Figure 1
3D structure of ptp-A as visualized by RasMol (helix, pink color; beta sheet, yellow; turns, white). 3D, three dimensional
Figure 2
Structure of the selected biocompounds from R. officinalis
Table 1
Molinspiration calculations of Rosmarinus officinalis biocompounds and drug likeliness of the R. officinalis against ptp-A of Porphyromonas gingivalis
| Compounds | Molecular weight | Molecular formula | Hydrogen bond donor | Hydrogen bond acceptor | LogP | Rotatable bonds | TPSA | Volume | N atoms | G protein-coupled receptors ligand | Ion channel modulator | Kinase inhibitor | Nuclear receptor ligand | Protease inhibitor | Enzyme inhibitor |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Carnosic acid | 332.44 | C20H28O4 | 3 | 4 | 4.60 | 2 | 77.75 | 322.31 | 24 | 0.41 | 0.24 | −0.24 | 0.72 | −0.01 | 0.32 |
| Rosmarinic acid | 360.318 | C18H16O8 | 5 | 8 | 1.63 | 7 | 144.52 | 303.54 | 26 | 0.17 | −0.08 | −0.18 | 0.57 | 0.15 | 0.24 |
| p-Coumaric acid | 164.16 | C9H8O3 | 2 | 3 | 1.43 | 2 | 57.53 | 146.48 | 12 | −0.56 | −0.26 | −0.91 | −0.12 | −0.87 | −0.15 |
| Luteolin | 286.239 | C15H10O6 | 4 | 6 | 1.97 | 1 | 111.12 | 232.07 | 21 | −0.02 | −0.07 | 0.26 | 0.39 | −0.22 | 0.28 |
| Amoxicillin | 365.404 | C16H19N3O5S | 5 | 8 | −1.32 | 4 | 132.96 | 306.89 | 25 | 0.07 | −0.42 | −0.65 | −0.47 | 0.84 | 0.27 |
[i] TPSA, topological polar surface area.
Table 2
Docking results of R. officinalis biocompounds with ptp-A of P. gingivalis (energy in kcal/mol)
| ptp-A docking with compounds | Number of hydrogen bonds | Binding energy | Ligand efficiency | Intermolecular energy | vdW + Hbond + desolv energy | Electrostatic energy | Torsional energy | Total internal unbound |
|---|---|---|---|---|---|---|---|---|
| Carnosic acid | 5 | −7.19 | −0.3 | −8.68 | −7.56 | −1.11 | 1.49 | −1.38 |
| Rosmarinic acid | 10 | −9.81 | −0.38 | −12.2 | −11.88 | −0.31 | 2.39 | −2.23 |
| p-Coumaric acid | 5 | −6.34 | −0.53 | −7.53 | −6.72 | −0.81 | 1.19 | −0.07 |
| Luteolin | 7 | −9.99 | −0.48 | −11.48 | −11.47 | −0.02 | 1.49 | −1.37 |
| Amoxicillin | 4 | −7.18 | −0.29 | −9.26 | −7.3 | −1.97 | 2.09 | −2.12 |
Table 3
Interactions of R. officinalis biocompounds with ptp-A of P. gingivalis
| PTPA docking with compounds | Hydrogen bond interactions | Van der Waals interactions | p–s, p–p T, amide–p interactions | Alkyl/p–alkyl interactions | Salt bridge/attractive charge |
|---|---|---|---|---|---|
| Carnosic acid | 5 (LYS210, TRP214, ASP153) | 6 (LEU289, SER290, PHE213, TRP214, PHE154, SER155) | – | 5 (TRP291, PRO340, PRO156) | – |
| Rosmarinic acid | 10 (HIS522, ASN558, ARG356, GLU564, GLN354) | 4 (SER355, TRP353, ALA523, ASN367) | – | 3 (ALA557, LEU338, ARG356) | 3 (GLU564, GLU336, GLU382) |
| p-Coumaric acid | 5 (SER603, TYR518, GLU45, TYR47) | 5 (TYR516, PHE46, ARG717, PHE49, HIS710) | 1 (TRP602) | – | – |
| Luteolin | 7 (HIS339, LEU388, GLN354, ARG356, TYR334, GLU564, GLN565) | 6 (GLU329, TRP353, ARG357, ASP331, LEU338, GLU336) | 2 (PRO337, SER355) 1 (ARG356) | 2 (VAL335, ARG 356) | – |
| Amoxicillin | 4 (GLU209, ASN288) | 6 (GLY207, ILE208, LEU289, TYR224, HIS339, HIS522) | – | 5 (LEU338, PHE213, PRO340) | – |
Figure 3
Biovia discovery studio visualization of the hydrogen interactions between ptp-A and (A) carnosic acid, (B) rosmarinic acid, (C) p-coumaric acid, (D) luteolin, and (E) amoxicillin