Design, synthesis, antifungal activity, and QM/MM docking study of two azole derivatives with indole ring

Abstract

Systemic candidiasis is a major health issue for immunocompromised individuals due to the increase in drug-resistance among Candida spp., which are prevalent pathogenic fungi responsible for many types of fungal infections. Azoles are among the most preferred antifungal class for systemic candidiasis with broad antifungal spectrum and systemic availability. In this study, we synthesized and tested antifungal effects of two new indole derivatives to investigate the impact of indole on the activity of azole antifungal compounds and to find potent derivatives against Candida spp. including resistant strains and biofilms. 1-(4-Chlorophenyl)-2-(1H-imidazol-1- yl)ethanol 1H-indole-2-carboxylate (4a) showed excellent antifungal profile with several times more potent activity against the tested species including a fluconazole-resistant C. tropicalis isolate. The minimum inhibitory concentration (MIC) of 4a was 0.03125 µg/ml against C. albicans, which was 0.5 µg/ml for fluconazole. The compound also showed promising biofilm inhibitory effect compared to amphotericin B. The importance of indole was demonstrated through molecular docking studies with the structure of C. albicans CYP51, the established target of azole antifungals, using different protocols. QM/MM docking approach yielded excellent results and accuracy, especially regarding metal interactions. As a result, indole could be a very useful fragment to design new and highly potent antifungal compounds in azole structure.

Keywords

• Azole
• antifungal
• biofilm
• Candida albicans
• CYP51
• indole
• induced fit docking
• QM/MM docking

References

1. [1] Wong SSW, Samaranayake LP, Seneviratne CJ. In pursuit of the ideal antifungal agent for Candida infections: highthroughput screening of small molecules. Drug Discov Today. 2014; 19(11): 1721-1730. [CrossRef]
2. [2] Graybill JR. Future directions of antifungal chemotherapy. Clin Infect Dis. 1992; 14(Suppl 1): S170-181. [CrossRef]
3. [3] Silva S, Rodrigues CF, Araujo D, Rodrigues ME, Henriques M. Candida Species Biofilms' Antifungal Resistance. J Fungi. 2017; 3(1): 8. [CrossRef]
4. [4] Maertens JA. History of the development of azole derivatives. Clin Microbiol Infect. 2004; 10(Suppl 1): 1-10. [CrossRef]
5. [5] Zhang J, Li L, Lv Q, Yan L, Wang Y, Jiang Y. The Fungal CYP51s: Their Functions, Structures, Related Drug Resistance, and Inhibitors. Front Microbiol. 2019; 10: 691. [CrossRef]
6. [6] Correia MA, Ortiz de Montellano PR. Inhibition of Cytochrome P450 Enzymes. In: Ortiz de Montellano PR. (Ed). Cytochrome P450: Structure, Mechanism, and Biochemistry. Springer US, Boston, 2005, pp. 247-322.
7. [7] Madhosingh H, Southwick FS. Infectious Diseases. In: Harward MP. (Ed). Medical Secrets. Mosby, Saint Louis, 2012, pp. 344-375.
8. [8] Hargrove TY, Friggeri L, Wawrzak Z, Qi A, Hoekstra WJ, Schotzinger RJ, York JD, Guengerich FP, Lepesheva GI. Structural analyses of Candida albicans sterol 14alpha-demethylase complexed with azole drugs address the molecular basis of azole-mediated inhibition of fungal sterol biosynthesis. J Biol Chem. 2017; 292(16): 6728-6743. [CrossRef]

9. [9] Hoekstra WJ, Hargrove TY, Wawrzak Z, da Gama Jaen Batista D, da Silva CF, Nefertiti AS, Rachakonda G, Schotzinger RJ, Villalta F, Soeiro Mde N, Lepesheva GI. Clinical Candidate VT-1161's Antiparasitic Effect In Vitro, Activity in a Murine Model of Chagas Disease, and Structural Characterization in Complex with the Target Enzyme CYP51 from Trypanosoma cruzi. Antimicrob Agents Chemother. 2016; 60(2): 1058-1066. [CrossRef]
10. [10] Monk BC, Tomasiak TM, Keniya MV, Huschmann FU, Tyndall JD, O'Connell JD, Cannon RD, McDonald JG, Rodriguez A, Finer-Moore JS, Stroud RM. Architecture of a single membrane spanning cytochrome P450 suggests constraints that orient the catalytic domain relative to a bilayer. Proc Natl Acad Sci U S A. 2014; 111(10): 3865-3870. [CrossRef]
11. [11] Sagatova AA, Keniya MV, Wilson RK, Sabherwal M, Tyndall JD, Monk BC. Triazole resistance mediated by mutations of a conserved active site tyrosine in fungal lanosterol 14alpha-demethylase. Sci Rep. 2016; 6: 26213. [CrossRef]
12. [12] Dogan IS, Sarac S, Sari S, Kart D, Gokhan SE, Vural I, Dalkara S. New azole derivatives showing antimicrobial effects and their mechanism of antifungal activity by molecular modeling studies. Eur J Med Chem. 2017; 130: 124-138. [CrossRef]
13. [13] Sari S, Kart D, Sabuncuoglu S, Dogan IS, Ozdemir Z, Bozbey I, Gencel M, Essiz S, Reynisson J, Karakurt A, Sarac S, Dalkara S. Antifungal screening and in silico mechanistic studies of an in-house azole library. Chem Biol Drug Des. 2019; 94(5): 1944-1955. [CrossRef]
14. [14] Sari S, Kart D, Ozturk N, Kaynak FB, Gencel M, Taskor G, Karakurt A, Sarac S, Essiz S, Dalkara S. Discovery of new azoles with potent activity against Candida spp. and Candida albicans biofilms through virtual screening. Eur J Med Chem. 2019; 179: 634-648. [CrossRef]
15. [15] Baji H, Flammang M, Kimny T, Gasquez F, Compagnon PL, Delcourt A. Synthesis and antifungal activity of novel (1-aryl-2-heterocyclyl)ethylideneaminooxymethyl-substituted dioxolanes. Eur J Med Chem. 1995; 30(7): 617-626. [CrossRef]A
16. [16] Godefroi EF, Heeres J, Van Cutsem J, Janssen PA. The preparation and antimycotic properties of derivatives of 1- phenethylimidazole. J Med Chem. 1969; 12(5): 784-791. [CrossRef]
17. [17] Immediata T, Day AR. β-Naphthyl derivatives of ethanolamine and n-substituted ethanolamines. J Org Chem. 1940; 05(5): 512-527. [CrossRef]
18. [18] Neises B, Steglich W. Simple Method for the Esterification of Carboxylic Acids. Angew Chem Int Ed. 1978; 17(7): 522- 524. [CrossRef]
19. [19] Cavalheiro M, Teixeira MC. Candida Biofilms: Threats, Challenges, and Promising Strategies. Front Med. 2018; 5: 28. [CrossRef]
20. [20] Kuhn DM, George T, Chandra J, Mukherjee PK, Ghannoum MA. Antifungal susceptibility of Candida biofilms: unique efficacy of amphotericin B lipid formulations and echinocandins. Antimicrob Agents Chemother. 2002; 46(6): 1773-1780. [CrossRef]
21. [21] Melo AS, Bizerra FC, Freymuller E, Arthington-Skaggs BA, Colombo AL. Biofilm production and evaluation of antifungal susceptibility amongst clinical Candida spp. isolates, including strains of the Candida parapsilosis complex. Med Mycol. 2011; 49(3): 253-262. [CrossRef]
22. [22] Wang J. Comprehensive assessment of ADMET risks in drug discovery. Curr Pharm Des. 2009; 15(19): 2195-2219. [CrossRef]
23. [23] Lipinski CA, Lombardo F, Dominy BW, Feeney PJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev. 2001; 46(1-3): 3-26. [CrossRef]
24. [24] Veber DF, Johnson SR, Cheng HY, Smith BR, Ward KW, Kopple KD. Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem. 2002; 45(12): 2615-2623. [CrossRef]
25. [25] Zhu F, Logan G, Reynisson J. Wine Compounds as a Source for HTS Screening Collections. A Feasibility Study. Mol Inform. 2012; 31(11-12): 847-855. [CrossRef]
26. [26] Baell J, Walters MA. Chemistry: Chemical con artists foil drug discovery. Nature. 2014; 513(7519): 481-483. [CrossRef],
27. [27] Schell WA, Jones AM, Garvey EP, Hoekstra WJ, Schotzinger RJ, Alexander BD. Fungal CYP51 Inhibitors VT-1161 and VT-1129 Exhibit Strong In Vitro Activity against Candida glabrata and C. krusei Isolates Clinically Resistant to Azole and Echinocandin Antifungal Compounds. Antimicrob Agents Chemother. 2017; 61(3): e01817-16. [CrossRef]
28. [28] Chau AS, Mendrick CA, Sabatelli FJ, Loebenberg D, McNicholas PM. Application of real-time quantitative PCR to molecular analysis of Candida albicans strains exhibiting reduced susceptibility to azoles. Antimicrob Agents Chemother. 2004; 48(6): 2124-2131. [CrossRef]
29. [29] Rupp B, Raub S, Marian C, Holtje HD. Molecular design of two sterol 14alpha-demethylase homology models and their interactions with the azole antifungals ketoconazole and bifonazole. J Comput Aided Mol Des. 2005; 19(3): 149- 163. [CrossRef]
30. [30] Zheng H, Langner KM, Shields GP, Hou J, Kowiel M, Allen FH, Murshudov G, Minor W. Data mining of iron(II) and iron(III) bond-valence parameters, and their relevance for macromolecular crystallography. Acta Crystallogr D Struct Biol. 2017; 73(Pt 4): 316-325. [CrossRef]
31. [31] Keniya MV, Sabherwal M, Wilson RK, Woods MA, Sagatova AA, Tyndall JDA, Monk BC. Crystal Structures of FullLength Lanosterol 14alpha-Demethylases of Prominent Fungal Pathogens Candida albicans and Candida glabrata Provide Tools for Antifungal Discovery. Antimicrob Agents Chemother. 2018; 62(11): e01134-18. [CrossRef]
32. [32] Friesner RA, Banks JL, Murphy RB, Halgren TA, Klicic JJ, Mainz DT, Repasky MP, Knoll EH, Shelley M, Perry JK, Shaw DE, Francis P, Shenkin PS. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem. 2004; 47(7): 1739-1749. [CrossRef]
33. [33] Friesner RA, Murphy RB, Repasky MP, Frye LL, Greenwood JR, Halgren TA, Sanschagrin PC, Mainz DT. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem. 2006; 49(21): 6177-6196. [CrossRef]
34. [34] Halgren TA, Murphy RB, Friesner RA, Beard HS, Frye LL, Pollard WT, Banks JL. Glide: a new approach for rapid, accurate docking and scoring. 2. Enrichment factors in database screening. J Med Chem. 2004; 47(7): 1750-1759. [CrossRef]
35. [35] Sherman W, Day T, Jacobson MP, Friesner RA, Farid R. Novel procedure for modeling ligand/receptor induced fit effects. J Med Chem. 2006; 49(2): 534-553. [CrossRef
36. [36] Cho AE, Guallar V, Berne BJ, Friesner R. Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. J Comput Chem. 2005; 26(9): 915-931. [CrossRef]
37. [37] Clinical and Laboratory Standards Institute (CLSI), Reference Method for Broth Dilution Antifungal Susceptibility Testing of Yeasts; Approved Standard, third ed. CLSI document M27-A3. Clinical and Laboratory Standards Institute, PA, USA 2008.
38. [38] Harder E, Damm W, Maple J, Wu C, Reboul M, Xiang JY, Wang L, Lupyan D, Dahlgren MK, Knight JL, Kaus JW, Cerutti DS, Krilov G, Jorgensen WL, Abel R, Friesner RA. OPLS3: A Force Field Providing Broad Coverage of Druglike Small Molecules and Proteins. J Chem Theory Comput. 2016; 12(1): 281-296. [CrossRef]
39. [39] Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The Protein Data Bank. Nucleic Acids Res. 2000; 28(1): 235-242. [CrossRef]
40. [40] Sastry GM, Adzhigirey M, Day T, Annabhimoju R, Sherman W. Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des. 2013; 27(3): 221-234. [CrossRef]
41. [41] Murphy RB, Philipp DM, Friesner RA. A mixed quantum mechanics/molecular mechanics (QM/MM) method for large-scale modeling of chemistry in protein environments. J Comput Chem. 2000; 21(16): 1442-1457. [CrossRef]
42. [42] Bochevarov AD, Harder E, Hughes TF, Greenwood JR, Braden DA, Philipp DM, Rinaldo D, Halls MD, Zhang J, Friesner RA. Jaguar: A high-performance quantum chemistry software program with strengths in life and materials sciences. Int J Quantum Chem. 2013; 113(18): 2110-2142. [CrossRef]