1
|
Chatterjee DR, Kapoor S, Jain M, Das R, Chowdhury MG, Shard A. PROTACting the kinome with covalent warheads. Drug Discov Today 2023; 28:103417. [PMID: 36306996 DOI: 10.1016/j.drudis.2022.103417] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 09/19/2022] [Accepted: 10/19/2022] [Indexed: 02/02/2023]
Abstract
The dawn of targeted degradation using proteolysis-targeting chimeras (PROTACs) against recalcitrant proteins has prompted numerous efforts to develop complementary drugs. Although many of these are specifically directed against undruggable proteins, there is increasing interest in small molecule-based PROTACs that target intracellular pathways, and some have recently entered clinical trials. Concurrently, small molecule-based PROTACs that target protumorigenic pathways in cancer cells, the tumor microenvironment (TME), and angiogenesis have been found to have potent effects that synergize with the action of antibodies. This has led to the augmentation of PROTACs with variable substitution patterns. Several combinations with small molecules targeting undruggable proteins are now under clinical investigation. In this review, we discuss the recent milestones achieved as well as challenges encountered in this area of drug development, as well as our opinion on the best path forward.
Collapse
Affiliation(s)
- Deep Rohan Chatterjee
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Saumya Kapoor
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Meenakshi Jain
- Department of Biotechnology, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Rudradip Das
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Moumita Ghosh Chowdhury
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India
| | - Amit Shard
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research-Ahmedabad, Gandhinagar, Gujarat 382355, India.
| |
Collapse
|
2
|
Hu J, Li G. Recent Progress in Fluorescent Chemosensors for Protein Kinases. Chem Asian J 2022; 17:e202200182. [PMID: 35486328 DOI: 10.1002/asia.202200182] [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: 02/24/2022] [Revised: 04/21/2022] [Indexed: 11/10/2022]
Abstract
Protein kinases are involved in almost all biological activities. The activities of different kinases reflect the normal or abnormal status of the human body. Therefore, detecting the activities of different kinases is important for disease diagnosis and drug discovery. Fluorescent probes offer opportunities for studying kinase behaviors at different times and spatial locations. In this review, we summarize different kinds of fluorescent chemosensors that have been used to detect the activities of many different kinases.
Collapse
Affiliation(s)
- Jun Hu
- Fujian Agriculture and Forestry University, College of Life Sciences, No.15 Shangxiadian Road, Cangshan District, 350002, Fuzhou, CHINA
| | - Gao Li
- Minjiang University, College of Material and Chemical Engineering, CHINA
| |
Collapse
|
3
|
Sarkes DA, Hurley MM, Stratis-Cullum DN. Unraveling the Roots of Selectivity of Peptide Affinity Reagents for Structurally Similar Ribosomal Inactivating Protein Derivatives. Molecules 2016; 21:E1504. [PMID: 27834872 PMCID: PMC6272918 DOI: 10.3390/molecules21111504] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 11/02/2016] [Accepted: 11/04/2016] [Indexed: 11/17/2022] Open
Abstract
Peptide capture agents have become increasingly useful tools for a variety of sensing applications due to their ease of discovery, stability, and robustness. Despite the ability to rapidly discover candidates through biopanning bacterial display libraries and easily mature them to Protein Catalyzed Capture (PCC) agents with even higher affinity and selectivity, an ongoing challenge and critical selection criteria is that the peptide candidates and final reagent be selective enough to replace antibodies, the gold-standard across immunoassay platforms. Here, we have discovered peptide affinity reagents against abrax, a derivative of abrin with reduced toxicity. Using on-cell Fluorescence Activated Cell Sorting (FACS) assays, we show that the peptides are highly selective for abrax over RiVax, a similar derivative of ricin originally designed as a vaccine, with significant structural homology to abrax. We rank the newly discovered peptides for strongest affinity and analyze three observed consensus sequences with varying affinity and specificity. The strongest (Tier 1) consensus was FWDTWF, which is highly aromatic and hydrophobic. To better understand the observed selectivity, we use the XPairIt peptide-protein docking protocol to analyze binding location predictions of the individual Tier 1 peptides and consensus on abrax and RiVax. The binding location profiles on the two proteins are quite distinct, which we determine is due to differences in pocket size, pocket environment (including hydrophobicity and electronegativity), and steric hindrance. This study provides a model system to show that peptide capture candidates can be quite selective for a structurally similar protein system, even without further maturation, and offers an in silico method of analysis for understanding binding and down-selecting candidates.
Collapse
Affiliation(s)
- Deborah A Sarkes
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| | - Margaret M Hurley
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| | - Dimitra N Stratis-Cullum
- Biotechnology Branch, Sensors and Electron Devices Directorate, US Army Research Laboratory, Adelphi, MD 20783, USA.
| |
Collapse
|
4
|
Das S, Nag A, Liang J, Bunck DN, Umeda A, Farrow B, Coppock MB, Sarkes DA, Finch AS, Agnew HD, Pitram S, Lai B, Yu MB, Museth AK, Deyle KM, Lepe B, Rodriguez‐Rivera FP, McCarthy A, Alvarez‐Villalonga B, Chen A, Heath J, Stratis‐Cullum DN, Heath JR. A General Synthetic Approach for Designing Epitope Targeted Macrocyclic Peptide Ligands. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505243] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Samir Das
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Arundhati Nag
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - JingXin Liang
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - David N. Bunck
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Aiko Umeda
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Blake Farrow
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Matthew B. Coppock
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Deborah A. Sarkes
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Amethist S. Finch
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Heather D. Agnew
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Suresh Pitram
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Bert Lai
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Mary Beth Yu
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - A. Katrine Museth
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Kaycie M. Deyle
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Bianca Lepe
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Frances P. Rodriguez‐Rivera
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Amy McCarthy
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Belen Alvarez‐Villalonga
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Ann Chen
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - John Heath
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Dimitra N. Stratis‐Cullum
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - James R. Heath
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| |
Collapse
|
5
|
Das S, Nag A, Liang J, Bunck DN, Umeda A, Farrow B, Coppock MB, Sarkes DA, Finch AS, Agnew HD, Pitram S, Lai B, Yu MB, Museth AK, Deyle KM, Lepe B, Rodriguez-Rivera FP, McCarthy A, Alvarez-Villalonga B, Chen A, Heath J, Stratis-Cullum DN, Heath JR. A General Synthetic Approach for Designing Epitope Targeted Macrocyclic Peptide Ligands. Angew Chem Int Ed Engl 2015; 54:13219-24. [PMID: 26377818 DOI: 10.1002/anie.201505243] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Revised: 08/12/2015] [Indexed: 12/20/2022]
Abstract
We describe a general synthetic strategy for developing high-affinity peptide binders against specific epitopes of challenging protein biomarkers. The epitope of interest is synthesized as a polypeptide, with a detection biotin tag and a strategically placed azide (or alkyne) presenting amino acid. This synthetic epitope (SynEp) is incubated with a library of complementary alkyne or azide presenting peptides. Library elements that bind the SynEp in the correct orientation undergo the Huisgen cycloaddition, and are covalently linked to the SynEp. Hit peptides are tested against the full-length protein to identify the best binder. We describe development of epitope-targeted linear or macrocycle peptide ligands against 12 different diagnostic or therapeutic analytes. The general epitope targeting capability for these low molecular weight synthetic ligands enables a range of therapeutic and diagnostic applications, similar to those of monoclonal antibodies.
Collapse
Affiliation(s)
- Samir Das
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Arundhati Nag
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - JingXin Liang
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - David N Bunck
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Aiko Umeda
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Blake Farrow
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Matthew B Coppock
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Deborah A Sarkes
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Amethist S Finch
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - Heather D Agnew
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Suresh Pitram
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Bert Lai
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Mary Beth Yu
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - A Katrine Museth
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Kaycie M Deyle
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Bianca Lepe
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Frances P Rodriguez-Rivera
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Amy McCarthy
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Belen Alvarez-Villalonga
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Ann Chen
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - John Heath
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Dimitra N Stratis-Cullum
- Biotechnology Branch, Sensors & Electronic Devices Directorate, U.S. Army Research Laboratory, 2800 Powder Mill Road, Adelphi, MD 20783 (USA)
| | - James R Heath
- Department of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA).
| |
Collapse
|
6
|
Farrow B, Wong M, Malette J, Lai B, Deyle KM, Das S, Nag A, Agnew HD, Heath JR. Epitope Targeting of Tertiary Protein Structure Enables Target-Guided Synthesis of a Potent In-Cell Inhibitor of Botulinum Neurotoxin. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201502451] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|
7
|
Farrow B, Wong M, Malette J, Lai B, Deyle KM, Das S, Nag A, Agnew HD, Heath JR. Epitope targeting of tertiary protein structure enables target-guided synthesis of a potent in-cell inhibitor of botulinum neurotoxin. Angew Chem Int Ed Engl 2015; 54:7114-9. [PMID: 25925721 DOI: 10.1002/anie.201502451] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Revised: 04/09/2015] [Indexed: 12/14/2022]
Abstract
Botulinum neurotoxin (BoNT) serotype A is the most lethal known toxin and has an occluded structure, which prevents direct inhibition of its active site before it enters the cytosol. Target-guided synthesis by in situ click chemistry is combined with synthetic epitope targeting to exploit the tertiary structure of the BoNT protein as a landscape for assembling a competitive inhibitor. A substrate-mimicking peptide macrocycle is used as a direct inhibitor of BoNT. An epitope-targeting in situ click screen is utilized to identify a second peptide macrocycle ligand that binds to an epitope that, in the folded BoNT structure, is active-site-adjacent. A second in situ click screen identifies a molecular bridge between the two macrocycles. The resulting divalent inhibitor exhibits an in vitro inhibition constant of 165 pM against the BoNT/A catalytic chain. The inhibitor is carried into cells by the intact holotoxin, and demonstrates protection and rescue of BoNT intoxication in a human neuron model.
Collapse
Affiliation(s)
- Blake Farrow
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA).,Department of Applied Physics and Materials Science, California Institute of Technology (USA)
| | - Michelle Wong
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Jacquie Malette
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Bert Lai
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - Kaycie M Deyle
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Samir Das
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Arundhati Nag
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA)
| | - Heather D Agnew
- Indi Molecular, 6162 Bristol Parkway, Culver City, CA 90230 (USA)
| | - James R Heath
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd, Pasadena, CA 91125 (USA).
| |
Collapse
|