Design, Synthesis and biological evaluation of novel triazole, urea and thiourea derivatives of Quinoline against Mycobacterium tuberculosis Ram Shankar Upadhayaya,a Girish M. Kulkarni,a Nageswara Rao Vasireddy,a Jaya Kishore Vandavasi,a Shailesh S. Dixit,a Vivek Sharma,a Jyoti Chattopadhyaya*,b aInstitute of Molecular Medicine, Pune 411 057, India b Program of Bioorganic Chemistry, Institute of Cell and Molecular Biology, Biomedical Centre, Uppsala University, Sweden S1 Table T1: Sr. No. Contents Page No. 1. 1 H-NMR spectra of compound 2 S8 2. D2O-NMR spectra of compound 2 S9 3. 13 C-NMR spectra of compound 2 S10 4. DEPT-NMR spectra of compound 2 S11 5. 1 S12 6. 13 C-NMR spectra of compound 3 S13 7. DEPT-NMR spectra of compound 3 S14 8. 1 S15 9. 13 C-NMR spectra of compound 4 S16 10. DEPT-NMR spectra of compound 4 S17 11. 1 H-NMR spectra of compound 5 S18 12. D2O-NMR spectra of compound 5 S19 13. 13 C-NMR spectra of compound 5 S20 14. DEPT-NMR spectra of compound 5 S21 15. 1 S22 17. 13 C-NMR spectra of compound 6 S23 18. DEPT-NMR spectra of compound 6 S24 19. 1 S25 20. 13 C-NMR spectra of compound 7 S26 21. DEPT-NMR spectra of compound 7 S27 22. 1 H-NMR spectra of compound 8 S28 23. D2O-NMR spectra of compound 8 S29 24. 13 S30 H-NMR spectra of compound 3 H-NMR spectra of compound 4 H-NMR spectra of compound 6 H-NMR spectra of compound 7 C-NMR spectra of compound 8 S2 25. DEPT-NMR spectra of compound 8 S31 26. 1 S32 27. 13 C-NMR spectra of compound 9 S33 28. DEPT-NMR spectra of compound 9 S34 29. 1 S35 30. 13 C-NMR spectra of compound 10 S36 31. DEPT-NMR spectra of compound 10 S37 32. 1 S38 33. 13 C-NMR spectra of compound 11 S39 34. DEPT-NMR spectra of compound 11 S40 35. 1 S41 36. 13 C-NMR spectra of compound 12 S42 37. DEPT-NMR spectra of compound 12 S43 38. 1 S44 39. 13 C-NMR spectra of compound 13 S45 40. DEPT-NMR spectra of compound 13 S46 41. 1 H-NMR spectra of compound 14 S47 42. D2O-NMR spectra of compound 14 S48 43. 13 C-NMR spectra of compound 14 S49 44. DEPT-NMR spectra of compound 14 S50 45. 1 H-NMR spectra of compound 15 S51 46. D2O-NMR spectra of compound 15 S52 47. 13 C-NMR spectra of compound 15 S53 48. DEPT-NMR spectra of compound 15 S54 49. 1 H-NMR spectra of compound 16 S55 50. D2O-NMR spectra of compound 16 S56 51. 13 S57 H-NMR spectra of compound 9 H-NMR spectra of compound 10 H-NMR spectra of compound 11 H-NMR spectra of compound 12 H-NMR spectra of compound 13 C-NMR spectra of compound 16 S3 52. DEPT-NMR spectra of compound 16 S58 53. 1 H-NMR spectra of compound 17 S59 54. D2O-NMR spectra of compound 17 S60 55. 13 C-NMR spectra of compound 17 S61 56. DEPT-NMR spectra of compound 17 S62 57. 1 H-NMR spectra of compound 18 S63 58. D2O-NMR spectra of compound 18 S64 59. 13 C-NMR spectra of compound 18 S65 60. DEPT-NMR spectra of compound 18 S66 61. 1 H-NMR spectra of compound 19 S67 62. D2O-NMR spectra of compound 19 S68 63. 13 C-NMR spectra of compound 19 S69 64. DEPT-NMR spectra of compound 19 S70 65. 1 H-NMR spectra of compound 20 S71 66 D2O-NMR spectra of compound 20 S72 67 13 C-NMR spectra of compound 20 S73 68 DEPT-NMR spectra of compound 20 S74 69 1 H-NMR spectra of compound 21 S75 70 D2O-NMR spectra of compound 21 S76 71 13 C-NMR spectra of compound 21 S77 72. DEPT-NMR spectra of compound 21 S78 73. 1 H-NMR spectra of compound 22 S79 74. D2O-NMR spectra of compound 22 S80 75. 13 C-NMR spectra of compound 22 S81 76. DEPT-NMR spectra of compound 22 S82 77. 1 H-NMR spectra of compound 23 S83 78. D2O-NMR spectra of compound 23 S84 S4 79. 13 C-NMR spectra of compound 23 S85 80. DEPT-NMR spectra of compound 23 S86 81. 1 H-NMR spectra of compound 24 S87 82. D2O-NMR spectra of compound 24 S88 83. 13 C-NMR spectra of compound 24 S89 84. DEPT-NMR spectra of compound 24 S90 85. 1 H-NMR spectra of compound 25 S91 86. D2O-NMR spectra of compound 25 S92 87. 13 C-NMR spectra of compound 25 S93 88. DEPT-NMR spectra of compound 25 S94 89. 1 H-NMR spectra of compound 26 S95 90. D2O-NMR spectra of compound 26 S96 91. 13 C-NMR spectra of compound 26 S97 92. DEPT-NMR spectra of compound 26 S98 93. 1 H-NMR spectra of compound 27 S99 94. D2O-NMR spectra of compound 27 S100 95. 13 C-NMR spectra of compound 27 S101 96. DEPT-NMR spectra of compound 27 S102 97. 1 H-NMR spectra of compound 28 S103 98. D2O-NMR spectra of compound 28 S104 99. 13 C-NMR spectra of compound 28 S105 100. DEPT-NMR spectra of compound 28 S106 101. 1 H-NMR spectra of compound 29 S107 102. D2O-NMR spectra of compound 29 S108 103. 13 C-NMR spectra of compound 29 S109 104. DEPT-NMR spectra of compound 29 S110 105. 1 S111 H-NMR spectra of compound 30 S5 106. 13 C-NMR spectra of compound 30 S112 107. DEPT-NMR spectra of compound 30 S113 108. 1 H-NMR spectra of compound 31 S114 109. D2O-NMR spectra of compound 31 S115 110. 13 C-NMR spectra of compound 31 S116 111. DEPT-NMR spectra of compound 31 S117 112. 1 H-NMR spectra of compound 32 S118 113. D2O-NMR spectra of compound 32 S119 114. 13 C-NMR spectra of compound 32 S120 115. DEPT-NMR spectra of compound 32 S121 116. 1 H-NMR spectra of compound 33 S122 117. D2O-NMR spectra of compound 33 S123 118. 13 C-NMR spectra of compound 33 S124 119. DEPT-NMR spectra of compound 33 S125 120. 1 H-NMR spectra of compound 34 S126 121. D2O-NMR spectra of compound 34 S127 122. 13 C-NMR spectra of compound 34 S128 123. DEPT-NMR spectra of compound 34 S129 124. 1 H-NMR spectra of compound 35 S130 125. D2O-NMR spectra of compound 35 S131 126. 13 C-NMR spectra of compound 35 S132 127. DEPT-NMR spectra of compound 35 S133 128. 1 H-NMR spectra of compound 36 S134 129. D2O-NMR spectra of compound 36 S135 130. 13 C-NMR spectra of compound 36 S136 131. DEPT-NMR spectra of compound 36 S137 132. 1 S138 H-NMR spectra of compound 37 S6 133. D2O-NMR spectra of compound 37 S139 134. 13 C-NMR spectra of compound 37 S140 135. DEPT-NMR spectra of compound 37 S141 136. 1 H-NMR spectra of compound 38 S142 137. D2O-NMR spectra of compound 38 S143 138. 13 C-NMR spectra of compound 38 S144 139. DEPT-NMR spectra of compound 38 S145 140. Biological methods S146 141. Table S1: % Inhibition and Standard Deviation data. S147 142. Theoretical methods S148 143. Cytotoxicity assay S149 144. References S150 S7 O2N 2 N H O S8 O2N 2 N H O S9 O2N 2 N H O S10 O2N 2 N H O S11 O2N N Cl 3 S12 O2N N Cl 3 S13 O2N N Cl 3 S14 O2N N O O 4 F S15 O2N N O O 4 F S16 O2N N O O 4 F S17 H2N N O O 5 F S18 H2N N O O 5 F S19 H2N N O O 5 F S20 H2N N O O 5 F S21 N3 N O O 6 F S22 N3 N O O 6 F S23 N3 N O O 6 F S24 N N N N O O 7 F S25 N N N N O O 7 F S26 N N N N O O 7 F S27 N N N N O OH 8 F S28 N N N N O OH 8 F S29 N N N N O OH 8 F S30 N N N N O OH 8 F S31 N N N N O Cl 9 F S32 N N N N O Cl 9 F S33 N N N N O Cl 9 F S34 N N N N N O N 10 F S35 N N N N N O N 10 F S36 N N N N N O N 10 F S37 N N N N O N 11 F S38 N N N N O N 11 F S39 N N N N O N 11 F S40 F N N N N N O N 12 F S41 F N N N N N O N 12 F S42 F N N N N N O N 12 F S43 N N N N N N O N 13 F S44 N N N N N N O N 13 F S45 N N N N N N O N 13 F S46 H N H N O NO 2 N O O 14 F S47 H N H N O NO 2 N O O 14 F S48 H N H N O NO 2 N O O 14 F S49 H N H N O NO 2 N O O 14 F S50 H N O H N O N O O 15 F S51 H N O H N O N O O 15 F S52 H N O H N O N O O 15 F S53 H N O H N O N O O 15 F S54 H N H N O O N O O 16 F S55 H N H N O O N O O 16 F S56 H N H N O O N O O 16 F S57 H N H N O O N O O 16 F S58 H N O H N O N O O 17 F S59 H N O H N O N O O 17 F S60 H N O H N O N O O 17 F S61 H N O H N O N O O 17 F S62 H N H N S N O O 18 Cl F S63 H N H N S N O O 18 Cl F S64 H N H N S N O 18 Cl F S65 O H N H N S N O O 18 Cl F S66 H N O H N S N O O 19 F S67 H N O H N S N O O 19 F S68 H N O H N S N O O 19 F S69 H N O H N S N O O 19 F S70 H N H N S O N O O 20 F S71 H N H N S O N O O 20 F S72 H N H N S O N O O 20 F S73 H N H N S O N O O 20 F S74 H N O H N S N O O 21 F S75 H N O H N S N O O 21 F S76 H N O H N S N O O 21 F S77 H N O H N S N O O 21 F S78 H N H N O NO 2 N O OH 22 F S79 H N H N O NO 2 N O OH 22 F S80 H N H N O NO 2 N O OH 22 F S81 H N H N O NO 2 N O OH 22 F S82 H N O H N O N O OH 23 F S83 H N O H N O N O OH 23 F S84 H N O H N O N O OH 23 F S85 H N O H N O N O OH 23 F S86 H N H N O O N O OH 24 F S87 H N H N O O N O OH 24 F S88 H N H N O O N O OH 24 F S89 H N H N O O N O OH 24 F S90 H N O H N O N O OH 25 F S91 H N O H N O N O OH 25 F S92 H N O H N O N O OH 25 F S93 H N O H N O N O OH 25 F S94 H N H N S N O OH 26 Cl F S95 H N H N S N O OH 26 Cl F S96 H N H N S N O OH 26 Cl F S97 H N H N S N O OH 26 Cl F S98 H N O H N S N O OH 27 F S99 H N O H N S N O OH 27 F S100 H N O H N S N O OH 27 F S101 H N O H N S N O OH 27 F S102 H N H N S O N O OH 28 F S103 H N H N S O N O OH 28 F S104 H N H N S O N O OH 28 F S105 H N H N S O N O OH 28 F S106 H N O H N S N O OH 29 F S107 H N O H N S N O OH 29 F S108 H N O H N S N O OH 29 F S109 H N O H N S N O OH 29 F S110 O2N N O O Br 30 F S111 O2N N O O Br 30 F S112 O2N N O O Br 30 F S113 O2N N O OH O N 31 F S114 O2N N O OH O N 31 F S115 O2N N O OH O N 31 F S116 O2N N O OH O N 31 F S117 O2N N O OH N 32 F S118 O2N N O OH N 32 F S119 O2N N O OH N 32 F S120 O2N N O OH N 32 F S121 O2N N O N OH N 33 F S122 O2N N O N OH N 33 F S123 O2N N O N OH N 33 F S124 O2N N O N OH N 33 F S125 O2N N O 34 OH N N F S126 O2N N O 34 OH N N F S127 O2N N O 34 OH N N F S128 O2N N O 34 OH N N F S129 O O2N N O OH N N 35 F S130 O O2N N O OH N N 35 F S131 O O2N N O OH N N 35 F S132 O O2N N O OH N N 35 F S133 O O 2N N O O H N N 36 F S134 O O2N N O 36 OH N N F S135 O O2N N O 36 OH N N F S136 O O 2N N O OH N N 36 F S137 F F F O2N N O 37 OH N N F S138 F F F O2N N O 37 OH N N F S139 F F F O2N N O 37 OH N N F S140 F F F O2N N O 37 OH N N F S141 Cl O2N N O 38 OH N N F S142 Cl O2N N O 38 OH N N F S143 Cl O2N N O 38 OH N N F S144 Cl O2N N O 38 OH N N F S145 Antimycobacterial activity: All the compounds were screened for antimycobacterial activity against mycobacterium tuberculosis by BACTEC 460 radiometric methods. The broth based BACTEC 460 TB system was used for the growth of Mycobacteria. In this growth system, Mycobacterium tuberculosis H37RV was grown in the C14 labelled substrate in 7H12 medium, substrate is utilized by growing mycobacteria and 14CO2 is produced, which is detected in the form of ‘Growth Index’ (GI), which reflects the rate and amount of growth in the medium vial. If an antituberculosis drug will be added to the medium vial, it will suppress the growth of the bacteria which is detected by the decrease of the GI values as compared to the control vial. The positive controls taken in the experiment were the standard therapeutic drugs presently used for the treatment of the tuberculosis, Isoniazid and Rifampin. The rate of increase in GI values or the change in GI over the previous day GI is called delta (∆) GI, is compared with that of control values. If ∆GI of the drug-containing vial is equal to or greater than (≥) than that in control vial the organisms are considered resistant to the drug. On the contrary if ∆GI of the drug-containing vial is less (<) than the control vial the organisms are considered susceptible. On the basis of the values calculated for ∆G, out of all screened compounds, four compounds i.e. 10, 22 and 24 were found to act as active antimycobacterial agents. Below given table depicts ∆G of the compounds tested. S146 Table S1: % Inhibition and Standard Deviation data. Days 1 2 3 4 5 6 7 8 9 10 11 GI 3 3 4 23 15 13 43 29 21 58 33 31 63 46 37 69 52 27 74 53 44 66 55 44 61 55 43 53 49 36 51 41 32 ∆ GI -2 -8 -4 9 16 31 8 18 43 6 21 41 9 21 40 9 18 32 8 16 36 8 17 33 8 15 29 9 15 30 - - 1 0 1 3 3 4 12 10 14 15 16 22 17 20 26 18 23 28 22 28 37 25 35 42 30 39 48 33 48 53 34 51 57 41 64 68 7 13 11 95.9 93.6 93.2 2.06 17 18 16 30 18 23 14 14 18 13 13 17 11 12 16 14 16 18 14 14 20 13 14 19 - - - -1 0 -1 20 26 18 40 46 34 61 70 52 93 101 80 152 152 134 220 232 219 345 344 346 466 446 450 605 618 547 617 719 720 813 818 796 196 99 76 99.7 99.6 98.0 0.53 - N N N N N O N 10 SD GI F H N H N O N O2N O OH SD % Inhibition 94.9 95.9 96.8 1.34 99.1 98.5 97.0 1.30 22 F GI H N H N O N O O OH SD 24 F Isoniazid GI Untreated Control SD GI S147 Theoretical methods: Homology model consisting of one subunit A and two subunit C of the ATP-synthase of M. tuberculosis was developed from corresponding subunits of Escherichia coli ATP synthase.1 MODELLER2 was used for generating homology model and protocol used is same as mentioned before.3 All acidic and basic residues were kept in their default protonation states i.e. arginine and lysine, protonated and glutamic and aspartic acid, deprotonated, except Glu61, which was protonated. 1,3 The selected ligand molecules were sketched (irrespective of stereochemistry) and energy minimized for 2500 steps in Ghemical.4 Subsequently a random conformational search was performed on each molecule with 2000 steps of conformational search and 300 steps of energy minimization. Final lowest energy structure of each ligand molecule was converted to *.pdbqt file using AutoDock Tools5 (http://mgltools.scripps.edu/) and used for automated docking in AutoDock 4.6 Same as discussed before,3 using AutoDock Tools and AutoDock 4, the ligand was docked into a cavity located near Arg186 (subunit A) and Glu61 (subunit C) of M. tuberculosis ATP-synthase. The grid dimensions used were 64Åx42Åx44Å. AutoDock parameters like population size, energy evaluations and number of Lamarckian Genetic Algorithm runs were 250, 25000000 and 100, respectively. Initial coordinates (tran0 option in AutoDock) were set to the defined grid center. The docked protein-ligand complex with lowest binding energy was selected for further analysis. Further we analyzed the intermolecular energies as calculated by AutoDock docking calculation as they give more precise description of binding. The docked complexes of certain compounds were subjected to forcefield-based refinement. The ligand coordinates were extracted from *.pdbqt files of complexes generated by AutoDock. Hydrogens were added with Ghemical and converted to *.mol2 format using Openbabel. The antechamber7 module of AMBER8 was used for writing the necessary files (*.prepin and *.frcmod) for ligand molecules. The AM1-BCC9 charge model was used for ligand molecules, which has been suggested to perform very well, relative to other well known methods for partial charge calculations.10 The General Amber Force Field (GAFF)11 and ff038 were used for ligand and protein, respectively. The complexes were minimized for 10000 steps using sander tool available in AMBER. The interaction energy (van der Waals and Electrostatic) between ligand and protein were computed using NAMDEnergy tool available in NAMD12 for the minimized complex. During analysis, hydrogen bond criteria used was Donor-H......Acceptor distance < 3Å and Donor...H...Acceptor angle > 150º. Visualization of molecules was done with the help of Visual Molecular Dynamics (VMD)13 and all simulations were run on 2.2GHz AMD Dual Core machine, running with Red Hat Enterprise Linux 5. S148 Cytotoxicity assay: Cellular viability in the presence and absence of test compounds was determined by MTT (3- (4,5-dimethylthiazol-2yl)-2,5-dimethyl tetrazolium bromide; Sigma-Aldrich) microcultured tetrazolium assay.14,15 The cells (monocytic cell line, THP-1) were plated in flatbottomed 96-well plates (10,000 cells/100µL) and cultured in controlled atmosphere (5% CO2 at 37 °C). Cells were cultured in the presence of medium along with DMSO (live controls). Different concentrations of compounds (1µg/100µl to 10µg/100µl) were added to the cells. After 24h and 72h, stock MTT solution (5 mg/mL) was added to the culture. Cells were again kept in CO2 incubator for 4h. After 4h, 100µl isopropanol was added and mixed 5-6 times. The absorbance was read at 540 nm in a plate reader (Bio-Rad— 450). The results were represented as percentage cell viability (Table 3). All the experiments were carried out in triplicates and the readings were the average mean of three readings. S149 References 1. Rastogi, V.; Girvin, M. Nature 1999, 402, 263. 2. Sali, A.; Blundell, T. L. J. Mol. Biol. 1993, 234, 779. 3. Upadhayaya, R. S.; Jaya Kishore, V.; Nageswar Rao, V.; Sharma, V.; Dixit, S. S.; Chattopadhyaya, J. Bioorg. Med. Chem. 2009, 17, 2830. 4. Hassinen, T.; Peräkylä, M. J. Comput. Chem. 2001, 22, 1229. http://www.uku.fi/~thassine/projects/ghemical/ 5. Sanner, M. F. J. Mol. Graph. Mod. 1999, 17, 57. 6. Morris, G. M.; Goodsell, D. S.; Halliday, R.S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. J. Comput. Chem. 1998, 19, 1639. 7. Wang, J.; Wang, W.; Kollman, P. A.; Case, D. A. J. Mol. Graph. Mod. 2006, 25, 247. 8. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. J. Comput. 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