1
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Geraud M, Cristini A, Salimbeni S, Bery N, Jouffret V, Russo M, Ajello AC, Fernandez Martinez L, Marinello J, Cordelier P, Trouche D, Favre G, Nicolas E, Capranico G, Sordet O. TDP1 mutation causing SCAN1 neurodegenerative syndrome hampers the repair of transcriptional DNA double-strand breaks. Cell Rep 2024; 43:114214. [PMID: 38761375 DOI: 10.1016/j.celrep.2024.114214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 03/05/2024] [Accepted: 04/24/2024] [Indexed: 05/20/2024] Open
Abstract
TDP1 removes transcription-blocking topoisomerase I cleavage complexes (TOP1ccs), and its inactivating H493R mutation causes the neurodegenerative syndrome SCAN1. However, the molecular mechanism underlying the SCAN1 phenotype is unclear. Here, we generate human SCAN1 cell models using CRISPR-Cas9 and show that they accumulate TOP1ccs along with changes in gene expression and genomic distribution of R-loops. SCAN1 cells also accumulate transcriptional DNA double-strand breaks (DSBs) specifically in the G1 cell population due to increased DSB formation and lack of repair, both resulting from abortive removal of transcription-blocking TOP1ccs. Deficient TDP1 activity causes increased DSB production, and the presence of mutated TDP1 protein hampers DSB repair by a TDP2-dependent backup pathway. This study provides powerful models to study TDP1 functions under physiological and pathological conditions and unravels that a gain of function of the mutated TDP1 protein, which prevents DSB repair, rather than a loss of TDP1 activity itself, could contribute to SCAN1 pathogenesis.
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Affiliation(s)
- Mathéa Geraud
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Agnese Cristini
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Simona Salimbeni
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France; Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Nicolas Bery
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Virginie Jouffret
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France; BigA Core Facility, Centre de Biologie Intégrative (CBI), Université de Toulouse, 31062 Toulouse, France
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Andrea Carla Ajello
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Lara Fernandez Martinez
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Jessica Marinello
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Pierre Cordelier
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Didier Trouche
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Gilles Favre
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Estelle Nicolas
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy.
| | - Olivier Sordet
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France.
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2
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Lee KY. Membrane-Driven Dimerization of the Peripheral Membrane Protein KRAS: Implications for Downstream Signaling. Int J Mol Sci 2024; 25:2530. [PMID: 38473778 DOI: 10.3390/ijms25052530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/14/2024] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
Transient homo-dimerization of the RAS GTPase at the plasma membrane has been shown to promote the mitogen-activated protein kinase (MAPK) signaling pathway essential for cell proliferation and oncogenesis. To date, numerous crystallographic studies have focused on the well-defined GTPase domains of RAS isoforms, which lack the disordered C-terminal membrane anchor, thus providing limited structural insight into membrane-bound RAS molecules. Recently, lipid-bilayer nanodisc platforms and paramagnetic relaxation enhancement (PRE) analyses have revealed several distinct structures of the membrane-anchored homodimers of KRAS, an isoform that is most frequently mutated in human cancers. The KRAS dimerization interface is highly plastic and altered by biologically relevant conditions, including oncogenic mutations, the nucleotide states of the protein, and the lipid composition. Notably, PRE-derived structures of KRAS homodimers on the membrane substantially differ in terms of the relative orientation of the protomers at an "α-α" dimer interface comprising two α4-α5 regions. This interface plasticity along with the altered orientations of KRAS on the membrane impact the accessibility of KRAS to downstream effectors and regulatory proteins. Further, nanodisc platforms used to drive KRAS dimerization can be used to screen potential anticancer drugs that target membrane-bound RAS dimers and probe their structural mechanism of action.
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Affiliation(s)
- Ki-Young Lee
- Department of Pharmacy, College of Pharmacy and Institute of Pharmaceutical Sciences, CHA University, Pocheon-si 11160, Gyeonggi-Do, Republic of Korea
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3
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Chan A, Tsourkas A. Intracellular Protein Delivery: Approaches, Challenges, and Clinical Applications. BME FRONTIERS 2024; 5:0035. [PMID: 38282957 PMCID: PMC10809898 DOI: 10.34133/bmef.0035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/14/2023] [Indexed: 01/30/2024] Open
Abstract
Protein biologics are powerful therapeutic agents with diverse inhibitory and enzymatic functions. However, their clinical use has been limited to extracellular applications due to their inability to cross plasma membranes. Overcoming this physiological barrier would unlock the potential of protein drugs for the treatment of many intractable diseases. In this review, we highlight progress made toward achieving cytosolic delivery of recombinant proteins. We start by first considering intracellular protein delivery as a drug modality compared to existing Food and Drug Administration-approved drug modalities. Then, we summarize strategies that have been reported to achieve protein internalization. These techniques can be broadly classified into 3 categories: physical methods, direct protein engineering, and nanocarrier-mediated delivery. Finally, we highlight existing challenges for cytosolic protein delivery and offer an outlook for future advances.
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Affiliation(s)
| | - Andrew Tsourkas
- Department of Bioengineering,
University of Pennsylvania, Philadelphia, PA, USA
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4
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Nussinov R, Jang H. Direct K-Ras Inhibitors to Treat Cancers: Progress, New Insights, and Approaches to Treat Resistance. Annu Rev Pharmacol Toxicol 2024; 64:231-253. [PMID: 37524384 DOI: 10.1146/annurev-pharmtox-022823-113946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2023]
Abstract
Here we discuss approaches to K-Ras inhibition and drug resistance scenarios. A breakthrough offered a covalent drug against K-RasG12C. Subsequent innovations harnessed same-allele drug combinations, as well as cotargeting K-RasG12C with a companion drug to upstream regulators or downstream kinases. However, primary, adaptive, and acquired resistance inevitably emerge. The preexisting mutation load can explain how even exceedingly rare mutations with unobservable effects can promote drug resistance, seeding growth of insensitive cell clones, and proliferation. Statistics confirm the expectation that most resistance-related mutations are in cis, pointing to the high probability of cooperative, same-allele effects. In addition to targeted Ras inhibitors and drug combinations, bifunctional molecules and innovative tri-complex inhibitors to target Ras mutants are also under development. Since the identities and potential contributions of preexisting and evolving mutations are unknown, selecting a pharmacologic combination is taxing. Collectively, our broad review outlines considerations and provides new insights into pharmacology and resistance.
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Affiliation(s)
- Ruth Nussinov
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland, USA;
- Department of Human Molecular Genetics and Biochemistry, Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hyunbum Jang
- Computational Structural Biology Section, Frederick National Laboratory for Cancer Research in the Cancer Innovation Laboratory, National Cancer Institute, Frederick, Maryland, USA;
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5
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Saitoh T, Kim HN, Narita R, Ohtsuka I, Mo W, Lee KY, Enomoto M, Gasmi-Seabrook GMC, Marshall CB, Ikura M. Biochemical and biophysical characterization of the RAS family small GTPase protein DiRAS3. Protein Expr Purif 2023; 212:106361. [PMID: 37652393 DOI: 10.1016/j.pep.2023.106361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/02/2023]
Abstract
DiRAS3, also called ARHI, is a RAS (sub)family small GTPase protein that shares 50-60% sequence identity with H-, K-, and N-RAS, with substitutions in key conserved G-box motifs and a unique 34 amino acid extension at its N-terminus. Unlike the RAS proto-oncogenes, DiRAS3 exhibits tumor suppressor properties. DiRAS3 function has been studied through genetics and cell biology, but there has been a lack of understanding of the biochemical and biophysical properties of the protein, likely due to its instability and poor solubility. To overcome this solubility issue, we engineered a DiRAS3 variant (C75S/C80S), which significantly improved soluble protein expression in E. coli. Recombinant DiRAS3 was purified by Ni-NTA and size exclusion chromatography (SEC). Concentration dependence of the SEC chromatogram indicated that DiRAS3 exists in monomer-dimer equilibrium. We then produced truncations of the N-terminal (ΔN) and both (ΔNC) extensions to the GTPase domain. Unlike full-length DiRAS3, the SEC profiles showed that ΔNC is monomeric while ΔN was monomeric with aggregation, suggesting that the N and/or C-terminal tail(s) contribute to dimerization and aggregation. The 1H-15N HSQC NMR spectrum of ΔNC construct displayed well-dispersed peaks similar to spectra of other GTPase domains, which enabled us to demonstrate that DiRAS3 has a GTPase domain that can bind GDP and GTP. Taken together, we conclude that, despite the substitutions in the G-box motifs, DiRAS3 can switch between nucleotide-bound states and that the N- and C-terminal extensions interact transiently with the GTPase domain in intra- and inter-molecular fashions, mediating weak multimerization of this unique small GTPase.
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Affiliation(s)
- Takashi Saitoh
- Faculty of Pharmaceutical Sciences, Hokkaido University of Science, Sapporo, Hokkaido, 006-8585, Japan; Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada.
| | - Ha-Neul Kim
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Riku Narita
- Faculty of Pharmaceutical Sciences, Hokkaido University of Science, Sapporo, Hokkaido, 006-8585, Japan
| | - Ibuki Ohtsuka
- Faculty of Pharmaceutical Sciences, Hokkaido University of Science, Sapporo, Hokkaido, 006-8585, Japan
| | - Weiyu Mo
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Ki-Young Lee
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | - Masahiro Enomoto
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada
| | | | - Christopher B Marshall
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada.
| | - Mitsuhiko Ikura
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, Toronto, Ontario, M5G 1L7, Canada.
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6
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Gomez-Gutierrez P, Rubio-Martinez J, Perez JJ. Discovery of Hit Compounds Targeting the P4 Allosteric Site of K-RAS, Identified through Ensemble-Based Virtual Screening. J Chem Inf Model 2023; 63:6412-6422. [PMID: 37824186 PMCID: PMC10598794 DOI: 10.1021/acs.jcim.3c01212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Indexed: 10/13/2023]
Abstract
Mutants of Ras are oncogenic drivers of a large number of human tumors. Despite being recognized as an attractive target for the treatment of cancer, the high affinity for its substrate tagged the protein as undruggable for a few years. The identification of cryptic pockets on the protein surface gave the opportunity to identify molecules capable of acting as allosteric modulators. Several molecules were disclosed in recent years, with sotorasib and adagrasib already approved for clinical use. The present study makes use of computational methods to characterize eight prospective allosteric pockets (P1-P8) in K-Ras, four of which (P1-P4) were previously characterized in the literature. The present study also describes the results of a virtual screening study focused on the discovery of hit compounds, binders of the P4 site that can be considered as peptidomimetics of a fragment of the SOS αI helix, a guanine exchange factor of Ras. After a detailed description of the computational procedure followed, we disclose five hit compounds, prospective binders of the P4 allosteric site that exhibit an inhibitory capability higher than 30% in a cell proliferation assay at 50 μM.
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Affiliation(s)
- Patricia Gomez-Gutierrez
- Department
of Chemical Engineering. ETSEIB, Universitat
Politecnica de Catalunya, Av. Diagonal, 647, Barcelona 08028, Spain
- Allinky
Biopharma, Madrid Scientific Park, Faraday, 7, Madrid 28049, Spain
| | - Jaime Rubio-Martinez
- Department
of Materials Science and Physical Chemistry, University of Barcelona and the Institut de Recerca en Quimica Teorica
i Computacional (IQTCUB), Marti i Franques, 1, Barcelona 08028, Spain
| | - Juan J. Perez
- Department
of Chemical Engineering. ETSEIB, Universitat
Politecnica de Catalunya, Av. Diagonal, 647, Barcelona 08028, Spain
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7
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Castells-Graells R, Meador K, Arbing MA, Sawaya MR, Gee M, Cascio D, Gleave E, Debreczeni JÉ, Breed J, Leopold K, Patel A, Jahagirdar D, Lyons B, Subramaniam S, Phillips C, Yeates TO. Cryo-EM structure determination of small therapeutic protein targets at 3 Å-resolution using a rigid imaging scaffold. Proc Natl Acad Sci U S A 2023; 120:e2305494120. [PMID: 37669364 PMCID: PMC10500258 DOI: 10.1073/pnas.2305494120] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/14/2023] [Indexed: 09/07/2023] Open
Abstract
Cryoelectron microscopy (Cryo-EM) has enabled structural determination of proteins larger than about 50 kDa, including many intractable by any other method, but it has largely failed for smaller proteins. Here, we obtain structures of small proteins by binding them to a rigid molecular scaffold based on a designed protein cage, revealing atomic details at resolutions reaching 2.9 Å. We apply this system to the key cancer signaling protein KRAS (19 kDa in size), obtaining four structures of oncogenic mutational variants by cryo-EM. Importantly, a structure for the key G12C mutant bound to an inhibitor drug (AMG510) reveals significant conformational differences compared to prior data in the crystalline state. The findings highlight the promise of cryo-EM scaffolds for advancing the design of drug molecules against small therapeutic protein targets in cancer and other human diseases.
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Affiliation(s)
- Roger Castells-Graells
- Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Kyle Meador
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Mark A. Arbing
- Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Michael R. Sawaya
- Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Morgan Gee
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Duilio Cascio
- Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Emma Gleave
- Discovery Sciences, R&D, AstraZeneca, CambridgeCB2 0AA, United Kingdom
| | | | - Jason Breed
- Discovery Sciences, R&D, AstraZeneca, CambridgeCB2 0AA, United Kingdom
| | - Karoline Leopold
- Gandeeva Therapeutics, Inc., Burnaby, British ColumbiaV5C 6N5, Canada
| | - Ankoor Patel
- Gandeeva Therapeutics, Inc., Burnaby, British ColumbiaV5C 6N5, Canada
| | | | - Bronwyn Lyons
- Gandeeva Therapeutics, Inc., Burnaby, British ColumbiaV5C 6N5, Canada
| | - Sriram Subramaniam
- Gandeeva Therapeutics, Inc., Burnaby, British ColumbiaV5C 6N5, Canada
- Department of Biochemistry and Molecular Biology, The University of British Columbia, Vancouver, BC V6T 1Z3, Canada
| | - Chris Phillips
- Discovery Sciences, R&D, AstraZeneca, CambridgeCB2 0AA, United Kingdom
| | - Todd O. Yeates
- Department of Energy, Institute for Genomics and Proteomics, University of California, Los Angeles, CA90095
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
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8
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David TI, Pestov NB, Korneenko TV, Barlev NA. Non-Immunoglobulin Synthetic Binding Proteins for Oncology. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:1232-1247. [PMID: 37770391 DOI: 10.1134/s0006297923090043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Revised: 08/01/2023] [Accepted: 08/01/2023] [Indexed: 09/30/2023]
Abstract
Extensive application of technologies like phage display in screening peptide and protein combinatorial libraries has not only facilitated creation of new recombinant antibodies but has also significantly enriched repertoire of the protein binders that have polypeptide scaffolds without homology to immunoglobulins. These innovative synthetic binding protein (SBP) platforms have grown in number and now encompass monobodies/adnectins, DARPins, lipocalins/anticalins, and a variety of miniproteins such as affibodies and knottins, among others. They serve as versatile modules for developing complex affinity tools that hold promise in both diagnostic and therapeutic settings. An optimal scaffold typically has low molecular weight, minimal immunogenicity, and demonstrates resistance against various challenging conditions, including proteolysis - making it potentially suitable for peroral administration. Retaining functionality under reducing intracellular milieu is also advantageous. However, paramount to its functionality is the scaffold's ability to tolerate mutations across numerous positions, allowing for the formation of a sufficiently large target binding region. This is achieved through the library construction, screening, and subsequent expression in an appropriate system. Scaffolds that exhibit high thermodynamic stability are especially coveted by the developers of new SBPs. These are steadily making their way into clinical settings, notably as antagonists of oncoproteins in signaling pathways. This review surveys the diverse landscape of SBPs, placing particular emphasis on the inhibitors targeting the oncoprotein KRAS, and highlights groundbreaking opportunities for SBPs in oncology.
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Affiliation(s)
- Temitope I David
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
- Laboratory of Molecular Oncology, Phystech School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, 141701, Russia
| | - Nikolay B Pestov
- Institute of Biomedical Chemistry, Moscow, 119121, Russia.
- Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Tatyana V Korneenko
- Group of Cross-Linking Enzymes, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow, 117997, Russia
| | - Nikolai A Barlev
- Institute of Biomedical Chemistry, Moscow, 119121, Russia
- Laboratory of Tick-Borne Encephalitis and Other Viral Encephalitides, Chumakov Federal Scientific Center for Research and Development of Immune-and-Biological Products, Russian Academy of Sciences, Moscow, 108819, Russia
- Institute of Cytology Russian Academy of Sciences, St.-Petersburg, 194064, Russia
- School of Medicine, Nazarbayev University, Astana, 010000, Kazakhstan
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9
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Shen F, Dassama LMK. Opportunities and challenges of protein-based targeted protein degradation. Chem Sci 2023; 14:8433-8447. [PMID: 37592990 PMCID: PMC10430753 DOI: 10.1039/d3sc02361c] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 07/02/2023] [Indexed: 08/19/2023] Open
Abstract
In the 20 years since the first report of a proteolysis targeting chimeric (PROTAC) molecule, targeted protein degradation (TPD) technologies have attempted to revolutionize the fields of chemical biology and biomedicine by providing exciting research opportunities and potential therapeutics. However, they primarily focus on the use of small molecules to recruit the ubiquitin proteasome system to mediate target protein degradation. This then limits protein targets to cytosolic domains with accessible and suitable small molecule binding pockets. In recent years, biologics such as proteins and nucleic acids have instead been used as binders for targeting proteins, thereby expanding the scope of TPD platforms to include secreted proteins, transmembrane proteins, and soluble but highly disordered intracellular proteins. This perspective summarizes the recent TPD platforms that utilize nanobodies, antibodies, and other proteins as binding moieties to deplete challenging targets, either through the ubiquitin proteasome system or the lysosomal degradation pathway. Importantly, the perspective also highlights opportunities and remaining challenges of current protein-based TPD technologies.
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Affiliation(s)
- Fangfang Shen
- Department of Chemistry, Sarafan ChEM-H Institute, Stanford University USA
| | - Laura M K Dassama
- Department of Chemistry, Sarafan ChEM-H Institute, Stanford University USA
- Department of Microbiology & Immunology, Stanford School of Medicine USA
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10
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Akkapeddi P, Hattori T, Khan I, Glasser E, Koide A, Ketavarapu G, Whaby M, Zuberi M, Teng KW, Lefler J, Maso L, Bang I, Ostrowski MC, O’Bryan JP, Koide S. Exploring switch II pocket conformation of KRAS(G12D) with mutant-selective monobody inhibitors. Proc Natl Acad Sci U S A 2023; 120:e2302485120. [PMID: 37399416 PMCID: PMC10334749 DOI: 10.1073/pnas.2302485120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 05/26/2023] [Indexed: 07/05/2023] Open
Abstract
The G12D mutation is among the most common KRAS mutations associated with cancer, in particular, pancreatic cancer. Here, we have developed monobodies, small synthetic binding proteins, that are selective to KRAS(G12D) over KRAS(wild type) and other oncogenic KRAS mutations, as well as over the G12D mutation in HRAS and NRAS. Crystallographic studies revealed that, similar to other KRAS mutant-selective inhibitors, the initial monobody bound to the S-II pocket, the groove between switch II and α3 helix, and captured this pocket in the most widely open form reported to date. Unlike other G12D-selective polypeptides reported to date, the monobody used its backbone NH group to directly recognize the side chain of KRAS Asp12, a feature that closely resembles that of a small-molecule inhibitor, MTRX1133. The monobody also directly interacted with H95, a residue not conserved in RAS isoforms. These features rationalize the high selectivity toward the G12D mutant and the KRAS isoform. Structure-guided affinity maturation resulted in monobodies with low nM KD values. Deep mutational scanning of a monobody generated hundreds of functional and nonfunctional single-point mutants, which identified crucial residues for binding and those that contributed to the selectivity toward the GTP- and GDP-bound states. When expressed in cells as genetically encoded reagents, these monobodies engaged selectively with KRAS(G12D) and inhibited KRAS(G12D)-mediated signaling and tumorigenesis. These results further illustrate the plasticity of the S-II pocket, which may be exploited for the design of next-generation KRAS(G12D)-selective inhibitors.
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Affiliation(s)
- Padma Akkapeddi
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
| | - Takamitsu Hattori
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
- Dertment of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY10016
| | - Imran Khan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC29425
- Ralph H. Johnson VA Medical Center, Charleston, SC29425
| | - Eliezra Glasser
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
| | - Akiko Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
- Department of Medicine, New York University Grossman School of Medicine, New York, NY10016
| | - Gayatri Ketavarapu
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
| | - Michael Whaby
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC29425
- Ralph H. Johnson VA Medical Center, Charleston, SC29425
| | - Mariyam Zuberi
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC29425
- Ralph H. Johnson VA Medical Center, Charleston, SC29425
| | - Kai Wen Teng
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
| | - Julia Lefler
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC29425
| | - Lorenzo Maso
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
| | - Injin Bang
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
| | - Michael C. Ostrowski
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC29425
| | - John P. O’Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC29425
- Ralph H. Johnson VA Medical Center, Charleston, SC29425
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY10016
- Dertment of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, NY10016
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11
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Tomazini A, Shifman JM. Targeting Ras with protein engineering. Oncotarget 2023; 14:672-687. [PMID: 37395750 DOI: 10.18632/oncotarget.28469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2023] Open
Abstract
Ras proteins are small GTPases that regulate cell growth and division. Mutations in Ras genes are associated with many types of cancer, making them attractive targets for cancer therapy. Despite extensive efforts, targeting Ras proteins with small molecules has been extremely challenging due to Ras's mostly flat surface and lack of small molecule-binding cavities. These challenges were recently overcome by the development of the first covalent small-molecule anti-Ras drug, sotorasib, highlighting the efficacy of Ras inhibition as a therapeutic strategy. However, this drug exclusively inhibits the Ras G12C mutant, which is not a prevalent mutation in most cancer types. Unlike the G12C variant, other Ras oncogenic mutants lack reactive cysteines, rendering them unsuitable for targeting via the same strategy. Protein engineering has emerged as a promising method to target Ras, as engineered proteins have the ability to recognize various surfaces with high affinity and specificity. Over the past few years, scientists have engineered antibodies, natural Ras effectors, and novel binding domains to bind to Ras and counteract its carcinogenic activities via a variety of strategies. These include inhibiting Ras-effector interactions, disrupting Ras dimerization, interrupting Ras nucleotide exchange, stimulating Ras interaction with tumor suppressor genes, and promoting Ras degradation. In parallel, significant advancements have been made in intracellular protein delivery, enabling the delivery of the engineered anti-Ras agents into the cellular cytoplasm. These advances offer a promising path for targeting Ras proteins and other challenging drug targets, opening up new opportunities for drug discovery and development.
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Affiliation(s)
- Atilio Tomazini
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
| | - Julia M Shifman
- Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem 9190401, Israel
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12
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Yin G, Huang J, Petela J, Jiang H, Zhang Y, Gong S, Wu J, Liu B, Shi J, Gao Y. Targeting small GTPases: emerging grasps on previously untamable targets, pioneered by KRAS. Signal Transduct Target Ther 2023; 8:212. [PMID: 37221195 DOI: 10.1038/s41392-023-01441-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/28/2023] [Accepted: 04/14/2023] [Indexed: 05/25/2023] Open
Abstract
Small GTPases including Ras, Rho, Rab, Arf, and Ran are omnipresent molecular switches in regulating key cellular functions. Their dysregulation is a therapeutic target for tumors, neurodegeneration, cardiomyopathies, and infection. However, small GTPases have been historically recognized as "undruggable". Targeting KRAS, one of the most frequently mutated oncogenes, has only come into reality in the last decade due to the development of breakthrough strategies such as fragment-based screening, covalent ligands, macromolecule inhibitors, and PROTACs. Two KRASG12C covalent inhibitors have obtained accelerated approval for treating KRASG12C mutant lung cancer, and allele-specific hotspot mutations on G12D/S/R have been demonstrated as viable targets. New methods of targeting KRAS are quickly evolving, including transcription, immunogenic neoepitopes, and combinatory targeting with immunotherapy. Nevertheless, the vast majority of small GTPases and hotspot mutations remain elusive, and clinical resistance to G12C inhibitors poses new challenges. In this article, we summarize diversified biological functions, shared structural properties, and complex regulatory mechanisms of small GTPases and their relationships with human diseases. Furthermore, we review the status of drug discovery for targeting small GTPases and the most recent strategic progress focused on targeting KRAS. The discovery of new regulatory mechanisms and development of targeting approaches will together promote drug discovery for small GTPases.
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Affiliation(s)
- Guowei Yin
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China.
| | - Jing Huang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Johnny Petela
- Wake Forest University School of Medicine, Winston-Salem, NC, 27101, USA
| | - Hongmei Jiang
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
| | - Yuetong Zhang
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Siqi Gong
- The Seventh Affiliated Hospital of Sun Yat-sen University, Shenzhen, 518107, China
- School of Medicine, Sun Yat-Sen University, Shenzhen, 518107, China
| | - Jiaxin Wu
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China
| | - Bei Liu
- National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, 100871, China
| | - Jianyou Shi
- Department of Pharmacy, Personalized Drug Therapy Key Laboratory of Sichuan Province, Sichuan Academy of Medical Sciences & Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology, Chengdu, 610072, China.
| | - Yijun Gao
- State Key Laboratory of Oncology in South China, Guangdong Key Laboratory of Nasopharyngeal Carcinoma Diagnosis and Therapy, Sun Yat-sen University Cancer Center, Guangzhou, 510060, China.
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13
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Haley RM, Chan A, Billingsley MM, Gong N, Padilla MS, Kim EH, Wang HH, Yin D, Wangensteen KJ, Tsourkas A, Mitchell MJ. Lipid Nanoparticle Delivery of Small Proteins for Potent In Vivo RAS Inhibition. ACS APPLIED MATERIALS & INTERFACES 2023; 15:21877-21892. [PMID: 37115558 PMCID: PMC10727849 DOI: 10.1021/acsami.3c01501] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Mutated RAS proteins are potent oncogenic drivers and have long been considered "undruggable". While RAS-targeting therapies have recently shown promise, there remains a clinical need for RAS inhibitors with more diverse targets. Small proteins represent a potential new therapeutic option, including K27, a designed ankyrin repeat protein (DARPin) engineered to inhibit RAS. However, K27 functions intracellularly and is incapable of entering the cytosol on its own, currently limiting its utility. To overcome this barrier, we have engineered a lipid nanoparticle (LNP) platform for potent delivery of functional K27-D30─a charge-modified version of the protein─intracellularly in vitro and in vivo. This system efficiently encapsulates charge-modified proteins, facilitates delivery in up to 90% of cells in vitro, and maintains potency after at least 45 days of storage. In vivo, these LNPs deliver K27-D30 to the cytosol of cancerous cells in the liver, inhibiting RAS-driven growth and ultimately reducing tumor load in an HTVI-induced mouse model of hepatocellular carcinoma. This work shows that K27 holds promise as a new cancer therapeutic when delivered using this LNP platform. Furthermore, this technology has the potential to broaden the use of LNPs to include new cargo types─beyond RNA─for diverse therapeutic applications.
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Affiliation(s)
- Rebecca M. Haley
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Alexander Chan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | | | - Ningqiang Gong
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Marshall S. Padilla
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Emily H. Kim
- Department of Chemical and Biomolecular Engineering, University of Pennsylvania
| | - Hejia Henry Wang
- Department of Biochemistry and Molecular Biophysics, University of Pennsylvania
| | - Dingzi Yin
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN 55902
| | - Kirk J. Wangensteen
- Division of Gastroenterology and Hepatology, Department of Medicine, Mayo Clinic, Rochester, MN 55902
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
| | - Michael J. Mitchell
- Department of Bioengineering, University of Pennsylvania, Philadelphia, PA 19104
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14
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Simanshu DK, Philips MR, Hancock JF. Consensus on the RAS dimerization hypothesis: Strong evidence for lipid-mediated clustering but not for G-domain-mediated interactions. Mol Cell 2023; 83:1210-1215. [PMID: 36990093 PMCID: PMC10150945 DOI: 10.1016/j.molcel.2023.03.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 02/24/2023] [Accepted: 03/07/2023] [Indexed: 03/30/2023]
Abstract
One of the open questions in RAS biology is the existence of RAS dimers and their role in RAF dimerization and activation. The idea of RAS dimers arose from the discovery that RAF kinases function as obligate dimers, which generated the hypothesis that RAF dimer formation might be nucleated by G-domain-mediated RAS dimerization. Here, we review the evidence for RAS dimerization and describe a recent discussion among RAS researchers that led to a consensus that the clustering of two or more RAS proteins is not due to the stable association of G-domains but, instead, is a consequence of RAS C-terminal membrane anchors and the membrane phospholipids with which they interact.
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Affiliation(s)
- Dhirendra K Simanshu
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
| | - Mark R Philips
- Perlmutter Cancer Center, NYU Grossman School of Medicine, New York, NY, USA.
| | - John F Hancock
- Department of Integrative Biology and Pharmacology, McGovern Medical School, University of Texas Health Science Center, Houston, TX, USA.
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15
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Intracellular Antibodies for Drug Discovery and as Drugs of the Future. Antibodies (Basel) 2023; 12:antib12010024. [PMID: 36975371 PMCID: PMC10044824 DOI: 10.3390/antib12010024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 03/03/2023] [Accepted: 03/06/2023] [Indexed: 03/19/2023] Open
Abstract
The application of antibodies in cells was first shown in the early 1990s, and subsequently, the field of intracellular antibodies has expanded to encompass antibody fragments and their use in target validation and as engineered molecules that can be fused to moieties (referred to as warheads) to replace the Fc effector region of a whole immunoglobulin to elicit intracellular responses, such as cell death pathways or protein degradation. These various forms of intracellular antibodies have largely been used as research tools to investigate function within cells by perturbing protein activity. New applications of such molecules are on the horizon, namely their use as drugs per se and as templates for small-molecule drug discovery. The former is a potential new pharmacology that could harness the power and flexibility of molecular biology to generate new classes of drugs (herein referred to as macrodrugs when used in the context of disease control). Delivery of engineered intracellular antibodies, and other antigen-binding macromolecules formats, into cells to produce a therapeutic effect could be applied to any therapeutic area where regulation, degradation or other kinds of manipulation of target proteins can produce a therapeutic effect. Further, employing single-domain antibody fragments as competitors in small-molecule screening has been shown to enable identification of drug hits from diverse chemical libraries. Compounds selected in this way can mimic the effects of the intracellular antibodies that have been used for target validation. The capability of intracellular antibodies to discriminate between closely related proteins lends a new dimension to drug screening and drug development.
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16
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Jung YH, Choi Y, Seo HD, Seo MH, Kim HS. A conformation-selective protein binder for a KRAS mutant inhibits the interaction between RAS and RAF. Biochem Biophys Res Commun 2023; 645:110-117. [PMID: 36682330 DOI: 10.1016/j.bbrc.2023.01.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/10/2023] [Indexed: 01/13/2023]
Abstract
Small GTPases are key signaling nodes that regulate the cellular processes and subcellular events, and their abnormal activities and dysregulations are closely linked with diverse cancers. Here, we report the development of conformation-selective protein binders for a KRAS mutant. The conformation-specific protein binders were selected from a repebody scaffold composed of LRR (Leucine-rich repeat) modules through phage display and modular engineering against constitute active conformation of KRAS. Epitope of the selected binders was mapped to be located close to switch I of KRAS. The conformation-selective protein binders were shown to effectively block the interaction between active KRAS and RAS-binding domain of BRAF, suppressing the KRAS-mediated downstream signaling.
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Affiliation(s)
- Youn Hee Jung
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, South Korea
| | - Yoonjoo Choi
- Combinatorial Tumor Immunotherapy MRC, Chonnam National University Medical School, Hwasun-gun, Jeollanam-do, 58128, South Korea
| | - Hyo-Deok Seo
- Aging and Metabolism Research Group, Korea Food Research Institute, Wanju-gun, Jeollabuk-do, 55365, South Korea
| | - Moon-Hyeong Seo
- Natural Product Research Center, Korea Institute of Science and Technology (KIST), Gangneung, 25451, South Korea.
| | - Hak-Sung Kim
- Department of Biological Sciences, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, South Korea.
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17
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Lam KK, Wong SH, Cheah PY. Targeting the 'Undruggable' Driver Protein, KRAS, in Epithelial Cancers: Current Perspective. Cells 2023; 12:cells12040631. [PMID: 36831298 PMCID: PMC9954350 DOI: 10.3390/cells12040631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 01/30/2023] [Accepted: 02/10/2023] [Indexed: 02/18/2023] Open
Abstract
This review summarizes recent development in synthetic drugs and biologics targeting intracellular driver genes in epithelial cancers, focusing on KRAS, and provides a current perspective and potential leads for the field. Compared to biologics, small molecule inhibitors (SMIs) readily penetrate cells, thus being able to target intracellular proteins. However, SMIs frequently suffer from pleiotropic effects, off-target cytotoxicity and invariably elicit resistance. In contrast, biologics are much larger molecules limited by cellular entry, but if this is surmounted, they may have more specific effects and less therapy-induced resistance. Exciting breakthroughs in the past two years include engineering of non-covalent KRAS G12D-specific inhibitor, probody bispecific antibodies, drug-peptide conjugate as MHC-restricted neoantigen to prompt immune response by T-cells, and success in the adoptive cell therapy front in both breast and pancreatic cancers.
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Affiliation(s)
- Kuen Kuen Lam
- Department of Colorectal Surgery, Singapore General Hospital, Singapore 169856, Singapore
| | | | - Peh Yean Cheah
- Department of Colorectal Surgery, Singapore General Hospital, Singapore 169856, Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore 117549, Singapore
- Duke-NUS Medical School, National University of Singapore, Singapore 169857, Singapore
- Correspondence:
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18
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Ismail M, Martin SR, George R, Houghton F, Kelly G, Chaleil RAG, Anastasiou P, Wang X, O'Reilly N, Federico S, Joshi D, Nagaraj H, Cooley R, Hui NS, Molina-Arcas M, Hancock DC, Tavassoli A, Downward J. Characterisation of a cyclic peptide that binds to the RAS binding domain of phosphoinositide 3-kinase p110α. Sci Rep 2023; 13:1889. [PMID: 36732563 PMCID: PMC9894841 DOI: 10.1038/s41598-023-28756-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 01/24/2023] [Indexed: 02/04/2023] Open
Abstract
P110α is a member of the phosphoinositide 3-kinase (PI3K) enzyme family that functions downstream of RAS. RAS proteins contribute to the activation of p110α by interacting directly with its RAS binding domain (RBD), resulting in the promotion of many cellular functions such as cell growth, proliferation and survival. Previous work from our lab has highlighted the importance of the p110α/RAS interaction in tumour initiation and growth. Here we report the discovery and characterisation of a cyclic peptide inhibitor (cyclo-CRVLIR) that interacts with the p110α-RBD and blocks its interaction with KRAS. cyclo-CRVLIR was discovered by screening a "split-intein cyclisation of peptides and proteins" (SICLOPPS) cyclic peptide library. The primary cyclic peptide hit from the screen initially showed a weak affinity for the p110α-RBD (Kd about 360 µM). However, two rounds of amino acid substitution led to cyclo-CRVLIR, with an improved affinity for p110α-RBD in the low µM (Kd 3 µM). We show that cyclo-CRVLIR binds selectively to the p110α-RBD but not to KRAS or the structurally-related RAF-RBD. Further, using biophysical, biochemical and cellular assays, we show that cyclo-CRVLIR effectively blocks the p110α/KRAS interaction in a dose dependent manner and reduces phospho-AKT levels in several oncogenic KRAS cell lines.
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Affiliation(s)
- Mohamed Ismail
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Stephen R Martin
- Structural Biology, Science Technology Platforms, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Roger George
- Structural Biology, Science Technology Platforms, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Francesca Houghton
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Geoff Kelly
- Structural Biology, Science Technology Platforms, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Raphaël A G Chaleil
- Biomolecular Modelling Lab, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Panayiotis Anastasiou
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Xinyue Wang
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Nicola O'Reilly
- Peptide Chemistry, Science Technology Platforms, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Stefania Federico
- Peptide Chemistry, Science Technology Platforms, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Dhira Joshi
- Peptide Chemistry, Science Technology Platforms, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Hemavathi Nagaraj
- Peptide Chemistry, Science Technology Platforms, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Rachel Cooley
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ning Sze Hui
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Miriam Molina-Arcas
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - David C Hancock
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Ali Tavassoli
- School of Chemistry, University of Southampton, Southampton, SO17 1BJ, UK
| | - Julian Downward
- Oncogene Biology Laboratory, Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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19
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Whaby M, Wallon L, Mazzei M, Khan I, Teng KW, Koide S, O’Bryan JP. Mutations in the α4-α5 allosteric lobe of RAS do not significantly impair RAS signaling or self-association. J Biol Chem 2022; 298:102661. [PMID: 36334633 PMCID: PMC9763690 DOI: 10.1016/j.jbc.2022.102661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 10/21/2022] [Accepted: 10/27/2022] [Indexed: 11/11/2022] Open
Abstract
Mutations in one of the three RAS genes (HRAS, KRAS, and NRAS) are present in nearly 20% of all human cancers. These mutations shift RAS to the GTP-loaded active state due to impairment in the intrinsic GTPase activity and disruption of GAP-mediated GTP hydrolysis, resulting in constitutive activation of effectors such as RAF. Because activation of RAF involves dimerization, RAS dimerization has been proposed as an important step in RAS-mediated activation of effectors. The α4-α5 allosteric lobe of RAS has been proposed as a RAS dimerization interface. Indeed, the NS1 monobody, which binds the α4-α5 region within the RAS G domain, inhibits RAS-dependent signaling and transformation as well as RAS nanoclustering at the plasma membrane. Although these results are consistent with a model in which the G domain dimerizes through the α4-α5 region, the isolated G domain of RAS lacks intrinsic dimerization capacity. Furthermore, prior studies analyzing α4-α5 point mutations have reported mixed effects on RAS function. Here, we evaluated the activity of a panel of single amino acid substitutions in the α4-α5 region implicated in RAS dimerization. We found that these proposed "dimerization-disrupting" mutations do not significantly impair self-association, signaling, or transformation of oncogenic RAS. These results are consistent with a model in which activated RAS protomers cluster in close proximity to promote the dimerization of their associated effector proteins (e.g., RAF) without physically associating into dimers mediated by specific molecular interactions. Our findings suggest the need for a nonconventional approach to developing therapeutics targeting the α4-α5 region.
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Affiliation(s)
- Michael Whaby
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA,Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Lauren Wallon
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA
| | - Megan Mazzei
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA,Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Imran Khan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA,Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA,Ralph H. Johnson VA Medical Center, Charleston, South Carolina, USA
| | - Kai Wen Teng
- Perlmutter Cancer Center, New York University Langone Health, New York, New York, USA
| | - Shohei Koide
- Department of Biochemistry and Molecular Pharmacology, New York University Grossman School of Medicine, New York, New York, USA,Perlmutter Cancer Center, New York University Langone Health, New York, New York, USA,For correspondence: John P. O’Bryan; Shohei Koide
| | - John P. O’Bryan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, South Carolina, USA,Hollings Cancer Center, Medical University of South Carolina, Charleston, South Carolina, USA,Ralph H. Johnson VA Medical Center, Charleston, South Carolina, USA,For correspondence: John P. O’Bryan; Shohei Koide
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20
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Wallon L, Khan I, Teng KW, Koide A, Zuberi M, Li J, Ketavarapu G, Traaseth NJ, O’Bryan JP, Koide S. Inhibition of RAS-driven signaling and tumorigenesis with a pan-RAS monobody targeting the Switch I/II pocket. Proc Natl Acad Sci U S A 2022; 119:e2204481119. [PMID: 36252024 PMCID: PMC9618066 DOI: 10.1073/pnas.2204481119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 08/25/2022] [Indexed: 11/18/2022] Open
Abstract
RAS mutants are major therapeutic targets in oncology with few efficacious direct inhibitors available. The identification of a shallow pocket near the Switch II region on RAS has led to the development of small-molecule drugs that target this site and inhibit KRAS(G12C) and KRAS(G12D). To discover other regions on RAS that may be targeted for inhibition, we have employed small synthetic binding proteins termed monobodies that have a strong propensity to bind to functional sites on a target protein. Here, we report a pan-RAS monobody, termed JAM20, that bound to all RAS isoforms with nanomolar affinity and demonstrated limited nucleotide-state specificity. Upon intracellular expression, JAM20 potently inhibited signaling mediated by all RAS isoforms and reduced oncogenic RAS-mediated tumorigenesis in vivo. NMR and mutation analysis determined that JAM20 bound to a pocket between Switch I and II, which is similarly targeted by low-affinity, small-molecule inhibitors, such as BI-2852, whose in vivo efficacy has not been demonstrated. Furthermore, JAM20 directly competed with both the RAF(RBD) and BI-2852. These results provide direct validation of targeting the Switch I/II pocket for inhibiting RAS-driven tumorigenesis. More generally, these results demonstrate the utility of tool biologics as probes for discovering and validating druggable sites on challenging targets.
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Affiliation(s)
- Lauren Wallon
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016
| | - Imran Khan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425
- Ralph H. Johnson VA Medical Center, Charleston, SC 29401
| | - Kai Wen Teng
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016
| | - Akiko Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016
- Department of Medicine, New York University School of Medicine, New York, NY 10016
| | - Mariyam Zuberi
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425
- Ralph H. Johnson VA Medical Center, Charleston, SC 29401
| | - Jianping Li
- Department of Chemistry, New York University, New York, NY 10003
| | - Gayatri Ketavarapu
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016
| | | | - John P. O’Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC 29425
- Ralph H. Johnson VA Medical Center, Charleston, SC 29401
| | - Shohei Koide
- Laura and Isaac Perlmutter Cancer Center, New York University Langone Health, New York, NY 10016
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016
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21
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Keller L, Tardy C, Ligat L, Le Pennec S, Bery N, Koraïchi F, Chinestra P, David M, Gence R, Favre G, Cabantous S, Olichon A. Tripartite split-GFP assay to identify selective intracellular nanobody that suppresses GTPase RHOA subfamily downstream signaling. Front Immunol 2022; 13:980539. [PMID: 36059552 PMCID: PMC9433928 DOI: 10.3389/fimmu.2022.980539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 07/29/2022] [Indexed: 11/24/2022] Open
Abstract
Strategies based on intracellular expression of artificial binding domains present several advantages over manipulating nucleic acid expression or the use of small molecule inhibitors. Intracellularly-functional nanobodies can be considered as promising macrodrugs to study key signaling pathways by interfering with protein-protein interactions. With the aim of studying the RAS-related small GTPase RHOA family, we previously isolated, from a synthetic phage display library, nanobodies selective towards the GTP-bound conformation of RHOA subfamily proteins that lack selectivity between the highly conserved RHOA-like and RAC subfamilies of GTPases. To identify RHOA/ROCK pathway inhibitory intracellular nanobodies, we implemented a stringent, subtractive phage display selection towards RHOA-GTP followed by a phenotypic screen based on F-actin fiber loss. Intracellular interaction and intracellular selectivity between RHOA and RAC1 proteins was demonstrated by adapting the sensitive intracellular protein-protein interaction reporter based on the tripartite split-GFP method. This strategy led us to identify a functional intracellular nanobody, hereafter named RH28, that does not cross-react with the close RAC subfamily and blocks/disrupts the RHOA/ROCK signaling pathway in several cell lines without further engineering or functionalization. We confirmed these results by showing, using SPR assays, the high specificity of the RH28 nanobody towards the GTP-bound conformation of RHOA subfamily GTPases. In the metastatic melanoma cell line WM266-4, RH28 expression triggered an elongated cellular phenotype associated with a loss of cellular contraction properties, demonstrating the efficient intracellular blocking of RHOA/B/C proteins downstream interactions without the need of manipulating endogenous gene expression. This work paves the way for future therapeutic strategies based on protein-protein interaction disruption with intracellular antibodies.
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Affiliation(s)
- Laura Keller
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Laboratoire de Biologie Médicale Oncologique, IUCT-Oncopôle, Toulouse, France
| | - Claudine Tardy
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Laetitia Ligat
- Le Pôle Technologique du Centre de Recherches en Cancérologie de Toulouse, Plateau de Protéomique, Toulouse, France
| | - Soazig Le Pennec
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Nicolas Bery
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Faten Koraïchi
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Patrick Chinestra
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Mélissa David
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Rémi Gence
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
| | - Gilles Favre
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Laboratoire de Biologie Médicale Oncologique, IUCT-Oncopôle, Toulouse, France
| | - Stéphanie Cabantous
- Laboratoire de Biologie Médicale Oncologique, IUCT-Oncopôle, Toulouse, France
- *Correspondence: Stéphanie Cabantous, ; Aurélien Olichon,
| | - Aurélien Olichon
- Centre de Recherche en Cancérologie de Toulouse (CRCT), Université de Toulouse, Institut National de la Santé et de la Recherche Médicale (INSERM), Centre National de la Recherche Scientifique (CNRS), Université Toulouse III-Paul Sabatier, Centre de Recherches en Cancérologie de Toulouse (CRCT), Toulouse, France
- Institut National de la Santé et de la Recherche Médicale (INSERM), Unité Mixte de Recherche (UMR) 1188 Diabète athérothrombose Réunion Océan Indien (DéTROI), Université de La Réunion, Saint Denis de La Réunion, France
- *Correspondence: Stéphanie Cabantous, ; Aurélien Olichon,
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22
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Böldicke T. Therapeutic Potential of Intrabodies for Cancer Immunotherapy: Current Status and Future Directions. Antibodies (Basel) 2022; 11:antib11030049. [PMID: 35892709 PMCID: PMC9326752 DOI: 10.3390/antib11030049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/29/2022] [Accepted: 07/12/2022] [Indexed: 12/04/2022] Open
Abstract
Tumor cells are characterized by overexpressed tumor-associated antigens or mutated neoantigens, which are expressed on the cell surface or intracellularly. One strategy of cancer immunotherapy is to target cell-surface-expressed tumor-associated antigens (TAAs) with therapeutic antibodies. For targeting TAAs or neoantigens, adoptive T-cell therapies with activated autologous T cells from cancer patients transduced with novel recombinant TCRs or chimeric antigen receptors have been successfully applied. Many TAAs and most neoantigens are expressed in the cytoplasm or nucleus of tumor cells. As alternative to adoptive T-cell therapy, the mRNA of intracellular tumor antigens can be depleted by RNAi, the corresponding genes or proteins deleted by CRISPR-Cas or inactivated by kinase inhibitors or by intrabodies, respectively. Intrabodies are suitable to knockdown TAAs and neoantigens without off-target effects. RNA sequencing and proteome analysis of single tumor cells combined with computational methods is bringing forward the identification of new neoantigens for the selection of anti-cancer intrabodies, which can be easily performed using phage display antibody repertoires. For specifically delivering intrabodies into tumor cells, the usage of new capsid-modified adeno-associated viruses and lipid nanoparticles coupled with specific ligands to cell surface receptors can be used and might bring cancer intrabodies into the clinic.
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Affiliation(s)
- Thomas Böldicke
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
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23
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Sorbara M, Cordelier P, Bery N. Antibody-Based Approaches to Target Pancreatic Tumours. Antibodies (Basel) 2022; 11:antib11030047. [PMID: 35892707 PMCID: PMC9326758 DOI: 10.3390/antib11030047] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 07/04/2022] [Accepted: 07/08/2022] [Indexed: 02/01/2023] Open
Abstract
Pancreatic cancer is an aggressive cancer with a dismal prognosis. This is due to the difficulty to detect the disease at an early and curable stage. In addition, only limited treatment options are available, and they are confronted by mechanisms of resistance. Monoclonal antibody (mAb) molecules are highly specific biologics that can be directly used as a blocking agent or modified to deliver a drug payload depending on the desired outcome. They are widely used to target extracellular proteins, but they can also be employed to inhibit intracellular proteins, such as oncoproteins. While mAbs are a class of therapeutics that have been successfully employed to treat many cancers, they have shown only limited efficacy in pancreatic cancer as a monotherapy so far. In this review, we will discuss the challenges, opportunities and hopes to use mAbs for pancreatic cancer treatment, diagnostics and imagery.
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24
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Thermal Shift Assay for Small GTPase Stability Screening: Evaluation and Suitability. Int J Mol Sci 2022; 23:ijms23137095. [PMID: 35806100 PMCID: PMC9266822 DOI: 10.3390/ijms23137095] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/01/2023] Open
Abstract
Thermal unfolding methods are commonly used as a predictive technique by tracking the protein's physical properties. Inherent protein thermal stability and unfolding profiles of biotherapeutics can help to screen or study potential drugs and to find stabilizing or destabilizing conditions. Differential scanning calorimetry (DSC) is a 'Gold Standard' for thermal stability assays (TSA), but there are also a multitude of other methodologies, such as differential scanning fluorimetry (DSF). The use of an external probe increases the assay throughput, making it more suitable for screening studies, but the current methodologies suffer from relatively low sensitivity. While DSF is an effective tool for screening, interpretation and comparison of the results is often complicated. To overcome these challenges, we compared three thermal stability probes in small GTPase stability studies: SYPRO Orange, 8-anilino-1-naphthalenesulfonic acid (ANS), and the Protein-Probe. We studied mainly KRAS, as a proof of principle to obtain biochemical knowledge through TSA profiles. We showed that the Protein-Probe can work at lower concentration than the other dyes, and its sensitivity enables effective studies with non-covalent and covalent drugs at the nanomolar level. Using examples, we describe the parameters, which must be taken into account when characterizing the effect of drug candidates, of both small molecules and Designed Ankyrin Repeat Proteins.
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25
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Parker MI, Meyer JE, Golemis EA, Dunbrack RL. Delineating The RAS Conformational Landscape. Cancer Res 2022; 82:2485-2498. [PMID: 35536216 DOI: 10.1158/0008-5472.can-22-0804] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/16/2022]
Abstract
Mutations in RAS isoforms (KRAS, NRAS, and HRAS) are among the most frequent oncogenic alterations in many cancers, making these proteins high priority therapeutic targets. Effectively targeting RAS isoforms requires an exact understanding of their active, inactive, and druggable conformations. However, there is no structural catalog of RAS conformations to guide therapeutic targeting or examining the structural impact of RAS mutations. Here we present an expanded classification of RAS conformations based on analyses of the catalytic switch 1 (SW1) and switch 2 (SW2) loops. From 721 human KRAS, NRAS, and HRAS structures available in the Protein Data Bank (206 RAS-protein co-complexes, 190 inhibitor-bound, and 325 unbound, including 204 WT and 517 mutated structures), we created a broad conformational classification based on the spatial positions of Y32 in SW1 and Y71 in SW2. Clustering all well-modeled SW1 and SW2 loops using a density-based machine learning algorithm defined additional conformational subsets, some previously undescribed. Three SW1 conformations and nine SW2 conformations were identified, each associated with different nucleotide states (GTP-bound, nucleotide-free, and GDP-bound) and specific bound proteins or inhibitor sites. The GTP-bound SW1 conformation could be further subdivided based on the hydrogen bond type made between Y32 and the GTP γ-phosphate. Further analysis clarified the catalytic impact of G12D and G12V mutations and the inhibitor chemistries that bind to each druggable RAS conformation. Overall, this study has expanded our understanding of RAS structural biology, which could facilitate future RAS drug discovery.
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Affiliation(s)
- Mitchell I Parker
- Drexel University College of Medicine, Philadelphia, PA, United States
| | - Joshua E Meyer
- Fox Chase Cancer Center, Philadelphia, PA, United States
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26
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Chan A, Wang HH, Haley RM, Song C, Gonzalez-Martinez D, Bugaj L, Mitchell MJ, Tsourkas A. Cytosolic Delivery of Small Protein Scaffolds Enables Efficient Inhibition of Ras and Myc. Mol Pharm 2022; 19:1104-1116. [PMID: 35225618 PMCID: PMC8983512 DOI: 10.1021/acs.molpharmaceut.1c00798] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The ability to deliver small protein scaffolds intracellularly could enable the targeting and inhibition of many therapeutic targets that are not currently amenable to inhibition with small-molecule drugs. Here, we report the engineering of small protein scaffolds with anionic polypeptides (ApPs) to promote electrostatic interactions with positively charged nonviral lipid-based delivery systems. Proteins fused with ApPs are either complexed with off-the-shelf cationic lipids or encapsulated within ionizable lipid nanoparticles for highly efficient cytosolic delivery (up to 90%). The delivery of protein inhibitors is used to inhibit two common proto-oncogenes, Ras and Myc, in two cancer cell lines. This report demonstrates the feasibility of combining minimally engineered small protein scaffolds with tractable nanocarriers to inhibit intracellular proteins that are generally considered "undruggable" with current small molecule drugs and biologics.
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Affiliation(s)
- Alexander Chan
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Hejia Henry Wang
- Department Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Rebecca M. Haley
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Cindy Song
- Department of Molecular Biology and Biochemistry, Rutgers University, New Brunswick, New Jersey 08901, United States
| | - David Gonzalez-Martinez
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Lukasz Bugaj
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Michael J. Mitchell
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Cardiovascular Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Institute for Regenerative Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Andrew Tsourkas
- Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Institute for Immunology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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27
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Ozdemir ES, Koester AM, Nan X. Ras Multimers on the Membrane: Many Ways for a Heart-to-Heart Conversation. Genes (Basel) 2022; 13:genes13020219. [PMID: 35205266 PMCID: PMC8872464 DOI: 10.3390/genes13020219] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 12/31/2022] Open
Abstract
Formation of Ras multimers, including dimers and nanoclusters, has emerged as an exciting, new front of research in the ‘old’ field of Ras biomedicine. With significant advances made in the past few years, we are beginning to understand the structure of Ras multimers and, albeit preliminary, mechanisms that regulate their formation in vitro and in cells. Here we aim to synthesize the knowledge accrued thus far on Ras multimers, particularly the presence of multiple globular (G-) domain interfaces, and discuss how membrane nanodomain composition and structure would influence Ras multimer formation. We end with some general thoughts on the potential implications of Ras multimers in basic and translational biology.
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Affiliation(s)
- E. Sila Ozdemir
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
| | - Anna M. Koester
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
| | - Xiaolin Nan
- Cancer Early Detection Advanced Research Center, Knight Cancer Institute, Oregon Health & Science University, 2720 S Moody Ave., Portland, OR 97201, USA;
- Program in Quantitative and Systems Biology, Department of Biomedical Engineering, Oregon Health & Science University, 2730 S Moody Ave., Portland, OR 97201, USA;
- Correspondence:
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28
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Khan I, Marelia-Bennet C, Lefler J, Zuberi M, Denbaum E, Koide A, Connor DM, Broome AM, Pécot T, Timmers C, Ostrowski MC, Koide S, O’Bryan JP. Targeting the KRAS α4-α5 allosteric interface inhibits pancreatic cancer tumorigenesis. Small GTPases 2022; 13:114-127. [PMID: 33949915 PMCID: PMC9707541 DOI: 10.1080/21541248.2021.1906621] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/10/2021] [Accepted: 03/17/2021] [Indexed: 02/07/2023] Open
Abstract
RAS is the most frequently mutated oncogene in human cancer with nearly ~20% of cancer patients possessing mutations in one of three RAS genes (K, N or HRAS). However, KRAS is mutated in nearly 90% of pancreatic ductal carcinomas (PDAC). Although pharmacological inhibition of RAS has been challenging, KRAS(G12C)-specific inhibitors have recently entered the clinic. While KRAS(G12C) is frequently expressed in lung cancers, it is rare in PDAC. Thus, more broadly efficacious RAS inhibitors are needed for treating KRAS mutant-driven cancers such as PDAC. A RAS-specific tool biologic, NS1 Monobody, inhibits HRAS- and KRAS-mediated signalling and oncogenic transformation both in vitro and in vivo by targeting the α4-α5 allosteric site of RAS and blocking RAS self-association. Here, we evaluated the efficacy of targeting the α4-α5 interface of KRAS as an approach to inhibit PDAC development using an immunocompetent orthotopic mouse model. Chemically regulated NS1 expression inhibited ERK and AKT activation in KRAS(G12D) mutant KPC PDAC cells and reduced the formation and progression of pancreatic tumours. NS1-expressing tumours were characterized by increased infiltration of CD4 + T helper cells. These results suggest that targeting the #x3B1;4-#x3B1;5 allosteric site of KRAS may represent a viable therapeutic approach for inhibiting KRAS-mutant pancreatic tumours.
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Affiliation(s)
- Imran Khan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
- Ralph H. Johnson VA Medical Center, Charleston, SC, USA
| | - Catherine Marelia-Bennet
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
- Department of Biochemistry and Molecular Biology, New York University School of Medicine, NY, New York, USA
| | - Julia Lefler
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
- Department of Biochemistry and Molecular Biology, New York University School of Medicine, NY, New York, USA
| | - Mariyam Zuberi
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
- Ralph H. Johnson VA Medical Center, Charleston, SC, USA
| | - Eric Denbaum
- Perlmutter Cancer Center, New York University Langone Health, NY, New York, USA
| | - Akiko Koide
- Perlmutter Cancer Center, New York University Langone Health, NY, New York, USA
- Department of Medicine, New York University School of Medicine, NY, New York, USA
| | - Dean M. Connor
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Ann-Marie Broome
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Thierry Pécot
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
- Department of Medicine, New York University School of Medicine, NY, New York, USA
| | - Cynthia Timmers
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
- Department of Medicine, New York University School of Medicine, NY, New York, USA
| | - Michael C. Ostrowski
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
- Department of Biochemistry and Molecular Biology, New York University School of Medicine, NY, New York, USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Health, NY, New York, USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, USA
| | - John P. O’Bryan
- Department of Cell and Molecular Pharmacology & Experimental Therapeutics, Medical University of South Carolina, Charleston, SC, USA
- Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
- Ralph H. Johnson VA Medical Center, Charleston, SC, USA
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29
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Bery N, Rabbitts T. A Cell-based Screening Method Using an Intracellular Antibody for Discovering Small Molecules Targeting Hard-to-drug Proteins. Bio Protoc 2022; 12:e4324. [DOI: 10.21769/bioprotoc.4324] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 08/19/2021] [Accepted: 01/12/2022] [Indexed: 11/02/2022] Open
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30
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Zhang J, Zhang J, Liu Q, Fan XX, Leung ELH, Yao XJ, Liu L. Resistance looms for KRAS G12C inhibitors and rational tackling strategies. Pharmacol Ther 2021; 229:108050. [PMID: 34864132 DOI: 10.1016/j.pharmthera.2021.108050] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/28/2021] [Accepted: 11/29/2021] [Indexed: 12/13/2022]
Abstract
KRAS mutations are one of the most frequent activating alterations in carcinoma. Recent efforts have witnessed a revolutionary strategy for KRAS G12C inhibitors with exhibiting conspicuous clinical responses across multiple tumor types, providing new impetus for renewed drug development and culminating in sotorasib with approximately 6-month median progression-free survival in KRAS G12C-driven lung cancer. However, diverse genomic and histological mechanisms conferring resistance to KRAS G12C inhibitors may limit their clinical efficacy. Herein, we first briefly discuss the recent resistance looms for KRAS G12C inhibitors, focusing on their clinical trials. We then comprehensively interrogate and underscore our current understanding of resistance mechanisms and the necessity of incorporating genomic analyses into the clinical investigation to further decipher resistance mechanisms. Finally, we highlight the future role of novel treatment strategies especially rational identification of targeted combinatorial approaches in tackling drug resistance, and propose our views on including the application of robust biomarkers to precisely guide combination medication regimens.
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Affiliation(s)
- Junmin Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau (SAR), China; School of Pharmacy, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China
| | - Juanhong Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau (SAR), China; School of Pharmacy, State Key Laboratory of Applied Organic Chemistry, College of Chemistry and Chemical Engineering, Lanzhou University, Lanzhou 730000, China; College of Life Science, Northwest Normal University, Lanzhou 730070, China
| | - Qing Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau (SAR), China
| | - Xing-Xing Fan
- State Key Laboratory of Quality Research in Chinese Medicine, Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau (SAR), China
| | - Elaine Lai-Han Leung
- State Key Laboratory of Quality Research in Chinese Medicine, Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau (SAR), China.
| | - Xiao-Jun Yao
- State Key Laboratory of Quality Research in Chinese Medicine, Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau (SAR), China.
| | - Liang Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Dr. Neher's Biophysics Laboratory for Innovative Drug Discovery, Macau University of Science and Technology, Macau (SAR), China.
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31
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Akkapeddi P, Teng KW, Koide S. Monobodies as tool biologics for accelerating target validation and druggable site discovery. RSC Med Chem 2021; 12:1839-1853. [PMID: 34820623 PMCID: PMC8597423 DOI: 10.1039/d1md00188d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/26/2021] [Indexed: 12/21/2022] Open
Abstract
Despite increased investment and technological advancement, new drug approvals have not proportionally increased. Low drug approval rates, particularly for new targets, are linked to insufficient target validation at early stages. Thus, there remains a strong need for effective target validation techniques. Here, we review the use of synthetic binding proteins as tools for drug target validation, with focus on the monobody platform among several advanced synthetic binding protein platforms. Monobodies with high affinity and high selectivity can be rapidly developed against challenging targets, such as KRAS mutants, using protein engineering technologies. They have strong tendency to bind to functional sites and thus serve as drug-like molecules, and they can serve as targeting ligands for constructing bio-PROTACs. Genetically encoded monobodies are effective "tool biologics" for validating intracellular targets. They promote crystallization and help reveal the atomic structures of the monobody-target interface, which can inform drug design. Using case studies, we illustrate the potential of the monobody technology in accelerating target validation and small-molecule drug discovery.
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Affiliation(s)
- Padma Akkapeddi
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Kai Wen Teng
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
| | - Shohei Koide
- Perlmutter Cancer Center, New York University Langone Medical Center New York NY USA
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine New York NY USA
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32
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Targeting small GTPases and their downstream pathways with intracellular macromolecule binders to define alternative therapeutic strategies in cancer. Biochem Soc Trans 2021; 49:2021-2035. [PMID: 34623375 DOI: 10.1042/bst20201059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/20/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022]
Abstract
The RAS superfamily of small GTPases regulates major physiological cellular processes. Mutation or deregulation of these small GTPases, their regulators and/or their effectors are associated with many diseases including cancer. Hence, targeting these classes of proteins is an important therapeutic strategy in cancer. This has been recently achieved with the approval of the first KRASG12C covalent inhibitors for the clinic. However, many other mutants and small GTPases are still considered as 'undruggable' with small molecule inhibitors because of a lack of well-defined pocket(s) at their surface. Therefore, alternative therapeutic strategies have been developed to target these proteins. In this review, we discuss the use of intracellular antibodies and derivatives - reagents that bind their antigen inside the cells - for the discovery of novel inhibitory mechanisms, targetable features and therapeutic strategies to inhibit small GTPases and their downstream pathways. These reagents are also versatile tools used to better understand the biological mechanisms regulated by small GTPases and to accelerate the drug discovery process.
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33
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RAS Dimers: The Novice Couple at the RAS-ERK Pathway Ball. Genes (Basel) 2021; 12:genes12101556. [PMID: 34680951 PMCID: PMC8535645 DOI: 10.3390/genes12101556] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 09/27/2021] [Accepted: 09/28/2021] [Indexed: 02/07/2023] Open
Abstract
Signals conveyed through the RAS-ERK pathway constitute a pivotal regulatory element in cancer-related cellular processes. Recently, RAS dimerization has been proposed as a key step in the relay of RAS signals, critically contributing to RAF activation. RAS clustering at plasma membrane microdomains and endomembranes facilitates RAS dimerization in response to stimulation, promoting RAF dimerization and subsequent activation. Remarkably, inhibiting RAS dimerization forestalls tumorigenesis in cellular and animal models. Thus, the pharmacological disruption of RAS dimers has emerged as an additional target for cancer researchers in the quest for a means to curtail aberrant RAS activity.
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Shin C, Kim SS, Jo YH. Extending traditional antibody therapies: Novel discoveries in immunotherapy and clinical applications. Mol Ther Oncolytics 2021; 22:166-179. [PMID: 34514097 PMCID: PMC8416972 DOI: 10.1016/j.omto.2021.08.005] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Immunotherapy has been well regarded as one of the safer and antigen-specific anti-cancer treatments compared to first-generation chemotherapy. Since Coley's discovery, researchers focused on engineering novel antibody-based therapies. Including artificial and modified antibodies, such as antibody fragments, antibody-drug conjugates, and synthetic mimetics, the variety of immunotherapy has been rapidly expanding in the last few decades. Genetic and chemical modifications to monoclonal antibody have been brought into academia, in vivo trials, and clinical applications. Here, we have looked around antibodies overall. First, we elucidate the antibody structure and its cytotoxicity mechanisms. Second, types of therapeutic antibodies are presented. Additionally, there is a summarized list of US Food and Drug Administration (FDA)-approved therapeutic antibodies and recent clinical trials. This review provides a comprehensive overview of both the general function of therapeutic antibodies and a few main variations in development, including recent advent with the proposed mechanism of actions, and we introduce types of therapeutic antibodies, clinical trials, and approved commercial immunotherapeutic drugs.
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Affiliation(s)
- Charles Shin
- Chadwick International, Incheon 22002, Republic of Korea
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Sung Soo Kim
- Biomedical Science Institute, Kyung Hee University, Seoul 02447, Republic of Korea
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
| | - Yong Hwa Jo
- Department of Biochemistry and Molecular Biology, School of Medicine, Kyung Hee University, Seoul 02447, Republic of Korea
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Abstract
RAS proteins represent critical drivers of tumor development and thus are the focus of intense efforts to pharmacologically inhibit these proteins in human cancer. Although recent success has been attained in developing clinically efficacious inhibitors to KRASG12C, there remains a critical need for developing approaches to inhibit additional mutant RAS proteins. A number of anti-RAS biologics have been developed which reveal novel and potentially therapeutically targetable vulnerabilities in oncogenic RAS. This review will discuss the growing field of anti-RAS biologics and potential development of these reagents into new anti-RAS therapies.
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Affiliation(s)
- Michael Whaby
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States
| | - Imran Khan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States; Ralph H. Johnson VA Medical Center, Charleston, SC, United States
| | - John P O'Bryan
- Department of Cell and Molecular Pharmacology and Experimental Therapeutics, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, United States; Ralph H. Johnson VA Medical Center, Charleston, SC, United States.
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Inhibition of RAS: proven and potential vulnerabilities. Biochem Soc Trans 2021; 48:1831-1841. [PMID: 32869838 DOI: 10.1042/bst20190023] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 07/31/2020] [Accepted: 08/05/2020] [Indexed: 02/07/2023]
Abstract
RAS is a membrane localized small GTPase frequently mutated in human cancer. As such, RAS has been a focal target for developing cancer therapeutics since its discovery nearly four decades ago. However, efforts to directly target RAS have been challenging due to the apparent lack of readily discernable deep pockets for binding small molecule inhibitors leading many to consider RAS as undruggable. An important milestone in direct RAS inhibition was achieved recently with the groundbreaking discovery of covalent inhibitors that target the mutant Cys residue in KRAS(G12C). Surprisingly, these G12C-reactive compounds only target mutant RAS in the GDP-bound state thereby locking it in the inactive conformation and blocking its ability to couple with downstream effector pathways. Building on this success, several groups have developed similar compounds that selectively target KRAS(G12C), with AMG510 and MRTX849 the first to advance to clinical trials. Both have shown early promising results. Though the success with these compounds has reignited the possibility of direct pharmacological inhibition of RAS, these covalent inhibitors are limited to treating KRAS(G12C) tumors which account for <15% of all RAS mutants in human tumors. Thus, there remains an unmet need to identify more broadly efficacious RAS inhibitors. Here, we will discuss the current state of RAS(G12C) inhibitors and the potential for inhibiting additional RAS mutants through targeting RAS dimerization which has emerged as an important step in the allosteric regulation of RAS function.
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Abstract
As a member of small GTPase family, KRAS protein is a key physiological modulator of various cellular activities including proliferation. However, mutations of KRAS present in numerous cancer types, most frequently in pancreatic (> 60%), colorectal (> 40%), and lung cancers, drive oncogenic processes through overactivation of proliferation. The G12C mutation of KRAS protein is especially abundant in the case of these types of malignancies. Despite its key importance in human disease, KRAS was assumed to be non-druggable for a long time since the protein seemingly lacks potential drug-binding pockets except the nucleotide-binding site, which is difficult to be targeted due to the high affinity of KRAS for both GDP and GTP. Recently, a new approach broke the ice and provided evidence that upon covalent targeting of the G12C mutant KRAS, a highly dynamic pocket was revealed. This novel targeting is especially important since it serves with an inherent solution for drug selectivity. Based on these results, various structure-based drug design projects have been launched to develop selective KRAS mutant inhibitors. In addition to the covalent modification strategy mostly applicable for G12C mutation, different innovative solutions have been suggested for the other frequently occurring oncogenic G12 mutants. Here we summarize the latest advances of this field, provide perspectives for novel approaches, and highlight the special properties of KRAS, which might issue some new challenges.
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Affiliation(s)
- Kinga Nyíri
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, 1111, Hungary.
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, 1117, Hungary.
| | - Gergely Koppány
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, 1111, Hungary
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, 1117, Hungary
| | - Beáta G Vértessy
- Department of Applied Biotechnology and Food Sciences, Budapest University of Technology and Economics, Budapest, 1111, Hungary.
- Institute of Enzymology, Research Centre for Natural Sciences, Hungarian Academy of Sciences, Budapest, 1117, Hungary.
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RAS-inhibiting biologics identify and probe druggable pockets including an SII-α3 allosteric site. Nat Commun 2021; 12:4045. [PMID: 34193876 PMCID: PMC8245420 DOI: 10.1038/s41467-021-24316-0] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 06/04/2021] [Indexed: 11/09/2022] Open
Abstract
RAS mutations are the most common oncogenic drivers across human cancers, but there remains a paucity of clinically-validated pharmacological inhibitors of RAS, as druggable pockets have proven difficult to identify. Here, we identify two RAS-binding Affimer proteins, K3 and K6, that inhibit nucleotide exchange and downstream signaling pathways with distinct isoform and mutant profiles. Affimer K6 binds in the SI/SII pocket, whilst Affimer K3 is a non-covalent inhibitor of the SII region that reveals a conformer of wild-type RAS with a large, druggable SII/α3 pocket. Competitive NanoBRET between the RAS-binding Affimers and known RAS binding small-molecules demonstrates the potential to use Affimers as tools to identify pharmacophores. This work highlights the potential of using biologics with small interface surfaces to select unseen, druggable conformations in conjunction with pharmacophore identification for hard-to-drug proteins. Oncogenic RAS mutants remain difficult to target with small molecules. Here, the authors show that RAS-binding Affimer proteins inhibit RAS signaling while binding diverse regions on the RAS surface, suggesting the potential to use Affimers as tools to identify new binding pockets and pharmacophores.
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Zhou Y, Gorfe AA, Hancock JF. RAS Nanoclusters Selectively Sort Distinct Lipid Headgroups and Acyl Chains. Front Mol Biosci 2021; 8:686338. [PMID: 34222339 PMCID: PMC8245699 DOI: 10.3389/fmolb.2021.686338] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/13/2021] [Indexed: 12/12/2022] Open
Abstract
RAS proteins are lipid-anchored small GTPases that switch between the GTP-bound active and GDP-bound inactive states. RAS isoforms, including HRAS, NRAS and splice variants KRAS4A and KRAS4B, are some of the most frequently mutated proteins in cancer. In particular, constitutively active mutants of KRAS comprise ∼80% of all RAS oncogenic mutations and are found in 98% of pancreatic, 45% of colorectal and 31% of lung tumors. Plasma membrane (PM) is the primary location of RAS signaling in biology and pathology. Thus, a better understanding of how RAS proteins localize to and distribute on the PM is critical to better comprehend RAS biology and to develop new strategies to treat RAS pathology. In this review, we discuss recent findings on how RAS proteins sort lipids as they undergo macromolecular assembly on the PM. We also discuss how RAS/lipid nanoclusters serve as signaling platforms for the efficient recruitment of effectors and signal transduction, and how perturbing the PM biophysical properties affect the spatial distribution of RAS isoforms and their functions.
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Affiliation(s)
- Yong Zhou
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX, United States
| | - Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX, United States
| | - John F. Hancock
- Department of Integrative Biology and Pharmacology, University of Texas Health Science Center, Houston, TX, United States
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Folding and Stability of Ankyrin Repeats Control Biological Protein Function. Biomolecules 2021; 11:biom11060840. [PMID: 34198779 PMCID: PMC8229355 DOI: 10.3390/biom11060840] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 05/25/2021] [Accepted: 06/01/2021] [Indexed: 01/04/2023] Open
Abstract
Ankyrin repeat proteins are found in all three kingdoms of life. Fundamentally, these proteins are involved in protein-protein interaction in order to activate or suppress biological processes. The basic architecture of these proteins comprises repeating modules forming elongated structures. Due to the lack of long-range interactions, a graded stability among the repeats is the generic properties of this protein family determining both protein folding and biological function. Protein folding intermediates were frequently found to be key for the biological functions of repeat proteins. In this review, we discuss most recent findings addressing this close relation for ankyrin repeat proteins including DARPins, Notch receptor ankyrin repeat domain, IκBα inhibitor of NFκB, and CDK inhibitor p19INK4d. The role of local folding and unfolding and gradual stability of individual repeats will be discussed during protein folding, protein-protein interactions, and post-translational modifications. The conformational changes of these repeats function as molecular switches for biological regulation, a versatile property for modern drug discovery.
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Han CW, Jeong MS, Jang SB. Understand KRAS and the Quest for Anti-Cancer Drugs. Cells 2021; 10:cells10040842. [PMID: 33917906 PMCID: PMC8068306 DOI: 10.3390/cells10040842] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Revised: 04/06/2021] [Accepted: 04/06/2021] [Indexed: 12/30/2022] Open
Abstract
The KRAS oncogene is mutated in approximately ~30% of human cancers, and the targeting of KRAS has long been highlighted in many studies. Nevertheless, attempts to target KRAS directly have been ineffective. This review provides an overview of the structure of KRAS and its characteristic signaling pathways. Additionally, we examine the problems associated with currently available KRAS inhibitors and discuss promising avenues for drug development.
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Affiliation(s)
- Chang Woo Han
- Institute of Systems Biology, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 46241, Korea;
| | - Mi Suk Jeong
- Institute for Plastic Information and Energy Materials and Sustainable Utilization of Photovoltaic Energy Research Center, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 46241, Korea
- Correspondence: (M.S.J.); (S.B.J.); Tel.: +82-51-510-2523 (M.S.J. & S.B.J.)
| | - Se Bok Jang
- Department of Molecular Biology, College of Natural Sciences, Pusan National University, Jangjeon-dong, Geumjeong-gu, Busan 46241, Korea
- Correspondence: (M.S.J.); (S.B.J.); Tel.: +82-51-510-2523 (M.S.J. & S.B.J.)
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42
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Bery N, Bataille CJR, Russell A, Hayes A, Raynaud F, Milhas S, Anand S, Tulmin H, Miller A, Rabbitts TH. A cell-based screening method using an intracellular antibody for discovering small molecules targeting the translocation protein LMO2. SCIENCE ADVANCES 2021; 7:eabg1950. [PMID: 33837087 PMCID: PMC8034850 DOI: 10.1126/sciadv.abg1950] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 02/19/2021] [Indexed: 05/07/2023]
Abstract
Intracellular antibodies are tools that can be used directly for target validation by interfering with properties like protein-protein interactions. An alternative use of intracellular antibodies in drug discovery is developing small-molecule surrogates using antibody-derived (Abd) technology. We previously used this strategy with an in vitro competitive surface plasmon resonance method that relied on high-affinity antibody fragments to obtain RAS-binding compounds. We now describe a novel implementation of the Abd method with a cell-based intracellular antibody-guided screening method that we have applied to the chromosomal translocation protein LMO2. We have identified a chemical series of anti-LMO2 Abd compounds that bind at the same LMO2 location as the inhibitory anti-LMO2 intracellular antibody combining site. Intracellular antibodies could therefore be used in cell-based screens to identify chemical surrogates of their binding sites and potentially be applied to any challenging proteins, such as transcription factors that have been considered undruggable.
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Affiliation(s)
- Nicolas Bery
- Weatherall Institute of Molecular Medicine MRC Molecular Haematology Unit, University of Oxford John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Carole J R Bataille
- University of Oxford Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Angela Russell
- University of Oxford Chemistry Research Laboratory, University of Oxford, Oxford OX1 3TA, UK
| | - Angela Hayes
- Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Florence Raynaud
- Institute of Cancer Research, 15 Cotswold Road, Sutton, London SM2 5NG, UK
| | - Sabine Milhas
- Weatherall Institute of Molecular Medicine MRC Molecular Haematology Unit, University of Oxford John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Sneha Anand
- Weatherall Institute of Molecular Medicine MRC Molecular Haematology Unit, University of Oxford John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Hanna Tulmin
- Weatherall Institute of Molecular Medicine MRC Molecular Haematology Unit, University of Oxford John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Ami Miller
- Weatherall Institute of Molecular Medicine MRC Molecular Haematology Unit, University of Oxford John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Terence H Rabbitts
- Weatherall Institute of Molecular Medicine MRC Molecular Haematology Unit, University of Oxford John Radcliffe Hospital, Oxford OX3 9DS, UK.
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43
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Bery N, Favre G, Olichon A. Protocol to select conformation-specific intracellular antibodies for targeted protein degradation in an engineered cell line. STAR Protoc 2021; 2:100249. [PMID: 33437969 PMCID: PMC7786126 DOI: 10.1016/j.xpro.2020.100249] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Here, we provide a protocol for the selection of conformation-specific intracellular antibody degraders using a cell-based screening method. We applied this protocol to select antibody-based degraders targeting the active form of the small GTPase RHOB (i.e., RHOB-GTP) using an engineered H2882 cell line. The protocol can be used to study the function of RHOB active conformation in various cellular settings. This protocol can be broadly applied to select any kind of intracellular antibody degraders, regardless of conformational state. For complete details on the use and execution of this protocol, please refer to Bery et al. (2019).
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Affiliation(s)
- Nicolas Bery
- Centre de Recherche en Cancérologie de Toulouse (CRCT), UMR1037 INSERM - Université Toulouse III - ERL5294 CNRS, Toulouse, 31100, France
| | - Gilles Favre
- Centre de Recherche en Cancérologie de Toulouse (CRCT), UMR1037 INSERM - Université Toulouse III - ERL5294 CNRS, Toulouse, 31100, France.,Département de Biologie, Institut Claudius Regaud, Toulouse, 31100, France
| | - Aurélien Olichon
- Centre de Recherche en Cancérologie de Toulouse (CRCT), UMR1037 INSERM - Université Toulouse III - ERL5294 CNRS, Toulouse, 31100, France
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Van QN, Prakash P, Shrestha R, Balius TE, Turbyville TJ, Stephen AG. RAS Nanoclusters: Dynamic Signaling Platforms Amenable to Therapeutic Intervention. Biomolecules 2021; 11:377. [PMID: 33802474 PMCID: PMC8000715 DOI: 10.3390/biom11030377] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 02/24/2021] [Accepted: 02/24/2021] [Indexed: 01/18/2023] Open
Abstract
RAS proteins are mutated in approximately 20% of all cancers and are generally associated with poor clinical outcomes. RAS proteins are localized to the plasma membrane and function as molecular switches, turned on by partners that receive extracellular mitogenic signals. In the on-state, they activate intracellular signal transduction cascades. Membrane-bound RAS molecules segregate into multimers, known as nanoclusters. These nanoclusters, held together through weak protein-protein and protein-lipid associations, are highly dynamic and respond to cellular input signals and fluctuations in the local lipid environment. Disruption of RAS nanoclusters results in downregulation of RAS-mediated mitogenic signaling. In this review, we discuss the propensity of RAS proteins to display clustering behavior and the interfaces that are associated with these assemblies. Strategies to therapeutically disrupt nanocluster formation or the stabilization of signaling incompetent RAS complexes are discussed.
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Affiliation(s)
| | | | | | | | | | - Andrew G. Stephen
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, National Cancer Institute RAS Initiative, Inc., Frederick, MD 21702, USA; (Q.N.V.); (P.P.); (R.S.); (T.E.B.); (T.J.T.)
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45
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Gorfe AA, Cho KJ. Approaches to inhibiting oncogenic K-Ras. Small GTPases 2021; 12:96-105. [PMID: 31438765 PMCID: PMC7849769 DOI: 10.1080/21541248.2019.1655883] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 07/29/2019] [Accepted: 08/06/2019] [Indexed: 02/06/2023] Open
Abstract
Activating somatic K-Ras mutations are associated with >15% all human tumors and up to 90% of specific tumor types such as pancreatic cancer. Successfully inhibiting abnormal K-Ras signaling would therefore be a game changer in cancer therapy. However, K-Ras has long been considered an undruggable target for various reasons. This view is now changing by the discovery of allosteric inhibitors that directly target K-Ras and inhibit its functions, and by the identification of new mechanisms to dislodge it from the plasma membrane and thereby abrogate its cellular activities. In this review, we will discuss recent progresses and challenges to inhibiting aberrant K-Ras functions by these two approaches. We will also provide a broad overview of other approaches such as inhibition of K-Ras effectors, and offer a brief perspective on the way forward.
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Affiliation(s)
- Alemayehu A. Gorfe
- Department of Integrative Biology and Pharmacology, McGovern Medical School, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Programs of Biochemistry & Cell and Therapeutics & Pharmacology, MD Anderson UTHealth Graduate School of Biomedical Sciences, Houston, TX, USA
| | - Kwang-Jin Cho
- Department of Biochemistry and Molecular Biology, Boonshoft School of Medicine, Wright State University, Dayton, OH, USA
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Lim S, Khoo R, Juang YC, Gopal P, Zhang H, Yeo C, Peh KM, Teo J, Ng S, Henry B, Partridge AW. Exquisitely Specific anti-KRAS Biodegraders Inform on the Cellular Prevalence of Nucleotide-Loaded States. ACS CENTRAL SCIENCE 2021; 7:274-291. [PMID: 33655066 PMCID: PMC7908030 DOI: 10.1021/acscentsci.0c01337] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Indexed: 05/05/2023]
Abstract
Mutations to RAS proteins (H-, N-, and K-RAS) are among the most common oncogenic drivers, and tumors harboring these lesions are some of the most difficult to treat. Although covalent small molecules against KRASG12C have shown promising efficacy against lung cancers, traditional barriers remain for drugging the more prevalent KRASG12D and KRASG12V mutants. Targeted degradation has emerged as an attractive alternative approach, but for KRAS, identification of the required high-affinity ligands continues to be a challenge. Another significant hurdle is the discovery of a hybrid molecule that appends an E3 ligase-recruiting moiety in a manner that satisfies the precise geometries required for productive polyubiquitin transfer while maintaining favorable druglike properties. To gain insights into the advantages and feasibility of KRAS targeted degradation, we applied a protein-based degrader (biodegrader) approach. This workflow centers on the intracellular expression of a chimeric protein consisting of a high-affinity target-binding domain fused to an engineered E3 ligase adapter. A series of anti-RAS biodegraders spanning different RAS isoform/nucleotide-state specificities and leveraging different E3 ligases provided definitive evidence for RAS degradability. Further, these established that the functional consequences of KRAS degradation are context dependent. Of broader significance, using the exquisite degradation specificity that biodegraders can possess, we demonstrated how this technology can be applied to answer questions that other approaches cannot. Specifically, application of the GDP-state specific degrader uncovered the relative prevalence of the "off-state" of WT and various KRAS mutants in the cellular context. Finally, if delivery challenges can be addressed, anti-RAS biodegraders will be exciting candidates for clinical development.
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PEG Linker Improves Antitumor Efficacy and Safety of Affibody-Based Drug Conjugates. Int J Mol Sci 2021; 22:ijms22041540. [PMID: 33546481 PMCID: PMC7913616 DOI: 10.3390/ijms22041540] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Revised: 01/27/2021] [Accepted: 01/28/2021] [Indexed: 12/13/2022] Open
Abstract
Antibody drug conjugates (ADCs) have become an important modality of clinical cancer treatment. However, traditional ADCs have some limitations, such as reduced permeability in solid tumors due to the high molecular weight of monoclonal antibodies, difficulty in preparation and heterogeneity of products due to the high drug/antibody ratio (4-8 small molecules per antibody). Miniaturized ADCs may be a potential solution, although their short circulation half-life may lead to new problems. In this study, we propose a novel design strategy for miniaturized ADCs in which drug molecules and small ligand proteins are site-specifically coupled via a bifunctional poly(ethylene glycol) (PEG) chain. The results showed that the inserted PEG chains significantly prolonged the circulation half-life but also obviously reduced the cytotoxicity of the conjugates. Compared with the conjugate ZHER2-SMCC-MMAE (HM), which has no PEG insertion, ZHER2-PEG4K-MMAE (HP4KM) and ZHER2-PEG10K-MMAE (HP10KM) with 4 or 10 kDa PEG insertions have 2.5- and 11.2-fold half-life extensions and 4.5- and 22-fold in vitro cytotoxicity reductions, respectively. The combined effect leads to HP10KM having the most ideal tumor therapeutic ability at the same dosages in the animal model, and its off-target toxicity was also reduced by more than 4 times compared with that of HM. These results may indicate that prolonging the half-life is very helpful in improving the therapeutic capacity of miniaturized ADCs. In the future, the design of better strategies that can prolong half-life without affecting cytotoxicity may be useful for further improving the therapeutic potential of these molecules.
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Kumar M, Joshi G, Chatterjee J, Kumar R. Epidermal Growth Factor Receptor and its Trafficking Regulation by Acetylation: Implication in Resistance and Exploring the Newer Therapeutic Avenues in Cancer. Curr Top Med Chem 2021; 20:1105-1123. [PMID: 32031073 DOI: 10.2174/1568026620666200207100227] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 01/17/2020] [Accepted: 01/24/2020] [Indexed: 12/13/2022]
Abstract
BACKGROUND The EGFR is overexpressed in numerous cancers. So, it becomes one of the most favorable drug targets. Single-acting EGFR inhibitors on prolong use induce resistance and side effects. Inhibition of EGFR and/or its interacting proteins by dual/combined/multitargeted therapies can deliver more efficacious drugs with less or no resistance. OBJECTIVE The review delves deeper to cover the aspects of EGFR mediated endocytosis, leading to its trafficking, internalization, and crosstalk(s) with HDACs. METHODS AND RESULTS This review is put forth to congregate relevant literature evidenced on EGFR, its impact on cancer prognosis, inhibitors, and its trafficking regulation by acetylation along with the current strategies involved in targeting these proteins (EGFR and HDACs) successfully by involving dual/hybrid/combination chemotherapy. CONCLUSION The current information on cross-talk of EGFR and HDACs would likely assist researchers in designing and developing dual or multitargeted inhibitors through combining the required pharmacophores.
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Affiliation(s)
- Manvendra Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151001, India
| | - Gaurav Joshi
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151001, India
| | - Joydeep Chatterjee
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151001, India
| | - Raj Kumar
- Laboratory for Drug Design and Synthesis, Department of Pharmaceutical Sciences and Natural Products, School of Basic and Applied Sciences, Central University of Punjab, Bathinda, 151001, India
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The type of KRAS mutation drives PI3Kα/γ signalling dependency: Implication for the choice of targeted therapy in pancreatic adenocarcinoma patients. Clin Res Hepatol Gastroenterol 2021; 45:101473. [PMID: 32593694 DOI: 10.1016/j.clinre.2020.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 05/20/2020] [Indexed: 02/04/2023]
Abstract
Pancreatic ductal adenocarcinoma PDAC is a complex disease with an important diversity of genetic alterations found between patients. KRAS mutation is considered as a major oncogenic driver in this cancer (around 90% of the patients), but there exists different KRAS mutation types. The type of KRAS mutation was recently shown to be of importance to detect signalling vulnerabilities in a subset of PDAC patients. We comment on these innovative results and discuss their importance when designing clinical trials with PI3K targeted therapies in this cancer.
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50
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Natural Products Attenuating Biosynthesis, Processing, and Activity of Ras Oncoproteins: State of the Art and Future Perspectives. Biomolecules 2020; 10:biom10111535. [PMID: 33182807 PMCID: PMC7698260 DOI: 10.3390/biom10111535] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/03/2020] [Accepted: 11/08/2020] [Indexed: 02/07/2023] Open
Abstract
RAS genes encode signaling proteins, which, in mammalian cells, act as molecular switches regulating critical cellular processes as proliferation, growth, differentiation, survival, motility, and metabolism in response to specific stimuli. Deregulation of Ras functions has a high impact on human health: gain-of-function point mutations in RAS genes are found in some developmental disorders and thirty percent of all human cancers, including the deadliest. For this reason, the pathogenic Ras variants represent important clinical targets against which to develop novel, effective, and possibly selective pharmacological inhibitors. Natural products represent a virtually unlimited resource of structurally different compounds from which one could draw on for this purpose, given the improvements in isolation and screening of active molecules from complex sources. After a summary of Ras proteins molecular and regulatory features and Ras-dependent pathways relevant for drug development, we point out the most promising inhibitory approaches, the known druggable sites of wild-type and oncogenic Ras mutants, and describe the known natural compounds capable of attenuating Ras signaling. Finally, we highlight critical issues and perspectives for the future selection of potential Ras inhibitors from natural sources.
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