Waste to drugs: identification of pyrolysis by-products as antifungal agents against Cryptococcus neoformans

References

• Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1–2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
   Google Scholar
• Al Ruheili, A. M., Al Sariri, T., & Al Subhi, A. M. (2022). Predicting the potential habitat distribution of parthenium weed (Parthenium hysterophorus) globally and in Oman under projected climate change. Journal of the Saudi Society of Agricultural Sciences, 21(7), 469–478. https://doi.org/10.1016/j.jssas.2021.12.004
   Google Scholar
• ASTM, D. (1993a). D3173, Standard test method for moisture in the analysis sample of coal and coke. ASTM.
   Google Scholar
• ASTM, D. (1993b). D3174, Standard test method for ash in the analysis sample of coal and coke from coal. ASTM.
   Google Scholar
• ASTM, D. (1993c). D3175, Standard test method for volatile matter in the analysis sample of coal and coke. ASTM.
   Google Scholar
• Belkhir, L., & Elmeligi, A. (2019). Carbon footprint of the global pharmaceutical industry and relative impact of its major players. Journal of Cleaner Production, 214, 185–194. https://doi.org/10.1016/j.jclepro.2018.11.204
   Web of Science ®Google Scholar
• Ben-Ami, R., & Kontoyiannis, D. P. (2021). Resistance to antifungal drugs. Infectious Disease Clinics of North America, 35(2), 279–311. https://doi.org/10.1016/j.idc.2021.03.003
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., van der Spoel, D., & van Drunen, R. (1995). GROMACS: A message-passing parallel molecular dynamics implementation. Computer Physics Communications, 91(1–3), 43–56. https://doi.org/10.1016/0010-4655(95)00042-E
   Web of Science ®Google Scholar
• de Oliveira, F. F. M., Paredes, V., de Sousa, H. R., D'Áurea Moura, Á. N., Riasco-Palacios, J., Casadevall, A., Felipe, M. S. S., & Nicola, A. M. (2020). Thioredoxin reductase 1 is a highly immunogenic cell surface antigen in Paracoccidioides spp., Candida albicans, and Cryptococcus neoformans. Frontiers in Microbiology, 10, 2930. https://doi.org/10.3389/fmicb.2019.02930
   PubMed Web of Science ®Google Scholar
• de Oliveira, H. C., & Rodrigues, M. L. (2021). Repurposing benzimidazoles to fight Cryptococcus. In Fungal Biology Reviews (Vol. 37, pp.27–40). Elsevier. https://doi.org/10.1016/j.fbr.2021.04.002
   Google Scholar
• Dhyani, V., & Bhaskar, T. (2019). Pyrolysis of biomass. In Biofuels: Alternative feedstocks and conversion processes for the production of liquid and gaseous biofuels (pp. 217–244). Elsevier. https://doi.org/10.1016/B978-0-12-816856-1.00009-9
   Google Scholar
• 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. (2004). Glide: A new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749. https://doi.org/10.1021/jm0306430
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Murphy, R. B., Repasky, M. P., Frye, L. L., Greenwood, J. R., Halgren, T. A., Sanschagrin, P. C., & Mainz, D. T. (2006). Extra precision glide: Docking and scoring incorporating a model of hydrophobic enclosure for protein − ligand complexes. Journal of Medicinal Chemistry, 49(21), 6177–6196. https://doi.org/10.1021/jm051256o
   PubMed Web of Science ®Google Scholar
• Gao, T., Bian, R., Joseph, S., Taherymoosavi, S., Mitchell, D. R. G., Munroe, P., Xu, J., & Shi, J. (2020). Wheat straw vinegar: A more cost-effective solution than chemical fungicides for sustainable wheat plant protection. The Science of the Total Environment, 725, 138359. https://doi.org/10.1016/j.scitotenv.2020.138359
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Gondil, V. S., Dube, T., Panda, J. J., Yennamalli, R. M., Harjai, K., & Chhibber, S. (2020). Comprehensive evaluation of chitosan nanoparticle based phage lysin delivery system; a novel approach to counter S. pneumoniae infections. International Journal of Pharmaceutics, 573, 118850. https://doi.org/10.1016/j.ijpharm.2019.118850
   PubMed Web of Science ®Google Scholar
• Halgren, T. A. (2009). Identifying and characterizing binding sites and assessing druggability. Journal of Chemical Information and Modeling, 49(2), 377–389. https://doi.org/10.1021/ci800324m
   PubMed Web of Science ®Google Scholar
• Harder, E., Damm, W., Maple, J., Wu, C., Reboul, M., Xiang, J. Y., Wang, L., Lupyan, D., Dahlgren, M. K., Knight, J. L., Kaus, J. W., Cerutti, D. S., Krilov, G., Jorgensen, W. L., Abel, R., & Friesner, R. A. (2016). OPLS3: A force field providing broad coverage of drug-like small molecules and proteins. Journal of Chemical Theory and Computation, 12(1), 281–296. https://doi.org/10.1021/acs.jctc.5b00864
   PubMed Web of Science ®Google Scholar
• Hassan, N. M., Alhossary, A. A., Mu, Y., & Kwoh, C.-K. (2017). Protein-Ligand blind docking using QuickVina-W with inter-process spatio-temporal integration. Scientific Reports, 7(1), 15451. https://doi.org/10.1038/s41598-017-15571-7
   PubMedGoogle Scholar
• Hetényi, C., & van der Spoel, D. (2006). Blind docking of drug-sized compounds to proteins with up to a thousand residues. FEBS Letters, 580(5), 1447–1450. https://doi.org/10.1016/j.febslet.2006.01.074
   PubMed Web of Science ®Google Scholar
• Ianiri, G., & Idnurm, A. (2015). Essential gene discovery in the basidiomycete Cryptococcus neoformans for antifungal drug target prioritization. mBio, 6(2) e02334-14. https://doi.org/10.1128/mBio.02334-14
   PubMed Web of Science ®Google Scholar
• Iyer, K. R., Revie, N. M., Fu, C., Robbins, N., & Cowen, L. E. (2021). Treatment strategies for cryptococcal infection: Challenges, advances and future outlook. Nature Reviews. Microbiology, 19(7), 454–466. https://doi.org/10.1038/s41579-021-00511-0
   PubMed Web of Science ®Google Scholar
• Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., & Bolton, E. E. (2021). PubChem in 2021: New data content and improved web interfaces. Nucleic Acids Research, 49(D1), D1388–D1395. https://doi.org/10.1093/nar/gkaa971
   PubMed Web of Science ®Google Scholar
• Knaggs, M. H., Salsbury, F. R., Edgell, M. H., & Fetrow, J. S. (2007). Insights into correlated motions and long-range interactions in CheY derived from molecular dynamics simulations. Biophysical Journal, 92(6), 2062–2079. https://doi.org/10.1529/biophysj.106.081950
   PubMed Web of Science ®Google Scholar
• Leng, L., Yang, L., Chen, J., Hu, Y., Li, H., Li, H., Jiang, S., Peng, H., Yuan, X., & Huang, H. (2021). Valorization of the aqueous phase produced from wet and dry thermochemical processing biomass: A review. Journal of Cleaner Production, 294, 126238. https://doi.org/10.1016/j.jclepro.2021.126238
   Web of Science ®Google Scholar
• Linstrom, P. J., & Mallard, W. G. (2014). NIST chemistry WebBook, NIST standard reference database number 69 (p. 20899). National Institute of Standards and Technology.
   Google Scholar
• Sastry, G. M., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: Parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. https://doi.org/10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Majewski, M., Ruiz-Carmona, S., & Barril, X. (2019). An investigation of structural stability in protein-ligand complexes reveals the balance between order and disorder. Communications Chemistry, 2(1), 110. https://doi.org/10.1038/s42004-019-0205-5
   Google Scholar
• Missall, T. A., & Lodge, J. K. (2005). Function of the thioredoxin proteins in Cryptococcus neoformans during stress or virulence and regulation by putative transcriptional modulators. Molecular Microbiology, 57(3), 847–858. https://doi.org/10.1111/j.1365-2958.2005.04735.x
   PubMed Web of Science ®Google Scholar
• Pal, P., Modi, M., Ravichandran, S., Yennamalli, R. M., & Priyadarshini, R. (2021). DNA-binding properties of YbaB, a putative nucleoid-associated protein from Caulobacter crescentus. Frontiers in Microbiology, 12, 733344. https://doi.org/10.3389/fmicb.2021.733344
   PubMed Web of Science ®Google Scholar
• Ramesh, N., & Somasundaram, M. (2022). Thermochemical conversion of Parthenium hysterophorus biomass for bio-oil synthesis: Kinetics and techno-economic analysis. Biomass Conversion and Biorefinery, 12(8), 3145–3159. https://doi.org/10.1007/s13399-020-00790-2
   Web of Science ®Google Scholar
• Ramos, M. L. N. S., Carregosa, I. S. C., Carvalho, M. P., da Costa, M. T., Gagliardi, P. R., & Wisniewski, A. (2020). Potential of cattle manure pyrolysis liquid as an alternative environmentally friendly source of agricultural fungicides. Journal of Analytical and Applied Pyrolysis, 149, 104862. https://doi.org/10.1016/j.jaap.2020.104862
   Web of Science ®Google Scholar
• Ravichandran, S., Avatapalli, S., Narasimhan, Y., Kaushik, K. S., & Yennamalli, R. M. (2022). “Targeting” the search: An upgraded structural and functional repository of antimicrobial peptides for biofilm studies (B-AMP v2.0) with a focus on biofilm protein targets. Frontiers in Cellular and Infection Microbiology, 12, 1020391. https://doi.org/10.3389/fcimb.2022.1020391
   PubMed Web of Science ®Google Scholar
• Schrödinger Release 2022-4. (2021). LigPrep. NY.
   Google Scholar
• Schrödinger Release 2022-3. (2021). Mastero. NY.
   Google Scholar
• Schrödinger, L., & DeLano, W. (2017). The PyMOL molecular graphics system, version 2.0 Schrödinger, LLC. Google Scholar There Is No Corresponding Record for This Reference
   Google Scholar
• Schüttelkopf, A. W., & Van Aalten, D. M. F. (2004). PRODRG: A tool for high-throughput crystallography of protein–ligand complexes. Acta Crystallographica Section D Biological Crystallography, 60(8), 1355–1363. https://doi.org/10.1107/S0907444904011679
   PubMedGoogle Scholar
• Shanmugam, S. R., Adhikari, S., & Shakya, R. (2017). Nutrient removal and energy production from aqueous phase of bio-oil generated via hydrothermal liquefaction of algae. Bioresource Technology, 230, 43–48. https://doi.org/10.1016/j.biortech.2017.01.031
   PubMed Web of Science ®Google Scholar
• Shelley, J. C., Cholleti, A., Frye, L. L., Greenwood, J. R., Timlin, M. R., & Uchimaya, M. (2007). Epik: A software program for pK a prediction and protonation state generation for drug-like molecules. Journal of Computer-Aided Molecular Design, 21(12), 681–691. https://doi.org/10.1007/s10822-007-9133-z
   PubMed Web of Science ®Google Scholar
• Su, P., Zhou, M., Song, G., Du, X., & Lu, X. (2020). Efficient H2O2 generation and spontaneous OH conversion for in-situ phenol degradation on nitrogen-doped graphene: Pyrolysis temperature regulation and catalyst regeneration mechanism. Journal of Hazardous Materials, 397, 122681. https://doi.org/10.1016/j.jhazmat.2020.122681
   PubMed Web of Science ®Google Scholar
• Teotia, D., Gaid, M., Saini, S. S., Verma, A., Yennamalli, R. M., Khare, S. P., Ambatipudi, K., Mir, J. I., Beuerle, T., Hänsch, R., Roy, P., Agrawal, P. K., Beerhues, L., & Sircar, D. (2019). Cinnamate‐CoA ligase is involved in biosynthesis of benzoate‐derived biphenyl phytoalexin in Malus × domestica ‘Golden Delicious’ cell cultures. The Plant Journal: For Cell and Molecular Biology, 100(6), 1176–1192. https://doi.org/10.1111/tpj.14506
   PubMed Web of Science ®Google Scholar
• Toor, S. S., Rosendahl, L., & Rudolf, A. (2011). Hydrothermal liquefaction of biomass: A review of subcritical water technologies. Energy, 36(5), 2328–2342. https://doi.org/10.1016/j.energy.2011.03.013
   Web of Science ®Google Scholar
• Upadhya, R., Campbell, L. T., Donlin, M. J., Aurora, R., & Lodge, J. K. (2013). Global transcriptome profile of Cryptococcus neoformans during exposure to hydrogen peroxide induced oxidative stress. PloS One, 8(1), e55110. https://doi.org/10.1371/journal.pone.0055110
   PubMed Web of Science ®Google Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. C. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
   PubMed Web of Science ®Google Scholar
• Varsha, K. K., Devendra, L., Shilpa, G., Priya, S., Pandey, A., & Nampoothiri, K. M. (2015). 2,4-Di-tert-butyl phenol as the antifungal, antioxidant bioactive purified from a newly isolated Lactococcus sp. International Journal of Food Microbiology, 211, 44–50. https://doi.org/10.1016/j.ijfoodmicro.2015.06.025
   PubMed Web of Science ®Google Scholar
• Waksman, G., Krishna, T. S., Williams, C. H. J., & Kuriyan, J. (1994). Crystal structure of Escherichia coli thioredoxin reductase refined at 2 A resolution. Implications for a large conformational change during catalysis. Journal of Molecular Biology, 236(3), 800–816. https://doi.org/10.1006/jmbi.1994.1190
   PubMed Web of Science ®Google Scholar
• Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, 8(2), 127–134. https://doi.org/10.1093/protein/8.2.127
   PubMedGoogle Scholar
• Zafar, H., Altamirano, S., Ballou, E. R., & Nielsen, K. (2019). A titanic drug resistance threat in Cryptococcus neoformans. Current Opinion in Microbiology, 52, 158–164. https://doi.org/10.1016/j.mib.2019.11.001
   PubMed Web of Science ®Google Scholar