Repurposing antiviral drugs against the human monkeypox virus DNA-dependent RNA polymerase; in silico perspective

Dear Editor,

We read with great interest the paper that was recently published in this journal by Orvis et al.¹ regarding the emerging outbreak of human monkeypox in Madrid, Spain. According to the Centers for Disease Control and Prevention surveillance, the virus is reported in 99 countries and territories, with 47,652 confirmed cases (until August 26, 2022). The DNA-dependent RNA polymerase (DdRp) of poxvirus is a promising drug target for developing new chemotherapeutic antiviral drugs against DNA viruses. In this study, the DdRp of the HMV is modeled using its vaccinia virus as a homolog. After that, we repurposed 29 antiviral drugs on the equilibrated model (after a 100 ns molecular dynamics simulation run). The results revealed The effectiveness of the two antiviral drugs (Norov-29 and bemnifosbuvir) in binding the HMV DdRp active site with a comparable binding affinity (-24.26 ±4.43 and -21.32 ±6.43 kcal/mol) with the positive control, guanosine triphosphate (GTP) (-21.03 ±7.55 kcal/mol). These results need further experimental validation but promising as it was previously tested clinically in other viruses and had good pharmacological profiles. This may also pave the way for finding new circulating HMV inhibitors.

Modeling and simulation dynamics of DdRp

The model of HMV was built via SWISS-MODEL server² based on the solved structure of the Vaccinia virus elongation complex (PDB ID: 6RID). The predicted model has good quality as judged by MolProbity analysis.³ Only 0.4% of residues (five) have phi or psi angles in the generously allowed region and no outliers in the Ramachandran plot. In HMV, the active site (D415, D417, and D419) was predicted in the Rpo147 chain at a β-turn between two helices.

The structure of the Apo DdRp was subjected to 100 ns molecular dynamics (MD) simulation⁴ run aiming to equilibrate the system and visit the available conformations of the protein during this time domain.

Molecular docking

The molecular docking of analogs was performed by AutoDock Vina.² All active site residues (Asp415, Asp417, and Asp419) were treated as flexible. The search box was centered at the metal ion of the active site, and the box dimensions were set to 30 × 30 × 30 Å. In addition, the exhaustiveness was increased to 256 to account for the high torsions of the ligands.⁵ The other parameters were accepted in their default values.

The average binding affinities of the nucleoside analogs against the active site of HMV DdRp ranged from −5.92 to −6.59 kcal/mol. The average scores of the top ten compounds (including the positive controls; ATP, CTP, GTP, and UTP) are depicted graphically in Fig. 1 . As shown in Fig. 1; Valopicitabine, HCV-1, and Bemnifosbuvir are the best compounds with average binding affinity values of -6.58 ±0.01 kcal/mol. These three compounds show lower binding energies than the four positive controls. At the same time, HCV-2 and Norov-29 compounds show lower binding energies than ATP, GTP, and UTP (-6.51 ±0.01 kcal/mol). Finally, BMS-986094 shows lower binding energies than ATP and GTP (-6.48 ±0.08 kcal/mol).

Fig. 1.

(A) Average calculated binding energies of the top six drugs along with the physiological substrates (ribonucleotides; ATP, CTP, GTP, and UTP). Error bars represent the standard deviation of binding affinity (kcal/mol) of three clusters of representative protein conformations after MD simulation. (B) Established interactions after docking the top compounds against DdRp of HMV. (1) HCV-1, (2) HCV-2, (3) Valopicitabine, (4) Norov-29, (5) Bemnifosbuvir, and (6) GTP.

The detailed interactions established upon docking are listed in Table 1 . The primary interaction type between the compounds and the DdRp is the formation of hydrogen bonds (at least six H-bonds). Additionally, all these drugs establish at least one salt bridge interaction with R380. The active site residues (D415, D417, and D419) are bolded in Table 1 and are involved in H-bond formation in all the formed complexes except for the Valopicitabine-DdRp complex. The interactions are graphically rendered in Fig. 1B, where the formed interactions are depicted by blue lines (H-bonds) and dashed yellow lines (salt bridges). Cyan sticks show the interacting residues of the DdRp, whereas the other sticks are the ligands.

Table 1.

The established interactions upon docking the top six drugs and the physiological ribonucleotides (ATP, CTP, GTP, and UTP) against HMV DdRp after dynamics.

Compound (PubChem ID)	Hydrogen bonds		Hydrophobic interactions		Others
	number	Residues	number	Residues	number	Residues
Valopicitabine (15940324)	7	R287, Q381, A414, F416, and E420	-	-	2	R380 a
HCV-1 (5276734)	11	R380, Q381, D415, G418, D419, E420, and E421	-	-	2	R380 a
Bemnifosbuvir (122527275)	13	R380, P382, S383, D415, G418, D419, and E421	1	R380	3	R380 a,b
CTP	7	R287, Q381, D415, E420, and W422	-	-	3	R287 a and R380 a
HCV-2 (11290467)	10	R380, Q381, D415, G418, D419, and E421	-	-	1	R380 a
Norov_29 (88571722)	9	Q381, D415, G418, D419, and E421	-	-	2	R380 a,b
UTP	6	R380, Q381, P382, D415, D419, and W422	-	-	3	R380 a
BMS-986094 (49862756)	7	P382, H385, D419, E420, W422, and R757	-	-	3	R287 a, R380 a
ATP	9	R380, P382, S383, D415, D417, D419, E420, and E421	-	-	3	R380 a,b
GTP	8	R380, Q381, L384, H385, D415, W422, and R757	-	-	3	R380 a

^asalt bridge and

^bπ-cations. Active site residues are in bold.

MD simulation of top analogs and binding free energy calculations

We performed another round of MD simulation for the best five hits (Valopicitabine, HCV-1, Bemnifosbuvir, HCV-2, and Norov-29) and the positive control GTP to study the protein dynamics upon ligand binding. We neglected the compounds BMS-986094 and Lumicitabine as their clinical trials were terminated for safety issues.^{6 , 7}

Fig. 2 shows the calculated MM/GBSA of the top four complexes (HCV-1-DdRp, HCV-2-DdRp, Norov-29-DdRp, and bemnifosbuvir-DdRp) in addition to the GTP-DdRp complex. Norov-29 (sky blue) and bemnifosbuvir (red) are the best two compounds based on the MM/GBSA calculations in binding DdRp of HMV with values (-24.26 ±4.43 and -21.32 ±6.43 kcal/mol) near the positive control (GTP) (blue) (-21.03 ±7.55 kcal/mol). These two drugs may be potential anti-DdRp and are suggested further analyzed by in vitro and in vivo assays.

Fig. 2.

The calculated MM/GBSA for the positive control (GTP) and the best four ligands (HCV-1, HCV-2, Norov-29, and bemnifosbuvir)-HMV DdRp.

Conclusively, we report the effectiveness of anti-norovirus (Norov-29) and the anti-HCV and flaviviruses (Bemnifosbuvir) against HMV. Based on our docking results, dynamics simulation, and calculated binding energies, we suggest these two drugs against the DdRp of HMV. This could help in fighting against the current outbreak that spreading worldwide during the last few months.

CRediT authorship contribution statement

Jameel M. Abduljalil: Software, Writing – original draft. Abdo A. Elfiky: Visualization, Supervision, Investigation, Writing – review & editing.

Declaration of Competing Interest

We declare that there is no conflict of interest regarding this paper's work or publication.