Discovery of chromen-2-one based hybrid molecules as potential anti-tubercular agents and their docking for MTB

Introduction

For the millennia, human civilizations have relied on nature and its products as medicine, with traditional healing practices across cultures drawing on the therapeutic properties of plants, animals, fungi, and microorganisms (Fokunang CN et.al, 2011) [1] . The diverse array of natural products they produce contains biologically active compounds that have been harnessed for treating various ailments and enhancing overall health and wellness (Ekiz E et.al, 2023) [2] . Plants have been a primary source of medicinal compounds. Plant species contain chemical compounds known as phytochemicals (Altemimi et.al, 2017) [3] . More than a thousand phytochemicals have been identified to date, and they can be obtained from a variety of sources including whole grains, fruits, vegetables, nuts, and herbs. They are plant-derived chemical with bioactive properties for example quinones, flavonoids, polyphenols, tannins, terpenoids, alkaloids, polypeptides, steroids, saponins, coumarins. These phytochemicals display antibacterial, antidiarrheal, anthelmintic, antiallergic, antispasmodic, and antiviral properties as well as significant antioxidant activity (Kumar A et al, 2023) [4] . Of these phytochemicals mentioned coumarin is widespread in nature and more than 1300 coumarins have been identified as secondary metabolites from plants, bacteria, and fungi (Tsivileva et.al, 2022) [5] . Coumarin is a colorless, crystalline substance that tastes bitter and has a sweet, vanilla-like aroma. It is utilized as a flavoring agent in food products such baked goods, alcoholic beverages, and tobacco as well as in the fragrance industry (Lončar et.al, 2020) [6] . It has wide range of pharmacological properties such as anti-inflammatory, anticoagulant, antibacterial, antifungal, antiviral, anticancer, antihypertensive, antitubercular, anticonvulsant, antiadipogenic, antihyperglycemic, antioxidant, and neuroprotective properties (Venugopala et.al, 2013) [7] . 'Coumarin', the name is derived from the plant Coumarouna odorata and was isolated by Vogal in 1820 (Lončar et.al, 2020) [6] . Coumarins belong to the benzopyrone family commonly found in many medicinal plants.

In this work, a total of 10 Amides are synthesized from anilines, pyridines and chloroacetyl chloride, Triethylamine and Dichloromethane (DCM).

General Reaction

Respective Anilne to N Phenyl Acetamide Respective Aniline/pyridine is taken as starting material the reagent used is chloroacetyl chloride, Triethyl amine and the solvent used is Dichloromethane (DCM).The progress of the reaction is checked through thin layer chromatography

Synthesis of chloroacetamides

Amides-These are functional groups in which a carbonyl carbon atom is connected to a nitrogen atom, an H-atom, or a C-atom by a single bond.

Materials and Methods

Tuberculosis (TB) is caused by bacterium Mycobacterium tuberculosis. TB affects the lungs, it can also affect other parts of the body like brain, the kidneys or the spine. TB is treated with a combination of antibiotics for a period of six to nine months or longer. The most common drugs used for TB treatment include isoniazid, rifampicin, pyrazinamide, and ethambutol.

Here, our study is to find molecule which is more effective than the marketly available drugs. Chromen-2-one is is a naturally occurring compound which has anticancer, anticonvulsant, antimicrobial, anticholinesterase, antituberculosis, and antidiabetic activities. Chromen-2-one is synthetically modified to produce 7-hydroxy-4-methyl-2Hchromen-2-one (7-Hydroxy-4-methyl-coumarin) to get a better antituberculosis activity. Series of amide was prepared and set of amide was coupled with 7-hydroxy-4-methy.l-2Hchromen-2-one. The objective is to check the biological activity of the coupled molecule and to know if it is a promising drug candidate.Insilico studies is to be done. Synthesis of chromen molecule (7-hydroxy-4-methyl-2hchromen-2-one) A mixture of resorcinol (1.101 g, 0.01 mole) and ethyl acetoacetate (1.274 ml, 0.01 mole) with 75% H2SO4 (10 ml) was heated for one hour. The resulting dark green solution was cooled and poured over crushed ice and filtered using vaccum pump. The thin-layer chromatography (TLC) was checked with reference, the reference taken is Umbelliferone (7-Hydroxy coumarin). The both compound exhibited fluorescence in UV light chamber. There was slight impurity in the compound formed, so the compound is to separated using column chromatography until clear spot is visible in the TLC plate. To identify whether the compound formed is chromen molecule the compound is sent to Mass spectroscopy and H1 NMR. The compound structure is elucidated. The next step is to couple this pure compound formed (7-hydroxy-4-methyl-2H-chromen-2-one) with the amide which shows best activity towards Tuberculosis (TB).

Experimental: General Reaction: Coupling of chromen molecule with chloroacetamide: In coupling reactions, two similar or different species react together to yield a new product. There is a common intermediate and a metal catalyst.

General Procedure of the synthesis of 7-hydroxy-4methyl-2H-chromen-2-one

molecule N-Phenyl acetamide: Here in the coupling reaction, the reactants taken are the 7-hydroxy-4-methyl-2H-chromen-2-one molecule (1eq) and the corresponding amide (1.3 eq) with K 2 CO 3 as base and DMF as solvent, the reaction is done at room temperature and kept overnight.

Scheme: 1-7-hydroxy-4-methyl-2H-chromen-2-one molecule N-Phenylacetamide.

Results and Conclusion

The main molecule used in the reaction is Chromen-2-one molecule. A series of intermediates (amides) are made and are coupled with the Chromen molecule. Insilico studies like molecular docking is performed to determine the receptorligand interaction. Drug likeness is validated through pharmokinectics and ADME studies. The coupled complex should be validated for their biological activity the complex giving positive results are taken for further studies.

Molecular Docking: Here in this work, the coupled final product is taken as ligand and the receptor used is DNA Gyrase receptor. First we have to prepare protein and ligand.

Preparation of protein (Receptor):

Protein was downloaded from Protein Data Bank and is downloaded in PDB format. The downloaded protein is prepared using AutoDock Vina(Version 1.5.7).The heteroatoms, water molecules should be removed, Polar H may be added while preparing protein.We can also select grid-box in the target protein and thus prepared protein can be saved as PDBQT (Protein Data Bank, Partial Charge (Q), & Atom Type (T) format.

Preparation of Ligand:

The ligands taken are the final coupled compound. The structure of the final compound is drawn by ChemBioDraw Ultra 14.0 tool and is saved is "mol" Files. These prepared ligands energy can be minimized by the Open Babel tool in the PyRx Software and these energy minimized ligands can be saved in PDBQT Format.

References

1. Fokunang CN, Ndikum V, Tabi OY, Jiofack RB, Ngameni B, Guedje NM, et al. Traditional medicine: past, present and future research and development prospects and integration in the National Health System of Cameroon. Afr J Tradit Complement Altern Med. 2011;8(3).
2. Ekiz E, Oz E, Abd El-Aty AM, Proestos C, Brennan C, Zeng M, et al. Exploring the potential medicinal benefits of Ganoderma lucidum: From metabolic disorders to coronavirus infections. Foods. 2023 Apr 3;12(7):1512.
3. Altemimi A, Lakhssassi N, Baharlouei A, Watson DG, Lightfoot DA. Phytochemicals: Extraction, isolation, and identification of bioactive compounds from plant extracts. Plants. 2017 Sep 22;6(4):42.
4. Kumar A, Gautam V, Sandhu A, Rawat K, Sharma A, Saha L. Current and emerging therapeutic approaches for colorectal cancer: A comprehensive review. World J Gastrointest Surg. 2023 Apr 27;15(4):495.
5. Tsivileva OM, Koftin OV, Evseeva NV. Coumarins as fungal metabolites with potential medicinal properties. Antibiotics. 2022 Aug 26;11(9):1156.
6. Lončar M, Jakovljević M, Šubarić D, Pavlić M, Buzjak Sluzek V, Cindrić I, et al. Coumarins in food and methods of their determination. Foods. 2020 May 18;9(5):645.
7. Venugopala KN, Rashmi V, Odhav B. Review on natural coumarin lead compounds for their pharmacological activity. Biomed Res Int. 2013;2013(1):963248.