Drug screening against F13 protein, the target of tecovirimat, as potential therapies for monkeypox virus

Dear editor,

The outbreak of monkeypox virus (MPXV) outside Africa has expanded worldwide since May 2022. To date, there is no approved treatment for MPXV. Tecovirimat (also known as TPOXX or ST-246) is approved for the treatment of the smallpox, another member of the orthopoxvirus family, by targeting VP37 protein. F13, as a viral structural protein of MPXV and the homolog of VP37 protein, plays an important role in the envelopment of the intracellular mature virus with Golgi-derived membrane to form enveloped virus before the release of the virus.¹ Daoqun Li et al. established the 3D structure prediction of F13 protein and analyzed the molecular dynamics simulation of tecovirimat-F13 complex,² Lam et al. found hypericin and naldemedine can be repurposable drugs for F13L protein of original european MPXV strain by QVina2.1.³ And Qiangzhen Yang et al. screened 5903 drugs for 10 proteins (without F13) of MPXV.⁴ Tecovirimat was demonstrated to be an effective anti-MPXV medicine clinically.⁵ Thus, we think the F13 protein, rather than other untested proteins of MPXV, is a practical and promising drug target for anti-MPXV therapy discovery and development. And we conducted drug screening for MPXV F13.

We utilized AlphaFold2 to predict the protein structure of the latest F13 of MPXV (GenBank ID URK20480.1).² The predicted local distance difference test (pLDDT) score of MPXV F13 was 92.22 (Fig. 1 b), and most pLDDTs of amino acid residues reached a confidential score, indicating the predicted F13 protein structure is highly accurate. Next, the CurPocket tool, a web-based protein-surface-curvature-based cavity detection approach, of CB-Dock2 was used to detect cavities on the predicted monkeypox virus F13 protein structure.⁶ The top 20 pockets were found and prepared as docking configs (pocket 1 shown in Fig. 1c, Table S1).

Fig. 1.

Drug screening for F13 protein of monkeypox virus.

(A). Workflow of this study.

(B). The F13 protein structure predicted by Aphafold2.

(C). Potential docking pocket 1 predicted by CurPocket.

(D). The tecovirimat and F13 docking pose in pocket 10.

(E,F). The tecovirimat and F13 docking pose and binding residues in pocket 1.

(G-I). The docking poses and binding residues of glecaprevir, dolutegravir, and bictegravir with MPXV F13 protein.

(J,K) The molecular dynamics simulation (RMSD and RMSF) of glecaprevir-F13, dolutegravir-F13, and bictegravir-F13 complexes.

Then, the docking between tecovirimat and the above-mentioned MPXV F13 model was conducted to verify the accuracy of pocket detecting based on CB-Dock2, a protein-ligand blind docking web server based on AutoDock Vina (version 1.1.2). We found the docking between tecovirimat and MPXV F13 protein gets a better Vina score in pocket 1 (Fig. 1e, f) than in pocket 10 (Fig. 1d), the binding pose previously described by Daoqun Li et al. (−8.5 vs −8.2)² and similar to the value Lam et al. reported (−8.4).³ A 50 ns molecular dynamics simulation of the tecovirimat-F13 complex was used to validate the binding stability of the docking pose by Gromacs (version 2019.3). And the RMSD and RMSF curves suggest the tecovirimat-F13 complex retained as a whole (Fig. 1j, k, green line).

We used DrugRep,⁷ an AutoDock Vina-based online virtual screening server, to screen 10,640 compounds (workflow showed in Fig. 1a), containing 3 libraries: FDA-approved drugs (N = 2315), experimental drugs (N = 5935), and traditional Chinese medicine (TCM) monomer compounds (N = 2390). The approved drug library and experimental drug library were accessed from the DrugBank database (version 5.1.7). And TCM library was obtained from Topscience Company, from ∼800 traditional Chinese medicines. 406 compounds were found to have a better or equal binding ability with MPXV F13 protein (Vina score ≤−8.5), including 86 approved drugs, 186 experimental drugs, and 134 monomer compounds from traditional Chinese medicine (top 20 s were listed in Table 1 , Table S2). Tucatinib and ubrogepant et al. from the approved drug library, zk-806,450 et al. from the experimental drug library, and protohypericin, hypericin, and bilobetin et al. from the TCM library showed good binding abilities with F13 protein of monkeypox (Table 1). In our result, hypericin and naldemedine, found by Lam et al.,³ were validated (−10.7 and −8.7 respectively).

Table 1.

Drug screening results targeting F13 protein of monkeypox virus. (Related to Table S1).

Library 1: Approved drugs (Score≤-9.0)
Drug Bank Accession Number	Score	Generic Name	ATC code
DB11652	-10.4	Tucatinib	L01EH — Human epidermal growth factor receptor 2 (HER2) tyrosine kinase inhibitors
DB15328	-10.3	Ubrogepant	N02CD — Calcitonin gene-related peptide (CGRP) antagonists
DB13879	-10.1	Glecaprevir	J05AP — Antivirals for treatment of HCV infections
DB08901	-9.8	Ponatinib	L01EA — BCR-ABL tyrosine kinase inhibitors
DB11986	-9.8	Entrectinib	L01EX — Other protein kinase inhibitors
DB04868	-9.7	Nilotinib	L01EA — BCR-ABL tyrosine kinase inhibitors
DB09280	-9.6	Lumacaftor	R07AX — Other respiratory system products
DB00872	-9.5	Conivaptan	C03XA — Vasopressin antagonists
DB01199	-9.5	Tubocurarine	M03AA — Curare alkaloids
DB00320	-9.4	Dihydroergotamine	N02CA — Ergot alkaloids
DB12457	-9.4	Rimegepant	N02CD — Calcitonin gene-related peptide (CGRP) antagonists
DB01259	-9.4	Lapatinib	L01EH — Human epidermal growth factor receptor 2 (HER2) tyrosine kinase inhibitors
DB12523	-9.3	Mizolastine	R06AX — Other antihistamines for systemic use
DB08871	-9.3	Eribulin	L01XX — Other antineoplastic agents
DB09074	-9.3	Olaparib	L01XK — Poly (ADP-ribose) polymerase (PARP) inhibitors
DB00563	-9.2	Methotrexate	L04AX — Other immunosuppressants
DB00762	-9.2	Irinotecan	L01CE — Topoisomerase 1 (TOP1) inhibitors
DB08815	-9.2	Lurasidone	N05AE — Indole derivatives
DB06605	-9.2	Apixaban	B01AF — Direct factor Xa inhibitors
DB00309	-9.1	Vindesine	L01CA — Vinca alkaloids and analogues
DB08930	-9.1	Dolutegravir	J05AJ — Integrase inhibitors
DB00696	-9.1	Ergotamine	N02CA — Ergot alkaloids
DB12001	-9.1	Abemaciclib	L01EF — Cyclin-dependent kinase (CDK) inhibitors
DB01126	-9	Dutasteride	G04CB — Testosterone-5-alpha reductase inhibitors
DB08896	-9	Regorafenib	L01EX — Other protein kinase inhibitors
DB15035	-9	Zanubrutinib	L01EL — Bruton's tyrosine kinase (BTK) inhibitors
DB11799	-9	Bictegravir	J05AR — Antivirals for treatment of HIV infections, combinations
DB01251	-9	Gliquidone	A10BB — Sulfonylureas
DB06210	-9	Eltrombopag	B02BX — Other systemic hemostatics
Library 2: Experimental drugs (Top 20)			Library 3: Traditional Chinese medicine(Top 20)
DrugBank Accession Number	Score	Generic Name or ZINC ID	ID	Score	Generic Name
DB02112	-10.2	Zk-806,450	TN2108	-11.2	Protohypericin
DB08512	-10	ZINC000016052484	T6S0923	-10.7	Hypericin
DB03571	-10	ZINC000013559919	T4S2128	-10.1	Bilobetin
DB08683	-9.8	ZINC000018183490	T3417	-10	Amentoflavone
DB03168	-9.7	Nicotinamide adenine dinucleotide cyclohexanone	T4S0111	-10	Hupehenine
DB03802	-9.7	ZINC000013607707	T7602	-9.7	Theaflavin
DB02729	-9.7	SD146	T5S1598	-9.6	Mulberroside C
DB04877	-9.6	Voacamine	T2775	-9.4	Baicalin
DB06888	-9.6	ZINC000003820290	T5S0788	-9.4	Oroxin A
DB03231	-9.6	ZINC000013559921	T4S1335	-9.4	Daphnoretin
DB04118	-9.6	N-Coeleneterazine	T3410	-9.4	Momordin Ic
DB07666	-9.5	ZINC000014958755	T4S2126	-9.3	Ginkgetin
DB03351	-9.5	Sri-9439	T6S2038	-9.3	Ziyuglycoside II
DB07220	-9.4	ZINC000020149031	T5S0106	-9.2	Peimisine
DB01669	-9.4	Virginiamycin M1	T2728	-9.2	Limonin
DB07833	-9.3	ZINC000029130381	T3S1251	-9.2	Neoruscogenin
DB04785	-9.3	Streptolydigin	T3850	-9.2	Luteolin-7-glucuronide
DB07514	-9.3	ZINC000016052723	TQ0287	-9.2	Chrysin-7-O-glucuronide
DB08091	-9.3	ZINC000003818635	T5S2129	-9.2	Sciadopitysin
DB08749	-9.3	ZINC000010339589	T0228	-9.2	Methyl hesperidin

Furthermore, Among those 406 compounds, some approved antiviral drugs displayed a high affinity with MPXV F13 protein. Glecaprevir, an anti-hepatitis C virus (HCV) drug that inhibits NS3/4A protease of HCV, was dosed as an oral combination therapy with the NS5A inhibitor pibrentasvir.⁸ The vina binding score for glecaprevir and F13 protein complex was −10.1 (Fig. 1g), suggesting a more stable binding than the tecovirimat-F13 complex. Dolutegravir, a second-generation integrase strand transfer inhibitor, was originally developed for the treatment of human immunodeficiency virus (HIV).⁹ The vina score of the dolutegravir-F13 complex was −9.1, showing good potential as an anti-monkeypox virus medicine (Fig. 1h). Bictegravir, another second-generation integrase strand transfer inhibitor approved for HIV treatment in fixed-dose combination with emtricitabine and tenofovir alafenamide,¹⁰ demonstrated to be a potential candidate for drug repurposing to be an anti-MPXV therapy for its bictegravir-F13 complex vina score was −9.0 (Fig. 1i). To validate the stability of F13 protein binding with glecaprevir, dolutegravir, or bictegravir, a molecular dynamics simulation of the complexes was conducted for 50 ns. And the results showed all 3 protein-drug complexes remained as a whole as the tecovirimat-F13 complex (Fig. 1j, k). Our virtual drug screening work found that many approved drugs can be repurposed for the treatment of monkeypox potentially. Those approved drugs have been studied comprehensively in pre-clinical research and clinical trials for their pharmacokinetics, pharmacodynamics, and toxicology. During the rapid global epidemic of the monkeypox virus, fast track of drug discovery and development can be vital for MPXV patients. Clinical studies for off-label use (unapproved use of an approved drug) of those drugs can be considered after ethical approval for those areas where effective treatment, especially tecovirimat and cidofovir et al., is not accessible.

In this work, we have predicted the structure of the monkeypox F13 protein and detected the potential binding pockets of the predicted protein structure. The docking of tecovirimat and F13 was verified. Then 10,640 compounds of the approved drug library, the experimental library, and the TCM library were virtual screened to dock F13 protein. Approved anti-viral medicines, including glecaprevir, dolutegravir, and bictegravir, other approved medicines, i.e. tucatinib and ubrogepant, and zk-806,450 et al. from experimental drug library, and protohypericin, hypericin, and bilobetin et al. from TCM library be indicated can be potentially repurposed for the treatment of MPXV.

Availability of data and materials

All data needed to evaluate the conclusions in the paper are present in the paper or the Additional files. The data are available from the corresponding author on reasonable request.

Declaration of competing interest

The authors declare that they have no competing interests.

Appendix. Supplementary materials

Table S1. 20 potential docking pockets predicted by CurPocket.

Table S2. 406 screened compounds.