Int J Pharm Pharm Sci, Vol 7, Issue 9, 46-50Original Article
DESIGN OF COX-2 INHIBITORS–AN IN-SILICO APPROACH
D. GILES*, SAI PRABHA, GURU BASAVARAJASWAMY PM.
Department of Pharmaceutical Chemistry, Acharya and BM Reddy College of Pharmacy, Soladevanahalli, ACHIT Nagar Post, Bangalore-107
Email: sahayagiles@yahoo.com
Received: 01 May 2015 Revised and Accepted: 15 Jul 2015
ABSTRACT
Objective: The aim of the present work was to design the novel series of chalcone derivatives of indane-1,3-dione for its inhibition towards COX-2.
Methods: COX-2 inhibitors were designed on the binding ability of the compounds with the target. Docking analysis was performed using Acclerys discovery studio 3.5. Molecular properties, ADME parameters, Toxicity parameters were analysed using the same in-silico tool.
Results: Most of the designed compounds were possessing good binding affinity towards the COX-2. Other in-silico parameters such as ADMET and TOPKAT were within the appreciable range. Among all the designed compounds several compounds possess good CDOCKER energy and CDOCKER interaction energy with specific amino acid indicating that it could possess good binding with the target. Most of the design compounds could act as COX-2 because it forms hydrogen bonding with ARG120.
Conclusion: Compound l possess good binding affinity indicating that the presence of hydroxyl group in the phenyl ring possess good activity which can be further optimized for its druggabality after its pharmacological activity.
Keywords: Anti-inflammatory, Docking, CDOCKER, Cyclooxygenase.
INTRODUCTION
Inflammation is a part of the defence mechanisms that involved in the inflammatory reactions associated with the release of histamine, bradykinin and prostaglandins [1, 2]. COX (Cyclooxygenase) was believed to be expressed constitutively with constant levels in individual tissues [3]. Prostaglandin synthesis was believed to increase in inflammation because of increased release of precursor [4]. COX activity increases in inflammation, and this increase can be prevented by corticosteroids [5].
X-ray crystallography of the 3-D structure of COX-1 and COX-2 has done much to show how NSAIDs work. COX-1 and COX-2 are very similar enzymes consisting of a long narrow channel with a hairpin bend [6]. Several observations have shown that NSAIDs act on COX to inhibit prostaglandin synthesis. X-ray crystallography suggested that this blocking occurs by hydrogen bonding to the polar arginine at position 120 [4].
Structure-based drug design helps in identifying the ligand with the target protein, in its complex [7]. The knowledge of binding site helps to design novel drug candidates with better potency. The goal of small-molecule drug discovery is to modulate the activity of a biological target via interactions with an externally administered molecule at optimal drug intervention points to afford the maximum therapeutic index [8].
This work is mainly planned to design derivatives of chalcone of indane-1,3-dione for its binding affinity towards COX-2 inhibition and also evaluate for its other in-silico parameters such as ADME and toxicity parameter. The chalcones were designed on the basis of binding with Arg 120, since the studies suggest [4] that blocking through hydrogen bond could inhibit COX activity.
MATERIALS AND METHODS
Molecular properties
Molecular properties were important in designing compounds [9]. It was studied using Acclerys Discovery studio 3.5 and was depicted in table 1.
Docking
Docking study was performed using Acclerys Discovery studio 3.5 versions running on windows 7 service pack 1 OS.
Protein preparation
The X-ray crystallographic structure of COX-2 (PDB ID, 1cx2) protein was obtained from the protein data bank at a resolution of 3.0Å [10]. The crystal structure of COX-2 inhibitor complex with SC-558 was obtained from protein data bank (pdb: 1CX2). The structure was tetramer. Chain A was used for docking after deleting water molecules. After importing, the chain A is subjected protein preparation wizard using CHARM force field [11].
Ligand preparation
The ligand molecules were drawn in Acclerys Discovery studio 3.5 and the energy was minimized using the same software [12]. The minimized protein and ligands were used for docking.
Docking using CDOCKER
To identify the molecular binding interaction of the designed compounds with the receptor all the compounds were docked into the active binding site of the enzyme COX-2. Docking was performed using CDOCKER for predicting the protein–ligand interactions [13]. CDOCKER energy, CDOCKER interaction energy, secondary bonding mainly hydrogen bonding and the amino acid involved in the binding were used to predict the effect of designed drug binding with the target. The docking result of the ligands was listed in table 2. The docking process involves a conformational search for compound which compliments a target binding site, with the aim of identifying the best matching pose along with the active site to perform docking. The stability of the docked ligand-protein complex is due to hydrogen bonding and Vanderwaals interactions.
ADME Parameters
The newly designed derivatives were studied for its ADME descriptors using Discovery Studio 3.5 in which Blood Brain Barrier Penetration, Intestinal Absorption, Aqueous solubility, Hepatotoxicity, Cytochrome P450 inhibition and Plasma Protein Binding level [14] were predicted and tabulated in table 3.
Toxicity parameter
Virtual toxicity study was performed for the designed molecules using TOPKAT. This uses a training set of structure library in the database, based on the structural features in the query chemical compounds to predict the toxicity. If the query structure does not belong to the training set, the software displays the result of the warning. Aerobic Bio-Degradability, AMES Mutagenicity, Developmental Toxicity Potential, Ocular Irritancy, Skin Irritancy, Carcinogenicity for Female Mouse, Male Mouse, Female Rat, Male Rat were calculated using TOPKAT [15]. The data of toxicity parameters were represented in table 4.
Table 1: Molecular properties of designed derivatives
Ligand code |
Substituent |
Mol MW |
Mol surface area |
No of HB donors |
No of HB acceptor |
AlogP |
a |
R1 =CH3 |
289.305 |
60.32 |
0 |
3 |
3.794 |
b |
R1=OH |
291.278 |
80.55 |
1 |
4 |
3.066 |
c |
R1=F |
293.269 |
60.32 |
0 |
3 |
3.513 |
d |
R=F,R1=F |
311.259 |
60.32 |
0 |
3 |
3.719 |
e |
R1=NH2 |
290.293 |
86.34 |
1 |
4 |
2.561 |
f |
R4=SH |
306.335 |
80.22 |
0 |
4 |
3.747 |
g |
R1=SO2NH2 |
354.357 |
128.86 |
1 |
5 |
2.013 |
h |
R1= NH2, R2=CH3 |
304.319 |
86.34 |
1 |
4 |
3.047 |
i |
R1= CH3, R4=CH3 |
303.331 |
60.32 |
0 |
3 |
4.28 |
j |
R1=NH2, R3=SO2NH2 |
385.437 |
169.9 |
2 |
6 |
2.165 |
k |
R1=Cl |
309.723 |
60.32 |
0 |
3 |
3.972 |
l |
R2=OH |
291.278 |
80.55 |
1 |
4 |
3.066 |
m |
R=NH2, R4=OH |
306.292 |
106.57 |
2 |
5 |
2.319 |
n |
R4=OH |
291.278 |
80.55 |
1 |
4 |
3.066 |
o |
R3=NH2 |
290.293 |
86.34 |
1 |
4 |
2.561 |
p |
R4=NH2 |
290.293 |
86.34 |
1 |
4 |
2.561 |
q |
R2=NH2 |
290.293 |
86.34 |
1 |
4 |
2.561 |
Table 2: Docking study of the designed compounds towards COX-2
Ligand code |
CDOCKER Energy |
CDOCKER interaction Energy |
Interactions ligand-residue |
H-bond distance in Å |
Interacting amino acids |
a |
9.0599 |
-17.3778 |
Carbonyl group of Indane-1,3-dione |
2.10267 |
TYR355 |
Carbonyl group in chalcone |
2.19809 |
ARG513 |
|||
b |
9.0485 |
-17.3098 |
Carbonyl group of Indane-1,3-dione |
2.48498 |
ARG120 |
Carbonyl group of Indane-1,3-dione |
2.09973 |
TYR355 |
|||
Carbonyl group of chalcone |
2.14781 |
ARG513 |
|||
c |
18.5690 |
-12.8565 |
Carbonyl group of Indane-1,3-dione |
1.91725 |
ARG120 |
Carbonyl group of chalcone |
1.85145 |
TYR355 |
|||
d |
11.6089 |
-18.3292 |
Fluoro group |
2.27749 |
LYS83 |
Fluoro group |
1.95839 |
LYS83 |
|||
Carbonyl group of Indane-1,3-dione |
2.17305 |
ARG120 |
|||
e |
9.6416 |
-17.9761 |
Carbonyl group of Indane-1,3-dione |
2.06582 |
TYR355 |
Carbonyl group of Indane-1,3-dione |
2.32664 |
ARG513 |
|||
Carbonyl group of chalcone |
2.33576 |
ARG513 |
|||
Carbonyl group of chalcone |
2.27727 |
ARG513 |
|||
Amino group |
2.38899 |
LEU352 |
|||
f |
11.0967 |
-15.8717 |
Carbonyl group of Indane-1,3-dione |
2.10059 |
TYR355 |
Carbonyl group of chalcone |
2.21046 |
ARG513 |
|||
g |
4.9758 |
-20.7633 |
Carbonyl group of Indane-1,3-dione |
2.33615 |
ARG120 |
Carbonyl group of chalcone |
2.47006 |
ARG513 |
|||
h |
17.7657 |
-16.0606 |
Carbonyl group of Indane-1,3-dione |
2.33615 |
ARG120 |
Carbonyl group of chalcone |
2.47006 |
ARG513 |
|||
i |
7.35517 |
-18.7047 |
Carbonyl group of Indane-1,3-dione |
2.08576 |
TYR355 |
Carbonyl group of chalcone |
2.27312 |
ARG513 |
|||
Carbonyl group of chalcone |
2.47683 |
ARG513 |
|||
j |
14.3217 |
-19.1173 |
SO2 group |
2.19495 |
LYS83 |
SO2 group |
1.83469 |
ARG120 |
|||
Carbonyl group of Indane-1,3-dione |
2.40013 |
ARG120 |
|||
Carbonyl group of chalcone |
2.09184 |
TYR355 |
|||
Carbonyl group of chalcone |
2.15722 |
ARG513 |
|||
k |
14.0117 |
-15.9032 |
Chlorine in phenyl group |
2.45276 |
LYS83 |
Carbonyl group of Indane-1,3-dione |
2.2244 |
ARG120 |
|||
Carbonyl group of chalcone |
2.46307 |
ARG513 |
|||
l |
3.3472 |
-27.0175 |
Hydroxyl group |
1.77567 |
TYR355 |
Hydroxyl group |
2.30609 |
ARG513 |
|||
m |
8.9326 |
-20.1671 |
Carbonyl group of Indane-1,3-dione |
2.1153 |
TYR355 |
Carbonyl group of Indane-1,3-dione |
2.26669 |
ARG513 |
|||
Carbonyl group of chalcone |
2.40243 |
ARG513 |
|||
NH2 group in phenyl ring |
2.19598 |
LEU352 |
|||
n |
7.8069 |
-18.8413 |
Carbonyl group of Indane-1,3-dione |
2.12029 |
TYR355 |
Carbonyl group of chalcone |
2.21078 |
ARG513 |
|||
Carbonyl group of chalcone |
2.48055 |
ARG513 |
|||
o |
7.9388 |
-18.2033 |
Carbonyl group of Indane-1,3-dione |
2.49774 |
ARG120 |
Carbonyl group of Indane-1,3-dione |
2.128 |
TYR355 |
|||
Carbonyl group of chalcone |
2.17392 |
ARG513 |
|||
p |
9.5658 |
-16.7614 |
Carbonyl group of Indane-1,3-dione |
2.14541 |
TYR355 |
Carbonyl group of Indane-1,3-dione |
2.28169 |
ARG513 |
|||
Carbonyl group of chalcone |
2.48836 |
ARG513 |
|||
q |
18.3698 |
-19.2464 |
- |
- |
- |
Table 3: ADME profile of the designed derivatives
Ligand code |
BBB level |
Absorption level |
Solubility level |
Hepatotoxicity level |
CYP2D6 level |
PPB level |
a |
0 |
0 |
2 |
0 |
0 |
1 |
b |
0 |
0 |
3 |
0 |
0 |
1 |
c |
0 |
0 |
2 |
0 |
0 |
1 |
d |
0 |
0 |
2 |
0 |
0 |
1 |
e |
0 |
0 |
3 |
0 |
0 |
1 |
f |
0 |
0 |
2 |
0 |
0 |
1 |
g |
- |
0 |
2 |
0 |
0 |
1 |
h |
0 |
0 |
2 |
1 |
0 |
1 |
i |
0 |
0 |
2 |
0 |
0 |
1 |
j |
- |
0 |
2 |
0 |
0 |
0 |
k |
0 |
0 |
2 |
0 |
0 |
1 |
l |
0 |
0 |
3 |
0 |
0 |
1 |
m |
1 |
0 |
3 |
0 |
0 |
1 |
n |
0 |
0 |
3 |
0 |
0 |
1 |
o |
0 |
0 |
3 |
0 |
0 |
1 |
p |
0 |
0 |
3 |
0 |
0 |
1 |
q |
0 |
0 |
3 |
0 |
0 |
1 |
Table 4: Toxicity profile of the designed derivatives
Ligand code |
Aerobic bio-degradability |
AMES mutagenicity |
Developmental toxicity potential |
Ocular irritancy |
Skin irritancy |
Carcinogenicity |
|||
Female mouse |
Male mouse |
Female rat |
Male rat |
||||||
a |
No |
No |
Yes |
Mild |
Yes |
No |
Yes |
No |
No |
b |
No |
No |
Yes |
Mild |
Yes |
No |
Yes |
No |
Yes |
c |
No |
No |
Yes |
Mild |
Yes |
No |
Yes |
No |
No |
d |
No |
No |
Yes |
Mild |
Yes |
No |
Yes |
No |
Yes |
e |
No |
No |
No |
.- |
Yes |
No |
Yes |
Yes |
Yes |
f |
No |
No |
Yes |
Mild |
Yes |
No |
Yes |
No |
Yes |
g |
No |
No |
Yes |
Mild |
Yes |
No |
Yes |
No |
No |
h |
No |
No |
No |
Mild |
Yes |
No |
Yes |
Yes |
Yes |
i |
No |
No |
Yes |
Mild |
No |
No |
Yes |
No |
No |
j |
No |
No |
No |
Mild |
Yes |
No |
Yes |
No |
Yes |
k |
No |
No |
Yes |
- |
Yes |
No |
Yes |
No |
No |
l |
No |
No |
Yes |
Mild |
Yes |
No |
Yes |
No |
Yes |
m |
No |
No |
Yes |
Mild |
Yes |
No |
Yes |
Yes |
Yes |
n |
No |
No |
Yes |
Mild |
Yes |
Yes |
Yes |
Yes |
Yes |
o |
No |
No |
No |
Mild |
Yes |
No |
Yes |
Yes |
Yes |
p |
No |
No |
No |
Mild |
No |
No |
Yes |
Yes |
Yes |
q |
No |
No |
Yes |
Mild |
Yes |
No |
Yes |
Yes |
Yes |
RESULTS AND DISCUSSION
All the compounds possess good molecular properties. The structural studies of the new series of NSAIDs were conducted by molecular docking with COX-2 using the protocol CDOCKER in Acclerys Discovery studio 3.5. CDOCKER energy of the compound ranges from 18.3698 to 3.34729 and the CDOCKER interaction energy ranges from-27.0175 to-12.8565. Most of the designed compounds binds with TYR355, ARG120, ARG513, LYS83, LEU352.
Other than compounds A, M, L and I, amino acid ARG120 was involved in binding with the carbonyl group of the designed derivatives. ARG120 is one of the important amino acid COX-2 inhibitors mainly act by forming hydrogen bonding. This indicates the importance of carbonyl compound in COX-2inhibitor. Amino group as substituent in phenyl ring of indane-1,3-dione processes five hydrogen bonding with the receptor in which both carbonyl and amino group were involved in the binding with ARG513, LEU352, TYR355. CDOCKER score of 9.6416 and CDOCKER interaction energy off-17.9761 was observed for the above said compounds. Binding with LEU352 is one of the main interaction with the target for COX-2 inhibition.
Presence of mono and difloro substituent in phenyl ring possess good binding with the target. Mono floral substituent processes CDOCKER energy of 18.5690 and CDOCKER interaction energy of-12.8565. The hydrogen bonding was formed between ARG120 and TYR355 between carbonyl groups. At the same time presence of difloro derivative processes CDOCKER energy of 11.6089 and CDOCKER interaction energy of-18.3292. The hydrogen bonding between ARG120 and LYS83 ranges between 1.9583–2.7749 this indicates. The effective substitution in the phenyl ring with amino group at ortho, meta and para position varies the binding energy of the designed derivative with the COX-2 receptor. Good binding affinity towards the receptor with CDOCKER energy of 18.3698 and CDOCKER energy-19.2464 was observed for the compound q possessing substitution of amino group at the ortho position but at the same time it does not process any hydrogen bonding with the receptor. Substitution of amino group at the meta position of the phenyl ring processes CDOCKER energy of 7.9388 and CDOCKER interaction energy of-18.2033. It forms hydrogen bond between carbonyl group of indane-1,3-dione and chalcone.
Fig. 1: Binding of compound a with 1CX2
Fig. 2: Binding of compound e with 1CX2
Meanwhile substitution of an amino group at the para position in phenyl ring binds with TYR355 and ARG513 in which both the carbonyl groups were involved in binding with the target. This indicates the presence of substituent changes the binding with the specified target. Attachment of amino group and hydroxyl group individually and separately binding affinity and the interaction energy with the target differs slightly. Sulphamino group in R1 and R4with and without the presence of an amino group varied docking score and varied binding with the COX-2. Presence of SH group moderately increases binding affinity when compared to that of OH group. Binding of ligand a and e were specified in fig. 1 and 2.
Most of the compounds possess good binding with the receptor through electrostatic interaction, Vander walls force. Most of the designed derivatives possess Pi interactions specified amino acids indicating the importance of the indane-1,3-dione nucleus, Phenyl group with the target.
ADMET predication properties like blood brain barrier (BBB) penetrability, human intestinal absorption (HIA), solubility, hepatotoxicity and the ability to bind to cytochrome P450 enzymes and plasma protein binding (PPB) results were specified in table 1. All the designed molecules have the high penetration level in BBB indicating reasonable permeability, good absorption level in the human intestine. Most of the molecules possessing mono or di substituted hydroxy and amino group were predicted as low solubility. Presence of both amino and methyl group as substituent in the ring likely to cause dose-dependent liver injuries. None of designed molecules was not a likely inhibitor CYP2D6 level. Except compound j, other derivatives were likely to bind with the plasma protein less than other derivatives.
Toxicity profile of the designed derivatives was predicted using TOPKAT. Profiles like Aerobic biodegradability, AMES mutagenicity, Developmental toxicity potential, ocular irritancy, skin irritancy, carcinogenicity in both male and female mouse and rat model were predicted for the designed derivatives. Most of the compounds were not within the standard limit because the query structure does not belong to the training set and hence the software displays the results with warnings. Some compounds were virtually found to be more toxic. virtual toxicity study determines did not predict the clear picture of the toxicity of the designed compounds since the query structure does not belong the training set.
In the light of above analysis, the COX-2 docked posess generated by Acclerys discovery studio produced best results. It forms hydrogen bonds, hydrophobic interaction with the important residues mainly with Arg120. Since most of the compounds were within the range of ADME and toxicity parameters it was expected to be a good drugabble target after optimization with pharmacological activity.
CONCLUSION
Our docking studies have demonstrated this new series of chalcone of indanedione derivatives for its binding affinity towards COX-2 inhibition. Among all the designed derivatives Compound l possess good binding affinity indicating that the presence of hydroxyl group in the phenyl ring possess good activity. Since the ADME parameters and toxicity study were within the limit of the compound indicating that the compound l would be an effective inhibitor of COX-2. But the durggability depends on the pharmacological studies which have to confirm it.
ACKNOWLEDGEMENT
The authors are thankful to the Chairman and the Principal of Acharya & BM Reddy College of Pharmacy, Bangalore for providing facilities for carrying out this work.
CONFLICT OF INTERESTS
Declared None
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