1
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Niedzialkowska E, Runyan LA, Kudryashova E, Egelman EH, Kudryashov DS. Stabilization of F-actin by Salmonella effector SipA resembles the structural effects of inorganic phosphate and phalloidin. Structure 2024; 32:725-738.e8. [PMID: 38518780 PMCID: PMC11162321 DOI: 10.1016/j.str.2024.02.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Revised: 02/08/2024] [Accepted: 02/26/2024] [Indexed: 03/24/2024]
Abstract
Entry of Salmonella into host enterocytes relies on its pathogenicity island 1 effector SipA. We found that SipA binds to F-actin in a 1:2 stoichiometry with sub-nanomolar affinity. A cryo-EM reconstruction revealed that SipA's globular core binds at the groove between actin strands, whereas the extended C-terminal arm penetrates deeply into the inter-strand space, stabilizing F-actin from within. The unusually strong binding of SipA is achieved by a combination of fast association via the core and very slow dissociation dictated by the arm. Similar to Pi, BeF3, and phalloidin, SipA potently inhibited actin depolymerization by actin depolymerizing factor (ADF)/cofilin, which correlated with increased filament stiffness, supporting the hypothesis that F-actin's mechanical properties contribute to the recognition of its nucleotide state by protein partners. The remarkably strong binding to F-actin maximizes the toxin's effects at the injection site while minimizing global influence on the cytoskeleton and preventing pathogen detection by the host cell.
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Affiliation(s)
- Ewa Niedzialkowska
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Lucas A Runyan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Elena Kudryashova
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Edward H Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA.
| | - Dmitri S Kudryashov
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA.
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2
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Ray CMP, Yang H, Spangler JB, Mac Gabhann F. Mechanistic computational modeling of monospecific and bispecific antibodies targeting interleukin-6/8 receptors. PLoS Comput Biol 2024; 20:e1012157. [PMID: 38848446 PMCID: PMC11189202 DOI: 10.1371/journal.pcbi.1012157] [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: 12/20/2023] [Revised: 06/20/2024] [Accepted: 05/10/2024] [Indexed: 06/09/2024] Open
Abstract
The spread of cancer from organ to organ (metastasis) is responsible for the vast majority of cancer deaths; however, most current anti-cancer drugs are designed to arrest or reverse tumor growth without directly addressing disease spread. It was recently discovered that tumor cell-secreted interleukin-6 (IL-6) and interleukin-8 (IL-8) synergize to enhance cancer metastasis in a cell-density dependent manner, and blockade of the IL-6 and IL-8 receptors (IL-6R and IL-8R) with a novel bispecific antibody, BS1, significantly reduced metastatic burden in multiple preclinical mouse models of cancer. Bispecific antibodies (BsAbs), which combine two different antigen-binding sites into one molecule, are a promising modality for drug development due to their enhanced avidity and dual targeting effects. However, while BsAbs have tremendous therapeutic potential, elucidating the mechanisms underlying their binding and inhibition will be critical for maximizing the efficacy of new BsAb treatments. Here, we describe a quantitative, computational model of the BS1 BsAb, exhibiting how modeling multivalent binding provides key insights into antibody affinity and avidity effects and can guide therapeutic design. We present detailed simulations of the monovalent and bivalent binding interactions between different antibody constructs and the IL-6 and IL-8 receptors to establish how antibody properties and system conditions impact the formation of binary (antibody-receptor) and ternary (receptor-antibody-receptor) complexes. Model results demonstrate how the balance of these complex types drives receptor inhibition, providing important and generalizable predictions for effective therapeutic design.
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Affiliation(s)
- Christina M. P. Ray
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Medical-Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Huilin Yang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jamie B. Spangler
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, Maryland, United States of America
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Feilim Mac Gabhann
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- Institute for Nano Biotechnology (INBT), Johns Hopkins University, Baltimore, Maryland, United States of America
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3
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Yeoh YQ, Amin A, Cuic B, Tomas D, Turner BJ, Shabanpoor F. Efficient systemic CNS delivery of a therapeutic antisense oligonucleotide with a blood-brain barrier-penetrating ApoE-derived peptide. Biomed Pharmacother 2024; 175:116737. [PMID: 38749176 DOI: 10.1016/j.biopha.2024.116737] [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: 02/27/2024] [Revised: 04/22/2024] [Accepted: 05/08/2024] [Indexed: 06/03/2024] Open
Abstract
Antisense oligonucleotide (ASO) has emerged as a promising therapeutic approach for treating central nervous system (CNS) disorders by modulating gene expression with high selectivity and specificity. However, the poor permeability of ASO across the blood-brain barrier (BBB) diminishes its therapeutic success. Here, we designed and synthesized a series of BBB-penetrating peptides (BPP) derived from either the receptor-binding domain of apolipoprotein E (ApoE) or a transferrin receptor-binding peptide (THR). The BPPs were conjugated to phosphorodiamidate morpholino oligomers (PMO) that are chemically analogous to the 2'-O-(2-methoxyethyl) (MOE)-modified ASO approved by the FDA for treating spinal muscular atrophy (SMA). The BPP-PMO conjugates significantly increased the level of full-length SMN2 in the patient-derived SMA fibroblasts in a concentration-dependent manner with minimal to no toxicity. Furthermore, the systemic administration of the most potent BPP-PMO conjugates significantly increased the expression of full-length SMN2 in the brain and spinal cord of SMN2 transgenic adult mice. Notably, BPP8-PMO conjugate showed a 1.25-fold increase in the expression of full-length functional SMN2 in the brain. Fluorescence imaging studies confirmed that 78% of the fluorescently (Cy7)-labelled BPP8-PMO reached brain parenchyma, with 11% uptake in neuronal cells. Additionally, the BPP-PMO conjugates containing retro-inverso (RI) D-BPPs were found to possess extended half-lives compared to their L-counterparts, indicating increased stability against protease degradation while preserving the bioactivity. This delivery platform based on BPP enhances the CNS bioavailability of PMO targeting the SMN2 gene, paving the way for the development of systemically administered neurotherapeutics for CNS disorders.
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Affiliation(s)
- Yuan Qi Yeoh
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia
| | - Azin Amin
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia
| | - Brittany Cuic
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia
| | - Doris Tomas
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia
| | - Bradley J Turner
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia
| | - Fazel Shabanpoor
- The Florey Institute of Neuroscience and Mental Health, University of Melbourne, Parkville, VIC 3010, Australia; School of Chemistry, University of Melbourne, VIC 3010, Australia.
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4
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Zimmer O, Goepferich A. On the uncertainty of the correlation between nanoparticle avidity and biodistribution. Eur J Pharm Biopharm 2024; 198:114240. [PMID: 38437906 DOI: 10.1016/j.ejpb.2024.114240] [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: 11/17/2023] [Revised: 02/05/2024] [Accepted: 02/28/2024] [Indexed: 03/06/2024]
Abstract
The specific delivery of a drug to its site of action also known as targeted drug delivery is a topic in the field of pharmaceutics studied for decades. One approach extensively investigated in this context is the use ligand functionalized nanoparticles. These particles are modified to carry receptor specific ligands, enabling them to accumulate at a desired target site. However, while this concept initially appears straightforward to implement, in-depth research has revealed several challenges hindering target site specific particle accumulation - some of which remain unresolved to this day. One of these challenges consists in the still incomplete understanding of how nanoparticles interact with biological systems. This knowledge gap significantly compromises the predictability of particle distribution in biological systems, which is critical for therapeutic efficacy. One of the most crucial steps in delivery is the attachment of nanoparticles to cells at the target site. This attachment occurs via the formation of multiple ligand receptor bonds. A process also referred to as multivalent interaction. While multivalency has been described extensively for individual molecules and macromolecules respectively, little is known on the multivalent binding of nanoparticles to cells. Here, we will specifically introduce the concept of avidity as a measure for favorable particle membrane interactions. Also, an overview about nanoparticle and membrane properties affecting avidity will be given. Thereafter, we provide a thorough review on literature investigating the correlation between nanoparticle avidity and success in targeted particle delivery. In particular, we want to analyze the currently uncertain data on the existence and nature of the correlation between particle avidity and biodistribution.
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Affiliation(s)
- Oliver Zimmer
- Department of Pharmaceutical Technology, University of Regensburg, Regensburg, Bavaria 93053, Germany
| | - Achim Goepferich
- Department of Pharmaceutical Technology, University of Regensburg, Regensburg, Bavaria 93053, Germany.
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5
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Liu N, Wan Q, Wu X, Zhao T, Jakobsson V, Yuan H, Chen X, Zhang J, Zhang W. A comparison of [ 18F]AlF- and 68Ga-labeled dual targeting heterodimer FAPI-RGD in malignant tumor: preclinical evaluation and pilot clinical PET/CT imaging. Eur J Nucl Med Mol Imaging 2024; 51:1685-1697. [PMID: 38246909 DOI: 10.1007/s00259-023-06587-5] [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: 10/16/2023] [Accepted: 12/12/2023] [Indexed: 01/23/2024]
Abstract
Due to the heterogeneity of tumors, strategies to improve the effectiveness of dual-targeting tracers in tumor diagnostics have been intensively practiced. In this study, the radiolabeled [18F]AlF-NOTA-FAPI-RGD (denoted as [18F]AlF-LNC1007), a dual-targeting heterodimer tracer targeting both fibroblast activation protein (FAP) and integrin αvβ3 to enhance specific tumor uptake and retention, was synthesized and evaluated. The tracer was compared with [68Ga]Ga-LNC1007 in preclinical and clinical settings. METHODS The preparation of [18F]AlF- and 68Ga-labeled FAPI-RGD was carried out with an optimized protocol. The stability was tested in PBS and fetal bovine serum (FBS). Cellular uptake and in vivo distribution of the two products were compared and carried out on the U87MG cell line and its xenograft model. The safety and dosimetry of [18F]AlF-LNC1007 PET/CT scan were evaluated in six patients with malignant tumors. RESULTS Two radiolabeling protocols of [18F]AlF-/[68Ga]Ga-LNC1007 were developed and optimized to give a high yield of tracers with good stability. In vivo microPET images showed that the two tracers exhibited comparable pharmacokinetic characteristics, with high tumor uptake and prolonged tumor retention. In vivo distribution data showed that the target-to-non-target ratios of [18F]AlF-LNC1007 were similar to[68Ga]Ga-LNC1007. A total of six patients underwent [18F]AlF-LNC1007 PET/CT evaluation while two had head-to-head [18F]FDG PET/CT scans. The total body effective dose was 9.94E-03 mSv/MBq. The biodistribution curve showed optimal normal organ uptake with high tumor uptake and long retention of up to 3h p.i., and notably, the tumor-to-background ratio increased over time. CONCLUSION We successfully prepared an [18F]AlF-LNC1007 dual-targeting PET probe with comparable performances as [68Ga]Ga-LNC1007. With prolonged tumor retention and tumor specificity, it produced good imaging quality in preclinical and clinical translational studies, indicating that [18F]AlF-LNC1007 is a promising non-invasive tracer for detecting tumors expressing FAP and/or integrin avβ3, with the prospect of clinical implementation.
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Affiliation(s)
- Nan Liu
- Department of Nuclear Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China
| | - Qiang Wan
- Department of Nuclear Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, 646000, China
| | - Xiaoming Wu
- College of Nuclear Science and Technology, Harbin Engineering University, Harbin, 150001, China
| | - Tianzhi Zhao
- Department of Diagnostic Radiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Vivianne Jakobsson
- Department of Diagnostic Radiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore
| | - Hongmei Yuan
- Department of Pharmaceutics, School of Pharmacy, Southwest Medical University, Jiangyang District, Luzhou, 646000, China
| | - Xiaoyuan Chen
- Department of Diagnostic Radiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
- Departments of Surgery, Chemical and Biomolecular Engineering, and Biomedical Engineering, Yong Loo Lin School of Medicine and College of Design and Engineering, National University of Singapore, Singapore, 119074, Singapore.
- Institute of Molecular and Cell Biology, Agency for Science, Technology, and Research (A*STAR), National University of Singapore, 61 Biopolis Drive, Proteos, Singapore, 138673, Singapore.
| | - Jingjing Zhang
- Department of Diagnostic Radiology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 119074, Singapore.
- Clinical Imaging Research Centre, Centre for Translational Medicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117599, Singapore.
- Nanomedicine Translational Research Program, NUS Center for Nanomedicine, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, 117597, Singapore.
| | - Wei Zhang
- Department of Nuclear Medicine, Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, 610072, China.
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6
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Kopp A, Dong S, Kwon H, Wang T, Desai AA, Linderman JJ, Tessier P, Thurber GM. In vivo Auto-tuning of Antibody-Drug Conjugate Delivery for Effective Immunotherapy using High-Avidity, Low-Affinity Antibodies. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.06.588433. [PMID: 38645231 PMCID: PMC11030390 DOI: 10.1101/2024.04.06.588433] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Antibody-drug conjugates (ADCs) have experienced a surge in clinical approvals in the past five years. Despite this success, a major limitation to ADC efficacy in solid tumors is poor tumor penetration, which leaves many cancer cells untargeted. Increasing antibody doses or co-administering ADC with an unconjugated antibody can improve tumor penetration and increase efficacy when target receptor expression is high. However, it can also reduce efficacy in low-expression tumors where ADC delivery is limited by cellular uptake. This creates an intrinsic problem because many patients express different levels of target between tumors and even within the same tumor. Here, we generated High-Avidity, Low-Affinity (HALA) antibodies that can automatically tune the cellular ADC delivery to match the local expression level. Using HER2 ADCs as a model, HALA antibodies were identified with the desired HER2 expression-dependent competitive binding with ADCs in vitro. Multi-scale distribution of trastuzumab emtansine and trastuzumab deruxtecan co-administered with the HALA antibody were analyzed in vivo, revealing that the HALA antibody increased ADC tumor penetration in high-expression systems with minimal reduction in ADC uptake in low-expression tumors. This translated to greater ADC efficacy in immunodeficient mouse models across a range of HER2 expression levels. Furthermore, Fc-enhanced HALA antibodies showed improved Fc-effector function at both high and low expression levels and elicited a strong response in an immunocompetent mouse model. These results demonstrate that HALA antibodies can expand treatment ranges beyond high expression targets and leverage strong immune responses.
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Affiliation(s)
- Anna Kopp
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Shujun Dong
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Hyeyoung Kwon
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Tiexin Wang
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109
| | - Alec A Desai
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109
| | - Jennifer J Linderman
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
| | - Peter Tessier
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
- Department of Pharmaceutical Sciences, University of Michigan, Ann Arbor, MI 48109
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
- Biointerfaces Institute, University of Michigan, Ann Arbor, MI 48109
| | - Greg M Thurber
- Department of Chemical Engineering, University of Michigan, Ann Arbor, MI 48109
- Department of Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109
- Rogel Cancer Center, University of Michigan, Ann Arbor, MI 48109
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7
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Morla-Folch J, Ranzenigo A, Fayad ZA, Teunissen AJP. Nanotherapeutic Heterogeneity: Sources, Effects, and Solutions. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307502. [PMID: 38050951 PMCID: PMC11045328 DOI: 10.1002/smll.202307502] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 10/30/2023] [Indexed: 12/07/2023]
Abstract
Nanomaterials have revolutionized medicine by enabling control over drugs' pharmacokinetics, biodistribution, and biocompatibility. However, most nanotherapeutic batches are highly heterogeneous, meaning they comprise nanoparticles that vary in size, shape, charge, composition, and ligand functionalization. Similarly, individual nanotherapeutics often have heterogeneously distributed components, ligands, and charges. This review discusses nanotherapeutic heterogeneity's sources and effects on experimental readouts and therapeutic efficacy. Among other topics, it demonstrates that heterogeneity exists in nearly all nanotherapeutic types, examines how nanotherapeutic heterogeneity arises, and discusses how heterogeneity impacts nanomaterials' in vitro and in vivo behavior. How nanotherapeutic heterogeneity skews experimental readouts and complicates their optimization and clinical translation is also shown. Lastly, strategies for limiting nanotherapeutic heterogeneity are reviewed and recommendations for developing more reproducible and effective nanotherapeutics provided.
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Affiliation(s)
- Judit Morla-Folch
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Anna Ranzenigo
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zahi Adel Fayad
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Abraham Jozef Petrus Teunissen
- Biomedical Engineering and Imaging Institute, Icahn School of Medicine at Mount Sinai, New York, 10029, NY, USA
- Cardiovascular Research Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
- Icahn Genomics Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
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8
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Kletzien OA, Wuttke DS, Batey RT. The RNA-Binding Domain of hnRNP U Extends beyond the RGG/RG Motifs. Biochemistry 2024. [PMID: 38329035 DOI: 10.1021/acs.biochem.3c00510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
Heterogeneous nuclear ribonucleoprotein U (hnRNP U) is a ubiquitously expressed protein that regulates chromatin architecture through its interactions with numerous DNA, protein, and RNA partners. The RNA-binding domain (RBD) of hnRNP U was previously mapped to an RGG/RG motif within its disordered C-terminal region, but little is understood about its binding mode and potential for selective RNA recognition. Analysis of publicly available hnRNP U enhanced UV cross-linking and immunoprecipitation (eCLIP) data identified high-confidence binding sites within human RNAs. We synthesized a set of diverse RNAs encompassing 11 of these identified cross-link sites for biochemical characterization using a combination of fluorescence anisotropy and electrophoretic mobility shift assays. These in vitro binding experiments with a rationally designed set of RNAs and hnRNP U domains revealed that the RGG/RG motif is a small part of a more expansive RBD that encompasses most of the disordered C-terminal region. This RBD contains a second, previously experimentally uncharacterized RGG/RG motif with RNA-binding properties comparable to those of the canonical RGG/RG motif. These RGG/RG motifs serve redundant functions, with neither serving as the primary RBD. While in isolation, each RGG/RG motif has modest affinity for RNA, together they significantly enhance the association of hnRNP U with RNA, enabling the binding of most of the designed RNA set with low to midnanomolar binding affinities. Identification and characterization of the complete hnRNP U RBD highlight the perils of a reductionist approach to defining biochemical activities in this system and pave the way for a detailed investigation of its RNA-binding specificity.
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Affiliation(s)
- Otto A Kletzien
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States
| | - Deborah S Wuttke
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States
| | - Robert T Batey
- Department of Biochemistry, University of Colorado, Boulder, Colorado 80309-0596, United States
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9
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Dai R, Cai Z, Hu R, Huang Y, Fu L, Yang J, Hu K, Li H. 177Lu-Labeled Bivalent Ligands of Prostate-Specific Membrane Antigen for Endoradiotherapy of Prostate Cancer. Mol Pharm 2024; 21:883-894. [PMID: 38155100 DOI: 10.1021/acs.molpharmaceut.3c00987] [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: 12/30/2023]
Abstract
Recently, we developed a bivalent prostate-specific membrane antigen (PSMA) radioligand ([18F]AlF-Bi-PSMA), which showed higher tumor uptake and retention in PSMA-positive mouse models than the clinically used radioligands, [68Ga]Ga-PSMA-11 and [18F]PSMA-1007. Here, we developed two 177Lu-labeled bivalent PSMA ligands with (DOTA-Alb-Bi-PSMA) or without an albumin-binding motif (DOTA-Bi-PSMA) to enhance radiotherapeutic efficacy with minimal toxicity. The results demonstrated that both 177Lu-labeled bivalent radioligands showed good stability, high binding affinity, and PSMA-targeting specificity in vitro. Compared with [177Lu]Lu-PSMA-617, both [177Lu]Lu-Bi-PSMA and [177Lu]Lu-Alb-Bi-PSMA showed a higher area under the curve (AUC) of tumor accumulation and superior therapeutic efficacy. However, [177Lu]Lu-Alb-Bi-PSMA exhibited a dose-dependent increase in acute damage to kidneys. In terms of the radionuclide therapy efficacy and side effects, [177Lu]Lu-Bi-PSMA exhibited well-balanced action with high tumor-to-organs AUC ratios, resulting in remarkable therapeutic efficacy and negligible side effects. These promising results warrant further investigations to achieve the clinical translation of [177Lu]Lu-Bi-PSMA.
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Affiliation(s)
- Ruoxue Dai
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
| | - Zhikai Cai
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
| | - Rui Hu
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
| | - Yueqi Huang
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
| | - Lilan Fu
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
| | - Jiaqi Yang
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
| | - Kongzhen Hu
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
- School of Pharmaceutical Sciences, Southern Medical University, Guangzhou 510515, P. R. China
| | - Hongsheng Li
- GDMPA Key Laboratory for Quality Control and Evaluation of Radiopharmaceuticals, Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, Guangzhou 510515, P. R. China
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10
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Zhong H, Jiang Q, Wu C, Yu H, Li B, Zhou X, Fu R, Wang W, Sheng W. Design, Synthesis, and Antitumor Activity Evaluation of Artemisinin Bivalent Ligands. Molecules 2024; 29:409. [PMID: 38257322 PMCID: PMC10818997 DOI: 10.3390/molecules29020409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 01/11/2024] [Accepted: 01/11/2024] [Indexed: 01/24/2024] Open
Abstract
Five artemisinin bivalent ligands molecules 4a-4e were designed, synthesized, and confirmed by 1H NMR, 13C NMR, and low-resolution mass spectrometry, and the bioactivities of the target compounds were investigated against four human tumor cell lines in vitro, including BGC-823, HepG-2, MCF-7, and HCT-116. The results showed 4a, 4d, and 4e exhibited significantly tumor cell inhibitory activity compared with the artemisinin and dihydroartemisinin; compound 4e has good biological activity inhibiting BGC-823 with an IC50 value of 8.30 μmol/L. Then, the good correlations with biological results were validated by molecular docking through the established bivalent ligands multi-target model, which showed that 4e could bind well with the antitumor protein MMP-9.
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Affiliation(s)
- Hui Zhong
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; (H.Z.); (Q.J.); (C.W.); (H.Y.); (B.L.); (X.Z.); (R.F.)
| | - Qi Jiang
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; (H.Z.); (Q.J.); (C.W.); (H.Y.); (B.L.); (X.Z.); (R.F.)
| | - Cong Wu
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; (H.Z.); (Q.J.); (C.W.); (H.Y.); (B.L.); (X.Z.); (R.F.)
| | - Huanghe Yu
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; (H.Z.); (Q.J.); (C.W.); (H.Y.); (B.L.); (X.Z.); (R.F.)
- TCM and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Bin Li
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; (H.Z.); (Q.J.); (C.W.); (H.Y.); (B.L.); (X.Z.); (R.F.)
- TCM and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Xudong Zhou
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; (H.Z.); (Q.J.); (C.W.); (H.Y.); (B.L.); (X.Z.); (R.F.)
- TCM and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Ronggeng Fu
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; (H.Z.); (Q.J.); (C.W.); (H.Y.); (B.L.); (X.Z.); (R.F.)
| | - Wei Wang
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; (H.Z.); (Q.J.); (C.W.); (H.Y.); (B.L.); (X.Z.); (R.F.)
- TCM and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China
| | - Wenbing Sheng
- School of Pharmacy, Hunan University of Chinese Medicine, Changsha 410208, China; (H.Z.); (Q.J.); (C.W.); (H.Y.); (B.L.); (X.Z.); (R.F.)
- TCM and Ethnomedicine Innovation and Development International Laboratory, Hunan University of Chinese Medicine, Changsha 410208, China
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11
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Arslan S, Garcia FJ, Guo M, Kellinger MW, Kruglyak S, LeVieux JA, Mah AH, Wang H, Zhao J, Zhou C, Altomare A, Bailey J, Byrne MB, Chang C, Chen SX, Cho B, Dennler CN, Dien VT, Fuller D, Kelley R, Khandan O, Klein MG, Kim M, Lajoie BR, Lin B, Liu Y, Lopez T, Mains PT, Price AD, Robertson SR, Taylor-Weiner H, Tippana R, Tomaney AB, Zhang S, Abtahi M, Ambroso MR, Bajari R, Bellizzi AM, Benitez CB, Berard DR, Berti L, Blease KN, Blum AP, Boddicker AM, Bondar L, Brown C, Bui CA, Calleja-Aguirre J, Cappa K, Chan J, Chang VW, Charov K, Chen X, Constandse RM, Damron W, Dawood M, DeBuono N, Dimalanta JD, Edoli L, Elango K, Faustino N, Feng C, Ferrari M, Frankie K, Fries A, Galloway A, Gavrila V, Gemmen GJ, Ghadiali J, Ghorbani A, Goddard LA, Guetter AR, Hendricks GL, Hentschel J, Honigfort DJ, Hsieh YT, Hwang Fu YH, Im SK, Jin C, Kabu S, Kincade DE, Levy S, Li Y, Liang VK, Light WH, Lipsher JB, Liu TL, Long G, Ma R, Mailloux JM, Mandla KA, Martinez AR, Mass M, McKean DT, Meron M, Miller EA, Moh CS, Moore RK, Moreno J, Neysmith JM, Niman CS, Nunez JM, Ojeda MT, Ortiz SE, Owens J, Piland G, Proctor DJ, Purba JB, Ray M, Rong D, Saade VM, Saha S, Tomas GS, Scheidler N, Sirajudeen LH, Snow S, Stengel G, Stinson R, Stone MJ, Sundseth KJ, Thai E, Thompson CJ, Tjioe M, Trejo CL, Trieger G, Truong DN, Tse B, Voiles B, Vuong H, Wong JC, Wu CT, Yu H, Yu Y, Yu M, Zhang X, Zhao D, Zheng G, He M, Previte M. Sequencing by avidity enables high accuracy with low reagent consumption. Nat Biotechnol 2024; 42:132-138. [PMID: 37231263 DOI: 10.1038/s41587-023-01750-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 03/15/2023] [Indexed: 05/27/2023]
Abstract
We present avidity sequencing, a sequencing chemistry that separately optimizes the processes of stepping along a DNA template and that of identifying each nucleotide within the template. Nucleotide identification uses multivalent nucleotide ligands on dye-labeled cores to form polymerase-polymer-nucleotide complexes bound to clonal copies of DNA targets. These polymer-nucleotide substrates, termed avidites, decrease the required concentration of reporting nucleotides from micromolar to nanomolar and yield negligible dissociation rates. Avidity sequencing achieves high accuracy, with 96.2% and 85.4% of base calls having an average of one error per 1,000 and 10,000 base pairs, respectively. We show that the average error rate of avidity sequencing remained stable following a long homopolymer.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Bill Lin
- Element Biosciences, San Diego, CA, USA
| | - Yu Liu
- Element Biosciences, San Diego, CA, USA
| | | | | | | | | | | | | | | | - Su Zhang
- Element Biosciences, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Xiyi Chen
- Element Biosciences, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | - Chao Feng
- Element Biosciences, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Yu Li
- Element Biosciences, San Diego, CA, USA
| | | | | | | | | | | | - Rui Ma
- Element Biosciences, San Diego, CA, USA
| | | | | | | | - Max Mass
- Element Biosciences, San Diego, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Ben Tse
- Element Biosciences, San Diego, CA, USA
| | | | | | | | | | - Hua Yu
- Element Biosciences, San Diego, CA, USA
| | | | - Ming Yu
- Element Biosciences, San Diego, CA, USA
| | - Xi Zhang
- Element Biosciences, San Diego, CA, USA
| | - Da Zhao
- Element Biosciences, San Diego, CA, USA
| | | | - Molly He
- Element Biosciences, San Diego, CA, USA
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12
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Niedzialkowska E, Runyan LA, Kudryashova E, Egelman EH, Kudryashov DS. Stabilization of F-actin by Salmonella effector SipA resembles the structural effects of inorganic phosphate and phalloidin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.26.573373. [PMID: 38234808 PMCID: PMC10793455 DOI: 10.1101/2023.12.26.573373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/19/2024]
Abstract
Entry of Salmonella into host enterocytes strictly relies on its pathogenicity island 1 effector SipA. We found that SipA binds to F-actin in a unique mode in a 1:2 stoichiometry with picomolar affinity. A cryo-EM reconstruction revealed that SipA's globular core binds at the grove between actin strands, whereas the extended C-terminal arm penetrates deeply into the inter-strand space, stabilizing F-actin from within. The unusually strong binding of SipA is achieved via a combination of fast association via the core and very slow dissociation dictated by the arm. Similarly to Pi, BeF3, and phalloidin, SipA potently inhibited actin depolymerization by ADF/cofilin, which correlated with the increased filament stiffness, supporting the hypothesis that F-actin's mechanical properties contribute to the recognition of its nucleotide state by protein partners. The remarkably strong binding to F-actin maximizes the toxin's effects at the injection site while minimizing global influence on the cytoskeleton and preventing pathogen detection by the host cell.
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Affiliation(s)
- Ewa Niedzialkowska
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Lucas A. Runyan
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Elena Kudryashova
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
| | - Edward H. Egelman
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA 22903, USA
| | - Dmitri S. Kudryashov
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, OH 43210, USA
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13
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Ray CMP, Yang H, Spangler JB, Mac Gabhann F. Mechanistic computational modeling of monospecific and bispecific antibodies targeting interleukin-6/8 receptors. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.12.18.570445. [PMID: 38187701 PMCID: PMC10769311 DOI: 10.1101/2023.12.18.570445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
The spread of cancer from organ to organ (metastasis) is responsible for the vast majority of cancer deaths; however, most current anti-cancer drugs are designed to arrest or reverse tumor growth without directly addressing disease spread. It was recently discovered that tumor cell-secreted interleukin-6 (IL-6) and interleukin-8 (IL-8) synergize to enhance cancer metastasis in a cell-density dependent manner, and blockade of the IL-6 and IL-8 receptors (IL-6R and IL-8R) with a novel bispecific antibody, BS1, significantly reduced metastatic burden in multiple preclinical mouse models of cancer. Bispecific antibodies (BsAbs), which combine two different antigen-binding sites into one molecule, are a promising modality for drug development due to their enhanced avidity and dual targeting effects. However, while BsAbs have tremendous therapeutic potential, elucidating the mechanisms underlying their binding and inhibition will be critical for maximizing the efficacy of new BsAb treatments. Here, we describe a quantitative, computational model of the BS1 BsAb, exhibiting how modeling multivalent binding provides key insights into antibody affinity and avidity effects and can guide therapeutic design. We present detailed simulations of the monovalent and bivalent binding interactions between different antibody constructs and the IL-6 and IL-8 receptors to establish how antibody properties and system conditions impact the formation of binary (antibody-receptor) and ternary (receptor-antibody-receptor) complexes. Model results demonstrate how the balance of these complex types drives receptor inhibition, providing important and generalizable predictions for effective therapeutic design.
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Affiliation(s)
- Christina MP Ray
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Medical-Scientist Training Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Huilin Yang
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Jamie B Spangler
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Sidney Kimmel Cancer Center, Johns Hopkins University, Baltimore, Maryland, United States of America
- Bloomberg Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Ophthalmology, Johns Hopkins School of Medicine, Baltimore, Maryland, United States of America
| | - Feilim Mac Gabhann
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
- Institute for Computational Medicine, Johns Hopkins University, Baltimore, Maryland, United States of America
- Institute for Nano Biotechnology (INBT), Johns Hopkins University, Baltimore, Maryland, United States of America
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14
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Bauer-Smith H, Sudol ASL, Beers SA, Crispin M. Serum immunoglobulin and the threshold of Fc receptor-mediated immune activation. Biochim Biophys Acta Gen Subj 2023; 1867:130448. [PMID: 37652365 PMCID: PMC11032748 DOI: 10.1016/j.bbagen.2023.130448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/23/2023] [Accepted: 08/23/2023] [Indexed: 09/02/2023]
Abstract
Antibodies can mediate immune recruitment or clearance of immune complexes through the interaction of their Fc domain with cellular Fc receptors. Clustering of antibodies is a key step in generating sufficient avidity for efficacious receptor recognition. However, Fc receptors may be saturated with prevailing, endogenous serum immunoglobulin and this raises the threshold by which cellular receptors can be productively engaged. Here, we review the factors controlling serum IgG levels in both healthy and disease states, and discuss how the presence of endogenous IgG is encoded into the functional activation thresholds for low- and high-affinity Fc receptors. We discuss the circumstances where antibody engineering can help overcome these physiological limitations of therapeutic antibodies. Finally, we discuss how the pharmacological control of Fc receptor saturation by endogenous IgG is emerging as a feasible mechanism for the enhancement of antibody therapeutics.
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Affiliation(s)
- Hannah Bauer-Smith
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK; Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK
| | - Abigail S L Sudol
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK
| | - Stephen A Beers
- Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton SO16 6YD, UK.
| | - Max Crispin
- School of Biological Sciences, University of Southampton, Southampton SO17 1BJ, UK.
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15
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Arras P, Yoo HB, Pekar L, Clarke T, Friedrich L, Schröter C, Schanz J, Tonillo J, Siegmund V, Doerner A, Krah S, Guarnera E, Zielonka S, Evers A. AI/ML combined with next-generation sequencing of VHH immune repertoires enables the rapid identification of de novo humanized and sequence-optimized single domain antibodies: a prospective case study. Front Mol Biosci 2023; 10:1249247. [PMID: 37842638 PMCID: PMC10575757 DOI: 10.3389/fmolb.2023.1249247] [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: 06/28/2023] [Accepted: 08/31/2023] [Indexed: 10/17/2023] Open
Abstract
Introduction: In this study, we demonstrate the feasibility of yeast surface display (YSD) and nextgeneration sequencing (NGS) in combination with artificial intelligence and machine learning methods (AI/ML) for the identification of de novo humanized single domain antibodies (sdAbs) with favorable early developability profiles. Methods: The display library was derived from a novel approach, in which VHH-based CDR3 regions obtained from a llama (Lama glama), immunized against NKp46, were grafted onto a humanized VHH backbone library that was diversified in CDR1 and CDR2. Following NGS analysis of sequence pools from two rounds of fluorescence-activated cell sorting we focused on four sequence clusters based on NGS frequency and enrichment analysis as well as in silico developability assessment. For each cluster, long short-term memory (LSTM) based deep generative models were trained and used for the in silico sampling of new sequences. Sequences were subjected to sequence- and structure-based in silico developability assessment to select a set of less than 10 sequences per cluster for production. Results: As demonstrated by binding kinetics and early developability assessment, this procedure represents a general strategy for the rapid and efficient design of potent and automatically humanized sdAb hits from screening selections with favorable early developability profiles.
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Affiliation(s)
- Paul Arras
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Han Byul Yoo
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Lukas Pekar
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Thomas Clarke
- Bioinformatics, EMD Serono, Billerica, MA, United States
| | - Lukas Friedrich
- Computational Chemistry and Biologics, Merck Healthcare KGaA, Darmstadt, Germany
| | | | - Jennifer Schanz
- ADCs & Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Jason Tonillo
- ADCs & Targeted NBE Therapeutics, Merck KGaA, Darmstadt, Germany
| | - Vanessa Siegmund
- Early Protein Supply and Characterization, Merck Healthcare KGaA, Darmstadt, Germany
| | - Achim Doerner
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Simon Krah
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Enrico Guarnera
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
| | - Stefan Zielonka
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
- Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Andreas Evers
- Antibody Discovery and Protein Engineering, Merck Healthcare KGaA, Darmstadt, Germany
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16
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Kletzien OA, Wuttke DS, Batey RT. The RNA-binding domain of hnRNP U extends beyond the RGG/RG motifs. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.20.558674. [PMID: 37786719 PMCID: PMC10541603 DOI: 10.1101/2023.09.20.558674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
Heterogeneous nuclear ribonucleoprotein U (hnRNP U) is a ubiquitously expressed protein that regulates chromatin architecture through its interactions with numerous DNA, protein, and RNA partners. The RNA-binding domain (RBD) of hnRNP U was previously mapped to an RGG/RG element within its disordered C-terminal region, but little is understood about its binding mode and potential for selective RNA recognition. Analysis of publicly available hnRNP U enhanced UV crosslinking and immunoprecipitation (eCLIP) data identified high-confidence binding sites within human RNAs. We synthesized a set of diverse RNAs encompassing eleven of these identified crosslink sites for biochemical characterization using a combination of fluorescence anisotropy and electrophoretic mobility shift assays. These in vitro binding experiments with a rationally designed set of RNAs and hnRNP U domains revealed that the RGG/RG element is a small part of a more expansive RBD that encompasses most of the disordered C-terminal region. This RBD contains a second, previously experimentally uncharacterized RGG/RG element with RNA-binding properties comparable to the canonical RGG/RG element. These RGG/RG elements serve redundant functions, with neither serving as the primary RBD. While in isolation each RGG/RG element has modest affinity for RNA, together they significantly enhance the association of hnRNP U with RNA, enabling binding of most of the designed RNA set with low to mid-nanomolar binding affinities. Identification and characterization of the complete hnRNP U RBD highlights the perils of a reductionist approach to defining biochemical activities in this system and paves the way for a detailed investigation of its RNA-binding specificity.
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Affiliation(s)
- Otto A. Kletzien
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Deborah S. Wuttke
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
| | - Robert T. Batey
- Department of Biochemistry, University of Colorado, Boulder, CO 80309-0596, USA
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17
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Harmsen MM, Cornelissen JC, van der Wal FJ, Bergervoet JHW, Koene M. Single-Domain Antibody Multimers for Detection of Botulinum Neurotoxin Serotypes C, D, and Their Mosaics in Endopep-MS. Toxins (Basel) 2023; 15:573. [PMID: 37755999 PMCID: PMC10535107 DOI: 10.3390/toxins15090573] [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: 08/21/2023] [Revised: 09/12/2023] [Accepted: 09/14/2023] [Indexed: 09/28/2023] Open
Abstract
Botulinum neurotoxins (BoNTs) are highly toxic proteins that require high-affinity immunocapture reagents for use in endopeptidase-based assays. Here, 30 novel and 2 earlier published llama single-domain antibodies (VHHs) against the veterinary-relevant BoNT serotypes C and D were yeast-produced. These VHHs recognized 10 independent antigenic sites, and many cross-reacted with the BoNT/DC and CD mosaic variants. As VHHs are highly suitable for genetically linking to increase antigen-binding affinity, 52 VHH multimers were produced and their affinity for BoNT/C, D, DC, and CD was determined. A selection of 15 multimers with high affinity (KD < 0.1 nM) was further shown to be resilient to a high salt wash that is used for samples from complex matrices and bound native BoNTs from culture supernatants as shown by Endopep-MS. High-affinity multimers suitable for further development of a highly sensitive Endopep-MS assay include four multimers that bind both BoNT/D and CD with KD of 14-99 pM, one multimer for BoNT/DC (65 pM) that also binds BoNT/C (75 pM), and seven multimers for BoNT/C (<1-19 pM), six of which also bind BoNT/DC with lower affinity (93-508 pM). In addition to application in diagnostic tests, these VHHs could be used for the development of novel therapeutics for animals or humans.
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Affiliation(s)
- Michiel M. Harmsen
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands (F.J.v.d.W.)
| | - Jan C. Cornelissen
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands (F.J.v.d.W.)
| | - Fimme J. van der Wal
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands (F.J.v.d.W.)
| | - Jan H. W. Bergervoet
- Wageningen Plant Research, Wageningen University & Research, 6708 PB Wageningen, The Netherlands
| | - Miriam Koene
- Wageningen Bioveterinary Research, Wageningen University & Research, 8221 RA Lelystad, The Netherlands (F.J.v.d.W.)
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18
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Li H, Peng W, Zhen Z, Zhang W, Liao S, Wu X, Wang L, Xuan A, Gao Y, Xu J. Integrin α vβ 3 and EGFR dual-targeted [ 64Cu]Cu-NOTA-RGD-GE11 heterodimer for PET imaging in pancreatic cancer mouse model. Nucl Med Biol 2023; 124-125:108364. [PMID: 37591041 DOI: 10.1016/j.nucmedbio.2023.108364] [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: 03/29/2023] [Revised: 07/02/2023] [Accepted: 07/03/2023] [Indexed: 08/19/2023]
Abstract
PURPOSE Radiolabeled heterodimeric peptide has emerged as a highly promising targeting strategy for PET imaging due to their superior properties. RGD and GE11 are two peptides binding to receptor integrin αvβ3 and EGFR, respectively, which both overexpress in many different types of tumors. This study focuses on the synthesis and evaluation of a RGD and GE11-containing heterodimeric radiotracer [64Cu]Cu-NOTA-RGD-GE11 for PET imaging of tumors that simultaneously overexpress integrin αvβ3 and EGFR. PROCEDURES [64Cu]Cu-NOTA-RGD-GE11 was prepared by the conjugation of RGD-PEG4-NOTA-N3 and GE11-PEG4-BCN via metal-free click chemistry, followed by radiolabeling with 64Cu. Cell uptake and efflux studies, saturation binding assay, the animal PET/CT and biodistribution studies were conducted to characterize the biological properties of [64Cu]Cu-NOTA-RGD-GE11. RESULTS [64Cu]Cu-NOTA-RGD-GE11 was synthesized with a radiochemical purity of >97 % and molar activity of 23 GBq/μmol at the end of synthesis. [64Cu]Cu-NOTA-RGD-GE11 showed moderate hydrophilicity, good stability in mouse serum and high specific uptake by the human pancreatic cancer cell line (BxPC3) in the in vitro studies. Compared to the two monomeric counterparts [64Cu]Cu-NOTA-RGD and [64Cu]Cu-NOTA-GE11, [64Cu]Cu-NOTA-RGD-GE11 demonstrated significantly improved tumor uptakes (e.g. 4.63 ± 0.25 %ID/g vs 1.24 ± 0.18 %ID/g and 0.77 ± 0.13 %ID/g, 2 h after injection, p < 0.05) in the subsequent in vivo evaluation in mice bearing BxPC3 xenograft. Tumor uptake could be blocked in the presence of both non-radioactive c(RGDyK) and GE11 peptides, indicating good tumor specificity of [64Cu]Cu-NOTA-RGD-GE11 in vivo. CONCLUSION The results suggested that the as-developed [64Cu]Cu-NOTA-RGD-GE11 could serve as a potential PET tracer for the noninvasive imaging of integrin αvβ3 and EGFR expression in tumors.
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Affiliation(s)
- Huiqiang Li
- Department of Nuclear Medicine, Henan Key Laboratory of Novel Molecular Probes and Clinical Translation in Nuclear Medicine, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Wenhua Peng
- Green Catalysis Center, College of Chemistry, Zhengzhou University, Zhengzhou 450001, China
| | - Zhifei Zhen
- Department of Nuclear Medicine, Henan Key Laboratory of Novel Molecular Probes and Clinical Translation in Nuclear Medicine, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Weifeng Zhang
- Department of Nuclear Medicine, Henan Key Laboratory of Novel Molecular Probes and Clinical Translation in Nuclear Medicine, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Shuguang Liao
- Department of Nuclear Medicine, Henan Key Laboratory of Novel Molecular Probes and Clinical Translation in Nuclear Medicine, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Xinyu Wu
- Department of Nuclear Medicine, Henan Key Laboratory of Novel Molecular Probes and Clinical Translation in Nuclear Medicine, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, Zhengzhou 450003, China
| | - Li Wang
- Henan Academy of Medical Sciences, Zhengzhou, 450003, China
| | - Ang Xuan
- Department of Nuclear Medicine, Henan Key Laboratory of Novel Molecular Probes and Clinical Translation in Nuclear Medicine, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, Zhengzhou 450003, China.
| | - Yongju Gao
- Department of Nuclear Medicine, Henan Key Laboratory of Novel Molecular Probes and Clinical Translation in Nuclear Medicine, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, Zhengzhou 450003, China.
| | - Junling Xu
- Department of Nuclear Medicine, Henan Key Laboratory of Novel Molecular Probes and Clinical Translation in Nuclear Medicine, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, Zhengzhou 450003, China.
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19
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Singh Y, Sarkar D, Duari S, G S, Indra Guru PK, M V H, Singh D, Bhardwaj S, Kalia J. Dissecting the contributions of membrane affinity and bivalency of the spider venom protein DkTx to its sustained mode of TRPV1 activation. J Biol Chem 2023; 299:104903. [PMID: 37302551 PMCID: PMC10404664 DOI: 10.1016/j.jbc.2023.104903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 06/03/2023] [Accepted: 06/05/2023] [Indexed: 06/13/2023] Open
Abstract
The spider venom protein, double-knot toxin (DkTx), partitions into the cellular membrane and binds bivalently to the pain-sensing ion channel, TRPV1, triggering long-lasting channel activation. In contrast, its monovalent single knots membrane partition poorly and invoke rapidly reversible TRPV1 activation. To discern the contributions of the bivalency and membrane affinity of DkTx to its sustained mode of action, here, we developed diverse toxin variants including those containing truncated linkers between individual knots, precluding bivalent binding. Additionally, by appending the single-knot domains to the Kv2.1 channel-targeting toxin, SGTx, we created monovalent double-knot proteins that demonstrated higher membrane affinity and more sustained TRPV1 activation than the single-knots. We also produced hyper-membrane affinity-possessing tetra-knot proteins, (DkTx)2 and DkTx-(SGTx)2, that demonstrated longer-lasting TRPV1 activation than DkTx, establishing the central role of the membrane affinity of DkTx in endowing it with its sustained TRPV1 activation properties. These results suggest that high membrane affinity-possessing TRPV1 agonists can potentially serve as long-acting analgesics.
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Affiliation(s)
- Yashaswi Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Debayan Sarkar
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Subhadeep Duari
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Shashaank G
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Pawas Kumar Indra Guru
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Hrishikesh M V
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Dheerendra Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India
| | - Sahil Bhardwaj
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India
| | - Jeet Kalia
- Department of Biology, Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India; Department of Chemistry, Indian Institute of Science Education and Research (IISER) Pune, Pune, Maharashtra, India; Department of Chemistry, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal, Madhya Pradesh, India.
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20
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Anbari S, Wang H, Zhang Y, Wang J, Pilvankar M, Nickaeen M, Hansel S, Popel AS. Using quantitative systems pharmacology modeling to optimize combination therapy of anti-PD-L1 checkpoint inhibitor and T cell engager. Front Pharmacol 2023; 14:1163432. [PMID: 37408756 PMCID: PMC10318535 DOI: 10.3389/fphar.2023.1163432] [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: 02/10/2023] [Accepted: 06/06/2023] [Indexed: 07/07/2023] Open
Abstract
Although immune checkpoint blockade therapies have shown evidence of clinical effectiveness in many types of cancer, the outcome of clinical trials shows that very few patients with colorectal cancer benefit from treatments with checkpoint inhibitors. Bispecific T cell engagers (TCEs) are gaining popularity because they can improve patients' immunological responses by promoting T cell activation. The possibility of combining TCEs with checkpoint inhibitors to increase tumor response and patient survival has been highlighted by preclinical and clinical outcomes. However, identifying predictive biomarkers and optimal dose regimens for individual patients to benefit from combination therapy remains one of the main challenges. In this article, we describe a modular quantitative systems pharmacology (QSP) platform for immuno-oncology that includes specific processes of immune-cancer cell interactions and was created based on published data on colorectal cancer. We generated a virtual patient cohort with the model to conduct in silico virtual clinical trials for combination therapy of a PD-L1 checkpoint inhibitor (atezolizumab) and a bispecific T cell engager (cibisatamab). Using the model calibrated against the clinical trials, we conducted several virtual clinical trials to compare various doses and schedules of administration for two drugs with the goal of therapy optimization. Moreover, we quantified the score of drug synergy for these two drugs to further study the role of the combination therapy.
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Affiliation(s)
- Samira Anbari
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Hanwen Wang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Yu Zhang
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
| | - Jun Wang
- Biotherapeutics Discovery Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Minu Pilvankar
- Biotherapeutics Discovery Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Masoud Nickaeen
- Biotherapeutics Discovery Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Steven Hansel
- Biotherapeutics Discovery Research, Boehringer Ingelheim Pharmaceuticals Inc., Ridgefield, CT, United States
| | - Aleksander S. Popel
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD, United States
- Department of Oncology, Sidney Kimmel Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD, United States
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21
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Tabaei SR, Fernandez-Villamarin M, Vafaei S, Rooney L, Mendes PM. Recapitulating the Lateral Organization of Membrane Receptors at the Nanoscale. ACS NANO 2023. [PMID: 37200265 DOI: 10.1021/acsnano.3c00683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Many cell membrane functions emerge from the lateral presentation of membrane receptors. The link between the nanoscale organization of the receptors and ligand binding remains, however, mostly unclear. In this work, we applied surface molecular imprinting and utilized the phase behavior of lipid bilayers to create platforms that recapitulate the lateral organization of membrane receptors at the nanoscale. We used liposomes decorated with amphiphilic boronic acids that commonly serve as synthetic saccharide receptors and generated three lateral modes of receptor presentation─random distribution, nanoclustering, and receptor crowding─and studied their interaction with saccharides. In comparison to liposomes with randomly dispersed receptors, surface-imprinted liposomes resulted in more than a 5-fold increase in avidity. Quantifying the binding affinity and cooperativity proved that the boost was mediated by the formation of the nanoclusters rather than a local increase in the receptor concentration. In contrast, receptor crowding, despite the presence of increased local receptor concentrations, prevented multivalent oligosaccharide binding due to steric effects. The findings demonstrate the significance of nanometric aspects of receptor presentation and generation of multivalent ligands including artificial lectins for the sensitive and specific detection of glycans.
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Affiliation(s)
- Seyed R Tabaei
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Stranmillis Road, Belfast, BT9 5AG, U.K
| | | | - Setareh Vafaei
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
| | - Lorcan Rooney
- School of Chemistry and Chemical Engineering, Queen's University Belfast, Stranmillis Road, Belfast, BT9 5AG, U.K
| | - Paula M Mendes
- School of Chemical Engineering, University of Birmingham, Edgbaston, Birmingham, B15 2TT, U.K
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22
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Bailly T, Bodin S, Goncalves V, Denat F, Morgat C, Prignon A, Valverde IE. Modular One-Pot Strategy for the Synthesis of Heterobivalent Tracers. ACS Med Chem Lett 2023; 14:636-644. [PMID: 37197474 PMCID: PMC10184157 DOI: 10.1021/acsmedchemlett.3c00057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 04/10/2023] [Indexed: 05/19/2023] Open
Abstract
Bivalent ligands, i.e., molecules having two ligands covalently connected by a linker, have been gathering attention since the first description of their pharmacological potential in the early 80s. However, their synthesis, particularly of labeled heterobivalent ligands, can still be cumbersome and time-consuming. We herein report a straightforward procedure for the modular synthesis of labeled heterobivalent ligands (HBLs) using dual reactive 3,6-dichloro-1,2,4,5-tetrazine as a starting material and suitable partners for sequential SNAr and inverse electron-demand Diels-Alder (IEDDA) reactions. This assembly method conducted in a stepwise or in a sequential one-pot manner provides quick access to multiple HBLs. A conjugate combining ligands toward the prostate-specific membrane antigen (PSMA) and the gastrin-releasing peptide receptor (GRPR) was radiolabeled, and its biological activity was assessed in vitro and in vivo (receptor binding affinity, biodistribution, imaging) as an illustration that the assembly methodology preserves the tumor targeting properties of the ligands.
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Affiliation(s)
- Thibaud Bailly
- Institut
de Chimie Moléculaire de l’Université de Bourgogne,
UMR CNRS 6302, Université de Bourgogne, 21000 Dijon, France
| | - Sacha Bodin
- University
of Bordeaux, CNRS, EPHE, INCIA, UMR 5287, Bordeaux F-33000, France
| | - Victor Goncalves
- Institut
de Chimie Moléculaire de l’Université de Bourgogne,
UMR CNRS 6302, Université de Bourgogne, 21000 Dijon, France
| | - Franck Denat
- Institut
de Chimie Moléculaire de l’Université de Bourgogne,
UMR CNRS 6302, Université de Bourgogne, 21000 Dijon, France
| | - Clément Morgat
- University
of Bordeaux, CNRS, EPHE, INCIA, UMR 5287, Bordeaux F-33000, France
- Nuclear
Medicine Department, University Hospital
of Bordeaux, Bordeaux F-33000, France
| | - Aurélie Prignon
- UMS28
Laboratoire d’Imagerie Moléculaire Positonique (LIMP), Sorbonne Université, Paris 75020, France
| | - Ibai E. Valverde
- Institut
de Chimie Moléculaire de l’Université de Bourgogne,
UMR CNRS 6302, Université de Bourgogne, 21000 Dijon, France
- Mailing
Address: Ibai E. Valverde,
Institut de Chimie Moléculaire de L’Université
de Bourgogne, UMR 6302, Univ. Bourgogne Franche-Comté, 9, Avenue
Alain Savary, 21078 Dijon Cedex, France; , Phone: +33 380 39 90 48
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23
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van den Bor J, Bergkamp ND, Anbuhl SM, Dekker F, Comez D, Perez Almeria CV, Bosma R, White CW, Kilpatrick LE, Hill SJ, Siderius M, Smit MJ, Heukers R. NanoB 2 to monitor interactions of ligands with membrane proteins by combining nanobodies and NanoBRET. CELL REPORTS METHODS 2023; 3:100422. [PMID: 37056381 PMCID: PMC10088090 DOI: 10.1016/j.crmeth.2023.100422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2022] [Revised: 01/31/2023] [Accepted: 02/17/2023] [Indexed: 03/14/2023]
Abstract
The therapeutic potential of ligands targeting disease-associated membrane proteins is predicted by ligand-receptor binding constants, which can be determined using NanoLuciferase (NanoLuc)-based bioluminescence resonance energy transfer (NanoBRET) methods. However, the broad applicability of these methods is hampered by the restricted availability of fluorescent probes. We describe the use of antibody fragments, like nanobodies, as universal building blocks for fluorescent probes for use in NanoBRET. Our nanobody-NanoBRET (NanoB2) workflow starts with the generation of NanoLuc-tagged receptors and fluorescent nanobodies, enabling homogeneous, real-time monitoring of nanobody-receptor binding. Moreover, NanoB2 facilitates the assessment of receptor binding of unlabeled ligands in competition binding experiments. The broad significance is illustrated by the successful application of NanoB2 to different drug targets (e.g., multiple G protein-coupled receptors [GPCRs] and a receptor tyrosine kinase [RTK]) at distinct therapeutically relevant binding sites (i.e., extracellular and intracellular).
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Affiliation(s)
- Jelle van den Bor
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Nick D. Bergkamp
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Stephanie M. Anbuhl
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- QVQ Holding B.V., Utrecht, the Netherlands
| | - Françoise Dekker
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Dehan Comez
- Cell Signalling Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
| | - Claudia V. Perez Almeria
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Reggie Bosma
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Carl W. White
- Cell Signalling Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
| | - Laura E. Kilpatrick
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
- Division of Bimolecular Science and Medicinal Chemistry, School of Pharmacy, Biodiscovery Institute, University of Nottingham, Nottingham, UK
| | - Stephen J. Hill
- Cell Signalling Research Group, Division of Physiology, Pharmacology and Neuroscience, School of Life Sciences, University of Nottingham, Nottingham, UK
- Centre of Membrane Proteins and Receptors (COMPARE), University of Birmingham and University of Nottingham, the Midlands, UK
| | - Marco Siderius
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Martine J. Smit
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Raimond Heukers
- Receptor Biochemistry and Signaling group, Division of Medicinal Chemistry, Amsterdam Institute for Molecular and Life Science (AIMMS), Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
- QVQ Holding B.V., Utrecht, the Netherlands
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24
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Yan Q, Zhong J, Liu Y, Peng S, Feng P, Zhong Y, Hu K. Synthesis and preclinical evaluation of a heterodimeric radioligand targeting fibroblast activation protein and integrin-α vβ 3. Eur J Med Chem 2023; 251:115279. [PMID: 36931125 DOI: 10.1016/j.ejmech.2023.115279] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/07/2023] [Accepted: 03/10/2023] [Indexed: 03/13/2023]
Abstract
Tumor progression is accompanied by intrinsic heterogeneity and different phenotypes, which implies a different expression of cell surface receptors. Fibroblast activation protein (FAP) and integrin αvβ3 are highly expressed in the cell surface of cancer-associated cells or cancer cells compared with normal cells. Therefore, a FAP/integrin αvβ3 bispecific heterodimer was developed for positron emission tomography (PET) diagnostic imaging and radiotherapy. The heterodimer DOTA-FAPI-RGD was labeled with the diagnostic radionuclide gallium-68 or the therapeutic radionuclide lutetium-177, with yields >80%, and high stability. The competitive displacement binding assay showed an IC50 = 6.8 ± 0.6 nM for DOTA-FAPI-RGD towards FAP and IC50 = 2.1 ± 0.4 nM towards integrin αvβ3. Radionuclide labeled DOTA-FAPI-RGD showed high specificity and rapid internalization into U87MG cells (FAP/αvβ3-positive) in vitro. Micro-PET and biodistribution studies of [68Ga]Ga-DOTA-FAPI-RGD in tumor-bearing mice demonstrated that a high and specific tumor uptake of the tracer and a fast body clearance, resulting in high contrast images. In addition to the imaging applications demonstrated in this study, the labeling of the heterodimeric ligand with the radionuclide lutetium-177 used in cancer treatment might allow the therapeutic application of this ligand.
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Affiliation(s)
- Qingsong Yan
- Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, Guangdong Province, 510515, China; Department of Chemistry, Jinan University, Guangzhou, 510632, China
| | - Jiawei Zhong
- Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, Guangdong Province, 510515, China; Department of Chemistry, Jinan University, Guangzhou, 510632, China
| | - Yang Liu
- Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, Guangdong Province, 510515, China
| | - Simin Peng
- Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, Guangdong Province, 510515, China
| | - Pengju Feng
- Department of Chemistry, Jinan University, Guangzhou, 510632, China
| | - Yuhua Zhong
- Department of Rehabilitation Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, Guangdong Province, 510515, China.
| | - Kongzhen Hu
- Department of Nuclear Medicine, Nanfang Hospital, Southern Medical University, 1838 Guangzhou North Road, Guangzhou, Guangdong Province, 510515, China.
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25
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Liu J, Maxwell M, Cuddihy T, Crawford T, Bassetti M, Hyde C, Peigneur S, Tytgat J, Undheim EAB, Mobli M. ScrepYard: An online resource for disulfide-stabilized tandem repeat peptides. Protein Sci 2023; 32:e4566. [PMID: 36644825 PMCID: PMC9885460 DOI: 10.1002/pro.4566] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 01/17/2023]
Abstract
Receptor avidity through multivalency is a highly sought-after property of ligands. While readily available in nature in the form of bivalent antibodies, this property remains challenging to engineer in synthetic molecules. The discovery of several bivalent venom peptides containing two homologous and independently folded domains (in a tandem repeat arrangement) has provided a unique opportunity to better understand the underpinning design of multivalency in multimeric biomolecules, as well as how naturally occurring multivalent ligands can be identified. In previous work, we classified these molecules as a larger class termed secreted cysteine-rich repeat-proteins (SCREPs). Here, we present an online resource; ScrepYard, designed to assist researchers in identification of SCREP sequences of interest and to aid in characterizing this emerging class of biomolecules. Analysis of sequences within the ScrepYard reveals that two-domain tandem repeats constitute the most abundant SCREP domain architecture, while the interdomain "linker" regions connecting the functional domains are found to be abundant in amino acids with short or polar sidechains and contain an unusually high abundance of proline residues. Finally, we demonstrate the utility of ScrepYard as a virtual screening tool for discovery of putatively multivalent peptides, by using it as a resource to identify a previously uncharacterized serine protease inhibitor and confirm its predicted activity using an enzyme assay.
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Affiliation(s)
- Junyu Liu
- Centre for Advanced ImagingThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Michael Maxwell
- Centre for Advanced ImagingThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Thom Cuddihy
- Queensland Cyber Infrastructure Foundation Ltd.The University of QueenslandSt. LuciaQueenslandAustralia,Centre for Clinical ResearchThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Theo Crawford
- Centre for Advanced ImagingThe University of QueenslandSt. LuciaQueenslandAustralia
| | - Madeline Bassetti
- Queensland Cyber Infrastructure Foundation Ltd.The University of QueenslandSt. LuciaQueenslandAustralia
| | - Cameron Hyde
- Queensland Cyber Infrastructure Foundation Ltd.The University of QueenslandSt. LuciaQueenslandAustralia,University of the Sunshine CoastMaroochydoreQueenslandAustralia
| | - Steve Peigneur
- Toxicology and PharmacologyUniversity of Leuven (KU Leuven)LeuvenBelgium
| | - Jan Tytgat
- Toxicology and PharmacologyUniversity of Leuven (KU Leuven)LeuvenBelgium
| | - Eivind A. B. Undheim
- Centre for Advanced ImagingThe University of QueenslandSt. LuciaQueenslandAustralia,Centre for Ecological and Evolutionary Synthesis, Department of BiosciencesUniversity of OsloOsloNorway
| | - Mehdi Mobli
- Centre for Advanced ImagingThe University of QueenslandSt. LuciaQueenslandAustralia
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26
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Macdonald R, Mahoney BJ, Soule J, Goring AK, Ford J, Loo JA, Cascio D, Clubb RT. The Shr receptor from Streptococcus pyogenes uses a cap and release mechanism to acquire heme-iron from human hemoglobin. Proc Natl Acad Sci U S A 2023; 120:e2211939120. [PMID: 36693107 PMCID: PMC9945957 DOI: 10.1073/pnas.2211939120] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 12/19/2022] [Indexed: 01/25/2023] Open
Abstract
Streptococcus pyogenes (group A Streptococcus) is a clinically important microbial pathogen that requires iron in order to proliferate. During infections, S. pyogenes uses the surface displayed Shr receptor to capture human hemoglobin (Hb) and acquires its iron-laden heme molecules. Through a poorly understood mechanism, Shr engages Hb via two structurally unique N-terminal Hb-interacting domains (HID1 and HID2) which facilitate heme transfer to proximal NEAr Transporter (NEAT) domains. Based on the results of X-ray crystallography, small angle X-ray scattering, NMR spectroscopy, native mass spectrometry, and heme transfer experiments, we propose that Shr utilizes a "cap and release" mechanism to gather heme from Hb. In the mechanism, Shr uses the HID1 and HID2 modules to preferentially recognize only heme-loaded forms of Hb by contacting the edges of its protoporphyrin rings. Heme transfer is enabled by significant receptor dynamics within the Shr-Hb complex which function to transiently uncap HID1 from the heme bound to Hb's β subunit, enabling the gated release of its relatively weakly bound heme molecule and subsequent capture by Shr's NEAT domains. These dynamics may maximize the efficiency of heme scavenging by S. pyogenes, enabling it to preferentially recognize and remove heme from only heme-loaded forms of Hb that contain iron.
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Affiliation(s)
- Ramsay Macdonald
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Brendan J. Mahoney
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Jess Soule
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Andrew K. Goring
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Jordan Ford
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
| | - Duilio Cascio
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
| | - Robert T. Clubb
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA90095
- University of California, Los Angeles-United States Department of Energy Institute of Genomics and Proteomics, University of California, Los Angeles, CA90095
- Molecular Biology Institute, University of California, Los Angeles, CA90095
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27
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Ito K, Matsuda Y, Mine A, Miyairi K, Kikuchi Y, Konishi A. Bacterially Secretable Single-Chain Tandem Macrocyclic Peptides for High Affinity and Inhibitory Activity. Chembiochem 2023; 24:e202200599. [PMID: 36409290 DOI: 10.1002/cbic.202200599] [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: 10/19/2022] [Revised: 11/21/2022] [Indexed: 11/23/2022]
Abstract
The inhibition of protein-protein interactions (PPIs) is an effective approach for therapy. Owing to their large binding surface areas to target proteins, macrocyclic peptides are suitable molecules for PPI inhibition. In this study, we developed single-chain tandem macrocyclic peptides (STaMPtides) that inhibits the vascular endothelial growth factor (VEGF) receptor 2 (VEGFR2). They were artificially designed to comprise two different VEGFR2-binding macrocyclic peptides linked in tandem by peptide linkers and secreted by Corynebacterium glutamicum. Most potent VEGFR2-inhibitory STaMPtides with length-optimized linkers exhibited >1000 times stronger inhibitory activity than their parental monomeric peptides, possibly due to the avidity effect of heterodimerization. Our approach of using STaMPtides for PPI inhibition may be used to inhibit other extracellular factors, such as growth factors and cytokines.
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Affiliation(s)
- Kenichiro Ito
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Yoshihiko Matsuda
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Ayako Mine
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Kyohei Miyairi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Yoshimi Kikuchi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
| | - Atsushi Konishi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki, 210-8681, Kanagawa, Japan
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28
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Huang C, Huang J, Zhu S, Tang T, Chen Y, Qian F. Multivalent nanobodies with rationally optimized linker and valency for intravitreal VEGF neutralization. Chem Eng Sci 2023. [DOI: 10.1016/j.ces.2023.118521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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29
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Du W, Janssens R, Mykytyn AZ, Li W, Drabek D, van Haperen R, Chatziandreou M, Rissmann M, van der Lee J, van Dortmondt M, Martin IS, van Kuppeveld FJM, Hurdiss DL, Haagmans BL, Grosveld F, Bosch BJ. Avidity engineering of human heavy-chain-only antibodies mitigates neutralization resistance of SARS-CoV-2 variants. Front Immunol 2023; 14:1111385. [PMID: 36895554 PMCID: PMC9990171 DOI: 10.3389/fimmu.2023.1111385] [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: 11/29/2022] [Accepted: 01/31/2023] [Indexed: 02/23/2023] Open
Abstract
Emerging SARS-CoV-2 variants have accrued mutations within the spike protein rendering most therapeutic monoclonal antibodies against COVID-19 ineffective. Hence there is an unmet need for broad-spectrum mAb treatments for COVID-19 that are more resistant to antigenically drifted SARS-CoV-2 variants. Here we describe the design of a biparatopic heavy-chain-only antibody consisting of six antigen binding sites recognizing two distinct epitopes in the spike protein NTD and RBD. The hexavalent antibody showed potent neutralizing activity against SARS-CoV-2 and variants of concern, including the Omicron sub-lineages BA.1, BA.2, BA.4 and BA.5, whereas the parental components had lost Omicron neutralization potency. We demonstrate that the tethered design mitigates the substantial decrease in spike trimer affinity seen for escape mutations for the hexamer components. The hexavalent antibody protected against SARS-CoV-2 infection in a hamster model. This work provides a framework for designing therapeutic antibodies to overcome antibody neutralization escape of emerging SARS-CoV-2 variants.
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Affiliation(s)
- Wenjuan Du
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Rick Janssens
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands.,Harbour BioMed, Rotterdam, Netherlands
| | - Anna Z Mykytyn
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Wentao Li
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Dubravka Drabek
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands.,Harbour BioMed, Rotterdam, Netherlands
| | - Rien van Haperen
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands.,Harbour BioMed, Rotterdam, Netherlands
| | - Marianthi Chatziandreou
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Melanie Rissmann
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands
| | - Joline van der Lee
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Melissa van Dortmondt
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Itziar Serna Martin
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Frank J M van Kuppeveld
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Daniel L Hurdiss
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Bart L Haagmans
- Department of Viroscience, Erasmus Medical Center, Rotterdam, Netherlands
| | - Frank Grosveld
- Department of Cell Biology, Erasmus Medical Center, Rotterdam, Netherlands.,Harbour BioMed, Rotterdam, Netherlands
| | - Berend-Jan Bosch
- Virology Section, Infectious Diseases and Immunology Division, Department of Biomolecular Health Sciences, Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
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Cifone MT, He Y, Basu R, Wang N, Davoodi S, Spagnuolo LA, Si Y, Daryaee T, Stivala CE, Walker SG, Tonge PJ. Heterobivalent Inhibitors of Acetyl-CoA Carboxylase: Drug Target Residence Time and Time-Dependent Antibacterial Activity. J Med Chem 2022; 65:16510-16525. [PMID: 36459397 PMCID: PMC10303036 DOI: 10.1021/acs.jmedchem.2c01380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
The relationship between drug-target residence time and the post-antibiotic effect (PAE) provides insights into target vulnerability. To probe the vulnerability of bacterial acetyl-CoA carboxylase (ACC), a series of heterobivalent inhibitors were synthesized based on pyridopyrimidine 1 and moiramide B (3) which bind to the biotin carboxylase and carboxyltransferase ACC active sites, respectively. The heterobivalent compound 17, which has a linker of 50 Å, was a tight binding inhibitor of Escherichia coli ACC (Kiapp 0.2 nM) and could be displaced from ACC by a combination of both 1 and 3 but not just by 1. In agreement with the prolonged occupancy of ACC resulting from forced proximity binding, the heterobivalent inhibitors produced a PAE in E. coli of 1-4 h in contrast to 1 and 3 in combination or alone, indicating that ACC is a vulnerable target and highlighting the utility of kinetic, time-dependent effects in the drug mechanism of action.
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Affiliation(s)
- Matthew T Cifone
- Center for Advanced Study of Drug Action, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - YongLe He
- Center for Advanced Study of Drug Action, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Rajeswari Basu
- Center for Advanced Study of Drug Action, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Nan Wang
- Center for Advanced Study of Drug Action, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Shabnam Davoodi
- Center for Advanced Study of Drug Action, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Lauren A Spagnuolo
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Yuanyuan Si
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Taraneh Daryaee
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Craig E Stivala
- Discovery Chemistry, Genentech Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Stephen G Walker
- Department of Oral Biology and Pathology, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
| | - Peter J Tonge
- Center for Advanced Study of Drug Action, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
- Department of Chemistry, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
- Department of Radiology, Stony Brook University, John S. Toll Drive, Stony Brook, New York 11794-3400, United States
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31
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Gupta S, Ward CL, Perera SS, Gowan CT, Dittrich TM, Allen MJ, McElmurry SP, Kodanko JJ. Development of a Highly Selective Ni(II) Chelator in Aqueous Solution. Inorg Chem 2022; 61:19492-19501. [PMID: 36414257 PMCID: PMC10391596 DOI: 10.1021/acs.inorgchem.2c03441] [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] [Indexed: 11/24/2022]
Abstract
The design, synthesis, and characterization of a novel Ni(II) chelator SG-20 is reported. SG-20 is selective in binding to Ni(II) versus other metal ions including Cu(II), Fe(II), Co(II), and Zn(II). At pH = 7.1, SG-20 binds Ni(II) with a Kd = 7.0 ± 0.4 μM. Job analysis indicates that SG-20 binds to both Ni(II) and Cu(II) with a 1:1 stoichiometry. Affinity of SG-20 for Ni(II) is pH dependent and decreases upon lowering to pH 4.0. A green solid was isolated from the reaction of SG-20 with NiCl2·6H2O in MeOH and characterized by X-ray photoelectron spectroscopy (XPS), electronic absorption and infrared (IR) spectroscopies, and mass spectrometry. Collectively, XPS and IR analysis revealed Ni-N and Ni-O interactions and a shift in C-O asymmetric and symmetric stretches consistent with Ni binding. Attempts to crystalize a mononuclear complex were unsuccessful, likely due to the Ni-SG-20 complex being in equilibrium with higher order species in solution. However, reaction of SG-20 with NiCl2·6H2O in water followed by slow evaporation yielded green crystals that were characterized by electronic absorption spectroscopy (λmax = 260 nm) and X-ray crystallography. These analyses revealed that SG-20 supports formation of a complex cluster containing six SG-20 ligands, 15 Ni(II), and three Na(I) centers, with two distinct types of Ni atoms in its outer and inner core. The nine Ni atoms present in the inner core were bound by oxo and carbonate bridges, whereas the six Ni atoms present in its outer shell were bound to N, O, and S donor atoms derived from SG-20. Overall, X-ray crystallographic analysis revealed that two chelator arms of SG-20 bind to one Ni(II) ion with an axial aqua ligand, whereas the third arm is free to interact with Ni ions within the central cluster, supporting the goal of Ni capture.
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Affiliation(s)
- Sayak Gupta
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Cassandra L Ward
- Lumigen Instrument Center, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - S Sameera Perera
- Lumigen Instrument Center, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Conor T Gowan
- Department of Civil and Environmental Engineering, Wayne State University, 5050 Anthony Wayne Dr, Detroit, Michigan 48202, United States
| | - Timothy M Dittrich
- Department of Civil and Environmental Engineering, Wayne State University, 5050 Anthony Wayne Dr, Detroit, Michigan 48202, United States
| | - Matthew J Allen
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
| | - Shawn P McElmurry
- Department of Civil and Environmental Engineering, Wayne State University, 5050 Anthony Wayne Dr, Detroit, Michigan 48202, United States
| | - Jeremy J Kodanko
- Department of Chemistry, Wayne State University, 5101 Cass Avenue, Detroit, Michigan 48202, United States
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Deactivatable Bisubstrate Inhibitors of Protein Kinases. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27196689. [PMID: 36235226 PMCID: PMC9573699 DOI: 10.3390/molecules27196689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/26/2022] [Accepted: 10/06/2022] [Indexed: 11/08/2022]
Abstract
Bivalent ligands, including bisubstrate inhibitors, are conjugates of pharmacophores, which simultaneously target two binding sites of the biomolecule. Such structures offer attainable means for the development of compounds whose ability to bind to the biological target could be modulated by an external trigger. In the present work, two deactivatable bisubstrate inhibitors of basophilic protein kinases (PKs) were constructed by conjugating the pharmacophores via linkers that could be cleaved in response to external stimuli. The inhibitor ARC-2121 incorporated a photocleavable nitrodibenzofuran-comprising β-amino acid residue in the structure of the linker. The pharmacophores of the other deactivatable inhibitor ARC-2194 were conjugated via reduction-cleavable disulfide bond. The disassembly of the inhibitors was monitored by HPLC-MS. The affinity and inhibitory potency of the inhibitors toward cAMP-dependent PK (PKAcα) were established by an equilibrium competitive displacement assay and enzyme activity assay, respectively. The deactivatable inhibitors possessed remarkably high 1-2-picomolar affinity toward PKAcα. Irradiation of ARC-2121 with 365 nm UV radiation led to reaction products possessing a 30-fold reduced affinity. The chemical reduction of ARC-2194 resulted in the decrease of affinity of over four orders of magnitude. The deactivatable inhibitors of PKs are valuable tools for the temporal inhibition or capture of these pharmacologically important enzymes.
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Hariri AA, Newman SS, Tan S, Mamerow D, Adams AM, Maganzini N, Zhong BL, Eisenstein M, Dunn AR, Soh HT. Improved immunoassay sensitivity and specificity using single-molecule colocalization. Nat Commun 2022; 13:5359. [PMID: 36097164 PMCID: PMC9468026 DOI: 10.1038/s41467-022-32796-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 08/12/2022] [Indexed: 11/29/2022] Open
Abstract
Enzyme-linked immunosorbent assays (ELISAs) are a cornerstone of modern molecular detection, but the technique still faces notable challenges. One of the biggest problems is discriminating true signal generated by target molecules versus non-specific background. Here, we developed a Single-Molecule Colocalization Assay (SiMCA) that overcomes this problem by employing total internal reflection fluorescence microscopy to quantify target proteins based on the colocalization of fluorescent signal from orthogonally labeled capture and detection antibodies. By specifically counting colocalized signals, we can eliminate the effects of background produced by non-specific binding of detection antibodies. Using TNF-α, we show that SiMCA achieves a three-fold lower limit of detection compared to conventional single-color assays and exhibits consistent performance for assays performed in complex specimens such as serum and blood. Our results help define the pernicious effects of non-specific background in immunoassays and demonstrate the diagnostic gains that can be achieved by eliminating those effects.
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Affiliation(s)
- Amani A Hariri
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Sharon S Newman
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Steven Tan
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Dan Mamerow
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
| | - Alexandra M Adams
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Nicolò Maganzini
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Brian L Zhong
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Michael Eisenstein
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA
| | - Alexander R Dunn
- Department of Chemical Engineering, Stanford University, Stanford, CA, 94305, USA.
| | - H Tom Soh
- Department of Radiology, Stanford University, Stanford, CA, 94305, USA.
- Department of Electrical Engineering, Stanford University, Stanford, CA, 94305, USA.
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA.
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Bruncsics B, Errington WJ, Sarkar CA. MVsim is a toolset for quantifying and designing multivalent interactions. Nat Commun 2022; 13:5029. [PMID: 36068204 PMCID: PMC9448752 DOI: 10.1038/s41467-022-32496-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 08/03/2022] [Indexed: 11/17/2022] Open
Abstract
Arising through multiple binding elements, multivalency can specify the avidity, duration, cooperativity, and selectivity of biomolecular interactions, but quantitative prediction and design of these properties has remained challenging. Here we present MVsim, an application suite built around a configurational network model of multivalency to facilitate the quantification, design, and mechanistic evaluation of multivalent binding phenomena through a simple graphical user interface. To demonstrate the utility and versatility of MVsim, we first show that both monospecific and multispecific multivalent ligand-receptor interactions, with their noncanonical binding kinetics, can be accurately simulated. Further, to illustrate the conceptual insights into multivalent systems that MVsim can provide, we apply it to quantitatively predict the ultrasensitivity and performance of multivalent-encoded protein logic gates, evaluate the inherent programmability of multispecificity for selective receptor targeting, and extract rate constants of conformational switching for the SARS-CoV-2 spike protein and model its binding to ACE2 as well as multivalent inhibitors of this interaction. MVsim and instructional tutorials are freely available at https://sarkarlab.github.io/MVsim/ .
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Affiliation(s)
- Bence Bruncsics
- Department of Measurement and Information Systems, Budapest University of Technology and Economics, Budapest, H-1111, Hungary
| | - Wesley J Errington
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, 55455-0215, USA
| | - Casim A Sarkar
- Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, 55455-0215, USA.
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35
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Judmann B, Braun D, Schirrmacher R, Wängler B, Fricker G, Wängler C. Toward the Development of GE11-Based Radioligands for Imaging of Epidermal Growth Factor Receptor-Positive Tumors. ACS OMEGA 2022; 7:27690-27702. [PMID: 35967067 PMCID: PMC9366781 DOI: 10.1021/acsomega.2c03407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
The epidermal growth factor receptor (EGFR) is closely associated with tumor development and progression and thus an important target structure for imaging and therapy of various tumors. As a result of its important role in malignancies of various origins and the fact that antibody-based compounds targeting the EGFR have significant drawbacks in terms of in vivo pharmacokinetics, several attempts have been made within the last five years to develop peptide-based EGFR-specific radioligands based on the GE11 scaffold. However, none of these approaches have shown convincing results so far, which has been proposed to be attributed to different potential challenges associated with the GE11 lead structure: first, an aggregation of radiolabeled peptides, which might prevent their interaction with their target receptor, or second, a relatively low affinity of monomeric GE11, necessitating its conversion into a multimeric or polymeric form to achieve adequate EGFR-targeting properties. In the present work, we investigated if these aforementioned points are indeed critical and if the EGFR-targeting ability of GE11 can be improved by choosing an appropriate hydrophilic molecular design or a peptide multimer system to obtain a promising radiopeptide for the visualization of EGFR-overexpressing malignancies by positron emission tomography (PET). For this purpose, we developed several monovalent 68Ga-labeled GE11-based agents, a peptide homodimer and a homotetramer to overcome the challenges associated with GE11. The developed ligands were successfully labeled with 68Ga3+ in high radiochemical yields of ≥97% and molar activities of 41-104 GBq/μmol. The resulting radiotracers presented log D(7.4) values between -2.17 ± 0.21 and -3.79 ± 0.04 as well as a good stability in human serum with serum half-lives of 112 to 217 min for the monovalent radiopeptides and 84 and 62 min for the GE11 homodimer and homotetramer, respectively. In the following in vitro studies, none of the 68Ga-labeled radiopeptides demonstrated a considerable EGF receptor-specific uptake in EGFR-positive A431 cells. Moreover, none of the agents was able to displace [125I]I-EGF from the EGFR in competitive displacement assays in the same cell line in concentrations of up to 1 mM, whereas the endogenous receptor ligand hEGF demonstrated a high affinity of 15.2 ± 3.3 nM. These results indicate that it is not the aggregation of the GE11 sequence that seems to be the factor limiting the usefulness of the peptide as basis for radiotracer design but the limited affinity of monovalent and small homomultivalent GE11-based radiotracers to the EGFR. This highlights that the development of small-molecule GE11-based radioligands is not promising.
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Affiliation(s)
- Benedikt Judmann
- Biomedical
Chemistry, Clinic of Radiology and Nuclear Medicine, Medical Faculty
Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
- Molecular
Imaging and Radiochemistry, Clinic of Radiology and Nuclear Medicine,
Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Diana Braun
- Biomedical
Chemistry, Clinic of Radiology and Nuclear Medicine, Medical Faculty
Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
- Molecular
Imaging and Radiochemistry, Clinic of Radiology and Nuclear Medicine,
Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Ralf Schirrmacher
- Department
of Oncology, Division of Oncological Imaging, University of Alberta, 11560 University Avenue, T6G 1Z2 Edmonton, AB, Canada
| | - Björn Wängler
- Molecular
Imaging and Radiochemistry, Clinic of Radiology and Nuclear Medicine,
Medical Faculty Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
| | - Gert Fricker
- Institute
of Pharmacy and Molecular Biotechnology, University of Heidelberg, Im Neuenheimer Feld 329, 69120 Heidelberg, Germany
| | - Carmen Wängler
- Biomedical
Chemistry, Clinic of Radiology and Nuclear Medicine, Medical Faculty
Mannheim, Heidelberg University, Theodor-Kutzer-Ufer 1-3, 68167 Mannheim, Germany
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36
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Peper-Gabriel JK, Pavlidou M, Pattarini L, Morales-Kastresana A, Jaquin TJ, Gallou C, Hansbauer EM, Richter M, Lelievre H, Scholer-Dahirel A, Bossenmaier B, Sancerne C, Riviere M, Grandclaudon M, Zettl M, Bel Aiba RS, Rothe C, Blanc V, Olwill SA. The PD-L1/4-1BB Bispecific Antibody-Anticalin Fusion Protein PRS-344/S095012 Elicits Strong T-Cell Stimulation in a Tumor-Localized Manner. Clin Cancer Res 2022; 28:3387-3399. [PMID: 35121624 PMCID: PMC9662934 DOI: 10.1158/1078-0432.ccr-21-2762] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Revised: 09/25/2021] [Accepted: 02/02/2022] [Indexed: 01/07/2023]
Abstract
PURPOSE While patients responding to checkpoint blockade often achieve remarkable clinical responses, there is still significant unmet need due to resistant or refractory tumors. A combination of checkpoint blockade with further T-cell stimulation mediated by 4-1BB agonism may increase response rates and durability of response. A bispecific molecule that blocks the programmed cell death 1 (PD-1)/programmed cell death 1 ligand 1 (PD-L1) axis and localizes 4-1BB costimulation to a PD-L1-positive (PD-L1+) tumor microenvironment (TME) or tumor draining lymph nodes could maximize antitumor immunity and increase the therapeutic window beyond what has been reported for anti-4-1BB mAbs. EXPERIMENTAL DESIGN We generated and characterized the PD-L1/4-1BB bispecific molecule PRS-344/S095012 for target binding and functional activity in multiple relevant in vitro assays. Transgenic mice expressing human 4-1BB were transplanted with human PD-L1-expressing murine MC38 cells to assess in vivo antitumoral activity. RESULTS PRS-344/S095012 bound to its targets with high affinity and efficiently blocked the PD-1/PD-L1 pathway, and PRS-344/S095012-mediated 4-1BB costimulation was strictly PD-L1 dependent. We demonstrated a synergistic effect of both pathways on T-cell stimulation with the bispecific PRS-344/S095012 being more potent than the combination of mAbs. PRS-344/S095012 augmented CD4-positive (CD4+) and CD8-positive (CD8+) T-cell effector functions and enhanced antigen-specific T-cell stimulation. Finally, PRS-344/S095012 demonstrated strong antitumoral efficacy in an anti-PD-L1-resistant mouse model in which soluble 4-1BB was detected as an early marker for 4-1BB agonist activity. CONCLUSIONS The PD-L1/4-1BB bispecific PRS-344/S095012 efficiently combines checkpoint blockade with a tumor-localized 4-1BB-mediated stimulation burst to antigen-specific T cells, more potent than the combination of mAbs, supporting the advancement of PRS-344/S095012 toward clinical development. See related commentary by Shu et al., p. 3182.
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Affiliation(s)
| | | | - Lucia Pattarini
- Institut de Recherches Servier, Center for Therapeutic Innovation Oncology, Croissy-sur-Seine, France
| | | | | | - Catherine Gallou
- Institut de Recherches Servier, Center for Therapeutic Innovation Oncology, Croissy-sur-Seine, France
| | | | | | - Helene Lelievre
- Institut de Recherches Internationales Servier Oncology R&D Unit, Suresnes, France
| | - Alix Scholer-Dahirel
- Institut de Recherches Internationales Servier Oncology R&D Unit, Suresnes, France
| | | | - Celine Sancerne
- Institut de Recherches Servier, Center for Therapeutic Innovation Oncology, Croissy-sur-Seine, France
| | - Matthieu Riviere
- Institut de Recherches Servier, Center for Therapeutic Innovation Oncology, Croissy-sur-Seine, France
| | - Maximilien Grandclaudon
- Institut de Recherches Servier, Center for Therapeutic Innovation Oncology, Croissy-sur-Seine, France
| | - Markus Zettl
- Pieris Pharmaceuticals GmbH, Hallbergmoos, Germany
| | | | | | - Veronique Blanc
- Institut de Recherches Servier, Center for Therapeutic Innovation Oncology, Croissy-sur-Seine, France
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37
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McComb S, Nguyen T, Shepherd A, Henry KA, Bloemberg D, Marcil A, Maclean S, Zafer A, Gilbert R, Gadoury C, Pon RA, Sulea T, Zhu Q, Weeratna RD. Programmable Attenuation of Antigenic Sensitivity for a Nanobody-Based EGFR Chimeric Antigen Receptor Through Hinge Domain Truncation. Front Immunol 2022; 13:864868. [PMID: 35935988 PMCID: PMC9354126 DOI: 10.3389/fimmu.2022.864868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 06/06/2022] [Indexed: 11/13/2022] Open
Abstract
Epidermal growth factor family receptor (EGFR) is commonly overexpressed in many solid tumors and an attractive target for chimeric antigen receptor (CAR)-T therapy, but as EGFR is also expressed at lower levels in healthy tissues a therapeutic strategy must balance antigenic responsiveness against the risk of on-target off-tumor toxicity. Herein, we identify several camelid single-domain antibodies (also known as nanobodies) that are effective EGFR targeting moieties for CARs (EGFR-sdCARs) with very strong reactivity to EGFR-high and EGFR-low target cells. As a strategy to attenuate their potent antigenic sensitivity, we performed progressive truncation of the human CD8 hinge commonly used as a spacer domain in many CAR constructs. Single amino acid hinge-domain truncation progressively decreased both EGFR-sdCAR-Jurkat cell binding to EGFR-expressing targets and expression of the CD69 activation marker. Attenuated signaling in hinge-truncated EGFR-sdCAR constructs increased selectivity for antigen-dense EGFR-overexpressing cells over an EGFR-low tumor cell line or healthy donor derived EGFR-positive fibroblasts. We also provide evidence that epitope location is critical for determining hinge-domain requirement for CARs, as hinge truncation similarly decreased antigenic sensitivity of a membrane-proximal epitope targeting HER2-CAR but not a membrane-distal EGFRvIII-specific CAR. Hinge-modified EGFR-sdCAR cells showed clear functional attenuation in Jurkat-CAR-T cells and primary human CAR-T cells from multiple donors in vitro and in vivo. Overall, these results indicate that hinge length tuning provides a programmable strategy for throttling antigenic sensitivity in CARs targeting membrane-proximal epitopes, and could be employed for CAR-optimization and improved tumor selectivity.
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Affiliation(s)
- Scott McComb
- Human Health Therapeutics Research Centre, National Research Council, Ottawa, ON, Canada
- Centre for Infection, Immunity and Inflammation, University of Ottawa, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, Canada
- *Correspondence: Scott McComb,
| | - Tina Nguyen
- Human Health Therapeutics Research Centre, National Research Council, Ottawa, ON, Canada
| | - Alex Shepherd
- Human Health Therapeutics Research Centre, National Research Council, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Kevin A. Henry
- Human Health Therapeutics Research Centre, National Research Council, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, ON, Canada
| | - Darin Bloemberg
- Human Health Therapeutics Research Centre, National Research Council, Ottawa, ON, Canada
| | - Anne Marcil
- Human Health Therapeutics Research Centre, National Research Council, Ottawa, ON, Canada
| | - Susanne Maclean
- Human Health Therapeutics Research Centre, National Research Council, Ottawa, ON, Canada
| | - Ahmed Zafer
- Human Health Therapeutics Research Centre, National Research Council, Ottawa, ON, Canada
| | - Rénald Gilbert
- Human Health Therapeutics Research Centre, National Research Council, Ottawa, ON, Canada
- Department of Bioengineering, McGill University, Montréal, QC, Canada
| | - Christine Gadoury
- Human Health Therapeutics Research Centre, National Research Council, Ottawa, ON, Canada
| | - Robert A. Pon
- Human Health Therapeutics Research Centre, National Research Council, Ottawa, ON, Canada
| | - Traian Sulea
- Human Health Therapeutics Research Centre, National Research Council, Ottawa, ON, Canada
- Institute of Parasitology, McGill University, Sainte-Anne-de-Bellevue, QC, Canada
| | - Qin Zhu
- Human Health Therapeutics Research Centre, National Research Council, Ottawa, ON, Canada
| | - Risini D. Weeratna
- Human Health Therapeutics Research Centre, National Research Council, Ottawa, ON, Canada
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38
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Taylor RJ, Aguilar Rangel M, Geeson MB, Sormanni P, Vendruscolo M, Bernardes GJL. π-Clamp-Mediated Homo- and Heterodimerization of Single-Domain Antibodies via Site-Specific Homobifunctional Conjugation. J Am Chem Soc 2022; 144:13026-13031. [PMID: 35834748 PMCID: PMC9335888 DOI: 10.1021/jacs.2c04747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
![]()
Post-translational protein–protein conjugation
produces
bioconjugates that are unavailable via genetic fusion approaches.
A method for preparing protein–protein conjugates using π-clamp-mediated
cysteine arylation with pentafluorophenyl sulfonamide functional groups
is described. Two computationally designed antibodies targeting the
SARS-CoV-2 receptor binding domain were produced (KD = 146, 581 nM) with a π-clamp sequence near the
C-terminus and dimerized using this method to provide a 10–60-fold
increase in binding (KD = 8–15
nM). When two solvent-exposed cysteine residues were present on the
second protein domain, the π-clamp cysteine residue was selectively
modified over an Asp-Cys-Glu cysteine residue, allowing for subsequent
small-molecule conjugation. With this strategy, we build molecule–protein–protein
conjugates with complete chemical control over the sites of modification.
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Affiliation(s)
- Ross J Taylor
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Mauricio Aguilar Rangel
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Michael B Geeson
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Pietro Sormanni
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Gonçalo J L Bernardes
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.,Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina, Universidade de Lisboa, Avenida Professor Egas Moniz, 1649-028 Lisboa, Portugal
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39
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Schriek AI, van Haaren MM, Poniman M, Dekkers G, Bentlage AEH, Grobben M, Vidarsson G, Sanders RW, Verrips T, Geijtenbeek TBH, Heukers R, Kootstra NA, de Taeye SW, van Gils MJ. Anti-HIV-1 Nanobody-IgG1 Constructs With Improved Neutralization Potency and the Ability to Mediate Fc Effector Functions. Front Immunol 2022; 13:893648. [PMID: 35651621 PMCID: PMC9150821 DOI: 10.3389/fimmu.2022.893648] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
The most effective treatment for HIV-1, antiretroviral therapy, suppresses viral replication and averts the disease from progression. Nonetheless, there is a need for alternative treatments as it requires daily administration with the possibility of side effects and occurrence of drug resistance. Broadly neutralizing antibodies or nanobodies targeting the HIV-1 envelope glycoprotein are explored as alternative treatment, since they mediate viral suppression and contribute to the elimination of virus-infected cells. Besides neutralization potency and breadth, Fc-mediated effector functions of bNAbs also contribute to the in vivo efficacy. In this study multivalent J3, 2E7 and 1F10 anti-HIV-1 broadly neutralizing nanobodies were generated to improve neutralization potency and IgG1 Fc fusion was utilized to gain Fc-mediated effector functions. Bivalent and trivalent nanobodies, coupled using long glycine-serine linkers, showed increased binding to the HIV-1 Env and enhanced neutralization potency compared to the monovalent variant. Fusion of an IgG1 Fc domain to J3 improved neutralization potency compared to the J3-bihead and restored Fc-mediated effector functions such as antibody-dependent cellular phagocytosis and trogocytosis, and natural killer cell activation. Due to their neutralization breadth and potency and their ability to induce effector functions these nanobody-IgG1 constructs may prove to be valuable towards alternative HIV-1 therapies.
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Affiliation(s)
- Angela I Schriek
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Marlies M van Haaren
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Meliawati Poniman
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | | | - Arthur E H Bentlage
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Marloes Grobben
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Gestur Vidarsson
- Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands
| | - Rogier W Sanders
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands.,Department of Microbiology and Immunology, Weill Medical College of Cornell University, New York, NY, United States
| | - Theo Verrips
- Department of Biology, Faculty of Sciences, Utrecht University, Utrecht, Netherlands.,VerLin BV, Utrecht, Netherlands
| | - Teunis B H Geijtenbeek
- Department of Experimental Immunology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | | | - Neeltje A Kootstra
- Department of Experimental Immunology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Steven W de Taeye
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
| | - Marit J van Gils
- Department of Medical Microbiology, Amsterdam UMC, Amsterdam Institute for Infection and Immunity, University of Amsterdam, Amsterdam, Netherlands
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40
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Gomez-Soler M, Gehring MP, Lechtenberg BC, Zapata-Mercado E, Ruelos A, Matsumoto MW, Hristova K, Pasquale EB. Ligands with different dimeric configurations potently activate the EphA2 receptor and reveal its potential for biased signaling. iScience 2022; 25:103870. [PMID: 35243233 PMCID: PMC8858996 DOI: 10.1016/j.isci.2022.103870] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Revised: 12/13/2021] [Accepted: 02/01/2022] [Indexed: 12/03/2022] Open
Abstract
The EphA2 receptor tyrosine kinase activates signaling pathways with different, and sometimes opposite, effects in cancer and other pathologies. Thus, highly specific and potent biased ligands that differentially control EphA2 signaling responses could be therapeutically valuable. Here, we use EphA2-specific monomeric peptides to engineer dimeric ligands with three different geometric configurations to combine a potential ability to differentially modulate EphA2 signaling responses with the high potency and prolonged receptor residence time characteristic of dimeric ligands. The different dimeric peptides readily induce EphA2 clustering, autophosphorylation and signaling, the best with sub-nanomolar potency. Yet, there are differences in two EphA2 signaling responses induced by peptides with different configurations, which exhibit distinct potency and efficacy. The peptides bias signaling when compared with the ephrinA1-Fc ligand and do so via different mechanisms. These findings provide insights into Eph receptor signaling, and proof-of-principle that different Eph signaling responses can be distinctly modulated.
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Affiliation(s)
- Maricel Gomez-Soler
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Marina P. Gehring
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Bernhard C. Lechtenberg
- Ubiquitin Signalling Division, The Walter and Eliza Hall Institute of Medical Research, Parkville Victoria 3052, Australia and Department of Medical Biology, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Elmer Zapata-Mercado
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Alyssa Ruelos
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Mike W. Matsumoto
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Kalina Hristova
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Elena B. Pasquale
- Cancer Center, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
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41
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Dunlap T, Cao Y. Physiological Considerations for Modeling in vivo Antibody-Target Interactions. Front Pharmacol 2022; 13:856961. [PMID: 35281913 PMCID: PMC8912916 DOI: 10.3389/fphar.2022.856961] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 02/10/2022] [Indexed: 11/25/2022] Open
Abstract
The number of therapeutic antibodies in development pipelines is increasing rapidly. Despite superior success rates relative to small molecules, therapeutic antibodies still face many unique development challenges. There is often a translational gap from their high target affinity and specificity to the therapeutic effects. Tissue microenvironment and physiology critically influence antibody-target interactions contributing to apparent affinity alterations and dynamic target engagement. The full potential of therapeutic antibodies will be further realized by contextualizing antibody-target interactions under physiological conditions. Here we review how local physiology such as physical stress, biological fluid, and membrane characteristics could influence antibody-target association, dissociation, and apparent affinity. These physiological factors in the early development of therapeutic antibodies are valuable toward rational antibody engineering, preclinical candidate selection, and lead optimization.
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Affiliation(s)
- Tyler Dunlap
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Yanguang Cao
- Division of Pharmacotherapy and Experimental Therapeutics, Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States.,Lineberger Comprehensive Cancer Center, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
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42
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Verkhivker G. Structural and Computational Studies of the SARS-CoV-2 Spike Protein Binding Mechanisms with Nanobodies: From Structure and Dynamics to Avidity-Driven Nanobody Engineering. Int J Mol Sci 2022; 23:ijms23062928. [PMID: 35328351 PMCID: PMC8951411 DOI: 10.3390/ijms23062928] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 03/06/2022] [Accepted: 03/07/2022] [Indexed: 11/28/2022] Open
Abstract
Nanobodies provide important advantages over traditional antibodies, including their smaller size and robust biochemical properties such as high thermal stability, high solubility, and the ability to be bioengineered into novel multivalent, multi-specific, and high-affinity molecules, making them a class of emerging powerful therapies against SARS-CoV-2. Recent research efforts on the design, protein engineering, and structure-functional characterization of nanobodies and their binding with SARS-CoV-2 S proteins reflected a growing realization that nanobody combinations can exploit distinct binding epitopes and leverage the intrinsic plasticity of the conformational landscape for the SARS-CoV-2 S protein to produce efficient neutralizing and mutation resistant characteristics. Structural and computational studies have also been instrumental in quantifying the structure, dynamics, and energetics of the SARS-CoV-2 spike protein binding with nanobodies. In this review, a comprehensive analysis of the current structural, biophysical, and computational biology investigations of SARS-CoV-2 S proteins and their complexes with distinct classes of nanobodies targeting different binding sites is presented. The analysis of computational studies is supplemented by an in-depth examination of mutational scanning simulations and identification of binding energy hotspots for distinct nanobody classes. The review is focused on the analysis of mechanisms underlying synergistic binding of multivalent nanobodies that can be superior to single nanobodies and conventional nanobody cocktails in combating escape mutations by effectively leveraging binding avidity and allosteric cooperativity. We discuss how structural insights and protein engineering approaches together with computational biology tools can aid in the rational design of synergistic combinations that exhibit superior binding and neutralization characteristics owing to avidity-mediated mechanisms.
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Affiliation(s)
- Gennady Verkhivker
- Graduate Program in Computational and Data Sciences, Keck Center for Science and Engineering, Schmid College of Science and Technology, Chapman University, Orange, CA 92866, USA; ; Tel.: +1-714-516-4586
- Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Irvine, CA 92618, USA
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43
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Thomas BJ, Porciani D, Burke DH. Cancer immunomodulation using bispecific aptamers. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:894-915. [PMID: 35141049 PMCID: PMC8803965 DOI: 10.1016/j.omtn.2022.01.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Evasion of immune destruction is a major hallmark of cancer. Recent US Food and Drug Administration (FDA) approvals of various immunomodulating therapies underline the important role that reprogramming the immune system can play in combating this disease. However, a wide range of side effects still limit the therapeutic potential of immunomodulators, suggesting a need for more precise reagents with negligible off-target and on-target/off-tumor effects. Aptamers are single-chained oligonucleotides that bind their targets with high specificity and affinity owing to their three-dimensional (3D) structures, and they are one potential way to address this need. In particular, bispecific aptamers (bsApts) have been shown to induce artificial immune synapses that promote T cell activation and subsequent tumor cell lysis in various in vitro and in vivo pre-clinical models. We discuss these advances here, along with gaps in bsApt biology at both the cellular and resident tissue levels that should be addressed to accelerate their translation into the clinic. The broad application, minimal production cost, and relative lack of immunogenicity of bsApts give them some ideal qualities for manipulating the immune system. Building upon lessons from other novel therapies, bsApts could soon provide clinicians with an immunomodulating toolbox that is not only potent and efficacious but exercises a wide therapeutic index.
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Affiliation(s)
- Brian J. Thomas
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65201, USA
| | - David Porciani
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65201, USA
| | - Donald H. Burke
- Department of Molecular Microbiology and Immunology, University of Missouri School of Medicine, Columbia, MO 65212, USA
- Bond Life Sciences Center, University of Missouri, Columbia, MO 65201, USA
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44
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Engineered protein-small molecule conjugates empower selective enzyme inhibition. Cell Chem Biol 2022; 29:328-338.e4. [PMID: 34363759 PMCID: PMC8807807 DOI: 10.1016/j.chembiol.2021.07.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/17/2021] [Accepted: 07/14/2021] [Indexed: 11/20/2022]
Abstract
Potent, specific ligands drive precision medicine and fundamental biology. Proteins, peptides, and small molecules constitute effective ligand classes. Yet greater molecular diversity would aid the pursuit of ligands to elicit precise biological activity against challenging targets. We demonstrate a platform to discover protein-small molecule (PriSM) hybrids to combine unique pharmacophore activities and shapes with constrained, efficiently engineerable proteins. In this platform, a fibronectin protein library is displayed on yeast with a single cysteine coupled to acetazolamide via a maleimide-poly(ethylene glycol) linker. Magnetic and flow cytometric sorts enrich specific binders to carbonic anhydrase isoforms. Isolated PriSMs exhibit potent, specific inhibition of carbonic anhydrase isoforms with efficacy superior to that of acetazolamide or protein alone, including an 80-fold specificity increase and 9-fold potency gain. PriSMs are engineered with multiple linker lengths, protein conjugation sites, and sequences against two different isoforms, which reveal platform flexibility and impacts of molecular designs. PriSMs advance the molecular diversity of efficiently engineerable ligands.
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45
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Root-Bernstein R. Biased, Bitopic, Opioid–Adrenergic Tethered Compounds May Improve Specificity, Lower Dosage and Enhance Agonist or Antagonist Function with Reduced Risk of Tolerance and Addiction. Pharmaceuticals (Basel) 2022; 15:ph15020214. [PMID: 35215326 PMCID: PMC8876737 DOI: 10.3390/ph15020214] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 02/02/2022] [Accepted: 02/07/2022] [Indexed: 01/03/2023] Open
Abstract
This paper proposes the design of combination opioid–adrenergic tethered compounds to enhance efficacy and specificity, lower dosage, increase duration of activity, decrease side effects, and reduce risk of developing tolerance and/or addiction. Combinations of adrenergic and opioid drugs are sometimes used to improve analgesia, decrease opioid doses required to achieve analgesia, and to prolong the duration of analgesia. Recent mechanistic research suggests that these enhanced functions result from an allosteric adrenergic binding site on opioid receptors and, conversely, an allosteric opioid binding site on adrenergic receptors. Dual occupancy of the receptors maintains the receptors in their high affinity, most active states; drops the concentration of ligand required for full activity; and prevents downregulation and internalization of the receptors, thus inhibiting tolerance to the drugs. Activation of both opioid and adrenergic receptors also enhances heterodimerization of the receptors, additionally improving each drug’s efficacy. Tethering adrenergic drugs to opioids could produce new drug candidates with highly desirable features. Constraints—such as the locations of the opioid binding sites on adrenergic receptors and adrenergic binding sites on opioid receptors, length of tethers that must govern the design of such novel compounds, and types of tethers—are described and examples of possible structures provided.
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46
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Ito K, Matsuda Y, Mine A, Shikida N, Takahashi K, Miyairi K, Shimbo K, Kikuchi Y, Konishi A. Single-chain tandem macrocyclic peptides as a scaffold for growth factor and cytokine mimetics. Commun Biol 2022; 5:56. [PMID: 35031676 PMCID: PMC8760323 DOI: 10.1038/s42003-022-03015-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/28/2021] [Indexed: 11/28/2022] Open
Abstract
Mimetics of growth factors and cytokines are promising tools for culturing large numbers of cells and manufacturing regenerative medicine products. In this study, we report single-chain tandem macrocyclic peptides (STaMPtides) as mimetics in a new multivalent peptide format. STaMPtides, which contain two or more macrocyclic peptides with a disulfide-closed backbone and peptide linkers, are successfully secreted into the supernatant by Corynebacterium glutamicum-based secretion technology. Without post-secretion modification steps, such as macrocyclization or enzymatic treatment, bacterially secreted STaMPtides form disulfide bonds, as designed; are biologically active; and show agonistic activities against respective target receptors. We also demonstrate, by cell-based assays, the potential of STaMPtides, which mimic growth factors and cytokines, in cell culture. The STaMPtide technology can be applied to the design, screening, and production of growth factor and cytokine mimetics.
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Affiliation(s)
- Kenichiro Ito
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan.
| | - Yoshihiko Matsuda
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Ayako Mine
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Natsuki Shikida
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Kazutoshi Takahashi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Kyohei Miyairi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Kazutaka Shimbo
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Yoshimi Kikuchi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
| | - Atsushi Konishi
- Research Institute for Bioscience Products & Fine Chemicals, Ajinomoto Co., Inc., 1-1, Suzuki-Cho, Kawasaki-ku, Kawasaki-shi, Kanagawa, 210-8681, Japan
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47
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Ambati S, Pham T, Lewis ZA, Lin X, Meagher RB. DC-SIGN targets amphotericin B-loaded liposomes to diverse pathogenic fungi. Fungal Biol Biotechnol 2021; 8:22. [PMID: 34952645 PMCID: PMC8709943 DOI: 10.1186/s40694-021-00126-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/17/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Life-threatening invasive fungal infections are treated with antifungal drugs such as Amphotericin B (AmB) loaded liposomes. Our goal herein was to show that targeting liposomal AmB to fungal cells with the C-type lectin pathogen recognition receptor DC-SIGN improves antifungal activity. DC-SIGN binds variously crosslinked mannose-rich and fucosylated glycans and lipomannans that are expressed by helminth, protist, fungal, bacterial and viral pathogens including three of the most life-threatening fungi, Aspergillus fumigatus, Candida albicans and Cryptococcus neoformans. Ligand recognition by human DC-SIGN is provided by a carbohydrate recognition domain (CRD) linked to the membrane transit and signaling sequences. Different combinations of the eight neck repeats (NR1 to NR8) expressed in different protein isoforms may alter the orientation of the CRD to enhance its binding to different glycans. RESULTS We prepared two recombinant isoforms combining the CRD with NR1 and NR2 in isoform DCS12 and with NR7 and NR8 in isoform DCS78 and coupled them to a lipid carrier. These constructs were inserted into the membrane of pegylated AmB loaded liposomes AmB-LLs to produce DCS12-AmB-LLs and DCS78-AmB-LLs. Relative to AmB-LLs and Bovine Serum Albumin coated BSA-AmB-LLs, DCS12-AmB-LLs and DCS78-AmB-LLs bound more efficiently to the exopolysaccharide matrices produced by A. fumigatus, C. albicans and C. neoformans in vitro, with DCS12-AmB-LLs performing better than DCS78-AmB-LLs. DCS12-AmB-LLs inhibited and/or killed all three species in vitro significantly better than AmB-LLs or BSA-AmB-LLs. In mouse models of invasive candidiasis and pulmonary aspergillosis, one low dose of DCS12-AmB-LLs significantly reduced the fungal burden in the kidneys and lungs, respectively, several-fold relative to AmB-LLs. CONCLUSIONS DC-SIGN's CRD specifically targeted antifungal liposomes to three highly evolutionarily diverse pathogenic fungi and enhanced the antifungal efficacy of liposomal AmB both in vitro and in vivo. Targeting significantly reduced the effective dose of antifungal drug, which may reduce drug toxicity, be effective in overcoming dose dependent drug resistance, and more effectively kill persister cells. In addition to fungi, DC-SIGN targeting of liposomal packaged anti-infectives have the potential to alter treatment paradigms for a wide variety of pathogens from different kingdoms including protozoans, helminths, bacteria, and viruses which express its cognate ligands.
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Affiliation(s)
- Suresh Ambati
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA.
| | - Tuyetnhu Pham
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - Zachary A Lewis
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - Xiaorong Lin
- Department of Microbiology, University of Georgia, Athens, GA, 30602, USA
| | - Richard B Meagher
- Department of Genetics, University of Georgia, Athens, GA, 30602, USA
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48
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Miyoshi T, Friedman TB, Watanabe N. Fast-dissociating but highly specific antibodies are novel tools in biology, especially useful for multiplex super-resolution microscopy. STAR Protoc 2021; 2:100967. [PMID: 34841279 PMCID: PMC8605432 DOI: 10.1016/j.xpro.2021.100967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Fast-dissociating, highly specific monoclonal antibodies (FDSAs) are single-molecule imaging probes useful for many biological assays including consecutive, multiplexable super-resolution microscopy. We developed a screening assay to characterize the kinetics of antibody-antigen interactions using single-molecule microscopy and established a pipeline to identify FDSAs from thousands of monoclonal candidates. Provided here are detailed protocols to prepare multi-well glass-bottom plates necessary for our assay to identify hybridoma clones secreting FDSAs. Synthesis of fluorescently labeled Fab fragments (Fab probes) from FDSAs is also described. For complete details on the use and execution of this protocol, please refer to Miyoshi et al. (2021).
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Affiliation(s)
- Takushi Miyoshi
- Laboratory of Single-Molecule Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Department of Pharmacology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Room 1F-143A, Bethesda, MD 20892, USA
- Department of Otolaryngology - Head and Neck Surgery, Graduate School of Medicine, Kyoto University, Kyoto 606-8507, Japan
| | - Thomas B. Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Porter Neuroscience Research Center, Room 1F-143A, Bethesda, MD 20892, USA
| | - Naoki Watanabe
- Laboratory of Single-Molecule Cell Biology, Graduate School of Biostudies, Kyoto University, Kyoto 606-8501, Japan
- Department of Pharmacology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
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49
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Groysbeck N, Donzeau M, Stoessel A, Haeberle AM, Ory S, Spehner D, Schultz P, Ersen O, Bahri M, Ihiawakrim D, Zuber G. Gold labelling of a green fluorescent protein (GFP)-tag inside cells using recombinant nanobodies conjugated to 2.4 nm thiolate-coated gold nanoparticles. NANOSCALE ADVANCES 2021; 3:6940-6948. [PMID: 36132366 PMCID: PMC9417625 DOI: 10.1039/d1na00256b] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 09/24/2021] [Indexed: 06/15/2023]
Abstract
Advances in microscopy technology have prompted efforts to improve the reagents required to recognize specific molecules within the intracellular environment. For high-resolution electron microscopy, conjugation of selective binders originating from the immune response arsenal to gold nanoparticles (AuNPs) as contrasting agents is the method of choice to obtain labeling tools. However, conjugation of the minimal sized 15 kDa nanobody (Nb) to AuNPs remains challenging in comparison to the conjugation of 150 kDa IgG to AuNPs. Herein, effective Nb-AuNP assemblies are built using the selective and almost irreversible non-covalent associations between two peptide sequences deriving from a p53 heterotetramer domain variant. The 15 kDa GFP-binding Nb is fused to one dimerizing motif to obtain a recombinant Nb dimer with improved avidity for GFP while the other complementing dimerizing motif is equipped with thiols and grafted to a 2.4 nm substituted thiobenzoate-coordinated AuNP via thiolate exchange. After pegylation, the modified AuNPs are able to non-covalently anchor Nb dimers and the subsequent complexes demonstrate the ability to form immunogold label GFP-protein fusions within various subcellular locations. These tools open an avenue for precise localization of targets at high resolution by electron microscopy.
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Affiliation(s)
- Nadja Groysbeck
- Université de Strasbourg - CNRS, UMR 7242 Laboratoire de Biotechnologie et Signalisation Cellulaire Boulevard Sébastien Brant 67400 Illkirch France
| | - Mariel Donzeau
- Université de Strasbourg - CNRS, UMR 7242 Laboratoire de Biotechnologie et Signalisation Cellulaire Boulevard Sébastien Brant 67400 Illkirch France
| | - Audrey Stoessel
- Université de Strasbourg - CNRS, UMR 7242 Laboratoire de Biotechnologie et Signalisation Cellulaire Boulevard Sébastien Brant 67400 Illkirch France
| | - Anne-Marie Haeberle
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives F-67000 Strasbourg France
| | - Stéphane Ory
- Centre National de la Recherche Scientifique, Université de Strasbourg, Institut des Neurosciences Cellulaires et Intégratives F-67000 Strasbourg France
| | - Danièle Spehner
- Université de Strasbourg - Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire 67400 Illkirch France
| | - Patrick Schultz
- Université de Strasbourg - Department of Integrated Structural Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire 67400 Illkirch France
| | - Ovidiu Ersen
- Université de Strasbourg - CNRS, UMR 7504, Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS) 23 rue de Loess 67034 Strasbourg France
| | - Mounib Bahri
- Université de Strasbourg - CNRS, UMR 7504, Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS) 23 rue de Loess 67034 Strasbourg France
| | - Dris Ihiawakrim
- Université de Strasbourg - CNRS, UMR 7504, Institut de Physique et Chimie des Matériaux de Strasbourg (IPCMS) 23 rue de Loess 67034 Strasbourg France
| | - Guy Zuber
- Université de Strasbourg - CNRS, UMR 7242 Laboratoire de Biotechnologie et Signalisation Cellulaire Boulevard Sébastien Brant 67400 Illkirch France
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50
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Yao J, Tu Y, Shen C, Zhou Q, Xiao H, Jia D, Sun Q. Nuclear import receptors and hnRNPK mediates nuclear import and stress granule localization of SIRLOIN. Cell Mol Life Sci 2021; 78:7617-7633. [PMID: 34689235 PMCID: PMC11073023 DOI: 10.1007/s00018-021-03992-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 02/08/2023]
Abstract
The majority of lncRNAs and a small fraction of mRNAs localize in the cell nucleus to exert their functions. A SIRLOIN RNA motif was previously reported to drive its nuclear localization by the RNA-binding protein hnRNPK. However, the underlying mechanism remains unclear. Here, we report crystal structures of hnRNPK in complex with SIRLOIN, and with the nuclear import receptor (NIR) Impα1, respectively. The protein hnRNPK bound to SIRLOIN with multiple weak interactions, and interacted Impα1 using an independent high-affinity site. Forming a complex with hnRNPK and Impα1 was essential for the nuclear import and stress granule localization of SIRLOIN in semi-permeabilized cells. Nuclear import of SIRLOIN enhanced with increasing NIR concentrations, but its stress granule localization peaked at a low NIR concentration. Collectively, we propose a mechanism of SIRLOIN localization, in which NIRs functioned as drivers/regulators, and hnRNPK as an adaptor.
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Affiliation(s)
- Jialin Yao
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, 610041, China
| | - Yingfeng Tu
- Division of Neurology, Department of Pediatrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Congcong Shen
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, 610041, China
| | - Qiao Zhou
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, 610041, China
| | - Hengyi Xiao
- Aging Research Lab, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, 610041, China
| | - Da Jia
- Division of Neurology, Department of Pediatrics, Key Laboratory of Birth Defects and Related Diseases of Women and Children, West China Second University Hospital, Sichuan University, Chengdu, 610041, China
| | - Qingxiang Sun
- Department of Pathology, State Key Laboratory of Biotherapy and Cancer Centre, West China Hospital, Sichuan University, and Collaborative Innovation Centre of Biotherapy, Chengdu, 610041, China.
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