1
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Smith MJ. Defining bone fide effectors of RAS GTPases. Bioessays 2023; 45:e2300088. [PMID: 37401638 DOI: 10.1002/bies.202300088] [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] [Received: 05/24/2023] [Revised: 06/20/2023] [Accepted: 06/22/2023] [Indexed: 07/05/2023]
Abstract
RAS GTPases play essential roles in normal development and are direct drivers of human cancers. Three decades of study have failed to wholly characterize pathways stimulated by activated RAS, driven by engagement with 'effector' proteins that have RAS binding domains (RBDs). Bone fide effectors must bind directly to RAS GTPases in a nucleotide-dependent manner, and this interaction must impart a clear change in effector activity. Despite this, for most proteins currently deemed effectors there is little mechanistic understanding of how binding to the GTPase alters protein function. There has also been limited effort to comprehensively resolve the specificity of effector binding to the full array of RAS superfamily GTPase proteins. This review will summarize what is known about RAS-driven activation for an array of potential effector proteins, focusing on structural and mechanistic effects and highlighting how little is still known regarding this key paradigm of cellular signal transduction.
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Affiliation(s)
- Matthew J Smith
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Québec, Canada
- Department of Pathology and Cell Biology, Faculty of Medicine, Université de Montréal, Montréal, Québec, Canada
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2
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Sugita M, Fujie T, Yanagisawa K, Ohue M, Akiyama Y. Lipid Composition Is Critical for Accurate Membrane Permeability Prediction of Cyclic Peptides by Molecular Dynamics Simulations. J Chem Inf Model 2022; 62:4549-4560. [PMID: 36053061 PMCID: PMC9516681 DOI: 10.1021/acs.jcim.2c00931] [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] [Indexed: 11/29/2022]
Abstract
Cyclic peptides have attracted attention as a promising pharmaceutical modality due to their potential to selectively inhibit previously undruggable targets, such as intracellular protein-protein interactions. Poor membrane permeability is the biggest bottleneck hindering successful drug discovery based on cyclic peptides. Therefore, the development of computational methods that can predict membrane permeability and support elucidation of the membrane permeation mechanism of drug candidate peptides is much sought after. In this study, we developed a protocol to simulate the behavior in membrane permeation steps and estimate the membrane permeability of large cyclic peptides with more than or equal to 10 residues. This protocol requires the use of a more realistic membrane model than a single-lipid phospholipid bilayer. To select a membrane model, we first analyzed the effect of cholesterol concentration in the model membrane on the potential of mean force and hydrogen bonding networks along the direction perpendicular to the membrane surface as predicted by molecular dynamics simulations using cyclosporine A. These results suggest that a membrane model with 40 or 50 mol % cholesterol was suitable for predicting the permeation process. Subsequently, two types of membrane models containing 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine and 40 and 50 mol % cholesterol were used. To validate the efficiency of our protocol, the membrane permeability of 18 ten-residue peptides was predicted. Correlation coefficients of R > 0.8 between the experimental and calculated permeability values were obtained with both model membranes. The results of this study demonstrate that the lipid membrane is not just a medium but also among the main factors determining the membrane permeability of molecules. The computational protocol proposed in this study and the findings obtained on the effect of membrane model composition will contribute to building a schematic view of the membrane permeation process. Furthermore, the results of this study will eventually aid the elucidation of design rules for peptide drugs with high membrane permeability.
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Affiliation(s)
- Masatake Sugita
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-Based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Takuya Fujie
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-Based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Keisuke Yanagisawa
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-Based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Masahito Ohue
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-Based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
| | - Yutaka Akiyama
- Department of Computer Science, School of Computing, Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan.,Middle-Molecule IT-Based Drug Discovery Laboratory (MIDL), Tokyo Institute of Technology, W8-76, 2-12-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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3
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Buyanova M, Cai S, Cooper J, Rhodes C, Salim H, Sahni A, Upadhyaya P, Yang R, Sarkar A, Li N, Wang QE, Pei D. Discovery of a Bicyclic Peptidyl Pan-Ras Inhibitor. J Med Chem 2021; 64:13038-13053. [PMID: 34415745 DOI: 10.1021/acs.jmedchem.1c01130] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The Ras subfamily of small GTPases is mutated in ∼30% of human cancers and represents compelling yet challenging anticancer drug targets owing to their flat protein surface. We previously reported a bicyclic peptidyl inhibitor, cyclorasin B3, which binds selectively to Ras-GTP with modest affinity and blocks its interaction with downstream effector proteins in vitro but lacks cell permeability or biological activity. In this study, optimization of B3 yielded a potent pan-Ras inhibitor, cyclorasin B4-27, which binds selectively to the GTP-bound forms of wild-type and mutant Ras isoforms (KD = 21 nM for KRasG12V-GppNHp) and is highly cell-permeable and metabolically stable (serum t1/2 > 24 h). B4-27 inhibits Ras signaling in vitro and in vivo by blocking Ras from interacting with downstream effector proteins and induces apoptosis of Ras-mutant cancer cells. When administered systemically (i.v.), B4-27 suppressed tumor growth in two different mouse xenograft models at 1-5 mg/kg of daily doses.
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Affiliation(s)
- Marina Buyanova
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Shurui Cai
- Department of Radiation Oncology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Jahan Cooper
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Curran Rhodes
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Heba Salim
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Ashweta Sahni
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Punit Upadhyaya
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Rui Yang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Amar Sarkar
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Na Li
- Department of Radiation Oncology, The Ohio State University, Columbus, Ohio 43210, United States
| | - Qi-En Wang
- Department of Radiation Oncology, The Ohio State University, Columbus, Ohio 43210, United States.,Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States.,Comprehensive Cancer Center, The Ohio State University, Columbus, Ohio 43210, United States
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4
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Takeuchi K, Misaki I, Tokunaga Y, Fujisaki M, Kamoshida H, Takizawa T, Hanzawa H, Shimada I. Conformational Plasticity of Cyclic Ras‐Inhibitor Peptides Defines Cell Permeabilization Activity. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202016647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute National Institute of Advanced Industrial Science and Technology 2-3-26 Aomi, Koto Tokyo 135-0063 Japan
| | - Imai Misaki
- Japan Biological Informatics Consortium 2-3-26 Aomi, Koto Tokyo 135-0063 Japan
| | - Yuji Tokunaga
- Cellular and Molecular Biotechnology Research Institute National Institute of Advanced Industrial Science and Technology 2-3-26 Aomi, Koto Tokyo 135-0063 Japan
| | - Miwa Fujisaki
- Japan Biological Informatics Consortium 2-3-26 Aomi, Koto Tokyo 135-0063 Japan
| | - Hajime Kamoshida
- Japan Biological Informatics Consortium 2-3-26 Aomi, Koto Tokyo 135-0063 Japan
| | - Takeshi Takizawa
- Biological Research Department Daiichi Sankyo RD Novare Co., Ltd. 1-16-13 Kitakasai, Edogawa-ku Tokyo 134-8630 Japan
| | - Hiroyuki Hanzawa
- Biological Research Department Daiichi Sankyo RD Novare Co., Ltd. 1-16-13 Kitakasai, Edogawa-ku Tokyo 134-8630 Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Center for Biosystems Dynamics Research RIKEN 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
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5
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Takeuchi K, Misaki I, Tokunaga Y, Fujisaki M, Kamoshida H, Takizawa T, Hanzawa H, Shimada I. Conformational Plasticity of Cyclic Ras‐Inhibitor Peptides Defines Cell Permeabilization Activity. Angew Chem Int Ed Engl 2021; 60:6567-6572. [DOI: 10.1002/anie.202016647] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 01/08/2021] [Indexed: 01/05/2023]
Affiliation(s)
- Koh Takeuchi
- Cellular and Molecular Biotechnology Research Institute National Institute of Advanced Industrial Science and Technology 2-3-26 Aomi, Koto Tokyo 135-0063 Japan
| | - Imai Misaki
- Japan Biological Informatics Consortium 2-3-26 Aomi, Koto Tokyo 135-0063 Japan
| | - Yuji Tokunaga
- Cellular and Molecular Biotechnology Research Institute National Institute of Advanced Industrial Science and Technology 2-3-26 Aomi, Koto Tokyo 135-0063 Japan
| | - Miwa Fujisaki
- Japan Biological Informatics Consortium 2-3-26 Aomi, Koto Tokyo 135-0063 Japan
| | - Hajime Kamoshida
- Japan Biological Informatics Consortium 2-3-26 Aomi, Koto Tokyo 135-0063 Japan
| | - Takeshi Takizawa
- Biological Research Department Daiichi Sankyo RD Novare Co., Ltd. 1-16-13 Kitakasai, Edogawa-ku Tokyo 134-8630 Japan
| | - Hiroyuki Hanzawa
- Biological Research Department Daiichi Sankyo RD Novare Co., Ltd. 1-16-13 Kitakasai, Edogawa-ku Tokyo 134-8630 Japan
| | - Ichio Shimada
- Graduate School of Pharmaceutical Sciences The University of Tokyo 7-3-1 Hongo Bunkyo-ku Tokyo 113-0033 Japan
- Center for Biosystems Dynamics Research RIKEN 1-7-22 Suehiro-cho, Tsurumi-ku Yokohama 230-0045 Japan
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6
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Tsubamoto M, Le TK, Li M, Watanabe T, Matsumi C, Parvatkar P, Fujii H, Kato N, Sun J, Ohkanda J. A Guanidyl-Based Bivalent Peptidomimetic Inhibits K-Ras Prenylation and Association with c-Raf. Chemistry 2019; 25:13531-13536. [PMID: 31393030 DOI: 10.1002/chem.201903129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2019] [Revised: 08/07/2019] [Indexed: 01/06/2023]
Abstract
Unusual lipid modification of K-Ras makes Ras-directed cancer therapy a challenging task. Aiming to disrupt electrostatic-driven protein-protein interactions (PPIs) of K-Ras with FTase and GGTase I, a series of bivalent dual inhibitors that recognize the active pocket and the common acidic surface of FTase and GGTase I were designed. The structure-activity-relationship study resulted in 8 b, in which a biphenyl-based peptidomimetic FTI-277 was attached to a guanidyl-containing gallate moiety through an alkyl linker. Cell-based evaluation demonstrated that 8 b exhibited substantial inhibition of K-Ras processing without apparent interference with Rap-1A processing. Fluorescent imaging showed that 8 b disrupts localization of K-Ras to the plasma membrane and impairs interaction with c-Raf, whereas only FTI-277 was found to be inactive. These results suggest that targeting the PPI interface of K-Ras may provide an alternative method of inhibiting K-Ras.
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Affiliation(s)
- Mai Tsubamoto
- The Institute of Scientific Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Toan Khanh Le
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano, 399-4598, Japan
| | - Minghua Li
- Department of Pharmaceutical Science, University of South Florida, Tampa, Florida, 33612, USA
| | - Taku Watanabe
- Ina Laboratory, Medical & Biological Laboratories, CO., Ltd., Ina, Nagano, 396-0002, Japan
| | - Chiemi Matsumi
- Ina Laboratory, Medical & Biological Laboratories, CO., Ltd., Ina, Nagano, 396-0002, Japan
| | - Prakash Parvatkar
- Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto, 611-0011, Japan
| | - Hiroshi Fujii
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano, 399-4598, Japan
| | - Nobuo Kato
- The Institute of Scientific Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka, 567-0047, Japan
| | - Jiazhi Sun
- Department of Pharmaceutical Science, University of South Florida, Tampa, Florida, 33612, USA
| | - Junko Ohkanda
- Academic Assembly, Institute of Agriculture, Shinshu University, 8304 Minami-Minowa, Kami-Ina, Nagano, 399-4598, Japan
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7
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Tan X, Bruchez MP, Armitage BA. Efficient Cytoplasmic Delivery of Antisense Probes Assisted by Cyclized-Peptide-Mediated Photoinduced Endosomal Escape. Chembiochem 2019; 20:727-733. [PMID: 30452106 DOI: 10.1002/cbic.201800709] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2018] [Indexed: 12/24/2022]
Abstract
Intracellular delivery and endosomal release of antisense oligonucleotides remain a significant challenge in the development of gene-targeted therapeutics. Previously, noncovalently cyclized TAT peptide (Cyc-TAT), in which the final ring-closing step is accomplished by hybridization of two short complementary γPNA segments, has been proven more efficient than its linear analogues at entering cells. As Cyc-TAT also readily accommodates a binding site, that is, an overhanging γPNA sequence, for codelivery of functional nucleic acid probes into cells, we were able to demonstrate that the overhang-Cyc-TAT penetrated into A549 cells when carrying an anti-telomerase γPNA that specifically reduced telomerase activity by over 97 %. Herein, we report that the cyclized TAT(FAM) can escape endosomes much more efficiently than the linear TAT(FAM) after LED illumination (490 nm). Based on this observation, the endosomal release of overhang-Cyc-TAT(FAM)/anti-telomerase γPNA complex can be greatly enhanced by photoactivation, thus shortening cell treatment time from 60 to 3 h, while keeping the same high efficiency in inhibiting telomerase activity inside A549 cells.
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Affiliation(s)
- Xiaohong Tan
- Departments of Chemistry, Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Marcel P Bruchez
- Departments of Chemistry, Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA.,Departments of Biological Sciences, Molecular Biosensor and Imaging Center, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
| | - Bruce A Armitage
- Departments of Chemistry, Center for Nucleic Acids Science and Technology, Carnegie Mellon University, 4400 Fifth Avenue, Pittsburgh, PA, 15213, USA
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8
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Ehrhorn H, Tamm M. Well-Defined Alkyne Metathesis Catalysts: Developments and Recent Applications. Chemistry 2018; 25:3190-3208. [PMID: 30346054 DOI: 10.1002/chem.201804511] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2018] [Indexed: 12/31/2022]
Abstract
Although alkyne metathesis has been known for 50 years, rapid progress in this field has mostly occurred during the last two decades. In this article, the development of several highly efficient and thoroughly studied alkyne metathesis catalysts is reviewed, which includes novel well-defined, in situ formed and heterogeneous systems. Various alkyne metathesis methodologies, including alkyne cross-metathesis (ACM), ring-closing alkyne metathesis (RCAM), cyclooligomerization, acyclic diyne metathesis polymerization (ADIMET), and ring-opening alkyne metathesis polymerization (ROAMP), are presented, and their application in natural product synthesis, materials science as well as supramolecular and polymer chemistry is discussed. Recent progress in the metathesis of diynes is also summarized, which gave rise to new methods such as ring-closing diyne metathesis (RCDM) and diyne cross-metathesis (DYCM).
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Affiliation(s)
- Henrike Ehrhorn
- Institut für Anorganische und Analytische Chemie, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
| | - Matthias Tamm
- Institut für Anorganische und Analytische Chemie, Technische Universität Braunschweig, Hagenring 30, 38106, Braunschweig, Germany
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9
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Qian Z, Rhodes CA, McCroskey LC, Wen J, Appiah-Kubi G, Wang DJ, Guttridge DC, Pei D. Enhancing the Cell Permeability and Metabolic Stability of Peptidyl Drugs by Reversible Bicyclization. Angew Chem Int Ed Engl 2016; 56:1525-1529. [PMID: 28035784 DOI: 10.1002/anie.201610888] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2016] [Revised: 12/01/2016] [Indexed: 12/27/2022]
Abstract
Therapeutic applications of peptides are currently limited by their proteolytic instability and impermeability to the cell membrane. A general, reversible bicyclization strategy is now reported to increase both the proteolytic stability and cell permeability of peptidyl drugs. A peptide drug is fused with a short cell-penetrating motif and converted into a conformationally constrained bicyclic structure through the formation of a pair of disulfide bonds. The resulting bicyclic peptide has greatly enhanced proteolytic stability as well as cell-permeability. Once inside the cell, the disulfide bonds are reduced to produce a linear, biologically active peptide. This strategy was applied to generate a cell-permeable bicyclic peptidyl inhibitor against the NEMO-IKK interaction.
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Affiliation(s)
- Ziqing Qian
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA
| | - Curran A Rhodes
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA
| | - Lucas C McCroskey
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA
| | - Jin Wen
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA
| | - George Appiah-Kubi
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA
| | - David J Wang
- Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Denis C Guttridge
- Department of Molecular Virology, Immunology, and Medical Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 484 West 12th Avenue, Columbus, OH, 43210, USA
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10
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Qian Z, Rhodes CA, McCroskey LC, Wen J, Appiah-Kubi G, Wang DJ, Guttridge DC, Pei D. Enhancing the Cell Permeability and Metabolic Stability of Peptidyl Drugs by Reversible Bicyclization. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201610888] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Ziqing Qian
- Department of Chemistry and Biochemistry; The Ohio State University; 484 West 12th Avenue Columbus OH 43210 USA
| | - Curran A. Rhodes
- Department of Chemistry and Biochemistry; The Ohio State University; 484 West 12th Avenue Columbus OH 43210 USA
| | - Lucas C. McCroskey
- Department of Chemistry and Biochemistry; The Ohio State University; 484 West 12th Avenue Columbus OH 43210 USA
| | - Jin Wen
- Department of Chemistry and Biochemistry; The Ohio State University; 484 West 12th Avenue Columbus OH 43210 USA
| | - George Appiah-Kubi
- Department of Chemistry and Biochemistry; The Ohio State University; 484 West 12th Avenue Columbus OH 43210 USA
| | - David J. Wang
- Department of Molecular Virology, Immunology, and Medical Genetics; The Ohio State University; Columbus OH 43210 USA
| | - Denis C. Guttridge
- Department of Molecular Virology, Immunology, and Medical Genetics; The Ohio State University; Columbus OH 43210 USA
| | - Dehua Pei
- Department of Chemistry and Biochemistry; The Ohio State University; 484 West 12th Avenue Columbus OH 43210 USA
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11
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Marín-Ramos NI, Piñar C, Vázquez-Villa H, Martín-Fontecha M, González Á, Canales Á, Algar S, Mayo PP, Jiménez-Barbero J, Gajate C, Mollinedo F, Pardo L, Ortega-Gutiérrez S, Viso A, López-Rodríguez ML. Development of a Nucleotide Exchange Inhibitor That Impairs Ras Oncogenic Signaling. Chemistry 2016; 23:1676-1685. [PMID: 27885731 DOI: 10.1002/chem.201604905] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Indexed: 12/11/2022]
Abstract
Despite more than three decades of intense effort, no anti-Ras therapies have reached clinical application. Contributing to this failure has been an underestimation of Ras complexity and a dearth of structural information. In this regard, recent studies have revealed the highly dynamic character of the Ras surface and the existence of transient pockets suitable for small-molecule binding, opening up new possibilities for the development of Ras modulators. Herein, a novel Ras inhibitor (compound 12) is described that selectively impairs mutated Ras activity in a reversible manner without significantly affecting wild-type Ras, reduces the Ras-guanosine triphosphate (GTP) levels, inhibits the activation of the mitogen-activated protein kinase (MAPK) pathway, and exhibits remarkable cytotoxic activity in Ras-driven cellular models. The use of molecular dynamics simulations and NMR spectroscopy experiments has enabled the molecular bases responsible for the interactions between compound 12 and Ras protein to be explored. The new Ras inhibitor binds partially to the GTP-binding region and extends into the adjacent hydrophobic pocket delimited by switch II. Hence, Ras inhibitor 12 could represent a new compound for the development of more efficacious drugs to target Ras-driven cancers; a currently unmet clinical need.
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Affiliation(s)
- Nagore I Marín-Ramos
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain.,CEI Campus Moncloa, UCM-UPM and CSIC, 28040, Madrid, Spain
| | - Carmen Piñar
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Henar Vázquez-Villa
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Mar Martín-Fontecha
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Ángel González
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Ángeles Canales
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Sergio Algar
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Paloma P Mayo
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Jesús Jiménez-Barbero
- CIC bioGUNE, Parque Tecnológico de Bizkaia, Edif. 801A, 48160, Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48103, Bilbao, Spain
| | - Consuelo Gajate
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Faustino Mollinedo
- Department of Cellular and Molecular Medicine, Centro de Investigaciones Biológicas, CSIC, 28040, Madrid, Spain
| | - Leonardo Pardo
- Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Silvia Ortega-Gutiérrez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
| | - Alma Viso
- Instituto de Química Orgánica General, IQOG-CSIC, Juan de la Cierva, 3, 28006, Madrid, Spain
| | - María L López-Rodríguez
- Departamento de Química Orgánica I, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040, Madrid, Spain
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12
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Sautier B, Nising CF, Wortmann L. Fortschritte bei der Ras-Inhibition aus medizinisch-chemischer Perspektive. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201608270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Brice Sautier
- Bayer Pharma AG, Drug Discovery; Medicinal Chemistry Berlin; Muellerstraße 178 13353 Berlin Deutschland
| | - Carl F. Nising
- Bayer Pharma AG, Drug Discovery; Medicinal Chemistry Berlin; Muellerstraße 178 13353 Berlin Deutschland
| | - Lars Wortmann
- Bayer Pharma AG, Drug Discovery; Medicinal Chemistry Berlin; Muellerstraße 178 13353 Berlin Deutschland
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13
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Sautier B, Nising CF, Wortmann L. Latest Advances Towards Ras Inhibition: A Medicinal Chemistry Perspective. Angew Chem Int Ed Engl 2016; 55:15982-15988. [PMID: 27635522 DOI: 10.1002/anie.201608270] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Indexed: 12/17/2022]
Abstract
Owing to their high occurrence rate across many human cancers and their lack of druggability so far, mutant forms of the signaling protein Ras are currently among the most attractive (and elusive) oncology targets. This strong appeal explains the sustained effort in the field, and the ensuing progress has rekindled optimism regarding the discovery of Ras inhibitors. In this Minireview, we discuss the most recent advances towards irreversible inhibitors, and highlight approaches to inhibitors of Ras-effector interactions that have been overshadowed by the current focus on direct Ras inhibition. At the same time, we provide a critical assessment from a medicinal chemistry perspective.
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Affiliation(s)
- Brice Sautier
- Bayer Pharma AG, Drug Discovery, Medicinal Chemistry Berlin, Muellerstrasse 178, 13353, Berlin, Germany
| | - Carl F Nising
- Bayer Pharma AG, Drug Discovery, Medicinal Chemistry Berlin, Muellerstrasse 178, 13353, Berlin, Germany
| | - Lars Wortmann
- Bayer Pharma AG, Drug Discovery, Medicinal Chemistry Berlin, Muellerstrasse 178, 13353, Berlin, Germany
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14
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Raz R, Burlina F, Ismail M, Downward J, Li J, Smerdon SJ, Quibell M, White PD, Offer J. HF-Free Boc Synthesis of Peptide Thioesters for Ligation and Cyclization. Angew Chem Int Ed Engl 2016; 55:13174-13179. [PMID: 27654901 PMCID: PMC5113665 DOI: 10.1002/anie.201607657] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Indexed: 01/03/2023]
Abstract
We have developed a convenient method for the direct synthesis of peptide thioesters, versatile intermediates for peptide ligation and cyclic peptide synthesis. The technology uses a modified Boc SPPS strategy that avoids the use of anhydrous HF. Boc in situ neutralization protocols are used in combination with Merrifield hydroxymethyl resin and TFA/TMSBr cleavage. Avoiding HF extends the scope of Boc SPPS to post-translational modifications that are compatible with the milder cleavage conditions, demonstrated here with the synthesis of the phosphorylated protein CHK2. Peptide thioesters give easy, direct, access to cyclic peptides, illustrated by the synthesis of cyclorasin, a KRAS inhibitor.
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Affiliation(s)
- Richard Raz
- The Francis Crick Institute, 1 Midland road, London, NW1 1AT, UK
| | - Fabienne Burlina
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS, Laboratoire des Biomolécules (LBM), Paris, France
- Département de Chimie, ENS, PSL Research University, UPMC, Univ Paris 06, CNRS, LBM, Paris, France
| | - Mohamed Ismail
- The Francis Crick Institute, 1 Midland road, London, NW1 1AT, UK
| | - Julian Downward
- The Francis Crick Institute, 1 Midland road, London, NW1 1AT, UK
| | - Jiejin Li
- The Francis Crick Institute, 1 Midland road, London, NW1 1AT, UK
| | | | - Martin Quibell
- The Francis Crick Institute, 1 Midland road, London, NW1 1AT, UK
| | - Peter D White
- Merck Chemicals, Padge Road, Beeston, Notts, NG9 2JR, UK
| | - John Offer
- The Francis Crick Institute, 1 Midland road, London, NW1 1AT, UK.
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Raz R, Burlina F, Ismail M, Downward J, Li J, Smerdon SJ, Quibell M, White PD, Offer J. HF-Free Boc Synthesis of Peptide Thioesters for Ligation and Cyclization. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201607657] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Richard Raz
- The Francis Crick Institute; 1 Midland road London NW1 1AT UK
| | - Fabienne Burlina
- Sorbonne Universités, UPMC Univ Paris 06, ENS, CNRS; Laboratoire des Biomolécules (LBM); Paris France
- Département de Chimie, ENS; PSL Research University, UPMC, Univ Paris 06, CNRS, LBM; Paris France
| | - Mohamed Ismail
- The Francis Crick Institute; 1 Midland road London NW1 1AT UK
| | - Julian Downward
- The Francis Crick Institute; 1 Midland road London NW1 1AT UK
| | - Jiejin Li
- The Francis Crick Institute; 1 Midland road London NW1 1AT UK
| | | | - Martin Quibell
- The Francis Crick Institute; 1 Midland road London NW1 1AT UK
| | | | - John Offer
- The Francis Crick Institute; 1 Midland road London NW1 1AT UK
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16
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Fouché M, Schäfer M, Blatter M, Berghausen J, Desrayaud S, Roth HJ. Pharmacokinetic Studies around the Mono- and Difunctionalization of a Bioavailable Cyclic Decapeptide Scaffold. ChemMedChem 2016; 11:1060-8. [DOI: 10.1002/cmdc.201600083] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2016] [Indexed: 12/15/2022]
Affiliation(s)
- Marianne Fouché
- Global Discovery Chemistry/Macrocycles; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Michael Schäfer
- Global Discovery Chemistry/CADD; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Markus Blatter
- Global Discovery Chemistry/Analytics (NMR); Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Jörg Berghausen
- Metabolism and Pharmacokinetics; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Sandrine Desrayaud
- Metabolism and Pharmacokinetics; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
| | - Hans-Jörg Roth
- Global Discovery Chemistry/Macrocycles; Novartis Institute for BioMedical Research; Basel 4002 Switzerland
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17
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Lu S, Jang H, Zhang J, Nussinov R. Inhibitors of Ras-SOS Interactions. ChemMedChem 2015; 11:814-21. [PMID: 26630662 DOI: 10.1002/cmdc.201500481] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Indexed: 12/18/2022]
Abstract
Activating Ras mutations are found in about 30 % of human cancers. Ras activation is regulated by guanine nucleotide exchange factors, such as the son of sevenless (SOS), which form protein-protein interactions (PPIs) with Ras and catalyze the exchange of GDP by GTP. This is the rate-limiting step in Ras activation. However, Ras surfaces lack any evident suitable pockets where a molecule might bind tightly, rendering Ras proteins still 'undruggable' for over 30 years. Among the alternative approaches is the design of inhibitors that target the Ras-SOS PPI interface, a strategy that is gaining increasing recognition for treating Ras mutant cancers. Herein we focus on data that has accumulated over the past few years pertaining to the design of small-molecule modulators or peptide mimetics aimed at the interface of the Ras-SOS PPI. We emphasize, however, that even if such Ras-SOS therapeutics are potent, drug resistance may emerge. To counteract this development, we propose "pathway drug cocktails", that is, drug combinations aimed at parallel (or compensatory) pathways. A repertoire of classified cancer, cell/tissue, and pathway/protein combinations would be beneficial toward this goal.
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Affiliation(s)
- Shaoyong Lu
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China
| | - Hyunbum Jang
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD, 21702, USA
| | - Jian Zhang
- Department of Pathophysiology, Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of Education, Shanghai Jiao Tong University, School of Medicine, Shanghai, 200025, China.
| | - Ruth Nussinov
- Cancer and Inflammation Program, Leidos Biomedical Research Inc., Frederick National Laboratory, National Cancer Institute, Frederick, MD, 21702, USA. .,Department of Human Genetics and Molecular Medicine, Sackler School of Medicine, Sackler Institute of Molecular Medicine, Tel Aviv University, Tel Aviv, 69978, Israel.
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Cardote TAF, Ciulli A. Cyclic and Macrocyclic Peptides as Chemical Tools To Recognise Protein Surfaces and Probe Protein-Protein Interactions. ChemMedChem 2015; 11:787-94. [PMID: 26563831 PMCID: PMC4848765 DOI: 10.1002/cmdc.201500450] [Citation(s) in RCA: 132] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Indexed: 01/25/2023]
Abstract
Targeting protein surfaces and protein-protein interactions (PPIs) with small molecules is a frontier goal of chemical biology and provides attractive therapeutic opportunities in drug discovery. The molecular properties of protein surfaces, including their shallow features and lack of deep binding pockets, pose significant challenges, and as a result have proved difficult to target. Peptides are ideal candidates for this mission due to their ability to closely mimic many structural features of protein interfaces. However, their inherently low intracellular stability and permeability and high in vivo clearance have thus far limited their biological applications. One way to improve these properties is to constrain the secondary structure of linear peptides by cyclisation. Herein we review various classes of cyclic and macrocyclic peptides as chemical probes of protein surfaces and modulators of PPIs. The growing interest in this area and recent advances provide evidence of the potential of developing peptide-like molecules that specifically target these interactions.
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Affiliation(s)
- Teresa A F Cardote
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK
| | - Alessio Ciulli
- Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, James Black Centre, Dow Street, Dundee, DD1 5EH, UK.
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Cromm PM, Spiegel J, Grossmann TN, Waldmann H. Direct Modulation of Small GTPase Activity and Function. Angew Chem Int Ed Engl 2015; 54:13516-37. [DOI: 10.1002/anie.201504357] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Indexed: 12/19/2022]
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