Synthesis, Develop and Characterization of New Quinoline-Sulfonamides derivatives as Specific Tumer-Related CARBONIC ANHYDRASE Isoform XII Inhibitors

 

Bayan Bahnasli1, Djamila Ben Hadda2, Amir Balash3, Mustapha Fawaz Chehna1

1Department of Pharmaceutical Chemistry & Drug Control, Faculty of Pharmacy,

Aleppo University, Aleppo, Syria.

2Department of Pharmaceutical Chemistry & Drug Control, Faculty of Pharmacy,

Ebla University, Aleppo, Syria.

3Department of Pharmaceutical Chemistry & Drug Control, Faculty of Pharmacy,

Philipps University, Marburg, Germany.

*Corresponding Author E-mail: bbahnasli@gmail.com, djamila.benhadda@ebla.edu.sy,  amir_balash@hotmail.com; mf.chehna@gmail.com

 

ABSTRACT:

Numerous studies highlight the significant responsibility of CARBONIC ANHYDRASE Isoform XII in the mechanisms underlying the onset and progression of cancer. Our research focuses on the synthesis of Quinoline-Sulfonamides, which are compounds designed to inhibit this enzyme, a key player in cancer development. Using Molegro Virtual Docker (MVD), we conducted molecular modeling of these compounds, targeting Carbonic Anhydrase Isoform XII, and calculated their binding energies to identify the most promising candidate. Among the compounds studied, compound 1..e exhibited the highest binding energy at -166.694kcal/mol in comparison to 4-propylthiobenzen sulfonamide (VD9), Which has a binding energy of -115kcal/mol , Several of these compounds were synthesized efficiently using an economical and environmentally friendly aqueous method with high yield ranging between 70 to 86%.Their physicochemical properties were studied using Marvin Sketch and structural identification were confirmed through different analytical methods, involving Mass Spectrography, Infrared Spectrography, and nuclear magnetic resonance.

 

KEYWORDS: CA XII enzyme - Sulfonamide-quinoline derivatives - Quinoline-8-sulfonyl chloride - Carbonic Anhydrase XII – Hypoxia.

 

 


INTRODUCTION:

Carbonic anhydrase (CAs) are enzymatic metalloproteins that promote the invertible process between CO₂ and HCO₃⁻ ions1. Human carbonic anhydrases (H-CAs) are classified within the α-CA group, which is one among the eight labeled groups of carbonic anhydrases2. Among the sixteen known isozymes, only 12 isoforms demonstrate catalytic activity3.

 

CAs play significant parts in physical and diseases mechanisms, including pH balance, respiration, epilepsy, bone resorption, obesity, and tumorigenesis4,5,6. The involvement of CAs in diverse diseases has been established, making various (H-CA) isoforms important targets to develop inhibitors with possible therapeutic applications, such as treatments for glaucoma, epilepsy, obesity, and cancer7,8,9,10,11,12,13,14.

 

Tumor progression leads to the establishment of a hypoxic microenvironment, which in turn causes extracellular acidosis due to the reliance on anaerobic glycolysis by tumor cells. This decrease in pH further promotes tumor development15,16,17,18. The isoforms H-CA IX and H-CA XII are widely recognized as "tumer-associated" carbonic anhydrase isoforms. Furthermore, H-CA XII shows a significant role in both cell propagation and intercellular communication. The overexpression of the H-CA IX isoform has been strongly linked to unfavorable prognoses across various cancer types19. Additionally, while H-CA XII is present in numerous tumor types, its association with hypoxic tumors is less pronounced compared to H-CA IX20.

 

Sulfonamides demonstrate a spectrum of biological processes, involving anti-inflammatory, antiviral, anticancer, and antimicrobial properties. Since their introduction in 1932, many studies have been undertaken to investigate these effects21,22. Quinoline-derived limited molecules have been recorded to exhibit diverse biological activities, involving notable anticancer characteristics23,24. These compounds have gained prominence as promising candidates within the pharmacological domain, especially concerning cancer treatment25. Their distinctive structural features endow them with various biological functions, and an increasing amount of research indicates their potential effectiveness in modulating critical molecular pathways associated with tumor development. Due to the importance of both Quinoline and Sulfonamide, our research concentrated on the synthesis of Quinoline-Sulfonamides, evaluating their anticancer activity with references.

 

Our research team at the University of Aleppo, Faculty of Pharmacy, has conducted extensive studies on the synthesis of innovative sulfonamide derivatives. These efforts have been directed toward designing compounds with broad pharmaceutical potential, particularly in the fields of antibacterial and anticancer therapies, as well as EGFR inhibition26,27,28,29.

 

METHODS AND MATERIALS:

Chemicals, Equipment and Instruments:

Quinoline-8-sulfonyl chloride, which was obtained from Ambeed Company, has a purity of 98% while the other primary materials were purchased from reputable providers such as Sigma Aldrich to complete the synthesis process. The enzyme carbonic anhydrase XII isozyme (PDB code: 4WW8) was extracted from the pdB. The modeling of the designed derivatives for activity testing and investigating binding with amino acid residues in the enzyme (binding energy results) was completed using the MVD program (version 5.5.2022). Structures of compounds were sketched in Marvin Sketch software and exported in mol2 format for MVD input. Melting points of the prepared derivatives were determined to confirm identity using a BUCHI melting point apparatus (MACHEREY-NAGEL, Germany). Tlc was conducted on aluminum plates with silica gel 60 F254 using mixed ethyl acetate and petroleum ether for Rf value calculations. FT-IR spectroscopy (Bruker, Billerica, Massachusetts) was utilized to record infrared spectra. Mass spectra were ocquired using a mass spectrometer and ¹H/¹³C Nmr spectra were logged via a JEOL ECA NMR spectrometer with all of the compounds dissolved in DMSO for analysis.

 

Synthesis of quinoline sulfonamide derivatives:

In a suitable 100ml round bottom flask under an ice bath, the amino derivatives (0.002mol) were dissolved, each one separately, in a 10% sodium bicarbonate solution. Then, in batches and slowly, the quinoline-8-sulfonyl chloride (0.002 mol) was added. The reaction solution was left for a full day while the reaction was monitored by TLC. The next day, a precipitate was formed, which was separated and treated several tims with cool water. Then, it was recrystallized using equal proportions of water and ethanol.

 

Protein preparation:

The 3D structure of the target Enzyme Carbonic Anhydrase XII (CA XII) in complex with VD9 from the pdB with code: 4WW8 has a resolution of 1.42 A", consists of 354 amino acids.

 

 

Figure 1: 3D Structure of CA XII

 

Ligand preparation:

Preparation of Chemical Structures For this research, the chemical structures were retrieved from the PubChem database. The compound was designed and optimized using Marvin Sketch software before finally exporting the IM structures in mol2 format. The following default parameters were used for structure preparation: - Bond and atom type - Addition of hydrogen bonds - Determining hybridization and bond orders - Assigning charges through MVD calculations - Torsional flexibility of the ligand

 

A table containing the sulfonamide-based compounds evaluated in this study can be found in the next section.

 

Molecular Docking:

Molecular Docking Methodology The molecular docking analysis of Carbonic Anhydrase Isoform XII (CA XII) with selected compounds was performed utilizing Molegro Virtual Docker (MVD) which is a freely available software package widely used in computational drug discovery. Docking parameters (including grid resolution, ligand flexibility, scoring functions, and number of iterations) were modified specifically for the CA XII active site which is presented in Table 1. These docking parameters are consistent with previously established protocols in order to ensure both reproducibility and accuracy in predicting binding pose and estimating affinity.

 

 

Figure 2: Carbonic anhydrase XII active site:

 

Table 1: Parameters of mvd:

Parameters

Values

Cavity Volume

Volume:73.216A°

Surface:229.12A°

Scoring Function

Moldock Score

(Gird)

binding site redius

9

gird resolution( A°)

0.3

number of runs

10

searching algorthum

moldock optimizer

max population size

50

max iterations

2000

max number of poses returned

5

energy thershold

1000

 

Validation docking method:

Molecular modeling was conducted to evaluate the possibility of Carbonic Anhydrase Isoform XII inhibition by compounds a..1-b..8 and to calculate their binding energies. Before performing molecular modeling, an appropriate protocol needed to be selected and validated. The validity of the protocol was verified by redocking the VD9 substrate with the Carbonic Anhydrase Isoform XII enzyme and calculating the RMSD. RMSD value for the protocol was satisfactory at 0.7849 Å. After protocol validation, molecular modeling was performed using this protocol for compounds 1-8..a/1-8..e, with all compounds docked in the same active pocket.

 

Figure 3: All derivatives are bound to the CA XII enzyme in the active site

RESULTS AND DISCUSSION:

Chemistry:

Quinoline-8-sulfonyl chloride reacts with amino derivatives including aniline, sulfanilamide, anthranilic acid, and 3-chloro-4-fluoroaniline to produce quinoline-sulfonamide derivatives that may exhibit potential activity as CA XII inhibitors.

 

The reaction should be performed in an alkaline environment, either in an aqueous solution containing sodium bicarbonate and sodium hydroxide or in an organic medium with pyridine or triethylamine. In acidic conditions, the amine group becomes protonated, decreasing the nucleophile's strength.

 

The nucleophilic attack represents the rate-limiting step of the reaction, involving formation of a trigonal bipyramidal transition state. The simultaneous presence of both nucleophile and halide in the compound weakens the sulfur-halogen bond, resulting in halogen removal.

 

In our laboratory, the reaction was conducted in an aqueous medium with sodium bicarbonate. Upon reaction completion, a precipitate formed, which was subsequently purified through recrystallization.

 

 

Figure 4. The mechanism of synthesis of compounds 2..a, 3..a, 4..a and 8..a.

 

Docking:

All structural formulas for the designed and synthesized derivatives were drawn using Marvin Sketch and stored in mol2 format for docking using MVD.

 

We noted that all designed and synthesized compounds bound to the CA XII enzyme, exhibiting varying binding energies - some higher and some lower than the reference ligand.

 

All compounds formed van der waals interactions and Hydrogen bonds with the enzyme's amino acids, with different binding energies and bond distances. Compounds containing SO₂NH₂ and COOH groups formed ionic bonds with zinc, which is crucial for the enzyme's catalytic function.

 

The modeling results interpretation revealed the following:

Compounds 2..a (-98.635kcal/mol), 3..a (-97.234 kcal/mol), 2..e (-104.176kcal/mol), and 3..e (-109.26 kcal/mol) showed lower binding energies compared to other compounds due to lacking ionizable functional groups at physiological pH. Consequently, they cannot form ionic bonds with zinc in carbonic anhydrase, which plays a vital role in the enzyme's mechanism by enhancing water's nucleophilicity for CO₂ attack.In contrast, the remaining compounds demonstrated higher binding energies because their functional groups can ionize under biological conditions, enabling ionic interactions with zinc.

 

Compounds 1..a (-165.674 kcal/mol) and 1..e (-166.583 kcal/mol) exhibited the highest binding energies compared to other compounds, highlighting the importance of the heterocyclic ring in forming hydrogen bonds with critical amino acids involved in the enzyme's mechanism of action, as well as ionic interactions with zinc.

 

The para positioned COOH group, as seen in compounds 5..a(-156.232 Kcal/mol) and 5..e(-144.653 Kcal/mo), resulted in higher binding energies compared to its presence in the ortho position compounds 4..a(-140.418 Kcal/mol) and 4..e(-143.002 Kcal/mol).

 

Compounds 6..a/8..a (-150.727 kcal/mol, -147.694 kcal/mol, -161.491 kcal/mol) and 6..e/8..e (-143.941 kcal/mol, -150.018 kcal/mol, -146.691 kcal/mol) showed favorable binding energies due to form hydrogen bonds with essential amino acids (Thr199, Thr198, His117, His91, His93) and establish ionic bonds with zinc.

 

Figure 5.6: Predicted binding interactions of compound 8..a with the amino acids in the active site of carbonic anhydrase XII (CAXII).

 

Table 2. The Binding energies (Kcal/mol) of compounds designed.

Derivative

energy binding

Derivative

energy binding

[kcal/mol]

[Kcal/mol]

1..a

-165.674

1..e

-166.583

2..a

-98.6335

2..e

-104.176

3..a

-97.243

3..e

-109.29

4..a

-140.418

4..e

-143.002

5..a

-156.232

5..e

-144.653

6..a

-150.727

6..e

-143.941

7..a

-147.694

7..e

-150.018

8..a

-161.491

8..e

-146.691

VD9

-115

 

 


 

Table 3. Shows Lipinski's rule and Polar Surface Area for the designed compounds.

Ligand

mw

accepter

donor

lipinski’s rules violation

Pola Surface Area

Log P

1..a

444.48

7

2

Yes

148.02

1.83

2..a

284.33

3

1

Yes

67.44

2.23

3..a

336.77

4

1

Yes

67.44

3.11

4..a

328.34

5

2

Yes

104.74

1.71

5..a

328.34

5

2

Yes

104.74

1.60

6..a

363.41

6

2

Yes

135.98

1.10

7..a

363.41

6

2

Yes

135.98

1.26

8..a

363.41

6

2

Yes

135.98

1.13

1..e

460.48

8

3

Yes

168.25

1.82

2..e

300.33

4

2

Yes

87.67

2.07

3..e

352.77

5

2

Yes

87.67

2.92

4..e

344.34

6

3

Yes

124.97

1.63

5..e

344.34

6

3

Yes

124.97

1.39

6..e

379.41

7

3

Yes

156.21

0.93

7..e

397.41

7

3

Yes

156.21

1.07

8..e

397.41

7

3

Yes

156.21

0.95

 

Table 4. The interaction of the compounds designed with Carbonic Anhydrase Isoform xii.

Ligand

Residue

Hydrogyn Bond

Distense

Energy

1..a

 

Thr199

Thr198

Thr198

Ser133

NH.....SO2(Ligand)

NH.....SO2(Ligand)

OH.....SO2(Ligand)

OH.....SO2(Ligand)

3.10

2.76

2.75

3.22

-0.82

-1.73

-2.50

-1.47

2..a

Thr 199

Thr 199

OH.....NH(Ligand)

OH.....N(Ligand)

2.61

3.03

-2.01

-2.50

3..a

Gln89

Gln 89

NH.....SO2(Ligand)

NH.....N(Ligand)

2.87

2.70

-1.58

-2.00

4..a

Gln89

His117

Thr199

Thr199

Thr198

NH.....N(Ligand)

NH.....OH(Ligand)

NH.....CO(Ligand)

OH.....CO(Ligand)

OH.....SO(Ligand)

3.18

3.45

2.96

3.22

2 .84

-0.74

-0.68

-0.83

-1.88

-0.74

5..a

Thr 198

Gln 89

His 117

NH.....CO(Ligand)

NH.....SO2(Ligand)

NH.....OH(Ligand)

2.87

2.54

2.62

-2.50

-0.78

-1.52

6..a

Thr199

Thr199

His91

NH.....SO2(Ligand)

OH.....SO2(Ligand)

NH.....NH(Ligand)

2.62

3.02

2.85

-0.96

-2.50

-2.50

7..a

Thr199

Thr199

Thr198

Asn64

OH.....SO2(Ligand)

NH.....SO2(Ligand)

OH.....NH(Ligand)

NH.....SO2(Ligand)

2.58

3.04

2.76

3.14

-0.84

-2.50

-2.50

-2.31

8..a

Thr198

Thr198

Gln89

OH.....NH(Ligand)

NH.....SO2(Ligand)

NH.....SO2(Ligand)

2.73

2.65

2.63

-2.50

-2.50

-0.69

 1..e

Thr199

Thr199

Thr199

His117

Thr198

Thr198

Asn64

NH.....SO2(Ligand)

OH.....N(Ligand)

OH.....O(Ligand)

NH.....SO2(Ligand)

NH.....SO2(Ligand)

OH......SO2(Ligand)

NH.....OH(Ligand)

3.06

3.05

3.23

3.05

2.50

2.84

3.08

-2.50

-1.08

-1.73

-0.75

-1.19

-1.24

-1.58

2..e

Asn64

Gln 89

NH.....N(Ligand)

NH.....SO2(Ligand)

3.20

2.90

-0.78

-0.92

3..e

Thr 198

OH.....OH(Ligand)

2.84

-1.08

4..e

Thr 199

Thr 198

Thr 198

His 117

His66

Gln 89

OH.....NH(Ligand)

NH......CO(Ligand))

OH.....CO(Ligand)

NH.....OH(Ligand)

NH.....OH(Ligand)

NH.....SO2(Ligand)

3.30

2.64

2.80

2.88

3.33

3.08

-1.06

-2.50

-2.50

-1.99

-1.35

-1.89

5..e

 

Gln89

His117

Thr198

Thr199

Pro200

Trp4

NH.....CO(Ligand)

NH.....CO(Ligand)

NH.....CO(Ligand)

OH.....N(Ligand)

O.....OH(Ligand)

NH.....OH(Ligand)

2.44

2.96

2.79

3.17

3.15

3.05

-0.75

-1.87

-2.50

-2.16

-2.30

-1.01

6..e

 

His 91

Thr 199

Thr 199

Thr 199

N.....NH(Ligand)

NH.....SO(Ligand)

OH.....SO(Ligand)

NH.....SO(Ligand)

2.94

3.30

3.08

3.06

-2.50

-0.79

-1.25

-2.50

7..e

 

His 91

Thr199

Thr199

Thr198

Asn64

NH.....NH(Ligand)

NH.....SO2(Ligand)

OH.....SO2(Ligand)

OH.....SO2(Ligand)

NH.....OH(Ligand)

2.75

2.85

3.26

2.18

3.17

-2.04

-1.35

-1.68

-1.46

-1.41

8..e

Thr198

Thr198

Thr199

Gln89

Pro200

Trp4

NH.....SO2(Ligand)

OH....NH(Ligand)

OH.....N(Ligand)

NH.....SO2(Ligand)

NH.....OH(Ligand)

NH.....OH(Ligand)

2.58

2.83

3.06

2.91

3.08

3.05

-2.32

-2.50

-2.50

-2.18

-2.42

-1.27

Ligand

Thr 199

Thr 199

His 91

NH.....SO(Ligand)

NH.....SO(Ligand)

NH.....NH(Ligand)

2.78

3.25

2.94

-1.10

-1.76

-2.32


Table 5. Ionic links of compounds with zinc and their energy.

Ligand

Distanse

Energy

1..a

2.52236

-26.01

4..a

1.86281

-41.5

5..a

1.59303

-41.5

6..a

1.92315

-41.5

7..a

1.7671

-41.5

8..a

1.8894

-41.5

1..e

2.00587

-41.5

4..e

1.53708

-41.5

5..e

1.62641

-40.91

6..e

1.88858

-41.5

7..e

2.01427

-40.91

8..e

1.75901

-41.26

 

Analytic Data:

N-phenyl quinoline-8-sulfonamide (2..a):

White powder, Yield: 75%, Melting point: 167-171°C, TLC: mobile phase mixture of Petroleum Ether:Ethyl Acetate (2.5:7.5), Rf value: 0.75. Infrared spectrum (νmax, cm⁻¹): 3235 (N-H str), 1589.39 (N-H bend), 1315.09 (S=O asym str), 1161.85 (S=O sym str). ¹H NMR Spectrum (dmso-d6, ppm): 6.80 (t, 2h, Ar-h), 6.82 (t, 1h, Ar-h), 7.08 (q, 2h, Ar-h), 7.62 (t, 1h, Ar-h), 7.93 (t, 1h, Ar-h), 8.29 (d, 1h, Ar-h), 8.46 (d, 1h, Ar-h), 8.50 (d, 1h, Ar-h), 8.94 (d, 1h, Ar-h), 10.20 (s, 1h, Nh). ¹³C NMR Spectrum (dmso-d6, ppm): 119, 119, 121.5, 122.4, 124.3, 127.3, 128.9, 129.5, 129.5, 131.5, 136.4, 140.0, 141.9, 149.9. Mass spectrum (M/Z, ESI): showed molecular ion [m+H] peak at 285.17 corresponding to the molecular formula of 284.33 and [m+Na] peak at 307.

 

N-(3-chloro-4-fluoro phenyl)quinoline-8-sulfonamide (3..a):

White powder, Yield: 86%, Melting point: 147-151°C, TLC: mobile phase mixture of Petroleum Ether:Ethyl Acetate (2.5:7.5), Rf value: 0.62. Infrared spectrum (νmax, cm⁻¹): 3367.12 (N-H str), 1582.70 (N-H bend), 1351.36 (S=O asym str), 1172 (S=O sym str). ¹H NMR Spectrum (dmso-d6, ppm): 6.66 (d, 1h, Ar-h), 7.00 (s, 1h, Ar-h), 7.14 (d, 1h, Ar-h), 7.62 (t, 1h, Ar-h), 7.93 (t, 1h, Ar-h), 8.29 (d, 1h, Ar-h), 8.46 (d, 1h, Ar-h), 8.50 (d, 1h, Ar-h), 8.94 (d, 1h, Ar-h), 10.20 (s, 1h, NH). ¹³C NMR Spectrum (dmso-d6, ppm): 114.2, 116.0, 118.3, 121.5, 121.5, 124.3, 127.3, 128.9, 131.5, 134.7, 136.4, 140.0, 141.9, 148.8, 149.9. Mass spectrum (M/Z, ESI): showed molecular ion [m+H]+ peak at 337 corresponding to the formula of 336.77 and [m+Na]+ peak at 359.

 

2-(quinoline-8-sulfonamido)benzoic acid (4..a):

White powder, Yield: 83%, Melting point: 272-275°C, TLC: mobile phase mixture of Petroleum Ether:Ethyl Acetate Ethyl (3:7), Rf value of compound 4..a is: 0.79. Infrared spectrum (νmax, cm⁻¹): 3337.20 (N-H str), 1641.05 (C=O str), 1571.21 (N-H bend), 1315.70 (S=O asym str), 1156.17 (S=O sym str). H NMR Spectrum (dmso-d6, ppm): 7.07 (t, 2h, Ar-h), 7.62 (t, 1h, Ar-h), 7.90 (d, 1h, Ar-h), 7.93 (t, 1h, Ar-h), 8.29 (d, 1h, Ar-h), 8.46 (d, 1h, Ar-h), 8.50 (d, 1h, Ar-h), 8.94 (d, 1h, Ar-h), 11.07 (s, 1h, Nh), 13.11 (s, 1H, OH). CNMR Spectrum (dmso-d6, ppm): 110.2, 116.2, 118.6, 121.5, 124.3, 127.3, 128.9, 131.1, 131.5, 134.7, 136.4, 140.0, 141.9, 148.3, 149.9, 169.3. Mass spectrum (M/Z, ESI): molecular ion [m+H]⁺ peak at 329 corresponding to the molecular formula 328 and [m+Na]+ peak to 351

 

N-(4-sulfamoyl phenyl)quinoline-8-sulfonamide (8..a):

White powder, Yield: 70%, Melting point: 293-295°C, TLC: mobile phase mixture of Petroleum Ether:Ethyl Acetate (6:4), Rf value of compound 8..a is 0.6. Infrared spectrum (νmax, cm⁻¹): 3287(N-H str),1595(N-H bend),1328(S=O asym str),1160(S=O sym str),HNMR spectrum (dmso-d6, ppm): 6.89 (s, 2h, Ar-h), 7.05 (t, 2h, Ar-h), 7.55 (t, 2h, Ar-h), 7.62 (t, 1h, Ar-h), 7.93 (t, 1h, Ar-h), 8.29 (d, 1h, Ar-h), 8.46 (d, 1h, Ar-h), 8.50 (d, 1h, Ar-h), 8.94 (d, 1h, Ar-h), 10.20 (s, 1h, Nh). CNMR spectrum (dmso-d6, ppm): 116.6,116.6,121.5,124.3,127.3,128.9,130.0,130.0,130.9,131.5,136.4,140.0,140.0,140.9,141.9,149.9.l. Mass spectrum (M/Z, ESI): showed molecular ion [m+H]+ peak at 364.16 corresponding to the molecular formula 363 and [m+Na]+ peak at 386.7.

 

CONCLUSION:

In our study, the development, synthesis, and characterization of a novel series of quinoline-sulfonamides derivatives (1-8..a, 1-8..e) were carried out, followed by evaluation of their carbonic anhydrase (CA) inhibitory activity against The Human Carbonic Anhydrase XII (H-CA XII) isoform. Most synthesized quinoline-sulfonamides demonstrated direct inhibition of the tumor-related hCA XII isoform. Among tested compounds, 1..a, 2..a, 3..a, and 8..a exhibited the most significant inhibitory effects on hCA XII.

 

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Received on 28.04.2025      Revised on 11.09.2025

Accepted on 27.11.2025      Published on 20.05.2026

Available online from May 25, 2026

Research J. Pharmacy and Technology. 2026;19(5):2121-2127.

DOI: 10.52711/0974-360X.2026.00305

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