1
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Zhang X, Chen R, Shu H, Liang P, Qin T, Wang K, Guo A, Craik DJ, Liao B, Zhang J. Gene-guided identifications of a structure-chimeric cyclotide viphi I from Viola philippica: Potential functions against cadmium and nematodes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 347:112185. [PMID: 38986912 DOI: 10.1016/j.plantsci.2024.112185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/20/2024] [Revised: 07/04/2024] [Accepted: 07/06/2024] [Indexed: 07/12/2024]
Abstract
The cyclic peptides, cyclotides, are identified mostly with 29-31-aa (amino acid residues) but rarely with ≥ 34-aa in plants. Viola philippica is a well-known medicinal plant but a rare metallophyte with cyclotides. A hypothesis was hence raised that the potential novel 34-aa cyclotide of Viola philippica would clearly broaden the structural and functional diversities of plant cyclotides. After homology-cloning the cyclotide precursor gene of VpCP5, a 34-aa cyclotide (viphi I) was identified to be larger than 22 other known cyclotides in V. philippica. It had a chimeric primary structure, due to its unusual loop structures (8 residues in loop 2 and 6 residues in loop 5) and aa composition (3 E and 5 R), by using phylogenetic analyses and an in-house cyclotide analysis tool, CyExcel_V1. A plasmid pCYC-viphi_I and a lab-used recombinant process were specially constructed for preparing viphi I. Typically, 0.12 or 0.25 mg ml-1 co-exposed viphi I could significantly remain cell activities with elevating Cd2+-exposed doses from 10-8 to 10-6 mol l-1 in MCF7 cells. In the model nematode Caenorhabditis elegans, IC50 values of viphi I to inhibit adult ratios and to induce death ratios, were 184.7 and 585.9 µg ml-1, respectively; the median lifespan of adult worms decreased from 14 to 2 d at viphi I doses ranging from 0.05 to 2 mg ml-1. Taken together, the newly identified viphi I exhibits functional potentials against cadmium and nematodes, providing new insights into structural and functional diversity of chimeric cyclotides in plants.
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Affiliation(s)
- Xiaojie Zhang
- Guangdong Pharmaceutical University, School of Life Sciences and Biopharmaceutics, Guangzhou 510006, China.
| | - Ruohong Chen
- Sun Yat-sen University, School of Life Sciences, Guangzhou 510275, China.
| | - Haoyue Shu
- Sun Yat-sen University, School of Life Sciences, Guangzhou 510275, China.
| | - Peihui Liang
- Guangdong Pharmaceutical University, School of Life Sciences and Biopharmaceutics, Guangzhou 510006, China.
| | - Ting Qin
- Guangdong Pharmaceutical University, School of Life Sciences and Biopharmaceutics, Guangzhou 510006, China.
| | - Kemei Wang
- Guangdong Pharmaceutical University, School of Life Sciences and Biopharmaceutics, Guangzhou 510006, China.
| | - Aimin Guo
- Guangdong Pharmaceutical University, School of Life Sciences and Biopharmaceutics, Guangzhou 510006, China.
| | - David J Craik
- The University of Queensland, Institute for Molecular Bioscience, Brisbane, QLD 4072, Australia.
| | - Bin Liao
- Sun Yat-sen University, School of Life Sciences, Guangzhou 510275, China.
| | - Jun Zhang
- Guangdong Pharmaceutical University, School of Life Sciences and Biopharmaceutics, Guangzhou 510006, China.
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2
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Mourenza A, Ganesan R, Camarero JA. Resistance is futile: targeting multidrug-resistant bacteria with de novo Cys-rich cyclic polypeptides. RSC Chem Biol 2023; 4:722-735. [PMID: 37799576 PMCID: PMC10549238 DOI: 10.1039/d3cb00015j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/27/2023] [Indexed: 10/07/2023] Open
Abstract
The search for novel antimicrobial agents to combat microbial pathogens is intensifying in response to rapid drug resistance development to current antibiotic therapeutics. The use of disulfide-rich head-to-tail cyclized polypeptides as molecular frameworks for designing a new type of peptide antibiotics is gaining increasing attention among the scientific community and the pharmaceutical industry. The use of macrocyclic peptides, further constrained by the presence of several disulfide bonds, makes these peptide frameworks remarkably more stable to thermal, biological, and chemical degradation showing better activities when compared to their linear analogs. Many of these novel peptide scaffolds have been shown to have a high tolerance to sequence variability in those residues not involved in disulfide bonds, able to cross biological membranes, and efficiently target complex biomolecular interactions. Hence, these unique properties make the use of these scaffolds ideal for many biotechnological applications, including the design of novel peptide antibiotics. This article provides an overview of the new developments in the use of several disulfide-rich cyclic polypeptides, including cyclotides, θ-defensins, and sunflower trypsin inhibitor peptides, among others, in the development of novel antimicrobial peptides against multidrug-resistant bacteria.
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Affiliation(s)
- Alvaro Mourenza
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy Los Angeles CA90033 USA +1-(323) 442-1417
| | - Rajasekaran Ganesan
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy Los Angeles CA90033 USA +1-(323) 442-1417
| | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy Los Angeles CA90033 USA +1-(323) 442-1417
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California Los Angeles CA90033 USA
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3
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Chaudhuri D, Lu T, Jacob B, Abraham S, Shankar P, Poss MA, Neamati N, Camarero JA. Lipidation of a bioactive cyclotide-based CXCR4 antagonist greatly improves its pharmacokinetic profile in vivo. J Control Release 2023; 359:26-32. [PMID: 37236320 PMCID: PMC10527528 DOI: 10.1016/j.jconrel.2023.05.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/28/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023]
Abstract
The CXCR4 chemokine is a key molecular regulator of many biological functions controlling leukocyte functions during inflammation and immunity, and during embryonic development. Overexpression of CXCR4 is also associated with many types of cancer where its activation promotes angiogenesis, tumor growth/survival, and metastasis. In addition, CXCR4 is involved in HIV replication, working as a co-receptor for viral entry, making CXCR4 a very attractive target for developing novel therapeutic agents. Here we report the pharmacokinetic profile in rats of a potent CXCR4 antagonist cyclotide, MCo-CVX-5c, previously developed in our group that displayed a remarkable in vivo resistance to biological degradation in serum. This bioactive cyclotide, however, was rapidly eliminated through renal clearance. Several lipidated versions of cyclotide MCo-CVX-5c showed a significant increase in the half-life when compared to the unlipidated form. The palmitoylated version of cyclotide MCo-CVX-5c displayed similar CXCR4 antagonistic activity as the unlipidated cyclotide, while the cyclotide modified with octadecanedioic (18-oxo-octadecanoic) acid exhibited a remarkable decrease in its ability to antagonize CXCR4. Similar results were also obtained when tested for its ability to inhibit growth in two cancer cell lines and HIV infection in cells. These results show that the half-life of cyclotides can be improved by lipidation although it can also affect their biological activity depending on the lipid employed.
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Affiliation(s)
- Dipankar Chaudhuri
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Tiangong Lu
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-2800, USA
| | - Binu Jacob
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Sojan Abraham
- Department of Biomedical Sciences, Center of Excellence in Infectious Disease, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79430, USA
| | - Premlata Shankar
- Department of Biomedical Sciences, Center of Excellence in Infectious Disease, Paul L. Foster School of Medicine, Texas Tech University Health Sciences Center, El Paso, TX 79430, USA
| | - Michael A Poss
- Bristol Myers Squibb Research and Development, P.O. Box 4000, Princeton, NJ 08543, USA
| | - Nouri Neamati
- Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, MI 48109-2800, USA
| | - Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089, USA; Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA9033, USA.
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4
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Ho TNT, Pham SH, Nguyen LTT, Nguyen HT, Nguyen LT, Dang TT. Insights into the synthesis strategies of plant-derived cyclotides. Amino Acids 2023:10.1007/s00726-023-03271-8. [PMID: 37142771 DOI: 10.1007/s00726-023-03271-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 04/18/2023] [Indexed: 05/06/2023]
Abstract
Cyclotides are plant peptides characterized with a head-to-tail cyclized backbone and three interlocking disulfide bonds, known as a cyclic cysteine knot. Despite the variations in cyclotides peptide sequences, this core structure is conserved, underlying their most useful feature: stability against thermal and chemical breakdown. Cyclotides are the only natural peptides known to date that are orally bioavailable and able to cross cell membranes. Cyclotides also display bioactivities that have been exploited and expanded to develop as potential therapeutic reagents for a wide range of conditions (e.g., HIV, inflammatory conditions, multiple sclerosis, etc.). As such, in vitro production of cyclotides is of the utmost importance since it could assist further research on this peptide class, specifically the structure-activity relationship and its mechanism of action. The information obtained could be utilized to assist drug development and optimization. Here, we discuss several strategies for the synthesis of cyclotides using both chemical and biological routes.
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Affiliation(s)
- Thao N T Ho
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam
| | - Son H Pham
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam
| | - Linh T T Nguyen
- Department of Chemistry, Ho Chi Minh City University of Education, 280 An Duong Vuong Street, District 5, Ho Chi Minh City, Viet Nam
| | - Ha T Nguyen
- National Key Laboratory of Polymer and Composite Materials, Department of Energy Materials, Faculty of Materials Technology, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Viet Nam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam
| | - Luan T Nguyen
- National Key Laboratory of Polymer and Composite Materials, Department of Energy Materials, Faculty of Materials Technology, Ho Chi Minh City University of Technology (HCMUT), 268 Ly Thuong Kiet Street, District 10, Ho Chi Minh City, Viet Nam
- Vietnam National University Ho Chi Minh City, Linh Trung Ward, Thu Duc District, Ho Chi Minh City, Viet Nam
| | - Tien T Dang
- Institute of Applied Materials Science, Vietnam Academy of Science and Technology, 1B TL29, District 12, Ho Chi Minh City, Viet Nam.
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5
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Jacob B, Vogelaar A, Cadenas E, Camarero JA. Using the Cyclotide Scaffold for Targeting Biomolecular Interactions in Drug Development. Molecules 2022; 27:molecules27196430. [PMID: 36234971 PMCID: PMC9570680 DOI: 10.3390/molecules27196430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/21/2022] [Accepted: 09/24/2022] [Indexed: 11/28/2022] Open
Abstract
This review provides an overview of the properties of cyclotides and their potential for developing novel peptide-based therapeutics. The selective disruption of protein–protein interactions remains challenging, as the interacting surfaces are relatively large and flat. However, highly constrained polypeptide-based molecular frameworks with cell-permeability properties, such as the cyclotide scaffold, have shown great promise for targeting those biomolecular interactions. The use of molecular techniques, such as epitope grafting and molecular evolution employing the cyclotide scaffold, has shown to be highly effective for selecting bioactive cyclotides.
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Affiliation(s)
- Binu Jacob
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
| | - Alicia Vogelaar
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
| | - Enrique Cadenas
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, CA 9033, USA
- Correspondence:
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6
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Ganesan R, Dughbaj MA, Ramirez L, Beringer S, Aboye TL, Shekhtman A, Beringer PM, Camarero JA. Engineered Cyclotides with Potent Broad in Vitro and in Vivo Antimicrobial Activity. Chemistry 2021; 27:12702-12708. [PMID: 34159664 PMCID: PMC8410672 DOI: 10.1002/chem.202101438] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Indexed: 12/18/2022]
Abstract
The search for novel antimicrobial agents to combat microbial pathogens is intensifying in response to the rapid development of drug resistance to current antibiotic therapeutics. Respiratory failure and septicemia are the leading causes of mortality among hospitalized patients. Here, the development of a novel engineered cyclotide with effective broad-spectrum antibacterial activity against several ESKAPE bacterial strains and clinical isolates is reported. The most active antibacterial cyclotide was extremely stable in serum, showed little hemolytic activity, and provided protection in vivo in a murine model of P. aeruginosa peritonitis. These results highlight the potential of the cyclotide scaffold for the development of novel antimicrobial therapeutic leads for the treatment of bacteremia.
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Affiliation(s)
- Rajasekaran Ganesan
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
| | - Mansour A. Dughbaj
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
| | - Lisa Ramirez
- Department of Chemistry, State University of New York, Albany, NY 12222, USA
| | - Steven Beringer
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
| | - Teshome L. Aboye
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York, Albany, NY 12222, USA
| | - Paul M. Beringer
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
- Department of Clinical Pharmacy, School of Pharmacy, University of Southern California, Los Angeles, CA 90033, USA
- Norris Comprehensive Cancer Center, Keck School of Medicine, University of Southern California, Los Angeles, CA90033, USA
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7
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Huang LSM, Snyder EY, Schooley RT. Strategies and progress in CXCR4-targeted anti-HIV therapeutic development. Clin Infect Dis 2021; 73:919-924. [PMID: 33624027 DOI: 10.1093/cid/ciab160] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 02/18/2021] [Indexed: 01/09/2023] Open
Abstract
The acquired immunodeficiency syndrome (AIDS), caused by the human immunodeficiency virus (HIV), has been a global public health challenge for several decades. The majority of HIV infection is caused by the human immunodeficiency virus type 1 (HIV-1) which enters and infects a host cell via the cell surface proteins of CD4 as the primary receptor, and chemokine receptors CXCR4 or CCR5 as the co-receptor-then undergoing replication using the cell's intracellular machinery. Whereas many drugs targeting CCR5-mediated entry or HIV-1 replication via reverse transcriptase or proteases have long been used clinically, agents targeting CXCR4 are yet to be advanced to clinical application. Here in this review we highlight some of the strategies for and progress made in the discovery of novel small molecules, peptides, and larger molecules that target CXCR4, and their future prospects for translation into the clinic as a new class of anti-HIV therapeutics.
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Affiliation(s)
- Lina S M Huang
- Center for Innovative Phage Applications and Therapeutics, Department of Medicine, Division of Infectious Diseases and Global Public Health, School of Medicine, University of California San Diego, La Jolla, U.S.A
| | - Evan Y Snyder
- Sanford Burnham Prebys Medical Discovery Institute, La Jolla, U.S.A.,Sanford Consortium for Regenerative Medicine.,Department of Pediatrics, School of Medicine, University of California San Diego, La Jolla U.S.A
| | - Robert T Schooley
- Center for Innovative Phage Applications and Therapeutics, Department of Medicine, Division of Infectious Diseases and Global Public Health, School of Medicine, University of California San Diego, La Jolla, U.S.A
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8
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Abstract
This Review explores the class of plant-derived macrocyclic peptides called cyclotides. We include an account of their discovery, characterization, and distribution in the plant kingdom as well as a detailed analysis of their sequences and structures, biosynthesis and chemical synthesis, biological functions, and applications. These macrocyclic peptides are around 30 amino acids in size and are characterized by their head-to-tail cyclic backbone and cystine knot motif, which render them to be exceptionally stable, with resistance to thermal or enzymatic degradation. Routes to their chemical synthesis have been developed over the past two decades, and this capability has facilitated a wide range of mutagenesis and structure-activity relationship studies. In turn, these studies have both led to an increased understanding of their mechanisms of action as well as facilitated a range of applications in agriculture and medicine, as ecofriendly crop protection agents, and as drug leads or scaffolds for pharmaceutical design. Our overall objective in this Review is to provide readers with a comprehensive overview of cyclotides that we hope will stimulate further work on this fascinating family of peptides.
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Affiliation(s)
- Simon J de Veer
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - Meng-Wei Kan
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
| | - David J Craik
- Institute for Molecular Bioscience , The University of Queensland , Brisbane , Queensland 4072 , Australia
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9
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Schmidt M, Huang YH, Texeira de Oliveira EF, Toplak A, Wijma HJ, Janssen DB, van Maarseveen JH, Craik DJ, Nuijens T. Efficient Enzymatic Cyclization of Disulfide-Rich Peptides by Using Peptide Ligases. Chembiochem 2019; 20:1524-1529. [PMID: 30735312 DOI: 10.1002/cbic.201900033] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Indexed: 12/18/2022]
Abstract
Disulfide-rich macrocyclic peptides-cyclotides, for example-represent a promising class of molecules with potential therapeutic use. Despite their potential their efficient synthesis at large scale still represents a major challenge. Here we report new chemoenzymatic strategies using peptide ligase variants-inter alia, omniligase-1-for the efficient and scalable one-pot cyclization and folding of the native cyclotides MCoTI-II, kalata B1 and variants thereof, as well as of the θ-defensin RTD-1. The synthesis of the kB1 variant T20K was successfully demonstrated at multi-gram scale. The existence of several ligation sites for each macrocycle makes this approach highly flexible and facilitates both the larger-scale manufacture and the engineering of bioactive, grafted cyclotide variants, therefore clearly offering a valuable and powerful extension of the existing toolbox of enzymes for peptide head-to-tail cyclization.
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Affiliation(s)
- Marcel Schmidt
- EnzyPep B.V., Brightlands Campus, Urmonderbaan 22, 6167 RD, Geleen, The Netherlands.,Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - Yen-Hua Huang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Eduardo F Texeira de Oliveira
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Ana Toplak
- EnzyPep B.V., Brightlands Campus, Urmonderbaan 22, 6167 RD, Geleen, The Netherlands
| | - Hein J Wijma
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Dick B Janssen
- Groningen Biomolecular Science and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Jan H van Maarseveen
- Van 't Hoff Institute for Molecular Sciences (HIMS), University of Amsterdam, Science Park 904, 1098 XH, Amsterdam, The Netherlands
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Timo Nuijens
- EnzyPep B.V., Brightlands Campus, Urmonderbaan 22, 6167 RD, Geleen, The Netherlands
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10
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Camarero JA, Campbell MJ. The Potential of the Cyclotide Scaffold for Drug Development. Biomedicines 2019; 7:biomedicines7020031. [PMID: 31010257 PMCID: PMC6631875 DOI: 10.3390/biomedicines7020031] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 04/13/2019] [Accepted: 04/15/2019] [Indexed: 12/11/2022] Open
Abstract
Cyclotides are a novel class of micro-proteins (≈30-40 residues long) with a unique topology containing a head-to-tail cyclized backbone structure further stabilized by three disulfide bonds that form a cystine knot. This unique molecular framework makes them exceptionally stable to physical, chemical, and biological degradation compared to linear peptides of similar size. The cyclotides are also highly tolerant to sequence variability, aside from the conserved residues forming the cystine knot, and are orally bioavailable and able to cross cellular membranes to modulate intracellular protein-protein interactions (PPIs), both in vitro and in vivo. These unique properties make them ideal scaffolds for many biotechnological applications, including drug discovery. This review provides an overview of the properties of cyclotides and their potential for the development of novel peptide-based therapeutics. The selective disruption of PPIs still remains a very challenging task, as the interacting surfaces are relatively large and flat. The use of the cell-permeable highly constrained polypeptide molecular frameworks, such as the cyclotide scaffold, has shown great promise, as it provides unique pharmacological properties. The use of molecular techniques, such as epitope grafting, and molecular evolution have shown to be highly effective for the selection of bioactive cyclotides. However, despite successes in employing cyclotides to target PPIs, some of the challenges to move them into the clinic still remain.
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Affiliation(s)
- Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA.
- Norris Comprehensive Cancer Center, University of Southern California, Los Angeles, Los Angeles, CA 9033, USA.
| | - Maria Jose Campbell
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 9033, USA.
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11
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Using backbone-cyclized Cys-rich polypeptides as molecular scaffolds to target protein-protein interactions. Biochem J 2019; 476:67-83. [PMID: 30635453 DOI: 10.1042/bcj20180792] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Revised: 12/07/2018] [Accepted: 12/11/2018] [Indexed: 12/23/2022]
Abstract
The use of disulfide-rich backbone-cyclized polypeptides, as molecular scaffolds to design a new generation of bioimaging tools and drugs that are potent and specific, and thus might have fewer side effects than traditional small-molecule drugs, is gaining increasing interest among the scientific and in the pharmaceutical industries. Highly constrained macrocyclic polypeptides are exceptionally more stable to chemical, thermal and biological degradation and show better biological activity when compared with their linear counterparts. Many of these relatively new scaffolds have been also found to be highly tolerant to sequence variability, aside from the conserved residues forming the disulfide bonds, able to cross cellular membranes and modulate intracellular protein-protein interactions both in vitro and in vivo These properties make them ideal tools for many biotechnological applications. The present study provides an overview of the new developments on the use of several disulfide-rich backbone-cyclized polypeptides, including cyclotides, θ-defensins and sunflower trypsin inhibitor peptides, in the development of novel bioimaging reagents and therapeutic leads.
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12
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Camarero JA. Cyclotides, a versatile ultrastable micro-protein scaffold for biotechnological applications. Bioorg Med Chem Lett 2017; 27:5089-5099. [PMID: 29110985 PMCID: PMC5812341 DOI: 10.1016/j.bmcl.2017.10.051] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2017] [Revised: 10/13/2017] [Accepted: 10/21/2017] [Indexed: 01/26/2023]
Abstract
Cyclotides are fascinating microproteins (≈30-40 residues long) with a unique head-to-tail cyclized backbone, stabilized by three disulfide bonds forming a cystine knot. This unique topology makes them exceptionally stable to chemical, thermal and biological degradation compared to other peptides of similar size. Cyclotides have been also found to be highly tolerant to sequence variability, aside from the conserved residues forming the cystine knot, able to cross cellular membranes and modulate intracellular protein-protein interactions both in vitro and in vivo. These properties make them ideal scaffolds for many biotechnological applications. This article provides and overview of the properties of cyclotides and their applications as molecular imaging agents and peptide-based therapeutics.
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Affiliation(s)
- Julio A Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121, USA; Department of Chemistry, University of Southern California, Los Angeles, CA 90089-9121, USA.
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13
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Lesniak WG, Aboye T, Chatterjee S, Camarero JA, Nimmagadda S. In vivo Evaluation of an Engineered Cyclotide as Specific CXCR4 Imaging Reagent. Chemistry 2017; 23:14469-14475. [PMID: 28771849 PMCID: PMC5812345 DOI: 10.1002/chem.201702540] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Indexed: 12/14/2022]
Abstract
The CXCR4 chemokine receptor plays a key regulatory role in many biological functions, including embryonic development and controlling leukocyte functions during inflammation and immunity. CXCR4 has been also associated with multiple types of cancers where its overexpression/activation promotes metastasis, angiogenesis, and tumor growth and/or survival. Furthermore, CXCR4 is involved in HIV replication, as it is a co-receptor for viral entry into host cells. Altogether, these features make CXCR4 a very attractive target for the development of imaging and therapeutic agents. Here, the in vivo evaluation of the MCoTI-based cyclotide, MCo-CVX-5c, for the development of imaging agents that target CXCR4 is reported. Cyclotide MCo-CVX-5c is a potent CXCR4 antagonist with a remarkable in vivo resistance to biological degradation in serum. A [64 Cu]-DOTA-labeled version of this cyclotide demonstrated high and significant uptake in U87-stb-CXCR4 tumors compared to the control U87 tumors. Furthermore, protracted imaging studies demonstrated radiotracer retention in the U87-stb-CXCR4 tumor at 24 h post injection. Uptake in U87-stb-CXCR4 tumors could be blocked by unlabeled MCo-CVX-5c, showing high in vivo specificity. These results demonstrate the in vivo specificity and retention of a bioactive molecularly targeted cyclotide and highlight the potential of bioactive cyclotides for the development of new imaging agents that target CXCR4.
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Affiliation(s)
- Wojciech G. Lesniak
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Teshome Aboye
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121, USA
| | - Samit Chatterjee
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, Baltimore, Maryland 21287, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, California 90089-9121, USA
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-9121, USA
| | - Sridhar Nimmagadda
- Russell H. Morgan Department of Radiology and Radiological Science, Johns Hopkins University, Baltimore, Maryland 21287, USA
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Abstract
Cyclotides are globular microproteins with a unique head-to-tail cyclized backbone, stabilized by three disulfide bonds forming a cystine knot. This unique circular backbone topology and knotted arrangement of three disulfide bonds makes them exceptionally stable to chemical, thermal, and biological degradation compared to other peptides of similar size. In addition, cyclotides have been shown to be highly tolerant to sequence variability, aside from the conserved residues forming the cystine knot. Cyclotides can also cross cellular membranes and are able to modulate intracellular protein-protein interactions, both in vitro and in vivo. All of these features make cyclotides highly promising as leads or frameworks for the design of peptide-based diagnostic and therapeutic tools. This article provides an overview on cyclotides and their applications as molecular imaging agents and peptide-based therapeutics.
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Affiliation(s)
- Andrew Gould
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90089-9121, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089-9121, USA
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15
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Abstract
Among the various molecules that plants produce for defense against pests and pathogens, cyclotides stand out as exceptionally stable and structurally unique. These ribosomally synthesized peptides are around 30 amino acids in size, and are stabilized by a head-to-tail cyclic peptide backbone and three disulfide bonds that form a cystine knot. They occur in certain plants of the Rubiaceae, Violaceae, Cucurbitaceae, Fabaceae, and Solanaceae families, with an individual plant producing up to hundreds of different cyclotides. Aside from being exploitable as crop protection agents based on their natural pesticidal activities, cyclotides are amenable to repurposing by chemists for use as drug leads or as tools in chemical biology. Their macrocyclic peptide backbone and knotted arrangement of three disulfide bonds engenders cyclotides with resistance to proteolytic degradation, high temperatures, and chemical chaotropes. Furthermore, their small size makes them accessible to synthesis using solid-phase peptide chemistry and so non-natural cyclotides can be designed and synthesized for a variety of applications. Our focus here is on cyclotides as tools in chemical biology, and there are four main areas of application that have appeared in the literature so far: (i) cyclotides as probes of membrane binding; (ii) cyclotides as probes of biosynthetic pathways for peptide cyclization; (iii) cyclotides as probes of protease specificity and function; and (iv) cyclotides as probes of receptor binding and specificity, with the potential for them to be developed as drug leads. The main methods used in these studies include solid-phase peptide chemistry for synthesis and NMR spectroscopy for structural characterization, as well as a wide range of biochemical and biophysical techniques for probing intermolecular interactions. In addition, cyclotides have been examined in diverse biological assays, ranging from enzyme inhibition to cell penetration, intracellular targeting and cytotoxicity. The main finding to have emerged from studies over the past decade is that cyclotides are exceptionally stable under a variety of conditions (in assay buffers, biological fluids, membranes, and recombinant expression systems). Furthermore, they are structurally very well-defined and amenable to sequence substitutions that can introduce new desired biological activities, generally without compromising their exceptional stability. Both features contribute to their use as peptide-based frameworks in drug design. Finally, they occupy a size niche between traditional small-molecule drugs (<500 Da in molecular weight) and protein-based biologics (>5000 Da) and thus can probe receptors, membranes, and protein-protein interactions in different ways to what is possible with either small molecules or biologics. Overall, cyclotides are an exciting class of peptides that have great potential as ultrastable chemical biology probes in a variety of applications. They have the advantage of specificity (typical of proteins) combined with the synthetic accessibility of small molecules.
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Affiliation(s)
- Simon J. de Veer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joachim Weidmann
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
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16
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Cyclotides as drug design scaffolds. Curr Opin Chem Biol 2017; 38:8-16. [DOI: 10.1016/j.cbpa.2017.01.018] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 01/27/2017] [Indexed: 11/21/2022]
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17
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Li Y, Gould A, Aboye T, Bi T, Breindel L, Shekhtman A, Camarero JA. Full Sequence Amino Acid Scanning of θ-Defensin RTD-1 Yields a Potent Anthrax Lethal Factor Protease Inhibitor. J Med Chem 2017; 60:1916-1927. [PMID: 28151653 DOI: 10.1021/acs.jmedchem.6b01689] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
θ-Defensin RTD-1 is a noncompetitive inhibitor of anthrax lethal factor (LF) protease (IC50 = 390 ± 20 nM, Ki = 365 ± 20 nM) and a weak inhibitor of other mammalian metalloproteases such as TNFα converting enzyme (TACE) (Ki = 4.45 ± 0.48 μM). Using full sequence amino acid scanning in combination with a highly efficient "one-pot" cyclization-folding approach, we obtained an RTD-1-based peptide that was around 10 times more active than wild-type RTD-1 in inhibiting LF protease (IC50 = 43 ± 3 nM, Ki = 18 ± 1 nM). The most active peptide was completely symmetrical, rich in Arg and Trp residues, and able to adopt a native RTD-1-like structure. These results show the power of optimized chemical peptide synthesis approaches for the efficient production of libraries of disulfide-rich backbone-cyclized peptides to quickly perform structure-activity relationship studies for optimizing protease inhibitors.
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Affiliation(s)
| | | | | | | | - Leonard Breindel
- Department of Chemistry, State University of New York , Albany, New York 12222, United States
| | - Alexander Shekhtman
- Department of Chemistry, State University of New York , Albany, New York 12222, United States
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18
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Sakamoto K, Tsuda S, Nishio H, Yoshiya T. 1,2,4-Triazole-aided native chemical ligation between peptide-N-acyl-N′-methyl-benzimidazolinone and cysteinyl peptide. Chem Commun (Camb) 2017; 53:12236-12239. [DOI: 10.1039/c7cc07817j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Novel thiol-additive-free NCL using easy-to-prepare peptide-MeNbz and 1,2,4-triazole can be readily combined with one-pot desulfurization and Cys-modification.
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Affiliation(s)
| | | | - Hideki Nishio
- Peptide Institute, Inc
- Osaka 567-0085
- Japan
- Graduate School of Science
- Osaka University
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19
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Qu H, Smithies BJ, Durek T, Craik DJ. Synthesis and Protein Engineering Applications of Cyclotides. Aust J Chem 2017. [DOI: 10.1071/ch16589] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Cyclotides are a group of plant-derived peptides with a head-to-tail cyclized backbone that is stabilized by three knotted disulfide bonds. Their exceptional stability and tolerance for residue substitutions have led to interest in their application as drug design scaffolds. To date, chemical synthesis has been the dominant methodology for producing cyclotides and their analogues. Native chemical ligation is the most common strategy to generate the cyclic backbone and has been highly successful at producing a wide range of cyclotides for studies of structure–activity relationships. Both this and other chemical approaches require a specific linker at the C-terminus and typically involve a non-directed folding (disulfide oxidation) regimen, which can sometimes be a limiting factor in final yields. Following the recent discovery of enzymes involved in peptide cyclization in planta, site-specific and highly efficient enzymatic ligations have been used for synthetic cyclotide backbone cyclization. In this review, chemical synthesis strategies and approaches involving cyclization via enzymes for the production of cyclotides are described.
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Li Y, Bi T, Camarero JA. Chemical and biological production of cyclotides. ADVANCES IN BOTANICAL RESEARCH 2015; 76:271-303. [PMID: 27064329 PMCID: PMC4822716 DOI: 10.1016/bs.abr.2015.08.006] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Cyclotides are fascinating naturally occurring micro-proteins (≈30 residues long) present in several plant families, and display various biological properties such as protease inhibitory, anti-microbial, insecticidal, cytotoxic, anti-HIV and hormone-like activities. Cyclotides share a unique head-to-tail circular knotted topology of three disulfide bridges, with one disulfide penetrating through a macrocycle formed by the two other disulfides and interconnecting peptide backbones, forming what is called a cystine knot topology. This cyclic cystine knot (CCK) framework gives the cyclotides exceptional rigidity, resistance to thermal and chemical denaturation, and enzymatic stability against degradation. Interestingly, cyclotides have been shown to be orally bioavailable, and other cyclotides have been shown to cross the cell membranes. Moreover, recent reports have also shown that engineered cyclotides can be efficiently used to target extracellular and intracellular protein-protein interactions, therefore making cyclotides ideal tools for drug development to selectively target protein-protein interactions. In this work we will review all the available methods for production of these interesting proteins using chemical or biological methods.
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Affiliation(s)
- Yilong Li
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033, USA
| | - Tao Bi
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033, USA
| | - Julio A. Camarero
- Department of Pharmacology and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA 90033, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90033, USA
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