Next Article in Journal
Facile Synthesis of Bio-Antimicrobials with “Smart” Triiodides
Next Article in Special Issue
Tristaenone A: A New Anti-Inflammatory Compound Isolated from the Australian Indigenous Plant Tristaniopsis laurina
Previous Article in Journal
Development of Antimicrobial Laser-Induced Photodynamic Therapy Based on Ethylcellulose/Chitosan Nanocomposite with 5,10,15,20-Tetrakis(m-Hydroxyphenyl)porphyrin
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Molecules
Volume 26
Issue 12
10.3390/molecules26123550
molecules-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

Crystallography, Molecular Modeling, and COX-2 Inhibition Studies on Indolizine Derivatives

by
Katharigatta N. Venugopala
1,2,*,
Sandeep Chandrashekharappa
3,4,*,
Christophe Tratrat
1,
Pran Kishore Deb
5,
Rahul D. Nagdeve
6,
Susanta K. Nayak
6,
Mohamed A. Morsy
1,7,
Pobitra Borah
8,
Fawzi M. Mahomoodally
9,
Raghu Prasad Mailavaram
10,
Mahesh Attimarad
1,
Bandar E. Aldhubiab
1,
Nagaraja Sreeharsha
1,11,
Anroop B. Nair
1,
Osama I. Alwassil
12,
Michelyne Haroun
1,
Viresh Mohanlall
2,
Pottathil Shinu
13,
Rashmi Venugopala
14,
Mahmoud Kandeel
15,16,
Belakatte P. Nandeshwarappa
17 and
Yasmine F. Ibrahim
7add Show full author list remove Hide full author list
1
Department of Pharmaceutical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
2
Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa
3
Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research (NIPER-R) Raebareli, Lucknow UP 226002, India
4
Institute for Stem Cell Science and Regenerative Medicine, NCBS, TIFR, GKVK, Bellary Road, Bangalore 560065, India
5
Faculty of Pharmacy, Philadelphia University, Amman 19392, Jordan
6
Department of Chemistry, Visvesvaraya National Institute of Technology, Nagpur 440010, Maharashtra, India
7
Department of Pharmacology, Faculty of Medicine, Minia University, El-Minia 61511, Egypt
8
Pratiksha Institute of Pharmaceutical Sciences, Chandrapur Road, Panikhaiti, Guwahati 781026, Assam, India
9
Department of Health Sciences, Faculty of Medicine and Health Sciences, University of Mauritius, Réduit 80835, Mauritius
10
Department of Pharmaceutical Chemistry, Shri Vishnu College of Pharmacy, Vishnupur, Bhimavaram 534202, India
11
Department of Pharmaceutics, Vidya Siri College of Pharmacy, Off Sarjapura Road, Bangalore 560035, India
12
Department of Pharmaceutical Sciences, College of Pharmacy, King Saud bin Abdulaziz University for Health Sciences, Riyadh 11481, Saudi Arabia
13
Department of Biomedical Sciences, College of Clinical Pharmacy, King Faisal University, Al-Ahsa 31982, Saudi Arabia
14
Department of Public Health Medicine, Howard College Campus, University of KwaZulu-Natal, Durban 4001, South Africa
15
Department of Biomedical Sciences, College of Veterinary Medicine, King Faisal University, Al-Ahsa 31982, Saudi Arabia
16
Department of Pharmacology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafrelsheikh 33516, Egypt
17
Department of Studies in Chemistry, Shivagangotri, Davangere University, Davangere, Karnataka 577007, India
 
add Show full affiliation list
 
remove Hide full affiliation list
*
Authors to whom correspondence should be addressed.
Molecules 2021, 26(12), 3550; https://doi.org/10.3390/molecules26123550
Submission received: 26 April 2021 / Revised: 2 June 2021 / Accepted: 8 June 2021 / Published: 10 June 2021
(This article belongs to the Special Issue Discovery of Anti-Inflammatory Compounds)
Browse Figures
Versions Notes

Abstract

:
The cyclooxygenase-2 (COX-2) enzyme is an important target for drug discovery and development of novel anti-inflammatory agents. Selective COX-2 inhibitors have the advantage of reduced side-effects, which result from COX-1 inhibition that is usually observed with nonselective COX inhibitors. In this study, the design and synthesis of a new series of 7-methoxy indolizines as bioisostere indomethacin analogues (5a–e) were carried out and evaluated for COX-2 enzyme inhibition. All the compounds showed activity in micromolar ranges, and the compound diethyl 3-(4-cyanobenzoyl)-7-methoxyindolizine-1,2-dicarboxylate (5a) emerged as a promising COX-2 inhibitor with an IC50 of 5.84 µM, as compared to indomethacin (IC50 = 6.84 µM). The molecular modeling study of indolizines indicated that hydrophobic interactions were the major contribution to COX-2 inhibition. The title compound diethyl 3-(4-bromobenzoyl)-7-methoxyindolizine-1,2-dicarboxylate (5c) was subjected for single-crystal X-ray studies, Hirshfeld surface analysis, and energy framework calculations. The X-ray diffraction analysis showed that the molecule (5c) crystallizes in the monoclinic crystal system with space group P 21/n with a = 12.0497(6)Å, b = 17.8324(10)Å, c = 19.6052(11)Å, α = 90.000°, β = 100.372(1)°, γ = 90.000°, and V = 4143.8(4)Å3. In addition, with the help of Crystal Explorer software program using the B3LYP/6-31G(d, p) basis set, the theoretical calculation of the interaction and graphical representation of energy value was measured in the form of the energy framework in terms of coulombic, dispersion, and total energy.

1. Introduction

Nonsteroidal anti-inflammatory drugs (NSAIDs) are one of the most commonly prescribed drugs for the treatment of inflammatory conditions worldwide [1]. NSAIDs exhibit their anti-inflammatory activity via inhibition of cyclooxygenase (COX), an enzyme involved in the biosynthesis of prostaglandin G2 (PGG2). By inhibiting the formation of PGG2, the pathway, which would ultimately lead to the inflammatory response, is blocked [2,3]. The COX enzyme has two important isoforms, namely, COX-1 and COX-2. The COX-1 isoform represents the constitutive type that is normally expressed in various regions of the body, such as the kidney and the gastrointestinal tract (GIT), where it is responsible for maintaining certain physiological functions including protection of the gastric mucosa [4,5,6,7]. On the other hand, the COX-2 isoform represents the inducible type that is expressed in response to various inflammatory stimuli and certain substances such as mitogens and cytokines that are produced during injuries. Nonselective NSAIDs that inhibit both COX-1 and COX-2 can have severe undesirable side-effects due to inhibition of the customarily expressed isoform, COX-1. For example, GIT ulceration is a commonly observed adverse effect associated with the use of nonselective NSAIDs [8,9]. Thus, in order to develop anti-inflammatory agents with reduced side-effects, compounds with high selectivity for inhibiting the COX-2 isoform over the COX-1 isoform are required.
Synthetic indolizine derivatives have been shown to interact with a wide range of drug targets such as calcium channels [10], histamine receptors [11], and phospholipase A2 [12]. In addition, they have shown numerous pharmacological properties [13] such as analgesic [14], COX-2-inhibitory [15,16,17,18], anticancer [19,20], antidiabetic [21], antihistaminic [11], antileishmanic [22], antimicrobial [23], antimutagenic [24], antioxidant [25], antiviral [26], larvicidal [27,28], herbicidal [29], antitubercular [30,31,32,33,34,35,36,37], and alpha-7 nicotinic acetylcholine receptor (α-7 nAChR)- [38], N-meningitidis-, N-acetylneuraminic acid synthese (NmeNANAS)-inhibitory activities [39].
In persistence of our interest in pharmacologically active heterocyclic compounds [40,41,42,43,44,45,46,47,48], polymorphism studies [49,50,51,52], and the discovery of anti-inflammatory agents [53,54,55,56,57,58,59], in the present investigation, we synthesized a range of 7-methoxy indolizine derivatives as indomethacin analogues (Figure 1 and Scheme 1) to evaluate their potential as anti-inflammatory agents. The title compounds (5a–e) were evaluated for their pharmacological activity against the COX-2 enzyme in order to study the influence of ethyl ester at the 1- and 2-positions, ethyl at the 2-position, and the diverse substituent on the benzoyl ring at the 3-positions of the indolizine core on the biological action.

2. Results and Discussion

2.1. Chemistry

The design of the target compounds (5a–e) was mainly based on the close chemical structural relationship with the commercially available NSAIDs indomethacin (Figure 1). The synthesis of the target compounds is depicted in Scheme 1. The intermediates (3a–e) were obtained by stirring a mixture of 4-methoxy pyridine and para- and meta-substituted phenacyl bromides in acetone medium at 5 h and were then further reacted with diethyl but-2-ynedioate in the existence of potassium carbonate in dimethylformamide solvent medium for 30 min. The resulting title compounds were purified by column chromatography using mixture of ethyl acetate and hexane as an eluent, and the purity of the compounds was more than 99% with a satisfactory yield (69% to 77%). The physicochemical property of the target compound ethyl 3-(4-bromobenzoyl)-2-ethyl-7-methoxyindolizine-1-carboxylate (5e) is presented in Table 1. The chemical structure of this compound (5e) was confirmed with spectroscopic techniques such as FT-IR, 1H-NMR and 13C-NMR, and LC–MS. The Fourier-transform infrared (FT-IR) spectroscopy revealed benzoyl and ester carbonyl groups at 1699 and 1668 cm−1, respectively (spectra are available as Electronic Supplementary Materials). The 1H-NMR spectra revealed the methoxy group at 3.86 ppm, ester peak triplet appearance of 1.34 ppm, and ester group quartet appearance of 4.30 ppm. The 13C-NMR spectra revealed the appearance of benzoyl and ester carbonyl groups at 186.00 and 166.07 ppm, respectively. The molecular ion peaks of this compound (5e) were in good agreement with its molecular mass. Title compounds diethyl 3-(4-cyanobenzoyl)-7-methoxyindolizine-1,2-dicarboxylate (5a), diethyl 3-(4-fluorobenzoyl)-7-methoxyindolizine-1,2-dicarboxylate (5b), diethyl 3-(4-bromobenzoyl)-7-methoxyindolizine-1,2-dicarboxylate (5c), and diethyl 7-methoxy-3-(3-methoxybenzoyl)indolizine-1,2-dicarboxylate (5d) were resynthesized [35], and their physicochemical properties are presented in Table 1. The proposed general reaction mechanism for the target compound (5e) is illustrated in Figure 2.
The construction of the final indolizine compound (5e) was achieved via 1,3-dipolar cycloaddition of intermediate pyridinium salt 3e, generating ylide 3e(1) using a base. This ylide carbanion subsequently attacks the electron-deficient acetylene triple bond of reactant (4). This triple bond anion then attacks the carbocation of compound 3e(1), yielding compound 3e(2). This loss of hydrogen through oxidation leads to the construction of indolizine nucleus 5e (Figure 2).

2.2. Crystallography

The crystallographic details of 5c are listed in Table 2. The crystal structure of 5c crystallized in the monoclinic space group P 21/n with eight molecules in the unit cell. The lattice parameters were a = 12.0497(6)Å, b = 17.8324(10)Å, c = 19.6052(11)Å, α = 90.000°, β = 100.372(1)°, γ = 90.000°, and V = 4143.8(4)Å3. The asymmetric unit of 5c crystal structure showed two molecules which preferred the intramolecular C–H···O interactions shown as a dotted line and 50% thermal ellipsoidal probability of non-hydrogen atoms (Table 3 and Figure 3). There were eight molecules in the unit cell of 5c, where intermolecular weak hydrogen bonds C2A–H2A···O6B and C4B–H4B1···O4A were the major interactions, along with C–H···π interactions that stabilized the molecular assembly, as shown in Figure 4 and Figure 5 (Table 3).

2.3. Hirshfeld Surface Analysis

The Hirshfeld surfaces of the crystal structure 5c were investigated to illustrate the nature of intermolecular interactions and visualization of intermolecular close contacts in its crystal structure using Crystal Explorer 17.5 [60], which mapped over de, dnorm, shape index, and curvedness, as shown in Figure 6. The contribution of individual intermolecular interactions on the Hirshfeld surface can be defined by color codes. On the dnorm surface, the red color shows the shorter molecular contacts and the blue color on the dnorm surface area represents the longer molecular contacts. The white color on the dnorm surface indicates the contact around the van der Waals radii. In the dnorm surfaces, the red color shows the hydrogen bonding H···O contacts, whereas the blue surface area represents the H···H contacts (Figure 6a). The de surface features appear as a relatively flat green region where the contact distances are similar (Figure 6b). The adjacent highlighted red and yellow regions on the shape index surface also show the strong hydrogen bonding interactions present in the molecule (Figure 6c), whereas the blue curved and yellow regions on the curvedness surfaces shows the H···H interactions (Figure 6d). The 2D fingerprint plots [61] show the sharp spike, which represents the intermolecular interactions present in the molecule (Figure 7a). Again, it shows that C–H···O interactions were predominant (23.2%) after the H···H contacts, which led to the highest contribution of 35.8% in comparison to other interactions, suggesting that weak C–H···O hydrogen bonding plays an essential role in its crystal packing. The percentage contributions of other intermolecular interactions in this crystal structure were as follows: C···H/H···C (18.4%), H···Br/Br···H (12.2%), C···O/O···C (2.5%), C···C (2.1%), N···H/H···N (1.7%), etc. (Figure 7b).

2.4. Energy Framework Calculation

Furthermore, the Crystal Explorer 17.5 software was used to evaluate the interaction energies for the crystal structure 5c. Energy frameworks have a strong and remarkable way of imagining the supramolecular existence of molecular crystal structures. The interaction energies between the molecules are obtained using monomer wave functions at the B3LYP/6-31G (d, p) level. [62]. As prescribed, the tube size used in all the energy frameworks was 80 (scale factor), and the cutoff for the energy threshold value was set to zero. In the 3D topological images, the diameter of the tube cylinder reflects the interaction energy in the molecular packing for the corresponding interaction. The molecules present within the 3.8 Å circle within 1 × 1 × 1 unit cell dimensions were selected for this calculation (Figure 8a).
Energies between molecular pairs are expressed as cylinders that connect molecular pair centroids with a cylindrical radius proportional to the energy interaction magnitude. The energy framework was outlined as red cylinders for Eelec, green cylinders for Edis, and blue cylinders for Etot, as shown in (Figure 8b–d), and the relative strength of molecular packing was expressed in various directions by these tubes. The supramolecular nature of the crystal structure was, thus, visualized by energy structures in a special way. The calculated energy values are listed in Table 4 for electrostatic, polarization, dispersion, and total interaction energy, which suggests that 5c crystal structure preferred dispersion energy over others.

2.5. Pharmacology

The COX-2-inhibitory activity of the target compounds (5a–5e) is presented in Table 5. As can be seen from Table 5, all the indolizines displayed interesting inhibitory activity against COX-2 similar to the commercially available drug indomethacin. Compound 5a with a 4-cyanobenzoyl group attached to the 3-position of the indolizine scaffold, having two ethyl carboxylate groups attached to the 1- and 2-position of the scaffold, emerged as the most promising compound with the highest COX-2-inhibitory activity (IC50 = 5.84 µM). Replacement of the electron-withdrawing nitrile group with halogens such as fluorine and bromine atoms at the 4-position of the benzoyl ring exhibited detrimental COX-2 inhibitory activity for compounds 5b and 5c with IC50 values 6.73 µM and 6.99 µM, respectively. It is remarkable to note that title compound 5e with only one ethyl ester moiety at the first position of the indolizine pharmacophore exhibited a further reduction in activity (IC50 = 7.38 µM) as compared to the structurally similar compound 5c (IC50 = 6.99 µM).
The compound 5d, substituted with a methoxy functional group at the 3-position of the benzoyl ring, displayed the least inhibitory activity (IC50 = 8.49 µM). In general, the availability of the electron-withdrawing functional groups at the para position of the benzoyl ring was found to be favorable for COX-2-inhibitory activity as compared to the presence of the electron-donating functional groups at the meta position. Previously these derivatives demonstrated excellent safety profiles [35]; thus, they could be considered as lead molecules for further improvement of novel potential COX-2 inhibitors.

2.6. Computational Studies

Molecular docking studies are considered an invaluable in silico approach to correlate the in vitro structure–activity relationship (SAR) of chemical compounds [63]. To gain insight into the inhibitory activity of indolizines (5a–e), we investigated their key interactions with the COX-2 receptor through a computational approach. The docking study was conducted with Accelrys Discovery Studio Client 4.0 software. The docking interaction energies and the residue interactions of indolizines 5a–e and indomethacin are reported in Table 6. All the compounds demonstrated favorable docking energy ranging from −38.22 to −53.29 kcal/mol, indicating that they have a good binding affinity with the COX-2 receptor, as demonstrated from their biological activities.
The predicted docking poses of indolizines 5a–e and indomethacin are depicted in Figure 9. All the compounds adopted a similar conformation to that of indomethacin, where the indolizine ring is taken into a sandwich between the amino-acid residues Ala527, Val523 and Val349, Leu352. The benzoyl ring is oriented toward the residues Tyr385 and Trp387, while the methoxy group is located in the deep region of the receptor. As can be observed from the binding poses, indolizines 5a, 5b, and 5d demonstrated favorable hydrogen bonding interaction between Arg120 with the ester group at the 1-position of the indolizine scaffold, while indomethacin showed hydrogen bonding and ionic bonding interactions between the same residue Arg120 and its carboxylic acid group. This indicated that the ionic interaction with Arg120 is not a requirement for maintaining the potency of the compounds. Furthermore, the indolizines 5c and 5e containing a bromine atom at the para position of the benzoyl ring showed no hydrogen bonding involvement with the residue Arg120. Therefore, the major contribution to the COX-2 activity of our compounds principally involves hydrophobic interactions with the indolizine ring and with the substituents at positions 2 and 3 of indolizine. It can be noted that only the bromine substituent on the benzoyl ring (5c and 5e) demonstrated hydrophobic interactions with residues Leu384 and Met522, while pi–pi interactions were observed for all indolizines with the exception of fluoro indolizine 5b and indomethacin. Therefore, the substituent in the benzoyl ring has a minor contribution to the activity of indolizine. However, it has been demonstrated that the benzoyl ring on indomethacin is important to bioactivity since the replacement of N-benzoyl by N-benzyl led to a reduction in COX-2 inhibition [64].
The molecular modeling study provided insight into the structural requirement of indolizines for COX-2-inhibitory activity. Moreover, indolizines 5a–e are more likely to be selective COX-2 inhibitors. It has been validated that COX-1 and COX-2 selectivity is mainly due to the ionic interaction with residue Arg120 since the corresponding ester and amide of indomethacin derivatives presented good selectivity in favor of COX-2 inhibition [64].

3. Materials and Methods

3.1. Chemistry

All the commercially offered chemicals and solvents were purchased from Sigma-Aldrich Co. (St. Louis, MO, USA). All the chemical reactions were performed in hot-air-dried glassware in the presence of a nitrogen atmosphere consuming dry solvents. A Shimadzu FT-IR spectrophotometer (Columbia, MD, USA) was used to record the FT-IR spectra. Furthermore, 1H- and 13C-NMR spectra were documented at ambient temperature on Bruker AVANCE III 400 MHz instruments (San Jose, CA, USA) using CDCl3 and DMSO-d6 as solvents. An Agilent 1200 series instrument (Santa Clara, CA, USA) in conjunction with a 6140 single-quadrupole mass spectrometer using positive and negative ESI mode with a mass selective detector (MSD) range of 100–2000, as well as 0.1% aqueous trifluoroacetic acid in an acetonitrile system on the C18-BDS column, was used to record liquid chromatography–mass spectrometry (LC–MS) spectra. Then, an elemental analysis was carried out using the analyzer FLASH EA 1112 CHN (Thermo Finnigan LLC, New York, NY, USA). A single-crystal X-ray diffraction study was performed using a Bruker KAPPA APEX II DUO diffractometer (Madison, WI, USA) equipped with a charge-coupled device (CCD) detector; monochromated Mo Kα radiation (λ = 0.71073 Å) was used. Data collection was carried out using an Oxford Cryostream cooling system featuring the Bruker Apex II software (Madison, WI, USA) at 173(2) K [16].

3.2. General Synthetic Procedure for 4-methoxy-1-(2-(substituted phenyl)-2-oxoethyl)pyridinium Bromides (3a–e)

To a solution of 4-methoxypyridine (1) (0.0091 mol, 1 g) in dry acetone solvent (10 mL), substituted-phenacylbromide (0.0091 mol, 2.03 g) was added and agitated at room temperature for 5 h. The completion of the reaction was observed on thin-layer chromatography (TLC). The product obtained was separated, filtered, and desiccated under vacuum to yield 92–99% 1-(2-(substituted phenyl)2-oxoethyl)-4-methoxypyridinium bromides.

3.3. Synthetic Procedure for the Synthesis of Ethyl 3-(4-bromobenzoyl)-2-ethyl-7-methoxyindolizine-1-carboxylate (5e)

To a stirred solution of 1-(2-(4-bromophenyl)-2-oxoethyl)-4-methoxypyridinium bromide (3e) (0.0026 mol, 1 g), in dry dimethylformamide, ethyl pent-2-ynoate (4) (0.0025 mol, 0.512 g) and K2CO3 (0.0051 mol, 0.713 g) were added. It was stirred at room temperature for 30 min. The completion of the reaction was monitored on TLC. After completion of the reaction, the solvent was evaporated under reduced pressure and diluted with ethyl acetate. The organic layer was washed with water, brine, and dried with sodium sulfate. The crude compound was purified by column chromatography to afford a 69% yield of compound 5e. The physicochemical characteristics are tabulated in Table 1. Appearance: light-yellow crystalline compound. FT-IR (KBR neat cm−1): 1699, 1668, 1639, 1602. 1H-NMR (400 MHz CDCl3) δ = 9.18 (d, J = 7.2 Hz, 1H), 7.69–7.60 (m, 3H), 7.10–7.05 (m, 2H), 6.57–6.54 (m, 1H), 4.30 (q, J = 7.2 Hz, 2H), 3.86 (s, 3H), 2.57 (q, J = 7.2 Hz, 2H), 1.34 (t, J = 7.2 Hz, 3H), 0.91 (t, J = 7.2 Hz, 3H). 13C-NMR (100 MHz CDCl3) δ = 186.00, 166.07, 165.01, 163.56, 159.37, 144.79, 142.77, 137.58, 137.55, 130.95, 130.86, 129.61, 121.61, 121.10, 115.64, 115.42, 108.20, 102.82, 97.57, 59.64, 55.57, 20.06, 15.99, 14.41. Analysis calculated for C21H20BrNO4: C, 58.62; H, 4.68; N, 3.26; found: C, 58.69: H, 4.52: N, 3.24. The spectra are available as Electronic Supplementary Materials.

3.4. Crystallography

Single-crystal X-ray diffraction data of 5c were collected on a Bruker KAPPA APEX II DUO diffractometer using graphite-monochromated Mo-Kα radiation (χ = 0.71073 Å). Data collection was carried out at 173(2) K. Oxford Cryostream was used to control temperature (Oxford Cryostat). The cell refinement and data reduction for 5c were performed using the program SAINT [65], and the absorption correction was performed using SADABS [65].
The crystal structure of 5c was solved by direct methods using SHELXS-18 [66] and refined by the full-matrix least-squares method based on F2 using SHELXL-2018 [66]. The program WinGx [67] was used to prepare molecular graphic images. All non-hydrogen atoms were refined anisotropically, and all hydrogen atoms were placed in idealized positions and refined in riding models with Uiso assigned 1.2 or 1.5 times Ueq of the parent atoms [67]. The C–H bond distances was constrained to 0.95 Å for aromatic hydrogen and 1.00 Å for methyl hydrogen. The crystallographic parameters are listed in Table 2.

3.5. In Vitro COX-2 Inhibition Assay

The title compounds 5a–e were tested for in vitro human recombinant COX-2 enzyme inhibition activity following our previously reported protocol [68].

3.6. Computational Studies

The computational study for test compounds 5a–e was conducted with Accelrys Discovery Studio Client 4.0 (Waltham, MA, USA) using the indomethacin crystal structure PDB 4COX following our previously reported protocol [68].

4. Conclusions

In this study, a series of diethyl 7-methoxy-3-(3-substituted benzoyl)indolizine-1,2-dicarboxylate derivatives (5a–d) and ethyl 3-(4-bromobenzoyl)-2-ethyl-7-methoxyindolizine-1-carboxylate (5e) were synthesized and evaluated for the inhibition of COX-2 enzyme activity. All the compounds were demonstrated to be active inhibitors of COX-2, with the most active compound (5a) having an IC50 value comparable to that of indomethacin, a marketed COX inhibitor. Computational studies were conducted to analyze the key interactions of these compounds with the amino-acid residues of the COX-2 receptor. Hydrophobic interactions were observed to be mainly responsible for the inhibitory COX-2 activity of indolizines. The compound 5c was crystallized in a monoclinic crystal system with space group P 21/n. The molecule was observed to have both intra- and intermolecular hydrogen bonds and exhibited C–H···π interactions for stability. In order to understand and visualize the contribution of different intermolecular interactions, Hirshfeld surface analysis with 2D fingerprint plots was carried out to provide insight into the stability of the crystal structure. In terms of electrostatic, dispersion, and total energy, the systematic and theoretical energy was calculated using the software program Crystal Explorer, which further provided 3D topological images. Indolizines 5a–e could be considered as lead compounds for developing novel COX-2 inhibitors.

Supplementary Materials

The following are available online: Figure S1. FT-IR of FT-IR of diethyl 3-(4-cyano benzoyl)7-methoxyindolizine-1,2-dicarboxylate (5a); Figure S2. 1H-NMR of diethyl 3-(4-cyano benzoyl)7-methoxyindolizine-1,2-dicarboxylate (5a); Figure S3. 13C-NMR of diethyl 3-(4-cyano benzoyl)7-methoxyindolizine-1,2-dicarboxylate (5a); Figure S4. FT-IR of diethyl 3-(4-fluoro benzoyl)7-methoxyindolizine-1,2-dicarboxylate (5b); Figure S5. 1H-NMR of diethyl 3-(4-fluoro benzoyl)7-methoxyindolizine-1,2-dicarboxylate (5b); Figure S6. 13C-NMR of diethyl 3-(4-fluoro benzoyl)7-methoxyindolizine-1,2-dicarboxylate (5b); Figure S7. FT-IR of diethyl 3-(4-bromobenzoyl)7-methoxyindolizine-1,2-dicarboxylate (5c); Figure S8. 1H-NMR of diethyl 3-(4-bromobenzoyl)7-methoxyindolizine-1,2-dicarboxylate (5c); Figure S9. 13C-NMR of diethyl 3-(4-bromobenzoyl)7-methoxyindolizine-1,2-dicarboxylate (5c); Figure S10. FT-IR of diethyl 7-methoxy-3-(3-methoxybenzoyl)indolizine-1,2-dicarboxylate (5d); Figure S11. 1H-NMR of diethyl 7-methoxy-3-(3-methoxy benzoyl)indolizine-1,2-dicarboxylate (5d); Figure S12. 13C-NMR of diethyl 7-methoxy-3-(3-methoxy benzoyl)indolizine-1,2-dicarboxylate (5d); Figure S13. FT-IR of ethyl 3-(4-bromobenzoyl)-2-ethyl-7-methoxyindolizine-1-carboxylate (5e); Figure S14. 1H-NMR of ethyl 3-(4-bromobenzoyl)-2-ethyl-7-methoxyindolizine-1-carboxylate (5e); Figure S15. 13C-NMR of ethyl 3-(4-bromobenzoyl)-2-ethyl-7-methoxyindolizine-1-carboxylate (5e); Figure S16. checkCIF/PLATON report of checkCIF/PLATON report of diethyl-3-(4-bromo benzoyl)7-methoxyindolizine-1,2-dicarboxylate (5c).

Author Contributions

Conceptualization, K.N.V. and C.T.; methodology, K.N.V., R.D.N., S.K.N., P.B., C.T., S.C., M.A., M.H., V.M., R.V., M.K., B.P.N. and P.S.; software, K.N.V., P.K.D., S.K.N. and C.T.; validation, K.N.V., P.K.D., R.D.N., C.T., S.C. and N.S.; formal analysis, K.N.V., F.M.M., C.T., S.C. and M.H.; investigation, K.N.V., R.D.N., S.C., R.P.M. and A.B.N.; resources, K.N.V., P.K.D., S.C., S.K.N., R.P.M., M.A.M., B.E.A., M.A., N.S., O.I.A., R.V., M.K., B.P.N. and Y.F.I.; data curation, K.N.V. and M.A.M.; writing—original draft preparation, K.N.V., P.K.D., S.K.N., P.B., R.D.N., F.M.M., C.T., S.C., R.P.M., M.A.M., B.E.A., M.A., A.B.N., N.S., O.I.A., M.H., V.M., P.S., R.V., M.K., B.P.N. and Y.F.I.; writing—review and editing, K.N.V., S.C., P.K.D., S.K.N., P.B., F.M.M., C.T., M.A.M., B.E.A., A.B.N., O.I.A., V.M., P.S., R.V., M.K., B.P.N. and Y.F.I.; visualization, K.N.V. and C.T.; supervision, K.N.V. and S.K.N.; project administration, K.N.V.; funding acquisition, K.N.V. All authors have read and agreed to the published version of the manuscript.

Funding

This research was funded by the Deanship of Scientific Research at King Faisal University, Al-Ahsa, Saudi Arabia (Nasher Track Grant No. 186333).

Data Availability Statement

Crystal data of compound 5c were deposited in the Cambridge Crystallographic Data Center (CCDC) (https://www.ccdc.cam.ac.uk/, accessed on 18 September 2020) with number 2045116.

Acknowledgments

The authors acknowledge the Deanship of Scientific Research at King Faisal University, Kingdom of Saudi Arabia, for their financial support under Nasher Track (Grant No. 186333) and their encouragement. The authors thank Hong Su, Center for Supramolecular Chemistry Research, Department of Chemistry, University of Cape Town, Rondebosch 7701, for single-crystal X-ray data collection. R.D.N and S.K.N. thank UGC-New Delhi for providing financial assistance under UGC-JRF (JUNE18-136885) through a fellowship and the Department of Chemistry, VNIT, Nagpur for research facilities and infrastructure.

Conflicts of Interest

The authors declare no conflict of interest. The funders had no role in the design of the study; in the collection, analyses, or interpretation of data; in the writing of the manuscript, or in the decision to publish the results.

Sample Availability

Samples of the compounds are available from the authors.

References

  1. Lipscomb, J. Management of Nonsteroidal Anti-inflammatory Drug-Induced Hypersensitivity Reactions. US Pharm. 2019, 44, 22–26. [Google Scholar]
  2. Ricciotti, E.; Tang, S.-Y.; Barekat, K.; Veglia, F.; Maseda, D.; Bittinger, K.; Bushman, F.; FitzGerald, G.A. The impact of cyclooxygenase-2 selective and non-isoform selective NSAIDs on the gut microbiota. FASEB J. 2019, 33, 516. [Google Scholar]
  3. Moro, M.G.; Oliveira, M.D.d.S.; Oliveira, L.R.d.; Teixeira, S.A.; Muscará, M.N.; Spolidorio, L.C.; Holzhausen, M. Effects of Selective Versus Non-Selective COX-2 Inhibition on Experimental Periodontitis. Braz. Dent. J. 2019, 30, 133–138. [Google Scholar] [CrossRef]
  4. Takeuchi, K.; Amagase, K. Roles of cyclooxygenase, prostaglandin E2 and EP receptors in mucosal protection and ulcer healing in the gastrointestinal tract. Curr. Pharm. Des. 2018, 24, 2002–2011. [Google Scholar] [CrossRef]
  5. Pannunzio, A.; Coluccia, M. Cyclooxygenase-1 (COX-1) and COX-1 inhibitors in cancer: A review of oncology and medicinal chemistry literature. Pharmaceuticals 2018, 11, 101. [Google Scholar] [CrossRef] [Green Version]
  6. Omar, Y.M.; Abdu-Allah, H.H.; Abdel-Moty, S.G. Synthesis, biological evaluation and docking study of 1, 3, 4-thiadiazole-thiazolidinone hybrids as anti-inflammatory agents with dual inhibition of COX-2 and 15-LOX. Bioorg. Chem. 2018, 80, 461–471. [Google Scholar] [CrossRef]
  7. Deb, P.K.; Mailabaram, R.P.; Al-Jaidi, B.; Saadh, M. Molecular basis of binding interactions of NSAIDs and computer-aided drug design approaches in the pursuit of the development of cyclooxygenase-2 (COX-2) selective inhibitors. Nonsteroidal Anti Inflamm. Drugs 2017, 6, 101–121. [Google Scholar]
  8. Zarghi, A.; Zebardast, T.; Daraie, B.; Hedayati, M. Design and synthesis of new 1, 3-benzthiazinan-4-one derivatives as selective cyclooxygenase (COX-2) inhibitors. Bioorg. Med. Chem. 2009, 17, 5369–5373. [Google Scholar] [CrossRef] [PubMed]
  9. Wallace, J.L. How do NSAIDs cause ulcer disease? Baillieres Best Pract. Res. Clin. Gastroenterol. 2000, 14, 147–159. [Google Scholar] [CrossRef] [Green Version]
  10. Gubin, J.; de Vogelaer, H.; Inion, H.; Houben, C.; Lucchetti, J.; Mahaux, J.; Rosseels, G.; Peiren, M.; Clinet, M. Novel heterocyclic analogs of the new potent class of calcium entry blockers: 1-[[4-(aminoalkoxy)phenyl]sulfonyl]indolizines. J. Med. Chem. 1993, 36, 1425–1433. [Google Scholar] [CrossRef] [PubMed]
  11. Cingolani, G.M.; Claudi, F.; Massi, M.; Venturi, F. Indolizine derivatives with biological activity VI 1-(2-aminoethyl)-3-benzyl-7-methoxy-2-methylindolizine, benanserin structural analogue. Cingolani 1990, 25, 709–712. [Google Scholar] [CrossRef]
  12. Hagishita, S.; Yamada, M.; Shirahase, K.; Okada, T.; Murakami, Y.; Ito, Y.; Matsuura, T.; Wada, M.; Kato, T.; Ueno, M.; et al. Potent Inhibitors of Secretory Phospholipase A2:  Synthesis and Inhibitory Activities of Indolizine and Indene Derivatives. J. Med. Chem. 1996, 39, 3636–3658. [Google Scholar] [CrossRef]
  13. Sandeep, C.; Venugopala, K.N.; Mohammed, A.K.; Mahesh, A.; Basavaraj, P.; Rashmi, S.K.; Rashmi, V.; Odhav, B. Review on chemistry of natural and synthetic indolizines with their chemical and pharmacological properties. J. Basic Clin. Pharm. 2016, 8, 49–61. [Google Scholar]
  14. Vaught, J.L.; Carson, J.R.; Carmosin, R.J.; Blum, P.S.; Persico, F.J.; Hageman, W.E.; Shank, R.P.; Raffa, R.B. Antinociceptive action of McN-5195 in rodents: A structurally novel (indolizine) analgesic with a nonopioid mechanism of action. J. Pharmacol. Exp. Ther. 1990, 255, 1–10. [Google Scholar]
  15. Bhat, M.A.; Al-Omar, M.A.; Alsaif, N.A.; Almehizia, A.A.; Naglah, A.M.; Razak, S.; Khan, A.A.; Ashraf, N.M. Novel sulindac derivatives: Synthesis, characterisation, evaluation of antioxidant, analgesic, anti-inflammatory, ulcerogenic and COX-2 inhibition activity. J. Enzyme Inhib. Med. Chem. 2020, 35, 921–934. [Google Scholar] [CrossRef]
  16. Venugopala, K.N.; Al-Attraqchi, O.H.A.; Tratrat, C.; Nayak, S.K.; Morsy, M.A.; Aldhubiab, B.E.; Attimarad, M.; Nair, A.B.; Sreeharsha, N.; Venugopala, R.; et al. Novel Series of methyl 3-(substituted benzoyl)-7-substituted-2-phenylindolizine-1-carboxylates as promising anti-inflammatory agents: Molecular modeling studies. Biomolecules 2019, 9, 661. [Google Scholar] [CrossRef] [Green Version]
  17. Sandeep, C.; Venugopala, K.N.; Khedr, M.A.; Padmashali, B.; Kulkarni, R.S.; Rashmi, V.; Odhav, B. Design and synthesis of novel indolizine analogues as COX-2 inhibitors: Computational perspective and in vitro screening. Indian J. Pharm. Educ. Res. 2017, 51, 452–460. [Google Scholar] [CrossRef] [Green Version]
  18. Shrivastava, S.K.; Srivastava, P.; Bandresh, R.; Tripathi, P.N.; Tripathi, A. Design, synthesis, and biological evaluation of some novel indolizine derivatives as dual cyclooxygenase and lipoxygenase inhibitor for anti-inflammatory activity. Bioorg. Med. Chem. 2017, 25, 4424–4432. [Google Scholar] [CrossRef] [PubMed]
  19. Sandeep, C.; Padmashali, B.; Venugopala, K.N.; Kulkarni, R.S.; Venugopala, R.; Odhav, B. Synthesis and characterization of ethyl 7-acetyl-2-substituted 3-(substituted benzoyl)indolizine-1-carboxylates for in vitro anticancer activity. Asian J. Chem. 2016, 28, 1043–1048. [Google Scholar] [CrossRef]
  20. Ghinet, A.; Abuhaie, C.-M.; Gautret, P.; Rigo, B.; Dubois, J.; Farce, A.; Belei, D.; Bîcu, E. Studies on indolizines. Evaluation of their biological properties as microtubule-interacting agents and as melanoma targeting compounds. Eur. J. Med. Chem. 2015, 89, 115–127. [Google Scholar] [CrossRef] [PubMed]
  21. Mederski, W.; Beier, N.; Burgdorf, L.T.; Gericke, R.; Klein, M.; Tsaklakidis, C. Indolizine Derivatives and the Use Thereof as Antidiabetics. U.S. Patent US-8106067-B2, 31 January 2012. [Google Scholar]
  22. Jaisankar, P.; Pal, B.; Manna, K.N.; Pradhan, P.K.; Medda, S.; Basu, M.K.; Giri, V.S. Synthesis of antileishmanial (5R)-(-)-5-carbomethoxy-3-formyl-5,6-dihydroindolo-[2,3-a]-indolizine. Arkivoc 2003, 9, 150–157. [Google Scholar] [CrossRef] [Green Version]
  23. Hazra, A.; Mondal, S.; Maity, A.; Naskar, S.; Saha, P.; Paira, R.; Sahu, K.B.; Paira, P.; Ghosh, S.; Sinha, C.; et al. Amberlite-IRA-402 (OH) ion exchange resin mediated synthesis of indolizines, pyrrolo [1,2-a] quinolines and isoquinolines: Antibacterial and antifungal evaluation of the products. Eur. J. Med. Chem. 2011, 46, 2132–2140. [Google Scholar] [CrossRef] [PubMed]
  24. Olejnikova, P.; Birosova, L.; Svorc, L. Antimicrobial and antimutagenic properties of newly synthesized derivatives of indolizine. Sci. Pharm. 2009, 77, 216. [Google Scholar] [CrossRef]
  25. Nasir, A.I.; Gundersen, L.L.; Rise, F.; Antonsen, O.; Kristensen, T.; Langhelle, B.; Bast, A.; Custers, I.; Haenen, G.R.; Wikstrom, H. Inhibition of lipid peroxidation mediated by indolizines. Bioorg. Med. Chem. Lett. 1998, 8, 1829–1832. [Google Scholar] [CrossRef]
  26. Mishra, B.B.; Tiwari, V.K. Natural products in drug discovery: Clinical evaluations and investigations. Oppor. Chall. Scope Nat. Prod. Med. Chem. 2011, 661, 1–61. [Google Scholar]
  27. Chandrashekharappa, S.; Venugopala, K.N.; Nayak, S.K.; Gleiser, R.M.; García, D.A.; Kumalo, H.M.; Kulkarni, R.S.; Mahomoodally, F.M.; Venugopala, R.; Mohan, M.K.; et al. One-pot microwave assisted synthesis and structural elucidation of novel ethyl 3-substituted-7-methylindolizine-1-carboxylates with larvicidal activity against Anopheles arabiensis. J. Mol. Struct. 2018, 1156, 377–384. [Google Scholar] [CrossRef]
  28. Sandeep, C.; Venugopala, K.N.; Gleiser, R.M.; Chetram, A.; Padmashali, B.; Kulkarni, R.S.; Venugopala, R.; Odhav, B. Greener synthesis of indolizine analogues using water as a base and solvent: Study for larvicidal activity against Anopheles arabiensis. Chem. Biol. Drug Des. 2016, 88, 899–904. [Google Scholar] [CrossRef]
  29. Smith, S.C.; Clarke, E.D.; Ridley, S.M.; Bartlett, D.; Greenhow, D.T.; Glithro, H.; Klong, A.Y.; Mitchell, G.; Mullier, G.W. Herbicidal indolizine-5,8-diones: Photosystem I redox mediators. Pest Manag. Sci. 2005, 61, 16–24. [Google Scholar] [CrossRef] [PubMed]
  30. Venugopala, K.N.; Uppar, V.; Sandeep, C.; Abdallah, H.H.; Pillay, M.; Deb, P.K.; Morsy, M.A.; Aldhubiab, B.E.; Attimarad, M.; Nair, A.B.; et al. Cytotoxicity and antimycobacterial properties of pyrrolo[1,2-a]quinoline derivatives: Molecular target identification and molecular docking studies. Antibiotics 2020, 9, 233. [Google Scholar] [CrossRef]
  31. Sandeep, C.; Venugopala, K.N. Novel Substituted Indolizine Scaffolds for MDR Strains of Mycobacterium tuberculosis, Synthetic Methodology and Chemical Structures Thereof. Indian Patent Application Number IN 201941002546 A, 3 April 2020. [Google Scholar]
  32. Hasija, A.; Bhandary, S.; Venugopala, K.N.; Chandrashekharappa, S.; Chopra, D. Structural investigation of methyl 3-(4-fluoro-benzo-yl)-7-methyl-2-phenyl-indolizine-1-carboxyl-ate, an inhibitory drug towards Mycobacterium tuberculosis. Acta Cryst. E Cryst. Commun. 2020, 76, 567–571. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  33. Venugopala, K.N.; Tratrat, C.; Chandrashekharappa, S.; Attimarad, M.; Sreeharsha, N.; Nair, A.B.; Pottathil, S.; Venugopala, R.; Al-Attraqchi, O.H.A.; Morsy, M.A.; et al. Anti-tubercular potency and computationally-assessed drug-likeness and toxicology of diversely substituted indolizines. Indian J. Pharm. Educ. Res. 2019, 53, 545–552. [Google Scholar] [CrossRef] [Green Version]
  34. Venugopala, K.N.; Tratrat, C.; Pillay, M.; Mahomoodally, F.M.; Bhandary, S.; Chopra, D.; Morsy, M.A.; Haroun, M.; Aldhubiab, B.E.; Attimarad, M.; et al. Anti-tubercular activity of substituted 7-methyl and 7-formylindolizines and in silico study for prospective molecular target identification. Antibiotics 2019, 8, 247. [Google Scholar] [CrossRef] [Green Version]
  35. Venugopala, K.N.; Chandrashekharappa, S.; Pillay, M.; Abdallah, H.H.; Mahomoodally, F.M.; Bhandary, S.; Chopra, D.; Attimarad, M.; Aldhubiab, B.E.; Nair, A.B.; et al. Computational, crystallographic studies, cytotoxicity and anti-tubercular activity of substituted 7-methoxy-indolizine analogues. PLoS ONE 2019, 14, e0217270. [Google Scholar] [CrossRef] [Green Version]
  36. Venugopala, K.N.; Khedr, M.A.; Pillay, M.; Nayak, S.K.; Chandrashekharappa, S.; Aldhubiab, B.E.; Harsha, S.; Attimard, M.; Odhav, B. Benzothiazole analogs as potential anti-TB agents: Computational input and molecular dynamics. J. Biomol. Struct. Dyn. 2019, 37, 1830–1842. [Google Scholar] [CrossRef]
  37. Khedr, M.A.; Pillay, M.; Chandrashekharappa, S.; Chopra, D.; Aldhubiab, B.E.; Attimarad, M.; Alwassil, O.I.; Mlisana, K.; Odhav, B.; Venugopala, K.N. Molecular modeling studies and anti-TB activity of trisubstituted indolizine analogues; molecular docking and dynamic inputs. J. Biomol. Struct. Dyn. 2018, 36, 2163–2178. [Google Scholar] [CrossRef] [PubMed]
  38. Xue, Y.; Tang, J.; Ma, X.; Li, Q.; Xie, B.; Hao, Y.; Jin, H.; Wang, K.; Zhang, G.; Zhang, L.; et al. Synthesis and biological activities of indolizine derivatives as alpha-7 nAChR agonists. Eur. J. Med. Chem. 2016, 115, 94–108. [Google Scholar] [CrossRef]
  39. Alwassil, O.I.; Chandrashekharappa, S.; Nayak, S.K.; Venugopala, K.N. Design, synthesis, and structural elucidation of novel NmeNANAS inhibitors for the treatment of meningococcal infection. PLoS ONE 2019, 14, e0223413. [Google Scholar] [CrossRef] [PubMed]
  40. Ingle, K.S.; Mohurle, S.A.; Bairagi, K.M.; Shaikh, T.R.; Venugopala, K.N.; Chandrashekharappa, S.; Gonnade, R.G.; Nayak, S.K. Synthesis, crystal structure and Hirshfeld surface analysis of the hydrated form of N′, N-(1,4-phenylenebis(methanylylidene) di(iso-nicotinic hydrazide). Chem. Data Collect. 2020, 28, 100401. [Google Scholar] [CrossRef]
  41. Chopra, D.; Venugopala, K.N.; Jayashree, B.S.; Guru Row, T.N. 3-(2-Anilino-1,3-thiazol-4-yl)-2H-chromen-2-one. Acta Crystallogr. Sect. E 2006, 62, o2663–o2665. [Google Scholar] [CrossRef]
  42. Maste, M.M.; Mahapatra, S.; Ramachandran, K.K.; Venugopala, K.N.; Bhat, A.R. N-(2-Amino-3,5-dibromobenzyl)-N-methylcyclohexan-1-aminium p-toluenesulfonate. Acta Crystallogr. Sect. E Struct. Rep. Online 2011, 67, o2032. [Google Scholar] [CrossRef] [PubMed]
  43. Chopra, D.; Venugopala, K.N.; Rao, G.K. (5S)-1,4-Bis{[(1E)-4-methylbenzylidene]amino}-5-(thien-2-yl)pyrrolidin-2-one. Acta Crystallogr. Sect. E 2007, 63, o2840. [Google Scholar] [CrossRef]
  44. Bhandary, S.; Girish, Y.R.; Venugopala, K.N.; Chopra, D. Crystal structure analysis of [5-(4-methoxyphenyl)-2-methyl-2H-1, 2, 3-triazol-4-yl](thiophen-2-yl) methanone. Acta Crystallogr. Sect. E Crystallogr. Commun. 2018, 74, 1178–1181. [Google Scholar] [CrossRef] [Green Version]
  45. Bairagi, K.M.; Kumar, V.B.S.; Bhandary, S.; Venugopala, K.N.; Nayak, S.K. Structural analysis of 2-iodobenzamide and 2-iodo-N-phenylbenzamide. Acta Crystallogr. Sect. E 2018, 74, 1130–1133. [Google Scholar] [CrossRef]
  46. Venugopala, K.N. Design, microwave assisted synthesis and characterization of substituted 1, 2, 4-oxadiazole analogues as promising pharmacological agents. Asian J. Chem. 2017, 29, 1767–1770. [Google Scholar] [CrossRef]
  47. Venugopala, K.N. Synthesis and structural elucidation of novel 2,4-disubstituted 1,3-oxazole analogues for pharmacological properties. Asian J. Chem. 2018, 30, 684–688. [Google Scholar] [CrossRef]
  48. Venugopala, K.N.; Ramachandra, P.; Tratrat, C.; Gleiser, R.M.; Bhandary, S.; Chopra, D.; Morsy, M.A.; Aldhubiab, B.E.; Attimarad, M.; Nair, A.B. Larvicidal activities of 2-aryl-2, 3-dihydroquinazolin-4-ones against malaria vector Anopheles arabiensis, In Silico ADMET prediction and molecular target investigation. Molecules 2020, 25, 1316. [Google Scholar] [CrossRef] [Green Version]
  49. Panini, P.; Venugopala, K.N.; Odhav, B.; Chopra, D. Polymorphism in two biologically active dihydropyrimidinium hydrochloride derivatives: Quantitative inputs towards the energetics associated with crystal packing. Acta Crystallogr. Sect. B Struct. Sci. Cryst. Eng. Mater. 2014, 70, 681–696. [Google Scholar] [CrossRef]
  50. Venugopala, K.N.; Rao, G.D.; Bhandary, S.; Pillay, M.; Chopra, D.; Aldhubiab, B.E.; Attimarad, M.; Alwassil, O.I.; Harsha, S.; Mlisana, K. Design, synthesis, and characterization of (1-(4-aryl)-1H-1, 2, 3-triazol-4-yl) methyl, substituted phenyl-6-methyl-2-oxo-1, 2, 3, 4-tetrahydropyrimidine-5-carboxylates against Mycobacterium tuberculosis. Drug Des. Devel. Ther. 2016, 10, 2681. [Google Scholar] [CrossRef] [Green Version]
  51. Munshi, P.; Venugopala, K.N.; Jayashree, B.S.; Guru Row, T.N. Concomitant Polymorphism in 3-Acetylcoumarin:  Role of Weak C–H···O and C–H···π Interactions. Cryst. Growth Des. 2004, 4, 1105–1107. [Google Scholar] [CrossRef]
  52. Nayak, S.K.; Venugopala, K.N.; Chopra, D.; Row, T.N.G. Insights into conformational and packing features in a series of aryl substituted ethyl-6-methyl-4-phenyl-2-oxo-1,2,3,4-tetrahydropyrimidine-5-carboxylates. CrystEngComm 2011, 13, 591–605. [Google Scholar] [CrossRef]
  53. Deb, P.K.; Kaur, R.; Chandrasekaran, B.; Bala, M.; Gill, D.; Kaki, V.R.; Akkinepalli, R.R.; Mailavaram, R. Synthesis, anti-inflammatory evaluation, and docking studies of some new thiazole derivatives. Med. Chem. Res. 2014, 23, 2780–2792. [Google Scholar] [CrossRef]
  54. Dhingra, M.S.; Deb, P.K.; Chadha, R.; Singh, T.; Karan, M. Synthesis, evaluation, and molecular docking studies of cycloalkyl/aryl-3, 4, 5-trimethylgallates as potent non-ulcerogenic and gastroprotective anti-inflammatory agents. Med. Chem. Res. 2014, 23, 87–106. [Google Scholar] [CrossRef]
  55. Kishore, D.P.; Maillabaram, R.; Rao, A.R.; Rao, P.M. Antiinflammatory evaluation and docking studies of some new thienopyrimidines. Asian J. Chem. 2013, 25, 10583. [Google Scholar] [CrossRef]
  56. Bali, A.; Ohri, R.; Deb, P.K. Synthesis, evaluation and docking studies on 3-alkoxy-4-methanesulfonamido acetophenone derivatives as non ulcerogenic anti-inflammatory agents. Eur. J. Med. Chem. 2012, 49, 397–405. [Google Scholar] [CrossRef] [PubMed]
  57. Balakumar, C.; Lamba, P.; Kishore, D.P.; Narayana, B.L.; Rao, K.V.; Rajwinder, K.; Rao, A.R.; Shireesha, B.; Narsaiah, B. Synthesis, anti-inflammatory evaluation and docking studies of some new fluorinated fused quinazolines. Eur. J. Med. Chem. 2010, 45, 4904–4913. [Google Scholar] [CrossRef]
  58. Venugopala, K.N.; Jayashree, B.S. Synthesis and characterization of Schiff bases of aminothiazolylbromocoumarin for their analgesic and anti-inflammatory activity. Asian J. Chem. 2004, 16, 407–411. [Google Scholar]
  59. Venugopala, K.N.; Jayashree, B.S.; Attimarad, M. Synthesis and evaluation of some substituted 2-arylamino coumarinyl thiazoles as potential NSAIDs. Asian J. Chem. 2004, 16, 872–876. [Google Scholar]
  60. Venugopala, K.N.; Chandrashekharappa, S.; Bhandary, S.; Chopra, D.; Khedr, M.A.; Aldhubiab, B.E.; Attimarad, M.; Odhav, B. Efficient synthesis and characterization of novel substituted 3-benzoylindolizine analogues via the cyclization of aromatic cycloimmoniumylides with electron-deficient alkenes. Curr. Org. Synth. 2018, 15, 388–395. [Google Scholar] [CrossRef]
  61. Spackman, M.A.; McKinnon, J.J.; Jayatilaka, D. Electrostatic potentials mapped on Hirshfeld surfaces provide direct insight into intermolecular interactions in crystals. CrystEngComm 2008, 10, 377–388. [Google Scholar] [CrossRef]
  62. Turner, M.J.; Grabowsky, S.; Jayatilaka, D.; Spackman, M.A. Accurate and Efficient Model Energies for Exploring Intermolecular Interactions in Molecular Crystals. J. Phys. Chem. Lett. 2014, 5, 4249–4255. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  63. Deb, P.K.; Al-Attraqchi, O.; Al-Qattan, M.N.; Raghu Prasad, M.; Tekade, R.K. Chapter 19—Applications of Computers in Pharmaceutical Product Formulation. In Dosage Form Design Parameters; Tekade, R.K., Ed.; Academic Press: Massachusetts, MA, USA, 2018; pp. 665–703. [Google Scholar] [CrossRef]
  64. Kalgutkar, A.S.; Crews, B.C.; Rowlinson, S.W.; Marnett, A.B.; Kozak, K.R.; Remmel, R.P.; Marnett, L.J. Biochemically based design of cyclooxygenase-2 (COX-2) inhibitors: Facile conversion of nonsteroidal antiinflammatory drugs to potent and highly selective COX-2 inhibitors. Proc. Natl. Acad. Sci. USA 2000, 97, 925–930. [Google Scholar] [CrossRef] [Green Version]
  65. APEX 2, SAINT; SADABS Bruker AXS Inc.: Madison, WI, USA, 2012. Available online: https://journals.iucr.org/e/services/stdswrefs.html (accessed on 9 June 2021).
  66. Sheldrick, G. Crystal structure refinement with SHELXL. Acta Crystallogr. Sect. C 2015, 71, 3–8. [Google Scholar] [CrossRef] [PubMed]
  67. Farrugia, L.J. WinGX and ORTEP for Windows: An update. J. Appl. Crystallogr. 2012, 45, 849–854. [Google Scholar] [CrossRef]
  68. Chandrashekharappa, S.; Venugopala, K.N.; Tratrat, C.; Mahomoodally, F.M.; Aldhubiab, B.E.; Haroun, M.; Venugopala, R.; Mohan, M.K.; Kulkarni, R.S.; Attimarad, M.V.; et al. Efficient synthesis and characterization of novel indolizines: Exploration of in vitro COX-2 inhibitory activity and molecular modelling studies. New J. Chem. 2018, 42, 4893–4901. [Google Scholar] [CrossRef]
Molecules 26 03550 g001 550
Figure 1. The proposed 7-methoxy indolizine analogues and commercially available nonselective cyclooxygenase (COX) inhibitor (indomethacin) for COX-2 inhibition action.
Figure 1. The proposed 7-methoxy indolizine analogues and commercially available nonselective cyclooxygenase (COX) inhibitor (indomethacin) for COX-2 inhibition action.
Molecules 26 03550 g001
Molecules 26 03550 sch001 550
Scheme 1. Synthetic outline for the construction of diethyl 7-methoxy-3-(3-substituedbenzoyl)indolizine-1,2-dicarboxylates (5a–d) [35] and ethyl 3-(4-bromobenzoyl)-2-ethyl-7-methoxyindolizine-1-carboxylates (5e).
Scheme 1. Synthetic outline for the construction of diethyl 7-methoxy-3-(3-substituedbenzoyl)indolizine-1,2-dicarboxylates (5a–d) [35] and ethyl 3-(4-bromobenzoyl)-2-ethyl-7-methoxyindolizine-1-carboxylates (5e).
Molecules 26 03550 sch001
Molecules 26 03550 g002 550
Figure 2. Plausible reaction mechanism for the construction of ethyl 3-(4-bromobenzoyl)-2-ethyl-7-methoxyindolizine-1-carboxylate (5e) [35,60].
Figure 2. Plausible reaction mechanism for the construction of ethyl 3-(4-bromobenzoyl)-2-ethyl-7-methoxyindolizine-1-carboxylate (5e) [35,60].
Molecules 26 03550 g002
Molecules 26 03550 g003 550
Figure 3. The ORTEP of 5c at 50% ellipsoidal probability and atom labeling of non-hydrogen atoms. The intramolecular C–H···O interactions are shown as green dotted lines.
Figure 3. The ORTEP of 5c at 50% ellipsoidal probability and atom labeling of non-hydrogen atoms. The intramolecular C–H···O interactions are shown as green dotted lines.
Molecules 26 03550 g003
Molecules 26 03550 g004 550
Figure 4. Crystal packing of 5c prefers the weak C–H···O interactions.
Figure 4. Crystal packing of 5c prefers the weak C–H···O interactions.
Molecules 26 03550 g004
Molecules 26 03550 g005 550
Figure 5. The C–H···π contacts exist in 5c crystal structure in its molecular assembly.
Figure 5. The C–H···π contacts exist in 5c crystal structure in its molecular assembly.
Molecules 26 03550 g005
Molecules 26 03550 g006 550
Figure 6. Hirshfeld surfaces of 5c mapped with (a) dnorm (b) de (c) shape index, and (d) curvedness.
Figure 6. Hirshfeld surfaces of 5c mapped with (a) dnorm (b) de (c) shape index, and (d) curvedness.
Molecules 26 03550 g006
Molecules 26 03550 g007a 550Molecules 26 03550 g007b 550
Figure 7. (a) The 2D fingerprint plots of the compound 5c with a percentage of interaction. (b) The short contact contributions derived from H···H, O···H/H···O, C···H/H···C, Br···H/H···Br, O···C/C···O, and C···C contacts. The values mentioned in the pie chart are in percentage form.
Figure 7. (a) The 2D fingerprint plots of the compound 5c with a percentage of interaction. (b) The short contact contributions derived from H···H, O···H/H···O, C···H/H···C, Br···H/H···Br, O···C/C···O, and C···C contacts. The values mentioned in the pie chart are in percentage form.
Molecules 26 03550 g007aMolecules 26 03550 g007b
Molecules 26 03550 g008 550
Figure 8. (a) Selected molecules for 5c present within 3.8 Å and cylindrical tube formation for the coulombic energy as red tubes (b), for dispersion energy as green tubes (c), and total energy as blue tubes (d).
Figure 8. (a) Selected molecules for 5c present within 3.8 Å and cylindrical tube formation for the coulombic energy as red tubes (b), for dispersion energy as green tubes (c), and total energy as blue tubes (d).
Molecules 26 03550 g008
Molecules 26 03550 g009a 550Molecules 26 03550 g009b 550
Figure 9. Predicted docking pose of indolizines (5a–e) and indomethacin (salmon-filled spheres) in the cyclooxygense-2 COX-2 domain (PDB 4COX). Hydrogen bonding and pi–pi interactions are represented in green and violet dotted lines, respectively.
Figure 9. Predicted docking pose of indolizines (5a–e) and indomethacin (salmon-filled spheres) in the cyclooxygense-2 COX-2 domain (PDB 4COX). Hydrogen bonding and pi–pi interactions are represented in green and violet dotted lines, respectively.
Molecules 26 03550 g009aMolecules 26 03550 g009b
Table
Table 1. Physicochemical properties of the target compound ethyl 3-(4-bromobenzoyl)-2-ethyl-7-methoxy-indolizine-1-carboxylate (5e).
Table 1. Physicochemical properties of the target compound ethyl 3-(4-bromobenzoyl)-2-ethyl-7-methoxy-indolizine-1-carboxylate (5e).
Molecules 26 03550 i001
CompoundMol Formulae (Mol Mass)RR1Yield (%) a,bm.p. (°C)cLogP c
5aC23H20N2O6 (420)4-CNCOOC2H5721713.4454
5bC22H20FNO6 (413)4-FCOOC2H5771474.0199
5cC22H20BrNO6 (473)4-BrCOOC2H5731344.7399
5dC23H23NO7 (425)3-OCH3COOC2H5751424.0294
5eC21H20BrNO4 (430)4-BrC2H5691086.2773
a The target compound was confirmed by physical and spectral data. b The final yield obtained after purification by column chromatography. c cLogP was calculated using ChemBioDraw Ultra 16.0v.
Table
Table 2. The crystallographic refinement parameters of 5c (diethyl 3-(4-bromobenzoyl)-7-methoxyindolizine-1,2-dicarboxylate).
Table 2. The crystallographic refinement parameters of 5c (diethyl 3-(4-bromobenzoyl)-7-methoxyindolizine-1,2-dicarboxylate).
DATA5c
FormulaC22H20BrNO6
Formula weight474.30
CCDC2,045,116
Temperature (K)173(2)
Wavelength (Å)0.71073
Crystal systemMonoclinic
Space groupP 21/n
a (Å)12.0479(6)
b (Å)17.8324(10)
c (Å)19.6052(11)
α (˚)90.000
β (˚)100.372(1)
γ (˚)90.000
V (Å3)4143.8(4)
Z’, Z2, 8
Density (g·cm−3)1.52
μ (mm−1)2.023
F (000)1936.0
θ (min, max)1.6, 28.3
hmin, max, kmin, max, lmin, max.−16, 15; −23, 23; −26, 26
No. of refl.10,282
No of unique ref./Obs. ref.10,282/6833
No. parameters576
Rall, Robs0.079, 0.041
wRall, wRobs0.100, 0.088
Δρmin, max(eÅ−3)−0.473, 0.393
G.O.O.F.1.024
Table
Table 3. Intra- and intermolecular interactions of 5c.
Table 3. Intra- and intermolecular interactions of 5c.
D–X···AD–X (Å)X···A (Å)D···A (Å)<D–X···A (o)
C21B–H21B···O1B i0.952.553.109(3)118
C1A–H1A···O6A i0.952.272.851(3)119
C1A–H1A···O6A i0.952.262.855(3)120
C2A–H2A···O6B ii0.952.523.466(3)174
C4B–H4B1···O4A iii0.982.503.442(3)162
C13B–H13C···π iv0.98(24)2.923.735(3)140
C13B–H13C···π* v0.98(24)2.863.785(3)156
Symmetry codes: (i) 1 + x, y, z; (ii) 3/2 − x, 1/2 + y, 1/2 − z; (iii) −1/2 + x, 1/2 − y, 1/2 + z; (iv) x, y, z; (v) x, y, z; Note: −π and π* are the centroids of the (N1A–C6A–C7A–C11A–C15A) and (N1A–C1A–C2A–C3A–C5A–C6A) aromatic rings, respectively.
Table
Table 4. Interaction energies as obtained from the Crystal Explorer 17.5 (in kJ/mol) for the 5c compound.
Table 4. Interaction energies as obtained from the Crystal Explorer 17.5 (in kJ/mol) for the 5c compound.
ColorNSymopRE_eleE_polE_disE_repE_tot
1-4.55−22.8−5.1−98.537.6−84.7
1-14.58−0.50−0.40−0.8
1-11.14.2−5.5−31.316.2−14.4
1-14.410.20−0.30−0.1
1-13.9800−1.30−1.3
1-17.790.20−0.200
1-11.161−4.4−22.68.9−15
1-16.730.10−0.100
1-18.830.30−0.200.2
1-12.40.80−0.800.1
1−x + 1/2, y + 1/2, −z + 1/211.15−16.2−1.2−22.849.62.5
1x + 1/2, −y + 1/2, z + 1/212.57−0.60−0.60−1.2
1−x, −y, −z18.250.30−0.100.2
2−x + 1/2, y + 1/2, −z + 1/212.35−0.3−0.1−2.10−2.3
1x + 1/2, −y + 1/2, z + 1/210.75−2.2−0.3−3.10−5.2
1x, y, z12.05−11.3−2.6−26.114.3−25.2
1−x, −y, −z23.430.10000.1
1x, y, z17.83−0.10−0.20−0.3
1−x, −y, −z16.07−0.30−0.10−0.4
1x + 1/2, −y + 1/2, z + 1/222.5400000
Table
Table 5. In vitro inhibitory study of cyclooxygenase-2 (COX-2) on diethyl 7-methoxy-3-(3-substitued-benzoyl)-indolizine-1,2-dicarboxylates (5a–d) and ethyl 3-(4-bromobenzoyl)-2-ethyl-7-methoxy-indolizine-1-carboxylate (5e).
Table 5. In vitro inhibitory study of cyclooxygenase-2 (COX-2) on diethyl 7-methoxy-3-(3-substitued-benzoyl)-indolizine-1,2-dicarboxylates (5a–d) and ethyl 3-(4-bromobenzoyl)-2-ethyl-7-methoxy-indolizine-1-carboxylate (5e).
CompoundCompound StructureIC50 * (µM)
5a Molecules 26 03550 i0025.84 ± 0.03 a
5b Molecules 26 03550 i0036.73 ± 0.03 a,b
5c Molecules 26 03550 i0046.99 ± 0.03 b
5d Molecules 26 03550 i0058.49 ± 0.03, b,c
5e Molecules 26 03550 i0067.38 ± 0.03 c,d
Indomethacin Molecules 26 03550 i0076.84 ± 0.03 b,d
Celecoxib Molecules 26 03550 i0080.05 ± 0.03 a
* IC50 value is defined as the concentration of test and standard substances required to produce 50% inhibition of human recombinant COX-2 enzyme by means of three determinations using the enzyme-linked immune sorbent assay kit. a–d Title compounds not sharing a letter vary significantly (p < 0.05).
Table
Table 6. Docking results of indolizines (5a–e) and indomethacin against cyclooxygense-2 (COX-2) receptor (PDB 4COX).
Table 6. Docking results of indolizines (5a–e) and indomethacin against cyclooxygense-2 (COX-2) receptor (PDB 4COX).
Molecules 26 03550 i009
EntryR1R2CDocker Interaction EnergyResidues Interaction
H-Bondingpi–pipi-alkyl
pi-halogen		Alkyl-alkyl
Alkyl-halogen
5aCO2Et4-CN39.51Arg120Trp387 Gly526Val349, Leu352, Ala527, Val523, Tyr355Val116, Val349, Leu531, Leu534
5bCO2Et4-F38.22Arg120 Val349, Leu352, Ala527, Val523, Tyr355Val116, Leu359, Leu531
5cCO2Et4-Br46.69-Tyr385Val349, Leu352, Ala527, Val523, Tyr385, Trp387, Phe381Val116, Val349, Leu359, Leu 531, Leu534, Leu384, Met522
5dCO2Et3-OCH353.29Arg120Tyr385 Trp387 Gly526Val349, Leu352, Ala527, Val523, Tyr355Val116, Leu359, Leu531
5eEt4-Br48.54-Trp387Val349, Leu352, Ala527, Val523, Tyr385, Trp387, Phe381Val116, Val349, Leu359, Leu 531, Leu534, Leu384, Met522
Indomethacin55.36Arg120 (ionic) Val349, Leu352, Ala527, Val523, Trp387Val349, Ala527, Leu531, Leu384, Met522
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Share and Cite

MDPI and ACS Style

Venugopala, K.N.; Chandrashekharappa, S.; Tratrat, C.; Deb, P.K.; Nagdeve, R.D.; Nayak, S.K.; Morsy, M.A.; Borah, P.; Mahomoodally, F.M.; Mailavaram, R.P.; et al. Crystallography, Molecular Modeling, and COX-2 Inhibition Studies on Indolizine Derivatives. Molecules 2021, 26, 3550. https://doi.org/10.3390/molecules26123550

AMA Style

Venugopala KN, Chandrashekharappa S, Tratrat C, Deb PK, Nagdeve RD, Nayak SK, Morsy MA, Borah P, Mahomoodally FM, Mailavaram RP, et al. Crystallography, Molecular Modeling, and COX-2 Inhibition Studies on Indolizine Derivatives. Molecules. 2021; 26(12):3550. https://doi.org/10.3390/molecules26123550

Chicago/Turabian Style

Venugopala, Katharigatta N., Sandeep Chandrashekharappa, Christophe Tratrat, Pran Kishore Deb, Rahul D. Nagdeve, Susanta K. Nayak, Mohamed A. Morsy, Pobitra Borah, Fawzi M. Mahomoodally, Raghu Prasad Mailavaram, and et al. 2021. "Crystallography, Molecular Modeling, and COX-2 Inhibition Studies on Indolizine Derivatives" Molecules 26, no. 12: 3550. https://doi.org/10.3390/molecules26123550

Article Metrics

Back to TopTop