1
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Krishna Sudhakar H, Yau JTK, Alcock LJ, Lau YH. Accessing diverse bicyclic peptide conformations using 1,2,3-TBMB as a linker. Org Biomol Chem 2024. [PMID: 39007293 DOI: 10.1039/d4ob00901k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Bicyclic peptides are a powerful modality for engaging challenging drug targets such as protein-protein interactions. Here, we use 1,2,3-tris(bromomethyl)benzene (1,2,3-TBMB) to access bicyclic peptides with diverse conformations that differ from conventional bicyclisation products formed with 1,3,5-TBMB. Bicyclisation at cysteine residues under aqueous buffer conditions proceeds efficiently, with broad substrate scope, compatibility with high-throughput screening, and clean conversion (>90%) for 96 of the 115 peptides tested. We envisage that the 1,2,3-TBMB linker will be applicable to a variety of peptide screening techniques in drug discovery.
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Affiliation(s)
| | - Jackie Tsz Ki Yau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia.
| | - Lisa J Alcock
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia.
| | - Yu Heng Lau
- School of Chemistry, The University of Sydney, Camperdown, NSW 2006, Australia.
- ARC Centre of Excellence for Innovations in Peptide and Protein Science, The University of Sydney, Camperdown, NSW 2006, Australia.
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2
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Xu X, Xu C, He W, Wei L, Li H, Zhou J, Zhang R, Wang Y, Xiong Y, Gao X. HELM-GPT: de novo macrocyclic peptide design using generative pre-trained transformer. Bioinformatics 2024; 40:btae364. [PMID: 38867692 PMCID: PMC11256930 DOI: 10.1093/bioinformatics/btae364] [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: 03/22/2024] [Revised: 05/08/2024] [Accepted: 06/10/2024] [Indexed: 06/14/2024] Open
Abstract
MOTIVATION Macrocyclic peptides hold great promise as therapeutics targeting intracellular proteins. This stems from their remarkable ability to bind flat protein surfaces with high affinity and specificity while potentially traversing the cell membrane. Research has already explored their use in developing inhibitors for intracellular proteins, such as KRAS, a well-known driver in various cancers. However, computational approaches for de novo macrocyclic peptide design remain largely unexplored. RESULTS Here, we introduce HELM-GPT, a novel method that combines the strength of the hierarchical editing language for macromolecules (HELM) representation and generative pre-trained transformer (GPT) for de novo macrocyclic peptide design. Through reinforcement learning (RL), our experiments demonstrate that HELM-GPT has the ability to generate valid macrocyclic peptides and optimize their properties. Furthermore, we introduce a contrastive preference loss during the RL process, further enhanced the optimization performance. Finally, to co-optimize peptide permeability and KRAS binding affinity, we propose a step-by-step optimization strategy, demonstrating its effectiveness in generating molecules fulfilling both criteria. In conclusion, the HELM-GPT method can be used to identify novel macrocyclic peptides to target intracellular proteins. AVAILABILITY AND IMPLEMENTATION The code and data of HELM-GPT are freely available on GitHub (https://github.com/charlesxu90/helm-gpt).
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Affiliation(s)
- Xiaopeng Xu
- Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia
| | - Chencheng Xu
- Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia
| | - Wenjia He
- Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia
| | - Lesong Wei
- Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia
| | - Haoyang Li
- Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia
| | - Juexiao Zhou
- Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia
| | | | - Yu Wang
- Syneron Technology, Guangzhou 510000, China
| | | | - Xin Gao
- Computer Science Program, Computer, Electrical and Mathematical Science and Engineering (CEMSE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Makkah, Kingdom of Saudi Arabia
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3
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Ye XW, Tian W, Han L, Li YJ, Liu S, Lai WJ, Liu YX, Wang L, Yang PP, Wang H. High-Throughput Screening of pH-Dependent β-sheet Self-Assembling Peptide. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2307963. [PMID: 38183362 DOI: 10.1002/smll.202307963] [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: 09/11/2023] [Revised: 12/20/2023] [Indexed: 01/08/2024]
Abstract
pH-dependent peptide biomaterials hold tremendous potential for cell delivery and tissue engineering. However, identification of responsive self-assembling sequences with specified secondary structure remains a challenge. In this work, An experimental procedure based on the one-bead one-compound (OBOC) combinatorial library is developed to rapidly screen self-assembling β-sheet peptides at neutral aqueous solution (pH 7.5) and disassemble at weak acidic condition (pH 6.5). Using the hydrophobic fluorescent molecule thioflavin T (ThT) as a probe, resin beads displaying self-assembling peptides show fluorescence under pH 7.5 due to the insertion of ThT into the hydrophobic domain, and are further cultured in pH 6.5 solution. The beads with extinguished fluorescence are selected. Three heptapeptides are identified that can self-assemble into nanofibers or nanoparticles at pH 7.5 and disassemble at pH 6.5. P1 (LVEFRHY) shows a rapid acid response and morphology transformation with pH modulation. Changes in the charges of histidine and hydrophobic phenyl motif of phenylalanine may play important roles in the formation of pH-responsive β-sheet nanofiber. This high-throughput screening method provides an efficient way to identify pH-dependent β-sheet self-assembling peptide and gain insights into structural design of such nanomaterials.
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Affiliation(s)
- Xin-Wei Ye
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- China Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, 100049, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wen Tian
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Lu Han
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Yi-Jing Li
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Shan Liu
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Wen-Jia Lai
- Division of Nanotechnology Development, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Yi-Xuan Liu
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Lei Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Pei-Pei Yang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
| | - Hao Wang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology (NCNST), No. 11 Beiyitiao, Zhongguancun, Beijing, 100190, China
- China Sino-Danish College, Sino-Danish Center for Education and Research, University of Chinese Academy of Sciences, Beijing, 100049, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences Institution, Beijing, 100049, China
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4
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Abstract
Cyclic peptides are fascinating molecules abundantly found in nature and exploited as molecular format for drug development as well as other applications, ranging from research tools to food additives. Advances in peptide technologies made over many years through improved methods for synthesis and drug development have resulted in a steady stream of new drugs, with an average of around one cyclic peptide drug approved per year. Powerful technologies for screening random peptide libraries, and de novo generating ligands, have enabled the development of cyclic peptide drugs independent of naturally derived molecules and now offer virtually unlimited development opportunities. In this review, we feature therapeutically relevant cyclic peptides derived from nature and discuss the unique properties of cyclic peptides, the enormous technological advances in peptide ligand development in recent years, and current challenges and opportunities for developing cyclic peptides that address unmet medical needs.
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Affiliation(s)
- Xinjian Ji
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Alexander L Nielsen
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, School of Basic Sciences, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
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5
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Pepanian A, Binbay FA, Roy S, Nubbemeyer B, Koley A, Rhodes CA, Ammer H, Pei D, Ghosh P, Imhof D. Bicyclic Peptide Library Screening for the Identification of Gαi Protein Modulators. J Med Chem 2023; 66:12396-12406. [PMID: 37587416 PMCID: PMC11000586 DOI: 10.1021/acs.jmedchem.3c00873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/18/2023]
Abstract
Noncanonical G protein activation and inactivation, particularly for the Gαi/s protein subfamilies, have long been a focus of chemical research. Combinatorial libraries were already effectively applied to identify modulators of the guanine-nucleotide exchange, as can be exemplified with peptides such as KB-752 and GPM-1c/d, the so-called guanine-nucleotide exchange modulators. In this study, we identified novel bicyclic peptides from a combinatorial library screening that show prominent properties as molecular switch-on/off modulators of Gαi signaling. Among the series of hits, the exceptional paradigm of GPM-3, a protein and state-specific bicyclic peptide, is the first chemically identified GAP (GTPase-activating protein) modulator with a high binding affinity for Gαi protein. Computational analyses identified and assessed the structure of the bicyclic peptides, novel ligand-protein interaction sites, and their subsequent impact on the nucleotide binding site. This approach can therefore lead the way for the development of efficient chemical biological probes targeting Gαi protein modulation within a cellular context.
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Affiliation(s)
- Anna Pepanian
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Furkan Ayberk Binbay
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Suchismita Roy
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Britta Nubbemeyer
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
| | - Amritendu Koley
- Department of Chemistry and Biochemistry, The Ohio State University, 578 Biological Sciences Building, 484 W 12th Avenue, Columbus, OH 43210, USA
| | - Curran A. Rhodes
- Department of Chemistry and Biochemistry, The Ohio State University, 578 Biological Sciences Building, 484 W 12th Avenue, Columbus, OH 43210, USA
| | - Hermann Ammer
- Institute of Pharmacology Toxicology and Pharmacy, Veterinary Faculty, Ludwig Maximilian University of Munich, Königinstr. 16, 80539 Munich, Germany
| | - Dehua Pei
- Department of Chemistry and Biochemistry, The Ohio State University, 578 Biological Sciences Building, 484 W 12th Avenue, Columbus, OH 43210, USA
| | - Pradipta Ghosh
- Department of Cellular and Molecular Medicine, University of California at San Diego, La Jolla, CA 92093, USA
- Department of Medicine, University of California San Diego, La Jolla, CA 92093
| | - Diana Imhof
- Pharmaceutical Biochemistry and Bioanalytics, Pharmaceutical Institute, University of Bonn, An der Immenburg 4, 53121 Bonn, Germany
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6
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Zhang Y, Guo J, Cheng J, Zhang Z, Kang F, Wu X, Chu Q. High-Throughput Screening of Stapled Helical Peptides in Drug Discovery. J Med Chem 2023; 66:95-106. [PMID: 36580278 DOI: 10.1021/acs.jmedchem.2c01541] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Therapeutic peptides have revolutionized treatment for a number of human diseases. In particular, the past two decades have witnessed rapid progress of stapled helical peptides in drug discovery. Stapled helical peptides are chemically modified and constrained in their bioactive α-helical conformation. Compared to unstabilized linear peptides, stapled helical peptides exhibit superior binding affinity and selectivity, enhanced membrane permeability, and improved metabolic stability, presenting exciting promise for targeting otherwise challenging protein-protein interfaces. In this Perspective, we summarize recent applications of high-throughput screening technologies for identification of potent stapled helical peptides with optimized binding properties. We expect to provide a broad reference to accelerate the development of stapled helical peptides as the next generation of therapeutic peptides for various human diseases.
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Affiliation(s)
- Yiwei Zhang
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiabei Guo
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Jiongjia Cheng
- Key Laboratory of Advanced Functional Materials of Nanjing, Nanjing Xiaozhuang University, Nanjing 211171, China
| | - Zhenghua Zhang
- Department of Chemistry, School of Science, China Pharmaceutical University, Nanjing 211198, China
| | - Fenghua Kang
- Xiangya School of Pharmaceutical Sciences, Central South University, Changsha 410013, China
| | - Xiaoxing Wu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China
| | - Qian Chu
- Department of Medicinal Chemistry, School of Pharmacy, China Pharmaceutical University, Nanjing 211198, China.,Jiangsu Key Laboratory of Drug Design and Optimization, China Pharmaceutical University, Nanjing 210009, China
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7
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Hampton JT, Lalonde TJ, Tharp JM, Kurra Y, Alugubelli YR, Roundy CM, Hamer GL, Xu S, Liu WR. Novel Regioselective Approach to Cyclize Phage-Displayed Peptides in Combination with Epitope-Directed Selection to Identify a Potent Neutralizing Macrocyclic Peptide for SARS-CoV-2. ACS Chem Biol 2022; 17:2911-2922. [PMID: 36174018 PMCID: PMC9528030 DOI: 10.1021/acschembio.2c00565] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 09/19/2022] [Indexed: 01/20/2023]
Abstract
Using the regioselective cyanobenzothiazole condensation reaction with an N-terminal cysteine and the chloroacetamide reaction with an internal cysteine, a phage-displayed macrocyclic 12-mer peptide library was constructed and subsequently validated. Using this library in combination with iterative selections against two epitopes from the receptor binding domain (RBD) of the novel severe acute respiratory syndrome virus 2 (SARS-CoV-2) Spike protein, macrocyclic peptides that strongly inhibit the interaction between the Spike RBD and angiotensin-converting enzyme 2 (ACE2), the human host receptor of SARS-CoV-2, were identified. The two epitopes were used instead of the Spike RBD to avoid selection of nonproductive macrocyclic peptides that bind RBD but do not directly inhibit its interactions with ACE2. Antiviral tests against SARS-CoV-2 showed that one macrocyclic peptide is highly potent against viral reproduction in Vero E6 cells with an EC50 value of 3.1 μM. The AlphaLISA-detected IC50 value for this macrocyclic peptide was 0.3 μM. The current study demonstrates that two kinetically controlled reactions toward N-terminal and internal cysteines, respectively, are highly effective in the construction of phage-displayed macrocyclic peptides, and the selection based on the SARS-CoV-2 Spike epitopes is a promising methodology in the identification of peptidyl antivirals.
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Affiliation(s)
- J. Trae Hampton
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Tyler J. Lalonde
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Jeffery M. Tharp
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Yadagiri Kurra
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Yugendar R. Alugubelli
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | | | - Gabriel L. Hamer
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Shiqing Xu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
| | - Wenshe Ray Liu
- Texas A&M Drug Discovery Laboratory, Department of Chemistry, Texas A&M University, College Station, TX 77843, USA
- Institute of Biosciences and Technology and Department of Translational Medical Sciences, College of Medicine, Texas A&M University, Houston, TX 77030, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
- Department of Molecular and Cellular Medicine, College of Medicine, Texas A&M University, College Station, TX 77843, USA
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8
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Experimental spectroscopic investigations, solute-solvent interactions, topological analysis and biological evaluations of N-(9-Fluorenylmethoxycarbonyloxy)succinimide: An effective agent in anti-breast cancer activity. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.119756] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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9
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Development of PVA/Chitosan-g-Poly (N-vinyl imidazole)/TiO2/curcumin nanofibers as high-performance wound dressing. Carbohydr Polym 2022; 296:119956. [DOI: 10.1016/j.carbpol.2022.119956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Revised: 07/28/2022] [Accepted: 08/02/2022] [Indexed: 12/29/2022]
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10
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Habeshian S, Merz ML, Sangouard G, Mothukuri GK, Schüttel M, Bognár Z, Díaz-Perlas C, Vesin J, Bortoli Chapalay J, Turcatti G, Cendron L, Angelini A, Heinis C. Synthesis and direct assay of large macrocycle diversities by combinatorial late-stage modification at picomole scale. Nat Commun 2022; 13:3823. [PMID: 35780129 PMCID: PMC9250534 DOI: 10.1038/s41467-022-31428-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 06/17/2022] [Indexed: 11/29/2022] Open
Abstract
Macrocycles have excellent potential as therapeutics due to their ability to bind challenging targets. However, generating macrocycles against new targets is hindered by a lack of large macrocycle libraries for high-throughput screening. To overcome this, we herein established a combinatorial approach by tethering a myriad of chemical fragments to peripheral groups of structurally diverse macrocyclic scaffolds in a combinatorial fashion, all at a picomole scale in nanoliter volumes using acoustic droplet ejection technology. In a proof-of-concept, we generate a target-tailored library of 19,968 macrocycles by conjugating 104 carboxylic-acid fragments to 192 macrocyclic scaffolds. The high reaction efficiency and small number of side products of the acylation reactions allowed direct assay without purification and thus a large throughput. In screens, we identify nanomolar inhibitors against thrombin (Ki = 44 ± 1 nM) and the MDM2:p53 protein-protein interaction (Kd MDM2 = 43 ± 18 nM). The increased efficiency of macrocycle synthesis and screening and general applicability of this approach unlocks possibilities for generating leads against any protein target. Macrocycles have potential as therapeutics, but their libraries are currently not large enough for high-throughput screening. Here, the authors show a combinatorial approach to generate a library of almost 20’000 macrocycles by conjugating carboxylic-acid fragments to macrocyclic scaffolds, identifying nanomolar inhibitors against thrombin and binders of MDM2.
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Affiliation(s)
- Sevan Habeshian
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Manuel Leonardo Merz
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Gontran Sangouard
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Ganesh Kumar Mothukuri
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Mischa Schüttel
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Zsolt Bognár
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Cristina Díaz-Perlas
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland
| | - Jonathan Vesin
- Biomolecular Screening Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Julien Bortoli Chapalay
- Biomolecular Screening Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gerardo Turcatti
- Biomolecular Screening Facility, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Laura Cendron
- Department of Biology, University of Padova, 35131, Padova, Italy
| | - Alessandro Angelini
- Department of Molecular Sciences and Nanosystems, Ca' Foscari University of Venice, Via Torino 155, Venezia Mestre, Venice, 30172, Italy.,European Centre for Living Technologies (ECLT), Ca' Bottacin, Dorsoduro 3911, Calle Crosera, Venice, 30124, Italy
| | - Christian Heinis
- Institute of Chemical Sciences and Engineering, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015, Lausanne, Switzerland.
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11
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Delivoria DC, Skretas G. The Discovery of Peptide Macrocycle Rescuers of Pathogenic Protein Misfolding and Aggregation by Integrating SICLOPPS Technology and Ultrahigh-Throughput Screening in Bacteria. Methods Mol Biol 2022; 2371:215-246. [PMID: 34596851 DOI: 10.1007/978-1-0716-1689-5_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The phenomenon of protein misfolding and aggregation has been widely associated with numerous human diseases, such as Alzheimer's disease, systemic amyloidosis and type 2 diabetes, the vast majority of which remain incurable. To advance early stage drug discovery against these diseases, investigation of molecular libraries with expanded diversities and ultrahigh-throughput screening methodologies that allow deeper investigation of chemical space are urgently required. Toward this, we describe how Escherichia coli can be engineered so as to enable (1) the production of expanded combinatorial libraries of short, drug-like, head-to-tail cyclic peptides and (2) their simultaneous functional screening for identifying effective inhibitors of protein misfolding and aggregation using a genetic assay that links protein folding and misfolding to cell fluorescence. In this manner, cyclic peptides with the ability to inhibit pathogenic protein misfolding and/or aggregation can be readily selected by flow cytometric cell sorting in an ultrahigh-throughput fashion. This biotechnological approach accelerates significantly the identification of hit/lead molecules with potentially therapeutic properties against devastating diseases.
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Affiliation(s)
- Dafni C Delivoria
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece.
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12
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Gu Y, Iannuzzelli JA, Fasan R. MOrPH-PhD: A Phage Display System for the Functional Selection of Genetically Encoded Macrocyclic Peptides. Methods Mol Biol 2022; 2371:261-286. [PMID: 34596853 PMCID: PMC8493807 DOI: 10.1007/978-1-0716-1689-5_14] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Macrocyclic peptides represent promising scaffolds for targeting biomolecules with high affinity and selectivity, making methods for the diversification and functional selection of these macrocycles highly valuable for drug discovery purposes. We recently reported a novel phage display platform (called MOrPH-PhD) for the creation and functional exploration of combinatorial libraries of genetically encoded cyclic peptides. In this system, spontaneous, posttranslational peptide cyclization by means of a cysteine-reactive non-canonical amino acid is integrated with M13 bacteriophage display, enabling the creation of genetically encoded macrocyclic peptide libraries displayed on phage particles. Using this system, it is possible to rapidly generate and screen large libraries of phage-displayed macrocyclic peptides (up to 108 to 1010 members) in order to identify high-affinity binders of a target protein of interest. Herein, we describe step-by-step protocols for the production of MOrPH-PhD libraries, the screening of these libraries against an immobilized protein target, and the isolation and characterization of functional macrocyclic peptides from these genetically encoded libraries.
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Affiliation(s)
- Yu Gu
- Department of Chemistry, University of Rochester, Rochester, NY, USA
| | | | - Rudi Fasan
- Department of Chemistry, University of Rochester, Rochester, NY, USA.
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13
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Preparation of Bacterial Cell-Surface Displayed Semisynthetic Cyclic Peptides. Methods Mol Biol 2021. [PMID: 34596850 DOI: 10.1007/978-1-0716-1689-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Semisynthetic cyclic peptides bearing both non-proteinogenic and genetically encoded amino acids are excellent ligands for peptide-based drug discovery. While semisynthesis expands the chemical space, genetic encoding allows access to a large library via randomization at the nucleic acid level. Selection of novel binders of such macrocyclic ligands requires linking their genotype to phenotype. In this chapter, we report a bacterial cell-surface display system to present cyclic peptides composed of synthetic and genetically encoded fragments. The synthetic fragment along with the split intein partner and an aminooxy moiety is ligated and cyclized with the recombinant backbone containing an unnatural amino acid by protein trans-splicing and intramolecular oxime ligation, respectively. A pH-shift protocol was applied to accelerate on surface cyclization. This method will enable generation of semisynthetic cyclic peptide libraries and their selection by fluorescence-activated cell sorting.
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14
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Goto Y, Suga H. The RaPID Platform for the Discovery of Pseudo-Natural Macrocyclic Peptides. Acc Chem Res 2021; 54:3604-3617. [PMID: 34505781 DOI: 10.1021/acs.accounts.1c00391] [Citation(s) in RCA: 75] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Although macrocyclic peptides bearing exotic building blocks have proven their utility as pharmaceuticals, the sources of macrocyclic peptide drugs have been largely limited to mimetics of native peptides or natural product peptides. However, the recent emergence of technologies for discovering de novo bioactive peptides has led to their reconceptualization as a promising therapeutic modality. For the construction and screening of libraries of such macrocyclic peptides, our group has devised a platform to conduct affinity-based selection of massive libraries (>1012 unique sequences) of in vitro expressed macrocyclic peptides, which is referred to as the random nonstandard peptides integrated discovery (RaPID) system. The RaPID system integrates genetic code reprogramming using the FIT (flexible in vitro translation) system, which is largely facilitated by flexizymes (flexible tRNA-aminoacylating ribozymes), with mRNA display technology.We have demonstrated that the RaPID system enables rapid discovery of various de novo pseudo-natural peptide ligands for protein targets of interest. Many examples discussed in this Account prove that thioether-closed macrocyclic peptides (teMPs) obtained by the RaPID system generally exhibit remarkably high affinity and specificity, thereby potently inhibiting or activating a specific function(s) of the target. Moreover, such teMPs are used for a wide range of biochemical applications, for example, as crystallization chaperones for intractable transmembrane proteins and for in vivo recognition of specific cell types. Furthermore, recent studies demonstrate that some teMPs exhibit pharmacological activities in animal models and that even intracellular proteins can be inhibited by teMPs, illustrating the potential of this class of peptides as drug leads.Besides the ring-closing thioether linkage in the teMPs, genetic code reprogramming by the FIT system allows for incorporation of a variety of other exotic building blocks. For instance, diverse nonproteinogenic amino acids, hydroxy acids (ester linkage), amino carbothioic acid (thioamide linkage), and abiotic foldamer units have been successfully incorporated into ribosomally synthesized peptides. Despite such enormous successes in the conventional FIT system, multiple or consecutive incorporation of highly exotic amino acids, such as d- and β-amino acids, is yet challenging, and particularly the synthesis of peptides bearing non-carbonyl backbone structures remains a demanding task. To upgrade the RaPID system to the next generation, we have engaged in intensive manipulation of the FIT system to expand the structural diversity of peptides accessible by our in vitro biosynthesis strategy. Semilogical engineering of tRNA body sequences led to a new suppressor tRNA (tRNAPro1E2) capable of effectively recruiting translation factors, particularly EF-Tu and EF-P. The use of tRNAPro1E2 in the FIT system allows for not only single but also consecutive and multiple elongation of exotic amino acids, such as d-, β-, and γ-amino acids as well as aminobenzoic acids. Moreover, the integration of the FIT system with various chemical or enzymatic posttranslational modifications enables us to expand the range of accessible backbone structures to non-carbonyl moieties prominent in natural products and peptidomimetics. In such systems, FIT-expressed peptides undergo multistep backbone conversions in a one-pot manner to yield designer peptides composed of modified backbones such as azolines, azoles, and ring-closing pyridines. Our current research endeavors focus on applying such in vitro biosynthesis systems for the discovery of bioactive de novo pseudo-natural products.
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Affiliation(s)
- Yuki Goto
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
| | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Bunkyo, Tokyo 113-0033, Japan
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15
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Vu QN, Young R, Sudhakar HK, Gao T, Huang T, Tan YS, Lau YH. Cyclisation strategies for stabilising peptides with irregular conformations. RSC Med Chem 2021; 12:887-901. [PMID: 34263169 PMCID: PMC8230030 DOI: 10.1039/d1md00098e] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 04/12/2021] [Indexed: 11/21/2022] Open
Abstract
Cyclisation is a common synthetic strategy for enhancing the therapeutic potential of peptide-based molecules. While there are extensive studies on peptide cyclisation for reinforcing regular secondary structures such as α-helices and β-sheets, there are remarkably few reports of cyclising peptides which adopt irregular conformations in their bioactive target-bound state. In this review, we highlight examples where cyclisation techniques have been successful in stabilising irregular conformations, then discuss how the design of cyclic constraints for irregularly structured peptides can be informed by existing β-strand stabilisation approaches, new computational design techniques, and structural principles extracted from cyclic peptide library screening hits. Through this analysis, we demonstrate how existing peptide cyclisation techniques can be adapted to address the synthetic design challenge of stabilising irregularly structured binding motifs.
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Affiliation(s)
- Quynh Ngoc Vu
- School of Chemistry, Eastern Ave, The University of Sydney NSW 2006 Australia
| | - Reginald Young
- School of Chemistry, Eastern Ave, The University of Sydney NSW 2006 Australia
| | | | - Tianyi Gao
- School of Chemistry, Eastern Ave, The University of Sydney NSW 2006 Australia
| | - Tiancheng Huang
- School of Chemistry, Eastern Ave, The University of Sydney NSW 2006 Australia
| | - Yaw Sing Tan
- Bioinformatics Institute, Agency for Science, Technology and Research (ASTAR) 30 Biopolis Street, #07-01, Matrix Singapore 138671 Singapore
| | - Yu Heng Lau
- School of Chemistry, Eastern Ave, The University of Sydney NSW 2006 Australia
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16
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Wu Y, Williams J, Calder EDD, Walport LJ. Strategies to expand peptide functionality through hybridisation with a small molecule component. RSC Chem Biol 2021; 2:151-165. [PMID: 34458778 PMCID: PMC8341444 DOI: 10.1039/d0cb00167h] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 11/09/2020] [Indexed: 02/04/2023] Open
Abstract
Combining different compound classes gives molecular hybrids that can offer access to novel chemical space and unique properties. Peptides provide ideal starting points for such molecular hybrids, which can be easily modified with a variety of molecular entities. The addition of small molecules can improve the potency, stability and cell permeability of therapeutically relevant peptides. Furthermore, they are often applied to create peptide-based tools in chemical biology. In this review, we discuss general methods that allow the discovery of this compound class and highlight key examples of peptide-small molecule hybrids categorised by the application and function of the small molecule entity.
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Affiliation(s)
- Yuteng Wu
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Jack Williams
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Ewen D D Calder
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
| | - Louise J Walport
- Protein-Protein Interaction Laboratory, The Francis Crick Institute London UK
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London London UK
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17
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Zane D, Feldman PL, Sawyer T, Sobol Z, Hawes J. Development and Regulatory Challenges for Peptide Therapeutics. Int J Toxicol 2020; 40:108-124. [PMID: 33327828 DOI: 10.1177/1091581820977846] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
There has been an increased interest in and activity for the use of peptide therapeutics to treat a variety of human diseases. The number of peptide drugs entering clinical development and the market has increased significantly over the past decade despite inherent challenges of peptide therapeutic discovery, development, and patient-friendly delivery. Disparities in interpretation and application of existing regulatory guidances to innovative synthetic and conjugated peptide assets have resulted in challenges for both regulators and sponsors. The Symposium on Development and Regulatory Challenges for Peptide Therapeutics at the 40th Annual Meeting of the American College of Toxicology held in November of 2019 focused on the following specific topics: (1) peptide therapeutic progress and future directions, and approaches to discover, optimize, assess, and deliver combination peptide therapeutics for treatment of diseases; (2) toxicological considerations to advance peptide drug-device combination products for efficient development and optimal patient benefit and adherence; (3) industry and regulatory perspectives on the regulation of synthetic and conjugated peptide products, including exploration of regulatory classifications, interpretations, and application of the existing guidances International Council for Harmonisation (ICH) M3(R2) and ICH S6(R1) in determining nonclinical study recommendations; and (4) presentation of the 2016 Health and Environmental Sciences Institute's Genetic Toxicology Technical Committee working group assessment of genotoxicity testing requirements. Perspectives were shared from industry and regulatory scientists working in the peptide therapeutics field followed by an open forum panel discussion to discuss questions drafted for the peptide therapeutics scientific community, which will be discussed in more detail.
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Affiliation(s)
- Doris Zane
- 435529Intarcia Therapeutics, Inc., Hayward, CA, USA
| | - Paul L Feldman
- 435529Intarcia Therapeutics, Inc., Research Triangle Park, NC, USA
| | | | - Zhanna Sobol
- Pfizer Inc., Worldwide Research and Development, Groton, CT, USA
| | - Jessica Hawes
- 4137Food and Drug Administration (FDA), Center for Drug Evaluation and Research (CDER), Silver Spring, MD, USA.,Hawes is now with Food and Drug Administration (FDA), National Center for Toxicological Research (NCTR), Jefferson, AR, USA
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18
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Bacon K, Blain A, Burroughs M, McArthur N, Rao BM, Menegatti S. Isolation of Chemically Cyclized Peptide Binders Using Yeast Surface Display. ACS COMBINATORIAL SCIENCE 2020; 22:519-532. [PMID: 32786323 DOI: 10.1021/acscombsci.0c00076] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Cyclic peptides with engineered protein-binding activity have gained increasing attention for use in therapeutic and biotechnology applications. We describe the efficient isolation and characterization of cyclic peptide binders from genetically encoded combinatorial libraries using yeast surface display. Here, peptide cyclization is achieved by disuccinimidyl glutarate-mediated cross-linking of amine groups within a linear peptide sequence that is expressed as a yeast cell surface fusion. Using this approach, we first screened a library of cyclic heptapeptides using magnetic selection, followed by fluorescence activated cell sorting (FACS) to isolate binders for a model target (lysozyme) with low micromolar binding affinity (KD ∼ 1.2-3.7 μM). The isolated peptides bind lysozyme selectively and only when cyclized. Importantly, we showed that yeast surface displayed cyclic peptides can be used to efficiently obtain quantitative estimates of binding affinity, circumventing the need for chemical synthesis of the selected peptides. Subsequently, to demonstrate broader applicability of our approach, we isolated cyclic heptapeptides that bind human interleukin-17 (IL-17) using yeast-displayed IL-17 as a target for magnetic selection, followed by FACS using recombinant IL-17. Molecular docking simulations and follow-up experimental analyses identified a candidate cyclic peptide that likely binds IL-17 in its receptor binding region with moderate apparent affinity (KD ∼ 300 nM). Taken together, our results show that yeast surface display can be used to efficiently isolate and characterize cyclic peptides generated by chemical modification from combinatorial libraries.
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Affiliation(s)
- Kaitlyn Bacon
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Box 7905, Engineering Building I, Raleigh, North Carolina 27695, United States
| | - Abigail Blain
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Box 7905, Engineering Building I, Raleigh, North Carolina 27695, United States
| | - Matthew Burroughs
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Box 7905, Engineering Building I, Raleigh, North Carolina 27695, United States
| | - Nikki McArthur
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Box 7905, Engineering Building I, Raleigh, North Carolina 27695, United States
| | - Balaji M Rao
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Box 7905, Engineering Building I, Raleigh, North Carolina 27695, United States
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Stefano Menegatti
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Box 7905, Engineering Building I, Raleigh, North Carolina 27695, United States
- Biomanufacturing Training and Education Center (BTEC), North Carolina State University, Raleigh, North Carolina 27695, United States
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19
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Shinbara K, Liu W, van Neer RHP, Katoh T, Suga H. Methodologies for Backbone Macrocyclic Peptide Synthesis Compatible With Screening Technologies. Front Chem 2020; 8:447. [PMID: 32626683 PMCID: PMC7314982 DOI: 10.3389/fchem.2020.00447] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 04/28/2020] [Indexed: 12/23/2022] Open
Abstract
Backbone macrocyclic structures are often found in diverse bioactive peptides and contribute to greater conformational rigidity, peptidase resistance, and potential membrane permeability compared to their linear counterparts. Therefore, such peptide scaffolds are an attractive platform for drug-discovery endeavors. Recent advances in synthetic methods for backbone macrocyclic peptides have enabled the discovery of novel peptide drug candidates against diverse targets. Here, we overview recent technical advancements in the synthetic methods including 1) enzymatic synthesis, 2) chemical synthesis, 3) split-intein circular ligation of peptides and proteins (SICLOPPS), and 4) in vitro translation system combined with genetic code reprogramming. We also discuss screening methodologies compatible with those synthetic methodologies, such as one-beads one-compound (OBOC) screening compatible with the synthetic method 2, cell-based assay compatible with 3, limiting-dilution PCR and mRNA display compatible with 4.
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Affiliation(s)
| | | | | | | | - Hiroaki Suga
- Department of Chemistry, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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20
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Methods for generating and screening libraries of genetically encoded cyclic peptides in drug discovery. Nat Rev Chem 2020; 4:90-101. [PMID: 37128052 DOI: 10.1038/s41570-019-0159-2] [Citation(s) in RCA: 107] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2019] [Indexed: 12/14/2022]
Abstract
Drug discovery has traditionally focused on using libraries of small molecules to identify therapeutic drugs, but new modalities, especially libraries of genetically encoded cyclic peptides, are increasingly used for this purpose. Several technologies now exist for the production of libraries of cyclic peptides, including phage display, mRNA display and split-intein circular ligation of peptides and proteins. These different approaches are each compatible with particular methods of screening libraries, such as functional or affinity-based screening, and screening in vitro or in cells. These techniques allow the rapid preparation of libraries of hundreds of millions of molecules without the need for chemical synthesis, and have therefore lowered the entry barrier to generating and screening for inhibitors of a given target. This ease of use combined with the inherent advantages of the cyclic-peptide scaffold has yielded inhibitors of targets that have proved difficult to drug with small molecules. Multiple reports demonstrate that cyclic peptides act as privileged scaffolds in drug discovery, particularly against 'undruggable' targets such as protein-protein interactions. Although substantial challenges remain in the clinical translation of hits from screens of cyclic-peptide libraries, progress continues to be made in this area, with an increasing number of cyclic peptides entering clinical trials. Here, we detail the various platforms for producing and screening libraries of genetically encoded cyclic peptides and discuss and evaluate the advantages and disadvantages of each approach when deployed for drug discovery.
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21
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Wang XS, Chen PC, Hampton JT, Tharp JM, Reed CA, Das SK, Wang D, Hayatshahi HS, Shen Y, Liu J, Liu WR. A Genetically Encoded, Phage‐Displayed Cyclic‐Peptide Library. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201908713] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
| | | | - J. Trae Hampton
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Jeffery M. Tharp
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Catrina A. Reed
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Sukant K. Das
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
| | - Duen‐Shian Wang
- Department of Pharmaceutical Sciences UNT Health Science Center Fort Worth TX 76107 USA
| | - Hamed S. Hayatshahi
- Department of Pharmaceutical Sciences UNT Health Science Center Fort Worth TX 76107 USA
| | - Yang Shen
- Department of Electrical and Computer Engineering Texas A&M University College Station TX 77843-3218 USA
| | - Jin Liu
- Department of Pharmaceutical Sciences UNT Health Science Center Fort Worth TX 76107 USA
| | - Wenshe Ray Liu
- Department of Chemistry Texas A&M University College Station TX 77843-3255 USA
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22
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Wang XS, Chen PHC, Hampton JT, Tharp JM, Reed CA, Das SK, Wang DS, Hayatshahi HS, Shen Y, Liu J, Liu WR. A Genetically Encoded, Phage-Displayed Cyclic-Peptide Library. Angew Chem Int Ed Engl 2019; 58:15904-15909. [PMID: 31398275 PMCID: PMC6803038 DOI: 10.1002/anie.201908713] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Indexed: 11/10/2022]
Abstract
Superior to linear peptides in biological activities, cyclic peptides are considered to have great potential as therapeutic agents. To identify cyclic-peptide ligands for therapeutic targets, phage-displayed peptide libraries in which cyclization is achieved by the covalent conjugation of cysteines have been widely used. To resolve drawbacks related to cysteine conjugation, we have invented a phage-display technique in which its displayed peptides are cyclized through a proximity-driven Michael addition reaction between a cysteine and an amber-codon-encoded Nϵ -acryloyl-lysine (AcrK). Using a randomized 6-mer library in which peptides were cyclized at two ends through a cysteine-AcrK linker, we demonstrated the successful selection of potent ligands for TEV protease and HDAC8. All selected cyclic peptide ligands showed 4- to 6-fold stronger affinity to their protein targets than their linear counterparts. We believe this approach will find broad applications in drug discovery.
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Affiliation(s)
- Xiaoshan Shayna Wang
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Peng-Hsun Chase Chen
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - J Trae Hampton
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Jeffery M Tharp
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Catrina A Reed
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Sukant K Das
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
| | - Duen-Shian Wang
- Department of Pharmaceutical Sciences, UNT Health Science Center, Fort Worth, TX, 76107, USA
| | - Hamed S Hayatshahi
- Department of Pharmaceutical Sciences, UNT Health Science Center, Fort Worth, TX, 76107, USA
| | - Yang Shen
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843-3218, USA
| | - Jin Liu
- Department of Pharmaceutical Sciences, UNT Health Science Center, Fort Worth, TX, 76107, USA
| | - Wenshe Ray Liu
- Department of Chemistry, Texas A&M University, College Station, TX, 77843-3255, USA
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23
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Jiang Z, Guan J, Qian J, Zhan C. Peptide ligand-mediated targeted drug delivery of nanomedicines. Biomater Sci 2019; 7:461-471. [PMID: 30656305 DOI: 10.1039/c8bm01340c] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Targeted drug delivery is emerging as a promising strategy to achieve better clinical outcomes. Actively targeted drug delivery that utilizes overexpressed receptors or antigens on diseased tissues is receiving increasing scrutiny, especially due to the uncertainty of existence of the enhanced permeability and retention (EPR) effect in cancer patients. Peptide ligands are advantageous over other classes of targeting ligands due to their accessibility of high-throughput screening, ease of synthesis, high specificity and affinity, etc. In this review, we briefly summarize the resources of peptide ligands and discuss the pitfalls and perspectives of peptide ligand-mediated targeted delivery of nanomedicines.
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Affiliation(s)
- Zhuxuan Jiang
- Department of Pharmacology, School of Basic Medical Sciences & State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200032, P.R. China.
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24
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Ottl J, Leder L, Schaefer JV, Dumelin CE. Encoded Library Technologies as Integrated Lead Finding Platforms for Drug Discovery. Molecules 2019; 24:E1629. [PMID: 31027189 PMCID: PMC6514559 DOI: 10.3390/molecules24081629] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/17/2019] [Accepted: 04/21/2019] [Indexed: 01/22/2023] Open
Abstract
The scope of targets investigated in pharmaceutical research is continuously moving into uncharted territory. Consequently, finding suitable chemical matter with current compound collections is proving increasingly difficult. Encoded library technologies enable the rapid exploration of large chemical space for the identification of ligands for such targets. These binders facilitate drug discovery projects both as tools for target validation, structural elucidation and assay development as well as starting points for medicinal chemistry. Novartis internalized two complementing encoded library platforms to accelerate the initiation of its drug discovery programs. For the identification of low-molecular weight ligands, we apply DNA-encoded libraries. In addition, encoded peptide libraries are employed to identify cyclic peptides. This review discusses how we apply these two platforms in our research and why we consider it beneficial to run both pipelines in-house.
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Affiliation(s)
- Johannes Ottl
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Lukas Leder
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
| | - Jonas V Schaefer
- Novartis Institutes for Biomedical Research, 4056 Basel, Switzerland.
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25
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Palei S, Becher KS, Nienberg C, Jose J, Mootz HD. Bacterial Cell-Surface Display of Semisynthetic Cyclic Peptides. Chembiochem 2018; 20:72-77. [PMID: 30216604 DOI: 10.1002/cbic.201800552] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2018] [Indexed: 01/20/2023]
Abstract
Semisynthetic cyclic peptides containing both non-proteinogenic building blocks, as the synthetic part, and a genetically encoded sequence amenable to DNA-based randomization hold great potential to expand the chemical space in the quest for novel bioactive peptides. Key to an efficient selection of novel binders to biomacromolecules is a robust method to link their genotype and phenotype. A novel bacterial cell surface display technology has been developed to present cyclic peptides composed of synthetic and genetically encoded fragments in their backbones. The fragments were combined by protein trans-splicing and intramolecular oxime ligation. To this end, a split intein half and an unnatural amino acid were displayed with the genetically encoded part on the surface of Escherichia coli. Addition of the synthetic fragment equipped with the split intein partner and an aminooxy moiety, as well as the application of a pH-shift protocol, resulted in the onsurface formation of the semisynthetic cyclic peptide. This approach will serve for the generation of cyclic peptide libraries suitable for selection by fluorescence-activated cell sorting, and more generally enables chemical modification of proteins on the bacterial surface.
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Affiliation(s)
- Shubhendu Palei
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany.,International Graduate School of Chemistry (GSC-MS), University of Münster, 48149, Münster, Germany
| | - Kira S Becher
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany
| | - Christian Nienberg
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, PharmaCampus, 48149, Münster, Germany
| | - Joachim Jose
- Institute of Pharmaceutical and Medicinal Chemistry, University of Muenster, PharmaCampus, 48149, Münster, Germany.,International Graduate School of Chemistry (GSC-MS), University of Münster, 48149, Münster, Germany
| | - Henning D Mootz
- Institute of Biochemistry, University of Muenster, Wilhelm-Klemm-Strasse 2, 48149, Münster, Germany.,International Graduate School of Chemistry (GSC-MS), University of Münster, 48149, Münster, Germany
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26
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McCarthy KA, Kelly MA, Li K, Cambray S, Hosseini AS, van Opijnen T, Gao J. Phage Display of Dynamic Covalent Binding Motifs Enables Facile Development of Targeted Antibiotics. J Am Chem Soc 2018; 140:6137-6145. [PMID: 29701966 DOI: 10.1021/jacs.8b02461] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Antibiotic resistance of bacterial pathogens poses an increasing threat to the wellbeing of our society and urgently calls for new strategies for infection diagnosis and antibiotic discovery. The antibiotic resistance problem at least partially arises from extensive use of broad-spectrum antibiotics. Ideally, for the treatment of infection, one would like to use a narrow-spectrum antibiotic that specifically targets and kills the disease-causing strain. This is particularly important considering the commensal bacterial species that are beneficial and sometimes even critical to the health of a human being. In this contribution, we describe a phage display platform that enables rapid identification of peptide probes for specific bacterial strains. The phage library described herein incorporates 2-acetylphenylboronic acid moieties to elicit dynamic covalent binding to the bacterial cell surface. Screening of the library against live bacterial cells yields submicromolar and highly specific binders for clinical strains of Staphylococcus aureus and Acinetobacter baumannii that display antibiotic resistance. We further show that the identified peptide probes can be readily converted to bactericidal agents that deliver generic toxins to kill the targeted bacterial strain with high specificity. The phage display platform described here is applicable to a wide array of bacterial strains, paving the way to facile diagnosis and development of strain-specific antibiotics.
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Affiliation(s)
- Kelly A McCarthy
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Michael A Kelly
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Kaicheng Li
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Samantha Cambray
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Azade S Hosseini
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Tim van Opijnen
- Department of Biology , Boston College , Chestnut Hill , Massachusetts 02467 , United States
| | - Jianmin Gao
- Department of Chemistry, Merkert Chemistry Center , Boston College , Chestnut Hill , Massachusetts 02467 , United States
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27
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CycLS: Accurate, whole-library sequencing of cyclic peptides using tandem mass spectrometry. Bioorg Med Chem 2018; 26:1232-1238. [DOI: 10.1016/j.bmc.2018.01.027] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Revised: 01/27/2018] [Accepted: 01/30/2018] [Indexed: 01/20/2023]
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28
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Abstract
Molecular imaging allows for the visualization of changes at the cellular level in diseases such as cancer. A successful molecular imaging agent must rely on disease-selective targets and ligands that specifically interact with those targets. Unfortunately, the translation of novel target-specific ligands into the clinic has been frustratingly slow with limitations including the complex design and screening approaches for ligand identification, as well as their subsequent optimization into useful imaging agents. This review focuses on combinatorial library approaches towards addressing these two challenges, with particular focus on phage display and one-bead one-compound (OBOC) libraries. Both of these peptide-based techniques have proven successful in identifying new ligands for cancer-specific targets and some of the success stories will be highlighted. New developments in screening methodology and sequencing technology have pushed the bounds of phage display and OBOC even further, allowing for even faster and more robust discovery of novel ligands. The combination of multiple high-throughput technologies will not only allow for more accurate identification, but also faster affinity maturation, while overall streamlining the process of translating novel ligands into clinical imaging agents.
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Wu CY, Wang DH, Wang X, Dixon SM, Meng L, Ahadi S, Enter DH, Chen CY, Kato J, Leon LJ, Ramirez LM, Maeda Y, Reis CF, Ribeiro B, Weems B, Kung HJ, Lam KS. Rapid Discovery of Functional Small Molecule Ligands against Proteomic Targets through Library-Against-Library Screening. ACS COMBINATORIAL SCIENCE 2016; 18:320-9. [PMID: 27053324 PMCID: PMC4908505 DOI: 10.1021/acscombsci.5b00194] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
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Identifying “druggable”
targets and their corresponding
therapeutic agents are two fundamental challenges in drug discovery
research. The one-bead-one-compound (OBOC) combinatorial library method
has been developed to discover peptides or small molecules that bind
to a specific target protein or elicit a specific cellular response.
The phage display cDNA expression proteome library method has been
employed to identify target proteins that interact with specific compounds.
Here, we combined these two high-throughput approaches, efficiently
interrogated approximately 1013 possible molecular interactions,
and identified 91 small molecule compound beads that interacted strongly
with the phage library. Of 19 compounds resynthesized, 4 were cytotoxic
against cancer cells; one of these compounds was found to interact
with EIF5B and inhibit protein translation. As more binding pairs
are confirmed and evaluated, the “library-against-library”
screening approach and the resulting small molecule–protein
domain interaction database may serve as a valuable tool for basic
research and drug development.
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Affiliation(s)
- Chun-Yi Wu
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
- Pharmacology
and Toxicology Graduate Group, University of California, Davis, Davis, California 95616, United States
| | - Don-Hong Wang
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
- Genetic
Graduate Group, University of California, Davis, California 95616, United States
| | - Xiaobing Wang
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Seth M. Dixon
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Liping Meng
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Sara Ahadi
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Daniel H. Enter
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
- Center
for Biophotonics Science and Technology, University of California, Davis, Sacramento, California 95817, United States
| | - Chao-Yu Chen
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
- Pharmacology
and Toxicology Graduate Group, University of California, Davis, Davis, California 95616, United States
| | - Jason Kato
- Pharmacology
and Toxicology Graduate Group, University of California, Davis, Davis, California 95616, United States
| | - Leonardo J. Leon
- Pharmacology
and Toxicology Graduate Group, University of California, Davis, Davis, California 95616, United States
| | - Laura M. Ramirez
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
- Center
for Biophotonics Science and Technology, University of California, Davis, Sacramento, California 95817, United States
| | - Yoshiko Maeda
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Carolina F. Reis
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Brianna Ribeiro
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Brittany Weems
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
| | - Hsing-Jien Kung
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
- National Health Research Institutes, Miaoli
County 35053, Taiwan
| | - Kit S. Lam
- Department
of Biochemistry and Molecular Medicine, University of California Davis School of Medicine, 2700 Stockton Boulevard, Suite 2102, Sacramento, California 95817, United States
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