6. Molecular dynamic screening of sesquiterpenoid/sesquiterpenoid alcohol Pogostemon herba as predicted cyclooxygenase inhibitor selective

After the results of the rigid docking to compute possible interaction COX-1 and COX-2 with (alpha-bulnesene (CID94275), alpha-guaiene (CID107152), and

Figure 6.

51

Modeling analysis alpha-patchouli alcohol isomer in complex with COX-1 and COX-2. (a1) – (l1) 3D active site structure of COX-1/COX-2-alpha-patchouli alcohol isomers complexes; (a2) to (l2) Ramachandran plot analysis of COX-1/COX-2-alpha-patchouli alcohol complexes using discovery studio 3.5 viewer Software.

Virtual Screening of Sesquiterpenoid Pogostemon herba as Predicted Cyclooxygenase Inhibitor

DOI: http://dx.doi.org/10.5772/intechopen.85319

## Virtual Screening of Sesquiterpenoid Pogostemon herba as Predicted Cyclooxygenase Inhibitor DOI: http://dx.doi.org/10.5772/intechopen.85319

#### Figure 6.

Modeling analysis alpha-patchouli alcohol isomer in complex with COX-1 and COX-2. (a1) – (l1) 3D active site structure of COX-1/COX-2-alpha-patchouli alcohol isomers complexes; (a2) to (l2) Ramachandran plot analysis of COX-1/COX-2-alpha-patchouli alcohol complexes using discovery studio 3.5 viewer Software.

6. Molecular dynamic screening of sesquiterpenoid/sesquiterpenoid alcohol Pogostemon herba as predicted cyclooxygenase inhibitor

Analysis of virtual modeling of COX-1/COX-2-sesquiterpenoid/sesquiterpenoid alcohol complexes.

COX-2 with (alpha-bulnesene (CID94275), alpha-guaiene (CID107152), and

After the results of the rigid docking to compute possible interaction COX-1 and

Amino acid residues in the active site (by Hex 8.0 software and then Discovery Studio 3.5 software) COX-1 COX-2

> TRP139A, GLU140A, SER143A, ASN144A, LEU145A, GLY235B, GLU236B, THR237B, LEU238B,

LYS211B, THR212B, ASP213B, HIS214B, LYS215B, ARG222B, ILE274B, GLN298B, GLU290B, VAL291B, HEM682B

TRP139A, GLU140A, SER143A, ASN144A, LEU145A, THR237B, LEU238B, GLY235B, GLU236B, GLN241B, GLN330B, LYS333B

TRP139A, SER143A, ASN144A, LEU145A, GLY235B, GLU236B, THR237B, LEU238B, GLN241B,

TRP139A, GLU140A, SER143A, ASN144A, LEU145A, GLY235B, GLU236B, THR237B, LEU238B, GLN241B, GLN330B, LYS33B

Electrostatic: SER143B. Van der Walls: GLY235A, GLU236A, THR237A, LEU238A, ASP239A, GLN241A, LYS333A, TRP139B, GLU140B, ASN144B,

Van der Walls: GLY225A, ASP229A, GLY235A, GLU236A, LEU238A, GLN241A, GLN330A, THR237A, LYS333A, SER143B, TRP139B, GLU140B, ASN144B,

Van der Walls: GLY225A, ASP229A, ASN231A, GLY235A, GLU236A, THR237A, GLN241A, GLN330A, LYS333A, TRP139B, GLU140B, SER143B, ASN144B,

LEU145B, LEU238A

Van der Walls: ASP213A, HIS214A, LYS215A,LYS211A, THR212A, ARG222A, ILE274A, GLN289A, GLU290A, VAL291A,

LYS333B

LEU145B

LEU145B

HEM682A

GLN241B, GLN330B

TRP141A, GLU142A, SER145A, ASN146A, LEU226B, GLY227B, ASP231B, GLN243B, GLY237B, ASN239B, LEU240B, ASP238B,

SER123A, ASN124A, LEU125A, ILE126A, PRO127A, SER128A, PRO129A, GLN372A, PHE373A, GLN274A, LYS534A, PRO544B,

TRP141A, GLU142A, SER145A, ASN146A, LEU226B, ASP231B, GLY237B, ASP238B, ASN239B, LEU240B, GLN243B, ARG335B

SER123A, ASN124A, ILE126A, PRO127A, SER128A, PRO129A, GLN372A, PHE373A, GLN374A, LYS534A, PRO544B, GLU545B

TRP141A, GLU142A, SER145A, ASN146A, LEU226B, ASP231B, GLY237B, ASP238B, ASN239B, LEU240B, GLN243B, ARG335B

Van der Walls: LEU226A, GLY237A, ASP238A, ASN239A, LEU240A, GLU241A, GLN243A, ARG335A, TRP141B, GLU142B,

Van der Walls: VAL147A, LYS224A, ALA225A, LEU226A, GLY227A, ASP231A, GLY233A, GLY237A, ASP238A, ASN239A, LEU240A, ARG335A, TRP141B, GLU142B,

Van der Walls: TRP141A, GLU142A, SER145A, ASN146A, LEU226B, GLY227B, ASP231B, GLY237B, ASN239B, ASP238B, LEU240B, GLU241B, GLN243B, ARG335B

Van der Walls: PRO544A, GLU545A, SER123B, ASN124B, LEU125B, ILE126B, PRO127B, SER128B, PHE373B, GLN372B,

GLN374B, LYS534B

SER145B, ASN146B, VAL147B

Electrostatic: ASN146B.

SER145B

ARG335B

Molecular Docking and Molecular Dynamics

GLU545B

selective

Table 2.

50

No. Virtual modeling

1. alpha-Patchouli alcohol CID442384

2. alpha-Patchouli alcohol CID521903

3. alpha-Patchouli alcohol CID643285

4. alpha-Patchouli alcohol CID3080622

5. alpha-Patchouli alcohol CID10955174

6. alpha-Patchouli alcohol CID56928117

7. alphabulnesene CID94275

8. alpha-guaiene CID107152

9. Seychellene CID519743

seychellene (CID519743). And also, sesquiterpenoid alcohol, such as alpha-Patchouli alcohol isomers (CID442384, CID521903, CID6432585, CID3080622, CID10955174, and CID56928117) to performed active visualization-interaction 2D and 3D, and binding energy using Discovery Studio 3.5 software. The output of the docking, visualization, and binding energy calculation using AMBER12 software and Virtual Molecular Dynamics 1.9.1 obtained the most possible native complex structure of sesquiterpenoid/sesquiterpenoid alcohol of CID94275, CID107152, CID519743, CID442384, CID521903, CID6432585, CID3080622, CID10955174, and CID56928117, respectively, that bind with COX-1 and COX-2 in molecular dynamic with Model Solvent of MM-PBSA (Molecular Mechanics Poisson-Boltzmann Surface Area), which included both backbone and side-chains movements. Therefore, we used AMBER12 to refine the candidate models according to a binding energy calculation for scoring of virtual screening sesquiterpenoid/sesquiterpenoid alcohol compounds as selective inhibitor for COX-1 and/or COX-2. Molecular dynamics (MD) were carried out using AMBER12 and the AMBER-99 force field. The initial structure of the sesquiterpenoid/sesquiterpenoid alcohol inhibitor complex was taken for each compound from the Hex 8.0 docking study. The ligand force fields parameters were taken from the General Amber force Field (GAFF), whereas AM1 ESP atomic partial charges were assigned to the inhibitors. Prior to the free MD simulations, two steps of relaxation were carried out; in the first step, we kept the protein fixed with a constraint of 500 Kcal�mol�<sup>1</sup> � °A�<sup>1</sup> . In the second step, the inhibitor structures were relaxed for 0.5 pico second, during which the protein atoms were restrained to the X-ray coordinates with a force constant of 500 Kcal�mol�<sup>1</sup> � °A�<sup>1</sup> . In the final step, all restraints were removed and the complexes were relaxed for 1 pico second. The temperature of the relaxed system was then equilibrated at 300 Kelvin through 20 pico second of MD using 2 fs time steps. A constant volume periodic boundary was set to equilibrate the temperature of the system by the Langevin dynamics using a collision frequency of 10 ps�<sup>1</sup> and a velocity limit of five temperature units. During the temperature equilibration routine, the complex in the solvent box was restrained to the initial coordinates with a weak force constant of 10 Kcal�mol�<sup>1</sup> � °A�<sup>1</sup> . The final coordinates of the temperature equilibration routine (after 20 ps) were then used to complete a 1 ns molecular dynamics routine using 2 fs time steps, during which the temperature was kept at 300 Kelvin. For the Langevin dynamics a collision frequency of 1 ps�<sup>1</sup> and a velocity limit of 20 temperature units were used. The pressure of the solvated system was equilibrated at 1 bar at a certain density in a constant pressure periodic boundary by an isotropic pressure scaling method employing a pressure relaxation time of 2 ps. The time step of the free MD simulations was 2 fs with a cut-off of 9°A for the non-bonded interaction, and SHAKE was employed to keep all bonds involving hydrogen atoms rigid. Calculation of binding energy was administered using this equation:

results of the analysis of 200 poses: the complex energy, energy ligand protein, and

Virtual Screening of Sesquiterpenoid Pogostemon herba as Predicted Cyclooxygenase Inhibitor

<sup>Δ</sup>Gbind <sup>¼</sup> Gcomplex � Gprotein <sup>þ</sup> Gligand

sesquiterpenoid/sesquiterpenoid alcohol are by Discovery Studio 3.5 and Amber 12,

The different position active site the complexes have led to interaction types, such as hydrogen bond, van der Waals, electrostatic and covalent bond. The different types of interactions in this complex will certainly affect its binding free energy. The use of Poisson-Boltzmann (PB) and Generalized Born (GB) characterized the binding free energy calculation model solvent MMPB/SA and MM-GB/SA in computing the electrostatic component of the solvation free energy. The following equation was employed in binding free energy of the protein-ligand complex.

T is the temperature of the system at 300 Kelvin. The free binding energy (ΔGbinds) of the protein-ligand-complex were evaluated using MMPBSA (Molecular Mechanics Poison Blotzmann Surface Area) method as implemented in Discovery Studio 3.5 and AMBER12. MMPBSA has always been considered as a proper method to compare binding energies of similar ligands. MMPBSA measures the

In (5.2), Gcomplex is the absolute free energy of the complex, Gprotein is the absolute free energy of the protein, and Gligand is the absolute free energy of the ligand [6, 8, 33, 38]. The free energy of each term was estimated as a sum of the three terms:

[GMM] is the molecular mechanics energy of the molecule expressed as the sum of the internal energy (bond, angle, and dihedral) (Eint), electrostatic energy (Eele),

[Eele] solvation energy can be categorized as polar and nonpolar part. Polar part gives electrostatic contribution to solvation by solving the linear Poisson Boltzmann equation within the solvent's continuum model [33]. The binding energy calculation in AMBER12 includes preparation, minimization, heating, and energy calculations (complex, protein, and ligand). We extracted 200 snapshots (at time intervals of 2 ps) for each species (complex, protein, and ligand). Furthermore, the visualization using virtual model dynamic (VMD 1.9.1 software) is shown in Figure 7(a–f) and (j–o), and then the binding energy calculation can be obtained from the data ligand energy, protein energy, and energy complex by AMBER12, 200 times/poses, respectively; next, the binding free energy calculation is calculated by Eq. (7.2) and shown in Figure 7(g), (h), (i), (p), (q), and (r) and summarized in Figure 5(s). Figure 5(s) shows that the binding energy calculation (PBSA Model

binding free energy based on thermodynamic cycle in which molecular mechanical energy and the continuum solvent approaches are simultaneously used [6, 8, 33, 38]. The calculation of binding free energy is computed as:

ΔG ¼ ΔH–TΔS (8)

<sup>Δ</sup>Gbind <sup>¼</sup> Gcomplex � Gprotein <sup>þ</sup> Gligand (9)

½ �¼ G ½ �þ EMM Gsol ½ �� T � ½ � S (10)

½ �¼ EMM Eint ½ �þ Eele ½ �þ ½ � Evdw (11)

energy. The binding energy was calculated use the following equation:

Analysis of the active site and the binding energies COX-1/COX-2-

as shown in Figure 7(g–i), (p–r) and (o).

summarized and presented in Figure 7 (s).

DOI: http://dx.doi.org/10.5772/intechopen.85319

and van der Waals term (Evdw):

53

$$
\Delta \mathbf{G}\_{\text{bind}} = \mathbf{G}\_{\text{complex}} - \left[ \mathbf{G}\_{\text{protein}} + \mathbf{G}\_{\text{ligand}} \right],
$$

[6, 8, 33–37].

We were using AMBER12 software and Virtual Molecular Dynamics 1.9.1 to simulate the most possible native complex structure of sesquiterpenoid/ sesquiterpenoid alcohol (CID94275, CID107152, CID519743, CID442384, CID521903, CID6432585, CID3080622, CID10955174, and CID56928117), respectively, that binds with COX-1 and COX-2 in molecular dynamic with MM-PBSA Model Solvent. The MD simulations of the sesquiterpenoid/sesquiterpenoid alcoholinhibitor, some of them are alpha-patchouli alcohol-COX-1/COX-2 complexes. The structure of the complexes is shown in Figure 7(a–f) and (j–o). We also acquire the Virtual Screening of Sesquiterpenoid Pogostemon herba as Predicted Cyclooxygenase Inhibitor DOI: http://dx.doi.org/10.5772/intechopen.85319

results of the analysis of 200 poses: the complex energy, energy ligand protein, and energy. The binding energy was calculated use the following equation:

$$
\Delta \mathbf{G}\_{\text{bind}} = \mathbf{G}\_{\text{complex}} - \left[ \mathbf{G}\_{\text{protein}} + \mathbf{G}\_{\text{ligand}} \right],
$$

as shown in Figure 7(g–i), (p–r) and (o).

seychellene (CID519743). And also, sesquiterpenoid alcohol, such as alpha-Patchouli alcohol isomers (CID442384, CID521903, CID6432585, CID3080622, CID10955174, and CID56928117) to performed active visualization-interaction 2D and 3D, and binding energy using Discovery Studio 3.5 software. The output of the docking, visualization, and binding energy calculation using AMBER12 software and Virtual Molecular Dynamics 1.9.1 obtained the most possible native complex structure of sesquiterpenoid/sesquiterpenoid alcohol of CID94275, CID107152, CID519743, CID442384, CID521903, CID6432585, CID3080622, CID10955174, and CID56928117, respectively, that bind with COX-1 and COX-2 in molecular dynamic with Model Solvent of MM-PBSA (Molecular Mechanics Poisson-Boltzmann Surface Area), which included both backbone and side-chains movements. Therefore, we used AMBER12 to refine the candidate models according to a binding energy calculation for scoring of virtual screening sesquiterpenoid/sesquiterpenoid alcohol compounds as selective inhibitor for COX-1 and/or COX-2. Molecular dynamics (MD) were carried out using AMBER12 and the AMBER-99 force field. The initial structure of the sesquiterpenoid/sesquiterpenoid alcohol inhibitor complex was taken for each compound from the Hex 8.0 docking study. The ligand force fields parameters were taken from the General Amber force Field (GAFF), whereas AM1 ESP atomic partial charges were assigned to the inhibitors. Prior to the free MD simulations, two steps of relaxation were carried out; in the first step, we kept the

Molecular Docking and Molecular Dynamics

protein fixed with a constraint of 500 Kcal�mol�<sup>1</sup> � °A�<sup>1</sup>

weak force constant of 10 Kcal�mol�<sup>1</sup> � °A�<sup>1</sup>

500 Kcal�mol�<sup>1</sup> � °A�<sup>1</sup>

using this equation:

[6, 8, 33–37].

52

inhibitor structures were relaxed for 0.5 pico second, during which the protein atoms were restrained to the X-ray coordinates with a force constant of

plexes were relaxed for 1 pico second. The temperature of the relaxed system was then equilibrated at 300 Kelvin through 20 pico second of MD using 2 fs time steps. A constant volume periodic boundary was set to equilibrate the temperature of the system by the Langevin dynamics using a collision frequency of 10 ps�<sup>1</sup> and a velocity limit of five temperature units. During the temperature equilibration routine, the complex in the solvent box was restrained to the initial coordinates with a

ture equilibration routine (after 20 ps) were then used to complete a 1 ns molecular dynamics routine using 2 fs time steps, during which the temperature was kept at 300 Kelvin. For the Langevin dynamics a collision frequency of 1 ps�<sup>1</sup> and a velocity limit of 20 temperature units were used. The pressure of the solvated system was equilibrated at 1 bar at a certain density in a constant pressure periodic boundary by an isotropic pressure scaling method employing a pressure relaxation time of 2 ps. The time step of the free MD simulations was 2 fs with a cut-off of 9°A for the non-bonded interaction, and SHAKE was employed to keep all bonds involving hydrogen atoms rigid. Calculation of binding energy was administered

ΔGbind ¼ Gcomplex � Gprotein þ Gligand

We were using AMBER12 software and Virtual Molecular Dynamics 1.9.1 to

CID521903, CID6432585, CID3080622, CID10955174, and CID56928117), respectively, that binds with COX-1 and COX-2 in molecular dynamic with MM-PBSA Model Solvent. The MD simulations of the sesquiterpenoid/sesquiterpenoid alcoholinhibitor, some of them are alpha-patchouli alcohol-COX-1/COX-2 complexes. The structure of the complexes is shown in Figure 7(a–f) and (j–o). We also acquire the

simulate the most possible native complex structure of sesquiterpenoid/ sesquiterpenoid alcohol (CID94275, CID107152, CID519743, CID442384,

. In the final step, all restraints were removed and the com-

. In the second step, the

. The final coordinates of the tempera-

Analysis of the active site and the binding energies COX-1/COX-2 sesquiterpenoid/sesquiterpenoid alcohol are by Discovery Studio 3.5 and Amber 12, summarized and presented in Figure 7 (s).

The different position active site the complexes have led to interaction types, such as hydrogen bond, van der Waals, electrostatic and covalent bond. The different types of interactions in this complex will certainly affect its binding free energy. The use of Poisson-Boltzmann (PB) and Generalized Born (GB) characterized the binding free energy calculation model solvent MMPB/SA and MM-GB/SA in computing the electrostatic component of the solvation free energy. The following equation was employed in binding free energy of the protein-ligand complex.

$$
\Delta \mathbf{G} = \Delta \mathbf{H} \mathbf{-T} \Delta \mathbf{S} \tag{8}
$$

T is the temperature of the system at 300 Kelvin. The free binding energy (ΔGbinds) of the protein-ligand-complex were evaluated using MMPBSA (Molecular Mechanics Poison Blotzmann Surface Area) method as implemented in Discovery Studio 3.5 and AMBER12. MMPBSA has always been considered as a proper method to compare binding energies of similar ligands. MMPBSA measures the binding free energy based on thermodynamic cycle in which molecular mechanical energy and the continuum solvent approaches are simultaneously used [6, 8, 33, 38]. The calculation of binding free energy is computed as:

$$
\Delta \mathbf{G}\_{\text{bind}} = \mathbf{G}\_{\text{complex}} - \left[ \mathbf{G}\_{\text{protein}} + \mathbf{G}\_{\text{ligand}} \right] \tag{9}
$$

In (5.2), Gcomplex is the absolute free energy of the complex, Gprotein is the absolute free energy of the protein, and Gligand is the absolute free energy of the ligand [6, 8, 33, 38]. The free energy of each term was estimated as a sum of the three terms:

$$\mathbf{[G]} = \mathbf{[E\_{MM}]} + \mathbf{[G\_{sol}]} - \mathbf{T} \cdot \mathbf{[S]} \tag{10}$$

[GMM] is the molecular mechanics energy of the molecule expressed as the sum of the internal energy (bond, angle, and dihedral) (Eint), electrostatic energy (Eele), and van der Waals term (Evdw):

$$\begin{aligned} \left[ \mathbf{E\_{MM}} \right] &= \left[ \mathbf{E\_{int}} \right] + \left[ \mathbf{E\_{ele}} \right] + \left[ \mathbf{E\_{vdw}} \right] \end{aligned} \tag{11}$$

[Eele] solvation energy can be categorized as polar and nonpolar part. Polar part gives electrostatic contribution to solvation by solving the linear Poisson Boltzmann equation within the solvent's continuum model [33]. The binding energy calculation in AMBER12 includes preparation, minimization, heating, and energy calculations (complex, protein, and ligand). We extracted 200 snapshots (at time intervals of 2 ps) for each species (complex, protein, and ligand). Furthermore, the visualization using virtual model dynamic (VMD 1.9.1 software) is shown in Figure 7(a–f) and (j–o), and then the binding energy calculation can be obtained from the data ligand energy, protein energy, and energy complex by AMBER12, 200 times/poses, respectively; next, the binding free energy calculation is calculated by Eq. (7.2) and shown in Figure 7(g), (h), (i), (p), (q), and (r) and summarized in Figure 5(s). Figure 5(s) shows that the binding energy calculation (PBSA Model

Solvent) of COX-1 CID442384 complexes (28.386 1.102 Kcal/mol) was smaller than the COX-2 CID442384 complexes (16.215 0.985 Kcal/mol) and also ligands CID6432585, CID3080622, CID10955174, and CID56928117. The similar research, docking studies ligand salicin compound from D. gangeticum to COX-1 and COX-2 protein receptor, showed high binding affinity COX-2 protein (5 Kcal/mol) and lesser interaction with COX-1 (3.79 Kcal/mol). Therefore, salicin could predict as COX-2 inhibitor selective and anti-cancerous compound [6].

Ebinds (ΔG) was determined on the basis of calculation of the Eq. (5.2). Gligand value is influenced by the type of ligand. Gligand will affect the value Ebinds and ratio of Ebinds COX-1 and Ebinds COX-2. Hence, in-silico analysis can be used as an approach to determine the selectivity of the ligand as an inhibitor of COX-1/COX-2. Ebinds (binding energy calculations) seychellene (CID519743) (Figure 7(s)) showed as candidate non-selective COX inhibitor and it's similar to value of selective IC50, as shown in Figure 8.

Figure 7.

55

Binding energy calculation of alpha-patchouli alcohol isomers binds to COX-1/COX-2. (a) and (f) and (j)–(o) virtual molecule dynamic complexes of COX-1/COX-2-alpha-patchouli alcohol isomers. (g), (h), (i), (p),(q), and (r) comparison of binding energy calculation of alpha-patchouli alcohol isomer-COX-1 (blue) and COX-2 (red) complexes. (s) Histogram of binding energy calculation of COX-1 (blue)/COX-2 (red) sesquiterpenoid/sesquiterpenoid alcohol complexes by discovery studio 3.5 (s-1) and Amber 12 (s-2).

Virtual Screening of Sesquiterpenoid Pogostemon herba as Predicted Cyclooxygenase Inhibitor

DOI: http://dx.doi.org/10.5772/intechopen.85319

## Virtual Screening of Sesquiterpenoid Pogostemon herba as Predicted Cyclooxygenase Inhibitor DOI: http://dx.doi.org/10.5772/intechopen.85319

#### Figure 7.

Solvent) of COX-1 CID442384 complexes (28.386 1.102 Kcal/mol) was smaller than the COX-2 CID442384 complexes (16.215 0.985 Kcal/mol) and also ligands CID6432585, CID3080622, CID10955174, and CID56928117. The similar research, docking studies ligand salicin compound from D. gangeticum to COX-1 and COX-2 protein receptor, showed high binding affinity COX-2 protein (5 Kcal/mol) and lesser interaction with COX-1 (3.79 Kcal/mol). Therefore, salicin could predict as

Ebinds (ΔG) was determined on the basis of calculation of the Eq. (5.2). Gligand value is influenced by the type of ligand. Gligand will affect the value Ebinds and ratio of Ebinds COX-1 and Ebinds COX-2. Hence, in-silico analysis can be used as an approach to determine the selectivity of the ligand as an inhibitor of COX-1/COX-2. Ebinds (binding energy calculations) seychellene (CID519743) (Figure 7(s)) showed as candidate non-selective COX inhibitor and it's similar to value of

COX-2 inhibitor selective and anti-cancerous compound [6].

selective IC50, as shown in Figure 8.

Molecular Docking and Molecular Dynamics

54

Binding energy calculation of alpha-patchouli alcohol isomers binds to COX-1/COX-2. (a) and (f) and (j)–(o) virtual molecule dynamic complexes of COX-1/COX-2-alpha-patchouli alcohol isomers. (g), (h), (i), (p),(q), and (r) comparison of binding energy calculation of alpha-patchouli alcohol isomer-COX-1 (blue) and COX-2 (red) complexes. (s) Histogram of binding energy calculation of COX-1 (blue)/COX-2 (red) sesquiterpenoid/sesquiterpenoid alcohol complexes by discovery studio 3.5 (s-1) and Amber 12 (s-2).

The relationship binding energy, Ki and IC50 is defined by Eq. (5.5) and (5.6) [39, 40].

$$\Delta \mathbf{G}\_{\text{bind}} = 2.303 \,\mathrm{R} \cdot \mathrm{T} \,\log \,\mathrm{K} \,\tag{12}$$

$$\text{For competitive inhibition } : \mathrm{K}\_{\mathrm{i}} = (\mathrm{IC}\_{50} - \mathrm{E}/2)/(\mathrm{S}/\mathrm{K}\mathrm{m} + 1)$$

$$\text{For uncompact inhibition inhibtion } : \mathrm{K}\_{\mathrm{i}} = (\mathrm{IC}\_{50} - \mathrm{E}/2)/(\mathrm{Km}/\mathrm{S} + 1)$$

$$\text{if } \mathrm{S} = \mathrm{Km}, \mathrm{K}\_{\mathrm{i}} = \mathrm{IC}\_{50}/2;$$

$$\text{if } \mathrm{S} >> \mathrm{K}\_{\mathrm{m}}, \mathrm{K}\_{\mathrm{i}} << \mathrm{IC}\_{50};$$

$$\text{if } \mathrm{S} << \mathrm{K}\_{\mathrm{m}} \,\mathrm{K}\_{\mathrm{i}} \approx \mathrm{IC}\_{50}.$$

For non-competitive inhibition: Ki = IC50 when S = Km or S < < Km and for tightly bound inhibitor:

$$\mathbf{K}\_{\mathbf{i}} = \mathbf{I}\mathbf{C}\_{\mathbf{5}0}\mathbf{-}\mathbf{E}/\mathbf{2} \tag{13}$$

According Eq. (5.5), selectivities Ebinds and selectivities IC50 some of them are complexes of CID442384, CID519743, CID3060622, CID107152, and CID94275 with

The relative selectivity of COX-1 and COX-2 inhibitors based on the IC80 ratio is declared logarithmic, so 0 is the baseline, that is, the compound in the line is equiactive to COX-1 and COX-2. Compounds above the COX-

Virtual Screening of Sesquiterpenoid Pogostemon herba as Predicted Cyclooxygenase Inhibitor

Collectively, our results suggest that alpha-Patchouli alcohol (CID442384) as candidate COX-2 inhibitor selective, alpha-guaiene (CID107152), alpha

bulnesene (CID94275), alpha patchouli alcohol isomers (CID3060622, CID6432585, CID10955174, and CID56928117) as candidate COX-1 inhibitor selective, and alpha-patchouli alcohol CID521903, seychellene as candidate COX non

selective. These in silico analysis data will be completed with the biological activity

Selectivities of IC50 versus Ebinds sesquiterpenoid/sesquiterpenoid alcohol Pogostemon herba to COX-1/COX-2.

COX-1/COX-2, as shown in Figure 10.

1-selective line and below are COX-2 selective [34].

DOI: http://dx.doi.org/10.5772/intechopen.85319

analysis.

Figure 10.

57

Figure 9.

where: E = enzyme, S = Substrate, P=Product.

The latest development is more selective selective COX-2 drugs, such as valdecoxib (Bextra™) and etoricoxib (Arcoxi™) and lumiracoxib (Prexige). Several COX-2-selective drugs in NSAIDs are presented in Figure 9. The classification of COX inhibition is based on the potential inhibition of COX isoforms and specifically the IC50 ratio of COX-1 and COX-2 (or selectivity index) [20].

Eq. (5.5) can be used as the COX-1/COX-2 selectivity approach in in-silico analysis, which without calculating for competitive, un-competitive and noncompetitive, shows that ΔGbind are directly proportional to IC50 values.

While the selectivity of COX-1/COX-2 is expressed in the equation:

$$\text{IC}\_{50} \text{ selecting, } \text{COX} - 1/\text{COX} - 2 = \log \left( \text{IC}\_{50}, \text{ratio} \left( \text{COX} - 2/\text{COX} - 1 \right) \right) \tag{14}$$

Therefore selectivity in in-silico analysis can be expressed as:

$$\text{E\_{bind}\,\text{selecttivity}}, \text{COX} - 1/\text{COX} - 2 = \log \left( \text{E}\_{\text{bind}}, \text{ratio} \left( \text{COX} - 2/\text{COX} - 1 \right) \right) \tag{15}$$

Figure 8.

Virtual Screening of Sesquiterpenoid Pogostemon herba as Predicted Cyclooxygenase Inhibitor DOI: http://dx.doi.org/10.5772/intechopen.85319

#### Figure 9.

The relationship binding energy, Ki and IC50 is defined by Eq. (5.5) and (5.6)

For competitive inhibition : Ki ¼ ð Þ IC50–E=2 =ð Þ S=Km þ 1 For uncompetitive inhibition : Ki ¼ ð Þ IC50–E=2 =ð Þ Km=S þ 1 if S ¼ Km,Ki ¼ IC50=2; if S>>Km,Ki <<IC50; if S<<Km Ki ≈ IC50:

For non-competitive inhibition: Ki = IC50 when S = Km or S < < Km and for

The latest development is more selective selective COX-2 drugs, such as valdecoxib (Bextra™) and etoricoxib (Arcoxi™) and lumiracoxib (Prexige). Several COX-2-selective drugs in NSAIDs are presented in Figure 9. The classification of COX inhibition is based on the potential inhibition of COX isoforms and specifically the IC50 ratio of COX-1 and COX-2 (or selectivity index) [20]. Eq. (5.5) can be used as the COX-1/COX-2 selectivity approach in in-silico analysis, which without calculating for competitive, un-competitive and noncompetitive, shows that ΔGbind are directly proportional to IC50 values. While the selectivity of COX-1/COX-2 is expressed in the equation:

IC50 selectivity,COX � 1=COX � 2 ¼ log ICð Þ <sup>50</sup>;ratio COX ð Þ � 2=COX � 1

Ebind selectivity,COX � 1=COX � 2 ¼ log Eð Þ bind;ratio COX ð Þ � 2=COX � 1

Therefore selectivity in in-silico analysis can be expressed as:

Regression linier analyses of IC50 fraction-5 to COX-1 and COX-2 [39].

ΔGbind ¼ 2:303 R � T log Ki (12)

Ki ¼ IC50–E=2 (13)

(14)

(15)

[39, 40].

Figure 8.

56

tightly bound inhibitor:

Molecular Docking and Molecular Dynamics

where: E = enzyme, S = Substrate, P=Product.

The relative selectivity of COX-1 and COX-2 inhibitors based on the IC80 ratio is declared logarithmic, so 0 is the baseline, that is, the compound in the line is equiactive to COX-1 and COX-2. Compounds above the COX-1-selective line and below are COX-2 selective [34].

According Eq. (5.5), selectivities Ebinds and selectivities IC50 some of them are complexes of CID442384, CID519743, CID3060622, CID107152, and CID94275 with COX-1/COX-2, as shown in Figure 10.

Collectively, our results suggest that alpha-Patchouli alcohol (CID442384) as candidate COX-2 inhibitor selective, alpha-guaiene (CID107152), alpha bulnesene (CID94275), alpha patchouli alcohol isomers (CID3060622, CID6432585, CID10955174, and CID56928117) as candidate COX-1 inhibitor selective, and alpha-patchouli alcohol CID521903, seychellene as candidate COX non selective. These in silico analysis data will be completed with the biological activity analysis.

#### Figure 10.

Selectivities of IC50 versus Ebinds sesquiterpenoid/sesquiterpenoid alcohol Pogostemon herba to COX-1/COX-2.
