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Singh AK, Lewis CD, Boas CAWV, Diebolder P, Jethva PN, Rhee A, Song JH, Goo YA, Li S, Nickels ML, Liu Y, Rogers BE, Kapoor V, Hallahan DE. Development of a [89Zr]Zr-labeled Human Antibody using a Novel Phage-displayed Human scFv Library. Clin Cancer Res 2024; 30:1293-1306. [PMID: 38277241 PMCID: PMC10984770 DOI: 10.1158/1078-0432.ccr-23-3647] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 01/28/2024]
Abstract
PURPOSE Tax-interacting protein 1 (TIP1) is a cancer-specific radiation-inducible cell surface antigen that plays a role in cancer progression and resistance to therapy. This study aimed to develop a novel anti-TIP1 human antibody for noninvasive PET imaging in patients with cancer. EXPERIMENTAL DESIGN A phage-displayed single-chain variable fragment (scFv) library was created from healthy donors' blood. High-affinity anti-TIP1 scFvs were selected from the library and engineered to human IgG1. Purified Abs were characterized by size exclusion chromatography high-performance liquid chromatography (SEC-HPLC), native mass spectrometry (native MS), ELISA, BIAcore, and flow cytometry. The labeling of positron emitter [89Zr]Zr to the lead Ab, L111, was optimized using deferoxamine (DFO) chelator. The stability of [89Zr]Zr-DFO-L111 was assessed in human serum. Small animal PET studies were performed in lung cancer tumor models (A549 and H460). RESULTS We obtained 95% pure L111 by SEC-HPLC. Native MS confirmed the intact mass and glycosylation pattern of L111. Conjugation of three molar equivalents of DFO led to the optimal DFO-to-L111 ratio of 1.05. Radiochemical purity of 99.9% and specific activity of 0.37 MBq/μg was obtained for [89Zr]Zr-DFO-L111. [89Zr]Zr-DFO-L111 was stable in human serum over 7 days. The immunoreactive fraction in cell surface binding studies was 96%. In PET, preinjection with 4 mg/kg cold L111 before [89Zr]Zr-DFO-L111 (7.4 MBq; 20 μg) significantly (P < 0.01) enhanced the tumor-to-muscle standard uptake values (SUVmax) ratios on day 5 compared with day 2 postinjection. CONCLUSIONS L111 Ab targets lung cancer cells in vitro and in vivo. [89Zr]Zr-DFO-L111 is a human antibody that will be evaluated in the first in-human study of safety and PET imaging.
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Affiliation(s)
- Abhay K Singh
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Calvin D Lewis
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Cristian A W V Boas
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Philipp Diebolder
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Prashant N Jethva
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri
| | - Aaron Rhee
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
| | - Jong Hee Song
- Mass Spectrometry Technology Access Center at the McDonnell Genome Institute (MTAC@MGI), Washington University in St. Louis, St. Louis, Missouri
| | - Young Ah Goo
- Mass Spectrometry Technology Access Center at the McDonnell Genome Institute (MTAC@MGI), Washington University in St. Louis, St. Louis, Missouri
| | - Shunqian Li
- Department of Medicine, Washington University in St. Louis, St. Louis, Missouri
| | - Michael L Nickels
- Mallinckrodt Institute of Radiology, Washington University in St. Louis, St. Louis, Missouri
- Cyclotron Facility, Mallinckrodt Institute of Radiology, Washington University School of Medicine, St. Louis, Missouri
| | - Yongjian Liu
- Mallinckrodt Institute of Radiology, Washington University in St. Louis, St. Louis, Missouri
| | - Buck E Rogers
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
- Siteman Cancer Center, St. Louis, Missouri
| | - Vaishali Kapoor
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
- Siteman Cancer Center, St. Louis, Missouri
| | - Dennis E Hallahan
- Department of Radiation Oncology, Washington University School of Medicine, St. Louis, Missouri
- Siteman Cancer Center, St. Louis, Missouri
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Singh AK, Dadey DY, Rau MJ, Fitzpatrick J, Shah HK, Saikia M, Townsend R, Thotala D, Hallahan DE, Kapoor V. Blocking the functional domain of TIP1 by antibodies sensitizes cancer to radiation therapy. Biomed Pharmacother 2023; 166:115341. [PMID: 37625322 DOI: 10.1016/j.biopha.2023.115341] [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: 06/25/2023] [Revised: 08/11/2023] [Accepted: 08/19/2023] [Indexed: 08/27/2023] Open
Abstract
Non-small-cell lung cancer (NSCLC) and glioblastoma (GB) have poor prognoses. Discovery of new molecular targets is needed to improve therapy. Tax interacting protein 1 (TIP1), which plays a role in cancer progression, is overexpressed and radiation-inducible in NSCLC and GB. We evaluated the effect of an anti-TIP1 antibody alone and in combination with ionizing radiation (XRT) on NSCLC and GB in vitro and in vivo. NSCLC and GB cells were treated with anti-TIP1 antibodies and evaluated for proliferation, colony formation, endocytosis, and cell death. The efficacy of anti-TIP1 antibodies in combination with XRT on tumor growth was measured in mouse models of NSCLC and GB. mRNA sequencing was performed to understand the molecular mechanisms involved in the action of anti-TIP1 antibodies. We found that targeting the functional domain of TIP1 leads to endocytosis of the anti-TIP1 antibody followed by reduced proliferation and increased apoptosis-mediated cell death. Anti-TIP1 antibodies bound specifically (with high affinity) to cancer cells and synergized with XRT to significantly increase cytotoxicity in vitro and reduce tumor growth in mouse models of NSCLC and GB. Importantly, downregulation of cancer survival signaling pathways was found in vitro and in vivo following treatment with anti-TIP1 antibodies. TIP1 is a new therapeutic target for cancer treatment. Antibodies targeting the functional domain of TIP1 exhibited antitumor activity and enhanced the efficacy of radiation both in vitro and in vivo. Anti-TIP1 antibodies interrupt TIP1 function and are effective cancer therapy alone or in combination with XRT in mouse models of human cancer.
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Affiliation(s)
- Abhay K Singh
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - David Ya Dadey
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Department of Neurosurgery, Stanford University School of Medicine, Stanford, CA, USA
| | - Michael J Rau
- Center for Cellular Imaging, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - James Fitzpatrick
- Center for Cellular Imaging, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Departments of Cell Biology & Physiology and Neuroscience, Washington University School of Medicine, St. Louis, MO, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO,USA
| | - Harendra K Shah
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Minakshi Saikia
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - Reid Townsend
- Department of Medicine, Washington University in St. Louis, St. Louis, MO,USA; Siteman Cancer Center, St. Louis, MO, USA
| | - Dinesh Thotala
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Siteman Cancer Center, St. Louis, MO, USA
| | - Dennis E Hallahan
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Siteman Cancer Center, St. Louis, MO, USA.
| | - Vaishali Kapoor
- Department of Radiation Oncology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA; Siteman Cancer Center, St. Louis, MO, USA.
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Sahandi Zangabad P, Abousalman Rezvani Z, Tong Z, Esser L, Vasani RB, Voelcker NH. Recent Advances in Formulations for Long-Acting Delivery of Therapeutic Peptides. ACS APPLIED BIO MATERIALS 2023; 6:3532-3554. [PMID: 37294445 DOI: 10.1021/acsabm.3c00193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Recent preclinical and clinical studies have focused on the active area of therapeutic peptides due to their high potency, selectivity, and specificity in treating a broad range of diseases. However, therapeutic peptides suffer from multiple disadvantages, such as limited oral bioavailability, short half-life, rapid clearance from the body, and susceptibility to physiological conditions (e.g., acidic pH and enzymolysis). Therefore, high peptide dosages and dose frequencies are required for effective patient treatment. Recent innovations in pharmaceutical formulations have substantially improved therapeutic peptide administration by providing the following advantages: long-acting delivery, precise dose administration, retention of biological activity, and improvement of patient compliance. This review discusses therapeutic peptides and challenges in their delivery and explores recent peptide delivery formulations, including micro/nanoparticles (based on lipids, polymers, porous silicon, silica, and stimuli-responsive materials), (stimuli-responsive) hydrogels, particle/hydrogel composites, and (natural or synthetic) scaffolds. This review further covers the applications of these formulations for prolonged delivery and sustained release of therapeutic peptides and their impact on peptide bioactivity, loading efficiency, and (in vitro/in vivo) release parameters.
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Affiliation(s)
- Parham Sahandi Zangabad
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutics Science, Monash University, Parkville Campus, Parkville, Victoria 3052, Australia
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, Victoria 3168, Australia
| | - Zahra Abousalman Rezvani
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutics Science, Monash University, Parkville Campus, Parkville, Victoria 3052, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Clayton, Victoria 3168, Australia
| | - Ziqiu Tong
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutics Science, Monash University, Parkville Campus, Parkville, Victoria 3052, Australia
| | - Lars Esser
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutics Science, Monash University, Parkville Campus, Parkville, Victoria 3052, Australia
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Clayton, Victoria 3168, Australia
| | - Roshan B Vasani
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutics Science, Monash University, Parkville Campus, Parkville, Victoria 3052, Australia
| | - Nicolas H Voelcker
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutics Science, Monash University, Parkville Campus, Parkville, Victoria 3052, Australia
- Melbourne Centre for Nanofabrication, Victorian Node of the Australian National Fabrication Facility, Clayton, Victoria 3168, Australia
- Department of Materials Science and Engineering, Monash University, Clayton, Victoria 3800, Australia
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Nhàn NTT, Yamada T, Yamada KH. Peptide-Based Agents for Cancer Treatment: Current Applications and Future Directions. Int J Mol Sci 2023; 24:12931. [PMID: 37629112 PMCID: PMC10454368 DOI: 10.3390/ijms241612931] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Revised: 08/10/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023] Open
Abstract
Peptide-based strategies have received an enormous amount of attention because of their specificity and applicability. Their specificity and tumor-targeting ability are applied to diagnosis and treatment for cancer patients. In this review, we will summarize recent advancements and future perspectives on peptide-based strategies for cancer treatment. The literature search was conducted to identify relevant articles for peptide-based strategies for cancer treatment. It was performed using PubMed for articles in English until June 2023. Information on clinical trials was also obtained from ClinicalTrial.gov. Given that peptide-based strategies have several advantages such as targeted delivery to the diseased area, personalized designs, relatively small sizes, and simple production process, bioactive peptides having anti-cancer activities (anti-cancer peptides or ACPs) have been tested in pre-clinical settings and clinical trials. The capability of peptides for tumor targeting is essentially useful for peptide-drug conjugates (PDCs), diagnosis, and image-guided surgery. Immunomodulation with peptide vaccines has been extensively tested in clinical trials. Despite such advantages, FDA-approved peptide agents for solid cancer are still limited. This review will provide a detailed overview of current approaches, design strategies, routes of administration, and new technological advancements. We will highlight the success and limitations of peptide-based therapies for cancer treatment.
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Affiliation(s)
- Nguyễn Thị Thanh Nhàn
- Department of Pharmacology & Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL 60612, USA;
| | - Tohru Yamada
- Department of Surgery, Division of Surgical Oncology, University of Illinois College of Medicine, Chicago, IL 60612, USA;
- Richard & Loan Hill Department of Biomedical Engineering, University of Illinois College of Engineering, Chicago, IL 60607, USA
| | - Kaori H. Yamada
- Department of Pharmacology & Regenerative Medicine, University of Illinois College of Medicine, Chicago, IL 60612, USA;
- Department of Ophthalmology & Visual Sciences, University of Illinois College of Medicine, Chicago, IL 60612, USA
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Multifunctional building elements for the construction of peptide drug conjugates. ENGINEERED REGENERATION 2022. [DOI: 10.1016/j.engreg.2022.02.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Novel Peptide Therapeutic Approaches for Cancer Treatment. Cells 2021; 10:cells10112908. [PMID: 34831131 PMCID: PMC8616177 DOI: 10.3390/cells10112908] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/12/2021] [Accepted: 10/21/2021] [Indexed: 11/17/2022] Open
Abstract
Peptides are increasingly being developed for use as therapeutics to treat many ailments, including cancer. Therapeutic peptides have the advantages of target specificity and low toxicity. The anticancer effects of a peptide can be the direct result of the peptide binding its intended target, or the peptide may be conjugated to a chemotherapy drug or radionuclide and used to target the agent to cancer cells. Peptides can be targeted to proteins on the cell surface, where the peptide–protein interaction can initiate internalization of the complex, or the peptide can be designed to directly cross the cell membrane. Peptides can induce cell death by numerous mechanisms including membrane disruption and subsequent necrosis, apoptosis, tumor angiogenesis inhibition, immune regulation, disruption of cell signaling pathways, cell cycle regulation, DNA repair pathways, or cell death pathways. Although using peptides as therapeutics has many advantages, peptides have the disadvantage of being easily degraded by proteases once administered and, depending on the mode of administration, often have difficulty being adsorbed into the blood stream. In this review, we discuss strategies recently developed to overcome these obstacles of peptide delivery and bioavailability. In addition, we present many examples of peptides developed to fight cancer.
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Abstract
Cancer is the second leading cause of death worldwide, and the search for specialised therapy options has been a challenge for decades. The emergence of active targeted therapies provides the opportunity to treat cancerous tissues without harming healthy ones due to peculiar physiological changes. Herein, peptides and peptide analogs have been gaining a lot of attention over the last decade, especially for the on-site delivery of therapeutics to target tissues in order to achieve efficient and reliable cancer treatment. Combining peptides with highly efficient drug delivery platforms could potentially eliminate off-target adverse effects encountered during active targeting of conventional chemotherapeutics. Small size, ease of production and characterisation, low immunogenicity and satisfactory binding affinity of peptides offer some advantages over other complex targeting moiety, no wonder the market of peptide-based drugs continues to expand expeditiously. It is estimated that the global peptide drug market will be worth around USD 48.04 billion by 2025, with a compound annual growth rate of 9.4%. In this review, the current state of art of peptide-based therapeutics with special interest on tumour targeting peptides has been discussed. Moreover, various active targeting strategies such as the use functionalised peptides or peptide analogs are also elaborated.
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Affiliation(s)
- Selin Seda Timur
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
| | - R Neslihan Gürsoy
- Department of Pharmaceutical Technology, Faculty of Pharmacy, Hacettepe University, Ankara, Turkey
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Effendi N, Mishiro K, Shiba K, Kinuya S, Ogawa K. Development of Radiogallium-Labeled Peptides for Platelet-Derived Growth Factor Receptor β (PDGFR β) Imaging: Influence of Different Linkers. Molecules 2020; 26:molecules26010041. [PMID: 33374773 PMCID: PMC7795354 DOI: 10.3390/molecules26010041] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 12/11/2022] Open
Abstract
The purpose of this study is to develop peptide-based platelet-derived growth factor receptor β (PDGFRβ) imaging probes and examine the effects of several linkers, namely un-natural amino acids (D-alanine and β-alanine) and ethylene-glycol (EG), on the properties of Ga-DOTA-(linker)-IPLPPPRRPFFK peptides. Seven radiotracers, 67Ga-DOTA-(linker)-IPLPPPRRPFFK peptides, were designed, synthesized, and evaluated. The stability and cell uptake in PDGFRβ positive peptide cells were evaluated in vitro. The biodistribution of [67Ga]Ga-DOTA-EG2-IPLPPPRRPFFK ([67Ga]27) and [67Ga]Ga-DOTA-EG4-IPLPPPRRPFFK ([67Ga]28), which were selected based on in vitro stability in murine plasma and cell uptake rates, were determined in BxPC3-luc-bearing nu/nu mice. Seven 67Ga-labeled peptides were successfully synthesized with high radiochemical yields (>85%) and purities (>99%). All evaluated radiotracers were stable in PBS (pH 7.4) at 37 °C. However, only [67Ga]27 and [67Ga]28 remained more than 75% after incubation in murine plasma at 37 °C for 1 h. [67Ga]27 exhibited the highest BxPC3-luc cell uptake among the prepared radiolabeled peptides. As regards the results of the biodistribution experiments, the tumor-to-blood ratios of [67Ga]27 and [67Ga]28 at 1 h post-injection were 2.61 ± 0.75 and 2.05 ± 0.77, respectively. Co-injection of [67Ga]27 and an excess amount of IPLPPPRRPFFK peptide as a blocking agent can significantly decrease this ratio. However, tumor accumulation was not considered sufficient. Therefore, further probe modification is required to assess tumor accumulation for in vivo imaging.
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Affiliation(s)
- Nurmaya Effendi
- Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; (N.E.); (K.M.)
- Faculty of Pharmacy, Universitas Muslim Indonesia, Urip Sumiharjo KM. 10, Makassar 90-231, Indonesia
| | - Kenji Mishiro
- Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; (N.E.); (K.M.)
| | - Kazuhiro Shiba
- Advanced Science Research Center, Kanazawa University, Takara-machi 13-1, Kanazawa, Ishikawa 920-8640, Japan;
| | - Seigo Kinuya
- Department of Nuclear Medicine, Institute of Medical, Pharmaceutical and Health Sciences, Kanazawa University, Takara-machi 13-1, Kanazawa, Ishikawa 920-8641, Japan;
| | - Kazuma Ogawa
- Institute for Frontier Science Initiative, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan; (N.E.); (K.M.)
- Graduate School of Medical Sciences, Kanazawa University, Kakuma-machi, Kanazawa, Ishikawa 920-1192, Japan
- Correspondence: ; Tel./Fax: +81-76-234-4460
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Synthesis and labeling of p-NH2-Bn-DTPA-(Dabcyl-Lys6,Phe7)-pHBSP with 99mTc as a radiopeptide scintigraphic agent to detect cardiac ischemia. J Radioanal Nucl Chem 2020. [DOI: 10.1007/s10967-020-07123-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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10
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Redirecting extracellular proteases to molecularly guide radiosensitizing drugs to tumors. Biomaterials 2020; 248:120032. [PMID: 32304937 DOI: 10.1016/j.biomaterials.2020.120032] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Revised: 04/02/2020] [Accepted: 04/03/2020] [Indexed: 12/21/2022]
Abstract
Patients with advanced cancers are treated with combined radiotherapy and chemotherapy, however curability is poor and treatment side effects severe. Drugs sensitizing tumors to radiotherapy have been developed to improve cell kill, but tumor specificity remains challenging. To achieve tumor selectivity of small molecule radiosensitizers, we tested as a strategy active tumor targeting using peptide-based drug conjugates. We attached an inhibitor of the DNA damage response to antibody or cell penetrating peptides. Antibody drug conjugates honed in on tumor overexpressed cell surface receptors with high specificity but lacked efficacy when conjugated to the DNA damage checkpoint kinase inhibitor AZD7762. As an alternative approach, we synthesized activatable cell penetrating peptide scaffolds that accumulated within tumors based on matrix metalloproteinase cleavage. While matrix metalloproteinases are integral to tumor progression, they have proven therapeutically elusive. We harnessed these pro-tumorigenic extracellular proteases to spatially guide radiosensitizer drug delivery using cleavable activatable cell penetrating peptides. Here, we tested the potential of these two drug delivery platforms targeting distinct tumor compartments in combination with radiotherapy and demonstrate the advantages of protease triggered cell penetrating peptide scaffolds over antibody drug conjugates to deliver small molecule amine radiosensitizers.
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Zhang Z, Zhang Y, Song S, Yin L, Sun D, Gu J. Recent advances in the bioanalytical methods of polyethylene glycols and PEGylated pharmaceuticals. J Sep Sci 2020; 43:1978-1997. [DOI: 10.1002/jssc.201901340] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Revised: 02/15/2020] [Accepted: 02/16/2020] [Indexed: 12/23/2022]
Affiliation(s)
- Zhi Zhang
- Research Center for Drug Metabolism, College of Life ScienceJilin University Changchun P. R. China
- Beijing Institute of Drug Metabolism Beijing P. R. China
| | - Yuyao Zhang
- Research Center for Drug Metabolism, College of Life ScienceJilin University Changchun P. R. China
- Beijing Institute of Drug Metabolism Beijing P. R. China
| | - Shiwen Song
- Research Center for Drug Metabolism, College of Life ScienceJilin University Changchun P. R. China
- Beijing Institute of Drug Metabolism Beijing P. R. China
| | - Lei Yin
- Research Center for Drug Metabolism, College of Life ScienceJilin University Changchun P. R. China
- Research Institute of Translational MedicineThe First Bethune Hospital of Jilin University Changchun P. R. China
| | - Dong Sun
- Department of Biopharmacy, College of Life ScienceJilin University Changchun P. R. China
- Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education”Yantai University Yantai P. R. China
| | - Jingkai Gu
- Research Center for Drug Metabolism, College of Life ScienceJilin University Changchun P. R. China
- Beijing Institute of Drug Metabolism Beijing P. R. China
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12
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Kumar V, Kumar R, Agrawal P, Patiyal S, Raghava GPS. A Method for Predicting Hemolytic Potency of Chemically Modified Peptides From Its Structure. Front Pharmacol 2020; 11:54. [PMID: 32153395 PMCID: PMC7045810 DOI: 10.3389/fphar.2020.00054] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Accepted: 01/20/2020] [Indexed: 01/23/2023] Open
Abstract
In the present study, a systematic effort has been made to predict the hemolytic potency of chemically modified peptides. All models have been trained, tested, and evaluated on a dataset that contains 583 modified hemolytic peptides and a balanced number of non-hemolytic peptides. Machine learning techniques have been used to build the classification models using an immense range of peptide features that include 2D, 3D descriptors, fingerprints, atom, and diatom compositions. Random Forest based model developed using fingerprints as an input feature achieved maximum accuracy of 78.33% with AUC of 0.86 on the main dataset and accuracy of 78.29% with AUC of 0.85 on the validation dataset. Models developed in this study have been incorporated in a web server “HemoPImod” to facilitate the scientific community (http://webs.iiitd.edu.in/raghava/hemopimod/).
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Affiliation(s)
- Vinod Kumar
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla, India.,Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Rajesh Kumar
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla, India.,Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Piyush Agrawal
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla, India.,Bioinformatics Centre, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sumeet Patiyal
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla, India
| | - Gajendra P S Raghava
- Department of Computational Biology, Indraprastha Institute of Information Technology, Okhla, India
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