1
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Novacek A, Ugaz B, Stephanopoulos N. Templating Peptide Chemistry with Nucleic Acids: Toward Artificial Ribosomes, Cell-Specific Therapeutics, and Novel Protein-Mimetic Architectures. Biomacromolecules 2024; 25:3865-3876. [PMID: 38860980 DOI: 10.1021/acs.biomac.4c00372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2024]
Abstract
In biology, nanomachines like the ribosome use nucleic acid templates to synthesize polymers in a sequence-specific, programmable fashion. Researchers have long been interested in using the programmable properties of nucleic acids to enhance chemical reactions via colocalization of reagents using complementary nucleic acid handles. In this review, we describe progress in using nucleic acid templates, handles, or splints to enhance the covalent coupling of peptides to other peptides or oligonucleotides. We discuss work in several areas: creating ribosome-mimetic systems, synthesizing bioactive peptides on DNA or RNA templates, linking peptides into longer molecules and bioactive antibody mimics, and scaffolding peptides to build protein-mimetic architectures. We close by highlighting the challenges that must be overcome in nucleic acid-templated peptide chemistry in two areas: making full-length, functional proteins from synthetic peptides and creating novel protein-mimetic architectures not possible through macromolecular folding alone.
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Affiliation(s)
- Alexandra Novacek
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85251, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe Arizona 85251, United States
| | - Bryan Ugaz
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85251, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe Arizona 85251, United States
| | - Nicholas Stephanopoulos
- School of Molecular Sciences, Arizona State University, Tempe, Arizona 85251, United States
- Biodesign Center for Molecular Design and Biomimetics, Arizona State University, Tempe Arizona 85251, United States
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2
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Yu M, Tang X, Li Z, Wang W, Wang S, Li M, Yu Q, Xie S, Zuo X, Chen C. High-throughput DNA synthesis for data storage. Chem Soc Rev 2024; 53:4463-4489. [PMID: 38498347 DOI: 10.1039/d3cs00469d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
With the explosion of digital world, the dramatically increasing data volume is expected to reach 175 ZB (1 ZB = 1012 GB) in 2025. Storing such huge global data would consume tons of resources. Fortunately, it has been found that the deoxyribonucleic acid (DNA) molecule is the most compact and durable information storage medium in the world so far. Its high coding density and long-term preservation properties make itself one of the best data storage carriers for the future. High-throughput DNA synthesis is a key technology for "DNA data storage", which encodes binary data stream (0/1) into quaternary long DNA sequences consisting of four bases (A/G/C/T). In this review, the workflow of DNA data storage and the basic methods of artificial DNA synthesis technology are outlined first. Then, the technical characteristics of different synthesis methods and the state-of-the-art of representative commercial companies, with a primary focus on silicon chip microarray-based synthesis and novel enzymatic DNA synthesis are presented. Finally, the recent status of DNA storage and new opportunities for future development in the field of high-throughput, large-scale DNA synthesis technology are summarized.
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Affiliation(s)
- Meng Yu
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Xiaohui Tang
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Zhenhua Li
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Weidong Wang
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Shaopeng Wang
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Min Li
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Qiuliyang Yu
- Shenzhen Key Laboratory for the Intelligent Microbial Manufacturing of Medicines, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, 518055, Shenzhen, China
| | - Sijia Xie
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 200127, Shanghai, China.
| | - Chang Chen
- Institute of Medical Chips, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, 200025, Shanghai, China.
- School of Microelectronics, Shanghai University, 201800, Shanghai, China
- Shanghai Industrial μTechnology Research Institute, 201800, Shanghai, China
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, 200050, Shanghai, China
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3
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Cao B, Zheng Y, Shao Q, Liu Z, Xie L, Zhao Y, Wang B, Zhang Q, Wei X. Efficient data reconstruction: The bottleneck of large-scale application of DNA storage. Cell Rep 2024; 43:113699. [PMID: 38517891 DOI: 10.1016/j.celrep.2024.113699] [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: 08/09/2023] [Revised: 11/15/2023] [Accepted: 01/05/2024] [Indexed: 03/24/2024] Open
Abstract
Over the past decade, the rapid development of DNA synthesis and sequencing technologies has enabled preliminary use of DNA molecules for digital data storage, overcoming the capacity and persistence bottlenecks of silicon-based storage media. DNA storage has now been fully accomplished in the laboratory through existing biotechnology, which again demonstrates the viability of carbon-based storage media. However, the high cost and latency of data reconstruction pose challenges that hinder the practical implementation of DNA storage beyond the laboratory. In this article, we review existing advanced DNA storage methods, analyze the characteristics and performance of biotechnological approaches at various stages of data writing and reading, and discuss potential factors influencing DNA storage from the perspective of data reconstruction.
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Affiliation(s)
- Ben Cao
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China; Centre for Frontier AI Research, Agency for Science, Technology, and Research (A(∗)STAR), 1 Fusionopolis Way, Singapore 138632, Singapore
| | - Yanfen Zheng
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China
| | - Qi Shao
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Zhenlu Liu
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Lei Xie
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Yunzhu Zhao
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Bin Wang
- Key Laboratory of Advanced Design and Intelligent Computing, Ministry of Education, School of Software Engineering, Dalian University, Xuefu Street, Dalian, Liaoning 116622, China
| | - Qiang Zhang
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China.
| | - Xiaopeng Wei
- School of Computer Science and Technology, Dalian University of Technology, Lingshui Street, Dalian, Liaoning 116024, China
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4
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Zhang G, Zhu TF. Mirror-image trypsin digestion and sequencing of D-proteins. Nat Chem 2024; 16:592-598. [PMID: 38238467 DOI: 10.1038/s41557-023-01411-x] [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: 02/21/2023] [Accepted: 11/28/2023] [Indexed: 04/07/2024]
Abstract
The development of mirror-image biology systems and related applications is hindered by the lack of effective methods to sequence mirror-image (D-) proteins. Although natural-chirality (L-) proteins can be sequenced by bottom-up liquid chromatography-tandem mass spectrometry (LC-MS/MS), the sequencing of long D-peptides and D-proteins with the same strategy requires digestion by a site-specific D-protease before mass analysis. Here we apply solid-phase peptide synthesis and native chemical ligation to chemically synthesize a mirror-image version of trypsin, a widely used protease for site-specific protein digestion. Using mirror-image trypsin digestion and LC-MS/MS, we sequence a mirror-image large subunit ribosomal protein (L25) and a mirror-image Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4), and distinguish between different mutants of D-Dpo4. We also perform writing and reading of digital information in a long D-peptide of 50 amino acids. Thus, mirror-image trypsin digestion in conjunction with LC-MS/MS may facilitate practical applications of D-peptides and D-proteins as potential therapeutic and informational tools.
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Affiliation(s)
- Guanwei Zhang
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- School of Life Sciences, New Cornerstone Science Laboratory, Research Center for Industries of the Future, Westlake University, Hangzhou, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China
| | - Ting F Zhu
- School of Life Sciences, New Cornerstone Science Laboratory, Research Center for Industries of the Future, Westlake University, Hangzhou, China.
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, China.
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5
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Qu A, Sun M, Xu L, Liu L, Guo L, Chen P, Wang Q, Du Z, Wu Z, Xu C, Kuang H. Chiral Nanomaterials for Cancer Vaccines. SMALL METHODS 2024; 8:e2301332. [PMID: 37997213 DOI: 10.1002/smtd.202301332] [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: 09/29/2023] [Revised: 11/01/2023] [Indexed: 11/25/2023]
Abstract
Chirality is a fundamental characteristic of living organisms and is commonly observed at the biomolecule, cellular, and tissue levels. Chiral nanomaterials play an irreplaceable role in nanomedicine and nanobiology because of their unique enantioselectivity with biological components. Here, research progress relating to chiral nanomaterials in the field of vaccines is reviewed, including antigen presenting systems, immune adjuvants, and cancer vaccines. First, the common synthesis methods are outlined for different types of chiral nanomaterials, as well as their chiral sources, optical properties, and potential biological applications. Then, the application of chiral nanomaterials are discussed in the field of vaccines with reference to the promotion of antigen presentation and activation of the immune system for tumor immunotherapy. Finally, the current obstacles and future research directions of chiral nanomaterials are revealed with regard to regulating the immune system.
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Affiliation(s)
- Aihua Qu
- International Joint Research Laboratory for Biointerface and Biodetection, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Maozhong Sun
- International Joint Research Laboratory for Biointerface and Biodetection, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Liguang Xu
- International Joint Research Laboratory for Biointerface and Biodetection, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Liqiang Liu
- International Joint Research Laboratory for Biointerface and Biodetection, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Lingling Guo
- International Joint Research Laboratory for Biointerface and Biodetection, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Panpan Chen
- International Joint Research Laboratory for Biointerface and Biodetection, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Qing Wang
- Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu, 214002, P. R. China
| | - Zhiyong Du
- Department of Neurosurgery, Jiangnan University Medical Center, Wuxi, Jiangsu, 214002, P. R. China
| | - Zhimeng Wu
- The Key Laboratory of Carbohydrate Chemistry & Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Chuanlai Xu
- International Joint Research Laboratory for Biointerface and Biodetection, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
| | - Hua Kuang
- International Joint Research Laboratory for Biointerface and Biodetection, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, Jiangsu, 214122, P. R. China
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6
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Callahan AJ, Gandhesiri S, Travaline TL, Reja RM, Lozano Salazar L, Hanna S, Lee YC, Li K, Tokareva OS, Swiecicki JM, Loas A, Verdine GL, McGee JH, Pentelute BL. Mirror-image ligand discovery enabled by single-shot fast-flow synthesis of D-proteins. Nat Commun 2024; 15:1813. [PMID: 38418820 PMCID: PMC10901774 DOI: 10.1038/s41467-024-45634-z] [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: 06/29/2023] [Accepted: 01/26/2024] [Indexed: 03/02/2024] Open
Abstract
Widespread adoption of mirror-image biological systems presents difficulties in accessing the requisite D-protein substrates. In particular, mirror-image phage display has the potential for high-throughput generation of biologically stable macrocyclic D-peptide binders with potentially unique recognition modes but is hindered by the individualized optimization required for D-protein chemical synthesis. We demonstrate a general mirror-image phage display pipeline that utilizes automated flow peptide synthesis to prepare D-proteins in a single run. With this approach, we prepare and characterize 12 D-proteins - almost one third of all reported D-proteins to date. With access to mirror-image protein targets, we describe the successful discovery of six macrocyclic D-peptide binders: three to the oncoprotein MDM2, and three to the E3 ubiquitin ligase CHIP. Reliable production of mirror-image proteins can unlock the full potential of D-peptide drug discovery and streamline the study of mirror-image biology more broadly.
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Affiliation(s)
- Alex J Callahan
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Satish Gandhesiri
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Tara L Travaline
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA
| | - Rahi M Reja
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Lia Lozano Salazar
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Stephanie Hanna
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Yen-Chun Lee
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Chemistry, National Cheng Kung University, No.1, University Road, Tainan City, 701, Taiwan
| | - Kunhua Li
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA
| | - Olena S Tokareva
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA
| | - Jean-Marie Swiecicki
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA
- Relay Therapeutics, Inc., 399 Binney Street, 2nd Floor, Cambridge, MA, 02139, USA
| | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Gregory L Verdine
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, 7 Divinity Avenue, Cambridge, MA, 02138, USA
- Department of Chemistry and Chemical Biology, Harvard University, 12 Oxford Street, Cambridge, MA, 02138, USA
- Department of Molecular and Cellular Biology, Harvard University, 52 Oxford Street, Cambridge, MA, 02138, USA
| | - John H McGee
- FOG Pharmaceuticals Inc., 30 Acorn Park Drive, Cambridge, MA, 02140, USA.
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, MA, 02142, USA.
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA, 02142, USA.
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7
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Wang S, Mao X, Wang F, Zuo X, Fan C. Data Storage Using DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307499. [PMID: 37800877 DOI: 10.1002/adma.202307499] [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: 07/27/2023] [Revised: 10/01/2023] [Indexed: 10/07/2023]
Abstract
The exponential growth of global data has outpaced the storage capacities of current technologies, necessitating innovative storage strategies. DNA, as a natural medium for preserving genetic information, has emerged as a highly promising candidate for next-generation storage medium. Storing data in DNA offers several advantages, including ultrahigh physical density and exceptional durability. Facilitated by significant advancements in various technologies, such as DNA synthesis, DNA sequencing, and DNA nanotechnology, remarkable progress has been made in the field of DNA data storage over the past decade. However, several challenges still need to be addressed to realize practical applications of DNA data storage. In this review, the processes and strategies of in vitro DNA data storage are first introduced, highlighting recent advancements. Next, a brief overview of in vivo DNA data storage is provided, with a focus on the various writing strategies developed to date. At last, the challenges encountered in each step of DNA data storage are summarized and promising techniques are discussed that hold great promise in overcoming these obstacles.
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Affiliation(s)
- Shaopeng Wang
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Xiuhai Mao
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
| | - Fei Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaolei Zuo
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
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8
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Brown SM, Mayer-Bacon C, Freeland S. Xeno Amino Acids: A Look into Biochemistry as We Do Not Know It. Life (Basel) 2023; 13:2281. [PMID: 38137883 PMCID: PMC10744825 DOI: 10.3390/life13122281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 11/18/2023] [Accepted: 11/20/2023] [Indexed: 12/24/2023] Open
Abstract
Would another origin of life resemble Earth's biochemical use of amino acids? Here, we review current knowledge at three levels: (1) Could other classes of chemical structure serve as building blocks for biopolymer structure and catalysis? Amino acids now seem both readily available to, and a plausible chemical attractor for, life as we do not know it. Amino acids thus remain important and tractable targets for astrobiological research. (2) If amino acids are used, would we expect the same L-alpha-structural subclass used by life? Despite numerous ideas, it is not clear why life favors L-enantiomers. It seems clearer, however, why life on Earth uses the shortest possible (alpha-) amino acid backbone, and why each carries only one side chain. However, assertions that other backbones are physicochemically impossible have relaxed into arguments that they are disadvantageous. (3) Would we expect a similar set of side chains to those within the genetic code? Many plausible alternatives exist. Furthermore, evidence exists for both evolutionary advantage and physicochemical constraint as explanatory factors for those encoded by life. Overall, as focus shifts from amino acids as a chemical class to specific side chains used by post-LUCA biology, the probable role of physicochemical constraint diminishes relative to that of biological evolution. Exciting opportunities now present themselves for laboratory work and computing to explore how changing the amino acid alphabet alters the universe of protein folds. Near-term milestones include: (a) expanding evidence about amino acids as attractors within chemical evolution; (b) extending characterization of other backbones relative to biological proteins; and (c) merging computing and laboratory explorations of structures and functions unlocked by xeno peptides.
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9
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Raza MH, Desai S, Aravamudhan S, Zadegan R. An outlook on the current challenges and opportunities in DNA data storage. Biotechnol Adv 2023; 66:108155. [PMID: 37068530 PMCID: PMC11060094 DOI: 10.1016/j.biotechadv.2023.108155] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 03/23/2023] [Accepted: 04/12/2023] [Indexed: 04/19/2023]
Abstract
Silicon is the gold standard for information storage systems. The exponential generation of digital information will exhaust the global supply of refined silicon. Therefore, investing in alternative information storage materials such as DNA has gained momentum. DNA as a memory material possesses several advantages over silicon-based data storage, including higher storage capacity, data retention, and lower operational energy. Routine DNA data storage approaches encode data into chemically synthesized nucleotide sequences. The scalability of DNA data storage depends on factors such as the cost and the generation of hazardous waste during DNA synthesis, latency of writing and reading, and limited rewriting capacity. Here, we review the current status of DNA data storage encoding, writing, storing, retrieving and reading, and discuss the technology's challenges and opportunities.
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Affiliation(s)
- Muhammad Hassan Raza
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, Greensboro, NC 27401, USA
| | - Salil Desai
- Department of Industrial & Systems Engineering, North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA; Center of Excellence in Product Design and Advanced Manufacturing (CEPDAM), North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA
| | - Shyam Aravamudhan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, Greensboro, NC 27401, USA; Center of Excellence in Product Design and Advanced Manufacturing (CEPDAM), North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA
| | - Reza Zadegan
- Department of Nanoengineering, Joint School of Nanoscience & Nanoengineering, Greensboro, NC 27401, USA; Center of Excellence in Product Design and Advanced Manufacturing (CEPDAM), North Carolina Agricultural & Technical State University, Greensboro, NC 27411, USA.
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10
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Zhang XE, Liu C, Dai J, Yuan Y, Gao C, Feng Y, Wu B, Wei P, You C, Wang X, Si T. Enabling technology and core theory of synthetic biology. SCIENCE CHINA. LIFE SCIENCES 2023; 66:1742-1785. [PMID: 36753021 PMCID: PMC9907219 DOI: 10.1007/s11427-022-2214-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 10/04/2022] [Indexed: 02/09/2023]
Abstract
Synthetic biology provides a new paradigm for life science research ("build to learn") and opens the future journey of biotechnology ("build to use"). Here, we discuss advances of various principles and technologies in the mainstream of the enabling technology of synthetic biology, including synthesis and assembly of a genome, DNA storage, gene editing, molecular evolution and de novo design of function proteins, cell and gene circuit engineering, cell-free synthetic biology, artificial intelligence (AI)-aided synthetic biology, as well as biofoundries. We also introduce the concept of quantitative synthetic biology, which is guiding synthetic biology towards increased accuracy and predictability or the real rational design. We conclude that synthetic biology will establish its disciplinary system with the iterative development of enabling technologies and the maturity of the core theory.
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Affiliation(s)
- Xian-En Zhang
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Chenli Liu
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Junbiao Dai
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Yingjin Yuan
- Frontiers Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072, China.
| | - Caixia Gao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Yan Feng
- State Key Laboratory of Microbial Metabolism, Shanghai Jiao Tong University, Shanghai, 200240, China.
| | - Bian Wu
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Ping Wei
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
| | - Chun You
- Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
| | - Xiaowo Wang
- Ministry of Education Key Laboratory of Bioinformatics; Center for Synthetic and Systems Biology; Bioinformatics Division, Beijing National Research Center for Information Science and Technology; Department of Automation, Tsinghua University, Beijing, 100084, China.
| | - Tong Si
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Shenzhen, 518055, China.
- Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
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11
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Kawamoto Y, Wu Y, Takahashi Y, Takakura Y. Development of nucleic acid medicines based on chemical technology. Adv Drug Deliv Rev 2023; 199:114872. [PMID: 37244354 DOI: 10.1016/j.addr.2023.114872] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/01/2023] [Accepted: 05/12/2023] [Indexed: 05/29/2023]
Abstract
Oligonucleotide-based therapeutics have attracted attention as an emerging modality that includes the modulation of genes and their binding proteins related to diseases, allowing us to take action on previously undruggable targets. Since the late 2010s, the number of oligonucleotide medicines approved for clinical uses has dramatically increased. Various chemistry-based technologies have been developed to improve the therapeutic properties of oligonucleotides, such as chemical modification, conjugation, and nanoparticle formation, which can increase nuclease resistance, enhance affinity and selectivity to target sites, suppress off-target effects, and improve pharmacokinetic properties. Similar strategies employing modified nucleobases and lipid nanoparticles have been used for developing coronavirus disease 2019 mRNA vaccines. In this review, we provide an overview of the development of chemistry-based technologies aimed at using nucleic acids for developing therapeutics over the past several decades, with a specific emphasis on the structural design and functionality of chemical modification strategies.
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Affiliation(s)
- Yusuke Kawamoto
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
| | - You Wu
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yuki Takahashi
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan
| | - Yoshinobu Takakura
- Department of Biopharmaceutics and Drug Metabolism, Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo, Kyoto 606-8501, Japan.
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12
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Saha A, Suga H, Brik A. Combining Chemical Protein Synthesis and Random Nonstandard Peptides Integrated Discovery for Modulating Biological Processes. Acc Chem Res 2023; 56:1953-1965. [PMID: 37312234 PMCID: PMC10357587 DOI: 10.1021/acs.accounts.3c00178] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Indexed: 06/15/2023]
Abstract
Chemical manipulation of naturally occurring peptides offers a convenient route for generating analogs to screen against different therapeutic targets. However, the limited success of the conventional chemical libraries has urged chemical biologists to adopt alternative methods such as phage and mRNA displays and create libraries of a large number of variants for the screening and selection of novel peptides. Messenger RNA (mRNA) display provides great advantages in terms of the library size and the straightforward recovery of the selected polypeptide sequences. Importantly, the integration of the flexible in vitro translation (FIT) system with the mRNA display provides the basis of the random nonstandard peptides integrated discovery (RaPID) approach for the introduction of diverse nonstandard motifs, such as unnatural side chains and backbone modifications. This platform allows the discovery of functionalized peptides with tight binding against virtually any protein of interest (POI) and therefore shows great potential in the pharmaceutical industry. However, this method has been limited to targets generated by recombinant expression, excluding its applications to uniquely modified proteins, particularly those with post-translational modifications.Chemical protein synthesis allows a wide range of changes to the protein's chemical composition to be performed, including side chain and backbone modifications and access to post-translationally modified proteins, which are often inaccessible or difficult to achieve via recombinant expression methods. Notably, d-proteins can be prepared via chemical synthesis, which has been used in mirror image phase display for the discovery of nonproteolytic d-peptide binders.Combining chemical protein synthesis with the RaPID system allows the production of a library of trillions of cyclic peptides and subsequent selection for novel cyclic peptide binders targeting a uniquely modified protein to assist in studying its unexplored biology and possibly the discovery of new drug candidates.Interestingly, the small post-translational modifier protein ubiquitin (Ub), with its various polymeric forms, regulates directly or indirectly many biochemical processes, e.g., proteasomal degradation, DNA damage repair, cell cycle regulation, etc. In this Account, we discuss combining the RaPID approach against various synthetic Ub chains for selecting effective and specific macrocyclic peptide binders. This offers an advancement in modulating central Ub pathways and provides opportunities in drug discovery areas associated with Ub signaling. We highlight experimental approaches and conceptual adaptations required to design and modulate the activity of Lys48- and Lys63-linked Ub chains by macrocyclic peptides. We also present the applications of these approaches to shed light on related biological activities and ultimately their activity against cancer. Finally, we contemplate future developments still pending in this exciting multidisciplinary field.
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Affiliation(s)
- Abhishek Saha
- Schulich
Faculty of Chemistry, Technion-Israel Institute
of Technology, Haifa 3200008, Israel
| | - Hiroaki Suga
- Department
of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo-ku, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan
| | - Ashraf Brik
- Schulich
Faculty of Chemistry, Technion-Israel Institute
of Technology, Haifa 3200008, Israel
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13
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Harrison K, Mackay AS, Kambanis L, Maxwell JWC, Payne RJ. Synthesis and applications of mirror-image proteins. Nat Rev Chem 2023; 7:383-404. [PMID: 37173596 DOI: 10.1038/s41570-023-00493-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/20/2023] [Indexed: 05/15/2023]
Abstract
The homochirality of biomolecules in nature, such as DNA, RNA, peptides and proteins, has played a critical role in establishing and sustaining life on Earth. This chiral bias has also given synthetic chemists the opportunity to generate molecules with inverted chirality, unlocking valuable new properties and applications. Advances in the field of chemical protein synthesis have underpinned the generation of numerous 'mirror-image' proteins (those comprised entirely of D-amino acids instead of canonical L-amino acids), which cannot be accessed using recombinant expression technologies. This Review seeks to highlight recent work on synthetic mirror-image proteins, with a focus on modern synthetic strategies that have been leveraged to access these complex biomolecules as well as their applications in protein crystallography, drug discovery and the creation of mirror-image life.
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Affiliation(s)
- Katriona Harrison
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Angus S Mackay
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Lucas Kambanis
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Joshua W C Maxwell
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Sydney, New South Wales, Australia.
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, New South Wales, Australia.
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14
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Gerecht K, Freund N, Liu W, Liu Y, Fürst MJLJ, Holliger P. The Expanded Central Dogma: Genome Resynthesis, Orthogonal Biosystems, Synthetic Genetics. Annu Rev Biophys 2023; 52:413-432. [PMID: 37159296 DOI: 10.1146/annurev-biophys-111622-091203] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Synthetic biology seeks to probe fundamental aspects of biological form and function by construction [i.e., (re)synthesis] rather than deconstruction (analysis). In this sense, biological sciences now follow the lead given by the chemical sciences. Synthesis can complement analytic studies but also allows novel approaches to answering fundamental biological questions and opens up vast opportunities for the exploitation of biological processes to provide solutions for global problems. In this review, we explore aspects of this synthesis paradigm as applied to the chemistry and function of nucleic acids in biological systems and beyond, specifically, in genome resynthesis, synthetic genetics (i.e., the expansion of the genetic alphabet, of the genetic code, and of the chemical make-up of genetic systems), and the elaboration of orthogonal biosystems and components.
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Affiliation(s)
- Karola Gerecht
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Niklas Freund
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Wei Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Yang Liu
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
| | - Maximilian J L J Fürst
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
- Current address: Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge, United Kingdom;
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15
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Xie XL, Qi JZ, Wan XC, Zhang SD, Zhang YN, Fang GM. Chemical Synthesis of Proteins Using an o-Nitrobenzyl Group as a Robust Temporary Protective Group for N-Terminal Cysteine Protection. Org Lett 2023; 25:3435-3439. [PMID: 37144961 DOI: 10.1021/acs.orglett.3c00998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
We report here a robust and practical strategy for chemical protein synthesis using an o-nitrobenzyl group as a temporary protective group for an N-terminal cysteine residue of intermediate hydrazide fragments. By reinvestigating the photoremoval of an o-nitrobenzyl group, we establish a robust and reliable strategy for its quantitative photodeprotection. The o-nitrobenzyl group is completely stable to oxidative NaNO2 treatment and has been applied to the convergent chemical synthesis of programmed death ligand 1 fragment, providing a practical avenue for hydrazide-based native chemical ligation.
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Affiliation(s)
- Xiao-Lei Xie
- School of Life Science, Institutes of Physical Science and Information Technology, Institute of Health Sciences, Anhui University, Hefei 230601, P.R. China
| | - Jing-Ze Qi
- School of Life Science, Institutes of Physical Science and Information Technology, Institute of Health Sciences, Anhui University, Hefei 230601, P.R. China
| | - Xiao-Cui Wan
- School of Life Science, Institutes of Physical Science and Information Technology, Institute of Health Sciences, Anhui University, Hefei 230601, P.R. China
| | - Suo-De Zhang
- Hefei KS-V Peptide Biological Technology Co., Ltd., Hefei 230031, P.R. China
| | - Yan-Ni Zhang
- School of Life Science, Institutes of Physical Science and Information Technology, Institute of Health Sciences, Anhui University, Hefei 230601, P.R. China
| | - Ge-Min Fang
- School of Life Science, Institutes of Physical Science and Information Technology, Institute of Health Sciences, Anhui University, Hefei 230601, P.R. China
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16
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Liu L, Xiong M, Rong Q, Zhang M, Zhang X. Nucleic acid sensors in vivo: challenges and opportunities. VIEW 2023. [DOI: 10.1002/viw.20220064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/31/2023] Open
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17
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Harel O, Jbara M. Chemical Synthesis of Bioactive Proteins. Angew Chem Int Ed Engl 2023; 62:e202217716. [PMID: 36661212 DOI: 10.1002/anie.202217716] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 01/21/2023]
Abstract
Nature has developed a plethora of protein machinery to operate and maintain nearly every task of cellular life. These processes are tightly regulated via post-expression modifications-transformations that modulate intracellular protein synthesis, folding, and activation. Methods to prepare homogeneously and precisely modified proteins are essential to probe their function and design new bioactive modalities. Synthetic chemistry has contributed remarkably to protein science by allowing the preparation of novel biomacromolecules that are often challenging or impractical to prepare via common biological means. The ability to chemically build and precisely modify proteins has enabled the production of new molecules with novel physicochemical properties and programmed activity for biomedical research, diagnostic, and therapeutic applications. This minireview summarizes recent developments in chemical protein synthesis to produce bioactive proteins, with emphasis on novel analogs with promising in vitro and in vivo activity.
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Affiliation(s)
- Omer Harel
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Muhammad Jbara
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, 69978, Israel
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18
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Saebi A, Brown JS, Marando VM, Hartrampf N, Chumbler NM, Hanna S, Poskus M, Loas A, Kiessling LL, Hung DT, Pentelute BL. Rapid Single-Shot Synthesis of the 214 Amino Acid-Long N-Terminal Domain of Pyocin S2. ACS Chem Biol 2023; 18:518-527. [PMID: 36821521 PMCID: PMC10460144 DOI: 10.1021/acschembio.2c00862] [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: 02/24/2023]
Abstract
The impermeable outer membrane of Pseudomonas aeruginosa is bypassed by antibacterial proteins known as S-type pyocins. Because of their properties, pyocins are investigated as a potential new class of antimicrobials against Pseudomonas infections. Their production and modification, however, remain challenging. To address this limitation, we employed automated fast-flow peptide synthesis for the rapid production of a pyocin S2 import domain. The N-terminal domain sequence (PyS2NTD) was synthesized in under 10 h and purified to yield milligram quantities of the desired product. To our knowledge, the 214 amino acid sequence of PyS2NTD is among the longest peptides produced from a "single-shot" synthesis, i.e., made in a single stepwise route without the use of ligation techniques. Biophysical characterization of the PyS2NTD with circular dichroism was consistent with the literature reports. Fluorescently labeled PyS2NTD binds to P. aeruginosa expressing the cognate ferripyoverdine receptor and is taken up into the periplasm. This selective uptake was validated with confocal and super resolution microscopy, flow cytometry, and fluorescence recovery after photobleaching. These modified, synthetic S-type pyocin domains can be used to probe import mechanisms of P. aeruginosa and leveraged to develop selective antimicrobial agents that bypass the outer membrane.
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Affiliation(s)
- Azin Saebi
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Joseph S Brown
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Victoria M Marando
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nina Hartrampf
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Nicole M Chumbler
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Stephanie Hanna
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Mackenzie Poskus
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Laura L Kiessling
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Deborah T Hung
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, United States
- Department of Molecular Biology and Center for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts 02114, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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19
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Lander AJ, Jin Y, Luk LYP. D-Peptide and D-Protein Technology: Recent Advances, Challenges, and Opportunities. Chembiochem 2023; 24:e202200537. [PMID: 36278392 PMCID: PMC10805118 DOI: 10.1002/cbic.202200537] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 10/23/2022] [Indexed: 11/08/2022]
Abstract
Total chemical protein synthesis provides access to entire D-protein enantiomers enabling unique applications in molecular biology, structural biology, and bioactive compound discovery. Key enzymes involved in the central dogma of molecular biology have been prepared in their D-enantiomeric forms facilitating the development of mirror-image life. Crystallization of a racemic mixture of L- and D-protein enantiomers provides access to high-resolution X-ray structures of polypeptides. Additionally, D-enantiomers of protein drug targets can be used in mirror-image phage display allowing discovery of non-proteolytic D-peptide ligands as lead candidates. This review discusses the unique applications of D-proteins including the synthetic challenges and opportunities.
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Affiliation(s)
- Alexander J. Lander
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
| | - Yi Jin
- Manchester Institute of BiotechnologyThe University of ManchesterManchesterM1 7DNUK
| | - Louis Y. P. Luk
- School of ChemistryCardiff UniversityMain Building, Park PlaceCardiffCF10 3ATUK
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20
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Mao C, Wang S, Li J, Feng Z, Zhang T, Wang R, Fan C, Jiang X. Metal-Organic Frameworks in Microfluidics Enable Fast Encapsulation/Extraction of DNA for Automated and Integrated Data Storage. ACS NANO 2023; 17:2840-2850. [PMID: 36728704 DOI: 10.1021/acsnano.2c11241] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
DNA as an exceptional data storage medium offers high information density. However, DNA storage requires specialized equipment and tightly controlled environments for storage. Fast encapsulation within minutes for enhanced DNA stability to do away with specialized equipment and fast DNA extraction remain a challenge. Here, we report a DNA microlibrary that can be encapsulated by metal-organic frameworks (MOFs) within 10 min and extracted (5 min) in a single microfluidic chip for automated and integrated DNA-based data storage. The DNA microlibrary@MOFs enhances the stability of data-encoded DNA against harsh environments. The encoded information can be read out perfectly after accelerated aging, equivalent to being readable after 10 years of storage at 25 °C, 50% relative humidity, and 10 000 lx sunlight radiation. Moreover, the library enables fast retrieval of target data via flow cytometry and can be reproduced after each access.
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Affiliation(s)
- Cuiping Mao
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Shuchen Wang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Jiankai Li
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Zhuowei Feng
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Tong Zhang
- Department of Electronic and Electrical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Rui Wang
- Department of Electronic and Electrical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
| | - Chunhai Fan
- Frontiers Science Center for Transformative Molecules, School of Chemistry and Chemical Engineering, Shanghai Jiao Tong University, No 800, DongChuan Road, Minhang District, Shanghai 200240, People's Republic of China
| | - Xingyu Jiang
- Guangdong Provincial Key Laboratory of Advanced Biomaterials, Shenzhen Key Laboratory of Smart Healthcare Engineering, Department of Biomedical Engineering, Southern University of Science and Technology, No 1088, Xueyuan Road, Nanshan District, Shenzhen, Guangdong 518055, People's Republic of China
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21
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Sharma K, Sharma KK, Sharma A, Jain R. Peptide-based drug discovery: Current status and recent advances. Drug Discov Today 2023; 28:103464. [PMID: 36481586 DOI: 10.1016/j.drudis.2022.103464] [Citation(s) in RCA: 38] [Impact Index Per Article: 38.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 11/28/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The progressive development of peptides from reaction vessels to life-saving drugs via rigorous preclinical and clinical assessments is fascinating. Peptide therapeutics have gained momentum with the evolution of techniques in peptide chemistry, such as microwave irradiation in solid- and solution-phase synthesis, ligation chemistry, recombinant synthesis, and amalgamation with synthetic tools, including metal catalysis. Diverse emerging technologies, such as DNA-encoded libraries (DELs) and display techniques, are changing the status quo in the discovery of peptide therapeutics. In this review, we analyzed US Food and Drug Administration (FDA)-approved peptide drugs and those in clinical trials, highlighting recent advances in peptide-based drug discovery.
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Affiliation(s)
- Komal Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Krishna K Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Anku Sharma
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India
| | - Rahul Jain
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Sector 67, S.A.S. Nagar, Punjab 160 062, India.
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22
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Xu Y, Zhu TF. Mirror-image T7 transcription of chirally inverted ribosomal and functional RNAs. Science 2022; 378:405-412. [DOI: 10.1126/science.abm0646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
To synthesize a chirally inverted ribosome with the goal of building mirror-image biology systems requires the preparation of kilobase-long mirror-image ribosomal RNAs that make up the structural and catalytic core and about two-thirds of the molecular mass of the mirror-image ribosome. Here, we chemically synthesized a 100-kilodalton mirror-image T7 RNA polymerase, which enabled efficient and faithful transcription of the full-length mirror-image 5
S
, 16
S
, and 23
S
ribosomal RNAs from enzymatically assembled long mirror-image genes. We further exploited the versatile mirror-image T7 transcription system for practical applications such as biostable mirror-image riboswitch sensor, long-term storage of unprotected kilobase-long
l
-RNA in water, and
l
-ribozyme–catalyzed
l
-RNA polymerization to serve as a model system for basic RNA research.
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Affiliation(s)
- Yuan Xu
- School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Tsinghua University, Beijing, China
- School of Life Sciences, Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Ting F. Zhu
- School of Life Sciences, Research Center for Industries of the Future, Westlake University, Hangzhou, Zhejiang, China
- Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
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23
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Guo C, Zhang LQ, Jiang W. Biodegrading plastics with a synthetic non-biodegradable enzyme. Chem 2022. [DOI: 10.1016/j.chempr.2022.09.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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24
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Li JZ, Dong LM, Zheng LL, Fu WL, Zhang JJ, Zhang L, Hu Q, Chen P, Gao ZF, Xia F. Molecular Visual Sensing, Boolean Logic Computing, and Data Security Using a Droplet-Based Superwetting Paradigm. ACS APPLIED MATERIALS & INTERFACES 2022; 14:40447-40459. [PMID: 36006781 DOI: 10.1021/acsami.2c11532] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Inspired by information processing and logic operations of life, many artificial biochemical systems have been designed for applications in molecular information processing. However, encoding the binary synergism between matter, energy, and information in a superwetting system remains challenging. Herein, a superwetting paradigm was proposed for multifunctional applications including molecular visual sensing and data security on a superhydrophobic surface. A Triton X-100-encapsulated gelatin (TeG) hydrogel was prepared and selectively decomposed by trypsin, releasing the surfactant to decrease the surface tension of a droplet. Integrating the droplet with the superhydrophobic surface, the superwetting behavior was utilized for visual detection and information encoding. Interestingly, the proposed TeG hydrogel can function as an artificial gelneuron for molecular-level logic computing, where the combination of matters (superhydrophobic surface, trypsin, and leupeptin) acts as inputs to interact with energy (liquid surface tension and solid surface energy) and information (binary character), resulting in superwettability transitions (droplet surface tension, contact angle, rolling angle, and bounce) as outputs. Impressively, the TeG gelneuron can be further developed as molecular-level double cryptographic steganography to encode, encrypt, and hide specific information (including the maze escape route and content of the classical literature) due to its programmability, stimuli responsive ability, and droplet concealment. This study will encourage the development of advanced molecular paradigms and their applications, such as superwetting visual sensing, molecular computing, interaction, and data security.
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Affiliation(s)
- Jin Ze Li
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Lu Ming Dong
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Lin Lin Zheng
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
| | - Wen Long Fu
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, P. R. China
| | - Jing Jing Zhang
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, P. R. China
| | - Lei Zhang
- Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L3G1, Canada
| | - Qiongzheng Hu
- School of Pharmaceutical Sciences, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, P. R. China
| | - Pu Chen
- Department of Chemical Engineering and Waterloo Institute for Nanotechnology, University of Waterloo, 200 University Avenue West, Waterloo, Ontario N2L3G1, Canada
| | - Zhong Feng Gao
- Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276005, P. R. China
- Advanced Materials Institute, Qilu University of Technology (Shandong Academy of Sciences), Jinan 250014, P. R. China
| | - Fan Xia
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, P. R. China
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25
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Abstract
![]()
There is a continuous demand to improve our
understanding of fundamental
processes that underlie human health and disease. Therefore, novel
strategies that can assist in these efforts are required. For example,
molecular biology and genetic approaches have revolutionized our understanding
of protein-mediated processes by facilitating their direct visualization
and analyses in living cells. Despite these developments, genetic
manipulation has limitations in controlling events that occur after
translation such as posttranslational modifications (PTMs), which
are imperative regulatory elements. As a result, developing new methods
to study PTMs in live cells is a major bottleneck in deciphering their
exact roles in the myriad cellular processes. Synthetic and
semisynthetic proteins are prepared by combining
solid phase peptide synthesis (SPPS) and chemoselective ligation approaches
with synthetic or recombinant peptides. Employing protein synthesis
allows chemists to incorporate natural and unnatural modifications
with virtually unlimited number of functional groups into the protein’s
sequence, such as PTMs and their mimics. In addition, synthetic proteins
can include additional elements such as fluorescent tags, reactive
groups, caged units, and enrichment handles. Therefore, harnessing
the power of chemical protein synthesis offers great opportunities
to study fundamental biological processes. Unfortunately, the
low cell permeability of proteins limits their
applications mainly to in vitro settings, excluding
live cell studies. As a result, chemical biologists have been attempting
to overcome these limitations by developing protein delivery methods
that would enable the study of custom-made proteins in a biological
context. Success with these strategies should enable accurate determination
of protein localization, degradation, folding, interactions, and involvement
in the assembly of membrane-less organelles formed by liquid–liquid
phase separation inside cells. Importantly, protein delivery approaches
are complementary to genetic manipulations, and combining these approaches
should pave the way to new discoveries. In this Account, we
describe recent developments in protein delivery
methods, with emphasis on those most compatible with synthetic proteins.
We highlight experimental approaches and conceptual adaptations required
to design and study synthetic proteins in live cells, with or without
genetic manipulation. In addition, we highlight the strength and weakness
of these approaches for both the delivery and the subsequent studies.
We also describe our endeavors to deliver synthetic proteins to cells
via cell penetrating peptides (CPPs) and multiplexed bead loading
(MBL), as showcases of the applications of these methods to shed light
on biological processes. Lastly, we contemplate other future applications
of synthetic proteins to answer questions that are currently unapproachable.
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Affiliation(s)
- Guy Mann
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Pradeep Sadhu
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
| | - Ashraf Brik
- Schulich Faculty of Chemistry, Technion-Israel Institute of Technology, Haifa 3200008, Israel
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26
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Posttranslational Chemical Mutagenesis Methods to Insert Posttranslational Modifications into Recombinant Proteins. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27144389. [PMID: 35889261 PMCID: PMC9316245 DOI: 10.3390/molecules27144389] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/27/2022] [Accepted: 07/06/2022] [Indexed: 11/17/2022]
Abstract
Posttranslational modifications (PTMs) dramatically expand the functional diversity of the proteome. The precise addition and removal of PTMs appears to modulate protein structure and function and control key regulatory processes in living systems. Deciphering how particular PTMs affect protein activity is a current frontier in biology and medicine. The large number of PTMs which can appear in several distinct positions, states, and combinations makes preparing such complex analogs using conventional biological and chemical tools challenging. Strategies to access homogeneous and precisely modified proteins with desired PTMs at selected sites and in feasible quantities are critical to interpreting their molecular code. Here, we summarize recent advances in posttranslational chemical mutagenesis and late-stage functionalization chemistry to transfer novel PTM mimicry into recombinant proteins with emphasis on novel transformations.
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27
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Zhang Y, Ren Y, Liu Y, Wang F, Zhang H, Liu K. Preservation and Encryption in DNA Digital Data Storage. Chempluschem 2022; 87:e202200183. [PMID: 35856827 DOI: 10.1002/cplu.202200183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 07/01/2022] [Indexed: 11/08/2022]
Abstract
The exponential growth of the total amount of global data presents a huge challenge to mainstream storage media. The emergence of molecular digital storage inspires the development of the new-generation higher-density digital data storage. In particular, DNA with high storage density, reproducibility, and long recoverable lifetime behaves the ideal representative of molecular digital storage media. With the development of DNA synthesis and sequencing technologies and the reduction of cost, DNA digital storage has attracted more and more attention and achieved significant breakthroughs. Herein, this Review briefly describes the workflow of DNA storage, and highlights the storage step of DNA digital data storage. Then, according to different information storage forms, the current DNA information encryption methods are emphatically expounded. Finally, the brief perspectives on the current challenges and optimizing proposals in DNA information preservation and encryption are presented.
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Affiliation(s)
- Yi Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Yubin Ren
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Yangyi Liu
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Fan Wang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
| | - Hongjie Zhang
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
| | - Kai Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, 130022, P. R. China
- Department of Chemistry, Tsinghua University, Beijing, 100084, P. R. China
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28
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Kulkarni SS, Watson EE, Maxwell JWC, Niederacher G, Johansen‐Leete J, Huhmann S, Mukherjee S, Norman AR, Kriegesmann J, Becker CFW, Payne RJ. Expressed Protein Selenoester Ligation. ANGEWANDTE CHEMIE (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 134:e202200163. [PMID: 38505698 PMCID: PMC10947028 DOI: 10.1002/ange.202200163] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Indexed: 03/21/2024]
Abstract
Herein, we describe the development and application of a novel expressed protein selenoester ligation (EPSL) methodology for the one-pot semi-synthesis of modified proteins. EPSL harnesses the rapid kinetics of ligation reactions between modified synthetic selenopeptides and protein aryl selenoesters (generated from expressed intein fusion precursors) followed by in situ chemoselective deselenization to afford target proteins at concentrations that preclude the use of traditional ligation methods. The utility of the EPSL technology is showcased through the efficient semi-synthesis of ubiquitinated polypeptides, lipidated analogues of the membrane-associated GTPase YPT6, and site-specifically phosphorylated variants of the oligomeric chaperone protein Hsp27 at high dilution.
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Affiliation(s)
- Sameer S. Kulkarni
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
| | - Emma E. Watson
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
| | - Joshua W. C. Maxwell
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
| | - Gerhard Niederacher
- Faculty of Chemistry, Institute of Biological ChemistryUniversity of ViennaViennaAustria
| | - Jason Johansen‐Leete
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
| | - Susanne Huhmann
- Faculty of Chemistry, Institute of Biological ChemistryUniversity of ViennaViennaAustria
| | - Somnath Mukherjee
- Faculty of Chemistry, Institute of Biological ChemistryUniversity of ViennaViennaAustria
| | - Alexander R. Norman
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
| | - Julia Kriegesmann
- Faculty of Chemistry, Institute of Biological ChemistryUniversity of ViennaViennaAustria
| | - Christian F. W. Becker
- Faculty of Chemistry, Institute of Biological ChemistryUniversity of ViennaViennaAustria
| | - Richard J. Payne
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein ScienceThe University of SydneySydneyNSW 2006Australia
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29
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Kulkarni SS, Watson EE, Maxwell JWC, Niederacher G, Johansen-Leete J, Huhmann S, Mukherjee S, Norman AR, Kriegesmann J, Becker CFW, Payne RJ. Expressed Protein Selenoester Ligation. Angew Chem Int Ed Engl 2022; 61:e202200163. [PMID: 35194928 PMCID: PMC9314092 DOI: 10.1002/anie.202200163] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Indexed: 12/23/2022]
Abstract
Herein, we describe the development and application of a novel expressed protein selenoester ligation (EPSL) methodology for the one‐pot semi‐synthesis of modified proteins. EPSL harnesses the rapid kinetics of ligation reactions between modified synthetic selenopeptides and protein aryl selenoesters (generated from expressed intein fusion precursors) followed by in situ chemoselective deselenization to afford target proteins at concentrations that preclude the use of traditional ligation methods. The utility of the EPSL technology is showcased through the efficient semi‐synthesis of ubiquitinated polypeptides, lipidated analogues of the membrane‐associated GTPase YPT6, and site‐specifically phosphorylated variants of the oligomeric chaperone protein Hsp27 at high dilution.
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Affiliation(s)
- Sameer S Kulkarni
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Emma E Watson
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Joshua W C Maxwell
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Gerhard Niederacher
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
| | - Jason Johansen-Leete
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Susanne Huhmann
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
| | - Somnath Mukherjee
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
| | - Alexander R Norman
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
| | - Julia Kriegesmann
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
| | - Christian F W Becker
- Faculty of Chemistry, Institute of Biological Chemistry, University of Vienna, Vienna, Austria
| | - Richard J Payne
- School of Chemistry and Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Sydney, NSW 2006, Australia
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30
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Bedding MJ, Kulkarni SS, Payne RJ. Diselenide-selenoester ligation in the chemical synthesis of proteins. Methods Enzymol 2022; 662:363-399. [PMID: 35101218 DOI: 10.1016/bs.mie.2021.10.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Peptides and proteins represent an important class of biomolecules responsible for a plethora of structural and functional roles in vivo. Following their translation on the ribosome, the majority of eukaryotic proteins are post-translationally modified, leading to a proteome that is much larger than the number of genes present in a given organism. In order to understand the functional role of a given protein modification, it is necessary to access peptides and proteins bearing homogeneous and site-specific modifications. Accordingly, there has been significant research effort centered on the development of peptide ligation methodologies for the chemical synthesis of modified proteins. In this chapter we outline the discovery and development of a contemporary methodology called the diselenide-selenoester ligation (DSL) that enables the rapid and efficient fusion of peptide fragments to generate synthetic proteins. The practical aspects of using DSL for the preparation of chemically modified peptides and proteins in the laboratory is described. In addition, recent advances in the application of the methodology are outlined, exemplified by the synthesis and biological evaluation of a number of complex protein targets.
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Affiliation(s)
- Max J Bedding
- School of Chemistry, The University of Sydney, Camperdown, NSW, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW, Australia
| | - Sameer S Kulkarni
- School of Chemistry, The University of Sydney, Camperdown, NSW, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW, Australia
| | - Richard J Payne
- School of Chemistry, The University of Sydney, Camperdown, NSW, Australia; Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW, Australia.
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31
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Schmidt N, Abendroth F, Vázquez O, Hantschel O. Synthesis of the l- and d-SH2 domain of the leukaemia oncogene Bcr-Abl. RSC Chem Biol 2022; 3:1008-1012. [PMID: 35975004 PMCID: PMC9347351 DOI: 10.1039/d2cb00108j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/01/2022] [Indexed: 11/29/2022] Open
Abstract
The d- and l-versions of the Bcr-Abl SH2 domain (12.7 kDa) were synthesized. Key optimizations included pseudoproline incorporation, N-terminal hydrophilic tail addition and mild N-acetoxy succinimide acetylation. Their folding and activity are as for the recombinant protein. Our results will enable engineering of mirror-image monobody antagonists of the central oncoprotein Bcr-Abl. The d- and l-versions of the Bcr-Abl SH2 domain (12.7 kDa) were synthesized successfully and show similar folding as compared to a recombinantly expressed version.![]()
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Affiliation(s)
- Nina Schmidt
- Institute of Physiological Chemistry, University of Marburg, 35032, Marburg, Germany
| | - Frank Abendroth
- Faculty of Chemistry, University of Marburg, 35032, Marburg, Germany
| | - Olalla Vázquez
- Faculty of Chemistry, University of Marburg, 35032, Marburg, Germany
- Center for Synthetic Microbiology (SYNMIKRO), University of Marburg, 35032, Marburg, Germany
| | - Oliver Hantschel
- Institute of Physiological Chemistry, University of Marburg, 35032, Marburg, Germany
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32
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Chen J, Chen M, Zhu TF. Directed evolution and selection of biostable L-DNA aptamers with a mirror-image DNA polymerase. Nat Biotechnol 2022; 40:1601-1609. [PMID: 35668324 PMCID: PMC9646512 DOI: 10.1038/s41587-022-01337-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 04/28/2022] [Indexed: 12/30/2022]
Abstract
Mirror-image aptamers made from chirally inverted nucleic acids are nuclease-resistant and exceptionally biostable, opening up opportunities for unique applications. However, the directed evolution and selection of mirror-image aptamers directly from large randomized L-DNA libraries has, to our knowledge, not been demonstrated previously. Here, we developed a 'mirror-image selection' scheme for the directed evolution and selection of biostable L-DNA aptamers with a mirror-image DNA polymerase. We performed iterative rounds of enrichment and mirror-image polymerase chain reaction (PCR) amplification of L-DNA sequences that bind native human thrombin, in conjunction with denaturing gradient gel electrophoresis (DGGE) to isolate individual aptamers and L-DNA sequencing-by-synthesis to determine their sequences. Based on the selected L-DNA aptamers, we designed biostable thrombin sensors and inhibitors, which remained functional in physiologically relevant nuclease-rich environments, even in the presence of human serum that rapidly degraded D-DNA aptamers. Mirror-image selection of biostable L-DNA aptamers directly from large randomized L-DNA libraries greatly expands the range of biomolecules that can be targeted, broadening their applications as biostable sensors, therapeutics and basic research tools.
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Affiliation(s)
- Ji Chen
- grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Mengyin Chen
- grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Ting F. Zhu
- grid.12527.330000 0001 0662 3178School of Life Sciences, Tsinghua-Peking Center for Life Sciences, Beijing Frontier Research Center for Biological Structure, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China ,grid.494629.40000 0004 8008 9315School of Life Sciences, Westlake University, Hangzhou, Zhejiang China ,grid.494629.40000 0004 8008 9315Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang China
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33
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Dantsu Y, Zhang Y, Zhang W. Advances in Therapeutic L-Nucleosides and L-Nucleic Acids with Unusual Handedness. Genes (Basel) 2021; 13:46. [PMID: 35052385 PMCID: PMC8774879 DOI: 10.3390/genes13010046] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 12/19/2022] Open
Abstract
Nucleic-acid-based small molecule and oligonucleotide therapies are attractive topics due to their potential for effective target of disease-related modules and specific control of disease gene expression. As the non-naturally occurring biomolecules, modified DNA/RNA nucleoside and oligonucleotide analogues composed of L-(deoxy)riboses, have been designed and applied as innovative therapeutics with superior plasma stability, weakened cytotoxicity, and inexistent immunogenicity. Although all the chiral centers in the backbone are mirror converted from the natural D-nucleic acids, L-nucleic acids are equipped with the same nucleobases (A, G, C and U or T), which are critical to maintain the programmability and form adaptable tertiary structures for target binding. The types of L-nucleic acid drugs are increasingly varied, from chemically modified nucleoside analogues that interact with pathogenic polymerases to nanoparticles containing hundreds of repeating L-nucleotides that circulate durably in vivo. This article mainly reviews three different aspects of L-nucleic acid therapies, including pharmacological L-nucleosides, Spiegelmers as specific target-binding aptamers, and L-nanostructures as effective drug-delivery devices.
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Affiliation(s)
- Yuliya Dantsu
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (Y.D.); (Y.Z.)
| | - Ying Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (Y.D.); (Y.Z.)
| | - Wen Zhang
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, 635 Barnhill Drive, Indianapolis, IN 46202, USA; (Y.D.); (Y.Z.)
- Melvin and Bren Simon Cancer Center, 535 Barnhill Drive, Indianapolis, IN 46202, USA
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34
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Freund N, Fürst MJLJ, Holliger P. New chemistries and enzymes for synthetic genetics. Curr Opin Biotechnol 2021; 74:129-136. [PMID: 34883451 DOI: 10.1016/j.copbio.2021.11.004] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/27/2021] [Accepted: 11/01/2021] [Indexed: 12/15/2022]
Abstract
Beyond the natural nucleic acids DNA and RNA, nucleic acid chemistry has unlocked a whole universe of modifications to their canonical chemical structure, which can in various ways modify and enhance nucleic acid function and utility for applications in biotechnology and medicine. Unlike the natural modifications of tRNA and rRNA or the epigenetic modifications in mRNA and genomic DNA, these altered chemistries are not found in nature and therefore these molecules are referred to as xeno-nucleic acids (XNAs). In this review we aim to focus specifically on recent progress in a subsection of this vast field-synthetic genetics-concerned with encoded synthesis, reverse transcription, and evolution of XNAs.
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Affiliation(s)
- Niklas Freund
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | | | - Philipp Holliger
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Francis Crick Avenue, Cambridge, CB2 0QH, UK.
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35
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Abstract
Informational macromolecules in biology are composed of subunits of a single handedness, d-nucleotides in nucleic acids and l-amino acids in proteins. Although this chiral uniformity may be expedient, it is not a chemical necessity, as demonstrated by the recent example of an RNA enzyme that catalyzes the RNA-templated polymerization of RNA molecules of the opposite handedness. This reaction, when carried out iteratively, can provide the basis for exponential amplification of RNA molecules and the information they contain. By carrying out thermal cycling, analogous to the polymerase chain reaction, and supplying oligonucleotide building blocks that comprise both the functional strand of RNA and its complement, cross-chiral exponential amplification was achieved. This process was used to amplify the l-RNA form of the hammerhead ribozyme, catalyzed by the d-RNA form of the polymerase. The resulting l-hammerhead exhibits the expected activity in cleaving a corresponding l-RNA substrate. Exponential amplification was also carried out within individual droplets of a water-in-oil emulsion. The ability to amplify enantio-RNAs, both in bulk solution and within compartments, provides a means to evolve cross-chiral RNA polymerases based on the function of the RNAs they produce.
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Affiliation(s)
- Grant A L Bare
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Gerald F Joyce
- The Salk Institute, 10010 North Torrey Pines Road, La Jolla, California 92037, United States
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36
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Dikici S, Yar M, Bullock AJ, Shepherd J, Roman S, MacNeil S. Developing Wound Dressings Using 2-deoxy- D-Ribose to Induce Angiogenesis as a Backdoor Route for Stimulating the Production of Vascular Endothelial Growth Factor. Int J Mol Sci 2021; 22:ijms222111437. [PMID: 34768868 PMCID: PMC8583821 DOI: 10.3390/ijms222111437] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/20/2021] [Accepted: 10/21/2021] [Indexed: 12/13/2022] Open
Abstract
2-deoxy-D-Ribose (2dDR) was first identified in 1930 in the structure of DNA and discovered as a degradation product of it later when the enzyme thymidine phosphorylase breaks down thymidine into thymine. In 2017, our research group explored the development of wound dressings based on the delivery of this sugar to induce angiogenesis in chronic wounds. In this review, we will survey the small volume of conflicting literature on this and related sugars, some of which are reported to be anti-angiogenic. We review the evidence of 2dDR having the ability to stimulate a range of pro-angiogenic activities in vitro and in a chick pro-angiogenic bioassay and to stimulate new blood vessel formation and wound healing in normal and diabetic rat models. The biological actions of 2dDR were found to be 80 to 100% as effective as VEGF in addition to upregulating the production of VEGF. We then demonstrated the uptake and delivery of the sugar from a range of experimental and commercial dressings. In conclusion, its pro-angiogenic properties combined with its improved stability on storage compared to VEGF, its low cost, and ease of incorporation into a range of established wound dressings make 2dDR an attractive alternative to VEGF for wound dressing development.
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Affiliation(s)
- Serkan Dikici
- Department of Bioengineering, Izmir Institute of Technology, 35430 Izmir, Turkey
- Department of Materials Science & Engineering, Kroto Research Institute, University of Sheffield, Sheffield S3 7HQ, UK; (A.J.B.); (S.R.)
- Correspondence: (S.D.); (S.M.)
| | - Muhammad Yar
- Interdisciplinary Research Centre in Biomedical Materials (IRCBM), COMSATS University Islamabad, Lahore Campus, Lahore 54000, Pakistan;
| | - Anthony J. Bullock
- Department of Materials Science & Engineering, Kroto Research Institute, University of Sheffield, Sheffield S3 7HQ, UK; (A.J.B.); (S.R.)
| | - Joanna Shepherd
- School of Clinical Dentistry, University of Sheffield, Sheffield S10 2TA, UK;
| | - Sabiniano Roman
- Department of Materials Science & Engineering, Kroto Research Institute, University of Sheffield, Sheffield S3 7HQ, UK; (A.J.B.); (S.R.)
| | - Sheila MacNeil
- Department of Materials Science & Engineering, Kroto Research Institute, University of Sheffield, Sheffield S3 7HQ, UK; (A.J.B.); (S.R.)
- Correspondence: (S.D.); (S.M.)
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37
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Erickson PW, Fulcher JM, Spaltenstein P, Kay MS. Traceless Click-Assisted Native Chemical Ligation Enabled by Protecting Dibenzocyclooctyne from Acid-Mediated Rearrangement with Copper(I). Bioconjug Chem 2021; 32:2233-2244. [PMID: 34619957 DOI: 10.1021/acs.bioconjchem.1c00403] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The scope of proteins accessible to total chemical synthesis via native chemical ligation (NCL) is often limited by slow ligation kinetics. Here we describe Click-Assisted NCL (CAN), in which peptides are incorporated with traceless "helping hand" lysine linkers that enable addition of dibenzocyclooctyne (DBCO) and azide handles. The resulting strain-promoted alkyne-azide cycloaddition (SPAAC) increases their effective concentration to greatly accelerate ligations. We demonstrate that copper(I) protects DBCO from acid-mediated rearrangement during acidic peptide cleavage, enabling direct production of DBCO synthetic peptides. Excitingly, triazole-linked model peptides ligated rapidly and accumulated little side product due to the fast reaction time. Using the E. coli ribosomal subunit L32 as a model protein, we further demonstrate that SPAAC, ligation, desulfurization, and linker cleavage steps can be performed in one pot. CAN is a useful method for overcoming challenging ligations involving sterically hindered junctions. Additionally, CAN is anticipated to be an important stepping stone toward a multisegment, one-pot, templated ligation system.
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Affiliation(s)
- Patrick W Erickson
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112, United States.,Institute for Protein Design, Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - James M Fulcher
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112, United States.,Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Paul Spaltenstein
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112, United States
| | - Michael S Kay
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, Utah 84112, United States
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38
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Wade JD, Jones JH. The life and work of Robert (Bob) C. Sheppard. J Pept Sci 2021; 28:e3369. [PMID: 34611959 DOI: 10.1002/psc.3369] [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: 08/24/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022]
Abstract
The life and work of Robert Charles Sheppard (1932-2019), Bob Sheppard informally among friends, is outlined. He was a leading pioneer of solid phase peptide synthesis and made the most significant and fundamental European contribution to the art of peptide synthesis since Emil Fischer.
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Affiliation(s)
- John D Wade
- Florey Institute of Neuroscience and Mental Health, Peptide and Protein Chemistry, The University of Melbourne, Parkville, Victoria, Australia.,School of Chemistry, University of Melbourne, Melbourne, Victoria, Australia
| | - John H Jones
- Balliol College, University of Oxford, Oxford, UK
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