1
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Komar AA, Samatova E, Rodnina MV. Translation Rates and Protein Folding. J Mol Biol 2024; 436:168384. [PMID: 38065274 DOI: 10.1016/j.jmb.2023.168384] [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: 10/20/2023] [Revised: 12/01/2023] [Accepted: 12/02/2023] [Indexed: 12/19/2023]
Abstract
The mRNA coding sequence defines not only the amino acid sequence of the protein, but also the speed at which the ribosomes move along the mRNA while making the protein. The non-uniform local kinetics - denoted as translational rhythm - is similar among mRNAs coding for related protein folds. Deviations from this conserved rhythm can result in protein misfolding. In this review we summarize the experimental evidence demonstrating how local translation rates affect cotranslational protein folding, with the focus on the synonymous codons and patches of charged residues in the nascent peptide as best-studied examples. Alterations in nascent protein conformations due to disturbed translational rhythm can persist off the ribosome, as demonstrated by the effects of synonymous codon variants of several disease-related proteins. Charged amino acid patches in nascent chains also modulate translation and cotranslational protein folding, and can abrogate translation when placed at the N-terminus of the nascent peptide. During cotranslational folding, incomplete nascent chains navigate through a unique conformational landscape in which earlier intermediate states become inaccessible as the nascent peptide grows. Precisely tuned local translation rates, as well as interactions with the ribosome, guide the folding pathway towards the native structure, whereas deviations from the natural translation rhythm may favor pathways leading to trapped misfolded states. Deciphering the 'folding code' of the mRNA will contribute to understanding the diseases caused by protein misfolding and to rational protein design.
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Affiliation(s)
- Anton A Komar
- Center for Gene Regulation in Health and Disease, Department of Biological, Geological and Environmental Sciences, Cleveland State University, 2121 Euclid Avenue, Cleveland, OH 44115, USA; Department of Biochemistry and Center for RNA Science and Therapeutics, School of Medicine, Case Western Reserve University, Cleveland, OH 44106, USA.
| | - Ekaterina Samatova
- Max Planck Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, 37077 Goettingen, Germany
| | - Marina V Rodnina
- Max Planck Department of Physical Biochemistry, Max Planck Institute for Multidisciplinary Sciences, 37077 Goettingen, Germany.
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2
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Nagar N, Naidu G, Mishra A, Poluri KM. Protein-Based Nanocarriers and Nanotherapeutics for Infection and Inflammation. J Pharmacol Exp Ther 2024; 388:91-109. [PMID: 37699711 DOI: 10.1124/jpet.123.001673] [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: 01/10/2023] [Revised: 08/04/2023] [Accepted: 08/21/2023] [Indexed: 09/14/2023] Open
Abstract
Infectious and inflammatory diseases are one of the leading causes of death globally. The status quo has become more prominent with the onset of the coronavirus disease 2019 (COVID-19) pandemic. To combat these potential crises, proteins have been proven as highly efficacious drugs, drug targets, and biomarkers. On the other hand, advancements in nanotechnology have aided efficient and sustained drug delivery due to their nano-dimension-acquired advantages. Combining both strategies together, the protein nanoplatforms are equipped with the advantageous intrinsic properties of proteins as well as nanoformulations, eloquently changing the field of nanomedicine. Proteins can act as carriers, therapeutics, diagnostics, and theranostics in their nanoform as fusion proteins or as composites with other organic/inorganic materials. Protein-based nanoplatforms have been extensively explored to target the major infectious and inflammatory diseases of clinical concern. The current review comprehensively deliberated proteins as nanocarriers for drugs and nanotherapeutics for inflammatory and infectious agents, with special emphasis on cancer and viral diseases. A plethora of proteins from diverse organisms have aided in the synthesis of protein-based nanoformulations. The current study specifically presented the proteins of human and pathogenic origin to dwell upon the field of protein nanotechnology, emphasizing their pharmacological advantages. Further, the successful clinical translation and current bottlenecks of the protein-based nanoformulations associated with the infection-inflammation paradigm have also been discussed comprehensively. SIGNIFICANCE STATEMENT: This review discusses the plethora of promising protein-based nanocarriers and nanotherapeutics explored for infectious and inflammatory ailments, with particular emphasis on protein nanoparticles of human and pathogenic origin with reference to the advantages, ADME (absorption, distribution, metabolism, and excretion parameters), and current bottlenecks in development of protein-based nanotherapeutic interventions.
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Affiliation(s)
- Nupur Nagar
- Department of Biosciences and Bioengineering (N.N., G.N., K.M.P.) and Centre for Nanotechnology (K.M.P.), Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; and Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India (A.M.)
| | - Goutami Naidu
- Department of Biosciences and Bioengineering (N.N., G.N., K.M.P.) and Centre for Nanotechnology (K.M.P.), Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; and Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India (A.M.)
| | - Amit Mishra
- Department of Biosciences and Bioengineering (N.N., G.N., K.M.P.) and Centre for Nanotechnology (K.M.P.), Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; and Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India (A.M.)
| | - Krishna Mohan Poluri
- Department of Biosciences and Bioengineering (N.N., G.N., K.M.P.) and Centre for Nanotechnology (K.M.P.), Indian Institute of Technology Roorkee, Roorkee, Uttarakhand, India; and Cellular and Molecular Neurobiology Unit, Indian Institute of Technology Jodhpur, Jodhpur, Rajasthan, India (A.M.)
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3
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Yu Y, Dong L, Dong C, Zhang X. Validation of a Proteomic-Based Prognostic Model for Breast Cancer and Immunological Analysis. Int J Genomics 2023; 2023:1738750. [PMID: 38145160 PMCID: PMC10748720 DOI: 10.1155/2023/1738750] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 10/07/2023] [Accepted: 11/25/2023] [Indexed: 12/26/2023] Open
Abstract
Breast cancer (BC) has emerged as an extremely destructive malignancy, causing significant harm to female patients and society at large. Proteomic research holds great promise for early diagnosis and treatment of diseases, and the integration of proteomics with genomics can offer valuable assistance in the early diagnosis, treatment, and improved prognosis of BC patients. In this study, we downloaded breast cancer protein expression data from The Cancer Genome Atlas (TCGA) and combined proteomics with genomics to construct a proteomic-based prognostic model for BC. This model consists of nine proteins (HEREGULIN, IDO, PEA15, MERIT40_pS29, CIITA, AKT2, CD171 DVL3, and CABL9). The accuracy of the model in predicting the survival prognosis of BC patients was further validated through risk curve analysis, survival curve analysis, and independent prognostic analysis. We further confirmed the impact of differential expression of these nine key proteins on overall survival in BC patients, and the differential expression of the key proteins and their encoding genes was validated using immunohistochemical staining. Enrichment analysis revealed functional associations primarily related to PPAR signaling pathway, steroid hormone metabolism, chemokine signaling pathway, DNA conformation changes, immunoglobulin production, and immunoglobulin complex in the high- and low-risk groups. Immune infiltration analysis revealed differential expression of immune cells between the high- and low-risk groups, providing a theoretical basis for subsequent immunotherapy. The model constructed in this study can predict the survival of BC patients, and the identified key proteins may serve as biomarkers to aid in the early diagnosis of BC. Enrichment analysis and immune infiltration analysis provide a necessary theoretical basis for further exploration of the molecular mechanisms and subsequent immunotherapy.
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Affiliation(s)
- Yunlin Yu
- Department of General Surgery, Affiliated Renhe Hospital of China Three Gorges University, Yichang 443000, China
| | - Linhuan Dong
- Department of General Surgery, Affiliated Renhe Hospital of China Three Gorges University, Yichang 443000, China
| | - Changjun Dong
- Department of General Surgery, Affiliated Renhe Hospital of China Three Gorges University, Yichang 443000, China
| | - Xianlin Zhang
- Department of General Surgery, Affiliated Renhe Hospital of China Three Gorges University, Yichang 443000, China
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4
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Li N, Han L, Wang X, Qiao O, Zhang L, Gong Y. Biotherapy of experimental acute kidney injury: emerging novel therapeutic strategies. Transl Res 2023; 261:69-85. [PMID: 37329950 DOI: 10.1016/j.trsl.2023.06.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 06/10/2023] [Accepted: 06/12/2023] [Indexed: 06/19/2023]
Abstract
Acute kidney injury (AKI) is a complex and heterogeneous disease with high incidence and mortality, posing a serious threat to human life and health. Usually, in clinical practice, AKI is caused by crush injury, nephrotoxin exposure, ischemia-reperfusion injury, or sepsis. Therefore, most AKI models for pharmacological experimentation are based on this. The current research promises to develop new biological therapies, including antibody therapy, non-antibody protein therapy, cell therapy, and RNA therapy, that could help mitigate the development of AKI. These approaches can promote renal repair and improve systemic hemodynamics after renal injury by reducing oxidative stress, inflammatory response, organelles damage, and cell death, or activating cytoprotective mechanisms. However, no candidate drugs for AKI prevention or treatment have been successfully translated from bench to bedside. This article summarizes the latest progress in AKI biotherapy, focusing on potential clinical targets and novel treatment strategies that merit further investigation in future pre-clinical and clinical studies.
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Affiliation(s)
- Ning Li
- Institute of Disaster and Emergency Medicine, Medical College, Tianjin University, Nankai District, Tianjin, China; Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin, China
| | - Lu Han
- Institute of Disaster and Emergency Medicine, Medical College, Tianjin University, Nankai District, Tianjin, China; Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin, China
| | - Xinyue Wang
- Institute of Disaster and Emergency Medicine, Medical College, Tianjin University, Nankai District, Tianjin, China; Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin, China
| | - Ou Qiao
- Institute of Disaster and Emergency Medicine, Medical College, Tianjin University, Nankai District, Tianjin, China; Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin, China
| | - Li Zhang
- Institute of Disaster and Emergency Medicine, Medical College, Tianjin University, Nankai District, Tianjin, China; Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin, China
| | - Yanhua Gong
- Institute of Disaster and Emergency Medicine, Medical College, Tianjin University, Nankai District, Tianjin, China; Tianjin Key Laboratory of Disaster Medicine Technology, Tianjin, China.
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5
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Jankowski W, Kidchob C, Bunce C, Cloake E, Resende R, Sauna ZE. The MHC Associated Peptide Proteomics assay is a useful tool for the non-clinical assessment of immunogenicity. Front Immunol 2023; 14:1271120. [PMID: 37915568 PMCID: PMC10616951 DOI: 10.3389/fimmu.2023.1271120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/13/2023] [Indexed: 11/03/2023] Open
Abstract
The propensity of therapeutic proteins to elicit an immune response, poses a significant challenge in clinical development and safety of the patients. Assessment of immunogenicity is crucial to predict potential adverse events and design safer biologics. In this study, we employed MHC Associated Peptide Proteomics (MAPPS) to comprehensively evaluate the immunogenic potential of re-engineered variants of immunogenic FVIIa analog (Vatreptacog Alfa). Our finding revealed the correlation between the protein sequence affinity for MHCII and the number of peptides identified in a MAPPS assay and this further correlates with the reduced T-cell responses. Moreover, MAPPS enable the identification of "relevant" T cell epitopes and may contribute to the development of biologics with lower immunogenic potential.
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Affiliation(s)
- Wojciech Jankowski
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | - Christopher Kidchob
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
| | | | | | | | - Zuben E. Sauna
- Hemostasis Branch 1, Division of Hemostasis, Office of Plasma Protein Therapeutics, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, United States
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6
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Rhodes KR, Tzeng SY, Iglesias M, Lee D, Storm K, Neshat SY, VanDyke D, Lowmaster SM, Spangler JB, Raimondi G, Green JJ. Bioengineered particles expand myelin-specific regulatory T cells and reverse autoreactivity in a mouse model of multiple sclerosis. SCIENCE ADVANCES 2023; 9:eadd8693. [PMID: 37267370 PMCID: PMC10413683 DOI: 10.1126/sciadv.add8693] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 04/27/2023] [Indexed: 06/04/2023]
Abstract
Multiple sclerosis (MS) is an autoimmune disease characterized by autoreactive immune cells damaging myelinated nerves, impairing brain function. Treatments aim for tolerance induction to reeducate the immune system to recognize myelin as "self" rather than "foreign." As peripheral immune tolerance is primarily mediated by regulatory T cells (Tregs), we developed a therapy to support Treg expansion and activity in vivo. To target, engage, and activate myelin-specific Tregs, we designed a biodegradable microparticle (MP) loaded with rapamycin and functionalized with a biased interleukin-2 (IL-2) fusion protein and a major histocompatibility complex (MHC) class II loaded with a myelin peptide. These tolerogenic MPs (Tol-MPs) were validated in vitro and then evaluated in a mouse model of MS, experimental autoimmune encephalomyelitis (EAE). Tol-MPs promoted sustained disease reversal in 100% of mice and full recovery in 38% of mice with symptomatic EAE. Tol-MPs are a promising platform for treatment of autoimmune diseases.
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Affiliation(s)
- Kelly R. Rhodes
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Stephany Y. Tzeng
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Marcos Iglesias
- Department of Plastic and Reconstructive Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Dongwoo Lee
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Kaitlyn Storm
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Sarah Y. Neshat
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Derek VanDyke
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Shirley M. Lowmaster
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Plastic and Reconstructive Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Jamie B. Spangler
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
- Institute for NanoBioTechnology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center and the Bloomberg~Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Molecular Microbiology and Immunology, Johns Hopkins University School of Public Health, Baltimore, MD 21231, USA
| | - Giorgio Raimondi
- Department of Plastic and Reconstructive Surgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Jordan J. Green
- Department of Biomedical Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Translational Tissue Engineering Center, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
- Institute for NanoBioTechnology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Ophthalmology, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center and the Bloomberg~Kimmel Institute for Cancer Immunotherapy, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
- Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, MD 21231, USA
- Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
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7
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McMullen P, Qiao Q, Luozhong S, Cai L, Fang L, Shao Q, Jiang S. Motif-based zwitterionic peptides impact their structure and immunogenicity. Chem Sci 2022; 13:10961-10970. [PMID: 36320710 PMCID: PMC9491220 DOI: 10.1039/d2sc03519g] [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: 06/23/2022] [Accepted: 08/30/2022] [Indexed: 12/18/2022] Open
Abstract
The linkage of zwitterionic peptides containing alternating glutamic acid (E) and lysine (K) amino acids exhibits protective effects on protein drugs due to their high hydration capacity. Previously, short EK peptides covering the surface of a protein drug showed significant protective effects and low immunogenicity. However, for high-molecular-weight single-chain (HMWSC) zwitterionic peptides, the incorporation of structure-disrupting amino acids such as proline (P), serine (S), and glycine (G) is necessary to improve their protective ability. Herein, we first probe the immunogenicity of eight EK-containing motif-based peptides, six of which incorporate structure-disrupting amino acids P, S, and G, linked to keyhole limpet hemocyanin (KLH). These studies uncover two sequence motifs, EKS and EKG, which show uniquely higher immunogenicity, while the other motifs, especially those containing P, exhibit lower immunogenicity. Additionally, the structure and dynamics of these sequence motifs are computationally modeled by Rosetta protein predictions and molecular dynamics (MD) simulations to predict properties of higher and lower immunogenicity peptides. These simulations revealed peptides with higher immunogenicity, namely EKS and EKG, exhibit regions of charge imbalance. Then, HMWSC zwitterionic sequences were linked to a typical protein drug, interferon-alpha 2a (IFN), which showed consistent immunogenic behaviors. Finally, epitope mapping and alanine scanning experiments using the serum collected from mice injected with HMWSC sequences also implicated a link between charge imbalance and peptide immunogenicity. Structure breaking amino acids, P, S, and G, are incorporated into low immunogenic unstructured zwitterionic peptide fusion proteins. We find unique sequence motifs that exhibit charge balanced conformations and low immunogenicity.![]()
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Affiliation(s)
- Patrick McMullen
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Qi Qiao
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, 40506, USA
| | - Sijin Luozhong
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Lirong Cai
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, 40506, USA
| | - Liang Fang
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
| | - Qing Shao
- Department of Chemical and Materials Engineering, University of Kentucky, Lexington, KY, 40506, USA
| | - Shaoyi Jiang
- Department of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA
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8
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Innate Immunity Modulating Impurities and the Immunotoxicity of Nanobiotechnology-Based Drug Products. Molecules 2021; 26:molecules26237308. [PMID: 34885886 PMCID: PMC8658779 DOI: 10.3390/molecules26237308] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/19/2021] [Accepted: 11/24/2021] [Indexed: 12/19/2022] Open
Abstract
Innate immunity can be triggered by the presence of microbial antigens and other contaminants inadvertently introduced during the manufacture and purification of bionanopharmaceutical products. Activation of these innate immune responses, including cytokine secretion, complement, and immune cell activation, can result in unexpected and undesirable host immune responses. These innate modulators can also potentially stimulate the activation of adaptive immune responses, including the formation of anti-drug antibodies which can impact drug effectiveness. To prevent induction of these adverse responses, it is important to detect and quantify levels of these innate immunity modulating impurities (IIMIs) that may be present in drug products. However, while it is universally agreed that removal of IIMIs from drug products is crucial for patient safety and to prevent long-term immunogenicity, there is no single assay capable of directly detecting all potential IIMIs or indirectly quantifying downstream biomarkers. Additionally, there is a lack of agreement as to which of the many analytical assays currently employed should be standardized for general IIMI screening. Herein, we review the available literature to highlight cellular and molecular mechanisms underlying IIMI-mediated inflammation and its relevance to the safety and efficacy of pharmaceutical products. We further discuss methodologies used for direct and indirect IIMI identification and quantification.
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9
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Intrinsic physicochemical profile of marketed antibody-based biotherapeutics. Proc Natl Acad Sci U S A 2021; 118:2020577118. [PMID: 34504010 PMCID: PMC8449350 DOI: 10.1073/pnas.2020577118] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/03/2021] [Indexed: 01/28/2023] Open
Abstract
Successful biologic drug discovery and development involves finding functional as well as developable candidates. Once a candidate has been demonstrated to be functional, the next step is to determine whether it can be translated into a drug product. This requires that the candidate can withstand stresses encountered during manufacturing, shipping, and storage. Additionally, it must be safe, efficacious, and possess good pharmacology. In silico analyses of the variable regions of 77 marketed antibody-based biotherapeutics have revealed five nonredundant physicochemical descriptors. Distributions of these descriptors, observed for marketed biotherapeutics, can help prioritize a drug candidate for experimental testing at early discovery stages, guide engineering efforts to further optimize it, and help increase the productivity of biologic drug discovery and development. Feeding biopharma pipelines with biotherapeutic candidates that possess desirable developability profiles can help improve the productivity of biologic drug discovery and development. Here, we have derived an in silico profile by analyzing computed physicochemical descriptors for the variable regions (Fv) found in 77 marketed antibody-based biotherapeutics. Fv regions of these biotherapeutics demonstrate significant diversities in their germlines, complementarity determining region loop lengths, hydrophobicity, and charge distributions. Furthermore, an analysis of 24 physicochemical descriptors, calculated using homology-based molecular models, has yielded five nonredundant descriptors whose distributions represent stability, isoelectric point, and molecular surface characteristics of their Fv regions. Fv regions of candidates from our internal discovery campaigns, human next-generation sequencing repertoires, and those in clinical-stages (CST) were assessed for similarity with the physicochemical profile derived here. The Fv regions in 33% of CST antibodies show physicochemical properties that are dissimilar to currently marketed biotherapeutics. In comparison, physicochemical characteristics of ∼29% of the Fv regions in human antibodies and ∼27% of our internal hits deviated significantly from those of marketed biotherapeutics. The early availability of this information can help guide hit selection, lead identification, and optimization of biotherapeutic candidates. Insights from this work can also help support portfolio risk assessment, in-licensing, and biopharma collaborations.
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10
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Komar AA. A Code Within a Code: How Codons Fine-Tune Protein Folding in the Cell. BIOCHEMISTRY (MOSCOW) 2021; 86:976-991. [PMID: 34488574 DOI: 10.1134/s0006297921080083] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genetic code sets the correspondence between the sequence of a given nucleotide triplet in an mRNA molecule, called a codon, and the amino acid that is added to the growing polypeptide chain during protein synthesis. With four bases (A, G, U, and C), there are 64 possible triplet codons: 61 sense codons (encoding amino acids) and 3 nonsense codons (so-called, stop codons that define termination of translation). In most organisms, there are 20 common/standard amino acids used in protein synthesis; thus, the genetic code is redundant with most amino acids (with the exception of Met and Trp) are being encoded by more than one (synonymous) codon. Synonymous codons were initially presumed to have entirely equivalent functions, however, the finding that synonymous codons are not present at equal frequencies in mRNA suggested that the specific codon choice might have functional implications beyond coding for amino acid. Observation of nonequivalent use of codons in mRNAs implied a possibility of the existence of auxiliary information in the genetic code. Indeed, it has been found that genetic code contains several layers of such additional information and that synonymous codons are strategically placed within mRNAs to ensure a particular translation kinetics facilitating and fine-tuning co-translational protein folding in the cell via step-wise/sequential structuring of distinct regions of the polypeptide chain emerging from the ribosome at different points in time. This review summarizes key findings in the field that have identified the role of synonymous codons and their usage in protein folding in the cell.
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Affiliation(s)
- Anton A Komar
- Center for Gene Regulation in Health and Disease and Department of Biological, Geological and Environmental Sciences, Cleveland State University, Cleveland, OH 44115, USA. .,Department of Biochemistry and Center for RNA Science and Therapeutics, Case Western Reserve University, Cleveland, OH 44106, USA.,Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA.,DAPCEL, Inc., Cleveland, OH 44106, USA
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11
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Parikh CR, Ponnampalam JK, Seligmann G, Coelewij L, Pineda-Torra I, Jury EC, Ciurtin C. Impact of immunogenicity on clinical efficacy and toxicity profile of biologic agents used for treatment of inflammatory arthritis in children compared to adults. Ther Adv Musculoskelet Dis 2021; 13:1759720X211002685. [PMID: 34188697 PMCID: PMC8212384 DOI: 10.1177/1759720x211002685] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 02/12/2021] [Indexed: 12/15/2022] Open
Abstract
The treatment of inflammatory arthritis has been revolutionised by the
introduction of biologic treatments. Many biologic agents are currently licensed
for use in both paediatric and adult patients with inflammatory arthritis and
contribute to improved disease outcomes compared with the pre-biologic era.
However, immunogenicity to biologic agents, characterised by an immune reaction
leading to the production of anti-drug antibodies (ADAs), can negatively impact
the therapeutic efficacy of biologic drugs and induce side effects to treatment.
This review explores for the first time the impact of immunogenicity against all
licensed biologic treatments currently used in inflammatory arthritis across
age, and will examine any significant differences between ADA prevalence, titres
and timing of development, as well as ADA impact on therapeutic drug levels,
clinical efficacy and side effects between paediatric and adult patients. In
addition, we will investigate factors associated with differences in
immunogenicity across biologic agents used in inflammatory arthritis, and their
potential therapeutic implications.
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Affiliation(s)
- Chinar R Parikh
- Centre for Adolescent Rheumatology versus Arthritis, University College London, London, UK
| | - Jaya K Ponnampalam
- Centre for Adolescent Rheumatology versus Arthritis, University College London, London, UK
| | - George Seligmann
- Centre for Adolescent Rheumatology versus Arthritis, University College London, London, UK
| | - Leda Coelewij
- Centre for Rheumatology Research, University College London, London, UK
| | - Ines Pineda-Torra
- Centre for Cardiometabolic and Vascular Science, University College London, London, UK
| | - Elizabeth C Jury
- Centre for Rheumatology Research, University College London, London, UK
| | - Coziana Ciurtin
- Centre for Adolescent Rheumatology Versus Arthritis, University College London, 3rd Floor Central, 250 Euston Road, London NW1 2PG, UK
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12
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Patel V, Efimov A, Baker D, Kang AS. Immunogenicity of biologics used in the treatment of moderate to severe psoriasis. Hum Antibodies 2021; 29:171-178. [PMID: 34151782 DOI: 10.3233/hab-210447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The number of biologic drugs available for the treatment of psoriasis continue to expand. However, being biological proteins and thus potentially immunogenic, there is evidence that anti-drug-antibodies develop against the various therapeutic proteins currently being utilised. Although chimeric antibodies that contain elements of the parental rodent monoclonal antibodies are immunogenic, anti-drug antibodies occur even if the biologic is a fully human protein and these can impact on clinical efficacy and safety. However, there is a wide variation in the reported level of anti-drug-antibodies for the same and different treatments that is highlighting issues with various assays used in anti-drug antibody detection. Here we review the available data on the occurrence of anti-drug antibodies in people with psoriasis treated with biologic agents.
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Affiliation(s)
- Visha Patel
- Centre for Oral Immunobiology and Regenerative Medicine, Dental Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Alex Efimov
- Camstech Ltd, Campus Technology Hub, Daresbury Laboratory, Science and Technology Facilities Council, Sci-Tech Daresbury, Daresbury, UK
| | - David Baker
- Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Angray S Kang
- Centre for Oral Immunobiology and Regenerative Medicine, Dental Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK.,Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London, UK
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