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Son A, Park J, Kim W, Lee W, Yoon Y, Ji J, Kim H. Integrating Computational Design and Experimental Approaches for Next-Generation Biologics. Biomolecules 2024; 14:1073. [PMID: 39334841 PMCID: PMC11430650 DOI: 10.3390/biom14091073] [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: 07/23/2024] [Revised: 08/13/2024] [Accepted: 08/26/2024] [Indexed: 09/30/2024] Open
Abstract
Therapeutic protein engineering has revolutionized medicine by enabling the development of highly specific and potent treatments for a wide range of diseases. This review examines recent advances in computational and experimental approaches for engineering improved protein therapeutics. Key areas of focus include antibody engineering, enzyme replacement therapies, and cytokine-based drugs. Computational methods like structure-based design, machine learning integration, and protein language models have dramatically enhanced our ability to predict protein properties and guide engineering efforts. Experimental techniques such as directed evolution and rational design approaches continue to evolve, with high-throughput methods accelerating the discovery process. Applications of these methods have led to breakthroughs in affinity maturation, bispecific antibodies, enzyme stability enhancement, and the development of conditionally active cytokines. Emerging approaches like intracellular protein delivery, stimulus-responsive proteins, and de novo designed therapeutic proteins offer exciting new possibilities. However, challenges remain in predicting in vivo behavior, scalable manufacturing, immunogenicity mitigation, and targeted delivery. Addressing these challenges will require continued integration of computational and experimental methods, as well as a deeper understanding of protein behavior in complex physiological environments. As the field advances, we can anticipate increasingly sophisticated and effective protein therapeutics for treating human diseases.
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Affiliation(s)
- Ahrum Son
- Department of Molecular Medicine, Scripps Research, La Jolla, CA 92037, USA;
| | - Jongham Park
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (J.P.); (W.K.); (W.L.); (Y.Y.)
| | - Woojin Kim
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (J.P.); (W.K.); (W.L.); (Y.Y.)
| | - Wonseok Lee
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (J.P.); (W.K.); (W.L.); (Y.Y.)
| | - Yoonki Yoon
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (J.P.); (W.K.); (W.L.); (Y.Y.)
| | - Jaeho Ji
- Department of Convergent Bioscience and Informatics, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea;
| | - Hyunsoo Kim
- Department of Bio-AI Convergence, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea; (J.P.); (W.K.); (W.L.); (Y.Y.)
- Department of Convergent Bioscience and Informatics, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea;
- Protein AI Design Institute, Chungnam National University, 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
- SCICS (Sciences for Panomics), 99 Daehak-ro, Yuseong-gu, Daejeon 34134, Republic of Korea
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Mariconti M, Dechamboux L, Heckmann M, Gros J, Morel M, Escriou V, Baigl D, Hoffmann C, Rudiuk S. Intracellular Delivery of Functional Proteins with DNA-Protein Nanogels-Lipids Complex. J Am Chem Soc 2024; 146:5118-5127. [PMID: 38363821 PMCID: PMC10910493 DOI: 10.1021/jacs.3c08000] [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: 07/25/2023] [Revised: 01/29/2024] [Accepted: 01/30/2024] [Indexed: 02/18/2024]
Abstract
Using functional proteins for therapeutic purposes due to their high selectivity and/or catalytic properties can enable the control of various cellular processes; however, the transport of active proteins inside living cells remains a major challenge. In contrast, intracellular delivery of nucleic acids has become a routine method for a number of applications in gene therapy, genome editing, or immunization. Here we report a functionalizable platform constituting of DNA-protein nanogel carriers cross-linked through streptavidin-biotin or streptactin-biotin interactions and demonstrate its applicability for intracellular delivery of active proteins. We show that the nanogels can be loaded with proteins bearing either biotin, streptavidin, or strep-tag, and the resulting functionalized nanogels can be delivered into living cells after complexation with cationic lipid vectors. We use this approach for delivery of alkaline phosphatase enzyme, which is shown to keep its catalytic activity after internalization by mouse melanoma B16 cells, as demonstrated by the DDAO-phosphate assay. The resulting functionalized nanogels have dimensions on the order of 100 nm, contain around 100 enzyme molecules, and are shown to be transfectable at low lipid concentrations (charge ratio R± = 0.75). This ensures the low toxicity of our system, which in combination with high local enzyme concentration (∼100 μM) underlines potential interest of this nanoplatform for biomedical applications.
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Affiliation(s)
- Marina Mariconti
- PASTEUR,
UMR8640, Department of Chemistry, PSL University,
Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005 France
| | | | - Marion Heckmann
- Université
Paris Cité, CNRS, INSERM, UTCBS, Paris 75006, France
| | - Julien Gros
- PASTEUR,
UMR8640, Department of Chemistry, PSL University,
Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005 France
| | - Mathieu Morel
- PASTEUR,
UMR8640, Department of Chemistry, PSL University,
Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005 France
| | | | - Damien Baigl
- PASTEUR,
UMR8640, Department of Chemistry, PSL University,
Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005 France
| | - Céline Hoffmann
- Université
Paris Cité, CNRS, INSERM, UTCBS, Paris 75006, France
| | - Sergii Rudiuk
- PASTEUR,
UMR8640, Department of Chemistry, PSL University,
Sorbonne Université, CNRS, Ecole Normale Supérieure, Paris 75005 France
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Abstract
Introduction: Prodrugs have been used to improve the selectivity and efficacy of cancer therapy by targeting unique abnormal markers that are overexpressed by cancer cells and are absent in normal tissues. In this context, different strategies have been exploited and new ones are being developed each year. Areas covered: In this review, an integrated view of the potential use of prodrugs in targeted cancer therapy is provided. Passive and active strategies are discussed in light of the advantages of each one and some successful examples are provided, as well as the clinical status of several prodrugs. Among them, antibody-drug conjugates (ADCs) are the most commonly used. However, several drawbacks, including limited prodrug uptake, poor pharmacokinetics, immunogenicity problems, difficulties in selective targeting and gene expression, and optimized bystander effects limit their clinical applications. Expert opinion: Despite the efforts of different companies and research groups, several drawbacks, such as the lack of relevant in vivo models, complexity of the human metabolism, and economic limitations, have hampered the development of new prodrugs for targeted cancer therapy. As a result, we believe that the combination of prodrugs with cancer nanotechnology and other newly developed approaches, such as aptamer-conjugated nanomaterials, are efficient strategies.
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Affiliation(s)
- Carla Souza
- a Center of Nanotechnology and Tissue Engineering, Department of Chemistry , School of Philosophy, Sciences and Letters of Ribeirão Preto- USP , Ribeirão Preto , Brazil
| | - Diogo Silva Pellosi
- b Department of Chemistry, Laboratory of Hybrid Materials , Federal University of São Paulo - UNIFESP , Diadema , Brazil
| | - Antonio Claudio Tedesco
- a Center of Nanotechnology and Tissue Engineering, Department of Chemistry , School of Philosophy, Sciences and Letters of Ribeirão Preto- USP , Ribeirão Preto , Brazil
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Drug Discovery by Molecular Imaging and Monitoring Therapy Response in Lymphoma. Int J Mol Sci 2017; 18:ijms18081639. [PMID: 28749424 PMCID: PMC5578029 DOI: 10.3390/ijms18081639] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/23/2017] [Accepted: 07/23/2017] [Indexed: 12/12/2022] Open
Abstract
Molecular imaging allows a noninvasive assessment of biochemical and biological processes in living subjects. Treatment strategies for malignant lymphoma depend on histology and tumor stage. For the last two decades, molecular imaging has been the mainstay diagnostic test for the staging of malignant lymphoma and the assessment of response to treatment. This technology enhances our understanding of disease and drug activity during preclinical and clinical drug development. Here, we review molecular imaging applications in drug development, with an emphasis on oncology. Monitoring and assessing the efficacy of anti-cancer therapies in preclinical or clinical models are essential and the multimodal molecular imaging approach may represent a new stage for pharmacologic development in cancer. Monitoring the progress of lymphoma therapy with imaging modalities will help patients. Identifying and addressing key challenges is essential for successful integration of molecular imaging into the drug development process. In this review, we highlight the general usefulness of molecular imaging in drug development and radionuclide-based reporter genes. Further, we discuss the different molecular imaging modalities for lymphoma therapy and their preclinical and clinical applications.
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Progress and problems with the use of suicide genes for targeted cancer therapy. Adv Drug Deliv Rev 2016; 99:113-128. [PMID: 26004498 DOI: 10.1016/j.addr.2015.05.009] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Revised: 02/19/2015] [Accepted: 05/14/2015] [Indexed: 12/16/2022]
Abstract
Among various gene therapy methods for cancer, suicide gene therapy attracts a special attention because it allows selective conversion of non-toxic compounds into cytotoxic drugs inside cancer cells. As a result, therapeutic index can be increased significantly by introducing high concentrations of cytotoxic molecules to the tumor environment while minimizing impact on normal tissues. Despite significant success at the preclinical level, no cancer suicide gene therapy protocol has delivered the desirable clinical significance yet. This review gives a critical look at the six main enzyme/prodrug systems that are used in suicide gene therapy of cancer and familiarizes readers with the state-of-the-art research and practices in this field. For each enzyme/prodrug system, the mechanisms of action, protein engineering strategies to enhance enzyme stability/affinity and chemical modification techniques to increase prodrug kinetics and potency are discussed. In each category, major clinical trials that have been performed in the past decade with each enzyme/prodrug system are discussed to highlight the progress to date. Finally, shortcomings are underlined and areas that need improvement in order to produce clinical significance are delineated.
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Jamin Y, Eykyn TR, Poon E, Springer CJ, Robinson SP. Detection of the prodrug-activating enzyme carboxypeptidase G2 activity with chemical exchange saturation transfer magnetic resonance. Mol Imaging Biol 2014; 16:152-7. [PMID: 23955100 PMCID: PMC4298162 DOI: 10.1007/s11307-013-0680-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
PURPOSE The purpose of this study is to evaluate if the differential exchange rates with bulk water between amine and amide protons can be exploited using chemical exchange saturation transfer magnetic resonance (CEST-MR) to monitor the release of glutamate induced by carboxypeptidase G2 (CPG2), an enzyme utilized in cancer gene therapy. PROCEDURES Z spectra of solutions of the CPG2 substrate, 3,5-difluorobenzoyl-L-glutamate (amide), and glutamate (amine) were acquired at 11.7 T, 37 °C, across different pH (5-8). The ability of CEST-MR to monitor CPG2-mediated release of glutamate was assessed in extracts of CPG2-expressing cancer cells and purified solution of CPG2. RESULTS The addition of CPG2 to a solution containing 3,5-difluorobenzoyl-L-glutamate led to a marked and progressively increasing CEST effect (+3 ppm), concomitant with the time-dependent release of glutamate induced by CPG2. CONCLUSION CEST-MR allows the detection of CPG2 activity in vitro and supports the translation of CEST-MRI to assess CPG2-based gene therapy in vivo.
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Affiliation(s)
- Yann Jamin
- Cancer Research UK and EPRSC Cancer Imaging Centre, Division of Radiotherapy and Imaging, The Institute of Cancer Research and Royal Marsden NHS Foundation Trust, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK,
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