). Figure 1 shows the 2D structures of the four nucleotide inhibitors which are Thuringiensin derivatives (CID: 99213, 194147, 20056441, and 102074352) and the positive control drugs (Sofosbuvir and Remdesivir). The FDA approves these drugs against RNA viruses such as Hepatitis C Virus, Ebola virus, and SARS-CoV-2 (37–41). The four Thuringiensin derivatives are based on the nucleotide adenosine (A), where the added moieties are present at the 5' position of the ribose ring. On the other hand, the positive controls drugs (remdesivir and Sofosbuvir) are adenosine triphosphate modified at position 1' of the ribose (C ≡ N) and uridine derivative modified at position 1' of the ribose (F, methyl), respectively.
Binding affinities of the nucleotide inhibitors against the pathogenic proteins
As shown in Fig. 2, the average binding affinities of the four nucleotide inhibitors (blue columns) (CID: 99213, 194147, 20056441, and 102074352) against SARS-CoV-2 RdRp (A), Rhizopus oryzae RdRp (B), and the human IMPDH (C) are in the same range of the positive control drugs. In Fig. 2, the error bars represent the standard deviations. Red columns in Fig. 2 represent the positive control drugs (Sofosbuvir and Remdesivir). The docking trials are performed on different conformations of the RdRp proteins generated from the 100 ns MDS runs, while Each conformation resembles a cluster from the trajectories. The MDS's role was to equilibrate the protein systems and ensure different possible conformations during the simulation period.
The average binding affinity for the four nucleotide inhibitors lies between − 6.84 kcal/mol (194147 versus SARS-CoV-2 RdRp) and − 9.8 kcal/mol (102074352 versus human IMPDH). For the SARS-CoV-2 RdRp, the average binding affinity for the four nucleotide inhibitors is -7.24 kcal/mol, while the average binding affinities of sofosbuvir and remdesivir against SARS-CoV-2 RdRp are − 7.4 and − 7.3 kcal/mol, respectively. Additionally, the average binding affinity of the four nucleotide inhibitors against R. oryzae RdRp is -7.63 kcal/mol, while it is -8.06 and − 7.8 kcal/mol for the sofosbuvir and remdesivir, respectively. These values indicate that the Thuringiensin derivatives have comparable average binding affinities to that of Sofosbuvir and Remdesivir against the viral and fungal RdRps.
On the other hand, the average binding affinity of the four nucleotide inhibitors against the human IMPDH is -8.71 kcal/mol, which is lower (better) than the average binding affinity of the positive controls (-8.3 and − 7.85 kcal/mol for sofosbuvir and remdesivir, respectively). The best compound from the Thuringiensin derivatives in binding all the proteins is the Thuringiensin 6,3-lactone (CID: 102074352). In order to check the binding mode of each ligand to the three proteins, the interaction map of the complexes is mined by the Discovery studio software. Based on the analysis, the compounds' binding modes against SARS-CoV-2 RdRp, R. oryzae RdRp, and human IMPDH are explored and tabulated.
Table 1 lists the interactions established for each ligand (Thuringiensin derivatives and the positive control drugs) after docking to the active site of the proteins. The main type of interaction that formed upon docking is the formation of Hydrogen bonds (H-bonds). An average of 13 H-bonds is formed between the positive control drugs and the protein. For the Thuringiensin derivatives, the average number of H-bonds formed is 14, while few hydrophobic contacts, salt bridges (red), and halogen bonds (green) are reported in Table 1. The residues shown in bold are the active site residues in each protein. For example, the most-reported residues from SARS-CoV-2 RdRp that take part in the interactions with the nucleotide inhibitors are D760(12), D761(9), D618(9), R555(8), E811(6), S814(6), and Y619(5), ranked by the number of reported interaction established upon docking. For the R. oryzae RdRp, the most reported residues to interact with the fungal RdRp are E27(15), D56(12), R14(10), D193(8), G142(5), S146(5), D194(5). On the other hand, the residues from the human IMPDH that reported to interact with the nucleotide inhibitors are D364(14), D274(12), S276(8), H93(6), G326(6), D256(5), C331(5), and T333(5).
Table 1
The interactions that were established after docking the four adenosine derivatives and positive controls (Sofosbuvir and Remdesivir) into the SARS-CoV-2 RdRp, Rhizopus oryzae RdRp, and the human IMPDH. Red-colored residues are residues that interact with salt bridges, while green-colored residues are that interact through halogen bonds. Bold residues are the active residues in each protein.
Protein target | Compound | Binding affinity (kcal/mol) | H-bonding | Hydrophobic interaction |
number | Amino acids involved | number | Amino acids involved |
SARS-CoV-2 RdRp | Sofosbuvir | -7.4 | 8 | S549, R555(2), R555, Y619, K621, C622, D623, and N691 | | |
Remdesivir | -7.3 | 10 | K551, R555(2), D618, Y619, K621, K621, D760(4), D761(2), and S814 | 1 | K551 |
CID: 99213 | -7.4 | 11 | D618(4), Y619, C622, D761(2), W800, and E811(2) | | |
CID: 194147 | -6.9 | 14 | K551(3), R555, W617, Y619(2), D760, W800, E811(2), S814(2), and R836 | | |
CID: 20056441 | -7.1 | 18 | R555(2), D618(3), D623, D760(6), D761(4), and S814(2) | | |
CID: 102074352 | -7.4 | 8 | K551, D618, D760, D761, W800, E811(2), and S814 | | |
Rhizopus oryzae RdRp | Sofosbuvir | -8.0 | 11 | P10, R14, Q141(2), S146, D193(3), and D194(3) | 4 | A11, Y13(2), and Y150 |
Remdesivir | -7.9 | 11 | E27(2), Q31, S53, D56(2), Y191, D193(2), and D194(2) | 5 | N12, R14, and E27(3) |
CID: 99213 | -7.1 | 17 | R14(2), E27(5), D56(4), Y88, G142, S146(3), and D193 | | |
CID: 194147 | -7.2 | 15 | R14(3), E27(2), D56(4), Q57, G142(2), S143(2), and Y191 | | |
CID: 20056441 | -7.5 | 15 | R14(2), D83(2), S86(2), Y88, T90, G142(2), P147(2), D193(2), and W222 | 1 | W222 |
CID: 102074352 | -8.3 | 12 | Y13, R14, E27(3), D56(2), Y88, Q141(2), S143, and S146 | | |
Human IMPDH | Sofosbuvir | -8.0 | 15 | D274(2), S276(2), M325, G326, S327, G328, C331, D364(4), G415(2), K438, and G442 | | |
Remdesivir | -7.8 | 23 | D274(4), S276(3), R322, G324(2), M325(2), G326(2), S327, C331, D364(2), M414, G415, K438(2), and Q441 | 1 | D274 |
CID: 99213 | -8.4 | 12 | S68(2), D256(2), D274, S276, R322, G326, C331, T333, and D364(2) | | |
CID: 194147 | -7.3 | 17 | S68, H93, D274(4), S275(2), S276, G326, S327, C331, T333, and D364(4) | | |
CID: 20056441 | -8.3 | 15 | H93(2), N94, D256(2), R259, S276, N303, G324(2), G326, S327, T333(2), and D364 | 3 | H93(3) |
CID: 102074352 | -9.8 | 11 | T252(2), D256, S275(2), Q277, N303, R322, C331, T333, and D364 | | |
Figure 3 shows the interactions that established between Thuringiensin 6,3-lactone (CID: 102074352), and the SARS-CoV-2 RdRp (top left), R. oryzae RdRp (top write), and the human IMPDH (down). This compound shows the best average binding affinities against the three proteins (see Fig. 2) compared to other nucleotide inhibitors. Figure 3 is represented by Discovery studio software, where the ligand is shown in the sticks, and the interacting residues are depicted in lines. The only type of interaction is the formation of H-bonds (dashed lines). Thuringiensin 6,3-lactone (CID: 102074352) formed 8 H-bonds to SARS-CoV-2 RdRp with residues K551, D618, D760, D761, W800, E811(2), and S814. For R. oryzae RdRp Y13, R14, E27(3), D56(2), Y88, Q141(2), S143, and S146 formed 12 H-bonds with Thuringiensin 6,3-lactone. At the same time, residues T252(2), D256, S275(2), Q277, N303, R322, C331, T333, and D364 of the human IMPDH formed 11 H-bonds with Thuringiensin 6,3-lactone.
The current work reveals the favorable binding affinity of four adenosine derivatives against the SARS-CoV-2 RdRp, Rhizopus oryzae RdRp, and the human IMPDH. Thuringiensin 6,3-lactone has the best binding affinity to the three proteins, hence can be a potential inhibitor against COVID-19/Mucormycosis coinfection, while experimental validation is yet to be performed.