Immunoinformatic and molecular docking approaches: siRNA prediction to silence cell surface binding protein of monkeypox virus

Beni-Suef University Journal of Basic and Applied Sciences

Table 6 Docking interaction analysis of the best binding complex S8 siRNA and human Argonaute-2

Alias	RNA oligo sequences 21nt guide (5′ → 3′)	Docking score	Interacting residues in Ago2 domains
Alias	RNA oligo sequences 21nt guide (5′ → 3′)	Docking score	N-terminal (36–166)	L1 (176–226)	PAZ (238–375)	Mid (429–511)	PIWI (517–818)
S8	UUAUGGAUCCAAUCACUUGAU	−408.24	GLU64	VAL177^b	MET275, LYS276	VAL434	LYS525^b, LYS550^b
			LYS65^b	GLY178^b	ARG277^a,b, LYS278^b	TRP435	VAL598^b, THR599^b
			CYS66^b		TYR279^b, PHE294^b	ASP436	HIS600, PRO601
			PRO67^b		GLU299, TYR311^b	ARG438	PRO602, ALA603
			LYS124^b		ARG315^a,b, VAL330		GLY604, ARG635
			ASP125^b		GLY331, GLN332^b		LYS709^a,b, ARG710^a,b
			ARG126		LYS335^b, HIS336^b		HIS753^b, GLN757^a,b
					THR337^b, ARG351^a,b		GLY758^b, THR759^a,b
					ILE353^a,b LYS355		SER760^b, ARG761^a,b
					THR357, ASP358		TYR790^b, ARG792^a,b
					ASN359, THR361		CYS793^b, ARG795^b
					SER362, ILE365^a,b		VAL797^b, SER798^a,b
					ARG366, THR368^b		ILE799, TYR804^a,b
							HIS807, PHE811^b
							ARG814, TYR815^b
Control	UUCACAUUGCCCAAGUCUUU	−1081.52	LYS65	PRO176	LYS266		LEU522, GLY524
			CYS66	VAL177	ILE269		LYS525, THR526
			PRO67	GLY178	ARG277		TYR529, LYS533
			ARG68	ARG179	LYS278		THR544, GLN545
			VAL70		TYR279		CYS546, VAL547
			ASP95		ARG280		GLN548, LYS550
			ARG97		PHE294		ASN551, GLN558
			GLY121		LEU296		THR559, ASN562
			GLY123		VAL308	N/A	LEU563, LYS566
			LYS124		TYR311		LYS570, VAL598
			ASP125		PHE312		THR599, HIS600
					ARG315		GLY670, VAL671
					HIS316		SER672, GLY674
					GLN332		GLN675, LYS709
					LYS335		ARG710, ARG714
					HIS336		HIS753, ALA754
					THR337		GLY755, ILE756
					TYR338		GLN757, GLY758
					LEU339		THR759, SER760
					PRO340		ARG761, PRO762
					ARG351		TYR790, ARG792
					MET364		CYS793, ARG795
					ILE365		SER796, VAL797
					THR368		SER798, TYR804
					ARG375		PHE811, ARG812
							TYR815, ALA859