Tanahashi N, Murakami Y, Minami Y, Shimbara N, Hendil KB, Tanaka K.Hybrid proteasomes: induction by interferon-γ and contribution to ATP-dependent proteolysis. J Biol Chem. 2000;275:14336–45. [DOI] [PubMed]
Voges D, Zwickl P, Baumeister W.The 26S proteasome: a molecular machine designed for controlled proteolysis. Annu Rev Biochem. 1999;68:1015–68. [DOI] [PubMed]
Hölzl H, Kapelari B, Kellermann J, Seemüller E, Sümegi M, Udvardy A, et al. The regulatory complex of Drosophila melanogaster 26s proteasomes. Subunit composition and localization of a deubiquitylating enzyme. J Cell Biol. 2000;150:119–30. [DOI] [PubMed] [PMC]
Hough R, Pratt G, Rechsteiner M.Purification of two high molecular weight proteases from rabbit reticulocyte lysate. J Biol Chem. 1987;262:8303–13. [DOI] [PubMed]
Inobe T, Genmei R.N-Terminal coiled-coil structure of ATPase subunits of 26S proteasome is crucial for proteasome function. PLoS One. 2015;10:e0134056. [DOI] [PubMed] [PMC]
Bard JAM, Goodall EA, Greene ER, Jonsson E, Dong KC, Martin A.Structure and function of the 26S proteasome. Annu Rev Biochem. 2018;87:697–724. [DOI] [PubMed] [PMC]
Adams J.The development of proteasome inhibitors as anticancer drugs. Cancer Cell. 2004;5:417–21. [DOI] [PubMed]
Chen L, Madura F.Increased proteasome activity, ubiquitin-conjugating enzymes, and eEF1A translation factor detected in breast cancer tissue. Cancer Res. 2005;65:5599–606. [DOI] [PubMed]
Voutsadakis IA.Proteasome expression and activity in cancer and cancer stem cells. Tumor Biol. 2017;39:1010428317692248. [DOI] [PubMed]
Bilalis AG, Papadimitriou K, Pouli A, Papanastasiou K, Tsakanikas S, Stefanitsi P, et al. Bortezomib in multiple myeloma: treatment and retreatment. A single center experience. Blood. 2007;110:4819. [DOI]
Kortuem KM, Stewart AK.Carfilzomib. Blood. 2013;121:893–7. [DOI] [PubMed]
Richardson PG, Zweegman S, O’Donnell EK, Laubach JP, Raje N, Voorhees P, et al. Ixazomib for the treatment of multiple myeloma. Expert Opin Pharmacother. 2018;19:1949–68. [DOI] [PubMed]
Borissenko L, Groll M.20S proteasome and its inhibitors: crystallographic knowledge for drug development. Chem Rev. 2007;107:687–717. [DOI] [PubMed]
Löwe J, Stock D, Jap B, Zwickl P, Baumeister W, Huber R.Crystal structure of the 20S proteasome from the archaeon T. acidophilum at 3.4 Å resolution. Science. 1995;268:533–9. [DOI] [PubMed]
Prudhomme J, McDaniel E, Ponts N, Bertani S, Fenical W, Jensen P, et al. Marine actinomycetes: a new source of compounds against the human malaria parasite. PLoS One. 2008;3:e2335. [DOI] [PubMed] [PMC]
Lin G, Li D, de Carvalho LP, Deng H, Tao H, Vogt G, et al. Inhibitors selective for mycobacterial versus human proteasomes. Nature. 2009;461:621–6. [DOI] [PubMed] [PMC]
Zhou J, Chng WJ.Novel mechanism of drug resistance to proteasome inhibitors in multiple myeloma. World J Clin Oncol. 2019;10:303–6. [DOI] [PubMed] [PMC]
Maccari R, Ettari R, Adornato I, Naß A, Wolber G, Bitto A, et al. Identification of 2-thioxoimidazolidin-4- one derivatives as novel noncovalent proteasome and immunoproteasome inhibitors. Bioorg Med Chem Lett. 2018;28:278–83. [DOI] [PubMed]
McDaniel TJ, Lansdell TA, Dissanayake AA, Azevedo LM, Claes J, Odom AL, et al. Substituted quinolines as noncovalent proteasome inhibitors. Bioorg Med Chem. 2016;24:2441–50. [DOI] [PubMed] [PMC]
Yu J, Xu L, Hong D, Zhang X, Liu J, Li D, et al. Design, synthesis, and biological evaluation of novel phenol ether derivatives as non-covalent proteasome inhibitors. Eur J Med Chem. 2019;161:543–58. [DOI] [PubMed]
Pandey S, Singh BK.De-novo drug design, molecular docking and in-silico molecular prediction of AChEI analogues through CADD approaches as anti-Alzheimer’s agents. Curr Comput Aided Drug Des. 2020;16:54–72. [DOI] [PubMed] [PMC]
Xu K, Wang K, Yang Y, Yan DA, Huang L, Chen CH, et al. Discovery of novel non-covalent inhibitors selective to the β5-subunit of the human 20S proteasome. Eur J Med Chem. 2015;98:61–8. [DOI] [PubMed]
Li A, Sun H, Du L, Wu X, Cao J, You Q, et al. Discovery of novel covalent proteasome inhibitors through a combination of pharmacophore screening, covalent docking, and molecular dynamics simulations. J Mol Model. 2014;20:2515. [DOI] [PubMed]
Yuan MA, Cheng P, Zhang SP.Structure-activity relationship analysis of a series of nonsteroidal analogues as androgen receptor antagonists. New J Chem. 2021;45:1176–86. [DOI]
Clark M, Cramer RD III, Van Opdenbosch N.Validation of the general purpose tripos 5.2 force field. J Comput Chem. 1989;10:982–1012. [DOI]
Gasteiger J, Marsili M.Iterative partial equalization of orbital electronegativity—a rapid access to atomic charges. Tetrahedron. 1980;36:3219–28. [DOI]
Klebe G, Abraham U, Mietzner T.Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J Med Chem. 1994;37:4130–46. [DOI] [PubMed]
Zhang Z, Cheng P, Zhu Y, Xia Q, Zhang S.3D-QSAR analysis of a series of 1,2,3-triazole-chromenone derivatives as an acetylcholinesterase inhibitor against Alzheimer’s disease. Chin J Struc Chem. 2020;39:1235–42. [DOI]
Cho SJ, Tropsha A.Cross-validated R2-guided region selection for comparative molecular field analysis: a simple method to achieve consistent results. J Med Chem. 1995;38:1060–6. [DOI] [PubMed]
Wang J, Yang Y, Li Y, Wang Y.Computational study exploring the interaction mechanism of benzimidazole derivatives as potent cattle bovine viral diarrhea virus inhibitors. J Agric Food Chem. 2016;64:5941–50. [DOI] [PubMed]
Gao Y, Chen Y, Tian Y, Zhao Y, Wu F, Luo X, et al. In silico study of 3-hydroxypyrimidine-2,4-diones as inhibitors of HIV RT-associated RNase H using molecular docking, molecular dynamics, 3D-QSAR, and pharmacophore models. New J Chem. 2019;43:17004–17. [DOI]
Mercado J, Gómez H, Vivas-Reyes R.Comparative molecular field analysis and comparative molecular similarity indices analysis studies of α-ketothiazole arginine analogues inhibitors of coagulation factor XIa. New J Chem. 2011;35:820–32. [DOI]
Han W, Li J.Structure-activity relationship analysis of 3-phenylpyrazole derivatives as androgen receptor antagonists. J Biomol Struct Dyn. 2020;38:2582–91. [DOI] [PubMed]
Ståhle L, Wold S.6 Multivariate data analysis and experimental design in biomedical research. Prog Med Chem. 1988;25:291–338. [DOI] [PubMed]
Good AC, Peterson SJ, Richards WG.QSAR’s from similarity matrices. Technique validation and application in the comparison of different similarity evaluation methods. J Med Chem. 1993;36:2929–37. [DOI] [PubMed]
Balasubramanian PK, Balupuri A, Gadhe CG, Cho SJ.3D QSAR modeling study on 7-aminofuro [2,3-c] pyridine derivatives as TAK1 inhibitors using CoMFA and COMSIA. Med Chem Res. 2015;24:2347–65. [DOI]
Wold S.Validation of QSAR’s. Quant Struc Act Rel. 1991;10:191–3. [DOI]
Cao D, Deng Z, Zhu M, Yao Z, Dong J, Zhao R.Ensemble partial least squares regression for descriptor selection, outlier detection, applicability domain assessment, and ensemble modeling in QSAR/QSPR modeling. J Chemom. 2017;31:e2922. [DOI]
Kim JH, Jeong JH.Structure-activity relationship studies based on 3D-QSAR CoMFA/CoMSIA for thieno-pyrimidine derivatives as triple negative breast cancer inhibitors. Molecules. 2022;27:7974. [DOI] [PubMed] [PMC]
Hadni H, Elhallaoui M.3D-QSAR, docking and ADMET properties of aurone analogues as antimalarial agents. Heliyon. 2020;6:e03580. [DOI] [PubMed] [PMC]
Roy PP, Paul S, Mitra I, Roy K.On two novel parameters for validation of predictive QSAR models. Molecules. 2009;14:1660–701. [DOI] [PubMed] [PMC]
Mitra I, Roy PP, Kar S, Ojha PK, Roy K.On further application of rm2 as a metric for validation of QSAR models. J Chemom. 2010;24:22–33. [DOI]
Ferreira LG, Dos Santos RN, Oliva G, Andricopulo AD.Molecular docking and structure-based drug design strategies. Molecules. 2015;20:13384–421. [DOI] [PubMed] [PMC]
Jones G, Willett P, Glen RC, Leach AR, Taylor R.Development and validation of a genetic algorithm for flexible docking. J Mol Biol. 1997;267:727–48. [DOI] [PubMed]
Eberhardt J, Santos-Martins D, Tillack AF, Forli S.AutoDock Vina 1.2.0: new docking methods, expanded force field, and python bindings. J Chem Inf Model. 2021;61:3891–8. [DOI] [PubMed] [PMC]
Yang X, Liu H, Liu J, Li F, Li X, Shi L, et al. Rational selection of the 3D structure of biomacromolecules for molecular docking studies on the mechanism of endocrine disruptor action. Chem Res Toxicol. 2016;29:1565–70. [DOI] [PubMed]
Blackburn C, Gigstad Kenneth M, Hales P, Garcia K, Jones M, Bruzzese Frank J, et al. Characterization of a new series of non-covalent proteasome inhibitors with exquisite potency and selectivity for the 20S β5-subunit. Biochem J. 2010;430:461–76. Erratum in: Biochem J. 2010;431:433. [DOI] [PubMed] [PMC]
Solis FJ, Wets RJB.Minimization by random search techniques. Math Oper Res. 1981;6:19–30. [DOI]
Waring MJ, Arrowsmith J, Leach AR, Leeson PD, Mandrell S, Owen RM, et al. An analysis of the attrition of drug candidates from four major pharmaceutical companies. Nat Rev Drug Discov. 2015;14:475–86. [DOI] [PubMed]
Sun D, Gao W, Hu H, Zhou S.Why 90% of clinical drug development fails and how to improve it?Acta Pharm Sin B. 2022;12:3049–62. [DOI] [PubMed] [PMC]
Ferreira LLG, Andricopulo AD.ADMET modeling approaches in drug discovery. Drug Discov Today. 2019;24:1157–65. [DOI] [PubMed]
Pires DE, Blundell TL, Ascher DB.pkCSM: predicting small-molecule pharmacokinetic and toxicity properties using graph-based signatures. J Med Chem. 2015;58:4066–72. [DOI] [PubMed] [PMC]
Daina A, Michielin O, Zoete V.SwissADME: a free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Sci Rep. 2017;7:42717. [DOI] [PubMed] [PMC]
Vidal-Limon A, Aguilar-Toalá JE, Liceaga AM.Integration of molecular docking analysis and molecular dynamics simulations for studying food proteins and bioactive peptides. J Agric Food Chem. 2022;70:934–43. [DOI] [PubMed]
Li Z, Zou CB, Yao Y, Hoyt MA, McDonough S, Mackey ZB, et al. An easily dissociated 26 S proteasome catalyzes an essential ubiquitin-mediated protein degradation pathway in Trypanosoma brucei*210. J Biol Chem. 2002;277:15486–98. [DOI] [PubMed]
Groll M, Ditzel L, Löwe J, Stock D, Bochtler M, Bartunik HD, et al. Structure of 20S proteasome from yeast at 2.4Å resolution. Nature. 1997;386:463–71. [DOI] [PubMed]
Gaczynska M, Osmulski PA.Characterization of noncompetitive regulators of proteasome activity. Methods Enzymol. 2005;398:425–38. [DOI] [PubMed]
Anbanandam A, Albarado DC, Tirziu DC, Simons M, Veeraraghavan S.Molecular basis for proline- and arginine-rich peptide inhibition of proteasome. J Mol Biol. 2008;384:219–27. [DOI] [PubMed] [PMC]
Chitra S, Nalini G, Rajasekhar G.The ubiquitin proteasome system and efficacy of proteasome inhibitors in diseases. Int J Rheum Dis. 2012;15:249–60. [DOI] [PubMed]