Prioritization and characterization of validated biofilm blockers targeting glucosyltransferase C of Streptococcus mutans

Figures & data

Figure 1. GtfC reaction scheme (Brenda enzyme database) [11].

Figure 2. GtfC monomer (A-chain) with active site.

Table 1. Details of the validated ligands: the compound name refers to the compound used in the respective study.

Compound name*	Figure SI	PubChem ID/IUPAC*	Molecular formula	Molecular weight	Reference
D-acarbose	L1	41774	C25H43NO18	645.6	[19]
6-Deoxysucrose	L2	146,374	C12H22O10	326.3	[26]
Trichloro-galactosucrose	L3	71,485	C12H19Cl3O8	397.6	[23]
Flavonoid myrecitin	L4	5281672	C15H10O8	318.23	[27,28]
Flavonoid new	L5	(6Z)-3-hydroxy-6-[(Z)-3-hydroxy-3-(3-hydroxyphenyl)prop-2- enylidene]cyclohexa-2,4-dien-1-one	C15H12O4	256.253	[27,28]
2-N,3-N-Bis[2-(4-methoxyphenyl)ethyl]quinoxaline-2,3-diamine	L6	1,023,772	C26H28N4O2	428.5	[28]
Flavonoid apigenin	L7	5,280,443	C15H10O5	270.24	[27,28]
D-mannosamine	L8	440,049	C6H13NO5	179.17	[29]
Stilbene piceatannol	L9	667,639	C14H12O4	244.24	[30]
1-Deoxynojirimycin	L10	29,435	C6H13NO4	163.17	[28]
Flavonoid (Z)-3-(2,4-Dihydroxyphenyl)-1-(3-hydroxyphenyl)- 2-propen-1-one	L11	(Z)-3-(2,4-Dihydroxyphenyl)-1-(3-hydroxyphenyl)-2-propen-1-one	C15 H11O4	255.253	[27,28]
D-galactosamine	L12	24,154	C6H13NO5	179.17	[29]
G16	L13	(6E)-3-(dihydroxymethyl)-6-[5-[4-[(4-fluorophenyl)-hydroxy-methylene]cyclohexa-2,5-dien- 1-ylidene]-4-phenyl-imidazol-2-ylidene]cyclohexa-2,4-dien-1-one	C29H21FN2O4	480.499	[31]
G43	L14	(2Z)-N-(2-carbamoylphenyl)-5-nitro-benzothiophene-2-carboximidic acid	C16H11N3O4S	341.351	[31]
Epiclusianone	L15	5,471,610	C33H42O4	502.7	[28]

Figure 3. Interaction profile of GtfC-D-Acarbose. (a) From 3AIC.pdb structure. (b) Docked complex.

Table 2. Summary of ligand interactions.

Ligand (inhibitor)	H	O	U	ALIS	%Efficiency @D-Acarbose	Target-ligand 2-D Interaction Diagram
D-Acarbose	10	3	0	7.66	100.00	Figure 3(b)
6-Deoxysucrose	4	6	0	5.84	76.24	Figure 5(a)
Trichloro-galactosucrose	6	9	0	5.81	75.88	Figure 5(b)
Flavonoid Myrecitin	2	10	0	5.79	75.59	Figure 5(c)
2-N,3-N-Bis[2-(4-methoxyphenyl)ethyl]quinoxaline-2,3-diamine	2	9	0	5.75	75.10	Figure 5(d)
Flavonoid new	3	4	0	5.58	72.85	Figure SI C1
G16	3	6	0	5.55	72.42	Figure SI C2
Flavonoid Apigenin	4	9	1	5.46	71.28	Figure SI C3
D-Mannosamine	6	6	0	5.20	67.82	Figure SI C4
G43	1	11	1	5.09	66.45	Figure SI C5
Stilbene Piceatannol	5	5	1	5.07	66.22	Figure SI C6
1-Deoxynojirimycin	3	7	0	4.62	60.28	Figure SI C7
Flavonoid (Z)-3-(2,4-Dihydroxyphenyl)-1-(3-hydroxyphenyl)-2-propen-1-one	3	2	2	4.32	56.36	Figure SI C8
D-Galactosamine	4	3	0	4.20	54.77	Figure SI C9
Epiclusianone	0	8	0	3.80	49.61	Figure SI C10

H: Number of possible HYDROGEN BONDS with GtfC Target; O: other possible non-covalent interactions, i.e. Van der Waal, Pi-Sigma, Carbon–Hydrogen, Pi-cation, Pi-anion, alkyl interaction and Pi-alkyl with GtfC Target; U: unfavourable Interaction. ALIS=(LigScore1_drieding+Ligscore2_drieding+LigScore1_CFF+ LigScore2_CFF)/4. (refer to Table 1-SI for ligand Pose Score) $\mathrm{\%}\mathrm{ }\mathit{efficiency}@\mathrm{Acarbose}=\left(\frac{{\mathit{ALIS}}_{\mathit{Ligand}}}{{\mathit{ALIS}}_{\text{Acarbose }}}\right)\times 100.$

Table 3. Summary of Interacting chemical fragments.

Ligand (inhibitor)	Interacting chemical fragment/s	Interacting critical amino acid residues
D-Acarbose	Hydroxyl group of the tetrahydropyran ring	Arg54O
	Hydroxyl and hydroxymethyl groups of the Cyclohex-2ene fragment	Gln960, Asp477, Asp909, His587, Arg475, Glu515, Asp588
	Amino Nitrogen interaction of cyclohex-2-en-1-yl] amino tetrahydropyran	Glu515, Leu433
	Carbonyl oxygen of the pyran ring	Asn481
6-Deoxysucrose	Hydroxyl group of the tetrahydropyran ring	Asp588
	Hydroxyl groups and hydrogen atoms of the tetrahydrofuran ring	Asp588, Asp909, Gln960, Asp477
Trichloro-galactosucrose	Hydroxyl groups of the chloro- tetrahydropyran ring	Arg475, His587, Asp588, Asp477
	Chlorine atoms of the chloro- tetrahydropyran ring	Tyr916, His587
	Hydroxyl groups of the di chloro- tetrahydrofuran ring	Asp588, Glu515
	Chlorine atoms of the di-chloro- tetrahydrofuran ring	Ala478, Tyr610, Trp517
Flavonoid Myrecitin	Hydroxyl groups of the chromen-4-one ring	His587, Tyr916, Arg475, Ala478
	Carbonyl oxygen of the chromen-4-one ring	Arg475
	pi Interactions of chromen-4-one ring	Tyr916, Asp588, Ala478
	pi Interactions of trihydroxyphenyl ring	Leu433, Asn481

Figure 4. Percentage efficiency of the validated ligands @αD-Acarbose.

Figure 5. GtfC-interaction profile. (a) 6-Deoxysucrose, (b) trichloro-galactosucrose, (c) flavonoid myrecitin, (d) 2-N,3-N-Bis(2-(4-methoxyphenyl) ethyl) quinoxaline-2,3-diamine.

Figure 6. Frequently interacting residues. (a) Hydrogen bonding; (b) favourable count.

Barthelmes J, Ebeling C, Chang A, et al. BRENDA, AMENDA and FRENDA: the enzyme information system in 2007. Nucleic Acids Res. 2007;35(Database issue):D511–4.

 PubMed Web of Science ®Google Scholar

Ito K, Ito S, Shimamura T, et al. Crystal structure of glucansucrase from the dental caries pathogen Streptococcus mutans. J Mol Biol. 2011;408(2):177–186.

 PubMed Web of Science ®Google Scholar

Binder TP, Robyt JF. Inhibition of Streptococcus mutans 6715 glucosyltransferases by sucrose analogs modified at positions 6 and 6'′. Carbohydr Res. 1985;140(1):9–20.

 PubMed Web of Science ®Google Scholar

Wunder D, Bowen WH. Action of agents on glucosyltransferases from Streptococcus mutans in solution and adsorbed to experimental pellicle. Arch Oral Biol. 1999;44(3):203–214.

 PubMed Web of Science ®Google Scholar

Nijampatnam B, Casals L, Zheng R, et al. Hydroxychalcone inhibitors of Streptococcus mutans glucosyl transferases and biofilms as potential anticaries agents. Bioorg Med Chem Lett. 2016;26(15):3508–3513.

 PubMed Web of Science ®Google Scholar

Ren Z, Chen L, Li J, et al. Inhibition of Streptococcus mutans polysaccharide synthesis by molecules targeting glycosyltransferase activity. J Oral Microbiol. 2016;8(1):31095.

 PubMed Web of Science ®Google Scholar

Lee CG, Park JK. Comparison of inhibitory activity of bioactive molecules on the dextransucrase from Streptococcus mutans. Appl Microbiol Biotechnol. 2015;99(18):7495–7503.

 PubMed Web of Science ®Google Scholar

Nijampatnam B, Zhang H, Cai X, et al. Inhibition of Streptococcus mutans biofilms by the natural stilbene piceatannol through the inhibition of glucosyltransferases. ACS Omega. 2018;3(7):8378–8385.

 PubMed Web of Science ®Google Scholar

Zhang Q, Nijampatnam B, Hua Z, et al. Structure-based discovery of small molecule inhibitors of cariogenic virulence. Sci Rep. 2017;7(1):1–0.

 PubMed Web of Science ®Google Scholar

Data availability statement

All the data required is available in supplementary Information and on request.