- Email: [email protected]
Discovery of new potent inhibitors for carbonic anhydrase IX by structure-based virtual screening
Bioorganic & Medicinal Chemistry Letters 23 (2013) 3496–3499
Contents lists available at SciVerse ScienceDirect
Bioorganic & Medicinal Chemistry Letters journal homepage: www.elsevier.com/locate/bmcl
Discovery of new potent inhibitors for carbonic anhydrase IX by structure-based virtual screening Liyan Wang , Chunmei Yang , Weiqiang Lu, Li Liu, Rui Gao, Sha Liao, Zhenjiang Zhao, Lili Zhu, Yufang Xu, Honglin Li ⇑, Jin Huang ⇑, Weiping Zhu ⇑ State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
a r t i c l e
i n f o
Article history: Received 25 March 2013 Revised 17 April 2013 Accepted 19 April 2013 Available online 29 April 2013 Keywords: Virtual screening Molecular docking Carbonic anhydrase inhibitors Sulfonamides
a b s t r a c t Through structure-based virtual screening, some dozen of benzene sulfonamides with novel scaffolds are identified as potent inhibitors against carbonic anhydrase (CA) IX with IC50 values ranging from 2.86 to 588.34 nM. Among them, compounds 1 and 9 show high selectivity against tumor-target CA IX over CA II (the selectivity ratios are 21.3 and 136.6, respectively). The possible binding poses of hit compounds are also explored and the selectivity is elucidated by molecular docking simulations. The hit compounds discovered in this work would provide novel scaffolds for further hit-to-lead optimization. Ó 2013 Elsevier Ltd. All rights reserved.
Carbonic anhydrases (CAs, EC 4.2.1.1) are an important family of zinc metalloenzymes widespread in a diversity of organisms.1,2 These CAs catalyze a fundamental physiological reaction, the interconversion between the carbon dioxide and bicarbonate.3,4 They play an important role in many physiological processes, such as carbon dioxide transport between metabolizing tissues and lung, pH homeostasis,5 and many other physiologic or pathologic processes.6–10 In mammals, there are 16 different CA isozymes or CArelated proteins (CARP): several cytosolic forms (such as CA I–III and CA VII), five membrane-bound isozymes (CA IV, CA IX, CA XII, CA XIV and CA XV), one mitochondrial form (CA V), as well as a secreted CA isozyme (CA VI).3 Recently, two tumor-associated membrane carbonic anhydrase isozymes (CA IX and CA XII) attract much more attention.11 The role of CA IX in tumor physiology has been reported by many papers, such as the control of tumor pH and the influence in the cell microenvironment that promote cell proliferation, invasion, and metastasis.12–16 From this point, great efforts have been made to design anticancer drugs against CA IX. Although there are many effective inhibitors against CAs, most of classical sulfonamides/sulfamates CA inhibitors and their derivatives, such as acetazolamide (AZA), ethoxzolamide (EZA), do not have a good selectivity of CA IX over the sulfonamide-avid isozyme CA II.17–19 Therefore, one of the main
⇑ Corresponding authors. Tel./fax: +86 21 64250213. E-mail addresses: [email protected] (H. Li), [email protected] (J. Huang), [email protected] (W. Zhu). These authors contributed equally to this work. 0960-894X/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.bmcl.2013.04.048
challenges in the development of CA IX inhibitors is to identify high selectivity inhibitors against CA IX over the isozyme CA II.3 In this study, thirteen hits with novel scaffolds from the commercial SPECS database are identified with potent inhibitory activities against CA IX with IC50 values ranging from 2.86 to 588.34 nM by structure-based virtual screening. Among them, two inhibitors show high selectivity against tumor-target CA IX over CA II (the selectivity ratios are 21.3 and 136.6, respectively). In details, the crystal structure of CA IX is retrieved from the Protein Data Bank (RCSB Protein Data Bank (PDB) database code: 3IAI), and then virtual screening is performed using Glide5.5 against the SPECS database (about 280,000 compounds). The standard-precision (SP) is performed for preliminary calculations, and extra-precision (XP) is used for the final calculations to generate the minimized pose. Then visual inspections are taken to select candidates for further biological assays. Thus the initial 280 thousands compounds are reduced to about 10,000 after SP mode. The top 500 compounds are selected with the XP mode from the 10,000, and then 49 compounds are picked out to be tested by the enzyme assays against CA IX (Table S1). Finally, thirteen compounds are identified to exhibit inhibitory potencies against CAs ( Fig. 1). The structures and IC50 values of the hits and the reported positive controls acetazolamide (AZA), ethoxzolamide (EZA) are provided in Figure 1 and Table 1. The protocol of the preparation of the protein and ligands, and all structures of compounds for biological assays are described in the Supplementary data. The inhibition assays against CAs in vitro are thoroughly described in our previous report.20
L. Wang et al. / Bioorg. Med. Chem. Lett. 23 (2013) 3496–3499
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Figure 1. Structures of AZA, EZA and compounds 1–13.
Table 1 Inhibitory activities of the compounds 1–14 against CA I, CA II and CA IX Compounds
IC50 (nM) CA I
1 2 3 4 5 6 7 8 9 10 11 12 13 EZA AZA a b
a
197.64 213.69 2.13 16.73 156.78 172.84 3.09 126.47 231.41 258.84 36.13 120.13 1194 15.71 161.11
a
Selectivity ratios b
CA II
CA IX
60.93 41.97 9.33 10.58 27.16 153.18 33.13 33.92 3873 670.72 48.09 12.54 808.81 0.3 20.02
2.86 3.11 4.53 10.42 14.95 18.81 19.09 21.64 28.35 68.46 198.98 341.71 588.34 0.99 2.58
CA I/CA IX
CA II/CA IX
68.9 68.71 0.47 1.61 10.48 9.19 0.16 5.84 8.16 3.78 0.18 0.35 2.03 15.87 62.45
21.3 13.49 2.06 1.02 1.82 8.14 1.74 1.57 136.6 9.8 0.24 0.037 1.37 0.3 7.76
Full length, from human erythrocytes. Catalytic domain with GST-tag, recombinant enzyme.
From the experimental results, only benzene sulfonamide compounds have potent inhibitory activity against CAs (Table S1). In particular, compounds 1 and 9 not only show excellent inhibitory activity against CA IX (IC50 = 2.86 and 28.35 nM, respectively), but also have high selectivity ratio against CA IX over CA II. Especially the compound 9 shows a superior selective property against CA IX over CA II (the selective ratio is 136). It is suggested that steric hindered groups of the compounds, interacting with the hydrophobic surface of the active site, are possibly the key factors in the selectivity. In order to explore the structure-activity relationships (SAR) of the benzene sulfonamide compounds 1–13 and explain the possible mechanism of selectivity, the docking studies are undertaken with the available human CA IX crystal structure. For example, the most potent compound 1 (Fig. 2) binds in a compact manner to the CA IX active site. The sulfamate nitrogen is deprotonated and has replaced the hydroxyl ion coordinated to the zinc ion, while the metal ion remains its stable tetrahedral geometry with one sulfamate nitrogen of the compound and three imidazolic nitrogens of His 94, His 96 and His 119. The proton of the coordi-
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L. Wang et al. / Bioorg. Med. Chem. Lett. 23 (2013) 3496–3499
Figure 2. The predicted binding pose of compound 1 in the binding site of CA IX (PDB code: 3IAI). Key residues with potential interactions are labeled out and shown in green, while compound 1 is exhibited with yellow sticks. The activity zinc ion is illustrated with gray sphere, and the hydrogen bonds are highlighted by the red dot lines.
nated sulfamate nitrogen atom also forms a hydrogen bond with the hydroxyl group of Thr 199, which in turn forms a hydrogen bond with the carboxylate of Glu106. One of the oxygen atoms of the sulfamate moiety makes a hydrogen bond with the backbone amide of Thr 199. All these hydrogen bonds form an extended network and make the ligand bind to the active site well. This situation makes the substrate (CO2) avoid being attacked in a favorable location, and the hydrogen bond network also prevents the proton transfer reaction taking place from the active site to the environment. Consequently, the sulfamate group is essential for these compounds reported here, which will lose inhibitory potencies without this group. As for the selectivity, the factor maybe is the smaller active site of CA I compared to the other isozymes CA II and CA IX, owing to the presence of two extra His residues (His 200 and His 67) ( Fig. 3). So the steric hindered groups would prevent most ligands binding to the CA I well, especially the benzene moiety of compound 1 (the selective ratio against CA IX over CA I is 68.9). The similar situation also happens to CA II and CA IX. Superposition of the crystal structures of CA II and CA IX clearly reveals that the amino acids at the position 131 in the hydrophobic areas of the active site are different (Fig. 4). The phenylalanine with big side chain locates in CA II, while the valine with small side chain locates in CA IX. The big hydrophobic groups of compounds 1 and 9 (benzene of the compound 1 and the benzo[cd]indol-2(1H)-one of the compound 9, respectively) can interact with Val 131 by hydrophobic contacts. On the contrary, the steric hindered groups of compounds 1 and 9 may form strong clash interactions with Phe 131, so that they can not bind to CA II well. This structure information of compounds would be helpful for further optimizing the compounds in the next step. In summary, a series of benzene sulfonamide compounds with novel scaffolds are identified as CAs inhibitors through structurebased virtual screening. Especially compounds 1, 2 and 3 have equivalent inhibitory activities with the reported positive controls
Figure 3. Superposition of the crystal structures of CA I (slate, PDB code: 2NMX) and CA IX (green, PDB code: 3IAI). The binding poses of the compound 1 (yellow stick) is predicted by the molecular docking.
Figure 4. Superposition of the crystal structures of CA II (orange, PDB code: 3R16) and CA IX (green, PDB code: 3IAI). The binding poses of the compound 1 (yellow stick) and the compound 9 (magenta stick) are predicted by the molecular docking.
AZA and EZA (their IC50 values against CA IX are equal to 2.86, 3.11 and 4.53 nM, respectively). Meanwhile, docking simulation analysis is performed to elucidate the inhibitory activities of them and superior selectivity against CA IX over CA II, which shows that the sulfamate group is important for the inhibitors of CAs, and several special steric hindered hydrophobic groups might cause the selectivity due to their clash with the residues of CAs. These inhibitors may serve as new lead compounds for further development to treat cancer.
L. Wang et al. / Bioorg. Med. Chem. Lett. 23 (2013) 3496–3499
Acknowledgments This work is supported by the National Natural Science Foundation of China (Grants 21173076, 81102420 and 81222046), the Innovation Program of Shanghai Municipal Education Commission (Grant 10ZZ41), the Shanghai Committee of Science and Technology (Grant 11DZ2260600), the Special Fund for Major State Basic Research Project (Grant 2009CB918501), the 863 Hi-Tech Program of China (Grant 2012AA020308), and the Fundamental Research Funds for the Central Universities. We thank Professor Seppo Parkkila (Institute of Medical Technology and School of Medicine, University of Tampere, Finland) for providing the plasmid of carbonic anhydrase IX. We also thank Ph.D Houqi Liu at the Suzhou Institute for Advanced Study, University of Science and Technology of China (USTC), for providing the Applied Photophysics SX 20 stopped-flow instrument. Supplementary data Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.bmcl.2013.04 .048. References and notes 1. 2. 3. 4.
Supuran, Supuran, Supuran, Supuran,
C. C. C. C.
T. Nat. Rev. Drug Disc. 2008, 7, 168. T. Curr. Pharm. Des. 2010, 16, 3233. T.; Scozzafava, A. Bioorg. Med. Chem. 2007, 15, 4336. T.; Scozzafava, A.; Casini, A. Med. Res. Rev. 2003, 23, 146.
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5. Svastov, E.; HulIkov, A.; Rafajov, M.; Zat’ovicov, M.; Gibadulinov, A.; Casini, A.; Cecchi, A.; Scozzafava, A.; Supuran, C. T.; Pastorek, J.; Pastorekov, S. FEBS Lett. 2004, 577, 439. 6. Avvaru, B. S.; Wagner, J. M.; Maresca, A.; Scozzafava, A.; Robbins, A. H.; Supuran, C. T.; McKenna, R. Bioorg. Med. Chem. Lett. 2010, 20, 4376. 7. Bertucci, A.; Innocenti, A.; Zoccola, D.; Scozzafava, A.; Tambutt, S.; Supuran, C. T. Bioorg. Med. Chem. 2009, 17, 5054. 8. Borras, J.; Scozzafava, A.; Menabuoni, L.; Mincione, F.; Briganti, F.; Mincione, G.; Supuran, C. T. Bioorg. Med. Chem. 1999, 7, 2397. 9. Brzozowski, Z.; Slawinski, J.; Innocenti, A.; Supuran, C. T. Eur. J. Med. Chem. 2010, 45, 3656. 10. Casini, A.; Scozzafava, A.; Mincione, F.; Menabuoni, L.; Ilies, M. A.; Supuran, C. T. J. Med. Chem. 2000, 43, 4884. 11. Winum, J. Y.; Rami, M.; Scozzafava, A.; Montero, J. L.; Supuran, C. Med. Res. Rev. 2008, 28, 445. 12. Marques, S.; Enyedy, É. A.; Supuran, C. T.; Krupenko, N. I.; Krupenko, S. A.; Amélia Santos, M. Bioorg. Med. Chem. 2010, 18, 5081. 13. Menabuoni, L.; Scozzafava, A.; Mincione, F.; Briganti, F.; Mincione, G.; Supuran, C. T. J. Enzyme Inhib. Med. Chem. 1999, 14, 457. 14. Mincione, F.; Benedini, F.; Biondi, S.; Cecchi, A.; Temperini, C.; Formicola, G.; Pacileo, I.; Scozzafava, A.; Masini, E.; Supuran, C. T. Bioorg. Med. Chem. Lett. 2011, 21, 3216. 15. Puccetti, L.; Fasolis, G.; Cecchi, A.; Winum, J.-Y.; Gamberi, A.; Montero, J.-L.; Scozzafava, A.; Supuran, C. T. Bioorg. Med. Chem. Lett. 2005, 15, 2359. 16. Rami, M.; Maresca, A.; Smaine, F.-Z.; Montero, J.-L.; Scozzafava, A.; Winum, J.Y.; Supuran, C. T. Bioorg. Med. Chem. Lett. 2011, 21, 2975. 17. Winum, J.-Y.; Pastorekova, S.; Jakubickova, L.; Montero, J.-L.; Scozzafava, A.; Pastorek, J.; Vullo, D.; Innocenti, A.; Supuran, C. T. Bioorg. Med. Chem. Lett. 2005, 15, 579. 18. McComsey, D. F.; Costanzo, M. J.; Hochman, C.; Smith-Swintosky, V.; Shank, R. P. J. Med. Chem. 1941, 2005, 48. 19. Ozensoy, O.; Puccetti, L.; Fasolis, G.; Arslan, O.; Scozzafava, A.; Supuran, C. T. Bioorg. Med. Chem. Lett. 2005, 15, 4862. 20. Zhang, S.; Yang, C.; Lu, W.; Huang, J.; Zhu, W.; Li, H.; Xu, Y.; Qian, X. Chem. Commun. (Camb) 2011, 47, 8301.
Contents lists available at SciVerse ScienceDirect
Bioorganic & Medicinal Chemistry Letters journal homepage: www.elsevier.com/locate/bmcl
Discovery of new potent inhibitors for carbonic anhydrase IX by structure-based virtual screening Liyan Wang , Chunmei Yang , Weiqiang Lu, Li Liu, Rui Gao, Sha Liao, Zhenjiang Zhao, Lili Zhu, Yufang Xu, Honglin Li ⇑, Jin Huang ⇑, Weiping Zhu ⇑ State Key Laboratory of Bioreactor Engineering, Shanghai Key Laboratory of Chemical Biology, Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology, Shanghai 200237, China
a r t i c l e
i n f o
Article history: Received 25 March 2013 Revised 17 April 2013 Accepted 19 April 2013 Available online 29 April 2013 Keywords: Virtual screening Molecular docking Carbonic anhydrase inhibitors Sulfonamides
a b s t r a c t Through structure-based virtual screening, some dozen of benzene sulfonamides with novel scaffolds are identified as potent inhibitors against carbonic anhydrase (CA) IX with IC50 values ranging from 2.86 to 588.34 nM. Among them, compounds 1 and 9 show high selectivity against tumor-target CA IX over CA II (the selectivity ratios are 21.3 and 136.6, respectively). The possible binding poses of hit compounds are also explored and the selectivity is elucidated by molecular docking simulations. The hit compounds discovered in this work would provide novel scaffolds for further hit-to-lead optimization. Ó 2013 Elsevier Ltd. All rights reserved.
Carbonic anhydrases (CAs, EC 4.2.1.1) are an important family of zinc metalloenzymes widespread in a diversity of organisms.1,2 These CAs catalyze a fundamental physiological reaction, the interconversion between the carbon dioxide and bicarbonate.3,4 They play an important role in many physiological processes, such as carbon dioxide transport between metabolizing tissues and lung, pH homeostasis,5 and many other physiologic or pathologic processes.6–10 In mammals, there are 16 different CA isozymes or CArelated proteins (CARP): several cytosolic forms (such as CA I–III and CA VII), five membrane-bound isozymes (CA IV, CA IX, CA XII, CA XIV and CA XV), one mitochondrial form (CA V), as well as a secreted CA isozyme (CA VI).3 Recently, two tumor-associated membrane carbonic anhydrase isozymes (CA IX and CA XII) attract much more attention.11 The role of CA IX in tumor physiology has been reported by many papers, such as the control of tumor pH and the influence in the cell microenvironment that promote cell proliferation, invasion, and metastasis.12–16 From this point, great efforts have been made to design anticancer drugs against CA IX. Although there are many effective inhibitors against CAs, most of classical sulfonamides/sulfamates CA inhibitors and their derivatives, such as acetazolamide (AZA), ethoxzolamide (EZA), do not have a good selectivity of CA IX over the sulfonamide-avid isozyme CA II.17–19 Therefore, one of the main
⇑ Corresponding authors. Tel./fax: +86 21 64250213. E-mail addresses: [email protected] (H. Li), [email protected] (J. Huang), [email protected] (W. Zhu). These authors contributed equally to this work. 0960-894X/$ - see front matter Ó 2013 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.bmcl.2013.04.048
challenges in the development of CA IX inhibitors is to identify high selectivity inhibitors against CA IX over the isozyme CA II.3 In this study, thirteen hits with novel scaffolds from the commercial SPECS database are identified with potent inhibitory activities against CA IX with IC50 values ranging from 2.86 to 588.34 nM by structure-based virtual screening. Among them, two inhibitors show high selectivity against tumor-target CA IX over CA II (the selectivity ratios are 21.3 and 136.6, respectively). In details, the crystal structure of CA IX is retrieved from the Protein Data Bank (RCSB Protein Data Bank (PDB) database code: 3IAI), and then virtual screening is performed using Glide5.5 against the SPECS database (about 280,000 compounds). The standard-precision (SP) is performed for preliminary calculations, and extra-precision (XP) is used for the final calculations to generate the minimized pose. Then visual inspections are taken to select candidates for further biological assays. Thus the initial 280 thousands compounds are reduced to about 10,000 after SP mode. The top 500 compounds are selected with the XP mode from the 10,000, and then 49 compounds are picked out to be tested by the enzyme assays against CA IX (Table S1). Finally, thirteen compounds are identified to exhibit inhibitory potencies against CAs ( Fig. 1). The structures and IC50 values of the hits and the reported positive controls acetazolamide (AZA), ethoxzolamide (EZA) are provided in Figure 1 and Table 1. The protocol of the preparation of the protein and ligands, and all structures of compounds for biological assays are described in the Supplementary data. The inhibition assays against CAs in vitro are thoroughly described in our previous report.20
L. Wang et al. / Bioorg. Med. Chem. Lett. 23 (2013) 3496–3499
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Figure 1. Structures of AZA, EZA and compounds 1–13.
Table 1 Inhibitory activities of the compounds 1–14 against CA I, CA II and CA IX Compounds
IC50 (nM) CA I
1 2 3 4 5 6 7 8 9 10 11 12 13 EZA AZA a b
a
197.64 213.69 2.13 16.73 156.78 172.84 3.09 126.47 231.41 258.84 36.13 120.13 1194 15.71 161.11
a
Selectivity ratios b
CA II
CA IX
60.93 41.97 9.33 10.58 27.16 153.18 33.13 33.92 3873 670.72 48.09 12.54 808.81 0.3 20.02
2.86 3.11 4.53 10.42 14.95 18.81 19.09 21.64 28.35 68.46 198.98 341.71 588.34 0.99 2.58
CA I/CA IX
CA II/CA IX
68.9 68.71 0.47 1.61 10.48 9.19 0.16 5.84 8.16 3.78 0.18 0.35 2.03 15.87 62.45
21.3 13.49 2.06 1.02 1.82 8.14 1.74 1.57 136.6 9.8 0.24 0.037 1.37 0.3 7.76
Full length, from human erythrocytes. Catalytic domain with GST-tag, recombinant enzyme.
From the experimental results, only benzene sulfonamide compounds have potent inhibitory activity against CAs (Table S1). In particular, compounds 1 and 9 not only show excellent inhibitory activity against CA IX (IC50 = 2.86 and 28.35 nM, respectively), but also have high selectivity ratio against CA IX over CA II. Especially the compound 9 shows a superior selective property against CA IX over CA II (the selective ratio is 136). It is suggested that steric hindered groups of the compounds, interacting with the hydrophobic surface of the active site, are possibly the key factors in the selectivity. In order to explore the structure-activity relationships (SAR) of the benzene sulfonamide compounds 1–13 and explain the possible mechanism of selectivity, the docking studies are undertaken with the available human CA IX crystal structure. For example, the most potent compound 1 (Fig. 2) binds in a compact manner to the CA IX active site. The sulfamate nitrogen is deprotonated and has replaced the hydroxyl ion coordinated to the zinc ion, while the metal ion remains its stable tetrahedral geometry with one sulfamate nitrogen of the compound and three imidazolic nitrogens of His 94, His 96 and His 119. The proton of the coordi-
3498
L. Wang et al. / Bioorg. Med. Chem. Lett. 23 (2013) 3496–3499
Figure 2. The predicted binding pose of compound 1 in the binding site of CA IX (PDB code: 3IAI). Key residues with potential interactions are labeled out and shown in green, while compound 1 is exhibited with yellow sticks. The activity zinc ion is illustrated with gray sphere, and the hydrogen bonds are highlighted by the red dot lines.
nated sulfamate nitrogen atom also forms a hydrogen bond with the hydroxyl group of Thr 199, which in turn forms a hydrogen bond with the carboxylate of Glu106. One of the oxygen atoms of the sulfamate moiety makes a hydrogen bond with the backbone amide of Thr 199. All these hydrogen bonds form an extended network and make the ligand bind to the active site well. This situation makes the substrate (CO2) avoid being attacked in a favorable location, and the hydrogen bond network also prevents the proton transfer reaction taking place from the active site to the environment. Consequently, the sulfamate group is essential for these compounds reported here, which will lose inhibitory potencies without this group. As for the selectivity, the factor maybe is the smaller active site of CA I compared to the other isozymes CA II and CA IX, owing to the presence of two extra His residues (His 200 and His 67) ( Fig. 3). So the steric hindered groups would prevent most ligands binding to the CA I well, especially the benzene moiety of compound 1 (the selective ratio against CA IX over CA I is 68.9). The similar situation also happens to CA II and CA IX. Superposition of the crystal structures of CA II and CA IX clearly reveals that the amino acids at the position 131 in the hydrophobic areas of the active site are different (Fig. 4). The phenylalanine with big side chain locates in CA II, while the valine with small side chain locates in CA IX. The big hydrophobic groups of compounds 1 and 9 (benzene of the compound 1 and the benzo[cd]indol-2(1H)-one of the compound 9, respectively) can interact with Val 131 by hydrophobic contacts. On the contrary, the steric hindered groups of compounds 1 and 9 may form strong clash interactions with Phe 131, so that they can not bind to CA II well. This structure information of compounds would be helpful for further optimizing the compounds in the next step. In summary, a series of benzene sulfonamide compounds with novel scaffolds are identified as CAs inhibitors through structurebased virtual screening. Especially compounds 1, 2 and 3 have equivalent inhibitory activities with the reported positive controls
Figure 3. Superposition of the crystal structures of CA I (slate, PDB code: 2NMX) and CA IX (green, PDB code: 3IAI). The binding poses of the compound 1 (yellow stick) is predicted by the molecular docking.
Figure 4. Superposition of the crystal structures of CA II (orange, PDB code: 3R16) and CA IX (green, PDB code: 3IAI). The binding poses of the compound 1 (yellow stick) and the compound 9 (magenta stick) are predicted by the molecular docking.
AZA and EZA (their IC50 values against CA IX are equal to 2.86, 3.11 and 4.53 nM, respectively). Meanwhile, docking simulation analysis is performed to elucidate the inhibitory activities of them and superior selectivity against CA IX over CA II, which shows that the sulfamate group is important for the inhibitors of CAs, and several special steric hindered hydrophobic groups might cause the selectivity due to their clash with the residues of CAs. These inhibitors may serve as new lead compounds for further development to treat cancer.
L. Wang et al. / Bioorg. Med. Chem. Lett. 23 (2013) 3496–3499
Acknowledgments This work is supported by the National Natural Science Foundation of China (Grants 21173076, 81102420 and 81222046), the Innovation Program of Shanghai Municipal Education Commission (Grant 10ZZ41), the Shanghai Committee of Science and Technology (Grant 11DZ2260600), the Special Fund for Major State Basic Research Project (Grant 2009CB918501), the 863 Hi-Tech Program of China (Grant 2012AA020308), and the Fundamental Research Funds for the Central Universities. We thank Professor Seppo Parkkila (Institute of Medical Technology and School of Medicine, University of Tampere, Finland) for providing the plasmid of carbonic anhydrase IX. We also thank Ph.D Houqi Liu at the Suzhou Institute for Advanced Study, University of Science and Technology of China (USTC), for providing the Applied Photophysics SX 20 stopped-flow instrument. Supplementary data Supplementary data associated with this article can be found, in the online version, at http://dx.doi.org/10.1016/j.bmcl.2013.04 .048. References and notes 1. 2. 3. 4.
Supuran, Supuran, Supuran, Supuran,
C. C. C. C.
T. Nat. Rev. Drug Disc. 2008, 7, 168. T. Curr. Pharm. Des. 2010, 16, 3233. T.; Scozzafava, A. Bioorg. Med. Chem. 2007, 15, 4336. T.; Scozzafava, A.; Casini, A. Med. Res. Rev. 2003, 23, 146.
3499
5. Svastov, E.; HulIkov, A.; Rafajov, M.; Zat’ovicov, M.; Gibadulinov, A.; Casini, A.; Cecchi, A.; Scozzafava, A.; Supuran, C. T.; Pastorek, J.; Pastorekov, S. FEBS Lett. 2004, 577, 439. 6. Avvaru, B. S.; Wagner, J. M.; Maresca, A.; Scozzafava, A.; Robbins, A. H.; Supuran, C. T.; McKenna, R. Bioorg. Med. Chem. Lett. 2010, 20, 4376. 7. Bertucci, A.; Innocenti, A.; Zoccola, D.; Scozzafava, A.; Tambutt, S.; Supuran, C. T. Bioorg. Med. Chem. 2009, 17, 5054. 8. Borras, J.; Scozzafava, A.; Menabuoni, L.; Mincione, F.; Briganti, F.; Mincione, G.; Supuran, C. T. Bioorg. Med. Chem. 1999, 7, 2397. 9. Brzozowski, Z.; Slawinski, J.; Innocenti, A.; Supuran, C. T. Eur. J. Med. Chem. 2010, 45, 3656. 10. Casini, A.; Scozzafava, A.; Mincione, F.; Menabuoni, L.; Ilies, M. A.; Supuran, C. T. J. Med. Chem. 2000, 43, 4884. 11. Winum, J. Y.; Rami, M.; Scozzafava, A.; Montero, J. L.; Supuran, C. Med. Res. Rev. 2008, 28, 445. 12. Marques, S.; Enyedy, É. A.; Supuran, C. T.; Krupenko, N. I.; Krupenko, S. A.; Amélia Santos, M. Bioorg. Med. Chem. 2010, 18, 5081. 13. Menabuoni, L.; Scozzafava, A.; Mincione, F.; Briganti, F.; Mincione, G.; Supuran, C. T. J. Enzyme Inhib. Med. Chem. 1999, 14, 457. 14. Mincione, F.; Benedini, F.; Biondi, S.; Cecchi, A.; Temperini, C.; Formicola, G.; Pacileo, I.; Scozzafava, A.; Masini, E.; Supuran, C. T. Bioorg. Med. Chem. Lett. 2011, 21, 3216. 15. Puccetti, L.; Fasolis, G.; Cecchi, A.; Winum, J.-Y.; Gamberi, A.; Montero, J.-L.; Scozzafava, A.; Supuran, C. T. Bioorg. Med. Chem. Lett. 2005, 15, 2359. 16. Rami, M.; Maresca, A.; Smaine, F.-Z.; Montero, J.-L.; Scozzafava, A.; Winum, J.Y.; Supuran, C. T. Bioorg. Med. Chem. Lett. 2011, 21, 2975. 17. Winum, J.-Y.; Pastorekova, S.; Jakubickova, L.; Montero, J.-L.; Scozzafava, A.; Pastorek, J.; Vullo, D.; Innocenti, A.; Supuran, C. T. Bioorg. Med. Chem. Lett. 2005, 15, 579. 18. McComsey, D. F.; Costanzo, M. J.; Hochman, C.; Smith-Swintosky, V.; Shank, R. P. J. Med. Chem. 1941, 2005, 48. 19. Ozensoy, O.; Puccetti, L.; Fasolis, G.; Arslan, O.; Scozzafava, A.; Supuran, C. T. Bioorg. Med. Chem. Lett. 2005, 15, 4862. 20. Zhang, S.; Yang, C.; Lu, W.; Huang, J.; Zhu, W.; Li, H.; Xu, Y.; Qian, X. Chem. Commun. (Camb) 2011, 47, 8301.