Chiến đấu với các đột biến BTK bằng các chất ức chế không đồng hóa trị vượt qua các đột biến Cys481 và Thr474 trong liệu pháp điều trị u tế bào Waldenström: những hiểu biết cơ chế cấu trúc về vai trò của fenebrutinib

Gertz MA (2019) Waldenström macroglobulinemia: 2019 update on diagnosis, risk stratification, and management. Am J Hematol 94(2):266–276 Pal Singh S, Dammeijer F, Hendriks RW (2018) Correction: role of Bruton’s tyrosine kinase in B cells and malignancies. Mol Cancer 17(1):57 Treon SP, Xu L, Yang G et al (2012) MYD88 L265P somatic mutation in Waldenström’s macroglobulinemia. N Engl J Med 367(9):826–833 Cao Y, Hunter ZR, Liu X et al (2015) The WHIM-like CXCR4S338X somatic mutation activates AKT and ERK, and promotes resistance to ibrutinib and other agents used in the treatment of Waldenstrom’s Macroglobulinemia. Leukemia 29(1):169–176 Roccaro AM, Sacco A, Jimenez C et al (2014) C1013G/CXCR4 acts as a driver mutation of tumor progression and modulator of drug resistance in lymphoplasmacytic lymphoma. Blood 123(26):4120–4131 Hunter ZR, Xu L, Yang G et al (2014) The genomic landscape of Waldenström macroglobulinemia is characterized by highly recurring MYD88 and WHIM-like CXCR4 mutations, and small somatic deletions associated with B-cell lymphomagenesis. Blood 123(11):1637–1646 Varettoni M, Arcaini L, Zibellini S et al (2013) Prevalence and clinical significance of the MYD88 (L265P) somatic mutation in Waldenström’s macroglobulinemia and related lymphoid neoplasms. Blood 121(13):2522–2528 Abeykoon JP, Paludo J, King RL et al (2018) MYD88 mutation status does not impact overall survival in Waldenström macroglobulinemia. Am J Hematol 93(2):187–194 Bagratuni T, Ntanasis-Stathopoulos I, Gavriatopoulou M et al (2018) Detection of MYD88 and CXCR4 mutations in cell-free DNA of patients with IgM monoclonal gammopathies. Leukemia 32(12):2617–2625 Smith CIE (2017) Enigmas in tumor resistance to kinase inhibitors and calculation of the drug resistance index for cancer (DRIC). Semin Cancer Biol 45:36–49 Burger JA, Wiestner A (2018) Targeting B cell receptor signalling in cancer: preclinical and clinical advances. Nat Rev Cancer 18(3):148–167 Herman SEM, Gordon AL, Hertlein E et al (2011) Bruton tyrosine kinase represents a promising therapeutic target for treatment of chronic lymphocytic leukemia and is effectively targeted by PCI-32765. Blood 117(23):6287–6296 Smith CIE (2017) From identification of the BTK kinase to effective management of leukemia. Oncogene 36(15):2045–2053 Lucas F, Woyach JA (2019) Inhibiting Bruton’s tyrosine kinase in CLL and other B-cell malignancies. Target Oncol 14(2):125–138 Treon SP, Gustine J, Meid K et al (2018) Ibrutinib monotherapy in symptomatic, treatment-naïve patients with Waldenström macroglobulinemia. J Clin Oncol 36(27):2755–2761 Charalambous A, Schwarzbich M-A, Witzens-Harig M (2018) Ibrutinib. Recent Results Cancer Res 133–168 Furman RR, Cheng S, Lu P et al (2014) Ibrutinib resistance in chronic lymphocytic leukemia. N Engl J Med 370(24):2352–2354 Woyach JA, Ruppert AS, Guinn D et al (2017) BTK C481S -Mediated resistance to ibrutinib in chronic lymphocytic leukemia. J Clin Oncol 35(13):1437–1443 Johnson AR, Kohli PB, Katewa A et al (2016) Battling Btk mutants with noncovalent inhibitors that overcome Cys481 and Thr474 mutations. ACS Chem Biol 11(10):2897–2907 Reiff SD, Muhowski EM, Guinn D et al (2018) Noncovalent inhibition of C481S Bruton tyrosine kinase by GDC-0853: a new treatment strategy for ibrutinib-resistant CLL. Blood 132(10):1039–1049 Crawford JJ, Johnson AR, Misner DL et al (2018) Discovery of GDC-0853: a potent, selective, and noncovalent Bruton’s tyrosine kinase inhibitor in early clinical development. J Med Chem 61(6):2227–2245 Kohrt HE, Sagiv-Barfi I, Rafiq S et al (2014) Ibrutinib antagonizes rituximab-dependent NK cell–mediated cytotoxicity. Blood 123(12):1957–1960 Herman AE, Chinn LW, Kotwal SG et al (2018) Safety, pharmacokinetics, and pharmacodynamics in healthy volunteers treated with GDC-0853, a selective reversible Bruton’s tyrosine kinase inhibitor. Clin Pharmacol Ther 103(6):1020–1028 Estupiñán HY, Wang Q, Berglöf A et al (2021) BTK gatekeeper residue variation combined with cysteine 481 substitution causes super-resistance to irreversible inhibitors acalabrutinib, ibrutinib and zanubrutinib. Leukemia 35(5):1317–1329 Usha T, Shanmugarajan D, Goyal AK, Kumar CS, Middha SK (2018) Recent updates on computer-aided drug discovery: time for a paradigm shift. Curr Top Med Chem 17(30):3296–3307 Berman HM, Battistuz T, Bhat TN et al (2002) The protein data bank. Acta Crystallogr D Biol Crystallogr 58(6):899–907 Pettersen EF, Goddard TD, Huang CC et al (2004) UCSF Chimera - a visualization system for exploratory research and analysis. J Comput Chem 25(13):1605–1612 Kusumaningrum S, Budianto E, Kosela S, Sumaryono W, Juniarti F (2014) The molecular docking of 1,4-naphthoquinone derivatives as inhibitors of Polo-like kinase 1 using Molegro Virtual Docker. J Appl Pharm Sci 4(11):47–53 Thomsen R, Christensen MH (2006) MolDock: a new technique for high-accuracy molecular docking. J Med Chem 49(11):3315–3321 Dunbrack RL (2002) Rotamer libraries in the 21st century. Curr Opin Struct Biol 12(4):431–440 Allouche A (2012) Software news and updates Gabedit — a graphical user interface for computational chemistry softwares. J Comput Chem 32:174–182 Trott O, Olson A (2010) Autodock vina: improving the speed and accuracy of docking. J Comput Chem 31(2):455–461 Sastry GM, Adzhigirey M, Day T, Annabhimoju R, Sherman W (2013) Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. J Comput Aided Mol Des 27(3):221–234 Mhlongo NN, Ebrahim M, Skelton AA, Kruger HG, Williams IH, Soliman MES (2015) Dynamics of the thumb-finger regions in a GH11 xylanase Bacillus circulans: comparison between the Michaelis and covalent intermediate. RSC Adv 5(100):82381–82394 Ramharack P, Oguntade S, Soliman MES (2017) Delving into Zika virus structural dynamics-a closer look at NS3 helicase loop flexibility and its role in drug discovery. RSC Adv 7(36):22133–22144 Case DA, Walker RC, Cheatham TE et al (2018) Amber 2018. University of California, San Francisco 2018:1–923 Wang J, Wolf RM, Caldwell JW, Kollman PA, Case DA (2004) Development and testing of a general amber force field. J Comput Chem 25(9):1157–1174 Grest GS, Kremer K (1986) Molecular dynamics simulation for polymers in the presence of a heat bath. Phys Rev A (Coll Park) 33(5):3628–3631 Berendsen HJC, Postma JPM, van Gunsteren WF, DiNola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81(8):3684–3690 Ryckaert J-P, Ciccotti G, Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes. J Comput Phys 23(3):327–341 Roe DR, Cheatham TE (2013) PTRAJ and CPPTRAJ: software for processing and analysis of molecular dynamics trajectory data. J Chem Theory Comput 9(7):3084–3095 Seifert E (2014) OriginPro 9.1: scientific data analysis and graphing software - software review. J Chem Inf Model 54(5):1552 Abdullahi M, Olotu FA, Soliman ME (2017) Dynamics of allosteric modulation of lymphocyte function associated antigen-1 closure-open switch: unveiling the structural mechanisms associated with outside-in signaling activation. Biotechnol Lett 39(12):1843–1851 Olotu FA, Soliman MES (2018) From mutational inactivation to aberrant gain-of-function: unraveling the structural basis of mutant p53 oncogenic transition. J Cell Biochem 119(3):2646–2652 Hou T, Wang J, Li Y, Wang W (2011) Assessing the performance of the MM/PBSA and MM/GBSA methods 1 The accuracy of binding free energy calculations based on molecular dynamics simulations. J Chem Inf Model 51(1):69–82 Homeyer N, Gohlke H (2012) Free energy calculations by the molecular mechanics Poisson−Boltzmann surface area method. Mol Inform 31(2):114–122 Mukherjee J, Gupta MN (2015) Increasing importance of protein flexibility in designing biocatalytic processes. Biotechnology Reports 6:119–123 Xie Y, An J, Yang G et al (2014) enhanced enzyme kinetic stability by increasing rigidity within the active site. J Biol Chem 289(11):7994–8006 Celej MS, Montich GG, Fidelio GD (2003) Protein stability induced by ligand binding correlates with changes in protein flexibility. Protein Sci 12(7):1496–1506 Liu K, Kokubo H (2017) Exploring the stability of ligand binding modes to proteins by molecular dynamics simulations: a cross-docking study. J Chem Inf Model 57(10):2514–2522 Agoni C, Salifu EY, Munsamy G, Olotu FA, Soliman M (2019) CF 3 -Pyridinyl substitution on antimalarial therapeutics: probing differential ligand binding and dynamical inhibitory effects of a novel triazolopyrimidine-based inhibitor on plasmodium falciparum dihydroorotate dehydrogenase. Chem Biodivers 16(12):e1900365 Genheden S, Ryde U (2015) The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opin Drug Discov 10(5):449–461 Zhang C, Feng L-J, Huang Y et al (2017) Discovery of novel phosphodiesterase-2a inhibitors by structure-based virtual screening, structural optimization, and bioassay. J Chem Inf Model 57(2):355–364 Kumalo HM, Soliman ME (2016) Per-residue energy footprints-based pharmacophore modeling as an enhanced in silico approach in drug discovery: a case study on the identification of novel β-secretase1 (BACE1) inhibitors as anti-Alzheimer agents. Cell Mol Bioeng 9(1):175–189 Patil R, Das S, Stanley A, Yadav L, Sudhakar A, Varma AK (2010) Optimized hydrophobic interactions and hydrogen bonding at the target-ligand interface leads the pathways of drug-designing. PLoS ONE 5(8):e12029 Azeyedo WD Jr (2010) MolDock applied to structure-based virtual screening. Curr Drug Targets 11(3):327–334 Wang S, Mondal S, Zhao C et al (2019) Noncovalent inhibitors reveal BTK gatekeeper and auto-inhibitory residues that control its transforming activity. JCI Insight 4(12):e127566 Salifu EY, Agoni C, Olotu FA, Dokurugu YM, Soliman MES (2019) Halting ionic shuttle to disrupt the synthetic machinery—structural and molecular insights into the inhibitory roles of bedaquiline towards Mycobacterium tuberculosis ATP synthase in the treatment of tuberculosis. J Cell Biochem 120(9):16108–16119 Karshikoff A, Nilsson L, Ladenstein R (2015) Rigidity versus flexibility: the dilemma of understanding protein thermal stability. FEBS J 282(20):3899–3917 Pitera JW (2014) Expected distributions of root-mean-square positional deviations in proteins. J Phys Chem B 118(24):6526–6530 Agoni C, Ramharack P, Munsamy G, Soliman MES (2020) Human rhinovirus inhibition through capsid “canyon” perturbation: structural insights into the role of a novel benzothiophene derivative. Cell Biochem Biophys 78(1):3–13 Agoni C, Ramharack P, Salifu EY, Soliman MES (2020) The dual-targeting activity of the metabolite substrate of para-amino salicyclic acid in the mycobacterial folate pathway: atomistic and structural perspectives. Protein J 39(2):106–117 Lobanov MYu, Bogatyreva NS, Galzitskaya O, v. (2008) Radius of gyration as an indicator of protein structure compactness. Mol Biol 42(4):623–628 Salleh AB, Rahim ASMA, Rahman RNZRA, Rahman TC, Leow MB (2012) The role of Arg157Ser in improving the compactness and stability of ARM lipase. J Comput Sci Syst Biol 5(2):38–46 Agoni C, Ramharack P, Soliman ME (2018) Co-inhibition as a strategic therapeutic approach to overcome rifampin resistance in tuberculosis therapy: atomistic insights. Future Med Chem 10(14):1665–1675