Repurposing FDA-approved drugs as NLRP3 inhibitors against inflammatory diseases: machine learning and molecular simulation approaches

References

• Alturki, N. A., Mashraqi, M. M., Alzamami, A., Alghamdi, Y. S., Alharthi, A. A., Asiri, S. A., Ahmad, S., & Alshamrani, S. (2022). In-silico screening and molecular dynamics simulation of drug bank experimental compounds against SARS-CoV-2. Molecules (Basel, Switzerland), 27(14), 4391. https://doi.org/10.3390/molecules27144391
   PubMed Web of Science ®Google Scholar
• Azzam, K. M., Negim, E. S., & Aboul-Enein, H. Y. (2022). ADME studies of TUG-770 (a GPR-40 inhibitor agonist) for the treatment of type 2 diabetes using SwissADME predictor: In silico study. Journal of Applied Pharmaceutical Science, 12(4), 159–169. https://doi.org/10.7324/JAPS.2022.120418
   Google Scholar
• Basnet, S., Prasad Ghimire, M., Lamichhane, T. R., Adhikari, R., & Adhikari, A. (2023). Identification of potential human pancreatic α-amylase inhibitors from natural products by molecular docking, MM/GBSA calculations, MD simulations, and ADMET analysis. PloS One, 18(3), e0275765. https://doi.org/10.1371/journal.pone.0275765
   PubMed Web of Science ®Google Scholar
• Bockstiegel, J., Wurnig, S. L., Engelhardt, J., Enns, J., Hansen, F. K., & Weindl, G. (2023). Pharmacological inhibition of HDAC6 suppresses NLRP3 inflammasome-mediated IL-1β release. Biochemical Pharmacology, 215, 115693. https://doi.org/10.1016/j.bcp.2023.115693
   PubMed Web of Science ®Google Scholar
• Coll, R. C., Robertson, A. A. B., Chae, J. J., Higgins, S. C., Muñoz-Planillo, R., Inserra, M. C., Vetter, I., Dungan, L. S., Monks, B. G., Stutz, A., Croker, D. E., Butler, M. S., Haneklaus, M., Sutton, C. E., Núñez, G., Latz, E., Kastner, D. L., Mills, K. H. G., Masters, S. L., … O'Neill, L. A. J. (2015). A small-molecule inhibitor of the NLRP3 inflammasome for the treatment of inflammatory diseases. Nature Medicine, 21(3), 248–255. https://doi.org/10.1038/nm.3806
   PubMed Web of Science ®Google Scholar
• Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. https://doi.org/10.1038/srep42717
   PubMed Web of Science ®Google Scholar
• Dekker, C., Mattes, H., Wright, M., Boettcher, A., Hinniger, A., Hughes, N., Kapps-Fouthier, S., Eder, J., Erbel, P., Stiefl, N., Mackay, A., & Farady, C. J. (2021). Crystal structure of NLRP3 NACHT domain with an inhibitor defines mechanism of inflammasome inhibition. Journal of Molecular Biology, 433(24), 167309. https://doi.org/10.1016/j.jmb.2021.167309
   PubMed Web of Science ®Google Scholar
• El-Sayed, S., Freeman, S., & Bryce, R. A. (2022). A selective review and virtual screening analysis of natural product inhibitors of the NLRP3 inflammasome. Molecules (Basel, Switzerland), 27(19), 6213. https://doi.org/10.3390/molecules27196213
   PubMed Web of Science ®Google Scholar
• Foss, F., Horwitz, S. M., Coiffier, B., Bartlett, N., Popplewell, L., Pro, B., Pinter-Brown, L. C., Shustov, A., Furman, R. R., Haioun, C., Koutsoukos, T., & O'Connor, O. A. (2012). Pralatrexate Is an effective treatment for relapsed or refractory transformed mycosis fungoides: A subgroup efficacy analysis from the PROPEL study. Clinical Lymphoma, Myeloma & Leukemia, 12(4), 238–243. https://doi.org/10.1016/j.clml.2012.01.010
   PubMed Web of Science ®Google Scholar
• Frampton, J. E. (2018). Empagliflozin: A review in type 2 diabetes. Drugs, 78(10), 1037–1048. https://doi.org/10.1007/s40265-018-0937-z
   PubMed Web of Science ®Google Scholar
• Galindez, G., Matschinske, J., Rose, T. D., Sadegh, S., Salgado-Albarrán, M., Späth, J., Baumbach, J., & Pauling, J. K. (2021). Lessons from the COVID-19 pandemic for advancing computational drug repurposing strategies. Nature Computational Science, 1(1), 33–41. https://doi.org/10.1038/s43588-020-00007-6
   PubMedGoogle Scholar
• González-Cofrade, L., Cuadrado, I., Amesty, Á., Estévez-Braun, A., de Las Heras, B., & Hortelano, S. (2022). Dehydroisohispanolone as a promising NLRP3 inhibitor agent: Bioevaluation and molecular docking. Pharmaceuticals (Basel, Switzerland), 15(7), 825. https://doi.org/10.3390/ph15070825
   PubMedGoogle Scholar
• Grieb, P., Jünemann, A., Rekas, M., & Rejdak, R. (2016). Citicoline: A food beneficial for patients suffering from or threated with glaucoma. Frontiers in Aging Neuroscience, 8, 73. https://doi.org/10.3389/fnagi.2016.00073
   PubMed Web of Science ®Google Scholar
• Hout, G. P. J. V., & Bosch, L. (2018). The inflammasomes in cardiovascular disease. Experientia Supplementum (2012), 108, 9–40. https://doi.org/10.1007/978-3-319-89390-7_2
   PubMedGoogle Scholar
• Huang, N., Kny, M., Riediger, F., Busch, K., Schmidt, S., Luft, F. C., Slevogt, H., & Fielitz, J. (2017). Deletion of Nlrp3 protects from inflammation-induced skeletal muscle atrophy. Intensive Care Medicine Experimental, 5(1), 3. https://doi.org/10.1186/s40635-016-0115-0
   PubMedGoogle Scholar
• Isyaku, Y., Uzairu, A., & Uba, S. (2020). Computational studies of a series of 2-substituted phenyl-2-oxo-, 2-hydroxyl- and 2-acylloxyethylsulfonamides as potent anti-fungal agents. Heliyon, 6(4), e03724. https://doi.org/10.1016/j.heliyon.2020.e03724
   PubMed Web of Science ®Google Scholar
• John, A., Umashankar, V., Krishnakumar, S., & Deepa, P. R. (2015). Comparative modeling and molecular dynamics simulation of substrate binding in human fatty acid synthase: Enoyl reductase and β-ketoacyl reductase catalytic domains. Genomics & Informatics, 13(1), 15–24. https://doi.org/10.5808/GI.2015.13.1.15
   PubMedGoogle Scholar
• Jones, J., & Taylor, K. (2011). Nicotinamide coenzyme regeneration. Flavin mononucleotide (riboflavin phosphate) as an efficient, economical, and enzyme-compatible recycling agent. Canadian Journal of Chemistry, 54(19), 2969–2973. https://doi.org/10.1139/v76-420
   Google Scholar
• Kar, S., & Leszczynski, J. (2020). Open access in silico tools to predict the ADMET profiling of drug candidates. Expert Opinion on Drug Discovery, 15(12), 1473–1487. https://doi.org/10.1080/17460441.2020.1798926
   PubMed Web of Science ®Google Scholar
• Kaufmann, H. (2017). Droxidopa for symptomatic neurogenic orthostatic hypotension: What can we learn? Clinical Autonomic Research: Official Journal of the Clinical Autonomic Research Society, 27(Suppl 1), 1–3. https://doi.org/10.1007/s10286-017-0426-6
   Google Scholar
• Kelly, K., Azzoli, C. G., Zatloukal, P., Albert, I., Jiang, P. Y. Z., Bodkin, D., Pereira, J. R., Juhász, E., Iannotti, N. O., Weems, G., Koutsoukos, T., & Patel, J. D. (2012). Randomized phase 2b study of pralatrexate versus erlotinib in patients with stage IIIB/IV non-small-cell lung cancer (NSCLC) after failure of prior platinum-based therapy. Journal of Thoracic Oncology: Official Publication of the International Association for the Study of Lung Cancer, 7(6), 1041–1048. https://doi.org/10.1097/JTO.0b013e31824cc66c
   PubMed Web of Science ®Google Scholar
• Kode, J., Maharana, J., Dar, A. A., Mukherjee, S., Gadewal, N., Sigalapalli, D. K., Kumar, S., Panda, D., Ghosh, S., Keshry, S. S., Mamidi, P., Chattopadhyay, S., Pradhan, T., Kailaje, V., Inamdar, S., & Gujjarwar, V. (2022). 6-shogaol exhibits anti-viral and anti-inflammatory activity in COVID-19-associated inflammation by regulating NLRP3 inflammasomes. ACS Omega, 8(2), 2618–2628. https://doi.org/10.1021/acsomega.2c07138
   Web of Science ®Google Scholar
• Kulthinee, S., Yano, N., Zhuang, S., Wang, L., & Zhao, T. C. (2022). Critical functions of histone deacetylases (HDACs) in modulating inflammation associated with cardiovascular diseases. Pathophysiology: The Official Journal of the International Society for Pathophysiology, 29(3), 471–485. https://doi.org/10.3390/pathophysiology29030038
   PubMedGoogle Scholar
• Kumar, A., Rathi, E., & Kini, S. G. (2019). E-pharmacophore modelling, virtual screening, molecular dynamics simulations and in-silico ADME analysis for identification of potential E6 inhibitors against cervical cancer. Journal of Molecular Structure, 1189, 299–306. https://doi.org/10.1016/j.molstruc.2019.04.023
   Web of Science ®Google Scholar
• Kumar, S., Sharma, R., & Roychowdhury, A. (2012). Modulation of cytochrome-P450 inhibition (CYP) in drug discovery: A medicinal chemistry perspective. Current Medicinal Chemistry, 19(21), 3605–3621. https://doi.org/10.2174/092986712801323180
   PubMed Web of Science ®Google Scholar
• Lee, H.-M., Yu, M.-S., Kazmi, S. R., Oh, S. Y., Rhee, K.-H., Bae, M.-A., Lee, B. H., Shin, D.-S., Oh, K.-S., Ceong, H., Lee, D., & Na, D. (2019). Computational determination of HERG-related cardiotoxicity of drug candidates. BMC Bioinformatics, 20(S10), 250. https://doi.org/10.1186/s12859-019-2814-5
   PubMedGoogle Scholar
• Lin, M., Li, L., Li, L., Pokhrel, G., Qi, G., Rong, R., & Zhu, T. (2014). The protective effect of baicalin against renal ischemia-reperfusion injury through inhibition of inflammation and apoptosis. BMC Complementary and Alternative Medicine, 14(1), 19. https://doi.org/10.1186/1472-6882-14-19
   PubMedGoogle Scholar
• Ma, Q. (2023). Pharmacological inhibition of the NLRP3 inflammasome: Structure, molecular activation, and inhibitor-NLRP3 interaction. Pharmacological Reviews, 75(3), 487–520. https://doi.org/10.1124/pharmrev.122.000629
   PubMed Web of Science ®Google Scholar
• Marchi, E., Paoluzzi, L., Scotto, L., Seshan, V. E., Zain, J. M., Zinzani, P. L., & O'Connor, O. A. (2010). Pralatrexate is synergistic with the proteasome inhibitor bortezomib in in vitro and in vivo models of T-cell lymphoid malignancies. Clinical Cancer Research: An Official Journal of the American Association for Cancer Research, 16(14), 3648–3658. https://doi.org/10.1158/1078-0432.CCR-10-0671
   PubMed Web of Science ®Google Scholar
• Mohammed, A. O., Abo-Idrees, M. I., Makki, A. A., Ibraheem, W., & Alzain, A. A. (2022). Drug repurposing against main protease and RNA-dependent RNA polymerase of SARS-CoV-2 using molecular docking, MM-GBSA calculations and molecular dynamics. Structural Chemistry, 33(5), 1553–1567. https://doi.org/10.1007/s11224-022-01999-9
   PubMed Web of Science ®Google Scholar
• Moossavi, M., Parsamanesh, N., Bahrami, A., Atkin, S. L., & Sahebkar, A. (2018). Role of the NLRP3 inflammasome in cancer. Molecular Cancer, 17(1), 158. https://doi.org/10.1186/s12943-018-0900-3
   PubMed Web of Science ®Google Scholar
• Ostacolo, C., Caruso, C., Tronino, D., Troisi, S., Laneri, S., Pacente, L., Del Prete, A., & Sacchi, A. (2013). Enhancement of corneal permeation of riboflavin-5′-phosphate through vitamin E TPGS: a promising approach in corneal trans-epithelial cross linking treatment. International Journal of Pharmaceutics, 440 (2), 148–153. https://doi.org/10.1016/j.ijpharm.2012.09.051
   PubMed Web of Science ®Google Scholar
• Patil, S. M., Manu, G., Shivachandra, J. C., Anil Kumar, K. M., Vigneswaran, J., Ramu, R., Shirahatti, P. S., & Lakshmi Ranganatha, V. (2022). Computational screening of benzophenone integrated derivatives (BIDs) targeting the NACHT domain of the potential target NLRP3 inflammasome. Advances in Cancer Biology - Metastasis, 5, 100056. https://doi.org/10.1016/j.adcanc.2022.100056
   Google Scholar
• Pires, D. E. V., Blundell, T. L., & Ascher, D. B. (2015). PkCSM: Predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. Journal of Medicinal Chemistry, 58(9), 4066–4072. https://doi.org/10.1021/acs.jmedchem.5b00104
   PubMed Web of Science ®Google Scholar
• Pirolli, D., Righino, B., Camponeschi, C., Ria, F., Di Sante, G., & De Rosa, M. C. (2023). Virtual screening and molecular dynamics simulations provide insight into repurposing drugs against SARS-CoV-2 variants spike protein/ACE2 interface. Scientific Reports, 13(1), 1494. https://doi.org/10.1038/s41598-023-28716-8
   PubMed Web of Science ®Google Scholar
• Revuelta, J. L., Ledesma-Amaro, R., Lozano-Martinez, P., Díaz-Fernández, D., Buey, R. M., & Jiménez, A. (2017). Bioproduction of riboflavin: a bright yellow history. Journal of Industrial Microbiology and Biotechnology, 44(4–5), 659–665. https://doi.org/10.1007/s10295-016-1842-7
   PubMed Web of Science ®Google Scholar
• Riva, L., Yuan, S., Yin, X., Martin-Sancho, L., Matsunaga, N., Pache, L., Burgstaller-Muehlbacher, S., De Jesus, P. D., Teriete, P., Hull, M. V., Chang, M. W., Chan, J. F.-W., Cao, J., Poon, V. K.-M., Herbert, K. M., Cheng, K., Nguyen, T.-T H., Rubanov, A., Pu, Y., … Chanda, S. K. (2020). Discovery of SARS-CoV-2 antiviral drugs through large-scale compound repurposing. Nature, 586(7827), 113–119. https://doi.org/10.1038/s41586-020-2577-1
   PubMed Web of Science ®Google Scholar
• Sharma, P. P., Bansal, M., Sethi, A., Pena, L., Goel, V. K., Grishina, M., Chaturvedi, S., Kumar, D., Rathi, B., & Poonam. (2021). Computational methods directed towards drug repurposing for COVID-19: Advantages and limitations. RSC Advances, 11(57), 36181–36198. https://doi.org/10.1039/d1ra05320e
   PubMed Web of Science ®Google Scholar
• Sirotnak, F. M., DeGraw, J. I., Colwell, W. T., & Piper, J. R. (1998). A new analogue of 10-deazaaminopterin with markedly enhanced curative effects against human tumor xenografts in mice. Cancer Chemotherapy and Pharmacology, 42(4), 313–318. https://doi.org/10.1007/s002800050823
   PubMed Web of Science ®Google Scholar
• Sun, D., Gao, W., Hu, H., & Zhou, S. (2022). Why 90% of clinical drug development fails and how to improve it? Acta Pharmaceutica Sinica. B, 12(7), 3049–3062. https://doi.org/10.1016/j.apsb.2022.02.002
   PubMed Web of Science ®Google Scholar
• Tang, Y., Li, X., Yuan, Y., Zhang, H., Zou, Y., Xu, Z., Xu, Q., Song, J., Deng, C., & Wang, Q. (2022). Network pharmacology-based predictions of active components and pharmacological mechanisms of Artemisia Annua L. for the treatment of the novel corona virus disease 2019 (COVID-19). BMC Complementary Medicine and Therapies, 22(1), 56. https://doi.org/10.1186/s12906-022-03523-2
   PubMedGoogle Scholar
• Ullah, S., Rahman, W., Ullah, F., Ullah, A., Jehan, R., Nasir Iqbal, M., Ali, I., & Tianshun, G. (2023). Identification of lead compound screened from the natural products atlas to treat renal inflammasomes using molecular docking and dynamics simulation. Journal of Biomolecular Structure & Dynamics, 1–11. Advance online publication. https://doi.org/10.1080/07391102.2023.2254397
   Google Scholar
• Wang, Z., Hu, W., Lu, C., Ma, Z., Jiang, S., Gu, C., Acuña-Castroviejo, D., & Yang, Y. (2018). Targeting NLRP3 (nucleotide-binding domain, leucine-rich-containing family, pyrin domain-containing-3) inflammasome in cardiovascular disorders. Arteriosclerosis, Thrombosis, and Vascular Biology, 38(12), 2765–2779. https://doi.org/10.1161/ATVBAHA.118.311916
   PubMed Web of Science ®Google Scholar
• Yadav, R., Imran, M., Dhamija, P., Kumar Chaurasia, D., & Handu, S. (2021). Virtual screening, ADMET prediction and dynamics simulation of potential compounds targeting the main protease of SARS-CoV-2. Journal of Biomolecular Structure & Dynamics, 39(17), 6617–6632. https://doi.org/10.1080/07391102.2020.1796812
   PubMed Web of Science ®Google Scholar
• Zahid, A., Li, B., John Kombe Kombe, A., Jin, T., & Tao, J. (2019). Pharmacological inhibitors of the Nlrp3 inflammasome. Frontiers in Immunology, 10, 2538. https://doi.org/10.3389/fimmu.2019.02538
   PubMed Web of Science ®Google Scholar
• Zeng, J., Xie, X., Feng, X.-L., Xu, L., Han, J.-B., Yu, D., Zou, Q.-C., Liu, Q., Li, X., Ma, G., Li, M.-H., & Yao, Y.-G. (2022). Specific inhibition of the NLRP3 inflammasome suppresses immune overactivation and alleviates COVID-19 like pathology in mice. EBioMedicine, 75, 103803. https://doi.org/10.1016/j.ebiom.2021.103803
   PubMed Web of Science ®Google Scholar