1
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Garcia-Maldonado E, Huber AD, Chai SC, Nithianantham S, Li Y, Wu J, Poudel S, Miller DJ, Seetharaman J, Chen T. Chemical manipulation of an activation/inhibition switch in the nuclear receptor PXR. Nat Commun 2024; 15:4054. [PMID: 38744881 PMCID: PMC11094003 DOI: 10.1038/s41467-024-48472-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 04/29/2024] [Indexed: 05/16/2024] Open
Abstract
Nuclear receptors are ligand-activated transcription factors that can often be useful drug targets. Unfortunately, ligand promiscuity leads to two-thirds of receptors remaining clinically untargeted. PXR is a nuclear receptor that can be activated by diverse compounds to elevate metabolism, negatively impacting drug efficacy and safety. This presents a barrier to drug development because compounds designed to target other proteins must avoid PXR activation while retaining potency for the desired target. This problem could be avoided by using PXR antagonists, but these compounds are rare, and their molecular mechanisms remain unknown. Here, we report structurally related PXR-selective agonists and antagonists and their corresponding co-crystal structures to describe mechanisms of antagonism and selectivity. Structural and computational approaches show that antagonists induce PXR conformational changes incompatible with transcriptional coactivator recruitment. These results guide the design of compounds with predictable agonist/antagonist activities and bolster efforts to generate antagonists to prevent PXR activation interfering with other drugs.
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Affiliation(s)
- Efren Garcia-Maldonado
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Andrew D Huber
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
| | - Sergio C Chai
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Stanley Nithianantham
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Yongtao Li
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jing Wu
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Shyaron Poudel
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Darcie J Miller
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Jayaraman Seetharaman
- Department of Structural Biology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, TN, 38105, USA.
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2
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Nithianantham S, Iwanski MK, Gaska I, Pandey H, Bodrug T, Inagaki S, Major J, Brouhard GJ, Gheber L, Rosenfeld SS, Forth S, Hendricks AG, Al-Bassam J. The kinesin-5 tail and bipolar minifilament domains are the origin of its microtubule crosslinking and sliding activity. Mol Biol Cell 2023; 34:ar111. [PMID: 37610838 PMCID: PMC10559304 DOI: 10.1091/mbc.e23-07-0287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 08/07/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023] Open
Abstract
Kinesin-5 crosslinks and slides apart microtubules to assemble, elongate, and maintain the mitotic spindle. Kinesin-5 is a tetramer, where two N-terminal motor domains are positioned at each end of the motor, and the coiled-coil stalk domains are organized into a tetrameric bundle through the bipolar assembly (BASS) domain. To dissect the function of the individual structural elements of the motor, we constructed a minimal kinesin-5 tetramer (mini-tetramer). We determined the x-ray structure of the extended, 34-nm BASS domain. Guided by these structural studies, we generated active bipolar kinesin-5 mini-tetramer motors from Drosophila melanogastor and human orthologues which are half the length of native kinesin-5. We then used these kinesin-5 mini-tetramers to examine the role of two unique structural adaptations of kinesin-5: 1) the length and flexibility of the tetramer, and 2) the C-terminal tails which interact with the motor domains to coordinate their ATPase activity. The C-terminal domain causes frequent pausing and clustering of kinesin-5. By comparing microtubule crosslinking and sliding by mini-tetramer and full-length kinesin-5, we find that both the length and flexibility of kinesin-5 and the C-terminal tails govern its ability to crosslink microtubules. Once crosslinked, stiffer mini-tetramers slide antiparallel microtubules more efficiently than full-length motors.
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Affiliation(s)
- Stanley Nithianantham
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - Malina K. Iwanski
- Departments of Biology and Bioengineering, McGill University, Montreal, Quebec Canada H3A 1B1
| | - Ignas Gaska
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Himanshu Pandey
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - Tatyana Bodrug
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - Sayaka Inagaki
- Department of Pharmacology, Mayo Clinic, Jacksonville, FL 32224
| | - Jennifer Major
- Department of Pharmacology, Mayo Clinic, Jacksonville, FL 32224
| | - Gary J. Brouhard
- Departments of Biology and Bioengineering, McGill University, Montreal, Quebec Canada H3A 1B1
| | - Larissa Gheber
- Department of Chemistry, The Ben Gurion University, Ber Sheva, Israel
| | | | - Scott Forth
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY 12180
| | - Adam G. Hendricks
- Departments of Biology and Bioengineering, McGill University, Montreal, Quebec Canada H3A 1B1
| | - Jawdat Al-Bassam
- Department of Molecular and Cellular Biology, University of California, Davis, CA 95616
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3
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Stachowski TR, Nithianantham S, Vanarotti M, Lopez K, Fischer M. Pan-Hsp90 ligand binding reveals isoform-specific differences in plasticity and water networks. Protein Sci 2023; 32:e4629. [PMID: 36938943 PMCID: PMC10108437 DOI: 10.1002/pro.4629] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Revised: 03/14/2023] [Accepted: 03/15/2023] [Indexed: 03/21/2023]
Abstract
Isoforms of heat shock protein 90 (HSP90) fold oncoproteins that facilitate all 10 hallmarks of cancer. However, its promise as a therapeutic target remains unfulfilled as there is still no FDA-approved drug targeting HSP90 in disease. Among the reasons hindering progress are side effects caused by pan-HSP90 inhibition. Selective targeting of the 4 isoforms is challenging due to high sequence and structural similarity. Surprisingly, while decades of drug discovery efforts have produced almost 400 human HSP90 structures, no single ligand has been structurally characterized across all 4 human isoforms to date, which could reveal structural differences to achieve selectivity. To better understand the HSP90 landscape relevant for ligand binding and design we take a 3-pronged approach. First, we solved the first complete set of structures of a single ligand bound to all 4 human isoforms. This enabled a systematic comparison of how side-chains and water networks respond to ligand binding across isoforms. Second, we expanded our analysis to publicly available, incomplete isoform-ligand series with distinct ligand chemistry. This highlighted general trends of protein and water mobility that differ among isoforms and impact ligand binding. Third, we further probed the Hsp90α conformational landscape for accommodating a congeneric series containing the purine scaffold common to HSP90 inhibitors. This revealed how minor ligand modifications flip ligand poses and perturb water and protein conformations. Taken together, this work illustrates how a systematic approach can shed new light on an "old" target and reveal hidden isoform-specific accommodations of congeneric ligands that may be exploited in ligand discovery and design.
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Affiliation(s)
- Timothy R Stachowski
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Stanley Nithianantham
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Murugendra Vanarotti
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
| | - Karlo Lopez
- School of Natural Sciences, Mathematics, and Engineering, California State University, Bakersfield, CA, 93311, USA
| | - Marcus Fischer
- Department of Chemical Biology & Therapeutics, St. Jude Children's Research Hospital, Memphis, TN, 38105, USA
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4
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Stachowski T, Vanarotti M, Nithianantham S, Jayaraman S, Lopez K, Fischer M. The big thaw: waters freed from cryo-cooling yield dynamic protein–ligand interactions. Acta Crystallogr A Found Adv 2022. [DOI: 10.1107/s2053273322099818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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5
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Alcock LJ, Chang Y, Jarusiewicz JA, Actis M, Nithianantham S, Mayasundari A, Min J, Maxwell D, Hunt J, Smart B, Yang JJ, Nishiguchi G, Fischer M, Mullighan CG, Rankovic Z. Development of Potent and Selective Janus Kinase 2/3 Directing PG-PROTACs. ACS Med Chem Lett 2022; 13:475-482. [PMID: 35300081 PMCID: PMC8919382 DOI: 10.1021/acsmedchemlett.1c00650] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 02/17/2022] [Indexed: 12/15/2022] Open
Abstract
Aberrant activation of the JAK-STAT signaling pathway has been implicated in the pathogenesis of a range of hematological malignancies and autoimmune disorders. Here we describe the design, synthesis, and characterization of JAK2/3 PROTACs utilizing a phenyl glutarimide (PG) ligand as the cereblon (CRBN) recruiter. SJ10542 displayed high selectivity over GSPT1 and other members of the JAK family and potency in patient-derived ALL cells containing both JAK2 fusions and CRLF2 rearrangements.
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Affiliation(s)
- Lisa J Alcock
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Yunchao Chang
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jamie A Jarusiewicz
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Marisa Actis
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Stanley Nithianantham
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Anand Mayasundari
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Dylan Maxwell
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jeremy Hunt
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Brandon Smart
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Jun J Yang
- Department of Pharmacy and Pharmaceutical Sciences, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Gisele Nishiguchi
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Marcus Fischer
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Charles G Mullighan
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States.,Hematological Malignancies Program, St. Jude Comprehensive Cancer Center, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
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6
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Min J, Mayasundari A, Keramatnia F, Jonchere B, Yang SW, Jarusiewicz J, Actis M, Das S, Young B, Slavish J, Yang L, Li Y, Fu X, Garrett SH, Yun M, Li Z, Nithianantham S, Chai S, Chen T, Shelat A, Lee RE, Nishiguchi G, White SW, Roussel MF, Potts PR, Fischer M, Rankovic Z. Phenyl‐Glutarimides: Alternative Cereblon Binders for the Design of PROTACs. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202108848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Jaeki Min
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Anand Mayasundari
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Fatemeh Keramatnia
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Barbara Jonchere
- Department of Tumor Cell Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Seung Wook Yang
- Department of Cell & Molecular Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Jamie Jarusiewicz
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Marisa Actis
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Sourav Das
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Brandon Young
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Jake Slavish
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Lei Yang
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Yong Li
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Xiang Fu
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Shalandus H. Garrett
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Mi‐Kyung Yun
- Department of Structural Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Zhenmei Li
- Department of Structural Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Stanley Nithianantham
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Sergio Chai
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Anang Shelat
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Gisele Nishiguchi
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Stephen W. White
- Department of Structural Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Martine F. Roussel
- Department of Tumor Cell Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Patrick Ryan Potts
- Department of Cell & Molecular Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Marcus Fischer
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
- Department of Structural Biology St. Jude Children's Research Hospital Memphis TN 38105 USA
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics St. Jude Children's Research Hospital Memphis TN 38105 USA
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7
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Min J, Mayasundari A, Keramatnia F, Jonchere B, Yang SW, Jarusiewicz J, Actis M, Das S, Young B, Slavish J, Yang L, Li Y, Fu X, Garrett SH, Yun MK, Li Z, Nithianantham S, Chai S, Chen T, Shelat A, Lee RE, Nishiguchi G, White SW, Roussel MF, Potts PR, Fischer M, Rankovic Z. Phenyl-Glutarimides: Alternative Cereblon Binders for the Design of PROTACs. Angew Chem Int Ed Engl 2021; 60:26663-26670. [PMID: 34614283 PMCID: PMC8648984 DOI: 10.1002/anie.202108848] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Indexed: 12/15/2022]
Abstract
Targeting cereblon (CRBN) is currently one of the most frequently reported proteolysis-targeting chimera (PROTAC) approaches, owing to favorable drug-like properties of CRBN ligands, immunomodulatory imide drugs (IMiDs). However, IMiDs are known to be inherently unstable, readily undergoing hydrolysis in body fluids. Here we show that IMiDs and IMiD-based PROTACs rapidly hydrolyze in commonly utilized cell media, which significantly affects their cell efficacy. We designed novel CRBN binders, phenyl glutarimide (PG) analogues, and showed that they retained affinity for CRBN with high ligand efficiency (LE >0.48) and displayed improved chemical stability. Our efforts led to the discovery of PG PROTAC 4 c (SJ995973), a uniquely potent degrader of bromodomain and extra-terminal (BET) proteins that inhibited the viability of human acute myeloid leukemia MV4-11 cells at low picomolar concentrations (IC50 =3 pM; BRD4 DC50 =0.87 nM). These findings strongly support the utility of PG derivatives in the design of CRBN-directed PROTACs.
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Affiliation(s)
- Jaeki Min
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Anand Mayasundari
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Fatemeh Keramatnia
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Barbara Jonchere
- Department of Tumor Cell Biology, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Seung Wook Yang
- Department of Cell & Molecular Biology, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Jamie Jarusiewicz
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Marisa Actis
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Sourav Das
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Brandon Young
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Jake Slavish
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Lei Yang
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Yong Li
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Xiang Fu
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Shalandus H. Garrett
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Mi-Kyung Yun
- Department of Structural Biology, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Zhenmei Li
- Department of Structural Biology, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Stanley Nithianantham
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Sergio Chai
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Taosheng Chen
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Anang Shelat
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Richard E. Lee
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Gisele Nishiguchi
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Stephen W. White
- Department of Structural Biology, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Martine F. Roussel
- Department of Tumor Cell Biology, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Patrick Ryan Potts
- Department of Cell & Molecular Biology, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Marcus Fischer
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
- Department of Structural Biology, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics, St. Jude
Children’s Research Hospital, Memphis, Tennessee 38105, United States
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8
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Chang Y, Min J, Jarusiewicz JA, Actis M, Yu-Chen Bradford S, Mayasundari A, Yang L, Chepyala D, Alcock LJ, Roberts KG, Nithianantham S, Maxwell D, Rowland L, Larsen R, Seth A, Goto H, Imamura T, Akahane K, Hansen BS, Pruett-Miller SM, Paietta EM, Litzow MR, Qu C, Yang JJ, Fischer M, Rankovic Z, Mullighan CG. Degradation of Janus kinases in CRLF2-rearranged acute lymphoblastic leukemia. Blood 2021; 138:2313-2326. [PMID: 34110416 PMCID: PMC8662068 DOI: 10.1182/blood.2020006846] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 04/02/2021] [Indexed: 11/20/2022] Open
Abstract
CRLF2-rearranged (CRLF2r) acute lymphoblastic leukemia (ALL) accounts for more than half of Philadelphia chromosome-like (Ph-like) ALL and is associated with a poor outcome in children and adults. Overexpression of CRLF2 results in activation of Janus kinase (JAK)-STAT and parallel signaling pathways in experimental models, but existing small molecule inhibitors of JAKs show variable and limited efficacy. Here, we evaluated the efficacy of proteolysis-targeting chimeras (PROTACs) directed against JAKs. Solving the structure of type I JAK inhibitors ruxolitinib and baricitinib bound to the JAK2 tyrosine kinase domain enabled the rational design and optimization of a series of cereblon (CRBN)-directed JAK PROTACs utilizing derivatives of JAK inhibitors, linkers, and CRBN-specific molecular glues. The resulting JAK PROTACs were evaluated for target degradation, and activity was tested in a panel of leukemia/lymphoma cell lines and xenograft models of kinase-driven ALL. Multiple PROTACs were developed that degraded JAKs and potently killed CRLF2r cell lines, the most active of which also degraded the known CRBN neosubstrate GSPT1 and suppressed proliferation of CRLF2r ALL in vivo, e.g. compound 7 (SJ988497). Although dual JAK/GSPT1-degrading PROTACs were the most potent, the development and evaluation of multiple PROTACs in an extended panel of xenografts identified a potent JAK2-degrading, GSPT1-sparing PROTAC that demonstrated efficacy in the majority of kinase-driven xenografts that were otherwise unresponsive to type I JAK inhibitors, e.g. compound 8 (SJ1008030). Together, these data show the potential of JAK-directed protein degradation as a therapeutic approach in JAK-STAT-driven ALL and highlight the interplay of JAK and GSPT1 degradation activity in this context.
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Affiliation(s)
| | - Jaeki Min
- Department of Chemical Biology and Therapeutics
| | | | | | | | | | - Lei Yang
- Department of Chemical Biology and Therapeutics
| | | | | | | | | | | | | | - Randolph Larsen
- Department of Pharmaceutical Sciences, and
- Graduate School of Biomedical Sciences, St Jude Children's Research Hospital, Memphis, TN
| | | | - Hiroaki Goto
- Division of Hemato-Oncology/Regenerative Medicine, Kanagawa Children's Medical Center, Yokohama, Japan
| | - Toshihiko Imamura
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Koshi Akahane
- Department of Pediatrics, School of Medicine, University of Yamanashi, Chuo, Japan
| | - Baranda S Hansen
- Center for Advanced Genome Engineering, St Jude Children's Research Hospital, Memphis, TN
| | | | - Elisabeth M Paietta
- Cancer Center, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY
| | - Mark R Litzow
- Division of Hematology, Department of Medicine, Mayo Clinic, Rochester, MN; and
| | | | - Jun J Yang
- Department of Pharmaceutical Sciences, and
- Hematological Malignancies Program, St Jude Children's Research Hospital, Memphis, TN
| | - Marcus Fischer
- Department of Chemical Biology and Therapeutics
- Department of Structural Biology
- Cancer Biology Program, and
| | - Zoran Rankovic
- Department of Chemical Biology and Therapeutics
- Cancer Biology Program, and
| | - Charles G Mullighan
- Department of Pathology
- Hematological Malignancies Program, St Jude Children's Research Hospital, Memphis, TN
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9
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Zahid H, Buchholz CR, Singh M, Ciccone MF, Chan A, Nithianantham S, Shi K, Aihara H, Fischer M, Schönbrunn E, Dos Santos CO, Landry JW, Pomerantz WCK. New Design Rules for Developing Potent Cell-Active Inhibitors of the Nucleosome Remodeling Factor (NURF) via BPTF Bromodomain Inhibition. J Med Chem 2021; 64:13902-13917. [PMID: 34515477 DOI: 10.1021/acs.jmedchem.1c01294] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The nucleosome remodeling factor (NURF) alters chromatin accessibility through interactions with its largest subunit,the bromodomain PHD finger transcription factor BPTF. BPTF is overexpressed in several cancers and is an emerging anticancer target. Targeting the BPTF bromodomain presents a potential strategy for its inhibition and the evaluation of its functional significance; however, inhibitor development for BPTF has lagged behind those of other bromodomains. Here we describe the development of pyridazinone-based BPTF inhibitors. The lead compound, BZ1, possesses a high potency (Kd = 6.3 nM) and >350-fold selectivity over BET bromodomains. We identify an acidic triad in the binding pocket to guide future designs. We show that our inhibitors sensitize 4T1 breast cancer cells to doxorubicin but not BPTF knockdown cells, suggesting a specificity to BPTF. Given the high potency and good physicochemical properties of these inhibitors, we anticipate that they will be useful starting points for chemical tool development to explore the biological roles of BPTF.
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Affiliation(s)
- Huda Zahid
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States
| | - Caroline R Buchholz
- Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
| | - Manjulata Singh
- The Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - Michael F Ciccone
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, United States
| | - Alice Chan
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Stanley Nithianantham
- Department of Chemical Biology & Therapeutics and Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ke Shi
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Hideki Aihara
- Department of Biochemistry, Molecular Biology, and Biophysics, University of Minnesota, 321 Church Street SE, Minneapolis, Minnesota 55455, United States
| | - Marcus Fischer
- Department of Chemical Biology & Therapeutics and Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee 38105, United States
| | - Ernst Schönbrunn
- Drug Discovery Department, H. Lee Moffitt Cancer Center and Research Institute, 12902 Magnolia Drive, Tampa, Florida 33612, United States
| | - Camila O Dos Santos
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, New York 11724, United States
| | - Joseph W Landry
- The Department of Human and Molecular Genetics, VCU Institute of Molecular Medicine, Massey Cancer Center, Virginia Commonwealth University, Richmond, Virginia 23298, United States
| | - William C K Pomerantz
- Department of Chemistry, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455, United States.,Department of Medicinal Chemistry, University of Minnesota, 308 Harvard Street SE, Minneapolis, Minnesota 55455, United States
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10
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Bodrug T, Wilson-Kubalek EM, Nithianantham S, Thompson AF, Alfieri A, Gaska I, Major J, Debs G, Inagaki S, Gutierrez P, Gheber L, McKenney RJ, Sindelar CV, Milligan R, Stumpff J, Rosenfeld SS, Forth ST, Al-Bassam J. The kinesin-5 tail domain directly modulates the mechanochemical cycle of the motor domain for anti-parallel microtubule sliding. eLife 2020; 9:e51131. [PMID: 31958056 PMCID: PMC7015671 DOI: 10.7554/elife.51131] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 01/16/2020] [Indexed: 12/29/2022] Open
Abstract
Kinesin-5 motors organize mitotic spindles by sliding apart microtubules. They are homotetramers with dimeric motor and tail domains at both ends of a bipolar minifilament. Here, we describe a regulatory mechanism involving direct binding between tail and motor domains and its fundamental role in microtubule sliding. Kinesin-5 tails decrease microtubule-stimulated ATP-hydrolysis by specifically engaging motor domains in the nucleotide-free or ADP states. Cryo-EM reveals that tail binding stabilizes an open motor domain ATP-active site. Full-length motors undergo slow motility and cluster together along microtubules, while tail-deleted motors exhibit rapid motility without clustering. The tail is critical for motors to zipper together two microtubules by generating substantial sliding forces. The tail is essential for mitotic spindle localization, which becomes severely reduced in tail-deleted motors. Our studies suggest a revised microtubule-sliding model, in which kinesin-5 tails stabilize motor domains in the microtubule-bound state by slowing ATP-binding, resulting in high-force production at both homotetramer ends.
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Affiliation(s)
- Tatyana Bodrug
- Department of Molecular and Cellular BiologyUniversity of California, DavisDavisUnited States
| | - Elizabeth M Wilson-Kubalek
- Department of Integrative Structural and Computational BiologyScripps Research InstituteLa JollaUnited States
| | - Stanley Nithianantham
- Department of Molecular and Cellular BiologyUniversity of California, DavisDavisUnited States
| | - Alex F Thompson
- Department of Molecular Physiology and BiophysicsUniversity of VermontBurlingtonUnited States
| | - April Alfieri
- Department of Biological SciencesRensselaer Polytechnic InstituteTroyUnited States
| | - Ignas Gaska
- Department of Biological SciencesRensselaer Polytechnic InstituteTroyUnited States
| | - Jennifer Major
- Department of Cancer BiologyLerner Research Institute, Cleveland ClinicLorainUnited States
- Department of PharmacologyMayo ClinicJacksonvilleUnited States
| | - Garrett Debs
- Department of Molecular Biophysics and BiochemistryYale UniversityNew HavenUnited States
| | - Sayaka Inagaki
- Department of PharmacologyMayo ClinicJacksonvilleUnited States
| | - Pedro Gutierrez
- Department of Molecular and Cellular BiologyUniversity of California, DavisDavisUnited States
| | - Larisa Gheber
- Department of Chemistry and Ilse Katz Institute for Nanoscale Science and TechnologyBen-Gurion University of the NegevNegevIsrael
| | - Richard J McKenney
- Department of Molecular and Cellular BiologyUniversity of California, DavisDavisUnited States
| | | | - Ronald Milligan
- Department of Integrative Structural and Computational BiologyScripps Research InstituteLa JollaUnited States
| | - Jason Stumpff
- Department of Molecular Physiology and BiophysicsUniversity of VermontBurlingtonUnited States
| | - Steven S Rosenfeld
- Department of Cancer BiologyLerner Research Institute, Cleveland ClinicLorainUnited States
- Department of PharmacologyMayo ClinicJacksonvilleUnited States
| | - Scott T Forth
- Department of Biological SciencesRensselaer Polytechnic InstituteTroyUnited States
| | - Jawdat Al-Bassam
- Department of Molecular and Cellular BiologyUniversity of California, DavisDavisUnited States
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11
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Nithianantham S, Cook BD, Chang F, Al-Bassam J. Structural basis of tubulin recruitment and assembly by microtubule polymerases. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319096041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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12
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Nithianantham S, Cook BD, Beans M, Guo F, Chang F, Al-Bassam J. Structural basis of tubulin recruitment and assembly by microtubule polymerases with tumor overexpressed gene (TOG) domain arrays. eLife 2018; 7:38922. [PMID: 30422110 PMCID: PMC6251626 DOI: 10.7554/elife.38922] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 10/31/2018] [Indexed: 12/21/2022] Open
Abstract
XMAP215/Stu2/Alp14 proteins accelerate microtubule plus-end polymerization by recruiting tubulins via arrays of tumor overexpressed gene (TOG) domains, yet their mechanism remains unknown. Here, we describe the biochemical and structural basis for TOG arrays in recruiting and polymerizing tubulins. Alp14 binds four tubulins via dimeric TOG1-TOG2 subunits, in which each domain exhibits a distinct exchange rate for tubulin. X-ray structures revealed square-shaped assemblies composed of pseudo-dimeric TOG1-TOG2 subunits assembled head-to-tail, positioning four unpolymerized tubulins in a polarized wheel-like configuration. Crosslinking and electron microscopy show Alp14-tubulin forms square assemblies in solution, and inactivating their interfaces destabilize this organization without influencing tubulin binding. An X-ray structure determined using approach to modulate tubulin polymerization revealed an unfurled assembly, in which TOG1-TOG2 uniquely bind to two polymerized tubulins. Our findings suggest a new microtubule polymerase model in which TOG arrays recruit tubulins by forming square assemblies that then unfurl, facilitating their concerted polymerization into protofilaments.
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Affiliation(s)
- Stanley Nithianantham
- Molecular Cellular Biology Department, University of California, Davis, United States
| | - Brian D Cook
- Molecular Cellular Biology Department, University of California, Davis, United States
| | - Madeleine Beans
- Molecular Cellular Biology Department, University of California, Davis, United States
| | - Fei Guo
- Molecular Cellular Biology Department, University of California, Davis, United States
| | - Fred Chang
- Department of Cell and Tissue Biology, University of California, San Francisco, United States
| | - Jawdat Al-Bassam
- Molecular Cellular Biology Department, University of California, Davis, United States
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13
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Nithianantham S, McNally FJ, Al-Bassam J. Structural basis for disassembly of katanin heterododecamers. J Biol Chem 2018; 293:10590-10605. [PMID: 29752405 DOI: 10.1074/jbc.ra117.001215] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2017] [Revised: 04/20/2018] [Indexed: 11/06/2022] Open
Abstract
The reorganization of microtubules in mitosis, meiosis, and development requires the microtubule-severing activity of katanin. Katanin is a heterodimer composed of an ATPase associated with diverse cellular activities (AAA) subunit and a regulatory subunit. Microtubule severing requires ATP hydrolysis by katanin's conserved AAA ATPase domains. Whereas other AAA ATPases form stable hexamers, we show that katanin forms only a monomer or dimers of heterodimers in solution. Katanin oligomers consistent with hexamers of heterodimers or heterododecamers were only observed for an ATP hydrolysis-deficient mutant in the presence of ATP. X-ray structures of katanin's AAA ATPase in monomeric nucleotide-free and pseudo-oligomeric ADP-bound states revealed conformational changes in the AAA subdomains that explained the structural basis for the instability of the katanin heterododecamer. We propose that the rapid dissociation of katanin AAA oligomers may lead to an autoinhibited state that prevents inappropriate microtubule severing or that cyclical disassembly into heterodimers may critically contribute to the microtubule-severing mechanism.
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Affiliation(s)
- Stanley Nithianantham
- From the Department of Molecular Cellular Biology University of California, Davis, California 95616
| | - Francis J McNally
- From the Department of Molecular Cellular Biology University of California, Davis, California 95616
| | - Jawdat Al-Bassam
- From the Department of Molecular Cellular Biology University of California, Davis, California 95616
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14
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Nithianantham S, Cook BD, Chang F, Al-Bassam J. Structural Basis of Microtubule Polymerases in Accelerating Tubulin Polymerization via Multiple Tog Domains. Biophys J 2016. [DOI: 10.1016/j.bpj.2015.11.746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022] Open
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15
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Nithianantham S, Le S, Seto E, Jia W, Leary J, Corbett KD, Moore JK, Al-Bassam J. Tubulin cofactors and Arl2 are cage-like chaperones that regulate the soluble αβ-tubulin pool for microtubule dynamics. eLife 2015. [PMID: 26208336 PMCID: PMC4574351 DOI: 10.7554/elife.08811] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Microtubule dynamics and polarity stem from the polymerization of
αβ-tubulin heterodimers. Five conserved tubulin cofactors/chaperones
and the Arl2 GTPase regulate α- and β-tubulin assembly into
heterodimers and maintain the soluble tubulin pool in the cytoplasm, but their
physical mechanisms are unknown. Here, we reconstitute a core tubulin chaperone
consisting of tubulin cofactors TBCD, TBCE, and Arl2, and reveal a cage-like
structure for regulating αβ-tubulin. Biochemical assays and electron
microscopy structures of multiple intermediates show the sequential binding of
αβ-tubulin dimer followed by tubulin cofactor TBCC onto this chaperone,
forming a ternary complex in which Arl2 GTP hydrolysis is activated to alter
αβ-tubulin conformation. A GTP-state locked Arl2 mutant inhibits
ternary complex dissociation in vitro and causes severe defects in microtubule
dynamics in vivo. Our studies suggest a revised paradigm for tubulin cofactors and
Arl2 functions as a catalytic chaperone that regulates soluble
αβ-tubulin assembly and maintenance to support microtubule
dynamics. DOI:http://dx.doi.org/10.7554/eLife.08811.001 Cells contain a network of protein filaments called microtubules. These filaments are
involved in many biological processes; for example, they help cells keep the right
shape, and they help to transport proteins and other materials inside cells. Two proteins called α-tubulin and β-tubulin are the building blocks of
microtubules. The filaments are very dynamic structures that can rapidly change
length as individual tubulin units are either added or removed to the filament ends.
Several proteins known as tubulin cofactors and an enzyme called Arl2 help to build a
vast pool of tubulin units that are able attach to the microtubules. These
units—called αβ-tubulin—are formed by α-tubulin
and β-tubulin binding to each other, but it not clear exactly what roles the
tubulin cofactors and Arl2 play in this process. Nithianantham et al. used a combination of microscopy and biochemical techniques to
study how the tubulin cofactors and Arl2 are organised, and their role in the
assembly of microtubules in yeast. The experiments show that Arl2 and two tubulin
cofactors associate with each other to form a stable ‘complex’ that has
a cage-like structure. A molecule of αβ-tubulin binds to the complex,
followed by another cofactor called TBCC. This activates the enzyme activity of Arl2,
which releases the energy needed to alter the shape of the αβ-tubulin.
Nithianantham et al. also found that yeast cells with a mutant form of Arl2 that
lacked enzyme activity had problems forming microtubules. Together, these findings show that the tubulin cofactors and Arl2 form a complex that
regulates the assembly and maintenance of αβ-tubulin. The next
challenge is to understand how this regulation influences the way that microtubules
grow and shrink inside cells. DOI:http://dx.doi.org/10.7554/eLife.08811.002
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Affiliation(s)
- Stanley Nithianantham
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Sinh Le
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Elbert Seto
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Weitao Jia
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Julie Leary
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
| | - Kevin D Corbett
- Ludwig Institute for Cancer Research, University of California, San Diego, San Diego, United States
| | - Jeffrey K Moore
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, United States
| | - Jawdat Al-Bassam
- Department of Molecular Cellular Biology, University of California, Davis, Davis, United States
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16
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Abstract
Chromosome segregation during mitosis depends upon Kinesin-5 motors, which display a conserved, bipolar homotetrameric organization consisting of two motor dimers at opposite ends of a central rod. Kinesin-5 motors crosslink adjacent microtubules to drive or constrain their sliding apart, but the structural basis of their organization is unknown. In this study, we report the atomic structure of the bipolar assembly (BASS) domain that directs four Kinesin-5 subunits to form a bipolar minifilament. BASS is a novel 26-nm four-helix bundle, consisting of two anti-parallel coiled-coils at its center, stabilized by alternating hydrophobic and ionic four-helical interfaces, which based on mutagenesis experiments, are critical for tetramerization. Strikingly, N-terminal BASS helices bend as they emerge from the central bundle, swapping partner helices, to form dimeric parallel coiled-coils at both ends, which are offset by 90°. We propose that BASS is a mechanically stable, plectonemically-coiled junction, transmitting forces between Kinesin-5 motor dimers during microtubule sliding. DOI: http://dx.doi.org/10.7554/eLife.02217.001.
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Affiliation(s)
- Jessica E Scholey
- Department of Molecular and Cellular Biology, University of California, Davis, Davis, United States
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17
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Nithianantham S, Le S, Ti S, Seto E, Al-Bassam J. Tubulin Cofactors Form a Multi-Protein Platforms that Regulate the Soluble Tubulin Pool and Promote Microtubule Polymerization. Biophys J 2014. [DOI: 10.1016/j.bpj.2013.11.2493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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18
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Sethuraman V, Nithianantham S, Muthiah PT. Self-assembly of hydrogen-bonded supramolecular structures based on hexafluorosilicate anion. J Fluor Chem 2012. [DOI: 10.1016/j.jfluchem.2011.07.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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19
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Fardini Y, Wang X, Témoin S, Nithianantham S, Lee D, Shoham M, Han YW. Fusobacterium nucleatum adhesin FadA binds vascular endothelial cadherin and alters endothelial integrity. Mol Microbiol 2011; 82:1468-80. [PMID: 22040113 DOI: 10.1111/j.1365-2958.2011.07905.x] [Citation(s) in RCA: 173] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Fusobacterium nucleatum is a Gram-negative oral anaerobe, capable of systemic dissemination causing infections and abscesses, often in mixed-species, at different body sites. We have shown previously that F. nucleatum adheres to and invades host epithelial and endothelial cells via a novel FadA adhesin. In this study, vascular endothelial (VE)-cadherin, a member of the cadherin family and a cell-cell junction molecule, was identified as the endothelial receptor for FadA, required for F. nucleatum binding to the cells. FadA colocalized with VE-cadherin on endothelial cells, causing relocation of VE-cadherin away from the cell-cell junctions. As a result, the endothelial permeability was increased, allowing the bacteria to cross the endothelium through loosened junctions. This crossing mechanism may explain why the organism is able to disseminate systemically to colonize in different body sites and even overcome the placental and blood-brain barriers. Co-incubation of F. nucleatum and Escherichia coli enhanced penetration of the endothelial cells by the latter in the transwell assays, suggesting F. nucleatum may serve as an 'enabler' for other microorganisms to spread systemically. This may explain why F. nucleatum is often found in mixed infections. This study reveals a possible novel dissemination mechanism utilized by pathogens.
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Affiliation(s)
- Yann Fardini
- Department of Periodontics, Case Western Reserve University, Cleveland, OH 44106, USA
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20
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Nithianantham S, Xu M, Yamada M, Ikegami A, Shoham M, Han YW. Crystal structure of FadA adhesin from Fusobacterium nucleatum reveals a novel oligomerization motif, the leucine chain. J Biol Chem 2008; 284:3865-72. [PMID: 18996848 DOI: 10.1074/jbc.m805503200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many bacterial appendages have filamentous structures, often composed of repeating monomers assembled in a head-to-tail manner. The mechanisms of such linkages vary. We report here a novel protein oligomerization motif identified in the FadA adhesin from the Gram-negative bacterium Fusobacterium nucleatum. The 2.0 angstroms crystal structure of the secreted form of FadA (mFadA) reveals two antiparallel alpha-helices connected by an intervening 8-residue hairpin loop. Leucine-leucine contacts play a prominent dual intra- and intermolecular role in the structure and function of FadA. First, they comprise the main association between the two helical arms of the monomer; second, they mediate the head-to-tail association of monomers to form the elongated polymers. This leucine-mediated filamentous assembly of FadA molecules constitutes a novel structural motif termed the "leucine chain." The essential role of these residues in FadA is corroborated by mutagenesis of selected leucine residues, which leads to the abrogation of oligomerization, filament formation, and binding to host cells.
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Affiliation(s)
- Stanley Nithianantham
- Department of Biochemistry, Case Western Reserve University, Cleveland, Ohio 44106, USA
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21
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Nithianantham S, Shilton BH. Analysis of the isolated SecA DEAD motor suggests a mechanism for chemical-mechanical coupling. J Mol Biol 2008; 383:380-9. [PMID: 18761349 DOI: 10.1016/j.jmb.2008.08.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2008] [Revised: 08/07/2008] [Accepted: 08/11/2008] [Indexed: 11/18/2022]
Abstract
The preprotein cross-linking domain and C-terminal domains of Escherichia coli SecA were removed to create a minimal DEAD motor, SecA-DM. SecA-DM hydrolyzes ATP and has the same affinity for ADP as full-length SecA. The crystal structure of SecA-DM in complex with ADP was solved and shows the DEAD motor in a closed conformation. Comparison with the structure of the E. coli DEAD motor in an open conformation (Protein Data Bank ID 2FSI) indicates main-chain conformational changes in two critical sequences corresponding to Motif III and Motif V of the DEAD helicase family. The structures that the Motif III and Motif V sequences adopt in the DEAD motor open conformation are incompatible with the closed conformation. Therefore, when the DEAD motor makes the transition from open to closed, Motif III and Motif V are forced to change their conformations, which likely functions to regulate passage through the transition state for ATP hydrolysis. The transition state for ATP hydrolysis for the SecA DEAD motor was modeled based on the conformation of the Vasa helicase in complex with adenylyl imidodiphosphate and RNA (Protein Data Bank ID 2DB3). A mechanism for chemical-mechanical coupling emerges, where passage through the transition state for ATP hydrolysis is hindered by the conformational changes required in Motif III and Motif V, and may be promoted by binding interactions with the preprotein substrate and/or other translocase domains and subunits.
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Affiliation(s)
- Stanley Nithianantham
- Department of Biochemistry, The University of Western Ontario, London, Ontario, Canada N6A 5C1
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22
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Nithianantham S, Xu M, Wu N, Han YW, Shoham M. Crystallization and preliminary X-ray data of the FadA adhesin from Fusobacterium nucleatum. Acta Crystallogr Sect F Struct Biol Cryst Commun 2006; 62:1215-7. [PMID: 17142900 PMCID: PMC2225358 DOI: 10.1107/s1744309106045593] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2006] [Accepted: 10/30/2006] [Indexed: 11/10/2022]
Abstract
Fusobacterium nucleatum is a gram-negative anaerobe prevalent in the oral cavity that is associated with periodontal disease, preterm birth and infections in other parts of the human body. The bacteria attach to and invade epithelial and endothelial cells in the gum tissue and elsewhere via a 13.7 kDa adhesin protein FadA (Fusobacterium adhesin A). FadA exists in two forms: the intact form (pre-FadA), consisting of 129 amino acids, and the mature form (mFadA), which lacks an 18-residue signal sequence. Both forms have been expressed in Escherichia coli and purified. mFadA has been crystallized. The crystals belong to the hexagonal space group P6(1) or P6(5), with unit-cell parameters a = b = 59.3, c = 125.7 A and one molecule per asymmetric unit. The crystals exhibit an unusually high solvent content of 74%. Synchrotron X-ray data have been collected to 1.9 A. The crystals are suitable for X-ray structure determination. The crystal structure of FadA may provide a basis for the development of therapeutic agents to combat periodontal disease and other infections associated with F. nucleatum.
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Affiliation(s)
- Stanley Nithianantham
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4935, USA
| | - Minghua Xu
- Department of Biological Sciences, School of Dentistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4905, USA
| | - Nan Wu
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4935, USA
| | - Yiping W. Han
- Department of Biological Sciences, School of Dentistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106-4905, USA
- Department of Pathology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, OH 44106, USA
- Correspondence e-mail: ,
| | - Menachem Shoham
- Department of Biochemistry, School of Medicine, Case Western Reserve University, Cleveland, OH 44106-4935, USA
- Correspondence e-mail: ,
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23
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Wu N, Macion-Dazard R, Nithianantham S, Xu Z, Hanson SM, Vishnivetskiy SA, Gurevich VV, Thibonnier M, Shoham M. Soluble mimics of the cytoplasmic face of the human V1-vascular vasopressin receptor bind arrestin2 and calmodulin. Mol Pharmacol 2006; 70:249-58. [PMID: 16574744 DOI: 10.1124/mol.105.018804] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Signal transduction by G protein-coupled receptors (GPCRs) is mediated by interactions between intracellular proteins and exposed motifs on the cytoplasmic face of these receptors. Arrestins bind to GPCRs and modulate receptor function either by interfering with heterotrimeric G protein signaling or by serving as signaling adaptors themselves. Calmodulin interacts with GPCRs triggering a calcium response. We have studied the interaction of arrestin2 and calmodulin with intracellular elements of the human V1-vascular vasopressin receptor (hV1R). For this purpose, we designed, expressed, and purified soluble fusion proteins with the maltose-binding protein (MBP) from Escherichia coli that mimic the intracellular surface of the hV1R. These MBP fusion proteins bind arrestin2 and calmodulin with affinities in the micromolar range. A different series of soluble receptor analogs, named vasopressin receptor 1 elements on a soluble scaffold (V1ROSS) proteins, consist of the third intracellular loop and/or the C-terminal segment of the hV1R receptor juxtaposed on the surface of the MBP. V1ROSS proteins bind calmodulin and a truncated, phosphorylation-independent form of arrestin2 more tightly than the corresponding linear fusion proteins. Thus, embedding receptor loops within the three-dimensional structure of the MBP yields a better representation of the active conformation of these receptor loops than linear receptor peptides fused onto the C terminus of the MBP. V1ROSS proteins provide a valuable tool to study receptor interactions because they are more amenable to structural analysis than the native membrane receptor. These findings set the stage for the detailed structural analysis of these protein-protein interactions that are important for understanding the mechanism of signaling.
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Affiliation(s)
- Nan Wu
- Department of Biochemistry, Case Western Reserve University, 10900 Euclid Ave., Cleveland, OH 44106-4935, USA
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