**Abstract**

Inflammation is the body's defense mechanism to eradicate the spread of injurious agents in the affected mammalian tissues with a number of cellular mediators. Nonsteroidal anti-inflammatory drugs (NSAIDs) are the most commonly used drugs worldwide in such situations. The mode of action of the non-steroid antiinflammatory drugs (NSAIDs) is attributed primarily to the inhibition of prostaglandin (PG) synthesis, and more specifically, to the inhibition of the COX enzyme system. This work can be considered as an effort to gain a deeper insight into the physiochemical properties of a few well-known NSAIDs namely; ketoprofen, fenoprofen, flurbiprofen and ibuprofen. A quantum computational approach was used to predict geometry, molecular electrostatic potential (MESP), polarizability, hyperpolarizability and molecular docking study of all selected NSAIDs with human COX-1 and COX-2 enzymes were done to predict the most active drug among the four and to demonstrate good selectivity profile with COX enzymes.

**Keywords:** organic chemistry, theoretical chemistry, pharmaceutical chemistry, DFT, molecular docking, propionic acid derivatives

## **1. Introduction**

Nonsteroidal anti-inflammatory drugs (NSAID) are a class of drugs that reduce pain, decrease fever, prevent blood clots and, in higher doses decrease inflammations too. NSAIDs have been widely used to treat a number of diseases such as heart disease, various cancers, and Alzheimer's, pathogenic conditions. The term nonsteroidal distinguishes these drugs from steroids, which having a similar eicosanoiddepressing, anti-inflammatory action and have a broad range of other effects [1]. NSAIDs obstruct the generation of prostaglandins (chemical messengers that regulate inflammation, fever, and the sensation of pain) by restraining the activity of a

format and were converted to GJF (Gaussian Job File) input files using the

*DFT and Molecular Docking Studies of a Set of Non-Steroidal Anti-Inflammatory Drugs…*

(NLO) properties of AMB were also calculated at the same level of theory.

defined for the active site and box sizes are set to 20 Å [2, 13, 14].

Further, molecular docking was also conducted to predict binding poses, bio affinity and virtual screening of the selected drugs into the 3D crystal structure of cyclooxygenase-2 (PDB ID: 1CX2) and cyclooxygenase-1 (PDB ID: 1EQG) using GLIDE Dock Program in Schrödinger Maestro software. The protein structure was refined using the protein preparation wizard, which employs under restrained minimization and heavy atoms were restrained by using OPLS 2003 force field. The ligands were subjected to ligand preparation using the ligand preparation wizard (Lig prep) of Schrödinger software in the Maestro interface (11.5). Grid center is

The optimized structures of (a) fenoprofen, (b) ketoprofen, (c) flurbiprofen and (d) ibuprofen were calculated using B3LYP/6311G++(d,p) level of the theory and shown in **Figure 2**. The optimized geometries were compared to crystallographic data in the Cambridge Crystallographic Data Center to correlation coefficient factor. The calculated Pearson correlation coefficient for ketoprofen, fenoprofen and Ibuprofen has given in **Table 1**; the crystallographic data for flurbiprofen is not available yet. The Pearson correlation coefficient (PCC), or Pearson's r, the Pearson product-moment correlation coefficient (PPMCC), or the bivariate correlation is a statistic that measures linear correlation between two variables X and Y. Here, this method is used to find out the linear regression between the experimental and computationally calculated geometric parameters. Normally, it has a value between +1 and 1, where +1 indicates total positive linear correlation, 0 is no linear correlation, and 1 is total negative linear correlation [15].

The thermo-chemical parameters, such as enthalpy (H), entropy (S), Gibb's free energy (G) were calculated to find which drug is more stable by comparing G and S

All the quantum calculations have been performed by density functional theory using a Gaussian 09 software package [9]. The initial geometries chosen for calculation was taken from the PubChem database and optimized with B3LYP/6311G++(d,p) level of the theory [7]. The B3LYP is Becke's three-parameter practical hybrid methods that add the exchange and electronic correlation terms in DFT, including the Lee, Yang Parr (LYP) functional. The optimized geometry was compared to crystallographic data in the Cambridge Crystallographic Data Center, such a comparison between the experimental and theoretical values helps to reduce the error in the optimized geometry. The optimized geometry was used for the calculations of harmonic vibrational frequencies at the B3LYP/6311G++(d,p) method, it also helps to ensure the systems to be local minimum number imaginary vibration frequencies. The thermochemical properties [10–12] like, hardness (η), softness (S), chemical potential (μ), electronegativity (χ) and electrophilicity index (ω), were calculated using Koopmans' theorem for closed-shell compounds. Electrostatic potential analysis has also been made to identify the mapping surface of drugs. Dipole moments, linear and non-linear optical

application Open Babel [8].

*DOI: http://dx.doi.org/10.5772/intechopen.93828*

**2.2 Computational details**

**3. Results and discussion**

**3.2 Thermo-chemical properties**

**75**

**3.1 Molecular geometry**

**Figure 1.** *Chemical structure of propionic acid derivatives.*

compound, cyclooxygenase (COX); COX-1 and COX-2. Both the COX-1 and COX-2 enzymes serve important homeostatic roles in the human body. Depending on their chemical structures, NSAIDs are broadly divided into two major classes like nonselective COX inhibitors and selective COX-2 inhibitors. The classification based on the chemical structure is non-selective COX inhibitors and selective COX-2 inhibitors [2–5]. The non-selective COX inhibitors are salicylates, propionic acid derivatives, enolic acid (oxicam) derivatives, anthranilic acid derivatives, selective COX-2 inhibitors, sulfonanilide, and others. In which, COX-1 is considered as important for the production of prostaglandins of homeostatic maintenance, such as platelet aggregation, the regulation of blood flow in the kidney and stomach, and the regulation of gastric acid secretion. While COX-2 is considered as an inducible isoenzyme, although there is some constitutive expression in the kidney, brain, bone, female reproductive system, and gastrointestinal (GI) tract. Thus, the COX-2 is an enzyme plays an important role in pain and inflammatory processes [1–3, 6].

The profen drugs are a category of nonselective, non-steroidal antiinflammatory drugs (NSAIDs), which reduce pain (analgesia), body temperature during fever (antipyretic), signs of inflammation (anti-inflammatory activity), and in mice, slow the development of cancers. They are one of the most commonly prescribed pain medications. The profen drugs are derivatives of 2 phenylpropanoic acid. In this work, we have preferred such propionic acid derivatives. 2-phenylpropanoic acid- profen drugs and their general chemical structure are depicted in **Figure 1**. Few drugs under this category are; ibuprofen, ketoprofen, naproxen, fenoprofen, flurbiprofen, and oxaprozin. In an effort to elucidate a more deeper insight on the physicochemical properties of 2-phenylpropanoic acid- profen drugs we present a detailed discussion on quantum computational calculations and predictions based on their structural geometry, frontier molecular orbitals nonlinear optical properties (NLO), of all selected compounds, were done using B3LYP/ 6311G++(d,p) level of theory. In addition, the computationally calculated electronic properties such as Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO), Bond Dissociation Enthalpy (BDE), ionization potential (IP), electron affinity (EA), hardness (η), softness (S), electronegativity (χ) and electrophilic index (ω) were also calculated to get an insight into its property by means of its anti-inflammatory activities. This study will offer knowledge of their action and also help us to design new drugs with therapeutic effects, experimental and thus computational studies are of interest for the rationale of the action mechanism of bioactive compounds. Further, in order to have a better understanding about the interaction with target proteins, molecular docking was also conducted by determining the probable binding modes of it by inserting all selected ligands into the active sites of the COX enzymes.

#### **2. Materials and method**

#### **2.1 Materials**

The input structures the drugs; ketoprofen (PubChem: 3825), ibuprofen (PubChem: 3672), fenoprofen (PubChem: 3342) and flurbiprofen (PubChem: 3394) were taken from the PubChem database [7] which are in SDF (Standard Data File)

*DFT and Molecular Docking Studies of a Set of Non-Steroidal Anti-Inflammatory Drugs… DOI: http://dx.doi.org/10.5772/intechopen.93828*

format and were converted to GJF (Gaussian Job File) input files using the application Open Babel [8].

## **2.2 Computational details**

compound, cyclooxygenase (COX); COX-1 and COX-2. Both the COX-1 and COX-2 enzymes serve important homeostatic roles in the human body. Depending on their chemical structures, NSAIDs are broadly divided into two major classes like nonselective COX inhibitors and selective COX-2 inhibitors. The classification based on the chemical structure is non-selective COX inhibitors and selective COX-2 inhibitors [2–5]. The non-selective COX inhibitors are salicylates, propionic acid derivatives, enolic acid (oxicam) derivatives, anthranilic acid derivatives, selective COX-2 inhibitors, sulfonanilide, and others. In which, COX-1 is considered as important for the production of prostaglandins of homeostatic maintenance, such as platelet aggregation, the regulation of blood flow in the kidney and stomach, and the regulation of gastric acid secretion. While COX-2 is considered as an inducible isoenzyme, although there is some constitutive expression in the kidney, brain, bone, female reproductive system, and gastrointestinal (GI) tract. Thus, the COX-2 is an enzyme plays an important role in pain and inflammatory processes [1–3, 6].

The profen drugs are a category of nonselective, non-steroidal antiinflammatory drugs (NSAIDs), which reduce pain (analgesia), body temperature during fever (antipyretic), signs of inflammation (anti-inflammatory activity), and in mice, slow the development of cancers. They are one of the most commonly

ing about the interaction with target proteins, molecular docking was also

ligands into the active sites of the COX enzymes.

**2. Materials and method**

**2.1 Materials**

**74**

**Figure 1.**

*Chemical structure of propionic acid derivatives.*

*Density Functional Theory Calculations*

conducted by determining the probable binding modes of it by inserting all selected

The input structures the drugs; ketoprofen (PubChem: 3825), ibuprofen (PubChem: 3672), fenoprofen (PubChem: 3342) and flurbiprofen (PubChem: 3394) were taken from the PubChem database [7] which are in SDF (Standard Data File)

phenylpropanoic acid. In this work, we have preferred such propionic acid derivatives. 2-phenylpropanoic acid- profen drugs and their general chemical structure are depicted in **Figure 1**. Few drugs under this category are; ibuprofen, ketoprofen, naproxen, fenoprofen, flurbiprofen, and oxaprozin. In an effort to elucidate a more deeper insight on the physicochemical properties of 2-phenylpropanoic acid- profen drugs we present a detailed discussion on quantum computational calculations and predictions based on their structural geometry, frontier molecular orbitals nonlinear optical properties (NLO), of all selected compounds, were done using B3LYP/ 6311G++(d,p) level of theory. In addition, the computationally calculated electronic properties such as Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO), Bond Dissociation Enthalpy (BDE), ionization potential (IP), electron affinity (EA), hardness (η), softness (S), electronegativity (χ) and electrophilic index (ω) were also calculated to get an insight into its property by means of its anti-inflammatory activities. This study will offer knowledge of their action and also help us to design new drugs with therapeutic effects, experimental and thus computational studies are of interest for the rationale of the action mechanism of bioactive compounds. Further, in order to have a better understand-

prescribed pain medications. The profen drugs are derivatives of 2-

All the quantum calculations have been performed by density functional theory using a Gaussian 09 software package [9]. The initial geometries chosen for calculation was taken from the PubChem database and optimized with B3LYP/6311G++(d,p) level of the theory [7]. The B3LYP is Becke's three-parameter practical hybrid methods that add the exchange and electronic correlation terms in DFT, including the Lee, Yang Parr (LYP) functional. The optimized geometry was compared to crystallographic data in the Cambridge Crystallographic Data Center, such a comparison between the experimental and theoretical values helps to reduce the error in the optimized geometry. The optimized geometry was used for the calculations of harmonic vibrational frequencies at the B3LYP/6311G++(d,p) method, it also helps to ensure the systems to be local minimum number imaginary vibration frequencies. The thermochemical properties [10–12] like, hardness (η), softness (S), chemical potential (μ), electronegativity (χ) and electrophilicity index (ω), were calculated using Koopmans' theorem for closed-shell compounds. Electrostatic potential analysis has also been made to identify the mapping surface of drugs. Dipole moments, linear and non-linear optical (NLO) properties of AMB were also calculated at the same level of theory.

Further, molecular docking was also conducted to predict binding poses, bio affinity and virtual screening of the selected drugs into the 3D crystal structure of cyclooxygenase-2 (PDB ID: 1CX2) and cyclooxygenase-1 (PDB ID: 1EQG) using GLIDE Dock Program in Schrödinger Maestro software. The protein structure was refined using the protein preparation wizard, which employs under restrained minimization and heavy atoms were restrained by using OPLS 2003 force field. The ligands were subjected to ligand preparation using the ligand preparation wizard (Lig prep) of Schrödinger software in the Maestro interface (11.5). Grid center is defined for the active site and box sizes are set to 20 Å [2, 13, 14].

#### **3. Results and discussion**

#### **3.1 Molecular geometry**

The optimized structures of (a) fenoprofen, (b) ketoprofen, (c) flurbiprofen and (d) ibuprofen were calculated using B3LYP/6311G++(d,p) level of the theory and shown in **Figure 2**. The optimized geometries were compared to crystallographic data in the Cambridge Crystallographic Data Center to correlation coefficient factor. The calculated Pearson correlation coefficient for ketoprofen, fenoprofen and Ibuprofen has given in **Table 1**; the crystallographic data for flurbiprofen is not available yet. The Pearson correlation coefficient (PCC), or Pearson's r, the Pearson product-moment correlation coefficient (PPMCC), or the bivariate correlation is a statistic that measures linear correlation between two variables X and Y. Here, this method is used to find out the linear regression between the experimental and computationally calculated geometric parameters. Normally, it has a value between +1 and 1, where +1 indicates total positive linear correlation, 0 is no linear correlation, and 1 is total negative linear correlation [15].

#### **3.2 Thermo-chemical properties**

The thermo-chemical parameters, such as enthalpy (H), entropy (S), Gibb's free energy (G) were calculated to find which drug is more stable by comparing G and S

values and the obtained values are given in **Table 2**. In general, more negative the value of G the drug is more stable and more active if the value of S is more positive. From the analysis, it is found that ketoprofen has more negative value for G (�5.29 � <sup>10</sup><sup>5</sup> kcal/mol) and flurbiprofen has more or less same G value

*Frontier molecular orbital of the selected NSAIDs was calculated using the DFT/B3LYP/6311G++(d,p) level*

(�5.21 � <sup>10</sup><sup>5</sup> kcal/mol). Hence, ketoprofen is a more stable and active drug compared to other selected drugs with enhanced entropy value of 136.08 cal/mol.

In computational chemistry, the frontier molecular orbitals play an important role in demonstrating active sites, kinetic stability and chemical reactivity of the molecule (**Table 3**). In the present work, frontier molecular orbital energies (EHOMO and ELUMO) of all selected drugs were calculated using DFT/B3LYP/6311G++(d,p) level of theory. The LUMO indicates the most likely site which would undergo a nucleophilic attack while the HOMO describes the most likely site for an electrophilic attack. The energy corresponding to HOMO represents the ionization potential of the molecule, while that of the LUMO represents the corresponding electron affinity. A high HOMO–LUMO energy gap indicates greater stability and low reactivity of the chemical system. On the basis of frontier molecular orbital analysis, ketoprofen is found to be more reactive with lower stability compared to

To understand the three-dimensional charge distributions over the drug molecules, to locate the most electronegative and electropositive site on their skeleton and to predict reactive sites for electrophilic and nucleophilic attack for the NSAIDs

The MESP map of ketoprofen shows that the negative potential sites are on electronegative atoms like oxygen atoms as well as the positive potential sites are around the hydrogen atoms. These sites give information about the region from

In order to have a deep insight about the reactive nature of selected NSAIDs, the global descriptive parameters like hardness, softness, chemical potential, electronegativity, and electrophilicity index were calculated using Koopmans' theorem for

where EHOMO is the energy of HOMO and ELUMO is the energy of LUMO.

Ionization potential IP ð Þ≈ � EHOMO (1) Electron affinity EA ð Þ≈ � ELUMO (2)

molecular electrostatic potential (MESP) mapping can sightsee.

where the compound can have noncovalent interactions (**Figure 3**).

**3.3 Frontier molecular orbital analysis**

**SAMPLE HOMO**

**Table 3.**

*of theory.*

**(eV)**

*DOI: http://dx.doi.org/10.5772/intechopen.93828*

**LUMO (eV)**

**HOMO-1 (eV)**

Ketoprofen �6.96 �2.10 �7.25 �1.02 �7.29 �0.88 4.86 Fenoprofen �6.26 �0.91 �7.01 �0.65 �7.10 �0.48 5.36 Flurbiprofen �6.54 �1.35 �7.15 �0.71 �7.21 �0.53 5.19 Ibuprofen �6.68 �0.77 �7.05 �0.50 �7.92 �0.34 5.90

*DFT and Molecular Docking Studies of a Set of Non-Steroidal Anti-Inflammatory Drugs…*

**LUMO+1 (eV)**

**HOMO-2 (eV)**

**LUMO+2 (eV)**

**BAND GAP (eV)**

other drug molecules in the family.

**3.4 Global descriptive parameters**

**77**

closed-shell compounds, as follows [11, 16]:

#### **Figure 2.**

*The optimized molecular structures of the selected drugs, calculated at DFT/B3LYP/6311G++(d,p). (a) Ketoprofen. (b) Fenoprofen. (c) Flurbiprofen. (d) Ibuprofen.*


#### **Table 1.**

*The Pearson coefficient between the experimental and computationally calculated geometric parameters.*


#### **Table 2.**

*Thermo-chemical properties of the selected drugs were calculated using the DFT/B3LYP/6311G++(d,p) level of theory.*


*DFT and Molecular Docking Studies of a Set of Non-Steroidal Anti-Inflammatory Drugs… DOI: http://dx.doi.org/10.5772/intechopen.93828*

**Table 3.**

*Frontier molecular orbital of the selected NSAIDs was calculated using the DFT/B3LYP/6311G++(d,p) level of theory.*

values and the obtained values are given in **Table 2**. In general, more negative the value of G the drug is more stable and more active if the value of S is more positive. From the analysis, it is found that ketoprofen has more negative value for G (�5.29 � <sup>10</sup><sup>5</sup> kcal/mol) and flurbiprofen has more or less same G value (�5.21 � <sup>10</sup><sup>5</sup> kcal/mol). Hence, ketoprofen is a more stable and active drug compared to other selected drugs with enhanced entropy value of 136.08 cal/mol.

#### **3.3 Frontier molecular orbital analysis**

In computational chemistry, the frontier molecular orbitals play an important role in demonstrating active sites, kinetic stability and chemical reactivity of the molecule (**Table 3**). In the present work, frontier molecular orbital energies (EHOMO and ELUMO) of all selected drugs were calculated using DFT/B3LYP/6311G++(d,p) level of theory. The LUMO indicates the most likely site which would undergo a nucleophilic attack while the HOMO describes the most likely site for an electrophilic attack. The energy corresponding to HOMO represents the ionization potential of the molecule, while that of the LUMO represents the corresponding electron affinity. A high HOMO–LUMO energy gap indicates greater stability and low reactivity of the chemical system. On the basis of frontier molecular orbital analysis, ketoprofen is found to be more reactive with lower stability compared to other drug molecules in the family.

To understand the three-dimensional charge distributions over the drug molecules, to locate the most electronegative and electropositive site on their skeleton and to predict reactive sites for electrophilic and nucleophilic attack for the NSAIDs molecular electrostatic potential (MESP) mapping can sightsee.

The MESP map of ketoprofen shows that the negative potential sites are on electronegative atoms like oxygen atoms as well as the positive potential sites are around the hydrogen atoms. These sites give information about the region from where the compound can have noncovalent interactions (**Figure 3**).

#### **3.4 Global descriptive parameters**

In order to have a deep insight about the reactive nature of selected NSAIDs, the global descriptive parameters like hardness, softness, chemical potential, electronegativity, and electrophilicity index were calculated using Koopmans' theorem for closed-shell compounds, as follows [11, 16]:

Ionization potential IP ð Þ≈ � EHOMO (1)

Electron affinity EA ð Þ≈ � ELUMO (2)

where EHOMO is the energy of HOMO and ELUMO is the energy of LUMO.

**Figure 2.**

**Table 1.**

**Table 2.**

**76**

*level of theory.*

**Sample Energy**

**105 (kcal/mol)**

*The optimized molecular structures of the selected drugs, calculated at DFT/B3LYP/6311G++(d,p).*

**Sample Pearson correlation coefficient**

**Enthalpy <sup>10</sup><sup>5</sup> (kcal/mol)**

*The Pearson coefficient between the experimental and computationally calculated geometric parameters.*

ketoprofen 5.29 5.29 5.29 136.08 254.09 fenoprofen 5.06 5.06 5.06 133.11 242.09 flurbiprofen 5.21 5.21 5.21 129.43 244.08 ibuprofen 4.12 4.12 4.12 128.56 206.13

*Thermo-chemical properties of the selected drugs were calculated using the DFT/B3LYP/6311G++(d,p)*

**Gibbs free energy 105 (kcal/mol)**

**Entropy (cal/mol)** **Molecular mass (amu)**

Ketoprofen 0.951 Fenoprofen 0.976 Ibuprofen 0.899

*(a) Ketoprofen. (b) Fenoprofen. (c) Flurbiprofen. (d) Ibuprofen.*

*Density Functional Theory Calculations*

**Figure 3.**

*The MESP structures of (a) ketoprofen, (b) fenoprofen, (c) flurbiprofen and (d) ibuprofen. The negative (red) regions of MESP were related to electrophilic reactivity and the positive (blue) regions to nucleophilic reactivity.*

$$\text{Hardness } (\eta) \approx \frac{IP - EA}{2} \tag{3}$$

$$\text{Electronegativity } (\chi) \approx \frac{IP + EA}{2} \tag{4}$$

$$\text{Softness } (\mathbf{S}) \approx \frac{1}{2\eta} \tag{5}$$

**Sample**

**79**

Ketoprofen Fenoprofen Flurbiprofen

Ibuprofen

**Table 4.** *Calculated*

 *global descriptors*

 *of the selected NSAIDs were calculated using the* 

6.96 6.26 6.54 6.68

2.100

0.90 1.35 0.77

2.96

3.73 *DFT/B3LYP/6311G++(d,p)*

 *level of theory.*

5.91

3.73

2.60

3.95

5.19

3.95

2.68

3.58

5.36

3.58

2.43

4.53

4.86

4.53

 **Ionization potential (Ip) Electron affinity (Ea) Hardness (***η***)** 

**Electronegativity**

 **(***χ***) Softness (S) Chemical potential (***μ***)** 

**Electrophilicity**

 **index (**

4.86

5.36

*DFT and Molecular Docking Studies of a Set of Non-Steroidal Anti-Inflammatory Drugs…*

5.19

5.91

*ω***)**

*DOI: http://dx.doi.org/10.5772/intechopen.93828*

$$\text{Chemical potential } (\mu) \approx -\chi \tag{6}$$

$$\text{Electropibility index } (\omega) \approx \frac{\mu^2}{2\eta} \tag{7}$$

The calculated global descriptors of AMB are given in **Table 4.**

According to the maximum hardness principle (MHP), at constant external potential, the stability of a molecule increases with hardness, and with the increase in stability, the reactivity decreases. Softness is just the reciprocal of hardness, so higher the softness, lower is the stability, *i.e*., higher is the reactivity. The hardness value of ketoprofen is 2.43; fenoprofen is 2.68, flurbiprofen is 2.60, and ibuprofen is 2.96. This study shows that ketoprofen has a lower hardness and a higher softness value which indicates that this drug is highly reactive compared to other drugs.

