Basak S, Li Y, Tao S, Daryaee F, Merino J, Gu C, Delker SL, Phan JN, Edwards TE, Walker SG, Tonge PJ (2022) Structure–kinetic relationship studies for the development of long residence time LpxC inhibitors. J Med Chem 65:11854–11875. https://doi.org/10.1021/acs.jmedchem.2c00974
Byeon IJ, Meng X, Jung J, Zhao G, Yang R, Ahn J, Shi J, Concel J, Aiken C, Zhang P, Gronenborn AM (2009) Structural convergence between cryo-EM and NMR reveals intersubunit interactions critical for HIV-1 capsid function. Cell 139:780–790. https://doi.org/10.1016/j.cell.2009.10.010
Claridge T (2009) Software review of MNova: NMR data processing, analysis, and prediction software. J Chem Inf Model 49:1136–1137. https://doi.org/10.1021/ci900090d
Copeland RA, Pompliano DL, Meek TD (2006) Drug–target residence time and its implications for lead optimization. Nat Rev Drug Discovery 5:730–739. https://doi.org/10.1038/nrd2082
Danielsson J, Mu X, Lang L, Wang H, Binolfi A, Theillet FX, Bekei B, Logan DT, Selenko P, Wennerström H, Oliveberg M (2015) Thermodynamics of protein destabilization in live cells. Proc Natl Acad Sci U S A 112:12402–12407. https://doi.org/10.1073/pnas.1511308112
Davis CM, Gruebele M (2021) Cellular sticking can strongly reduce complex binding by speeding dissociation. J Phys Chem B 125:3815–3823. https://doi.org/10.1021/acs.jpcb.1c00950
Davis DG, Perlman ME, London RE (1994) Direct measurements of the Dissociation-Rate constant for Inhibitor-Enzyme complexes via the T1ρ and T2 (CPMG) methods. J Magn Reson Ser B 104:266–275. https://doi.org/10.1006/jmrb.1994.1084
Fanghänel J, Fischer G (2002) Thermodynamic characterization of the interaction of human Cyclophilin 18 with cyclosporin A. Biophys Chem 100:351–366. https://doi.org/10.1016/S0301-4622(02)00292-2
Freeman R, Hill HDW (1971) Fourier transform study of NMR spin–lattice relaxation by progressive saturation. J Chem Phys 54:3367–3377. https://doi.org/10.1063/1.1675352
Article ADS MATH Google Scholar
Gaither LA, Borawski J, Anderson LJ, Balabanis KA, Devay P, Joberty G, Rau C, Schirle M, Bouwmeester T, Mickanin C, Zhao S, Vickers C, Lee L, Deng G, Baryza J, Fujimoto RA, Lin K, Compton T, Wiedmann B (2010) Multiple cyclophilins involved in different cellular pathways mediate HCV replication. Virology 397:43–55. https://doi.org/10.1016/j.virol.2009.10.043
Gebre ST, Cameron SA, Li L, Babu YS, Schramm VL (2017) Intracellular rebinding of transition-state analogues provides extended in vivo Inhibition lifetimes on human purine nucleoside phosphorylase. J Biol Chem 292:15907–15915. https://doi.org/10.1074/jbc.M117.801779
Guo D, Mulder-Krieger T, IJzerman AP, Heitman LH (2012) Functional efficacy of adenosine A2a receptor agonists is positively correlated to their receptor residence time. Br J Pharmacol 166:1846–1859. https://doi.org/10.1111/j.1476-5381.2012.01897.x
Husi H, Zurini MGM (1994) Comparative binding studies of cyclophilins to cyclosporine A and derivatives by fluorescence measurements. Anal Biochem 222:251–255. https://doi.org/10.1006/abio.1994.1481
Jackson JC, Hammill JT, Mehl RA (2007) Site-specific incorporation of a 19F-amino acid into proteins as an NMR probe for characterizing protein structure and reactivity. J Am Chem Soc 129:1160–1166. https://doi.org/10.1021/ja064661t
Jarmoskaite I, AlSadhan I, Vaidyanathan PP, Herschlag D (2020) How to measure and evaluate binding affinities. eLife 9:e57264. https://doi.org/10.7554/eLife.57264
Lin W, Quintero A, Zhang Y (2016) Conformational heterogeneity of cyclosporin A in Cyclophilin 18 binding. PLoS ONE 11:e0153669. https://doi.org/10.1371/journal.pone.0153669
Lu H, Tonge PJ (2010) Drug–target residence time: critical information for lead optimization. Curr Opin Chem Biol 14:467–474. https://doi.org/10.1016/j.cbpa.2010.06.176
Lu H, England K, am Ende C, Truglio JJ, Luckner S, Reddy BG, Marlenee NL, Knudson SE, Knudson DL, Bowen RA, Kisker C, Slayden RA, Tonge PJ (2009) Slow-onset Inhibition of the FabI Enoyl reductase from Francisella tularensis: residence time and in vivo activity. ACS Chem Biol 4:221–231. https://doi.org/10.1021/cb800306y
Lu H, Iuliano JN, Tonge PJ (2018) Structure–kinetic relationships that control the residence time of drug–target complexes: insights from molecular structure and dynamics. Curr Opin Chem Biol 44:101–109. https://doi.org/10.1016/j.cbpa.2018.06.002
Lu M, Ishima R, Polenova T, Gronenborn AM (2019) 19F NMR relaxation studies of fluorosubstituted Tryptophans. J Biomol NMR 73:401–409. https://doi.org/10.1007/s10858-019-00268-y
Luchinat E, Barbieri L, Cremonini M, Nocentini A, Supuran CT, Banci L (2020a) Intracellular binding/unbinding kinetics of approved drugs to carbonic anhydrase II observed by in-cell NMR. ACS Chem Biol 15:2792–2800. https://doi.org/10.1021/acschembio.0c00590
Luchinat E, Barbieri L, Cremonini M, Nocentini A, Supuran CT, Banci L (2020b) Drug screening in human cells by NMR spectroscopy allows the early assessment of drug potency. Angew Chem Int Ed 59:6535–6539. https://doi.org/10.1002/anie.201913436
Luchinat E, Barbieri L, Davis B, Brough PA, Pennestri M, Banci L (2024) Ligand-Based competition binding by Real-Time 19F NMR in human cells. J Med Chem 67:1115–1126. https://doi.org/10.1021/acs.jmedchem.3c01600
Maschera B, Darby G, Palú G, Wright LL, Tisdale M, Myers R, Blair ED, Furfine ES (1996) Human immunodeficiency virus: mutations in the viral protease that confer resistance to saquinavir increase the dissociation rate constant of the protease-saquinavir complex. J Biol Chem 271:33231–33235. https://doi.org/10.1074/jbc.271.52.33231
Moschen T, Grutsch S, Juen MA, Wunderlich CH, Kreutz C, Tollinger M (2016) Measurement of Ligand–Target residence times by 1H relaxation dispersion NMR spectroscopy. J Med Chem 59:10788–10793. https://doi.org/10.1021/acs.jmedchem.6b01110
Niklasson M, Otten R, Ahlner A, Andresen C, Schlagnitweit J, Petzold K, Lundström P (2017) Comprehensive analysis of NMR data using advanced line shape fitting. J Biomol NMR 69:93–99. https://doi.org/10.1007/s10858-017-0141-6
Nishizawa M, Walinda E, Morimoto D, Kohn B, Scheler U, Shirakawa M, Sugase K (2021) Effects of weak nonspecific interactions with ATP on proteins. J Am Chem Soc 143:11982–11993. https://doi.org/10.1021/jacs.0c13118
Papaneophytou CP, Grigoroudis AI, McInnes C, Kontopidis G (2014) Quantification of the effects of ionic strength, viscosity, and hydrophobicity on protein–ligand binding affinity. ACS Med Chem Lett 5:931–936. https://doi.org/10.1021/ml500204e
Phillip Y, Kiss V, Schreiber G (2012) Protein-binding dynamics imaged in a living cell. Proc Natl Acad Sci U S A 109:1461–1466. https://doi.org/10.1073/pnas.1112171109
Article ADS MATH Google Scholar
Robers MB, Dart ML, Woodroofe CC, Zimprich CA, Kirkland TA, Machleidt T, Kupcho KR, Levin S, Hartnett JR, Zimmerman K, Niles AL, Ohana RF, Daniels DL, Slater M, Wood MG, Cong M, Cheng YQ, Wood KV (2015) Target engagement and drug residence time can be observed in living cells with BRET. Nat Commun 6:10091. https://doi.org/10.1038/ncomms10091
Sakakibara D, Sasaki A, Ikeya T, Hamatsu J, Hanashima T, Mishima M, Yoshimasu M, Hayashi N, Mikawa T, Wälchli M, Smith BO, Shirakawa M, Güntert P, Ito Y (2009) Protein structure determination in living cells by in-cell NMR spectroscopy. Nature 458:102–105. https://doi.org/10.1038/nature07814
Shuman CF, Markgren PO, Hämäläinen M, Danielson UH (2003) Elucidation of HIV-1 protease resistance by characterization of interaction kinetics between inhibitors and enzyme variants. Antiviral Res 58:235–242. https://doi.org/10.1016/S0166-3542(03)00002-0
Song X, Lv T, Chen J, Wang J, Yao L (2019) Characterization of residue specific protein folding and unfolding dynamics in cells. J Am Chem Soc 141:11363–11366. https://doi.org/10.1021/jacs.9b04435
Spagnuolo LA, Eltschkner S, Yu W, Daryaee F, Davoodi S, Knudson SE, Allen EKH, Merino J, Pschibul A, Moree B, Thivalapill N, Truglio JJ, Salafsky J, Slayden RA, Kisker C, Tonge PJ (2017) Evaluating the contribution of transition-state destabilization to changes in the residence time of triazole-based InhA inhibitors. J Am Chem Soc 139:3417–3429. https://doi.org/10.1021/jacs.6b11148
Speer SL, Zheng W, Jiang X, Chu IT, Guseman AJ, Liu M, Pielak GJ, Li C (2021) The intracellular environment affects protein–protein interactions. Proc Natl Acad Sci U S A 118:e2019918118. https://doi.org/10.1073/pnas.2019918118
Comments (0)