Skip to content
2000
image of Targeting Fructosamine Oxidase (Amadoriase II) in Aspergillus fumigatus: Comprehensive Virtual Screening, ADMET Analysis, and Molecular Dynamics Simulation of Triazole Derivatives

Abstract

Introduction

Aspergillus fumigatus, a significant fungal pathogen, poses a threat to human health, especially in immunocompromised individuals. Addressing the need for novel antifungal strategies, this study employs virtual screening to identify potential inhibitors of Fructosamine oxidase, also known as Amadoriase II, a crucial enzyme in A. fumigatus (PDB ID: 3DJE).

Method

Virtual screening of 81,197 triazole derivatives was subjected to computational analysis, aiming to pinpoint molecules with high binding affinity to the active site of Fructosamine oxidase. Subsequently, an in-depth ADMET analysis assessed the pharmacokinetic properties of lead compounds, ensuring their viability for further development. Molecular dynamics simulations were performed to evaluate the stability of top-ranked compounds over time.

Results

The results unveil a subset of triazole derivatives displaying promising interactions, suggesting their potential as inhibitors for further investigation.

Conclusion

This approach contributes to the development of targeted antifungal agents, offering a rational starting point for experimental validation and drug development against Aspergillus fumigatus infections.

Loading

Article metrics loading...

/content/journals/cmc/10.2174/0109298673321782240829082610
2024-09-12
2024-11-26
Loading full text...

Full text loading...

References

  1. Arastehfar A. Carvalho A. Houbraken J. Lombardi L. Garcia-Rubio R. Jenks J.D. Rivero-Menendez O. Aljohani R. Jacobsen I.D. Berman J. Osherov N. Hedayati M.T. Ilkit M. Armstrong-James D. Gabaldón T. Meletiadis J. Kostrzewa M. Pan W. Lass-Flörl C. Perlin D.S. Hoenigl M. Aspergillus fumigatus and aspergillosis: From basics to clinics. Stud. Mycol. 2021 100 1 100115 100115 10.1016/j.simyco.2021.100115 34035866
    [Google Scholar]
  2. Janbon G. Quintin J. Lanternier F. d’Enfert C. Studying fungal pathogens of humans and fungal infections: fungal diversity and diversity of approaches. Genes Immun. 2019 20 5 403 414 10.1038/s41435‑019‑0071‑2 31019254
    [Google Scholar]
  3. Bandres M.V. Modi P. Sharma S. Aspergillus Fumigatus (Archived). StatPearls Treasure Island (FL): StatPearls Publishing 2024
    [Google Scholar]
  4. Perfect J.R. The antifungal pipeline: a reality check. Nat. Rev. Drug Discov. 2017 16 9 603 616 10.1038/nrd.2017.46 28496146
    [Google Scholar]
  5. Roemer T. Krysan D.J. Antifungal drug development: challenges, unmet clinical needs, and new approaches. Cold Spring Harb. Perspect. Med. 2014 4 5 a019703 a019703 10.1101/cshperspect.a019703 24789878
    [Google Scholar]
  6. Fernández de Ullivarri M. Arbulu S. Garcia-Gutierrez E. Cotter P.D. Antifungal Peptides as Therapeutic Agents. Front. Cell. Infect. Microbiol. 2020 10 105 10.3389/fcimb.2020.00105 32257965
    [Google Scholar]
  7. Houšť J. Spížek J. Havlíček V. Antifungal Drugs. Metabolites 2020 10 3 106 10.3390/metabo10030106 32178468
    [Google Scholar]
  8. Rauseo A.M. Coler-Reilly A. Larson L. Spec A. Hope on the Horizon: Novel Fungal Treatments in Development. Open Forum Infect. Dis. 2020 7 2 ofaa016 10.1093/ofid/ofaa016 32099843
    [Google Scholar]
  9. Choudhary M. Kumar V. Naik B. Verma A. Saris P.E.J. Kumar V. Gupta S. Antifungal metabolites, their novel sources, and targets to combat drug resistance. Front. Microbiol. 2022 13 1061603 10.3389/fmicb.2022.1061603 36532457
    [Google Scholar]
  10. Pianalto K. Alspaugh J. New Horizons in Antifungal Therapy. J. Fungi (Basel) 2016 2 4 26 10.3390/jof2040026 29376943
    [Google Scholar]
  11. Collard F. Zhang J. Nemet I. Qanungo K.R. Monnier V.M. Yee V.C. Crystal structure of the deglycating enzyme fructosamine oxidase (amadoriase II). J. Biol. Chem. 2008 283 40 27007 27016 10.1074/jbc.M804885200 18667417
    [Google Scholar]
  12. Shimasaki T. Yoshida H. Kamitori S. Sode K. X-ray structures of fructosyl peptide oxidases revealing residues responsible for gating oxygen access in the oxidative half reaction. Sci. Rep. 2017 7 1 2790 10.1038/s41598‑017‑02657‑5 28584265
    [Google Scholar]
  13. Zheng J. Guan H. Xu L. Yang R. Lin Z. Engineered amadoriase II exhibiting expanded substrate range. Appl. Microbiol. Biotechnol. 2010 86 2 607 613 10.1007/s00253‑009‑2319‑7 19888573
    [Google Scholar]
  14. Nilsson R.H. Anslan S. Bahram M. Wurzbacher C. Baldrian P. Tedersoo L. Mycobiome diversity: high-throughput sequencing and identification of fungi. Nat. Rev. Microbiol. 2019 17 2 95 109 10.1038/s41579‑018‑0116‑y 30442909
    [Google Scholar]
  15. Zhang M. Analysis of LOXL1 expression in gastric cancer and mining of Traditional Chinese Medicine Based on bioinformatics. Cancer Cell Research 2024 11 41 10.54762/CCR2024.933‑942
    [Google Scholar]
  16. Yamari I. Mouhib A. Es-Sounni B. Nejjari R. Mazoir N. Bakhouch M. Mouzdahir A. Benharref A. El Kouali M. Chtita S. Oxidative functionalization of triterpenes isolated from Euphorbia resinifera latex: Semisynthesis, ADME-Tox, molecular docking, and molecular dynamics simulations. Chemical Physics Impact 2023 7 100372 10.1016/j.chphi.2023.100372
    [Google Scholar]
  17. Abchir O. Daoui O. Belaidi S. Ouassaf M. Qais F.A. ElKhattabi S. Belaaouad S. Chtita S. Design of novel benzimidazole derivatives as potential α-amylase inhibitors using QSAR, pharmacokinetics, molecular docking, and molecular dynamics simulation studies. J. Mol. Model. 2022 28 4 106 10.1007/s00894‑022‑05097‑9 35352175
    [Google Scholar]
  18. Yamari I. Abchir O. Mali S.N. Errougui A. Talbi M. Kouali M.E. Chtita S. The anti-SARS-CoV-2 activity of novel 9, 10-dihydrophenanthrene derivatives: an insight into molecular docking, ADMET analysis, and molecular dynamics simulation. Sci. Am. 2023 21 e01754 10.1016/j.sciaf.2023.e01754 37332393
    [Google Scholar]
  19. Nour H. Hashmi M.A. Belaidi S. Errougui A. El Kouali M. Talbi M. Chtita S. Design of Acetylcholinesterase Inhibitors as Promising Anti‐Alzheimer’s Agents Based on QSAR, Molecular Docking, and Molecular Dynamics Studies of Liquiritigenin Derivatives. ChemistrySelect 2023 8 32 e202301466 10.1002/slct.202301466
    [Google Scholar]
  20. Khedraoui M. Nour H. Yamari I. Abchir O. Errougui A. Chtita S. Design of a new potent Alzheimer’s disease inhibitor based on QSAR, molecular docking and molecular dynamics investigations. Chemical Physics Impact 2023 7 100361 10.1016/j.chphi.2023.100361
    [Google Scholar]
  21. Abchir O. Yamari I. Nour H. Daoui O. Elkhattabi S. Errougui A. Chtita S. Structure‐Based Virtual Screening, ADMET analysis, and Molecular Dynamics Simulation of Moroccan Natural Compounds as Candidates α‐Amylase Inhibitors. ChemistrySelect 2023 8 26 e202301092 10.1002/slct.202301092
    [Google Scholar]
  22. Serafini M. Pirali T. Tron G.C. Chapter Three - Click 1,2,3-triazoles in drug discovery and development: From the flask to the clinic? Advances in Heterocyclic Chemistry Academic Press Inc. 2021 134 101 148 10.1016/bs.aihch.2020.10.001
    [Google Scholar]
  23. Gao F. Wang T. Xiao J. Huang G. Antibacterial activity study of 1,2,4-triazole derivatives. Eur. J. Med. Chem. 2019 173 274 281 10.1016/j.ejmech.2019.04.043 31009913
    [Google Scholar]
  24. Matin M.M. Matin P. Rahman M.R. Ben Hadda T. Almalki F.A. Mahmud S. Ghoneim M.M. Alruwaily M. Alshehri S. Triazoles and Their Derivatives: Chemistry, Synthesis, and Therapeutic Applications. Front. Mol. Biosci. 2022 9 864286 10.3389/fmolb.2022.864286 35547394
    [Google Scholar]
  25. Staśkiewicz A. Ledwoń P. Rovero P. Papini A.M. Latajka R. Triazole-Modified Peptidomimetics: An Opportunity for Drug Discovery and Development. Front Chem. 2021 9 674705 10.3389/fchem.2021.674705 34095086
    [Google Scholar]
  26. Tian G. Song Q. Liu Z. Guo J. Cao S. Long S. Recent advances in 1,2,3- and 1,2,4-triazole hybrids as antimicrobials and their SAR: A critical review. Eur. J. Med. Chem. 2023 259 115603 10.1016/j.ejmech.2023.115603 37478558
    [Google Scholar]
  27. Schrödinger, System, Maestro-Desmond Interoperability Tools, Software. 2021 Available from: https://doi.org/software
  28. Friesner R.A. Banks J.L. Murphy R.B. Halgren T.A. Klicic J.J. Mainz D.T. Repasky M.P. Knoll E.H. Shelley M. Perry J.K. Shaw D.E. Francis P. Shenkin P.S. 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 10.1021/jm0306430 15027865
    [Google Scholar]
  29. Pubchem Available from: https://doi.org/https://pubchem.ncbi.nlm.nih.gov/
  30. Schrödinger Release 2024-1: LigPrep, Schrödinger, LLC, New York, NY. Available from: https://newsite.schrodinger.com/platform/products/ligprep/
  31. Roos K. Wu C. Damm W. Reboul M. Stevenson J.M. Lu C. Dahlgren M.K. Mondal S. Chen W. Wang L. Abel R. Friesner R.A. Harder E.D. OPLS3e: Extending Force Field Coverage for Drug-Like Small Molecules. J. Chem. Theory Comput. 2019 15 3 1863 1874 10.1021/acs.jctc.8b01026 30768902
    [Google Scholar]
  32. Shelley J.C. Cholleti A. Frye L.L. Greenwood J.R. Timlin M.R. Uchimaya M. Epik: a software program for pK a prediction and protonation state generation for drug-like molecules. J. Comput. Aided Mol. Des. 2007 21 12 681 691 10.1007/s10822‑007‑9133‑z 17899391
    [Google Scholar]
  33. Procheck Available from: https://saves.mbi.ucla.edu/
  34. Laskowski R.A. MacArthur M.W. Moss D.S. Thornton J.M. PROCHECK: a program to check the stereochemical quality of protein structures. J. Appl. Cryst. 1993 26 2 283 291 10.1107/S0021889892009944
    [Google Scholar]
  35. Laskowski R. Rullmann J.A.C. MacArthur M. Kaptein R. Thornton J. AQUA and PROCHECK-NMR: Programs for checking the quality of protein structures solved by NMR. J. Biomol. NMR 1996 8 4 477 486 10.1007/BF00228148 9008363
    [Google Scholar]
  36. Berman H.M. Westbrook J. Feng Z. Gilliland G. Bhat T.N. Weissig H. Shindyalov I.N. Bourne P.E. The Protein Data Bank. Nucleic Acids Res. 2000 28 1 235 242 10.1093/nar/28.1.235 10592235
    [Google Scholar]
  37. Schrödinger Release 2018-4, Protein Preparation Wizard Epik Schrödinger, LLC: New York, NY 2018
    [Google Scholar]
  38. Tripathi N.M. Bandyopadhyay A. High throughput virtual screening (HTVS) of peptide library: Technological advancement in ligand discovery. Eur. J. Med. Chem. 2022 243 114766 10.1016/j.ejmech.2022.114766 36122548
    [Google Scholar]
  39. Du J. Sun H. Xi L. Li J. Yang Y. Liu H. Yao X. Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM–GBSA calculation. J. Comput. Chem. 2011 32 13 2800 2809 10.1002/jcc.21859 21717478
    [Google Scholar]
  40. Genheden S. Ryde U. The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin. Drug Discov. 2015 10 5 449 461 10.1517/17460441.2015.1032936 25835573
    [Google Scholar]
  41. Pires D.E.V. Blundell T.L. Ascher D.B. pkCSM: Predicting Small-Molecule Pharmacokinetic and Toxicity Properties Using Graph-Based Signatures. J. Med. Chem. 2015 58 9 4066 4072 10.1021/acs.jmedchem.5b00104 25860834
    [Google Scholar]
  42. Mark P. Nilsson L. Structure and Dynamics of the TIP3P, SPC, and SPC/E Water Models at 298 K. J. Phys. Chem. A 2001 105 43 9954 9960 10.1021/jp003020w
    [Google Scholar]
  43. Ke Q. Gong X. Liao S. Duan C. Li L. Effects of thermostats/barostats on physical properties of liquids by molecular dynamics simulations. J. Mol. Liq. 2022 365 120116 10.1016/j.molliq.2022.120116
    [Google Scholar]
  44. Lipinski C.A. Lombardo F. Dominy B.W. Feeney P.J. 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 10.1016/S0169‑409X(00)00129‑0 11259830
    [Google Scholar]
/content/journals/cmc/10.2174/0109298673321782240829082610
Loading
/content/journals/cmc/10.2174/0109298673321782240829082610
Loading

Data & Media loading...


  • Article Type:
    Research Article
Keywords: Aspergillus fumigatus ; ADMET ; molecular dynamics ; Molecular docking
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error
Please enter a valid_number test