1
|
Cornish J, Owen D, Mott HR. RLIP76: A Structural and Functional Triumvirate. Cancers (Basel) 2021; 13:cancers13092206. [PMID: 34064388 PMCID: PMC8124665 DOI: 10.3390/cancers13092206] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 04/12/2021] [Accepted: 04/29/2021] [Indexed: 11/16/2022] Open
Abstract
RLIP76/RalBP1 is an ATP-dependent transporter of glutathione conjugates, which is overexpressed in various human cancers, but its diverse functions in normal cells, which include endocytosis, stress response and mitochondrial dynamics, are still not fully understood. The protein can be divided into three distinct regions, each with its own structural properties. At the centre of the protein are two well-defined domains, a GTPase activating protein domain targeting Rho family small G proteins and a small coiled-coil that binds to the Ras family small GTPases RalA and RalB. In engaging with Rho and Ral proteins, RLIP76 bridges these two distinct G protein families. The N-terminal region is predicted to be disordered and is rich in basic amino acids, which may mediate membrane association, consistent with its role in transport. RLIP76 is an ATP-dependent transporter with ATP-binding sites within the N-terminus and the Ral binding domain. Furthermore, RLIP76 is subject to extensive phosphorylation, particularly in the N-terminal region. In contrast, the C-terminal region is thought to form an extensive coiled-coil that could mediate dimerization. Here, we review the structural features of RLIP76, including experimental data and computational predictions, and discuss the implications of its various post-translational modifications.
Collapse
|
2
|
Hurd CA, Brear P, Revell J, Ross S, Mott HR, Owen D. Affinity maturation of the RLIP76 Ral binding domain to inform the design of stapled peptides targeting the Ral GTPases. J Biol Chem 2021; 296:100101. [PMID: 33214225 PMCID: PMC7949049 DOI: 10.1074/jbc.ra120.015735] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 11/10/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
Ral GTPases have been implicated as critical drivers of cell growth and metastasis in numerous Ras-driven cancers. We have previously reported stapled peptides, based on the Ral effector RLIP76, that can disrupt Ral signaling. Stapled peptides are short peptides that are locked into their bioactive form using a synthetic brace. Here, using an affinity maturation of the RLIP76 Ral-binding domain, we identified several sequence substitutions that together improve binding to Ral proteins by more than 20-fold. Hits from the selection were rigorously analyzed to determine the contributions of individual residues and two 1.5 Å cocrystal structures of the tightest-binding mutants in complex with RalB revealed key interactions. Insights gained from this maturation were used to design second-generation stapled peptides based on RLIP76 that exhibited vastly improved selectivity for Ral GTPases when compared with the first-generation lead peptide. The binding of second-generation peptides to Ral proteins was quantified and the binding site of the lead peptide on RalB was determined by NMR. Stapled peptides successfully competed with multiple Ral-effector interactions in cellular lysates. Our findings demonstrate how manipulation of a native binding partner can assist in the rational design of stapled peptide inhibitors targeting a protein-protein interaction.
Collapse
Affiliation(s)
- Catherine A Hurd
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Paul Brear
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jefferson Revell
- AstraZeneca, Sir Aaron Klug Building, Granta Park, Cambridge, UK
| | - Sarah Ross
- Research and Early Development, Oncology R&D, AstraZeneca, Cambridge, UK
| | - Helen R Mott
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
| | - Darerca Owen
- Department of Biochemistry, University of Cambridge, Cambridge, UK.
| |
Collapse
|
3
|
Shafiq A, Campbell LJ, Owen D, Mott HR. NMR resonance assignments for the active and inactive conformations of the small G protein RalA. BIOMOLECULAR NMR ASSIGNMENTS 2020; 14:87-91. [PMID: 31916136 PMCID: PMC7069931 DOI: 10.1007/s12104-019-09925-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 12/26/2019] [Indexed: 06/10/2023]
Abstract
The Ral proteins (RalA and RalB) are small G proteins of the Ras family that have been implicated in exocytosis, endocytosis, transcriptional regulation and mitochondrial fission, as well as having a role in tumourigenesis. RalA and RalB are activated downstream of the master regulator, Ras, which causes the nucleotide exchange of GDP for GTP. Here we report the 1H, 15 N and 13C resonance assignments of RalA in its active form bound to the GTP analogue GMPPNP. We also report the backbone assignments of RalA in its inactive, GDP-bound form. The assignments give insight into the switch regions, which change conformation upon nucleotide exchange. These switch regions are invisible in the spectra of the active, GMPPNP bound form but the residues proximal to the switches can be monitored. RalA is also an important drug target due to its over activation in some cancers and these assignments will be extremely useful for NMR-based screening approaches.
Collapse
Affiliation(s)
- Arooj Shafiq
- Department of Biochemistry, 80, Tennis Court Road, Cambridge, CB2 1GA, UK
- Barrett Hodgson University, Korangi Creek, Salim Habib Campus, NC-24, Deh Dih, Korangi Creek, Karachi, 74900, Sindh, Pakistan
| | - Louise J Campbell
- Department of Biochemistry, 80, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Darerca Owen
- Department of Biochemistry, 80, Tennis Court Road, Cambridge, CB2 1GA, UK
| | - Helen R Mott
- Department of Biochemistry, 80, Tennis Court Road, Cambridge, CB2 1GA, UK.
| |
Collapse
|
4
|
Tetley GJN, Murphy NP, Bonetto S, Ivanova-Berndt G, Revell J, Mott HR, Cooley RN, Owen D. The discovery and maturation of peptide biologics targeting the small G-protein Cdc42: A bioblockade for Ras-driven signaling. J Biol Chem 2020; 295:2866-2884. [PMID: 31959628 DOI: 10.1074/jbc.ra119.010077] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Revised: 12/24/2019] [Indexed: 01/10/2023] Open
Abstract
Aberrant Ras signaling drives 30% of cancers, and inhibition of the Rho family small GTPase signaling has been shown to combat Ras-driven cancers. Here, we present the discovery of a 16-mer cyclic peptide that binds to Cdc42 with nanomolar affinity. Affinity maturation of this sequence has produced a panel of derived candidates with increased affinity and modulated specificity for other closely-related small GTPases. The structure of the tightest binding peptide was solved by NMR, and its binding site on Cdc42 was determined. Addition of a cell-penetrating sequence allowed the peptides to access the cell interior and engage with their target(s), modulating signaling pathways. In Ras-driven cancer cell models, the peptides have an inhibitory effect on proliferation and show suppression of both invasion and motility. As such, they represent promising candidates for Rho-family small GTPase inhibitors and therapeutics targeting Ras-driven cancers. Our data add to the growing literature demonstrating that peptides are establishing their place in the biologics arm of drug discovery.
Collapse
Affiliation(s)
- George J N Tetley
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd., Cambridge CB2 1GA, United Kingdom
| | - Natasha P Murphy
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd., Cambridge CB2 1GA, United Kingdom
| | - Stephane Bonetto
- Isogenica Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Gabriela Ivanova-Berndt
- Isogenica Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Jefferson Revell
- MedImmune, Sir Aaron Klug Building, Granta Park, Cambridge CB21 6GH, United Kingdom
| | - Helen R Mott
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd., Cambridge CB2 1GA, United Kingdom.
| | - R Neil Cooley
- Isogenica Ltd., Chesterford Research Park, Little Chesterford, Essex CB10 1XL, United Kingdom
| | - Darerca Owen
- Department of Biochemistry, University of Cambridge, 80 Tennis Court Rd., Cambridge CB2 1GA, United Kingdom.
| |
Collapse
|
5
|
Thomas JC, Cooper JM, Clayton NS, Wang C, White MA, Abell C, Owen D, Mott HR. Inhibition of Ral GTPases Using a Stapled Peptide Approach. J Biol Chem 2016; 291:18310-25. [PMID: 27334922 DOI: 10.1074/jbc.m116.720243] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Indexed: 01/31/2023] Open
Abstract
Aberrant Ras signaling drives numerous cancers, and drugs to inhibit this are urgently required. This compelling clinical need combined with recent innovations in drug discovery including the advent of biologic therapeutic agents, has propelled Ras back to the forefront of targeting efforts. Activated Ras has proved extremely difficult to target directly, and the focus has moved to the main downstream Ras-signaling pathways. In particular, the Ras-Raf and Ras-PI3K pathways have provided conspicuous enzyme therapeutic targets that were more accessible to conventional drug-discovery strategies. The Ras-RalGEF-Ral pathway is a more difficult challenge for traditional medicinal development, and there have, therefore, been few inhibitors reported that disrupt this axis. We have used our structure of a Ral-effector complex as a basis for the design and characterization of α-helical-stapled peptides that bind selectively to active, GTP-bound Ral proteins and that compete with downstream effector proteins. The peptides have been thoroughly characterized biophysically. Crucially, the lead peptide enters cells and is biologically active, inhibiting isoform-specific RalB-driven cellular processes. This, therefore, provides a starting point for therapeutic inhibition of the Ras-RalGEF-Ral pathway.
Collapse
Affiliation(s)
- Jemima C Thomas
- From the Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Jonathan M Cooper
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390-9039
| | - Natasha S Clayton
- From the Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Chensu Wang
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390-9039
| | - Michael A White
- Department of Cell Biology, UT Southwestern Medical Center, Dallas, Texas 75390-9039
| | - Chris Abell
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Darerca Owen
- From the Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom,
| | - Helen R Mott
- From the Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom,
| |
Collapse
|