1
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Ali Y, Khan AA, Alanazi AM, Fatima S, Kozmon S. A novel Imidazo[1,2-a]pyridine derivative modulates active KRAS G12D through off-like conformational shifts in switch-I and switch-II regions, mimicking inactive KRAS G12D. Int J Biol Macromol 2024; 270:132477. [PMID: 38772459 DOI: 10.1016/j.ijbiomac.2024.132477] [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: 01/15/2024] [Revised: 05/05/2024] [Accepted: 05/15/2024] [Indexed: 05/23/2024]
Abstract
KRASG12D are the most prevalent oncogenic mutations and a promising target for solid tumor therapies. However, its inhibition exhibits tremendous challenge due to the necessity of high binding affinity to obviate the need for covalent binders. Here we report the evidence of a novel class of Imidazo[1,2-a]pyridine derivative as potentially significant novel inhibitors of KRASG12D, discovered through extensive ligand-based screening against 2-[(2R)-piperidin-2-yl]-1H-indole, an important scaffold for KRASG12D inhibition via switch-I/II (S-I/II) pocket. The proposed compounds exhibited similar binding affinities and overlapped pose configurations to 2-[(2R)-piperidin-2-yl]-1H-indole, serving as a reliable starting point for drug discovery. Comparative free energy profiles demonstrated that C4 [2-methyl-3-((5-phenyl-1H-1,2,4-triazol-3-yl)methyl)imidazo[1,2-a]pyridine] effectively shifted the protein to a stable low-energy conformation via a prominent transition state. The conformational changes across the transition revealed the conformational shift of switch-I and II to a previously known off-like conformation of inactive KRASG12D with rmsd of 0.91 Å. These conformations were even more prominent than the privileged scaffold 2-[(2R)-piperidin-2-yl]-1H-indole. The representative structure overlay of C4 and another X-ray crystallography solved BI-2852 bound inactive KRASG12D revealed that Switch-I and II exhibited off-like conformations. The cumulative variance across the first eigenvalue that accounted for 57 % of the collective variance validated this on-to-off transition. In addition, the relative interaction of C4 binding showed consistent patterns with BI-2852. Taken together, our results support the inhibitory activity of [2-methyl-3-((5-phenyl-1H-1,2,4-triazol-3-yl)methyl)imidazo[1,2-a]pyridine] by shifting active KRASG12D to an inactive conformation.
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Affiliation(s)
- Yasir Ali
- Institute of Chemistry Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia.
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Amer M Alanazi
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia.
| | - Shabeen Fatima
- Institute of Chemistry Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia.
| | - Stanislav Kozmon
- Institute of Chemistry Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia.
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2
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Eliminating oncogenic RAS: back to the future at the drawing board. Biochem Soc Trans 2023; 51:447-456. [PMID: 36688434 PMCID: PMC9987992 DOI: 10.1042/bst20221343] [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: 11/30/2022] [Revised: 01/11/2023] [Accepted: 01/12/2023] [Indexed: 01/24/2023]
Abstract
RAS drug development has made enormous strides in the past ten years, with the first direct KRAS inhibitor being approved in 2021. However, despite the clinical success of covalent KRAS-G12C inhibitors, we are immediately confronted with resistances as commonly found with targeted drugs. Previously believed to be undruggable due to its lack of obvious druggable pockets, a couple of new approaches to hit this much feared oncogene have now been carved out. We here concisely review these approaches to directly target four druggable sites of RAS from various angles. Our analysis focuses on the lessons learnt during the development of allele-specific covalent and non-covalent RAS inhibitors, the potential of macromolecular binders to facilitate the discovery and validation of targetable sites on RAS and finally an outlook on a future that may engage more small molecule binders to become drugs. We foresee that the latter could happen mainly in two ways: First, non-covalent small molecule inhibitors may be derived from the development of covalent binders. Second, reversible small molecule binders could be utilized for novel targeting modalities, such as degraders of RAS. Provided that degraders eliminate RAS by recruiting differentially expressed E3-ligases, this approach could enable unprecedented tissue- or developmental stage-specific destruction of RAS with potential advantages for on-target toxicity. We conclude that novel creative ideas continue to be important to exterminate RAS in cancer and other RAS pathway-driven diseases, such as RASopathies.
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3
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Kaguchi R, Katsuyama A, Sato T, Takahashi S, Horiuchi M, Yokota SI, Ichikawa S. Discovery of Biologically Optimized Polymyxin Derivatives Facilitated by Peptide Scanning and In Situ Screening Chemistry. J Am Chem Soc 2023; 145:3665-3681. [PMID: 36708325 DOI: 10.1021/jacs.2c12971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Peptides can be converted to highly active compounds by introducing appropriate substituents on the suitable amino acid residue. Although modifiable residues in peptides can be systematically identified by peptide scanning methodologies, there is no practical method for optimization at the "scanned" position. With the purpose of using derivatives not only for scanning but also as a starting point for further chemical functionalization, we herein report the "scanning and direct derivatization" strategy through chemoselective acylation of embedded threonine residues by a serine/threonine ligation (STL) with the help of in situ screening chemistry. We have applied this strategy to the optimization of the polymyxin antibiotics, which were selected as a model system to highlight the power of the rapid derivatization of active scanning derivatives. Using this approach, we explored the structure-activity relationships of the polymyxins and successfully prepared derivatives with activity against polymyxin-resistant bacteria and those with Pseudomonas aeruginosa selective antibacterial activity. This strategy opens up efficient structural exploration and further optimization of peptide sequences.
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Affiliation(s)
- Rintaro Kaguchi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo060-0812, Japan
| | - Akira Katsuyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo060-0812, Japan.,Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo060-0812, Japan
| | - Toyotaka Sato
- Laboratory of Veterinary Hygiene, School/Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo060-0818, Japan.,Graduate School of Infectious Diseases, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo060-0818, Japan.,One Health Research Center, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo060-0818, Japan
| | - Satoshi Takahashi
- Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Minami-1, Nishi-16, Chuo-ku, Sapporo060-8543, Japan.,Division of Laboratory Medicine, Sapporo Medical University Hospital, Minami-1, Nishi-16, Chuo-ku, Sapporo060-8543, Japan
| | - Motohiro Horiuchi
- Laboratory of Veterinary Hygiene, School/Faculty of Veterinary Medicine, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo060-0818, Japan.,Graduate School of Infectious Diseases, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo060-0818, Japan.,One Health Research Center, Hokkaido University, Kita-18, Nishi-9, Kita-ku, Sapporo060-0818, Japan
| | - Shin-Ichi Yokota
- Department of Microbiology, Sapporo Medical University School of Medicine, Minami-1, Nishi-17, Chuo-ku, Sapporo060-8556, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo060-0812, Japan.,Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo060-0812, Japan.,Global Station for Biosurfaces and Drug Discovery, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Kita-12, Nishi-6, Kita-ku, Sapporo060-0812, Japan
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4
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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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5
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Nanoformulation of the K-Ras(G12D)-inhibitory peptide KS-58 suppresses colorectal and pancreatic cancer-derived tumors. Sci Rep 2023; 13:518. [PMID: 36627374 PMCID: PMC9832047 DOI: 10.1038/s41598-023-27825-8] [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: 10/13/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023] Open
Abstract
Single amino acid mutations of Ras occur in 30% of human cancers. In particular, K-Ras(G12D) has been detected in the majority of intractable colorectal and pancreatic cancers. Although efforts to target K-Ras(G12D) are currently underway, no effective drugs are available. We previously found that the K-Ras(G12D)-inhibitory bicyclic peptide KS-58 exhibits antitumor activity against syngeneic colon and orthotopic grafted pancreatic tumors; however, pristine KS-58 is difficult to handle because of low water solubility and it requires frequent administration to obtain sufficient antitumor activity. In this study, we used a nanoformulation of KS-58 prepared with the highly biocompatible surfactant Cremophor® EL (CrEL) to improve water solubility and reduce the dosing frequency. Nanoformulations of KS-58 with CrEL dramatically improved its water solubility and increased its stability. Weekly intravenous administration of KS-58 nanoparticles (NPs) suppressed the growth of CT26 and PANC-1 cell-derived tumors in vivo, and fluorescent bioimaging indicated that the NP-encapsulated near-infrared fluorescent probe indocyanine green selectively accumulated in the tumor and was safely excreted through the kidneys following intravenous injection. Histopathological analysis of CT26 tumors and Western blotting of PANC-1 tumors revealed that KS-58 NPs reduced ERK phosphorylation, a downstream signal of K-Ras(G12D). Our results suggest that KS-58 NPs represent a novel therapeutic agent for treating colorectal and pancreatic cancers.
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6
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In Silico Strategies for Designing of Peptide Inhibitors of Oncogenic K-Ras G12V Mutant: Inhibiting Cancer Growth and Proliferation. Cancers (Basel) 2022; 14:cancers14194884. [PMID: 36230807 PMCID: PMC9564332 DOI: 10.3390/cancers14194884] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/02/2022] [Accepted: 10/03/2022] [Indexed: 12/12/2022] Open
Abstract
Simple Summary The most well-known oncogene and one with the highest rates of mutation across all cancers is K-Ras, also known as the Kirsten rat sarcoma viral oncogene homologue. It is also linked to certain cancers with a high mortality rate, including pancreatic ductal adenocarcinoma (PDAC), non-small-cell lung cancer (NSCLC), and colorectal cancer (CRC). The aim of this study was to make peptides that inhibit K-Ras G12V by computer-aided drug design methods. Our results showed that the top four selected peptides interact with K-Ras more strongly than the reference-peptide and can stop K-Ras from activating. Our binding affinity analyses demonstrated that the developed peptides can inhibit K-Ras and slow cancer growth. Abstract Ras plays a pivotal function in cell proliferation and is an important protein in signal transduction pathways. Mutations in genes encoding the Ras protein drive the signaling cascades essential for malignant transformation, tumour angiogenesis, and metastasis and are responsible for above 30% of all human cancers. There is evidence that N-Ras, K-Ras, and H-Ras play significant roles in human cancer. The mutated K-Ras protein is typically observed in malignant growths. Mutant K-Ras is the most common in lung, colon, and pancreatic cancers. The purpose of this research was to create peptides that inhibit K-Ras G12V. The crystal structure of the mutant K-Ras G12V-H-REV107 complex was obtained from a protein data bank. Further, we used a residue scan approach to create unique peptides from the reference peptide (H-REV107). AMBER molecular dynamics simulations were used to test the stability of the top four proposed peptides (based on binding free energies). Our findings showed that the top four selected peptides had stronger interactions with K-Ras than the reference peptide and have the ability to block the activation function of K-Ras. Our extensive analyses of binding affinities showed that our designed peptide possesses the potential to inhibit K-Ras and to reduce the progression of cancer.
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7
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Rapid label-free cell-based Approach Membrane Permeability Assay using MALDI-hydrogen-deuterium exchange mass spectrometry for peptides. Anal Chim Acta 2022; 1225:340234. [DOI: 10.1016/j.aca.2022.340234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 07/14/2022] [Accepted: 08/01/2022] [Indexed: 11/17/2022]
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8
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Garrigou M, Sauvagnat B, Duggal R, Boo N, Gopal P, Johnston JM, Partridge A, Sawyer T, Biswas K, Boyer N. Accelerated Identification of Cell Active KRAS Inhibitory Macrocyclic Peptides using Mixture Libraries and Automated Ligand Identification System (ALIS) Technology. J Med Chem 2022; 65:8961-8974. [PMID: 35707970 PMCID: PMC9289880 DOI: 10.1021/acs.jmedchem.2c00154] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
![]()
Macrocyclic
peptides can disrupt previously intractable protein–protein
interactions (PPIs) relevant to oncology targets such as KRAS. Early
hits often lack cellular activity and require meticulous improvement
of affinity, permeability, and metabolic stability to become viable
leads. We have validated the use of the Automated Ligand Identification
System (ALIS) to screen oncogenic KRASG12D (GDP) against
mass-encoded mini-libraries of macrocyclic peptides and accelerate
our structure–activity relationship (SAR) exploration. These
mixture libraries were generated by premixing various unnatural amino
acids without the need for the laborious purification of individual
peptides. The affinity ranking of the peptide sequences provided SAR-rich
data sets that led to the selection of novel potency-enhancing substitutions
in our subsequent designs. Additional stability and permeability optimization
resulted in the identification of peptide 7 that inhibited
pERK activity in a pancreatic cancer cell line. More broadly, this
methodology offers an efficient alternative to accelerate the fastidious
hit-to-lead optimization of PPI peptide inhibitors.
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Affiliation(s)
| | | | - Ruchia Duggal
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Nicole Boo
- MSD International, Singapore 138665, Singapore
| | - Pooja Gopal
- MSD International, Singapore 138665, Singapore
| | | | | | - Tomi Sawyer
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Kaustav Biswas
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | - Nicolas Boyer
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
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9
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Sakamoto K, Lin B, Nunomura K, Izawa T, Nakagawa S. The K-Ras(G12D)-inhibitory peptide KS-58 suppresses growth of murine CT26 colorectal cancer cell-derived tumors. Sci Rep 2022; 12:8121. [PMID: 35581303 PMCID: PMC9114382 DOI: 10.1038/s41598-022-12401-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 04/26/2022] [Indexed: 11/24/2022] Open
Abstract
Mutations in the cell proliferation regulator K-Ras are found with a variety of cancer types, so drugs targeting these mutant proteins could hold great clinical potential. Very recently, a drug targeting the K-Ras(G12C) mutant observed in lung cancer gained regulatory approval and several clinical trials are currently underway to examine the efficacy of this agent when combined with other drugs such as a monoclonal antibody inhibitor of programmed cell death 1 receptor (anti-PD-1). Alternatively, there are currently no approved drugs targeting K-Ras(G12D), the most common cancer-associated K-Ras mutant. In 2020, we described the development of the K-Ras(G12D) inhibitory bicyclic peptide KS-58 and presented evidence for anticancer activity against mouse xenografts derived from the human pancreatic cancer cell line PANC-1 stably expressing K-Ras(G12D). Here, we show that KS-58 also possess anticancer activity against mouse tumors derived from the colorectal cancer cell line CT26 stably expressing K-Ras(G12D). Further, KS-58 treatment reduced phosphorylation of ERK, a major downstream signaling factor in the Ras pathway, confirming that KS-58 inhibits K-Ras(G12D) function. Unexpectedly; however, KS-58 did not show additive or synergistic anticancer activity with mouse anti-PD-1. Morphological analysis and immunostaining demonstrated no obvious differences in CD8+ cells infiltration or PD-L1 expression levels in CT26-derived tumors exposed to monotherapy or combination treatment. Nonetheless, KS-58 demonstrated reasonable stability in blood (t1/2 ≈ 30 min) and no obvious systemic adverse effects, suggesting clinical potential as a lead molecule against colorectal cancer.
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Affiliation(s)
- Kotaro Sakamoto
- grid.459582.7Research & Development Department, Ichimaru Pharcos Company Limited, 318-1 Asagi, Motosu, Gifu 501-0475 Japan
| | - Bangzhong Lin
- grid.136593.b0000 0004 0373 3971Center for Supporting Drug Discovery and Life Science Research, Graduate School of Pharmaceutical Science, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Kazuto Nunomura
- grid.136593.b0000 0004 0373 3971Center for Supporting Drug Discovery and Life Science Research, Graduate School of Pharmaceutical Science, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
| | - Takeshi Izawa
- grid.261455.10000 0001 0676 0594Laboratory of Veterinary Pathology, Osaka Prefecture University, 1-58 Rinku-Orai-Kita, Izumisano, Osaka 598-8531 Japan
| | - Shinsaku Nakagawa
- grid.136593.b0000 0004 0373 3971Center for Supporting Drug Discovery and Life Science Research, Graduate School of Pharmaceutical Science, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan ,grid.136593.b0000 0004 0373 3971Laboratory of Biopharmaceutics, Osaka University, 1-6 Yamadaoka, Suita, Osaka 565-0871 Japan
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10
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KRAS is vulnerable to reversible switch-II pocket engagement in cells. Nat Chem Biol 2022; 18:596-604. [PMID: 35314814 PMCID: PMC9135634 DOI: 10.1038/s41589-022-00985-w] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 01/28/2022] [Indexed: 12/15/2022]
Abstract
Current small-molecule inhibitors of KRAS(G12C) bind irreversibly in the switch-II pocket (SII-P), exploiting the strong nucleophilicity of the acquired cysteine as well as the preponderance of the GDP-bound form of this mutant. Nevertheless, many oncogenic KRAS mutants lack these two features, and it remains unknown whether targeting the SII-P is a practical therapeutic approach for KRAS mutants beyond G12C. Here we use NMR spectroscopy and a cellular KRAS engagement assay to address this question by examining a collection of SII-P ligands from the literature and from our own laboratory. We show that the SII-Ps of many KRAS hotspot (G12, G13, Q61) mutants are accessible using noncovalent ligands, and that this accessibility is not necessarily coupled to the GDP state of KRAS. The results we describe here emphasize the SII-P as a privileged drug-binding site on KRAS and unveil new therapeutic opportunities in RAS-driven cancer. ![]()
The use of NMR spectroscopy and development of a cellular BRET KRAS engagement assay revealed that noncovalent ligands can access the switch-II pocket of KRAS hotspot mutants.
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11
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Affinity Selection from Synthetic Peptide Libraries Enabled by De Novo MS/MS Sequencing. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10370-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractRecently, de novo MS/MS peptide sequencing has enabled the application of affinity selections to synthetic peptide mixtures that approach the diversity of phage libraries (> 108 random peptides). In conjunction with ‘split-mix’ solid phase synthesis to access equimolar peptide mixtures, this approach provides a straightforward means to examine synthetic peptide libraries of considerably higher diversity than has been feasible historically. Here, we offer a critical perspective on this work, report emerging data, and highlight opportunities for further methods refinement. With continued development, ‘affinity selection–mass spectrometry’ may become a complimentary approach to phage display, in vitro selection, and DNA-encoded libraries for the discovery of synthetic ligands that modulate protein function.
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12
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Rajpurohit T, Bhattacharya S. Moving Towards Dawn: KRas Signaling and Treatment in Pancreatic Ductal Adenocarcinoma. Curr Mol Pharmacol 2022; 15:904-928. [PMID: 35088684 DOI: 10.2174/1874467215666220128161647] [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: 07/26/2021] [Revised: 10/20/2021] [Accepted: 11/17/2021] [Indexed: 12/24/2022]
Abstract
"Pancreatic ductal adenocarcinoma (PDAC)" is robust, nearly clueless, and all-around deadly among all tumors. Below 10 %, the general 5-year endurance period has remained adamantly unaltered in the last 30 years, regardless of enormous clinical and therapeutic endeavors. The yearly number of deaths is more than the number of recently analyzed cases. Not a classic one, but "Carbohydrate Antigen CA19- 9" remains the prevailing tool for diagnosis. MicroRNAs and non-invasive techniques are now incorporated for the effective prognosis of PDAC than just CA19-9. Mutated "Rat sarcoma virus Ras" conformation "V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog KRas" is 95 % accountable for PDAC, and its active (GTP-bound) formation activates signaling cascade comprising "Rapidly accelerated fibrosarcoma Raf"/"Mitogen-activated protein kinase MEK"/ "Extracellular signal-regulated kinase ERK" with "Phosphoinositide 3-kinase PI3K"/ "protein kinase B Akt"/ "mammalian target of rapamycin mTOR" pathways. KRas has acquired the label of 'undruggable' since the crosstalk in the nexus of pathways compensates for Raf and PI3K signaling cascade blocking. It is arduous to totally regulate KRascoordinated PDAC with traditional medicaments like "gemcitabine GEM" plus nabpaclitaxel/ FOLFIRINOX. For long-haul accomplishments aiming at KRas, future endeavors should be directed to combinatorial methodologies to adequately block KRas pathways at different standpoints. Currently they are contributing to healing PDAC. In this review article, we outline the function of KRas in carcinogenesis in PDAC, its signaling cascade, former techniques utilized in hindering Kras, current and future possibilities for targeting Kras.
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Affiliation(s)
- Tarun Rajpurohit
- Department of Pharmaceutics, School of Pharmacy & Technology Management, SVKM'S NMIMS Deemed-to-be University, Shirpur, Maharashtra 425405, India
| | - Sankha Bhattacharya
- Department of Pharmaceutics, School of Pharmacy & Technology Management, SVKM'S NMIMS Deemed-to-be University, Shirpur, Maharashtra 425405, India
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13
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Lim S, Boyer N, Boo N, Huang C, Venkatachalam G, Angela Juang YC, Garrigou M, Kaan HYK, Duggal R, Peh KM, Sadruddin A, Gopal P, Yuen TY, Ng S, Kannan S, Brown CJ, Verma CS, Orth P, Peier A, Ge L, Yu X, Bhatt B, Chen F, Wang E, Li NJ, Gonzales RJ, Stoeck A, Henry B, Sawyer TK, Lane DP, Johannes CW, Biswas K, Partridge AW. Discovery of cell active macrocyclic peptides with on-target inhibition of KRAS signaling. Chem Sci 2021; 12:15975-15987. [PMID: 35024121 PMCID: PMC8672774 DOI: 10.1039/d1sc05187c] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/20/2021] [Indexed: 12/13/2022] Open
Abstract
Macrocyclic peptides have the potential to address intracellular protein–protein interactions (PPIs) of high value therapeutic targets that have proven largely intractable to small molecules. Here, we report broadly applicable lessons for applying this modality to intracellular targets and specifically for advancing chemical matter to address KRAS, a protein that represents the most common oncogene in human lung, colorectal and pancreatic cancers yet is one of the most challenging targets in human disease. Specifically, we focused on KRpep-2d, an arginine-rich KRAS-binding peptide with a disulfide-mediated macrocyclic linkage and a protease-sensitive backbone. These latter redox and proteolytic labilities obviated cellular activity. Extensive structure–activity relationship studies involving macrocyclic linker replacement, stereochemical inversion, and backbone α-methylation, gave a peptide with on-target cellular activity. However, we uncovered an important generic insight – the arginine-dependent cell entry mechanism limited its therapeutic potential. In particular, we observed a strong correlation between net positive charge and histamine release in an ex vivo assay, thus making this series unsuitable for advancement due to the potentially fatal consequences of mast cell degranulation. This observation should signal to researchers that cationic-mediated cell entry – an approach that has yet to succeed in the clinic despite a long history of attempts – carries significant therapy-limiting safety liabilities. Nonetheless, the cell-active molecules identified here validate a unique inhibitory epitope on KRAS and thus provide valuable molecular templates for the development of therapeutics that are desperately needed to address KRAS-driven cancers – some of the most treatment-resistant human malignancies. Targeting undruggable intracellular proteins with peptides: novel on-target macrocyclic peptide inhibitors of KRAS with broad inhibition of proliferation of multiple KRAS-dependent cancer cell lines.![]()
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Affiliation(s)
- Shuhui Lim
- MSD International Singapore 138665 Singapore
| | | | - Nicole Boo
- MSD International Singapore 138665 Singapore
| | | | | | | | | | | | | | | | | | - Pooja Gopal
- MSD International Singapore 138665 Singapore
| | - Tsz Ying Yuen
- Agency for Science, Technology and Research (ASTAR) Singapore 138665 Singapore
| | - Simon Ng
- Agency for Science, Technology and Research (ASTAR) Singapore 138665 Singapore
| | | | - Christopher J Brown
- Agency for Science, Technology and Research (ASTAR) Singapore 138665 Singapore
| | - Chandra S Verma
- Agency for Science, Technology and Research (ASTAR) Singapore 138665 Singapore
| | - Peter Orth
- Merck & Co., Inc. Kenilworth New Jersey 07033 USA
| | - Andrea Peier
- Merck & Co., Inc. Kenilworth New Jersey 07033 USA
| | - Lan Ge
- Merck & Co., Inc. Kenilworth New Jersey 07033 USA
| | - Xiang Yu
- Merck & Co., Inc. West Point Pennsylvania 19486 USA
| | | | - Feifei Chen
- Merck & Co., Inc. West Point Pennsylvania 19486 USA
| | - Erjia Wang
- Merck & Co., Inc. West Point Pennsylvania 19486 USA
| | | | | | | | - Brian Henry
- MSD International Singapore 138665 Singapore
| | | | - David P Lane
- Agency for Science, Technology and Research (ASTAR) Singapore 138665 Singapore
| | - Charles W Johannes
- Agency for Science, Technology and Research (ASTAR) Singapore 138665 Singapore
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14
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Wang X, Allen S, Blake JF, Bowcut V, Briere DM, Calinisan A, Dahlke JR, Fell JB, Fischer JP, Gunn RJ, Hallin J, Laguer J, Lawson JD, Medwid J, Newhouse B, Nguyen P, O'Leary JM, Olson P, Pajk S, Rahbaek L, Rodriguez M, Smith CR, Tang TP, Thomas NC, Vanderpool D, Vigers GP, Christensen JG, Marx MA. Identification of MRTX1133, a Noncovalent, Potent, and Selective KRAS G12D Inhibitor. J Med Chem 2021; 65:3123-3133. [PMID: 34889605 DOI: 10.1021/acs.jmedchem.1c01688] [Citation(s) in RCA: 244] [Impact Index Per Article: 81.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
KRASG12D, the most common oncogenic KRAS mutation, is a promising target for the treatment of solid tumors. However, when compared to KRASG12C, selective inhibition of KRASG12D presents a significant challenge due to the requirement of inhibitors to bind KRASG12D with high enough affinity to obviate the need for covalent interactions with the mutant KRAS protein. Here, we report the discovery and characterization of the first noncovalent, potent, and selective KRASG12D inhibitor, MRTX1133, which was discovered through an extensive structure-based activity improvement and shown to be efficacious in a KRASG12D mutant xenograft mouse tumor model.
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Affiliation(s)
- Xiaolun Wang
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Shelley Allen
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - James F Blake
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Vickie Bowcut
- Mirati Therapeutics, San Diego, California 92121, United States
| | - David M Briere
- Mirati Therapeutics, San Diego, California 92121, United States
| | | | - Joshua R Dahlke
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Jay B Fell
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - John P Fischer
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Robin J Gunn
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Jill Hallin
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Jade Laguer
- Mirati Therapeutics, San Diego, California 92121, United States
| | - J David Lawson
- Mirati Therapeutics, San Diego, California 92121, United States
| | - James Medwid
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Brad Newhouse
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Phong Nguyen
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Jacob M O'Leary
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Peter Olson
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Spencer Pajk
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Lisa Rahbaek
- Mirati Therapeutics, San Diego, California 92121, United States
| | - Mareli Rodriguez
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | | | - Tony P Tang
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | - Nicole C Thomas
- Mirati Therapeutics, San Diego, California 92121, United States
| | | | - Guy P Vigers
- Pfizer Boulder Research & Development, Boulder, Colorado 80301, United States
| | | | - Matthew A Marx
- Mirati Therapeutics, San Diego, California 92121, United States
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15
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Fumagalli G, Carbajo RJ, Nissink JWM, Tart J, Dou R, Thomas AP, Spring DR. Targeting a Novel KRAS Binding Site: Application of One-Component Stapling of Small (5-6-mer) Peptides. J Med Chem 2021; 64:17287-17303. [PMID: 34787423 DOI: 10.1021/acs.jmedchem.1c01334] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
RAS proteins are central in the proliferation of many types of cancer, but a general approach toward the identification of pan-mutant RAS inhibitors has remained unresolved. In this work, we describe the application of a binding pharmacophore identified from analysis of known RAS binding peptides to the design of novel peptides. Using a chemically divergent approach, we generated a library of small stapled peptides from which we identified compounds with weak binding activity. Exploration of structure-activity relationships (SARs) and optimization of these early compounds led to low-micromolar binders of KRAS that block nucleotide exchange.
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Affiliation(s)
- Gabriele Fumagalli
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K.,Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | | | | | - Jonathan Tart
- Discovery Sciences, BioPharmaceuticals R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - Rongxuan Dou
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Andrew P Thomas
- Chemistry, Oncology R&D, AstraZeneca, Cambridge CB4 0WG, U.K
| | - David R Spring
- Department of Chemistry, Cambridge University, Lensfield Road, Cambridge CB2 1EW, U.K
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16
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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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17
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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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18
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Generation of KS-58 as the first K-Ras(G12D)-inhibitory peptide presenting anti-cancer activity in vivo. Sci Rep 2020; 10:21671. [PMID: 33303890 PMCID: PMC7730438 DOI: 10.1038/s41598-020-78712-5] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 11/25/2020] [Indexed: 12/22/2022] Open
Abstract
Ras mutations (e.g., occur in K-Ras, N-Ras, and H-Ras) are one of the most desirable and promising drug targets in chemotherapy treatments for cancer. However, there are still no approved drugs directly targeting mutated Ras. In 2017, an artificial cyclic peptide, KRpep-2d, was discovered as the first selective inhibitor of K-Ras(G12D), the most frequent K-Ras mutation. Here, we report the generation of KS-58, a KRpep-2d derivative that is identified as a bicyclic peptide and possess unnatural amino acid structures. Our in vitro data and molecular dynamics simulations suggest that KS-58 enters cells and blocks intracellular Ras–effector protein interactions. KS-58 selectively binds to K-Ras(G12D) and suppresses the in vitro proliferation of the human lung cancer cell line A427 and the human pancreatic cancer cell line PANC-1, both of which express K-Ras(G12D). Moreover, KS-58 exhibits anti-cancer activity when given as an intravenous injection to mice with subcutaneous or orthotropic PANC-1 cell xenografts. The anti-cancer activity is further improved by combination with gemcitabine. To the best of our knowledge, this is the first report of K-Ras(G12D)-selective inhibitory peptide presenting in vivo anti-cancer activity. KS-58 is an attractive lead molecule for the development of novel cancer drugs that target K-Ras(G12D).
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19
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Zhang Z, Gao R, Hu Q, Peacock H, Peacock DM, Dai S, Shokat KM, Suga H. GTP-State-Selective Cyclic Peptide Ligands of K-Ras(G12D) Block Its Interaction with Raf. ACS CENTRAL SCIENCE 2020; 6:1753-1761. [PMID: 33145412 PMCID: PMC7596874 DOI: 10.1021/acscentsci.0c00514] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Indexed: 05/08/2023]
Abstract
We report the identification of three cyclic peptide ligands of K-Ras(G12D) using an integrated in vitro translation-mRNA display selection platform. These cyclic peptides show preferential binding to the GTP-bound state of K-Ras(G12D) over the GDP-bound state and block Ras-Raf interaction. A co-crystal structure of peptide KD2 with K-Ras(G12D)·GppNHp reveals that this peptide binds in the Switch II groove region with concomitant opening of the Switch II loop and a 40° rotation of the α2 helix, and that a threonine residue (Thr10) on KD2 has direct access to the mutant aspartate (Asp12) on K-Ras. Replacing this threonine with non-natural amino acids afforded peptides with improved potency at inhibiting the interaction between Raf1-RBD and K-Ras(G12D) but not wildtype K-Ras. The union of G12D over wildtype selectivity and GTP state/GDP state selectivity is particularly desirable, considering that oncogenic K-Ras(G12D) exists predominantly in the GTP state in cancer cells, and wildtype K-Ras signaling is important for the maintenance of healthy cells.
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Affiliation(s)
- Ziyang Zhang
- Department of Cellular
and Molecular Pharmacology, Howard Hughes Medical Institute, University of California—San Francisco, San Francisco, California 94158, United States
| | - Rong Gao
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Qi Hu
- Department of Cellular
and Molecular Pharmacology, Howard Hughes Medical Institute, University of California—San Francisco, San Francisco, California 94158, United States
| | - Hayden Peacock
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - D. Matthew Peacock
- Department of Cellular
and Molecular Pharmacology, Howard Hughes Medical Institute, University of California—San Francisco, San Francisco, California 94158, United States
| | - Shizhong Dai
- Department of Cellular
and Molecular Pharmacology, Howard Hughes Medical Institute, University of California—San Francisco, San Francisco, California 94158, United States
| | - Kevan M. Shokat
- Department of Cellular
and Molecular Pharmacology, Howard Hughes Medical Institute, University of California—San Francisco, San Francisco, California 94158, United States
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
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20
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McAllister TE, Coleman OD, Roper G, Kawamura A. Structural diversity in
de novo
cyclic peptide ligands from genetically encoded library technologies. Pept Sci (Hoboken) 2020. [DOI: 10.1002/pep2.24204] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Tom E. McAllister
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Oliver D. Coleman
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
| | - Grace Roper
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Chemistry Research Laboratory, Department of Chemistry University of Oxford Oxford UK
| | - Akane Kawamura
- Chemistry – School of Natural and Environmental Sciences Newcastle University Newcastle upon Tyne UK
- Chemistry Research Laboratory, Department of Chemistry University of Oxford Oxford UK
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21
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Ng S, Juang YC, Chandramohan A, Kaan HYK, Sadruddin A, Yuen TY, Ferrer-Gago FJ, Lee XC, Liew X, Johannes CW, Brown CJ, Kannan S, Aronica PG, Berglund NA, Verma CS, Liu L, Stoeck A, Sawyer TK, Partridge AW, Lane DP. De-risking Drug Discovery of Intracellular Targeting Peptides: Screening Strategies to Eliminate False-Positive Hits. ACS Med Chem Lett 2020; 11:1993-2001. [PMID: 33062184 DOI: 10.1021/acsmedchemlett.0c00022] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/01/2020] [Indexed: 12/14/2022] Open
Abstract
Nonspecific promiscuous compounds can mislead researchers and waste significant resources. This phenomenon, though well-documented for small molecules, has not been widely explored for the peptide modality. Here we demonstrate that two purported peptide-based KRas inhibitors, SAH-SOS1 A and cyclorasin 9A5, exemplify false-positive molecules-in terms of both their binding affinities and cellular activities. Through multiple gold-standard biophysical techniques, we unambiguously show that both peptides lack specific binding to KRas and instead induce protein unfolding. Although these peptides inhibited cellular proliferation, the activities appeared to be off-target on the basis of a counterscreen with KRas-independent cell lines. We further demonstrate that their cellular activities are derived from membrane disruption. Accordingly, we propose that to de-risk false-positive molecules, orthogonal binding assays and cellular counterscreens are indispensable.
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Affiliation(s)
| | | | | | | | | | - Tsz Ying Yuen
- Institute of Chemical and Engineering Sciences, A*STAR, Singapore 138665
| | | | - Xue’Er Cheryl Lee
- Institute of Chemical and Engineering Sciences, A*STAR, Singapore 138665
| | - Xi Liew
- Institute of Chemical and Engineering Sciences, A*STAR, Singapore 138665
| | | | | | | | | | | | | | - Lijuan Liu
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
| | | | - Tomi K. Sawyer
- Merck & Co., Inc., Boston, Massachusetts 02115, United States
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22
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How to make an undruggable enzyme druggable: lessons from ras proteins. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020. [PMID: 32951811 DOI: 10.1016/bs.apcsb.2020.05.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2023]
Abstract
Significant advances have been made toward discovering allosteric inhibitors for challenging drug targets such as the Ras family of membrane-associated signaling proteins. Malfunction of Ras proteins due to somatic mutations is associated with up to a quarter of all human cancers. Computational techniques have played critical roles in identifying and characterizing allosteric ligand-binding sites on these proteins, and to screen ligand libraries against those sites. These efforts, combined with a wide range of biophysical, structural, biochemical and cell biological experiments, are beginning to yield promising inhibitors to treat malignancies associated with mutated Ras proteins. In this chapter, we discuss some of these developments and how the lessons learned from Ras might be applied to similar other challenging drug targets.
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23
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Uprety D, Adjei AA. KRAS: From undruggable to a druggable Cancer Target. Cancer Treat Rev 2020; 89:102070. [DOI: 10.1016/j.ctrv.2020.102070] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 07/04/2020] [Accepted: 07/06/2020] [Indexed: 02/07/2023]
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24
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Affiliation(s)
| | - Helen R. Mott
- Department of Biochemistry University of Cambridge Cambridge UK
| | - Darerca Owen
- Department of Biochemistry University of Cambridge Cambridge UK
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25
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Ghufran M, Rehman AU, Shah M, Ayaz M, Ng HL, Wadood A. In-silico design of peptide inhibitors of K-Ras target in cancer disease. J Biomol Struct Dyn 2019; 38:5488-5499. [DOI: 10.1080/07391102.2019.1704880] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Mehreen Ghufran
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Ashfaq Ur Rehman
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
- State Key Laboratory of Microbial Metabolism, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Masaud Shah
- Department of Molecular Science and Technology, Ajou University, South Korea
| | - Muhammad Ayaz
- Department of Pharmacy, University of Malakand, Pakistan
| | - Ho Leung Ng
- Department of Biochemistry and Molecular Biophysics, Kansas State University, Manhattan, KS, USA
| | - Abdul Wadood
- Department of Biochemistry, Abdul Wali Khan University Mardan, Mardan, Pakistan
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26
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Malde AK, Hill TA, Iyer A, Fairlie DP. Crystal Structures of Protein-Bound Cyclic Peptides. Chem Rev 2019; 119:9861-9914. [DOI: 10.1021/acs.chemrev.8b00807] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alpeshkumar K. Malde
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Timothy A. Hill
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Abishek Iyer
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David P. Fairlie
- Division of Chemistry and Structural Biology, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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27
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Stout MC, Campbell PM. RASpecting the oncogene: New pathways to therapeutic advances. Biochem Pharmacol 2018; 158:217-228. [PMID: 30352234 DOI: 10.1016/j.bcp.2018.10.022] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 10/19/2018] [Indexed: 12/13/2022]
Abstract
RAS is the most commonly mutated driver of tumorigenesis, seen in about 30% of all cancer cases. There is a subset of tumors termed RAS-driven cancers in which RAS mutation or overactivation is evident, including as much as 95% in pancreatic and 50% in colon cancer. RAS is a family of small membrane bound GTPases that act as a signaling node to control both normal and cancer biology. Since the discovery of RAS' overall prominence in many tumor types and specifically in RAS-dependent cancers, it has been an obvious therapeutic target for drug development. However, RAS has proved a very elusive target, and after a few prominent RAS targeted drugs failed in clinical trials after decades of research, RAS was termed "undruggable" and research in this field was greatly hampered. An increase in knowledge about basic RAS biology has led to a resurgence in the generation of novel therapeutics targeting RAS signaling utilizing various and distinct approaches. These new drugs target RAS activation directly, block downstream signaling effectors and inhibit proper post-translational processing and trafficking/recycling of RAS. This review will cover how these new drugs were developed and how they have fared in preclinical and early phase clinical trials.
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Affiliation(s)
- Matthew C Stout
- Department of Pharmacology and Physiology, College of Medicine, Drexel University, USA; Cancer Biology Program and The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, USA
| | - Paul M Campbell
- Cancer Biology Program and The Marvin & Concetta Greenberg Pancreatic Cancer Institute, Fox Chase Cancer Center, USA.
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28
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Marín-Ramos NI, Ortega-Gutiérrez S, López-Rodríguez ML. Blocking Ras inhibition as an antitumor strategy. Semin Cancer Biol 2018; 54:91-100. [PMID: 29409706 DOI: 10.1016/j.semcancer.2018.01.017] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 01/25/2018] [Accepted: 01/29/2018] [Indexed: 12/17/2022]
Abstract
Ras proteins are among the most frequently mutated drivers in human cancer and remain an elusive pharmaceutical targeting. Previous studies have improved the understanding of Ras structure, processing, and signaling pathways in cancer cells and have opened new possibilities for inhibiting Ras function. In this review we discuss the most recent advances towards inhibiting Ras activity with small molecules, highlighting the two approaches: (i) compounds that bind directly to Ras protein and (ii) inhibitors of the enzymes involved in the post-translational modifications of Ras. In the former, we analyze the most recent contributions in each of the main classes of Ras direct binders, including the different types of nucleotide exchange inhibitors, allosteric compounds, and molecules that interfere with the interaction between Ras and its effectors. In the latter, we examine the compounds that inhibit Ras activation by blocking any of its post-translational modifications. Also, a special focus is made on those molecules that have progressed the farthest from medicinal chemistry and drug development points of view. Finally, the current scene regarding the clinical trials of Ras inhibitors, together with the future promising avenues for further development of the challenging Ras field are reviewed.
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Affiliation(s)
- Nagore I Marín-Ramos
- Department of Neurosurgery, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States
| | - Silvia Ortega-Gutiérrez
- Department of Organic Chemistry I, Universidad Complutense de Madrid, Av. Complutense s/n, E-28040 Madrid, Spain
| | - María L López-Rodríguez
- Department of Organic Chemistry I, Universidad Complutense de Madrid, Av. Complutense s/n, E-28040 Madrid, Spain.
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Mott HR, Owen D. Bioblockades join the assault on small G protein signalling. Semin Cancer Biol 2018; 54:149-161. [PMID: 29307570 DOI: 10.1016/j.semcancer.2018.01.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 01/04/2018] [Indexed: 01/06/2023]
Abstract
Inhibition of Ras signalling has been a goal almost since its central role in cell signalling and its deregulation in disease were discovered. Early attempts at inhibiting its post-translational modification using peptidomimetics were successful in cell culture but failed spectacularly in clinical trials, making industry wary of targeting this critical oncoprotein. Small molecule inhibition of the protein-protein interactions involving Ras has also been difficult due to the nature of the interaction interface. Recent improvements in design, synthesis and selection of stabilised peptides, peptidomimetics and macrocycles have suggested that these biologics may represent a new hope in Ras inhibition. Here we review the various ways in which Ras has been targeted with these molecules. We also describe work on related small G proteins of the Ras superfamily, since many of the principles may be applicable to Ras, and these also provide inhibition of pathways downstream of Ras.
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Affiliation(s)
- Helen R Mott
- Department of Biochemistry, 80, Tennis Court Road, Cambridge CB2 1GA, UK.
| | - Darerca Owen
- Department of Biochemistry, 80, Tennis Court Road, Cambridge CB2 1GA, UK.
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Sogabe S, Kamada Y, Miwa M, Niida A, Sameshima T, Kamaura M, Yonemori K, Sasaki S, Sakamoto JI, Sakamoto K. Crystal Structure of a Human K-Ras G12D Mutant in Complex with GDP and the Cyclic Inhibitory Peptide KRpep-2d. ACS Med Chem Lett 2017; 8:732-736. [PMID: 28740607 DOI: 10.1021/acsmedchemlett.7b00128] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 05/10/2017] [Indexed: 11/28/2022] Open
Abstract
The Ras proteins play roles in cell differentiation, proliferation, and survival. Aberrant signaling through Ras-mediated pathways in tumor cells occurs as a result of several types of mutational damage, which most frequently affects the amino acids G12, G13, and Q61. Recently, KRpep-2d was identified as a K-Ras(G12D) selective inhibitory peptide against the G12D mutant of K-Ras, which is a key member of the Ras protein family and an attractive cancer therapeutic target. In this study, the crystal structure of the human K-Ras(G12D) mutant was determined in complex with GDP and KRpep-2d at 1.25 Å resolution. This structure revealed that the peptide binds near Switch II and allosterically blocks protein-protein interactions with the guanine nucleotide exchange factor. This discovery of a unique binding pocket provides valuable information that will facilitate the design of direct Ras inhibitors.
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Affiliation(s)
- Satoshi Sogabe
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Yusuke Kamada
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masanori Miwa
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Ayumu Niida
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Tomoya Sameshima
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Masahiro Kamaura
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kazuko Yonemori
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Shigekazu Sasaki
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Jun-ichi Sakamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
| | - Kotaro Sakamoto
- Pharmaceutical Research Division, Takeda Pharmaceutical Company Limited, 26-1, Muraoka-Higashi 2-chome, Fujisawa, Kanagawa 251-8555, Japan
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