Novel 3-cyclopentylidene-5-(methylsulfonyl)indolin-2-one derivatives as Anti-tubercular Agents: Design, Synthesis, Docking, Molecular Dynamic Simulation, and Biological Evaluation

doi:10.21203/rs.3.rs-3916647/v1

Nearly 3 million people die from tuberculosis (TB), which affects the lungs and other regions of the body. It is the most common bacterial infectious agent. We report the molecular docking, molecular dynamic simulations, synthesis, characterization, and biological activity of indolin-2-one derivatives as a novel anti-mycobacterial series identified from MABA (Microplate Alamar Blue Assay )method. The docking method was employed to investigate the intermolecular interactions between each compound and the enzyme Decaprenyl phosphoryl-D-ribose 2′-epimerase(DprE1). The results revealed significant binding interaction energies between these compounds and the enzyme. The stability of the interaction was evaluated using a standard 20 ns dynamic simulation study. For the protein-ligand complex's stability under the dynamic settings, parameters generated from MD simulation trajectories were computed and validated. The three compounds showed significant anti-mycobacterial activity, with MICs of 3.12 μg/ml against M. tuberculosis. All the compounds have favourable in vitroabsorption-distribution-metabolism-excretion (ADME). Evaluation of all the new compounds for in vitroanti-mycobacterial activity against Mycobacterium tuberculosis H37Rv (ATCC27294) resulted in 9b, 9c, and 15a (MIC: 3.125μg/mL) as promising lead analogues.

The bacterium that causes tuberculosis (TB), Mycobacterium tuberculosis (Mtb), most usually attacks the lungs and can also affect the kidneys, the brain, and the spine. Based on World Health Organisation estimates, the number of individuals diagnosed with tuberculosis (TB) reached 10.6 million last year, resulting in a mortality rate above 1 million [1]. Due to Mtb's propensity for adapting to treatments, there are a growing number of XDR (Extreme drug resistance) and MDR (Multi-drug resistance) strains that are resistant to all currently available antibiotics [2]. One of the difficulties is that Mtb has a peculiar mycobacterial cell wall composition and structure that limits the effective entrance of antibiotic medications and promotes resistance. MDR-TB patients need to receive treatment with a combination of 6–8 drugs for a lengthy period, up to 24 months [3]. Even though curative antituberculosis therapy has been available for almost 50 years, improper and insufficient care has allowed M. tuberculosis to develop resistance to our most potent antituberculosis medications [4]. To reduce the treatment length, a new TB drug will probably need to show that it can eradicate both replicating and non-replicating Mtb.

One of the areas of interest in treating tuberculosis is the mycobacterial cell wall. Decaprenyl phosphoryl-D-ribose 2′-epimerase, also known as DprE1, is a crucial flavoenzyme that contributes to the formation of the Mtb cell wall [5]. The heteromeric protein decaprenyl-phospho-ribose 2′-epimerase catalyses the epimerization conversion of decaprenyl phosphoryl-D-ribose (DPR) into decaprenyl phosphoryl-D-arabinose (DPA). [6]. When the FAD cofactor is reduced to FADH2, DprE1 catalyses the first step of epimerization, which is the oxidation of DPR to an intermediate decaprenyl-phospho-20-keto-D-arabinose (DPX). The NADH-dependent decaprenylphosphoryl-D-2-keto erythro pentose reductase (DprE2) then converts DPX to DPA [7]. Since the epimerization occurs in the periplasmic region, which explains DprE1's vulnerability as a target, this DprE1 is a promising target for developing novel therapeutic candidates to cure TB [8].

The oxindole nucleus has become crucial in several synthetic and natural chemicals that produce a range of pharmacological reactions [9]. The primary pharmacological properties of oxindole derivatives include antibacterial [10], anticancer [11, 12], anti-tubercular [13], anti-leishmanial [14], spermicidal [15], neuroprotective [16], etc. Some of the examples are shown in the Fig. 1. Due to the broad spectrum of biological activities and the abundance of synthetic options, numerous research groups have been involved in the design and synthesis of novel oxindole derivatives.

As part of our investigation into newly developed, effective synthetic compounds that target the DprE1 protein, we plan to create derivatives of indolin-2-one. We have applied a molecular docking technique on the enzyme DprE1 (PDB-ID-4NCR) to identify essential interactions and hit molecules. Two groups, piperidine and propane-1,3-diamine were introduced at region-1, while different acid chlorides were introduced at region-2, as shown in Fig. 2. The novel molecular design was anticipated to produce better anti-tubercular agents due to the combination of these active groups. In this communication, we describe the synthesis of newly synthesized 3-cyclopentylidene-2-oxo-N-(piperidin-4-yl)indoline-5-sulfonamide derivatives (9a-9f) and N-(3-aminopropyl)-3-cyclopentylidene-2-oxoindoline-5-sulfonamide derivatives (15a-15f) and analysed their anti-tubercular properties.

2.1: Rational Design: Structure-based designing was carried out to generate anti-tubercular compounds against DPrE1 protein ( PDB-ID: 4NCR), shown in Fig. 4. The ZINC Database was initially screened with the oxindole moiety [17]. Around 550 molecules were selected from the ZINC Database and docked using PyRx docking software, taking DPrE1protein, a vital enzyme for Mycobacterium tuberculosis, to produce its cell walls [18]. The best-scored molecules were further modified based on the synthetic feasibility. Out of which, 12 molecules were synthesized, which showed the best docking score shown in Table 1. The schematic representation of the workflow is shown in Fig. 3. The docking interactions between the ligand and protein are shown in Fig. 5. The determination of ADME qualities simplifies the drug development process by providing information on drug-likeness rules. We utilized Swiss ADME to evaluate the ADME characteristics. All the compounds have good ADME properties (Absorption, Distribution, Metabolism, Elimination), as shown in Table 1. Based on the Lipinski rule of five, the molecular weight should not exceed 500 g/mol. With the exception of three compounds, all the others met this requirement. All the compounds have adhered to the criterion that the topological polar surface area must be below 130 Å. And that the number of hydrogen bond donors should be less than 5 and the number of hydrogen bond acceptors should be less than 10. All compounds should have a logP (log of the partition coefficient) value that is less than 5, which is considered good. The molar refractivity (MR) of the four compounds is somewhat elevated, suggesting a little greater polarizability of the ion.

2.2: Molecular Dynamic Simulations

MD simulations at 20 ns were performed for the complex compounds 9C-4NCR and 15a-4NCR. The ligand's protonation state, the ligands' conformation, water molecules, cofactors, ions, and conformational and solvation entropies will all have an unanticipated pattern on docking predictions. Numerous studies supports using MD simulations to filter docking findings [19]. The Protein-Ligand RMSD (Root Mean Square Deviation) measure the average change in displacement of a selection of atoms for a particular frame with respect to a reference frame, as shown in Fig. 6. Throughout the simulations, the protein's secondary structural elements (SSE) were seen given in the supplementary material. The overall SSE percentages for the compounds 9c and 15a were 41.47% and 42.82%, respectively.

Table 1

Showing ADME Properties with Docking score
Molecules	MW	TPSA	LOGP	BBB permeant	Lipinski #violations	MR	Free energy binding (Kcal/Mol)	# Hydrogen bond acceptor	#Hydrogen bond donor
9a	533.56	103.96	3.12	No	1	138.51	-9.4	8	2
9b	483.56	103.96	3.34	No	0	133.47	-11.2	6	2
9c	445.57	103.96	3.13	No	0	128.03	-11.1	5	2
9d	431.55	103.96	2.86	No	0	123.22	-10.6	5	2
9e	465.56	103.96	2.84	No	0	133.51	-9.7	5	2
9f	544.46	103.96	3.05	No	1	141.21	-11.0	5	2
15a	507.53	112.75	2.6	No	1	127	-11.3	8	3
15b	457.52	112.75	2.88	No	0	121.96	-10.9	6	3
15c	419.54	112.75	2.87	No	0	116.52	-10.2	5	3
15d	405.51	112.75	2.49	No	0	111.71	-9.5	5	3
15e	377.46	112.75	2.48	No	0	102.1	-10.4	5	3
15f	439.53	112.75	2.12	No	0	122	-9.5	5	3
Co-crystal (PBTZ169)	-	-	-	-	-	-	-9.5	-	-

The sulphonamide group of the compound 9c formed an ionic bond through the water molecule with LYS-418 and a hydrogen bond with GLN-336 through the water molecule. The amino group of piperidine-4-amine forms a hydrogen bond with HIS-132. The carbonyl group of valeroyl moiety forms a bond with GLY-117. The other amino acids VAL-365, TYR-60, GLY-117, TYR-415, CYS-387, ILE-131, and LYS-134 for hydrophobic interactions in the ligand vicinity are shown in Fig. 7. In the compound 15a, the sulphonamide group formed an ionic bond through water molecule with LYS-418 and GLN-336. The LYS-418 also bonds with the benzene group of indolin-2-one through hydrophobic interaction with water molecules. The amino group hydrogen forms a hydrogen bond with HIS-132. The hydrogen group of other amino groups forms a bond with LEU-115. The benzene group of 3-fluorobenzamide forms a hydrophobic bond with TYR-314. The amino group in indoline-2-one forms a bond with TYR-60 through water type being hydrophobic interaction shown in Fig. 8. The timeline representation of the interactions and contacts (H-bonds, Hydrophobic, Ionic, Water bridges), ligand atom interactions with the protein residues, ligand torsions plot, and RMSF values are given in the supplementary material.

2.3: Synthesis

Economically available oxindole was used as the basis for synthesizing 5-substituted oxindole derivatives. Added oxindole, in portions, to the chlorosulfonic acid and stirred for 30 minutes at room temperature. The mixture was heated to 70°C using an oil bath to afford 2-oxoindoline-5-sulfonyl chloride 2 [20, 21]. The sulfonyl chloride intermediate 2 was coupled to N-amino-Boc piperidine 3 in the presence of pyridine [22, 23], resulting in the N-amino-Boc 4-(2-oxoindoline-5-sulfonamido) piperidine 4. By adding pyrrolidine as a base, the intermediate 4 in ethanol was subjected to Knoevenagel condensation with cyclopentanone 5, affording the intermediate 6. [24, 25]. The protecting group tertiary butyl carbonyl of intermediate 6 was removed by treating it with 4M HCl in ethyl acetate to yield the critical scaffold 7 as an HCl salt. The analogues 9a-9f were synthesized by amide coupling with different acid chlorides 8a-8f in the presence of di isopropyl ethyl amine shown in Scheme 1. The base diisopropylethylamine was added to the process to neutralise the generated hydrochloric acid. Similarly, in place of N amino-Boc piperidine 3, tert-butyl (3-aminopropyl)carbamate was taken and synthesized 15a- 15f following the procedure shown in Scheme 2.

2.3.1: Synthesis of 2-oxoindoline-5-sulfonyl chloride (2): The chlorosulfonic acid (HClSO₃) (20 ml) was taken in a two-neck round-bottomed flask and cooled to 0°C. Add indoline-2-one (5gm, 37.5mmole) portion-wise and stir for 30 min. at room temperature (rt). The reaction mixture temperature was increased to 70°C and stirred for 1 hr. The reaction mixture was cooled to RT and then poured into a beaker containing cold water (200 mL) slowly, and the precipitate formed was filtered and washed with water (3x 20 mL). The solid was then dried using reduced pressure to obtain the compound 2 (7.7g, 87.6%) as light brown solid: ¹H NMR (300 MHz, DMSO‒d₆): δ 10.55 (s, 1H), 7.49–7.46 (m, 2H), 6.79 (d, J = 7.8 Hz, 1H), 3.49 (s, 2H); MS (ESI + APCI): m/z = 231.9 [M + H]⁺.

2.3.2: Synthesis of tert-butyl-4-(2-oxo-1,3-dihydroindole-5-sulfonamido)piperidine-1-carboxylate (4): To a solution of 2-oxoindoline-5-sulfonyl chloride 2 (2.00 g, 8.63 mmol) and tert-butyl-4-amino-piperidine-1-carboxylate (1.92 gm, 8.71 mmol) in 1,4-dioxane(20ml) and was basified with pyridine (1.93 mL,24.7 mmol) and stirred for 2 hr at rt. The resultant mixture was diluted with water (20 mL) and pH adjusted to 6 by adding 2N HCL solution, then extracted with ethyl acetate (3x 50mL). The separated organic layer dried over Na₂SO₄ evaporated in rotavapors under reduced pressure. The obtained solid was washed with hexane (20 mL) to afford the compound 4 (2.8 g, 87%) as a light brown solid (crude directly used for the next step without any purification); MS (ESI + APCI): m/z = 395.30 [M -H]⁺.

2.3.3: Synthesis of tert-butyl-4‐(3‐ cyclopentylidene‐2‐oxo‐2,3‐dihydro‐1H‐indole‐5‐ sulfo- namido) piperidine‐1‐carboxylate (6): The compound 4 (2 g, 50.6 mmol) was added to cyclopentanone 5 (0.85 g, 10.10 mmol) in EtOH (10 mL). The reaction mixture was charged with pyrrolidine, stirred for 1hr at rt, and heated at 50°C for 1hr. The reaction mixture was cooled to room temperature, filtered the solid and washed with hexanes (50 mL) to afford compound 6 (1.2 g, 41.3%) as brown colour solid: ¹H NMR (400 MHz, CDCl₃) δ 7.73 (s, 1H, -NH), 7.68–7.66 (d, J = 6.8Hz, 1H, Ar-H), 7.62 (s, 1H, -ArH), 7.34–7.33 (d, J = 4 Hz, 1H, Ar-H), 7.03–7.01 (d, J = 8 Hz, 1H, Ar-H), 3.66–3.63 ( m, 4H, -NCH₂-CH₂-), 3.50 (m, H, -C = CH₂-CH₂-), 1.46–1.42 (t, 4H, -CH₂-CH₂-), 1.27 (3CH₃-O-C), 0.91 − 0.87 (m, 4H, -CH₂-CH₂-, cyclopentylidene). MS (ESI + APCI): m/z = 460 [M -H]⁺.

2.3.4: Synthesis of 3-cyclopentylidene‐1‐methyl‐2‐oxo‐N‐(piperidin‐4‐yl) indole‐5‐sulfon-amide hydrochloride (7): To the compound 6 (1.2 g, 2.60 mmol) in CH₂Cl₂ (10 mL) was added 4M HCl in 1,4-dioxane (10 mL) resultant reaction mixture stirred at room temperature for 16 h. The reaction mixture was concentrated under reduced pressure, and the resulting solid was washed with MTBE (20 mL) and dried to afford compound 7 (1.1 g, 91.6%); MS (ESI + APCI): m/z = 362.6 [M + H]⁺.

2.3.5: Synthesis of 3-cyclopentylidene-2-oxo-N-(piperidin-4-yl)indoline-5-sulfonamide derivatives (9): To the compound 7 ( 80 mg ) in CH₂Cl₂ (3 mL) was added DIPEA (3.0 equiv.) followed by RCOCl ( compound 8 ) (1.2 equiv.) at rt. The resultant reaction stirred at rt for 3 h. The reaction mass was quenched with water and extracted with EtOAc (5 mL). The organic layer dried over Na₂SO₄ and concentrated under reduced pressure to afford compound 9. All series of compounds 9a-j were synthesized using the same procedure.

2.3.5.1: 3-cyclopentylidene-2-oxo-N-(1-(3-(trifluoromethyl)benzoyl)piperidin-4-yl)indoline − 5-sulfonamide (9a): The compound (9a) was obtained from the 3-cyclopentylidene-2-oxo-N-(piperidin-4-yl)indoline-5-sulfonamide hydrochloride (7) (80 mg, 0.00220 mmol) and 3-(trifluoromethyl) benzoyl chloride (8a) (55.21 mg, 0.00264 mmol) as light cream solid; yield: 77.4 mg, 72%; HPLC purity: 97.80%; Melting point (MP): 160-162⁰C; IR (KBr): υ (cm^‒1): 3169, 1705, 1603, 1434, 1323, 1124; ¹H-NMR (400 MHz, CDCl₃): ¹H-NMR (400 MHz,CDCl₃): δ 8.34 (s, 1H, -NH), 7.91–7.89 (s, 1H, NH), 7.79–7.77 (d, J = 8 Hz, 1H, Ar-H), 7.49–7.44 (m, 1H, Ar-H), 7.38–7.37 (d, J = 4 Hz, 1H, Ar-H), 7.14–7.12 (d, J = 8 Hz, 1H, Ar-H), 7.08–7.06 (d, J = 8 Hz, 1H, Ar-H), 7.01–6.99 (d, J = 8 Hz, 1H, Ar-H) 3.79–3.15 (m, 4H, -NCH₂-CH₂-), 2.94 (m, 1H, CH₂-CH-CH₂- piperazine), 1.87–1.56 (m, 4H, -CH₂-CH₂- piperazine), 1.92–1.87 (m, 4H, -CH₂-CH₂- cyclopentylidene), 1.47–1.42 (m, 2H, -CH₂-CH₂- cyclopentylidene), 1.26–1.20 (m, 2H, -CH₂-CH₂- cyclopentylidene); ¹³C NMR (600 MHz, CDCl₃) 171.18, 169.89, 169.31, 169.04, 163.30, 163.38, 161.74, 143.07, 137.53, 133.91, 131.93, 130.12, 127.06, 125.85, 122.56, 121.23, 120.67, 120.53, 117.02, 116.87, 109.83, 50.50, 45.07, 35.62, 35.18, 26.16, 25.77; MS (ESI + APCI): m/z = 532.3 [M - H]⁺

2.3.5.2: 3-cyclopentylidene-N-(1-(3-fluorobenzoyl)piperidin-4-yl)-2-oxoindoline-5-sulfo- namide (9b): The compound (9b) was obtained from the 3-cyclopentylidene-2-oxo-N-(piperidin-4-yl)indoline-5-sulfonamide hydrochloride (7) (80 mg, 0.00220 mmol) and 3-flouro benzoyl chloride (8b) (41.85 mg, 0.00264 mmol) as a light cream solid; yield : 72.9 mg, 74.8%; HPLC purity: 92.71%; Melting point (MP): 172-174⁰C; IR (KBr): υ (cm^‒1): 3430, 1700, 1615, 1435, 1325, 1110; ¹H NMR (400 MHz, CDCl₃) δ 8.45 (s, 1H, -NH), 8.37 (s, 1H, -NH), 8.29–8.27 (d, (1H)), 7.91 (s, 1H, Ar-H), 7.88–7.85 (d, J = 8 Hz, 1H, Ar-H), 7.77–7.75 (d, J = 8 Hz, 1H, Ar-H), 7.70–7.67 (m, 1H), 7.63 (s, 1H, Ar-H), 7.54–7.53 (m, 1H), 7.00-6.98 (d, J = 8 Hz, 1H, Ar-H), 3.78–3.62 (m, 2H, piperidine), 3.45–3.40 (m, 2H, piperidine), 3.17–3.14 (m, 2H, piperidine), 2.94–2.91 (m, 1H, piperidine), 1.94–1.86 (m, 4H, -CH₂-CH₂-, cyclopentylidene), 1.59–1.54 (m, 2H, piperidine), 1.46–1.41 (m, 2H, -CH₂-CH₂-, cyclopentylidene), 1.28–1.25 (m, 2H-CH₂-CH₂- cyclopentylidene); ¹³C NMR (600 MHz, CDCl₃) δ 171.38, 169.92, 169.28, 168.95, 143.03, 136.26, 133.89, 130.60, 129.20, 126.99,126.67, 124.77, 123.92, 121.21, 118.72, 109.75, 53.90, 50.41, 45.01, 35.57, 35.11, 26.13, 25.73, 18.67, 17.44; MS (ESI + APCI): m/z = 482.3 [M - H]⁺

2.3.5.3: 3-cyclopentylidene-2-oxo-N-(1-pentanoylpiperidin-4-yl)indoline-5-sulfonamide(9c): The compound (9c) was obtained from the 3-cyclopentylidene-2-oxo-N-(piperidin-4-yl)indoline-5-sulfonamide hydrochloride (7) (80 mg, 0.00220 mmol) and valeroyl chloride (8c) (31.8 mg, 0.00264 mmol) as a light brown solid; yield : 81.7 mg, 82.8%; HPLC purity: 97.09%; Melting point (MP): 168-170⁰C; IR (KBr): υ (cm^‒1): 3425, 1705, 1610, 1460, 1315, 1075; ¹H NMR (400 MHz, CDCl3) δ 8.23 (s, 1H, -NH), 7.97–7.95 (d, J = 8 Hz, 1H, Ar-H), 7.90–7.88 (d, J = 8 Hz, 1H, Ar-H), 7.76 (s, 1H, Ar-H), 3.71–3.40(m, 4H, piperidine), 3.00-2.97 (m, 2H, piperidine), 2.93–2.91 (m, 2H, piperidine), 2.99–2.97 (m, 1H, Piperidine), 2.95–2.92(m, 2H, alkyl chain), 1.89–1.87 (m, 4H, cyclopentylidene), 1.57–1.53 (m, 4H, cyclopentylidene), 1.49–1.47 (m, 2H, alkyl chain), 1.29–1.26 (m, 2H, alkyl chain), 0.90 − 0.86 (m, 3H, alkyl chain); ¹³C NMR (600 MHz, CDCl₃) δ 171.74, 170.06, 169.28, 143.32, 133.54, 126.86, 124.72, 121.16, 118.86, 109.60, 53.80, 50.74, 45.01, 40.06, 34.93, 32.30, 26.95, 25.76, 22.55, 18.71, 17.48, 13.62, 12.06; MS (ESI + APCI): m/z = 444.3 [M - H]⁺

2.3.5.4: 3-cyclopentylidene-N-(1-isobutyrylpiperidin-4-yl)2-oxoindoline-5-sulfonamide (9d): The compound (9d) was obtained from the 3-cyclopentylidene-2-oxo-N-(piperidin-4-yl)indoline-5-sulfonamide hydrochloride (7) (80 mg, 0.00220 mmol) and isobutyryl chloride (8d) (28.1 mg, 0.00264 mmol) as a light cream solid; yield : 73.4 mg, 76.8%; HPLC purity: 98.17%; Melting point (MP): 170-172⁰C; IR (KBr): υ (cm^‒1): 3180, 1705, 1640, 1465, 1330, 1215, 1075; ¹H NMR (400 MHz, CDCl₃) δ 8.37(s, 1H, -NH), 7.90 (s, 1H, -Ar-H), 7.77–7.74 (d, J = 12 Hz, 1H, Ar-H), 7.00-6.98 (d, J = 8 Hz, 1H, Ar-H), 3.83–3.80 (m, 2H, piperidine), 3.38–3.36 (m, 2H, piperidine), 3.17–3.13 (m, 2H, piperidine), 2.94–2.91(m, 2H, piperidine), 2.75–2.73 (m, 1H, piperidine), 2.64–2.57 (m, 1H, Isobutyryl), 1.94–1.86 (m, 4H, cyclopentylidene), 1.46–1.44 (m, 4H, cyclopentylidene), 1.09–1.08 (d, J = 8Hz, 6H, Isobutyl); ¹³C NMR (600 MHz, CDCl₃) δ 175.50, 170.33, 169.37, 143.23, 133.84, 126.94, 124.73, 121.16, 118.81, 109.61, 53.80, 50.68, 43.73, 42.06, 40.28, 35.45, 34.96, 33.72, 32.36, 30.04, 26.15, 19.37, 18.91, 17.46, 12.03; MS (ESI + APCI): m/z = 432.2 [M - H]⁺

2.3.5.5: 3-cyclopentylidene N-(1-benzoylpiperidin-4-yl)-2-oxoindoline-5-sulfonamide (9e): The compound (9e) was obtained from the 3-cyclopentylidene-2-oxo-N-(piperidin-4-yl)indoline-5-sulfonamide hydrochloride (7) (80 mg, 0.00220 mmol) and benzoyl chloride (8e) (37.1 mg, 0.00264 mmol) as a brown solid; yield : 75 mg, 72.8%; Melting point (MP): 170-172⁰C; IR (KBr): υ (cm^‒1): 3247, 1696, 1609, 1458, 1143, 1075; ¹H NMR (400 MHz, CDCl₃) δ 8.32 (s, 1H, -NH), 7.98–7.96 (d, J = 12 1H, - Ar-H), 7.91 (s, 1H, -NH), 7.73–7.70 (d, J = 8, 2H, - Ar-H), 7.58–7.55 (m, 1H, - Ar-H), 7.03–7.01(m, 1H, - Ar-H), 3.50–3.41 (m, 3H, piperidine), 3.23–3.15 (m, 4H, piperidine), 2.95–2.92 (m, 2H, piperidine), 1.95–1.89 (m, 4H, cyclopentylidene), 1.20 (m, 4H, cyclopentylidene); ¹³C NMR (600 MHz, CDCl₃) δ 170.62, 169.40, 143.11, 135.52, 133.87, 133.42, 129.86, 126.83, 124.79, 121.16, 118.72, 109.55, 50.64, 35.47, 35.01, 26.14, 25.74; MS (ESI + APCI): m/z = 464.0 [M + H]⁺

2.3.5.6: 3-cyclopentylidene N-(1-(2-bromobenzoyl) piperidin-4-yl)-2-oxoindoline-5-sulfonamide (9f): The compound (9f ) was obtained from the 3-cyclopentylidene-2-oxo-N-(piperidin-4-yl)indoline-5-sulfonamide hydrochloride (7) (80 mg, 0.00220 mmol) and 2 bromo benzoyl chloride (8f) (57.9 mg, 0.00264 mmol) as a light cream solid; yield : 84.6 mg, 70.2%; Melting point (MP): 105-107⁰C; IR (KBr): υ (cm^‒1): 3189, 2946, 1697, 1610, 1443, 1298, 1146, 1072; ¹H NMR (400 MHz, CDCl₃) δ 8.77 (s, 1H, -NH), 8.11–8.09 (d, 1H, - Ar-H), 7.90 (s, 1H, -NH), 7.76–7.74 (d, 2H, - Ar-H), 7.62–7.59 (m, 1H, - Ar-H, 7.49–7.46 (m, 1H, - Ar-H), 7.40–7.35 (m, 1H, - Ar-H), 6.99–6.97 (m, 1H, - Ar-H), 3.42–3.41 (m, 2H, piperidine), 3.17–3.14 (m, 2H, piperidine), 2.93–2.90 (m, 1H, piperidine), 1.94–1.86 (m, 4H, cyclopentylidene), 1.67–1.47 (m, 4H, piperidine), 1.25–1.19 (m, 4H, cyclopentylidene); 13C NMR (600 MHz, CDCl3) δ 193.71, 191.98, 167.03, 161.66, 158.75, 156.84, 156.21, 155.09, 154.50, 151.04, 148.73, 146.32, 145.23, 143.09, 142.81, 134.01, 73.45, 69.50, 64.20, 62.46, 59.20, 56.19, 55.16, 51.01, 49.78. MS (ESI + APCI): m/z = 544.0 [M + H]⁺

2.3.6: Synthesis of tert-butyl (3-(2-oxoindoline-5-sulfonamido)propyl)carbamate (11): 1,4-dioxane (20ml) was taken and to that added 2-oxoindoline-5-sulfonyl chloride 2 (3.00 g, 12.9 mmol) and tert-butyl (3-aminopropyl)carbamate 10 (2.69 g, 15.45 mmol) and is basified with pyridine (2.04 mL, 26.15 mmol) and stirred for 2 hr at rt. 20 ml of water was added to the resulting mixture, which was then extracted with ethyl acetate after being acidified to a pH of 6 using a 2N HCl solution. (3 x 50 mL). Na₂SO₄ was used to dry the resultant reaction mixture and washed with hexane (2 x 5.0 mL). The resulting mixture was evaporated using the rotavapor to afford the compound 11 (4.16 g, 87%) as a light brown solid (crude directly used for nest step without any purification); MS (ESI + APCI): m/z = 369.30 [M -H]⁺.

2.3.7: Synthesis of tert-butyl (3-(3-cyclopentylidene-2-oxoindoline-5-sulfonamido)propyl) carbamate (12): The compound 11 (1.8 g, 4.80 mmol) was added to cyclopentanone 5 ( 0.49 g, 5.8 mmol) in EtOH (8 mL). To the reaction mixture, pyrrolidine (0.570g, 8.02 mmol) was added, stirred for 1hr at rt, and heated for 1hr at 50 ⁰C. The reaction mixture was cooled to room temperature, filtered, and washed with hexanes (50 mL) to afford compound 12 (0.94g, 44%) as white colour solid: ¹H-NMR (400 MHz, CDCl₃): δ 8.17 (s, 1H, -NH, Ar-H ), 7.90 (s, 2H, -Ar-H), 7.74–7.71 (d, J = 8Hz, 2H, -NH), 6.95–6.93 (d, J = 8Hz, 2H, -Ar-H), 3.19–3.14 (m, 2H, -NH-CH2), 2.98–2.94 (m, 2H, -CH2-CH2), 1.95–1.83 (m, 6H, cyclopentylidene, -CH2-CH2), 1.66–1.61 (m, 4H, cyclopentylidene), 1.36 (s, 9H, -CH3-CH3-CH3); MS(ESI + APCI): m/z = 434.30 [M -H]⁺.

2.3.8: Synthesis of N-(3-aminopropyl)-3-cyclopentylidene-2-oxoindoline-5-sulfonamide (13): To the compound 12 (1.2 g, 2.75 mmol) in CH₂Cl₂ (10 mL) was added 4M HCl in ethyl acetate (10 mL) resultant reaction mixture stirred at room temperature for 16 h. The reaction mixture was concentrated under reduced pressure, and the resulting solid was washed with MTBE (20 mL) and dried to afford compound 13 (1.1g, 91.6%). MS (ESI + APCI): m/z = 336 [M + H]⁺.

2.3.9: Synthesis of 3-cyclopentylidene-N-(3-(amino)propyl)-2-oxoindoline-5-sulfonamide derivatives (15): To the compound 13 (80 mg), CH₂Cl₂ (3 mL) was added DIPEA (3.0 equiv.) followed by different acids (RCOCl) (1.2 equiv.) at RT. The resultant reaction was stirred at RT for 3 h. The reaction mass was quenched with water and extracted with EtOAc (5 mL). The organic layer dried over Na₂SO₄ and concentrated under reduced pressure to afford compound 15. All series of compounds 15 a-f were synthesized using the same procedure.

2.3.9.1: Synthesis of N-(3-(3-cyclopentylidene-2-oxoindoline-5-sulfonamido)propyl)-3-(tri-fluoromethyl)benzamide(15a): The compound (15a) was obtained from the 3-cyclopentylidene-N-(3-(amino)propyl)-2-oxoindoline-5-sulfonamide (13) (80 mg, 0.00238 mmol) and 3-(trifluoromethyl)benzoyl chloride (14a) (59.56 mg, 0.00285 mmol) as a brown solid; yield : 81.3 mg, 74.3%; Melting point (MP): 115-117⁰C; IR (KBr): υ (cm^‒1): 3373, 1706, 1638, 1542, 1328, 1129; ¹H-NMR (400 MHz, CDCl₃):δ 8.03 (s, 2H, -NH, Ar-H ), 7.97–7.93 (m, 2H, -Ar-H), 7.89 (s, 1H, -NH), 7.77–7.72 (m, 2H, -Ar-H), 7.58–7.52 (m, 1H, -Ar-H), 6.94–6.92(m, 1H, -Ar-H), 3.65–3.62 (m, 2H, -NH-CH2), 3.14-3.00 (m, 2H, -NH-CH2), 2.93–2.89 (m, 2H, -CH2-CH2), 1.90–1.83 (m, 4H, cyclopentylidene), 1.56–1.44 (m, 4H,cyclopentylidene); ¹³C NMR (600 MHz, CDCl₃) δ 170.73, 166.64, 142.83, 134.87, 133.25, 132.87, 130.25, 129.24, 129.17, 128.21, 127.00, 124.73, 121.38, 118.62, 109.36, 53.84, 39.97, 36.49, 35.39, 35.00, 29.39, 26.12, 25.72, 12.01; MS(ESI + APCI): m/z = 506.30 [M + H]⁺.

2.3.9.2: Synthesis of N-(3-(3-cyclopentylidene-2-oxoindoline-5-sulfonamido)propyl)-3-fluoro -benzamide (15b): The compound (15b) was obtained from the 3-cyclopentylidene-N-(3-(amino)propyl)-2-oxoindoline-5-sulfonamide (13) (80 mg, 0.00238 mmol) and 3 fluoro benzoyl chloride (14b) (45.28 mg, 0.00285 mmol) as white solid; yield: 66.6 mg, 67.6%; Melting point (MP): 150-152⁰C; IR (KBr): υ (cm^‒1): 3409, 1739, 1649, 1519, 1449, 1329, 1124; ¹H-NMR (400 MHz, CDCl₃):¹H NMR (400 MHz, cdcl₃) δ 7.97 (s, 1H, -NH), 7.95 (s, 1H, -NH), 7.89 (s, 1H, -NH), 7.84–7.81 (d, J = 12Hz, 1H, -Ar-H), 7.74–7.72 (d, J = 8Hz, 2H, -Ar-H), 7.54–7.51 (m, 1H, -Ar-H), 7.48–7.45 (m, 1H, -Ar-H), 7.44–7.37 (m, 2H, -Ar-H), 6.94–6.92 (d, J = 8Hz, 2H, -Ar-H), 3.69–3.57 (m, 2H, -NH-CH2), 3.15–3.08 (M, 2H, -CH2-CH2) 2.97–2.91 (m, 2H, -CH2-CH2), 1.91–1.79 (m, 4H, cyclopentylidene), 1.58–1.44 (m, 4H, cyclopentylidene); ¹³C NMR (600 MHz, CDCl₃) δ 182.44, 163.39, 131.52, 130.19, 130.14, 125.88, 122.31, 121.49, 120.78, 120.64, 118.59, 117.08, 116.93, 77.23, 77.02, 76.81, 53.74, 41.98, 36.32, 35.43, 29.49, 17.41, 12.00; MS(ESI + APCI): m/z = 458.2[M + H]⁺.

2.3.9.3: Synthesis of N-(3-(3-cyclopentylidene-2-oxoindoline-5-sulfonamido)propyl)pentan-amide (15c) : The compound (15c) was obtained from the 3-cyclopentylidene-N-(3-(amino)propyl)-2-oxoindoline-5-sulfonamide (13) (80 mg, 0.00238 mmol) and valeroyl chloride (14c) (34.43 mg, 0.00285 mmol) white solid; yield: 71.71 mg, 79.3%; HPLC purity: 98.38%; Melting point (MP): 178-180⁰C; IR (KBr): υ (cm^‒1): 3340, 1705, 1655, 1544, 1457, 1329, 1148; ¹H-NMR (400 MHz, CDCl₃): δ 7.92 (s, 1H, ArH), 7.90 (s, 1H, -NH), 7.74–7.72 (d, J = 8Hz, 2H, -NH), 6.95–6.93 (d, J = 8Hz 1H, -Ar-H), 3.37–3.32 (m, 1H, -NH-CH2), 3.16–3.13 (m, 2H, -NH-CH2), 2.99–2.96 (m, 2H, -CH2-CH2), 2.94–2.89 (m, 2H, -CH2-CH2), 2.13–2.09 (m, 2H, -CH2-CH2), 1.94–1.85 (m, 4H, cyclopentylidene), 1.68–1.64 (m, 2H, -CH2-CH2), 1.54–1.47 (m, 2H, -CH2-CH2, Cyclopentylidene) 1.29–1.23 (m, 2H, -CH2-CH2, Cyclopentylidene), 0.92 − 0.84 (m, 3H, CH3-CH2-); ¹³C NMR (600 MHz, CDCl₃) δ 193.15, 163.76, 127.06, 121.53, 39.71, 36.42, 35.37, 27.82, 26.19, 25.80, 22.36, 13.76 ; MS(ESI + APCI): m/z = 418.4 [M + H]⁺.

2.3.9.4: Synthesis of N-(3-(3-cyclopentylidene-2-oxoindoline-5-sulfonamido)propyl) isobutyl-amide (15d) : The compound (15d) was obtained from the 3-cyclopentylidene-N-(3-(amino)propyl)-2-oxoindoline-5-sulfonamide (13) (80 mg, 0.00238 mmol) and isobutyryl chloride (14d) (30.43 mg, 0.00285 mmol) brown solid; yield: 65.4mg, 74.8%; Melting point (MP): 125-127⁰C; IR (KBr): υ (cm^‒1): 3474, 1705, 1652, 1545, 1468, 1324, 1145; ¹H-NMR (400 MHz, CDCl₃):¹H NMR (400 MHz, cdcl₃) δ 8.03 (s, 1H, -NH), 7.90(s, 1H, -NH), 7.74–7.72 (d, J = 8Hz, 2H, -NH), 6.94–6.93 (d, 1H, -NH),3.37–3.33 (m, 2H, -NH-CH2), 3.16–3.13 (m, 2H, -NH-CH2), 2.99–2.89 (m, 1H, CH3-CH-CH3), 2.35–2.28 (m, 2H, -CH2-CH2), 1.94–1.68 (m, 4H, cyclopentylidene), 1.54–1.45 (m, 4H, cyclopentylidene, 1.07–1.06 (m, 6H, Isobutyryl); ¹³C NMR (400 MHz, CDCl₃) δ 178.24, 170.29, 133.09, 127.03, 121.47, 118.76, 109.32, 77.24, 77.03, 76.82, 53.77, 42.01, 39.74, 38.39, 34.95, 33.70, 26.18, 25.77, 23.24, 19.57, 18.87, 12.01; MS(ESI + APCI): m/z = 404.3 [M + H]⁺.

2.3.9.5: Synthesis of N-(3-(3-cyclopentylidene-2-oxoindoline-5-sulfonamido)propyl)acet- amide (15e) : The compound (15e) was obtained from the3-cyclopentylidene-N-(3-(amino)propyl)-2-oxoindoline-5-sulfonamide (13) (80 mg, 0.00238 mmol) and acetyl chloride (14e) ( 22.41mg, 0.00285 mmol) light brown solid; yield: 50.7 mg, 62.3%; Melting point (MP): 132-134⁰C; IR (KBr): υ (cm^‒1): 3458, 1708, 1651, 1544, 1465, 1322, 1156; ¹H NMR (400 MHz, CDCl₃) δ 7.89 (s, 1H, -NH), 7.75–7.74 (d, J = 8Hz, 1H, -NH), 7.73–7.72 (d, J = 8Hz, 1H, ArH), 7.69 (s, 1H, ArH), 7.52 (s, 1H, -ArH), 6.95–6.93 (d, J = 8Hz, 1H, -ArH), 3.37–3.32 (m, 2H, -NH-CH2), 3.17–3.14 (m, 2H, -NH-CH2), 2.99–2.91 (m, 2H, -CH2-CH2), 1.93 (s, 3H, methyl) 1.90–1.85 (m, 4H, cyclopentylidene), 0.90–1.84 (m, 3H, CH3-C = O); ¹³C NMR (600MHz, DMSO) δ 169.55, 168.56, 167.81, 144.25, 132.92, 127.31, 124.37, 121.04, 119.12, 109.36, 40.97, 36.56, 35.03, 34.57, 29.71, 26.18, 25.70, 22.98; MS(ESI + APCI): m/z = 376.3 [M + H]⁺.

2.3.9.6: Synthesis of N-(3-(3-cyclopentylidene-2-oxoindoline-5-sulfonamido) propyl)benz-amide (15f) : The compound (15f) was obtained from the3-cyclopentylidene-N-(3-(amino)propyl)-2-oxoindoline-5-sulfonamide (13) (80 mg, 0.00238 mmol) and benzoyl chloride (14f) (40.14 mg, 0.00285 mmol) as light brown solid; yield : 66.9 mg, 70.6%; HPLC purity: 98.32%; Melting point (MP): 180- 182⁰C; IR (KBr): υ (cm^‒1): 3281, 1706, 1648, 1521, 1308, 1153; ¹H NMR (600 MHz, CDCl₃) δ 8.18–8.16 (m, 1H, -NH), 8.11–8.09 (m, 1H, -NH), 7.94 (s, 1H, -NH), 7.90 (s, 1H, -NH), 7.74–7.72 (d, J = 8Hz, 2H, -Ar-H), 7.69–7.67 (d, J = 8Hz, 1H, -Ar-H), 7.56–7.54 (m, 2H, -Ar-H), 7.51–7.47 (m, 1H, -ArH), 7.42–7.38 (d, J = 16 Hz, 1H, -Ar-H), 6.92–6.90 (d, J = 8Hz, 1H, -Ar-H), 3.67–3.56 (m, 2H, -CH₂-NH₂), 3.15–3.11 (m, 2H, -CH₂-CH₂), 3.01–2.92 (m, 2H, -CH₂-NH₂), 1.90–1.78 (m, 4H, cyclopentylidene), 1.53–1.44 (m, 4H, cyclopentylidene); ¹³C NMR (400 MHz, CDCl₃) δ 170.76, 133.69, 131.72, 130.19, 129.31, 128.62, 128.50, 126.83, 53.75, 39.85, 29.71, 25.77, 18.74, 17.49; MS(ESI + APCI): m/z = 438.3 [M + H]⁺.

2.4. Pharmacology

The MABA (Microplate Alamar Blue Assay) method was used to test twelve newly synthesized indoline-5-sulfonamide derivatives for in vitro anti-mycobacterial activity against M. tuberculosis H37Rv (ATCC27294). The MIC is defined as the minimum concentration of compound required to inhibit bacterial growth completely. Table 2 lists the MIC values (g/mL) of all compounds 9a-9f, 15a-15f, and three common anti-tubercular medications that were evaluated in triplicate at pH 7.40. All the new compounds screened have shown in vitro activity against Mtb with MICs ranging from 3.125-25 µg/mL. Among them, six analogues displayed MIC values below 6.25µg/mL, a figure proposed as an upper cutoff for evaluating novel M. tuberculosis treatments by the global program for discovering new anti-tubercular medicines. Three compounds, 9b, 9c, and 15a, inhibited Mtb with MIC 3.125 µg/mL. The 3(trifluoromethyl) benzoyl moieties group in compound 9a attached to the piperidine moiety shows promising activity with MIC of 6.25 µM. Replacing it with the 3-fluorobenzoyl group in compound 9b and the valeroyl group at the same position in compound 9c showed good activity with MIC of 3.125 µM. The isobutyryl group in compound 9d attached to the piperidine moiety shows less activity with MIC of 12.5 µM. The compounds 9e and 9f had benzoyl and 3-bromobenzoyl groups attached to piperidine moiety and showed similar activity with MIC of 6.25 µM. New compounds' structure-activity relationships related to their anti-tubercular activity have revealed that the compounds with N-amino piperidine showed more potency than those with an alkyl chain attached to the indoline-5-sulfonamide. Compound 15a has a trifluoro methyl benzoyl group, and the amino alkyl group showed good activity with MIC of 3.125 µM. Whereas 15d has an isobutyryl group and showed promising activity with MIC of 6.25 µM. The compounds 15b and 15c, having a 3-fluorobenzoyl group and valeroyl group, showed significantly less activity with MIC of 12.5 µM. The compounds 15e and 15f, having acetyl and benzoyl groups, led to more than 25 µM MIC value. At the same time, the compounds with short alkyl chains showed less potency. The compounds 9a, 9e, 9f, and 15d showed promising activity, a standard evaluation value of 6.25 µg/mL.

Table 2

MIC (minimum inhibitory concentration)of compounds against *Mycobacterium tuberculosis* H37Rv.
S.No	Compounds	MIC (µg/mL)
1	9a	6.25
2	9b	3.125
3	9c	3.125
4	9d	12.5
5	9e	6.25
6	9f	6.25
7	15a	3.125
8	15b	12.5
9	15c	12.5
10	15d	6.25
11	15e	> 25
12	15f	> 25
13	Isoniazid	0.05
14	Rifampicin	0.1
15	Ethambutol	1.56

3.1 Molecular Docking studies

The widely used computer technique known as molecular docking can be used to view the conformation of a receptor-ligand complex, which typically consists of a protein or a nucleic acid molecule as the receptor and either a small molecule or another protein as the ligand. The docking of a specific ligand to the active site of a precise protein was done using the PyRx-v0.8 virtual screening tool. The Lamarckian genetic approach was used to do the molecular docking analysis. We used a ligand fit docking approach to predict the binding modes and docking energies. The box dimensions were set as center_x = 14.83 Å, center_y = -10.55 Å, center_z = 2.55 Å, size_x = 45.65 Å, size_y = 41.50 Å, size_z = 43.78 Å. According to the root-mean-square deviation (RMSD) criterion, the findings were clustered, and this study selected the ligands with zero RMSD modes. The "exhaustiveness" preset for the docking was set to 8. The software's default values were employed for all other docking parameters. Nine poses in total were produced utilizing the receptor, ligand, and configuration files, which contained grid box attributes. When docking poses interacted with active site residues, the pose with the highest binding affinity was chosen and synthesized.

3.2. Ligand and Protein Preparation:

All the ligands were drawn using ChemDraw and saved as SDF files. The crystal structure of protein Decaprenylphosphoribose 2′epimerase (DprE1) (PDB-ID-4NCR, Resolution: 1.88 Å, R-Value Free: 0.234 and R-Value Work: 0.187, No mutations) was retrieved from the protein data bank. The protein was prepared Using Swiss PDB Viewer by removing its co-crystallized ligand and water molecules and adding missing residues [26]. For virtual screening, the SDF files from the ZINC15 database were utilized as it is.

3.3. ADME Properties

Numerous molecular descriptors, including lipophilicity, molecular flexibility, hydrogen-bonding capability, and molecular weight, have been used to characterise various molecular features and have been proven to help predict ADME characteristics. In this study, we have used Swiss ADME to predict the physio-chemical properties [27].

3.4. Molecular dynamic simulations

Molecular dynamics (MD) studies were conducted for the complex structures of the 4NCR protein with the selected compound 9c and 15a using Desmond Software Release 2018-4 for academic licensing (Schrödinger, LLC, New York, NY, USA to check the stability of binding for the complexes [28]. The simulations used the 0.15 M NaCl and TIP3P water model to mimic a physiological ionic concentration. Desmond's Protein Preparation, Ligand Preparation, and Epik tools were used to check the chemical structures' accuracy. Energy minimization was conducted for 100 Pico seconds (ps). At 300 K temperature and standard pressure (1.01325 bar), the MD simulations were run for 20 ns with a dimension buffer of 10 Å × 10 Å × 10 Å, an orthorhombic box, and an NPT ensemble. The energies were captured at 1.2 ps intervals. By incorporating Na⁺ or Cl^- ions, the protein-ligand complex's net charge system was balanced. All MD systems were kept at a temperature of 300 K and a pressure of 1.01325 bar using the Nose-Hoover chain and Martyna-Tobias-Klein algorithms.

3.5. Synthesis

All the reagents and solvents utilised in the synthesis were obtained from commercial suppliers (Sigma Aldrich, Avra, TCI, Combi-blocks) and used without additional purification. Using 20 × 20 cm, 200 m thick Merck classic aluminium silica plates, all reactions were monitored by TLC and detected at UV 254 nm. All the synthesised compounds were purified using silica gel (60–100#) columns in column chromatography. On an SA-AGILENT 400MHz NMR and (Ascend) AVANCE NEO 600 MHz FT-NMR spectrometer, proton 1H and 13C NMR spectra were captured. Tetramethyl silane (TMS) is used as a standard reference, and proton NMR chemical shifts are reported in parts per million (δ). ESI + was used to record ESI spectra on the Micro mass, Quattro LC. software with a capillary voltage of 3.98 kV and ESI mode positive ion trap detector. Melting points were measured in °C and reported.

3.6. Microplate Alamar Blue Assay (MABA)

Using MABA, the anti-TB effects of the title analogues 9a-f and 15a-f were assessed against the Mtb H37Rv (ATCC 27294) strain. As positive controls, isoniazid, rifampicin, and pyrazinamide are employed. The final test concentrations ranged from 50 to 0.78 g/mL, with compound stock solutions produced in DMSO at a concentration of 100 mg/mL. Fresh LJ medium was used to make the inoculum, which was then re-suspended in 7H9-S medium (which contains 7H9 broth, 0.1% casitone, 0.5% glycerol, and added oleic acid, albumin, dextrose, and catalase [OADC]), adjusted to an OD590 1.0, and diluted 1:20; 100 µl was used as the inoculum. The final highest concentration tested was achieved after each drug's stock solution had been thawed and diluted in 7H9-S four times. Using 100 µl 7H9-S, serial two-fold dilutions of each medication were prepared immediately in a sterile 96-well microtiter plate. On each plate, a sterile control and an antibiotic-free growth control were also created. All perimeter wells received sterile water addition to prevent evaporation throughout the incubation. The plate was covered, sealed up, and heated to 37°C in a typical environment. Each well received 30 µl of Alamar blue solution after the first 7 days of incubation, and the plate was then given another overnight incubation. The minimum inhibitory concentration (MIC) was defined as the lowest concentration of the drug that prevented the colour change from blue (an oxidised state) to pink (a reduced state), which indicated the growth of bacteria.

In this investigation, we attempted to derivatize oxindole lead compounds as potential DprE1 inhibitors employing virtual screening from the ZINC database. The most probable hits were subjected to molecular docking, and then to MD simulations to determine the interaction pattern and interaction strength. The results of docking followed by MD simulations of the compounds 9c and 15a showed that the obtained hits maintained the reported interactions with key amino acid residues, namely His 132 and Gln 336, which are required for the inhibition of DprE1. Based on in silico analysis and synthetic possibilities, the top twelve molecules were chosen, successfully synthesised, and tested for their anti-TB activity against the Mycobacterium tuberculosis H37Rv. Among series of twelve compounds, compound 9b, 9c and 15a are found to be effective with MIC 3.125 (µg/mL). Further exploration of the structure-activity studies of novel 3-cyclopentylidene-5-(methylsulfonyl)indolin-2-one derivatives can serve as a viable tool in developing drugs for antitubercular therapy.

Author Contributions Statement:

VVM: Investigation, Methodology, Data curation and Writing – original draft; NKK: Visualization and Writing – review & editing; GSK: Formal analysis, Validation and Resources; RG: Software, Conceptualization, Project administration and Supervision.

https:// (accessed April,30 2023)
Abubakar, I., Zignol, M., Falzon, D., Raviglione, M., Ditiu, L., Masham, S., Adetifa,I., Ford, N., Cox, H., Lawn, S. D., Marais, B. J., McHugh, T. D., Mwaba, P., Bates,M., Lipman, M., Zijenah, L., Logan, S., McNerney, R., Zumla, A., … Zumla, A. (2013).Drug-resistant tuberculosis: Time for visionary political leadership. The Lancet Infectious Diseases, 13(6), 529–539. https://doi.org/10.1016/S1473-3099(13)70030-6
Daley CL, Caminero JA (2013) Management of multidrug resistant tuberculosis. Semin Respir Crit Care Med 34(1):44–59. https://doi.org/10.1055/s-0032-1333546
Singh R, Dwivedi SP, Gaharwar US, Meena R, Rajamani P, Prasad T (2020) Recent updates on drug resistance in Mycobacterium tuberculosis. J Appl Microbiol 128(6):1547–1567. https://doi.org/10.1111/jam.14478
Huang H, Yagi T, Holsters M, Vereecke D, Haeze WD, Scherman MS, Brennan PJ, Mcneil MR, Crick DC (2005) Decaprenylphosphoryl Arabinofuranose, the Donor of the D -Arabinofuranosyl Residues of Mycobacterial Arabinan, Is Formed via a Two-Step Epimerization of Decaprenylphosphoryl Ribose. J Bacteriol 187(23):8020–8025. https://doi.org/10.1128/JB.187.23.8020
Manina G, Pasca R, Buroni M, De Rossi S, E., Riccardi G (2010) Decaprenylphosphoryl - β -D-Ribose 2-Epimerase from Mycobacterium tuberculosis is a Magic Drug Target. Curr Med Chem 17(27):3099–3108. https://doi.org/10.2174/092986710791959693
Gawad J, Bonde C (2018) Decaprenyl-phosphoryl-ribose 2′-epimerase (DprE1): Challenging target for antitubercular drug discovery. Chem Cent J 12(1):1–12. https://doi.org/10.1186/s13065-018-0441-2
Amado PSM, Woodley C, Cristiano MLS, O’Neill PM (2022) Recent Advances of DprE1 Inhibitors against Mycobacterium tuberculosis: Computational Analysis of Physicochemical and ADMET Properties. ACS Omega 7(45):40659–40681. https://doi.org/10.1021/acsomega.2c05307
Kaur M, Singh M, Chadha N, Silakari O (2016) Oxindole: A chemical prism carrying plethora of therapeutic benefits. Eur J Med Chem 123. https://doi.org/10.1016/j.ejmech.2016.08.011. Elsevier Ltd
Sharma P, Thummuri D, Reddy TS, Senwar KR, Naidu VGM, Srinivasulu G, Bharghava SK, Shankaraiah N (2016) New (E)-1-alkyl-1H-benzo[d]imidazol-2-yl)methylene)indolin-2-ones: Synthesis, in vitro cytotoxicity evaluation and apoptosis inducing studies. Eur J Med Chem 122:584–600. https://doi.org/10.1016/j.ejmech.2016.07.019
Roskoski R (2007) Sunitinib: A VEGF and PDGF receptor protein kinase and angiogenesis inhibitor. Biochem Biophys Res Commun 356(2):323–328. https://doi.org/10.1016/j.bbrc.2007.02.156
Kamal A, Ramakrishna G, Raju P, Rao AVS, Viswanath A, Nayak VL, Ramakrishna S (2011) Synthesis and anticancer activity of oxindole derived imidazo[1,5-a] pyrazines. Eur J Med Chem 46(6):2427–2435. https://doi.org/10.1016/j.ejmech.2011.03.027
Mohsen UABU (2014) Original article Synthesis and Antimicrobial Activity of Some Piperazine Dithiocarbamate Derivatives. Turk J Pharm Sci 11(3):347–354
Scala A, Cordaro M, Grassi G, Piperno A, Barberi G, Cascio A et al (2014) Direct synthesis of C3-mono-functionalized oxindoles from N-unprotected 2-oxindole and their antileishmanial activity. Bioorg Med Chem [Internet] 22(3):1063–1069. http://dx.doi.org/10.1016/j.bmc.2013.12.039
Paira P, Hazra A, Kumar S, Paira R, Sahu KB, Naskar S, saha P, Mondal S, Maity A, Banerjee S, Mondal NB (2009) Efficient synthesis of 3,3-diheteroaromatic oxindole analogues and their in vitro evaluation for spermicidal potential. Bioorg Med Chem Lett 19(16):4786–4789. https://doi.org/10.1016/j.bmcl.2009.06.049
Chowdhury S, Chafeev M, Liu S, Sun J, Raina V, Chui R, Young W, Kwan R, Fu J, Cadieux JA (2011) Discovery of XEN907, a spirooxindole blocker of Na V1.7 for the treatment of pain. Bioorg Med Chem Lett 21(12):3676–3681. https://doi.org/10.1016/j.bmcl.2011.04.088
Sterling T, Irwin JJ (2015) ZINC 15 - Ligand Discovery for Everyone. J Chem Inf Model 55(11):2324–2337. https://doi.org/10.1021/acs.jcim.5b00559
Dallakyan S, Olson AJ (2015) Small-Molecule Library Screening by Docking with PyRx. Methods Mol Biol. https://doi.org/10.1007/978-1-4939-2269-7_19
Andér M, Luzhkov VB, Åqvist J (2008) Ligand binding to the voltage-gated Kv1.5 potassium channel in the open state - Docking and computer simulations of a homology model. Biophys J 94(3):820–831. 10.1529/biophysj.107.112045
Sestito S, Nesi G, Daniele S, Martelli A, Digiacomo M, Borghini A, Pietra D, Calderone V, Lapucci A, Falasca M, Parrella P (2015) Design and synthesis of 2-oxindole based multi-targeted inhibitors of PDK1/Akt signaling pathway for the treatment of glioblastoma multiform. Eur J Med Chem 105:274–288. https://doi.org/10.1016/j.ejmech.2015.10.020
Guan H, Laird AD, Blake RA, Tang C, Liang C (2004) Design and synthesis of aminopropyltetrahydroindole-based indolin-2-ones as selective and potent inhibitors of Src and Yes tyrosine kinase. Bioorg Med Chem Lett 14:187–190. https://doi.org/10.1016/j.bmcl.2003.09.069
Kravchenko DV, Kuzovkova YA, Kysil VM, Tkachenko SE, Maliarchouk S, Okun IM, Balakin KV, Ivachtchenko AV (2005) Synthesis, and Structure-Activity Relationship of 4-Substituted 2-(2-Acetyloxyethyl)-8-(morpholine-4-sulfonyl) pyrrolo [3, 4-c] quinoline-1, 3-diones as Potent Caspase-3 Inhibitors. J Med Chem 48:3680–3683. https://doi.org/10.1021/jm048987t
Kim MH, Tsuhako AL, Co EW, Aftab DT, Bentzien F, Chen J, Cheng W, Engst S, Goon L, Klein RR, Le DT (2012) The design, synthesis, and biological evaluation of potent receptor tyrosine kinase inhibitors, Bioorganic Med. Chem Lett 22:4979–4985. https://doi.org/10.1016/j.bmcl.2012.06.029
Islam I, Bryant J, Chou YL, Kochanny MJ, Lee W, Phillips GB, Yu H, Adler M, Whitlow M, Ho E, Lentz D (2007) Indolinone based phosphoinositide-dependent kinase-1 (PDK1) inhibitors, Part 1: design, synthesis and biological activity. Bioorg Med Chem Lett 17:3814–3818. https://doi.org/10.1016/j.bmcl.2007.04.071
Liu CW, Lai CL, Lin YH, Teng LW, Yang SC, Wei WY, Lin SF, Yang JY, Huang HJ, Wang RW, Chiang CC (2014) Design and synthesis of pyrrole–5-(2, 6-dichloro benzyl) sulfonylindolin-2-ones with C-3′ side chains as potent Met kinase inhibitors. RSC Adv 4:58990–58998. https://doi.org/10.1039/C4RA08720H
Daina A, Michielin O, Zoete V (2017) SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(October 2016), 1–13. https://doi.org/10.1038/srep42717
Veber DF, Johnson SR, Cheng HY, Smith BR, Ward KW, Kopple KD (2002) Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem 45(12):2615–2623. https://doi.org/10.1021/jm020017n
(a) Desmond Molecular Dynamics System, Schrödinger Release 2020-1; D. E. Shaw Research: New York, 2020. (b) Maestro-Desmond Interoperability Tools; Schrödinger: New York, (2020)
Collins LA, Franzblau SG (1997) Microplate Alamar blue assay versus BACTEC 460 system for high- throughput screening of compounds against Mycobacterium tuberculosis and Mycobacterium avium. Antimicrob Agents Chemother 41(5):1004–1009. https://doi.org/10.1128/aac.41.5.1004
Krishna VS, Zheng S, Rekha EM, Guddat LW, Sriram D (2019) Discovery and evaluation of novel Mycobacterium tuberculosis ketol-acid reductoisomerase inhibitors as therapeutic drug leads. J Comput Aided Mol Des 33(3):357–366. https://doi.org/10.1007/s10822-019-00184-1

Schemes 1 and 2 are available in the Supplementary Files section

No competing interests reported.

GA.png
Graphical Abstract
Scheme1.png
Scheme 1: Synthesis of 9a-9f compounds
Scheme2.png
Scheme 2: Synthesis of 15a- 15f compounds
SupplementaryFile.docx

Novel 3-cyclopentylidene-5-(methylsulfonyl)indolin-2-one derivatives as Anti-tubercular Agents: Design, Synthesis, Docking, Molecular Dynamic Simulation, and Biological Evaluation

Status:

Version 1

Abstract

Figures

Introduction

Results and Discussion

2.2: Molecular Dynamic Simulations

2.3: Synthesis

2.4. Pharmacology

Materials and Method

3.1 Molecular Docking studies

3.2. Ligand and Protein Preparation:

3.3. ADME Properties

3.4. Molecular dynamic simulations

3.5. Synthesis

Conclusion

Declarations

Author Contributions Statement:

References

Schemes

Additional Declarations

Supplementary Files

Status:

Version 1