A biophysical framework for double- drugging kinases

被引:11
作者
Kim, Chansik [1 ,2 ,3 ]
Ludewig, Hannes [1 ,2 ,4 ]
Hadzipasic, Adelajda [1 ,2 ]
Kutter, Steffen [1 ,2 ,5 ]
Nguyen, Vy [1 ,2 ,6 ]
Kern, Dorothee [1 ,2 ]
机构
[1] Brandeis Univ, Dept Biochem, Waltham, MA 02454 USA
[2] Brandeis Univ, HHMI, Waltham, MA 02454 USA
[3] NoveltyNobility, Seongnam 13477, Gyeonggi Do, South Korea
[4] Novartis Inst Biomed Res Inc, Oncol Drug Discovery, Cambridge, MA 02139 USA
[5] Schrodinger Inc, Natick, MA 01760 USA
[6] Relay Therapeut, Cambridge, MA 02139 USA
关键词
kinase; conformational equilibrium; cooperativity; double-drugging; STRUCTURAL BASIS; ATP-SITE; ABL; INHIBITOR; AURORA; ACTIVATION; ASCIMINIB; BINDING; SELECTIVITY; RESISTANCE;
D O I
10.1073/pnas.2304611120
中图分类号
O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];
学科分类号
07 ; 0710 ; 09 ;
摘要
Selective orthosteric inhibition of kinases has been challenging due to the conserved active site architecture of kinases and emergence of resistance mutants. Simultaneous inhibition of distant orthosteric and allosteric sites, which we refer to as "double-drugging", has recently been shown to be effective in overcoming drug resistance. However, detailed biophysical characterization of the cooperative nature between orthosteric and allosteric modulators has not been undertaken. Here, we provide a quantitative framework for double-drugging of kinases employing isothermal titration calorimetry, Forster resonance energy transfer, coupled-enzyme assays, and X -ray crystallography. We discern positive and negative cooperativity for Aurora A kinase (AurA) and Abelson kinase (Abl) with different combinations of orthosteric and allosteric modulators. We find that a confor-mational equilibrium shift is the main principle governing cooperativity. Notably, for both kinases, we find a synergistic decrease of the required orthosteric and allosteric drug dosages when used in combination to inhibit kinase activities to clinically relevant inhibition levels. X -ray crystal structures of the double-drugged kinase complexes reveal the molecular principles underlying the cooperative nature of double-drugging AurA and Abl with orthosteric and allosteric inhibitors. Finally, we observe a fully closed confor-mation of Abl when bound to a pair of positively cooperative orthosteric and allosteric modulators, shedding light on the puzzling abnormality of previously solved closed Abl structures. Collectively, our data provide mechanistic and structural insights into rational design and evaluation of double-drugging strategies.
引用
收藏
页数:11
相关论文
共 73 条
[1]   PHENIX: a comprehensive Python']Python-based system for macromolecular structure solution [J].
Adams, Paul D. ;
Afonine, Pavel V. ;
Bunkoczi, Gabor ;
Chen, Vincent B. ;
Davis, Ian W. ;
Echols, Nathaniel ;
Headd, Jeffrey J. ;
Hung, Li-Wei ;
Kapral, Gary J. ;
Grosse-Kunstleve, Ralf W. ;
McCoy, Airlie J. ;
Moriarty, Nigel W. ;
Oeffner, Robert ;
Read, Randy J. ;
Richardson, David C. ;
Richardson, Jane S. ;
Terwilliger, Thomas C. ;
Zwart, Peter H. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :213-221
[2]   Towards automated crystallographic structure refinement with phenix.refine [J].
Afonine, Pavel V. ;
Grosse-Kunstleve, Ralf W. ;
Echols, Nathaniel ;
Headd, Jeffrey J. ;
Moriarty, Nigel W. ;
Mustyakimov, Marat ;
Terwilliger, Thomas C. ;
Urzhumtsev, Alexandre ;
Zwart, Peter H. ;
Adams, Paul D. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2012, 68 :352-367
[3]   PH-INDUCED DENATURATION OF PROTEINS - A SINGLE SALT BRIDGE CONTRIBUTES 3-5 KCAL MOL TO THE FREE-ENERGY OF FOLDING OF T4-LYSOZYME [J].
ANDERSON, DE ;
BECKTEL, WJ ;
DAHLQUIST, FW .
BIOCHEMISTRY, 1990, 29 (09) :2403-2408
[4]   Molecular dynamics simulations of water and biomolecules with a Monte Carlo constant pressure algorithm [J].
Åqvist, J ;
Wennerström, P ;
Nervall, M ;
Bjelic, S ;
Brandsdal, BO .
CHEMICAL PHYSICS LETTERS, 2004, 384 (4-6) :288-294
[5]   Making it Rain: Cloud-Based Molecular Simulations for Everyone [J].
Arantes, Pablo R. ;
Poleto, Marcelo D. ;
Pedebos, Conrado ;
Ligabue-Braun, Rodrigo .
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2021, 61 (10) :4852-4856
[6]   The selectivity of protein kinase inhibitors: a further update [J].
Bain, Jenny ;
Plater, Lorna ;
Elliott, Matt ;
Shpiro, Natalia ;
Hastie, C. James ;
Mclauchlan, Hilary ;
Klevernic, Iva ;
Arthur, J. Simon C. ;
Alessi, Dario R. ;
Cohen, Philip .
BIOCHEMICAL JOURNAL, 2007, 408 :297-315
[7]   Structural basis of Aurora-A activation by TPX2 at the mitotic spindle [J].
Bayliss, R ;
Sardon, T ;
Vernos, I ;
Conti, E .
MOLECULAR CELL, 2003, 12 (04) :851-862
[8]  
Berendsen J.J.C., 1981, INTERMOLECULAR FORCE, P331, DOI DOI 10.1007/978-94-015-7658-1_21
[9]   Molecular basis for cooperative binding and synergy of ATP-site and allosteric EGFR inhibitors [J].
Beyett, Tyler S. ;
To, Ciric ;
Heppner, David E. ;
Rana, Jaimin K. ;
Schmoker, Anna M. ;
Jang, Jaebong ;
De Clercq, Dries J. H. ;
Gomez, Gabriel ;
Scott, David A. ;
Gray, Nathanael S. ;
Janne, Pasi A. ;
Eck, Michael J. .
NATURE COMMUNICATIONS, 2022, 13 (01)
[10]  
Case D. A., 2021, Amber 2021