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Targeting prolyl tripeptidyl peptidase from Porphyromonas gingivalis with the bioactive compounds from Rosmarinus officinalis

Ashwin Kumar Ramalingam
Ashwin Kumar Ramalingam
, 
Smiline Girija Aseervatham Selvi
Smiline Girija Aseervatham Selvi
 and 
Vijayashree Priyadharsini Jayaseelan
Vijayashree Priyadharsini Jayaseelan
   | Jun 04, 2020
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Article Category: Technical report
Published Online: Jun 04, 2020
Page range: 197 - 203
DOI: https://doi.org/10.1515/abm-2019-0061
Keywords
© 2019 Ashwin Kumar Ramalingam et al., published by Sciendo
This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Figure 1

3D structure of ptp-A as visualized by RasMol (helix, pink color; beta sheet, yellow; turns, white). 3D, three dimensional
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
Structure of the selected biocompounds from R. officinalis

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
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

Molinspiration calculations of Rosmarinus officinalis biocompounds and drug likeliness of the R. officinalis against ptp-A of Porphyromonas gingivalis

CompoundsMolecular weightMolecular formulaHydrogen bond donorHydrogen bond acceptorLogPRotatable bondsTPSAVolumeN atomsG protein-coupled receptors ligandIon channel modulatorKinase inhibitorNuclear receptor ligandProtease inhibitorEnzyme inhibitor
Carnosic acid332.44C20H28O4344.60277.75322.31240.410.24−0.240.72−0.010.32
Rosmarinic acid360.318C18H16O8581.637144.52303.54260.17−0.08−0.180.570.150.24
p-Coumaric acid164.16C9H8O3231.43257.53146.4812−0.56−0.26−0.91−0.12−0.87−0.15
Luteolin286.239C15H10O6461.971111.12232.0721−0.02−0.070.260.39−0.220.28
Amoxicillin365.404C16H19N3O5S58−1.324132.96306.89250.07−0.42−0.65−0.470.840.27

Docking results of R. officinalis biocompounds with ptp-A of P. gingivalis (energy in kcal/mol)

ptp-A docking with compoundsNumber of hydrogen bondsBinding energyLigand efficiencyIntermolecular energyvdW + Hbond + desolv energyElectrostatic energyTorsional energyTotal internal unbound
Carnosic acid5−7.19−0.3−8.68−7.56−1.111.49−1.38
Rosmarinic acid10−9.81−0.38−12.2−11.88−0.312.39−2.23
p-Coumaric acid5−6.34−0.53−7.53−6.72−0.811.19−0.07
Luteolin7−9.99−0.48−11.48−11.47−0.021.49−1.37
Amoxicillin4−7.18−0.29−9.26−7.3−1.972.09−2.12

Interactions of R. officinalis biocompounds with ptp-A of P. gingivalis

PTPA docking with compoundsHydrogen bond interactionsVan der Waals interactionsp–s, p–p T, amide–p interactionsAlkyl/p–alkyl interactionsSalt bridge/attractive charge
Carnosic acid5 (LYS210, TRP214, ASP153)6 (LEU289, SER290, PHE213, TRP214, PHE154, SER155)–5 (TRP291, PRO340, PRO156)–
Rosmarinic acid10 (HIS522, ASN558, ARG356, GLU564, GLN354)4 (SER355, TRP353, ALA523, ASN367)–3 (ALA557, LEU338, ARG356)3 (GLU564, GLU336, GLU382)
p-Coumaric acid5 (SER603, TYR518, GLU45, TYR47)5 (TYR516, PHE46, ARG717, PHE49, HIS710)1 (TRP602)––
Luteolin7 (HIS339, LEU388, GLN354, ARG356, TYR334, GLU564, GLN565)6 (GLU329, TRP353, ARG357, ASP331, LEU338, GLU336)2 (PRO337, SER355)1 (ARG356)2 (VAL335, ARG 356)–
Amoxicillin4 (GLU209, ASN288)6 (GLY207, ILE208, LEU289, TYR224, HIS339, HIS522)–5 (LEU338, PHE213, PRO340)–
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