Anti-biofilm activity of Salvadora persica on cariogenic isolates of Streptococcus mutans: in vitro and molecular docking studies

Figures & data

Figure 1. GC–MS chromatogram of antibiofilm methanol extract of S. persica showing the compounds and their percentage abundance (parenthesis) 1. benzaldehyde (13.2); 2. benzyl chloride (1.6); 3. ethanone, 2-hydroxy-1-phenyl-(0.09); 4. benzyl isocyanate (7.2); 5. benzyl nitrile (2.0); 6. benzenecarboxylic acid (24.5); 7. l-[-]-4-hydroxy-1-methylproline(0.1); 8. benzaldehyde, 4-methoxy-(0.1); 9. benzaldehyde, 3-methoxy-(0.5); 10. 2-coumaranone (0.4); 11. benzeneacetic acid (0.07); 12. 3-benzyloxy-1-nitro-butan-2-Ol (0.01); 13. benzaldehyde, 4-(phenylmethoxy)- (0.3); 14. benzene isothiocyanate (18.1); 15. 2-(3’-phenylpropyl)-5-ethylpyridine (0.8); 16. (Z,Z)-à-farnesene (0.3); 17. N- benzylacetamide (10.9); 18. benzyl (6Z,9Z,12Z)-6,9,12-octadecatrienoate (0.02); 19. 1,3-cyclohexanedicarbohydrazide (0.01); 20. benzylidenebenzylamine (12.1); 21. 3à-hydroxy-3-methyl-6-phenyl-4-piperidone (0.8); 22. decanoic acid, methyl ester (0.1); 23. docosanoic acid, ethyl ester (0.08); 24. acetophenone benzyloxime (0.43); 25. benzamide, N-(4-methylphenyl)- (0.45); 26. pyrrole-2-carboxylic acid, 4-hydrazonomethyl-3,5-dimethyl-, ethyl ester(0.3).

Figure 2. Crystal structure of quorum sensing response regulator (PDB ID: INXO) (R) and its super imposed structures of (a) benzaldehyde, 4-methoxy-; (b) benzaldehyde, 3-methoxy-; (c) benzeneacetic acid; (d) benzyloxy-1-nitro-butan-2-ol; (e) benzaldehyde, 4-(phenylmethoxy)-; (f,g) N-benzylacetamide; (h) 1,3-cyclohexane dicarbo hydrazide; (i) decanoic acid, methyl ester; (j) docosanoic acid, ethyl ester; (k) benzamide, N-(4-methylphenyl)-; (l) benzyl (6Z,9Z,12Z)-6,9,12-octadecatrienoate; (m) benzyl isocyanate; (n) acetophenone benzyloxime; (o) chlorohexidine. The illustration demonstrates close alignment of molecular components of S.persica phytochemicals and the QS protein. The antibiotic chlorhexidine (2o) also interacts in the same manner as most of the phytochemicals.

Table 1. Growth inhibition and biofilm inhibiting activity of S. persica extracts on caries causing S. mutans.

Extract	Growth inhibition (Zone of inhibition/diameter in mm)	Biofilm inhibition activity
		Mean	SD	CV	Percentage reduction
Control	–	1.89	–		–
Methanol	24 ± 3	0.30	0.04	13.51	87.92
Ethanol	21 ± 2	0.33	0.04	12.17	85.75
Chloroform	16 ± 3	0.55	0.05	9.92	72.44
Acetone	15 ± 3	0.37	0.21	57.51	61.66
Aqueous	19 ± 2	0.52	0.14	27.81	58.68

Table 2. Ligandfit docking scores of the bioactive compounds of S. persica and the antibiotic chlorhexidine with the active site of the DNA-binding response regulator (PDB ID: 1NXO).

S. no	S. persica bioactive compound	PUBCHEM–ID (CID)	LIG SCORE1	LIG SCORE2	-PMF	Pose no.	Dock score	Internal energy	Amino acid with position	Distance
1	Benzaldehyde	240	1.589	106.122	0	1	1	0.155	–	–
2	Benzyl chloride	7503	2.43	126.583	0	0	1	0	–	–
3	Ethanone, 2-hydroxy-1-phenyl-	8375	1.327	136.148	1	2	1	0.263	–	–
4	Benzyl isocyanate	76639	1.697	133.147	0	2	2	0.212	LYS 81	1.792
5	Benzyl nitrile	8794	1.743	117.148	0	1	1	0.182	–	–
6	Benzenecarboxylic acid	243	1.459	122.121	1	2	1	0.304	–	–
7	l-[-]-4-Hydroxy-1-methylproline	237040	−3.728	145.156	2	4	1	0.404	–	–
8	Benzaldehyde, 4-methoxy-	31244	1.573	136.148	0	2	2	0.184	LYS 81	1.776
9	Benzaldehyde, 3-methoxy-	11569	1.573	136.148	0	2	2	0.184	LYS 81	1.654
10	2-Coumaranone	68382	1.466	134.132	0	2	0	0.216	–	–
11	Benzeneacetic acid	999	1.494	136.148	1	2	2	0.268	LYS 81	1.774
12	3-Benzyloxy-1-Nitro-Butan-2-ol	562214	1.61	225.241	1	4	6	0.321	ALA 80 LYS 81	1.846 2.792
13	Benzaldehyde, 4-(phenylmethoxy)-	78109	3.156	212.244	0	2	4	0.126	ALA 80 LYS 81 LYS 101	1.969 1.961 1.951
14	2-(3′-Phenylpropyl)-5-ethylpyridine	562461	4.515	225.329	0	1	5	0.054	–	–
15	Benzene, (isothiocyanatomethyl)-	12149	3.075	149.213	0	2	1	0.29	–	–
16	(Z,Z)-à-Farnesene	5317320	5.46	204.351	0	0	6	0	–	–
17	Acetamide, N-(phenylmethyl)-	11500	0.957	149.19	1	1	2	0.182	LEU 53 LYS 81	2.999 1.762
18	6,9,12-Octadecatrienoic acid, phenylmethyl ester, (Z,Z,Z)-	5368209	7.78	368.552	0	2	16	0.065	LYS 81	1.808
19	1,3-Cyclohexanedicarbohydrazide	598077	−1.133	200.238	4	4	2	0.535	LYS 81	1.988
20	Benzylidenebenzylamine	95831	3.433	195.26	0	1	3	0.061	–	–
21	Decanoic acid, methyl ester	8050	3.881	186.291	0	2	9	0.119	LYS 81	2.110 2.194 1.948
22	Docosanoic acid, ethyl ester	22199	9.704	368.637	0	2	22	0.061	LYS 81	2.369 2.194 1.948
23	Acetophenone benzyloxime	9602263	3.259	225.286	0	2	4	0.094	LYS 81	2.365 2.384
24	Benzamide, N-(4-methylphenyl)-	68497	3.1	211.259	1	1	2	0.137	LYS 81	2.154
25	Acetamide, N-(phenylmethyl)-	11500	0.957	149.19	1	1	2	0.182	LEU 153 LYS 81	2.941 1.812
26	Chlorhexidine	9552079	3.727	505.447	6	10	13	0.348	LYS 81	2.234 1.965

Figure 3. The DNA-binding response regulator (PDB ID: 3B2N) (R), LuxR family from S. aureus that was used for docking experiments with the bioactive compounds of S. persica 3-benzyloxy-1-nitro-butan-2-ol (a) and 1,3-cyclohexanedicarbohydrazide (b). The illustration demonstrates close alignment of the molecular components.

Table 3. Docking scores (highest) of the bioactive compounds of S. persica in the active site of 3B2N, the DNA-binding response regulator, Luxr family.

S. no	S. persica bioactive compound	PUBCHEM–ID (CID)	LIG score 1	LIG score 2	PMF	Pose no.	Dock score	Internal energy	Amino acid with position	Distance
1	3-Benzyloxy-1-nitro-butan-2-ol	CID: 562214	1.63	3.36	13.9	1	26.985	−2.548	ARG108	3.206
2	1,3-Cyclohexanedicarbohydrazide	CID :598077	0.68	3.12	−1.42	1	24.032	−1.622	ARG108	2.824