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Research Article

Decoding molecular mechanism of species-selective targeting of fungal versus human HSP90 using multiple replica molecular dynamics simulations and binding free energy calculations

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Received 31 Jul 2023, Accepted 09 Oct 2023, Published online: 18 Oct 2023

References

  • Ancuceanu, R., Hovaneț, M. V., Cojocaru-Toma, M., Anghel, A. I., & Dinu, M. (2022). Potential antifungal targets for Aspergillus sp. from the calcineurin and heat shock protein pathways. International Journal of Molecular Sciences, 23(20), 12543. https://doi.org/10.3390/ijms232012543
  • Banerjee, M., Hatial, I., Keegan, B. M., & Blagg, B. S. J. (2021). Assay design and development strategies for finding Hsp90 inhibitors and their role in human diseases. Pharmacology & Therapeutics, 221, 107747. https://doi.org/10.1016/j.pharmthera.2020.107747
  • Bao, H., Wang, W., Sun, H., & Chen, J. (2023). Probing mutation-induced conformational transformation of the GTP/M-RAS complex through Gaussian accelerated molecular dynamics simulations. Journal of Enzyme Inhibition and Medicinal Chemistry, 38(1), 2195995. https://doi.org/10.1080/14756366.2023.2195995
  • Basha, G. M., Parulekar, R. S., Al-Sehemi, A. G., Pannipara, M., Siddaiah, V., Kumari, S., Choudhari, P. B., & Tamboli, Y. (2022). Design and in silico investigation of novel Maraviroc analogues as dual inhibition of CCR-5/SARS-CoV-2 Mpro. Journal of Biomolecular Structure & Dynamics, 40(21), 11095–11110. https://doi.org/10.1080/07391102.2021.1955742
  • Bitencourt-Ferreira, G., Duarte da Silva, A., & Filgueira de Azevedo, W. (2021). Application of machine learning techniques to predict binding affinity for drug targets: A study of cyclin-dependent kinase 2. Current Medicinal Chemistry, 28(2), 253–265. https://doi.org/10.2174/2213275912666191102162959
  • Chatterjee, S., & Tatu, U. (2017). Heat shock protein 90 localizes to the surface and augments virulence factors of Cryptococcus neoformans. PLoS Neglected Tropical Diseases, 11(8), e0005836. https://doi.org/10.1371/journal.pntd.0005836
  • Chen, J., Pang, L., Wang, W., Wang, L., Zhang, J. Z. H., & Zhu, T. (2020). Decoding molecular mechanism of inhibitor bindings to CDK2 using molecular dynamics simulations and binding free energy calculations. Journal of Biomolecular Structure & Dynamics, 38(4), 985–996. https://doi.org/10.1080/07391102.2019.1591304
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N.long(N)method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. https://doi.org/10.1063/1.464397
  • dos Reis, T. F., de Castro, P. A., Bastos, R. W., Pinzan, C. F., Souza, P. F. N., Ackloo, S., Hossain, M. A., Drewry, D. H., Alkhazraji, S., Ibrahim, A. S., Jo, H., Lightfoot, J. D., Adams, E. M., Fuller, K. K., deGrado, W. F., & Goldman, G. H. (2023). A host defense peptide mimetic, brilacidin, potentiates caspofungin antifungal activity against human pathogenic fungi. Nature Communications, 14(1), 2052. https://doi.org/10.1038/s41467-023-37573-y
  • Eswar, N., Webb, B., Marti‐Renom, M. A., Madhusudhan, M. S., Eramian, D., Shen, M., Pieper, U., & Sali, A. (2006). Comparative protein structure modeling using modeller. Current Protocols in Bioinformatics, Chapter 5(1), Unit–UnU5.6. https://doi.org/10.1002/0471250953.bi0506s15
  • Gaziano, R., Campione, E., Iacovelli, F., Marino, D., Pica, F., Di Francesco, P., Aquaro, S., Menichini, F., Falconi, M., & Bianchi, L. (2018). Antifungal activity of Cardiospermum halicacabum L. (Sapindaceae) against Trichophyton rubrum occurs through molecular interaction with fungal Hsp90. Drug Design, Development and Therapy, 12, 2185–2193. https://doi.org/10.2147/DDDT.S155610
  • Girstmair, H., Tippel, F., Lopez, A., Tych, K., Stein, F., Haberkant, P., Schmid, P. W. N., Helm, D., Rief, M., Sattler, M., & Buchner, J. (2019). The Hsp90 isoforms from S. cerevisiae differ in structure, function and client range. Nature Communications, 10(1), 3626. https://doi.org/10.1038/s41467-019-11518-w
  • Jorgensen, W. L., Chandrasekhar, J., Madura, J. D., Impey, R. W., & Klein, M. L. (1983). Comparison of simple potential functions for simulating liquid water. The Journal of Chemical Physics, 79(2), 926–935. https://doi.org/10.1063/1.445869
  • Kim, S. H., Iyer, K. R., Pardeshi, L., Muñoz, J. F., Robbins, N., Cuomo, C. A., Koon, C., Wong, H., & Cowen, L. E. (2019). Genetic analysis of Candida auris implicates Hsp90 in morphogenesis and azole tolerance and Cdr1 in azole resistance. mBio, 10(1), e02529-18. https://doi.org/10.1128/mBio
  • Lu, S., Chen, Y., Wei, J., Zhao, M., Ni, D., He, X., & Zhang, J. (2021). Mechanism of allosteric activation of SIRT6 revealed by the action of rationally designed activators. Acta Pharmaceutica Sinica. B, 11(5), 1355–1361. https://doi.org/10.1016/j.apsb.2020.09.010
  • Lu, S., He, X., Yang, Z., Chai, Z., Zhou, S., Wang, J., Rehman, A. U., Ni, D., Pu, J., Sun, J., & Zhang, J. (2021). Activation pathway of a G protein-coupled receptor uncovers conformational intermediates as targets for allosteric drug design. Nature Communications, 12(1), 4721. https://doi.org/10.1038/s41467-021-25020-9
  • Lu, S., Ni, D., Wang, C., He, X., Lin, H., Wang, Z., & Zhang, J. (2019). Deactivation pathway of ras GTPase underlies conformational substates as targets for drug design. ACS Catalysis, 9(8), 7188–7196. https://doi.org/10.1021/acscatal.9b02556
  • Maier, J. A., Martinez, C., Kasavajhala, K., Wickstrom, L., Hauser, K. E., & Simmerling, C. (2015). ff14SB: Improving the accuracy of protein side chain and backbone parameters from ff99SB. Journal of Chemical Theory and Computation, 11(8), 3696–3713. https://doi.org/10.1021/acs.jctc.5b00255
  • Mayandi, V., Kang, W. T., Ting, D. S. J., Goh, E. T. L., Lynn, M. N., Aung, T. T., Vadivelu, J., Barathi, V. A., Chan, A. S. Y., & Lakshminarayanan, R. (2023). Propranolol ameliorates the antifungal activity of azoles in invasive Candidiasis. Pharmaceutics, 15(4), 1044. https://doi.org/10.3390/pharmaceutics15041044
  • Morris, G. M., Ruth, H., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). Software news and updates AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
  • Nakamoto, H., Yokoyama, Y., Suzuki, T., Miyamoto, Y., Fujishiro, T., Morikawa, M., & Miyata, Y. (2021). A cyclic lipopeptide surfactin is a species-selective Hsp90 inhibitor that suppresses cyanobacterial growth. Journal of Biochemistry, 170(2), 255–264. https://doi.org/10.1093/jb/mvab037
  • Ni, D., Wei, J., He, X., Rehman, A. U., Li, X., Qiu, Y., Pu, J., Lu, S., & Zhang, J. (2020). Discovery of cryptic allosteric sites using reversed allosteric communication by a combined computational and experimental strategy. Chemical Science, 12(1), 464–476. https://doi.org/10.1039/D0SC05131D
  • O’Meara, T. R., Robbins, N., & Cowen, L. E. (2017). The Hsp90 chaperone network modulates candida virulence traits. Trends in Microbiology, 25(10), 809–819. Elsevier Ltd. https://doi.org/10.1016/j.tim.2017.05.003
  • Penkler, D. L., & Tastan Bishop, Ö. (2019). Modulation of human Hsp90α conformational dynamics by allosteric ligand interaction at the C-terminal domain. Scientific Reports, 9(1), 1600. https://doi.org/10.1038/s41598-018-35835-0
  • Posfai, D., Eubanks, A. L., Keim, A. I., Lu, K. Y., Wang, G. Z., Hughes, P. F., Kato, N., Haystead, T. A., & Derbyshire, E. R. (2018). Identification of Hsp90 inhibitors with Anti-Plasmodium activity. Antimicrobial Agents and Chemotherapy, 62(4), e01799-17. https://doi.org/10.1128/AAC.01799-17
  • Qi, X., Li, G., Liu, J., Mou, L., Zhang, Y., Guo, S., Chen, X., & Li, W. (2023). Structural and energetic insights into the selective inhibition of PKMYT1 against WEE1. Journal of Biomolecular Structure & Dynamics, 1–9. https://doi.org/10.1080/07391102.2023.2225106
  • Qiu, Y., Yin, X., Li, X., Wang, Y., Fu, Q., Huang, R., & Lu, S. (2021). Untangling dual-targeting therapeutic mechanism of epidermal growth factor receptor (EGFR) based on reversed allosteric communication. Pharmaceutics, 13(5), 747. https://doi.org/10.3390/pharmaceutics13050747
  • Ravindranath, P. A., Forli, S., Goodsell, D. S., Olson, A. J., & Sanner, M. F. (2015). AutoDockFR: Advances in protein-ligand docking with explicitly specified binding site flexibility. PLoS Computational Biology, 11(12), e1004586. https://doi.org/10.1371/journal.pcbi.1004586
  • Roe, D. R., & Cheatham, T. E. (2013). PTRAJ and CPPTRAJ: Software for processing and analysis of molecular dynamics trajectory data. Journal of Chemical Theory and Computation, 9(7), 3084–3095. https://doi.org/10.1021/ct400341p
  • Ryckaert, J.-P., Ciccotti, G., & Berendsen, H. J. C. (1977). Numerical integration of the Cartesian equations of motion of a system with constraints: Molecular dynamics of n-alkanes. Journal of Computational Physics, 23(3), 327–341. https://doi.org/10.1016/0021-9991(77)90098-5
  • Sabe, V. T., Ntombela, T., Jhamba, L. A., Maguire, G. E. M., Govender, T., Naicker, T., & Kruger, H. G. (2021). Current trends in computer aided drug design and a highlight of drugs discovered via computational techniques: A review. European Journal of Medicinal Chemistry, 224, 113705. https://doi.org/10.1016/j.ejmech.2021.113705
  • Salomon-Ferrer, R., Case, D. A., & Walker, R. C. (2013). An overview of the Amber biomolecular simulation package. WIREs Computational Molecular Science, 3(2), 198–210. https://doi.org/10.1002/wcms.1121
  • Shi, Y., Yasen, M., Wang, Z., Du, T., Ding, Y., Li, X., Chai, Z., Jie, C., Ju, G., & Ji, M. (2023). The allosteric effect of the upper half of SENP1 contributes to its substrate selectivity for SUMO1 over SUMO2. Journal of Biomolecular Structure & Dynamics, 1–15. https://doi.org/10.1080/07391102.2023.2166997
  • Tassone, G., Mangani, S., Botta, M., & Pozzi, C. (2018). Probing the role of Arg97 in Heat shock protein 90 N-terminal domain from the parasite Leishmania braziliensis through site-directed mutagenesis on the human counterpart. Biochimica et Biophysica Acta. Proteins and Proteomics, 1866(11), 1190–1198. https://doi.org/10.1016/j.bbapap.2018.09.005
  • Vitiello, A., Ferrara, F., Boccellino, M., Ponzo, A., Cimmino, C., Comberiati, E., Zovi, A., Clemente, S., & Sabbatucci, M. (2023). Antifungal drug resistance: An emergent health threat. Biomedicines, 11(4), 1063. https://doi.org/10.3390/biomedicines11041063
  • Wang, E., Sun, H., Wang, J., Wang, Z., Liu, H., Zhang, J. Z. H., & Hou, T. (2019). End-point binding free energy calculation with MM/PBSA and MM/GBSA: Strategies and applications in drug design. Chemical Reviews, 119(16), 9478–9508. https://doi.org/10.1021/acs.chemrev.9b00055
  • Wang, J., Wolf, R. M., Caldwell, J. W., Kollman, P. A., & Case, D. A. (2004). Development and testing of a general amber force field. Journal of Computational Chemistry, 25(9), 1157–1174. https://doi.org/10.1002/jcc.20035
  • Whitesell, L., Robbins, N., Huang, D. S., McLellan, C. A., Shekhar-Guturja, T., LeBlanc, E. V., Nation, C. S., Hui, R., Hutchinson, A., Collins, C., Chatterjee, S., Trilles, R., Xie, J. L., Krysan, D. J., Lindquist, S., Porco, J. A., Tatu, U., Brown, L. E., Pizarro, J., & Cowen, L. E. (2019). Structural basis for species-selective targeting of Hsp90 in a pathogenic fungus. Nature Communications, 10(1), 402. https://doi.org/10.1038/s41467-018-08248-w
  • Wu, X., & Brooks, B. R. (2003). Self-guided Langevin dynamics simulation method. Chemical Physics Letters, 381(3-4), 512–518. https://doi.org/10.1016/j.cplett.2003.10.013
  • Yin, W., Wu, T., Liu, L., Jiang, H., Zhang, Y., Cui, H., Sun, Y., Qin, Q., Sun, Y., Gao, Z., Zhao, L., Su, X., Zhao, D., & Cheng, M. (2022). Species-selective targeting of fungal Hsp90: Design, synthesis, and evaluation of novel 4,5-diarylisoxazole derivatives for the combination treatment of azole-resistant candidiasis. Journal of Medicinal Chemistry, 65(7), 5539–5564. https://doi.org/10.1021/acs.jmedchem.1c01991
  • Yuan, R., Tu, J., Sheng, C., Chen, X., & Liu, N. (2021). Effects of Hsp90 inhibitor ganetespib on inhibition of azole-resistant Candida albicans. Frontiers in Microbiology, 12, 680382. https://doi.org/10.3389/fmicb.2021.680382
  • Zhang, H., Chu, G., Wang, G., Yao, M., Lu, S., & Chen, T. (2022). Mechanistic understanding of the palmitoylation of Go protein in the allosteric regulation of adhesion receptor GPR97. Pharmaceutics, 14(9), 1856. https://doi.org/10.3390/pharmaceutics14091856
  • Zhang, Z., Bills, G. F., & An, Z. (2023). Advances in the treatment of invasive fungal disease. PLoS Pathogens, 19(5), e1011322. https://doi.org/10.1371/journal.ppat.1011322
  • Zhen, C., Lu, H., & Jiang, Y. (2022). Novel promising antifungal target proteins for conquering invasive fungal infections. Frontiers in Microbiology, 13, 911322. https://doi.org/10.3389/fmicb.2022.911322

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