Hepatitis C Virus NS3 Protease and Helicase Inhibitors from Red Sea Sponge (Amphimedon) Species in Green Synthesized Silver Nanoparticles Assisted by in Silico Modeling and Metabolic Profiling

Figures & data

Table 1 In vitro Anti–NS3 Helicase and Protease Activities of Total Extract and Fractions of Amphimedon sp.

	IC50, µg/mL
	NS3 helicase	NS3 protease
Petroleum ether	0.296063	3.875308
Total extract	2.066837	13.29783
Butanol	2.346521	35.29088
Ethyl acetate	2.782707	43.69913
DCM	11.09016	29.79358

Table 2 In vitro Anti–NS3 Helicase and Protease Activities of the SNP Total Extract and Petroleum Ether Fraction of Amphimedon sp.

	IC50, µg/mL
	NS3 Helicase	NS3 Protease
Petroleum ether	0.11±0.62	2.38±0.57
Total extract	1.52 ±1.18	9.76±0.58
AgNO3	77.72 ±4.57	52.67±0.33
Telaprevir (375 mg Tab)	—	4.77±0.26
Ribavirin	4.66±0.29	—

Figure 1 Compounds identified and dereplicated from high-resolution mass-spectra data sets of Amphimedon sp.

Figure 2 Structures of isolated compounds 1–14.

Figure 3 TEM for shape and size of produced SNPs of (A) total extract of Amphimedon sp. and (B) Petroleum ether fraction of Amphimedon.

Abbreviations: TEM, transmission electron microscopy; SNPs, silver NPs

Figure 4 Ultraviolet-visible spectra analysis and color intensity of biosynthesized SNPs of (A) petroleum ether fraction of Amphimedon spp. and (B) total extract of Amphimedon.

Figure 5 FTIR spectra after synthesis of nanoparticles of (A) petroleum ether fraction of Amphimedon sp. and (B) total extract of Amphimedon.

Table 3 Docking Scores (kcal/Mol) of the 14 Tested Compounds, Paritaprevir, and Ribavirin 5ʹ-Triphosphate Against Full-Length HCV NS3-4A Protease–Helicase (4A92), HCV NS3/NS4A Protease (3P82), and HCV NS3 Helicase (4WXR)

	S-Score
	4A92	3P82	4WXR
Methyl 2-methoxyhexadecanoate	−5.07427	−4.75656	−5.51035
Icrinol A	−5.34033	−5.30877	−5.47285
6-hydroxymanzamine A	−5.49333	−5.37674	−6.26323
Pyrinodemin D	−6.98161	−5.14564	−7.64613
7-methyl-6-hexadecenoic acid	−5.09503	−4.49901	−5.4961
Amphimedine	−5.51757	−4.60604	−5.1061
Amphimedoside C	−5.84524	−5.22292	−5.84337
Keramaphidin B	—	—	—
20-hepacosenoic acid	−5.31298	−5.68273	−5.73547
3,4-dihydro-6-hydroxymanzamine A	−6.25434	−5.9257	−6.62751
3,4-dihydromanzamine A, J N-oxide	−6.26893	−4.72766	−5.56533
Nakinadine B	−6.4761	−6.17759	−6.80996
11,15-icosadienoic acid	−5.61213	−4.6286	−5.78322
Manzamine D	−5.62775	−5.10746	—
Paritaprevir		−5.95468	—
Ribavirin 5ʹ-triphosphate			−5.94529

Figure 6 2-D interaction diagrams of docked compounds and ribavirin 5ʹ-triphosphate (M) with the active sites of HCV NS3 helicase (4WXR). Green arrows represent side-chain acceptor/donor; blue arrows represent backbone acceptor/donor; blue shadows represent ligand exposure.

Figure 7 Analysis of physicochemical properties for the 14 isolated compounds by (A) molecular weight, (B) log P, (C) HBD, (D) HBA, (E) tPSA, and (F) number of rotatable bonds. The green line indicates the maximum desirable value for oral bioavailability defined by Lipinski’s rule of five and Veber’s oral bioavailability rule.