Robust anti-inflammatory activity of genistein against neutrophil elastase: a microsecond molecular dynamics simulation study

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
• Accerlrys Enterprise Platform. (2005). Introduction to the discovery studio visualizer (pp. 1–7).
   Google Scholar
• Ahmad, S. S., Sinha, M., Ahmad, K., Khalid, M., & Choi, I. (2020). Study of Caspase 8 inhibition for the management of Alzheimer’s Disease: A molecular docking and dynamics simulation. Molecules, 25(9). https://doi.org/10.3390/MOLECULES25092071
   Web of Science ®Google Scholar
• Alamanos, Y., Voulgari, P. V., & Drosos, A. A. (2006). Incidence and prevalence of rheumatoid arthritis, based on the 1987 American College of Rheumatology Criteria: A systematic review. Seminars in Arthritis and Rheumatism. https://doi.org/10.1016/j.semarthrit.2006.08.006
   PubMed Web of Science ®Google Scholar
• Ali, M. A., Vuree, S., Goud, H., Hussain, T., Nayarisseri, A., & Singh, S. K. (2019). Identification of high-affinity small molecules targeting gamma secretase for the treatment of Alzheimer’s disease. Current Topics in Medicinal Chemistry, 19(13), 1173–1187. https://doi.org/10.2174/1568026619666190617155326
   PubMed Web of Science ®Google Scholar
• Amadei, A., Linssen, A. B. M., & Berendsen, H. J. C. (1993). Essential dynamics of proteins. Proteins, 17(4), 412–425. https://doi.org/10.1002/PROT.340170408
   PubMed Web of Science ®Google Scholar
• Andersen, H. C. (1980). Molecular dynamics simulations at constant pressure and/or temperature. The Journal of Chemical Physics, 72(4), 2384–2393. https://doi.org/10.1063/1.439486
   Web of Science ®Google Scholar
• Andersen, H. C. (1983). Rattle: A “velocity” version of the shake algorithm for molecular dynamics calculations. Journal of Computational Physics, 52(1), 24–34. https://doi.org/10.1016/0021-9991(83)90014-1
   Web of Science ®Google Scholar
• Angew Chem Int Ed Engl - Latest PubMed articles - NCBI. (n.d.). Retrieved October 27, 2022, from https://www.ncbi.nlm.nih.gov/search/journals/0370543/
   Google Scholar
• António, J. P. M., Gonçalves, L. M., Guedes, R. C., Moreira, R., & Gois, P. M. P. (2018). Diazaborines as new inhibitors of human neutrophil elastase. ACS Omega, 3(7), 7418–7423. https://doi.org/10.1021/acsomega.8b00702
   PubMed Web of Science ®Google Scholar
• Aparoy, P., Reddy, K. K., & Reddanna, P. (2012). Structure and ligand based drug design strategies in the development of novel 5-LOX inhibitors. Current Medicinal Chemistry, 19(22), 3763. https://doi.org/10.2174/092986712801661112
   PubMed Web of Science ®Google Scholar
• Åqvist, J., Medina, C., & Samuelsson, J. E. (1994). A new method for predicting binding affinity in computer-aided drug design. Protein Engineering, Design and Selection, 7(3), 385–391. https://doi.org/10.1093/protein/7.3.385
   Google Scholar
• Azer, K., Kaddi, C. D., Barrett, J. S., Bai, J. P. F., McQuade, S. T., Merrill, N. J., Piccoli, B., Neves-Zaph, S., Marchetti, L., Lombardo, R., Parolo, S., Immanuel, S. R. C., & Baliga, N. S. (2021). History and future perspectives on the discipline of quantitative systems pharmacology modeling and its applications. Frontiers in Physiology, 12, 637999. https://doi.org/10.3389/FPHYS.2021.637999/BIBTEX
   PubMed Web of Science ®Google Scholar
• Babar, M. M., Zaidi, N., Us, S. S., Pothineni, V. R., Ali, Z., Faisal, S., Hakeem, K. R., & Gul, A. (2017). Application of bioinformatics and system biology in medicinal plant studies. Plant Bioinformatics: Decoding the Phyta, 375–393. https://doi.org/10.1007/978-3-319-67156-7_15
   Google Scholar
• Bae, S.‑C., & Lee, Y. H. (2019). Alcohol intake and risk of rheumatoid arthritis: a Mendelian randomization study. Zeitschrift fur Rheumatologie, 78(8), 791–796. https://doi.org/10.1007/s00393-018-0537-z
   PubMed Web of Science ®Google Scholar
• Berendsen, H. J. C., Postma, J. P. M., Van Gunsteren, W. F., Dinola, A., & Haak, J. R. (1984). Molecular dynamics with coupling to an external bath. The Journal of Chemical Physics, 81(8), 3684–3690. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Bernard, N. J. (2018). Synergy of environmental and genetic risk in RA. Nature Reviews. Rheumatology, 14(6), 319–319. https://doi.org/10.1038/s41584-018-0015-7
   PubMed Web of Science ®Google Scholar
• Brglez Mojzer, E., Knez Hrnčič, M., Škerget, M., Knez, Ž., & Bren, U. (2016). Polyphenols: Extraction methods, antioxidative action, bioavailability and anticarcinogenic effects. Molecules, 21(7). https://doi.org/10.3390/molecules21070901
   Google Scholar
• Cai, Y., Huang, T., & Yang, J. (2018). Applications of bioinformatics and systems biology in precision medicine and immunooncology. BioMed Research International, 2018, 1427978. https://doi.org/10.1155/2018/1427978
   PubMed Web of Science ®Google Scholar
• Cheng, F., Li, W., Zhou, Y., Shen, J., Wu, Z., Liu, G., Lee, P. W., & Tang, Y. (2012). admetSAR: a comprehensive source and free tool for assessment of chemical ADMET properties. Journal of Chemical Information and Modeling, 52(11), 3099–3105. https://doi.org/10.1021/CI300367A
   PubMed Web of Science ®Google Scholar
• Choy, E., Ganeshalingam, K., Semb, A. G., Szekanecz, Z., & Nurmohamed, M. (2014). Cardiovascular risk in rheumatoid arthritis: Recent advances in the understanding of the pivotal role of inflammation, risk predictors and the impact of treatment. Rheumatology (United Kingdom), 53(12), 2143–2154. https://doi.org/10.1093/RHEUMATOLOGY/KEU224
   PubMed Web of Science ®Google Scholar
• Chung, Y.-M., Chang, F.-R., Tseng, T.-F., Hwang, T.-L., Chen, L.-C., Wu, S.-F., Lee, C.-L., Lin, Z.-Y., Chuang, L.-Y., Su, J.-H., & Wu, Y.-C. (2011). A novel alkaloid, aristopyridinone A and anti-inflammatory phenanthrenes isolated from Aristolochia manshuriensis. Bioorganic & Medicinal Chemistry Letters, 21(6), 1792–1794. https://doi.org/10.1016/j.bmcl.2011.01.067
   PubMed Web of Science ®Google Scholar
• Clarke, J. (2020). NETs directly injure cartilage in RA. Nature Reviews. Rheumatology, 16(8), 410–410. https://doi.org/10.1038/s41584-020-0459-4
   PubMed Web of Science ®Google Scholar
• Cross, M., Smith, E., Hoy, D., Carmona, L., Wolfe, F., Vos, T., Williams, B., Gabriel, S., Lassere, M., Johns, N., Buchbinder, R., Woolf, A., & March, L. (2014). The global burden of rheumatoid arthritis: Estimates from the Global Burden of Disease 2010 study. Annals of the Rheumatic Diseases, 73(7), 1316–1322. https://doi.org/10.1136/annrheumdis-2013-204627
   PubMed Web of Science ®Google Scholar
• Dahlgren, C., Karlsson, A., & Bylund, J. (2019). Intracellular neutrophil oxidants: From laboratory curiosity to clinical reality. Journal of Immunology (Baltimore, MD: 1950), 202(11), 3127–3134. https://doi.org/10.4049/JIMMUNOL.1900235
   PubMed Web of Science ®Google Scholar
• Daien, C. I., Hua, C., Combe, B., & Landewe, R. (2017). Non-pharmacological and pharmacological interventions in patients with early arthritis: A systematic literature review informing the 2016 update of EULAR recommendations for the management of early arthritis. RMD Open, 3(1). https://doi.org/10.1136/RMDOPEN-2016-000404
   Google Scholar
• Daura, X., Jaun, B., Seebach, D., Van Gunsteren, W. F., & Mark, A. E. (1998). Reversible peptide folding in solution by molecular dynamics simulation. Journal of Molecular Biology, 280(5), 925–932. https://doi.org/10.1006/JMBI.1998.1885
   PubMed Web of Science ®Google Scholar
• Den Broeder, A. A., Van Herwaarden, N., & Van Den Bemt, B. J. F. (2018). Therapeutic drug monitoring of biologicals in rheumatoid arthritis: A disconnect between beliefs and facts. Current Opinion in Rheumatology, 30(3), 266–275. https://doi.org/10.1097/BOR.0000000000000487
   PubMed Web of Science ®Google Scholar
• Domon, H., Nagai, K., Maekawa, T., Oda, M., Yonezawa, D., Takeda, W., Hiyoshi, T., Tamura, H., Yamaguchi, M., Kawabata, S., & Terao, Y. (2018). Neutrophil elastase subverts the immune response by cleaving toll-like receptors and cytokines in pneumococcal pneumonia. Frontiers in Immunology, 9(APR), 732. https://doi.org/10.3389/FIMMU.2018.00732
   PubMedGoogle Scholar
• Dundas, J., Ouyang, Z., Tseng, J., Binkowski, A., Turpaz, Y., & Liang, J. (2006). CASTp: Computed atlas of surface topography of proteins with structural and topographical mapping of functionally annotated residues. Nucleic Acids Research, 34(WEB. SERV. ISS). https://doi.org/10.1093/NAR/GKL282
   PubMedGoogle Scholar
• El Aissouq, A., Chedadi, O., Bouachrine, M., & Ouammou, A. (2021). Identification of novel SARS-CoV-2 inhibitors: A structure-based virtual screening approach. Journal of Chemistry. https://doi.org/10.1155/2021/1901484
   Google Scholar
• Emery, P., Mankia, K., & Nam, J. L. (2017). Individuals at risk of rheumatoid arthritis – The evolving story. Best practice & research. Clinical Rheumatology, 31(1), 1–2. https://doi.org/10.1016/j.berh.2017.11.003
   Web of Science ®Google Scholar
• Engkvist, O., Wrede, P., & Ulrich, R. (2003). Prediction of CNS activity of compound libraries using substructure analysis. Journal of Chemical Information and Computer Sciences, 43(1), 155–160. https://doi.org/10.1021/ci0102721
   PubMedGoogle Scholar
• Eslami, M., Hashemianzadeh, S. M., Bagherzadeh, K., & Seyed Sajadi, S. A. (2016). Molecular perception of interactions between bis(7)tacrine and cystamine-tacrine dimer with cholinesterases as the promising proposed agents for the treatment of Alzheimer’s disease. Journal of Biomolecular Structure & Dynamics, 34(4), 855–869. https://doi.org/10.1080/07391102.2015.1057526
   PubMed Web of Science ®Google Scholar
• Friedman, B., & Cronstein, B. (2019). Methotrexate mechanism in treatment of rheumatoid arthritis. Joint Bone Spine, 86(3), 301–307. https://doi.org/10.1016/J.JBSPIN.2018.07.004
   PubMed Web of Science ®Google Scholar
• Fu, Z., Thorpe, M., Akula, S., Chahal, G., & Hellman, L. T. (2018). Extended cleavage specificity of human neutrophil elastase, human proteinase 3, and their distant ortholog clawed frog PR3-three elastases with similar primary but different extended specificities and stability. Frontiers in Immunology, 9(OCT), 2387. https://doi.org/10.3389/fimmu.2018.02387
   PubMedGoogle Scholar
• Furlan, V., & Bren, U. (2021). Insight into inhibitory mechanism of pde4d by dietary polyphenols using molecular dynamics simulations and free energy calculations. Biomolecules, 11(3), 1–23. https://doi.org/10.3390/biom11030479
   Web of Science ®Google Scholar
• Gabarro-Arpa, J., & Revilla, R. (2000). Clustering of a molecular dynamics trajectory with a Hamming distance. Computers & Chemistry, 24(6), 693–698. https://doi.org/10.1016/S0097-8485(00)00067-X
   PubMedGoogle Scholar
• Gibofsky, A. (2012). Overview of epidemiology, pathophysiology, and diagnosis of rheumatoid arthritis. The American Journal of Managed Care.
   Web of Science ®Google Scholar
• Guo, Q., Wang, Y., Xu, D., Nossent, J., Pavlos, N. J., & Xu, J. (2018a). Rheumatoid arthritis: pathological mechanisms and modern pharmacologic therapies. Bone Research, 6(1), 1–14. https://doi.org/10.1038/s41413-018-0016-9
   PubMedGoogle Scholar
• Guo, Q., Wang, Y., Xu, D., Nossent, J., Pavlos, N. J., & Xu, J. (2018b). Rheumatoid arthritis: pathological mechanisms and modern pharmacologic therapies. Bone Research, 6(1). https://doi.org/10.1038/S41413-018-0016-9
   Google Scholar
• Hallowell, R. W., & Horton, M. R. (2014). Interstitial lung disease in patients with rheumatoid arthritis: spontaneous and drug induced. Drugs, 74(4), 443–450. https://doi.org/10.1007/s40265-014-0190-z
   PubMed Web of Science ®Google Scholar
• Hartman, E., Wallblom, K., van der Plas, M. J. A., Petrlova, J., Cai, J., Saleh, K., Kjellström, S., & Schmidtchen, A. (2020). Bioinformatic analysis of the wound peptidome reveals potential biomarkers and antimicrobial peptides. Frontiers in Immunology, 11, 620707. https://doi.org/10.3389/FIMMU.2020.620707/FULL
   PubMed Web of Science ®Google Scholar
• Henriksen, P. A. (2014). The potential of neutrophil elastase inhibitors as anti-inflammatory therapies. Current opinion in Hematology, 21(1), 23–28. https://doi.org/10.1097/MOH.0000000000000001
   PubMed Web of Science ®Google Scholar
• Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12 < 1463::AID-JCC4 > 3.0.CO;2-H
   Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Ikram, N., Mirza, M. U., Vanmeert, M., Froeyen, M., Salo-Ahen, O. M. H., Tahir, M., … Ahmad, S. (2019). Inhibition of oncogenic kinases. An in vitro validated computational approach identified potential multi-target anticancer compounds. Biomolecules, 9(4), 124. https://doi.org/10.3390/BIOM9040124
   PubMed Web of Science ®Google Scholar
• Jugniot, N., Voisin, P., Bentaher, A., & Mellet, P. (2019). Neutrophil elastase activity imaging: Recent approaches in the design and applications of activity-based probes and substrate-based probes. Contrast Media and Molecular Imaging. Hindawi Limited, 2019, 1–12. https://doi.org/10.1155/2019/7417192
   Google Scholar
• Jukič, M., Janežič, D., & Bren, U. (2020). Ensemble docking coupled to linear interaction energy calculations for identification of coronavirus main protease (3CLpro) non-covalent small-molecule inhibitors. Molecules, 25(24). https://doi.org/10.3390/MOLECULES25245808
   PubMed Web of Science ®Google Scholar
• Kahler, J. P., Vanhoutte, R., & Verhelst, S. H. L. (2020). Activity-based protein profiling of serine proteases in immune cells. Archivum Immunologiae et Therapiae Experimentalis. https://doi.org/10.1007/s00005-020-00586-2
   PubMed Web of Science ®Google Scholar
• Kim, J., Hu, C., Moufawad El Achkar, C., Black, L. E., Douville, J., Larson, A., Pendergast, M. K., Goldkind, S. F., Lee, E. A., Kuniholm, A., Soucy, A., Vaze, J., Belur, N. R., Fredriksen, K., Stojkovska, I., Tsytsykova, A., Armant, M., DiDonato, R. L., Choi, J., … Yu, T. W. (2019). Patient-customized oligonucleotide therapy for a rare genetic disease. The New England Journal of Medicine, 381(17), 1644–1652. https://doi.org/10.1056/NEJMOA1813279/SUPPL_FILE/NEJMOA1813279_DISCLOSURES.PDF
   PubMed Web of Science ®Google Scholar
• Kim, J. W., & Suh, C. H. (2020). Systemic manifestations and complications in patients with rheumatoid arthritis. Journal of Clinical Medicine, 9(6), 1–5. https://doi.org/10.3390/JCM9062008
   Web of Science ®Google Scholar
• Kim, J. Y., Wang, Y., Uddin, Z., Song, Y. H., Li, Z. P., Jenis, J., & Park, K. H. (2018). Competitive neutrophil elastase inhibitory isoflavones from the roots of Flemingia philippinensis. Bioorganic Chemistry, 78, 249–257. https://doi.org/10.1016/j.bioorg.2018.03.024
   PubMed Web of Science ®Google Scholar
• Krotova, K., Khodayari, N., Oshins, R., Aslanidi, G., & Brantly, M. L. (2020). Neutrophil elastase promotes macrophage cell adhesion and cytokine production through the integrin-Src kinases pathway. Scientific Reports, 10(1), 1–10. https://doi.org/10.1038/s41598-020-72667-3
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., & Lynn, A., Open Source Drug Discovery Consortium. (2014). g_mmpbsa–a GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Laforge, M., Elbim, C., Frère, C., Hémadi, M., Massaad, C., Nuss, P., Benoliel, J.-J., & Becker, C. (2020). Tissue damage from neutrophil-induced oxidative stress in COVID-19. Nature Reviews. Immunology, 20(9), 515–516. https://doi.org/10.1038/s41577-020-0407-1
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A. (2009). PDBsum new things. Nucleic Acids Research, 37(SUPPL. 1). https://doi.org/10.1093/NAR/GKN860
   PubMedGoogle Scholar
• Lauper, K., Courvoisier, D. S., Chevallier, P., Finckh, A., & Gabay, C. (2018). Incidence and prevalence of major adverse cardiovascular events in rheumatoid arthritis, psoriatic arthritis, and axial spondyloarthritis. Arthritis Care & Research, 70(12), 1756–1763. https://doi.org/10.1002/ACR.23567
   Web of Science ®Google Scholar
• Lindahl, A., Hess, & Spoel, V. D. (2020). GROMACS 2019.6 Manual. https://zenodo.org/record/3685925
   Google Scholar
• Liou, J. R., El-Shazly, M., Du, Y. C., Tseng, C. N., Hwang, T. L., Chuang, Y. L., … Wu, Y. C. (2013). 1,5-Diphenylpent-3-en-1-ynes and methyl naphthalene carboxylates from Lawsonia inermis and their anti-inflammatory activity. Phytochemistry. https://doi.org/10.1016/j.phytochem.2012.11.010
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 46(1–3), 3–26. https://doi.org/10.1016/S0169-409X(00)00129-0
   PubMed Web of Science ®Google Scholar
• Liu, D., Ahmet, A., Ward, L., Krishnamoorthy, P., Mandelcorn, E. D., Leigh, R., … Kim, H. (2013). A practical guide to the monitoring and management of the complications of systemic corticosteroid therapy. Allergy, Asthma and Clinical Immunology, 9(1). https://doi.org/10.1186/1710-1492-9-30
   Google Scholar
• Longo, D. L. (2019). Personalized medicine for primary treatment of serous ovarian cancer. The New England Journal of Medicine, 381(25), 2471–2474. https://doi.org/10.1056/NEJME1914488/SUPPL_FILE/NEJME1914488_DISCLOSURES.PDF
   PubMed Web of Science ®Google Scholar
• Malmström, V., Catrina, A. I., & Klareskog, L. (2017). The immunopathogenesis of seropositive rheumatoid arthritis: from triggering to targeting. Nature Reviews. Immunology, 17(1), 60–75. https://doi.org/10.1038/nri.2016.124
   PubMed Web of Science ®Google Scholar
• Marigliano, B., Soriano, A., Margiotta, D., Vadacca, M., & Afeltra, A. (2013). Lung involvement in connective tissue diseases: a comprehensive review and a focus on rheumatoid arthritis. Autoimmunity Reviews, 12(11), 1076–1084. https://doi.org/10.1016/j.autrev.2013.05.001
   PubMed Web of Science ®Google Scholar
• Martyna, G. J., Tobias, D. J., & Klein, M. L. (1994). Constant pressure molecular dynamics algorithms. The Journal of Chemical Physics, 101(5), 4177–4189. https://doi.org/10.1063/1.467468
   Web of Science ®Google Scholar
• Martyna, G. J., Tuckerman, M. E., Tobias, D. J., & Klein, M. L. (1996). Explicit reversible integrators for extended systems dynamics. Molecular Physics, 87(5), 1117–1157. https://doi.org/10.1080/00268979600100761
   Web of Science ®Google Scholar
• Maughan, T. (2017). The promise and the hype of ‘personalised medicine. The New Bioethics, 23(1), 13. https://doi.org/10.1080/20502877.2017.1314886
   PubMed Web of Science ®Google Scholar
• 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
   PubMed Web of Science ®Google Scholar
• Nishina, K., Mikawa, K., Takao, Y., Maekawa, N., Shiga, M., & Obara, H. (1997). ONO-5046, an elastase inhibitor, attenuates endotoxin-induced acute lung injury in rabbits. Anesthesia and Analgesia, 84(5), 1097–1103. https://doi.org/10.1097/00000539-199705000-00026
   PubMed Web of Science ®Google Scholar
• O'Dwyer, D. N., Armstrong, M. E., Cooke, G., Dodd, J. D., Veale, D. J., & Donnelly, S. C. (2013). Rheumatoid arthritis (RA) associated interstitial lung disease (ILD. European Journal of Internal Medicine, 24(7), 597–603. https://doi.org/10.1016/j.ejim.2013.07.004
   PubMed Web of Science ®Google Scholar
• Okada, Y., Eyre, S., Suzuki, A., Kochi, Y., & Yamamoto, K. (2019). Genetics of rheumatoid arthritis: 2018 status. Annals of the Rheumatic Diseases, 78(4), 446–453. https://doi.org/10.1136/annrheumdis-2018-213678
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera - A visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/JCC.20084
   PubMed Web of Science ®Google Scholar
• Polverino, E., Rosales-Mayor, E., Dale, G. E., Dembowsky, K., & Torres, A. (2017). The role of neutrophil elastase inhibitors in lung diseases. Chest, 152(2), 249–262. https://doi.org/10.1016/J.CHEST.2017.03.056
   PubMed Web of Science ®Google Scholar
• Postma, J. C., Van Gunsteren, J. P. M., Di Nola, W. F., & Haak, A. (1984). Molecular dynamics with coupling to an external bath. Studies in Molecular Dynamics. I. General Method the Journal of Chemical Physics, 81(8), 234505. https://doi.org/10.1063/1.448118
   Web of Science ®Google Scholar
• Protein Data Bank. (2019). RCSB PDB: Homepage. Rcsb Pdb.
   Google Scholar
• Radner, H., Lesperance, T., Accortt, N. A., & Solomon, D. H. (2017). Incidence and prevalence of cardiovascular risk factors among patients with rheumatoid arthritis, psoriasis, or psoriatic arthritis. Arthritis Care & Research, 69(10), 1510–1518. https://doi.org/10.1002/ACR.23171/ABSTRACT
   Web of Science ®Google Scholar
• Rosas, E. C., Correa, L. B., & GraçasHenriques, M. d. (2017). Neutrophils in rheumatoid arthritis: A target for discovering new therapies based on natural products. In Role of neutrophils in disease pathogenesis. https://doi.org/10.5772/INTECHOPEN.68617
   Google Scholar
• Rotondo, S., Krauze-Brzósko, K., Manarini, S., Martelli, N., Pecce, R., Evangelista, V., Benedetta Donati, M., & Cerletti, C. (2008). Inhibition by soya isoflavones of human polymorphonuclear leukocyte function: Possible relevance for the beneficial effects of soya intake. The British Journal of Nutrition, 99(2), 240–247. https://doi.org/10.1017/S0007114507797052
   PubMed Web of Science ®Google Scholar
• Safiri, S., Kolahi, A. A., Hoy, D., Smith, E., Bettampadi, D., Mansournia, M. A., Almasi-Hashiani, A., Ashrafi-Asgarabad, A., Moradi-Lakeh, M., Qorbani, M., Collins, G., Woolf, A. D., March, L., & Cross, M. (2019). Global, regional and national burden of rheumatoid arthritis 1990–2017: a systematic analysis of the Global Burden of Disease study 2017. Annals of the Rheumatic Diseases, 78(11), 1463–1471. https://doi.org/10.1136/ANNRHEUMDIS-2019-215920
   PubMed Web of Science ®Google Scholar
• Schrödinger, LLC. (2015). The {PyMOL} Molecular Graphics System, Version∼1.8.
   Google Scholar
• Shao, J., Tanner, S. W., Thompson, N., & Cheatham, T. E. (2007). Clustering molecular dynamics trajectories: 1. Characterizing the performance of different clustering algorithms. Undefined, 3(6), 2312–2334. https://doi.org/10.1021/CT700119M
   Google Scholar
• Shaw, M., Collins, B. F., Ho, L. A., & Raghu, G. (2015). Rheumatoid arthritis-associated lung disease. European Respiratory Review: An Official Journal of the European Respiratory Society, 24(135), 1–16. https://doi.org/10.1183/09059180.00008014
   PubMedGoogle Scholar
• Siedle, B. (2007). Natural compounds as inhibitors of human neutrophil elastase. https://doi.org/10.1055/s-2007-967183
   Google Scholar
• Siedle, B., Hrenn, A., & Merfort, I. (2007). Natural compounds as inhibitors of human neutrophil elastase. Planta Medica, 73(5), 401–420. https://doi.org/10.1055/s-2007-967183
   PubMed Web of Science ®Google Scholar
• Smolen, J. S., Aletaha, D., Barton, A., Burmester, G. R., Emery, P., Firestein, G. S., … Yamamoto, K. (2018). Rheumatoid arthritis. Nature Reviews Disease Primers, 4(1), 1–23. https://doi.org/10.1038/nrdp.2018.1
   PubMedGoogle Scholar
• Srinivasan, E., & Rajasekaran, R. (2018). Comparative binding of kaempferol and kaempferide on inhibiting the aggregate formation of mutant (G85R) SOD1 protein in familial amyotrophic lateral sclerosis: A quantum chemical and molecular mechanics study. BioFactors (Oxford, England), 44(5), 431–442. https://doi.org/10.1002/BIOF.1441
   PubMed Web of Science ®Google Scholar
• Standish, A. J., & Weiser, J. N. (2009). Human neutrophils kill Streptococcus pneumoniae via serine proteases. Journal of Immunology (Baltimore, MD: 1950), 183(4), 2602–2609. https://doi.org/10.4049/jimmunol.0900688
   PubMed Web of Science ®Google Scholar
• Stjernschantz, E., & Oostenbrink, C. (2010). Improved ligand-protein binding affinity predictions using multiple binding modes. Biophysical Journal, 98(11), 2682–2691. https://doi.org/10.1016/j.bpj.2010.02.034
   PubMed Web of Science ®Google Scholar
• Tremblay, G. M., Janelle, M. F., & Bourbonnais, Y. (2003). Anti-inflammatory activity of neutrophil elastase inhibitors. Current Opinion in Investigational Drugs (London, England: 2000), 4(5), 556–565.
   PubMedGoogle Scholar
• Trott, O., & Olson, A. J. (2010). AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/JCC.21334
   PubMed Web of Science ®Google Scholar
• Van Gunsteren, W. F., & Berendsen, H. J. C. (1988). A leap-frog algorithm for stochastic dynamics. Molecular Simulation, 1(3), 173–185. https://doi.org/10.1080/08927028808080941
   Web of Science ®Google Scholar
• van Gunsteren, W., Daura, X., & Mark, A. (2002). GROMOS force field. In Encyclopedia of computational chemistry (vol. 2). https://doi.org/10.1002/0470845015.cga011
   Google Scholar
• Wang, L., Wu, Y., Yao, S., Ge, H., Zhu, Y., Chen, K., … Bai, F. (2021). Discovery of potential small molecular SARS-CoV-2 entry blockers targeting the spike protein. Acta Pharmacologica Sinica. http://www.ncbi.nlm.nih.gov/pubmed/34349236
   Google Scholar
• Yang, M., Chen, Q., Mei, L., Wen, G., An, W., Zhou, X., Niu, K., Liu, C., Ren, M., Sun, K., Xiao, Q., & Zhang, L. (2021). Neutrophil elastase promotes neointimal hyperplasia by targeting toll-like receptor 4 (TLR4)-NF-κB signalling. British Journal of Pharmacology, 178(20), 4048–4068. https://doi.org/10.1111/BPH.15583
   PubMed Web of Science ®Google Scholar
• Zou, J., Zheng, M. W., Li, G., & Su, Z. G. (2013). Advanced systems biology methods in drug discovery and translational biomedicine. BioMed Research International, 2013, 742835. https://doi.org/10.1155/2013/742835
   PubMed Web of Science ®Google Scholar