1
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Stability and Safety of Inhibitor Cystine Knot Peptide, GTx1-15, from the Tarantula Spider Grammostola rosea. Toxins (Basel) 2021; 13:toxins13090621. [PMID: 34564625 PMCID: PMC8473062 DOI: 10.3390/toxins13090621] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 08/29/2021] [Accepted: 09/01/2021] [Indexed: 12/19/2022] Open
Abstract
Inhibitor cystine knot (ICK) peptides are knotted peptides with three intramolecular disulfide bonds that affect several types of ion channels. Some are proteolytically stable and are promising scaffolds for drug development. GTx1-15 is an ICK peptide that inhibits the voltage-dependent calcium channel Cav3.1 and the voltage-dependent sodium channels Nav1.3 and Nav1.7. As a model molecule to develop an ICK peptide drug, we investigated several important pharmaceutical characteristics of GTx1-15. The stability of GTx1-15 in rat and human blood plasma was examined, and no GTx1-15 degradation was observed in either rat or human blood plasma for 24 h in vitro. GTx1-15 in blood circulation was detected for several hours after intravenous and intramuscular administration, indicating high stability in plasma. The thermal stability of GTx1-15 as examined by high thermal incubation and protein thermal shift assays indicated that GTx1-15 possesses high heat stability. The cytotoxicity and immunogenicity of GTx1-15 were examined using the human monocytic leukemia cell line THP-1. GTx1-15 showed no cytotoxicity or immunogenicity even at high concentrations. These results indicate that GTx1-15 itself is suitable for peptide drug development and as a peptide library scaffold.
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2
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Fu Y, Jaarsma AH, Kuipers OP. Antiviral activities and applications of ribosomally synthesized and post-translationally modified peptides (RiPPs). Cell Mol Life Sci 2021; 78:3921-3940. [PMID: 33532865 PMCID: PMC7853169 DOI: 10.1007/s00018-021-03759-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2020] [Revised: 12/15/2020] [Accepted: 01/08/2021] [Indexed: 12/15/2022]
Abstract
The emergence and re-emergence of viral epidemics and the risks of antiviral drug resistance are a serious threat to global public health. New options to supplement or replace currently used drugs for antiviral therapy are urgently needed. The research in the field of ribosomally synthesized and post-translationally modified peptides (RiPPs) has been booming in the last few decades, in particular in view of their strong antimicrobial activities and high stability. The RiPPs with antiviral activity, especially those against enveloped viruses, are now also gaining more interest. RiPPs have a number of advantages over small molecule drugs in terms of specificity and affinity for targets, and over protein-based drugs in terms of cellular penetrability, stability and size. Moreover, the great engineering potential of RiPPs provides an efficient way to optimize them as potent antiviral drugs candidates. These intrinsic advantages underscore the good therapeutic prospects of RiPPs in viral treatment. With the aim to highlight the underrated antiviral potential of RiPPs and explore their development as antiviral drugs, we review the current literature describing the antiviral activities and mechanisms of action of RiPPs, discussing the ongoing efforts to improve their antiviral potential and demonstrate their suitability as antiviral therapeutics. We propose that antiviral RiPPs may overcome the limits of peptide-based antiviral therapy, providing an innovative option for the treatment of viral disease.
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Affiliation(s)
- Yuxin Fu
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
| | - Ate H Jaarsma
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands
- Department of Environmental Science, Aarhus University, 4000, Roskilde, Denmark
| | - Oscar P Kuipers
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG, Groningen, The Netherlands.
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3
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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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4
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Jones PM, Mazzio E, Soliman K, George AM. In Silico Investigation of the Binding of MCoTI-II Plant Defense Knottin to the γ-NGF Serine Protease of the 7S Nerve Growth Factor Complex and Biological Activity of Its NGF Mimetic Properties. J Phys Chem B 2019; 123:9104-9110. [PMID: 31580077 DOI: 10.1021/acs.jpcb.9b07547] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nerve growth factor (NGF) is an endogenously produced polypeptide that promotes the differentiation, survival, and repair of neurons in the central and peripheral nervous systems. While trophic proteins hold promise for the treatment of neuronal injury and disease, use of NGF is limited by its large molecular weight, lack of permeability through the blood-brain barrier, and peripheral side effects. Previously, we found that an extract of the Momordica cochinchinensis seed stimulated PC-12 neurite outgrowth. Bioactivity-guided fractioning of the seed extract suggested that the NGF mimetic agent was one of few defined proteins from this plant: one group being the defense Knottins and the other group of the lowest mass is the potent trypsin inhibitor MCoTI-II. Here, the NGF mimetic potential of this latter protein was investigated using two concurrent but different approaches. A biological study used recombinant purified MCoTI-II, which when tested in rat PC-12 cells grown on collagen, failed to initiate outgrowth relative to the positive control 7S NGF. In a separate computational study, the possibility was investigated such that MCoTI-II could exert an effect through binding to the serine protease γ-NGF subunit of the 7S NGF complex, analogous to its binding to its native receptor trypsin. Molecular dynamics simulations showed that MCoTI-II can bind stably to γ-NGF for >350 ns. Modeling indicated that this interaction could sterically inhibit 7S NGF complex formation, potentially altering the equilibrium between inactive complexed and free active NFG protein. In conclusion, the biological study now excludes the MCoTI-II protein as the NGF mimetic factor in the Momordica extract, an important and required step to identify the active component in this seed. On the other hand, the theoretical study has revealed a novel observation that may be of use in the development of strategies to affect NGF activity.
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Affiliation(s)
- Peter M Jones
- School of Life Sciences , University of Technology Sydney , P.O. Box 123, Broadway , New South Wales 2007 , Australia
| | - Elizabeth Mazzio
- College of Pharmacy and Pharmaceutical Sciences , Florida Agricultural and Mechanical University , 241 Fred Humphries Science Research Facility , Tallahassee , Florida 32307 , United States
| | - Karam Soliman
- College of Pharmacy and Pharmaceutical Sciences , Florida Agricultural and Mechanical University , 241 Fred Humphries Science Research Facility , Tallahassee , Florida 32307 , United States
| | - Anthony M George
- School of Life Sciences , University of Technology Sydney , P.O. Box 123, Broadway , New South Wales 2007 , Australia
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5
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Poth AG, Huang YH, Le TT, Kan MW, Craik DJ. Pharmacokinetic characterization of kalata B1 and related therapeutics built on the cyclotide scaffold. Int J Pharm 2019; 565:437-446. [DOI: 10.1016/j.ijpharm.2019.05.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 04/24/2019] [Accepted: 05/03/2019] [Indexed: 02/08/2023]
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6
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Werle M, Föger F. Peroral peptide delivery: Peptidase inhibition as a key concept for commercial drug products. Bioorg Med Chem 2018; 26:2906-2913. [DOI: 10.1016/j.bmc.2017.08.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Revised: 08/10/2017] [Indexed: 11/16/2022]
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7
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Abstract
Chemical methods have enabled the total synthesis of protein molecules of ever-increasing size and complexity. However, methods to engineer synthetic proteins comprising noncanonical amino acids have not kept pace, even though this capability would be a distinct advantage of the total synthesis approach to protein science. In this work, we report a platform for protein engineering based on the screening of synthetic one-bead one-compound protein libraries. Screening throughput approaching that of cell surface display was achieved by a combination of magnetic bead enrichment, flow cytometry analysis of on-bead screens, and high-throughput MS/MS-based sequencing of identified active compounds. Direct screening of a synthetic protein library by these methods resulted in the de novo discovery of mirror-image miniprotein-based binders to a ∼150-kDa protein target, a task that would be difficult or impossible by other means.
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8
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Abstract
Antibodies have proved to be a valuable mode of therapy for numerous diseases, mainly owing to their high target binding affinity and specificity. Unfortunately, antibodies are also limited in several respects, chief amongst those being the extremely high cost of manufacture. Therefore, non-antibody binding proteins have long been sought after as alternative therapies. New binding protein scaffolds are constantly being designed or discovered with some already approved for human use by the FDA. This review focuses on protein scaffolds that are either already being used in humans or are currently being evaluated in clinical trials. Although not all are expected to be approved, the significant benefits ensure that these molecules will continue to be investigated and developed as therapeutic alternatives to antibodies. Based on the location of the amino acids that mediate ligand binding, we place all the protein scaffolds under clinical development into two general categories: scaffolds with ligand-binding residues located in exposed flexible loops, and those with the binding residues located in protein secondary structures, such as α-helices. Scaffolds that fall under the first category include adnectins, anticalins, avimers, Fynomers, Kunitz domains, and knottins, while those belonging to the second category include affibodies, β-hairpin mimetics, and designed ankyrin repeat proteins (DARPins). Most of these scaffolds are thermostable and can be easily produced in microorganisms or completely synthesized chemically. In addition, many of these scaffolds derive from human proteins and thus possess very low immunogenic potential. Additional advantages and limitations of these protein scaffolds as therapeutics compared to antibodies will be discussed.
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Affiliation(s)
- Rudo Simeon
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, TX, 77845, USA
| | - Zhilei Chen
- Department of Microbial Pathogenesis and Immunology, Texas A&M University Health Science Center, College Station, TX, 77845, USA.
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9
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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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10
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Chittoor B, Krishnarjuna B, Morales RAV, MacRaild CA, Sadek M, Leung EWW, Robinson SD, Pennington MW, Norton RS. The Single Disulfide-Directed β-Hairpin Fold. Dynamics, Stability, and Engineering. Biochemistry 2017; 56:2455-2466. [PMID: 28437072 DOI: 10.1021/acs.biochem.7b00120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Grafting bioactive peptide sequences onto small cysteine-rich scaffolds is a promising strategy for enhancing their stability and value as novel peptide-based therapeutics. However, correctly folded disulfide-rich peptides can be challenging to produce by either recombinant or synthetic means. The single disulfide-directed β-hairpin (SDH) fold, first observed in contryphan-Vc1, provides a potential alternative to complex disulfide-rich scaffolds. We have undertaken recombinant production of full-length contryphan-Vc1 (rCon-Vc1[Z1Q]) and a truncated analogue (rCon-Vc11-22[Z1Q]), analyzed the backbone dynamics of rCon-Vc1[Z1Q], and probed the conformational and proteolytic stability of these peptides to evaluate the potential of contryphan-Vc1 as a molecular scaffold. Backbone 15N relaxation measurements for rCon-Vc1[Z1Q] indicate that the N-terminal domain of the peptide is ordered up to Thr19, whereas the remainder of the C-terminal region is highly flexible. The solution structure of truncated rCon-Vc11-22[Z1Q] was similar to that of the full-length peptide, indicating that the flexible C-terminus does not have any effect on the structured domain of the peptide. Contryphan-Vc1 exhibited excellent proteolytic stability against trypsin and chymotrypsin but was susceptible to pepsin digestion. We have investigated whether contryphan-Vc1 can accept a bioactive epitope while maintaining the structure of the peptide by introducing peptide sequences based on the DINNN motif of inducible nitric oxide synthase. We show that sCon-Vc11-22[NNN12-14] binds to the iNOS-binding protein SPSB2 with an affinity of 1.3 μM while maintaining the SDH fold. This study serves as a starting point in utilizing the SDH fold as a peptide scaffold.
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Affiliation(s)
- Balasubramanyam Chittoor
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Bankala Krishnarjuna
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Rodrigo A V Morales
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Christopher A MacRaild
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Maiada Sadek
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Eleanor W W Leung
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | - Samuel D Robinson
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
| | | | - Raymond S Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University , Parkville, Victoria 3052, Australia
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11
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Treggiari D, Zoccatelli G, Chignola R, Molesini B, Minuz P, Pandolfini T. Tomato cystine-knot miniproteins possessing anti-angiogenic activity exhibit in vitro gastrointestinal stability, intestinal absorption and resistance to food industrial processing. Food Chem 2016; 221:1346-1353. [PMID: 27979099 DOI: 10.1016/j.foodchem.2016.11.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2016] [Revised: 10/07/2016] [Accepted: 11/02/2016] [Indexed: 02/04/2023]
Abstract
The cystine-knot miniproteins present in tomato fruit (TCMPs) have been shown to exert anti-angiogenic effects by inhibiting endothelial cell migration and to display resistance to gastrointestinal proteolytic attack. To better define the pharmacological potential of TCMPs, their oral bioavailability and their resistance to industrial processing must be assessed. To explore the intestinal transport of TCMPs we used the differentiated Caco-2 cells model. After 24h incubation, 37.73±9.34% of TCMPs crossed the epithelium, without altering the integrity of the cell layer. To assess the effects of the industrial processing on the biochemical features and the biological activity of TCMPs, we developed a method for purifying the proteins from tomato paste. The tomato-paste purified TCMPs retained the resistance to gastrointestinal digestion and the inhibitory activity towards endothelial cell migration. Our previous and present results collectively demonstrate that TCMPs possess interesting features for drug development.
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Affiliation(s)
- Davide Treggiari
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona Italy; Department of Medicine, Section of Internal Medicine, University of Verona, P.le L.A. Scuro 10, 37134 Verona Italy.
| | - Gianni Zoccatelli
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona Italy.
| | - Roberto Chignola
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona Italy.
| | - Barbara Molesini
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona Italy.
| | - Pietro Minuz
- Department of Medicine, Section of Internal Medicine, University of Verona, P.le L.A. Scuro 10, 37134 Verona Italy.
| | - Tiziana Pandolfini
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona Italy.
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12
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Simon MD, Maki Y, Vinogradov AA, Zhang C, Yu H, Lin YS, Kajihara Y, Pentelute BL. d-Amino Acid Scan of Two Small Proteins. J Am Chem Soc 2016; 138:12099-111. [DOI: 10.1021/jacs.6b03765] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Mark D. Simon
- Department
of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Yuta Maki
- Department
of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1,
Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Alexander A. Vinogradov
- Department
of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Chi Zhang
- Department
of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
| | - Hongtao Yu
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Yu-Shan Lin
- Department
of Chemistry, Tufts University, 62 Talbot Avenue, Medford, Massachusetts 02155, United States
| | - Yasuhiro Kajihara
- Department
of Chemistry, Graduate School of Science, Osaka University, 1-1,
Machikaneyama-cho, Toyonaka, Osaka 560-0043, Japan
| | - Bradley L. Pentelute
- Department
of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts
Avenue, Cambridge, Massachusetts 02139, United States
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13
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Kuznetsova SS, Kolesanova EF, Talanova AV, Veselovsky AV. [Prospects for the design of new therapeutically significant protease inhibitors based on knottins and sunflower seed trypsin inhibitor (SFTI 1)]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2016; 62:353-68. [PMID: 27562989 DOI: 10.18097/pbmc20166204353] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Plant seed knottins, mainly from the Cucurbitacea family, and sunflower seed trypsin inhibitor (SFTI 1) are the most low-molecular canonical peptide inhibitors of serine proteases. High efficiency of inhibition of various serine proteases, structure rigidity together with the possibility of limited variations of amino acid sequences, high chemical stability, lack of toxic properties, opportunity of production by either chemical synthesis or use of heterologous expression systems make these inhibitors attractive templates for design of new compounds for regulation of therapeutically significant serine protease activities. Hence the design of such compounds represents a prospective research field. The review considers structural characteristics of these inhibitors, their properties, methods of preparation and design of new analogs. Examples of successful employment of natural serine protease inhibitors belonging to knottin family and SFTI 1 as templates for the design of highly specific inhibitors of certain proteases are given.
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Affiliation(s)
| | | | - A V Talanova
- Institute of Biomedical Chemistry, Moscow, Russia; Pirogov Russian National Research Medical University, Moscow, Russia
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14
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Cox N, Kintzing JR, Smith M, Grant GA, Cochran JR. Integrin-Targeting Knottin Peptide-Drug Conjugates Are Potent Inhibitors of Tumor Cell Proliferation. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201603488] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Nick Cox
- Stanford ChEM-H Medicinal Chemistry Knowledge Center; Stanford University; Stanford CA 94305 USA
| | - James R. Kintzing
- Department of Bioengineering; Stanford University; Stanford CA 94305 USA
| | - Mark Smith
- Stanford ChEM-H Medicinal Chemistry Knowledge Center; Stanford University; Stanford CA 94305 USA
| | - Gerald A. Grant
- Department of Neurosurgery; Stanford University; Stanford CA 94305 USA
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15
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Cox N, Kintzing JR, Smith M, Grant GA, Cochran JR. Integrin-Targeting Knottin Peptide-Drug Conjugates Are Potent Inhibitors of Tumor Cell Proliferation. Angew Chem Int Ed Engl 2016; 55:9894-7. [PMID: 27304709 DOI: 10.1002/anie.201603488] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2016] [Revised: 05/16/2016] [Indexed: 01/05/2023]
Abstract
Antibody-drug conjugates (ADCs) offer increased efficacy and reduced toxicity compared to systemic chemotherapy. Less attention has been paid to peptide-drug delivery, which has the potential for increased tumor penetration and facile synthesis. We report a knottin peptide-drug conjugate (KDC) and demonstrate that it can selectively deliver gemcitabine to malignant cells expressing tumor-associated integrins. This KDC binds to tumor cells with low-nanomolar affinity, is internalized by an integrin-mediated process, releases its payload intracellularly, and is a highly potent inhibitor of brain, breast, ovarian, and pancreatic cancer cell lines. Notably, these features enable this KDC to bypass a gemcitabine-resistance mechanism found in pancreatic cancer cells. This work expands the therapeutic relevance of knottin peptides to include targeted drug delivery, and further motivates efforts to expand the drug-conjugate toolkit to include non-antibody protein scaffolds.
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Affiliation(s)
- Nick Cox
- Stanford ChEM-H Medicinal Chemistry Knowledge Center, Stanford University, Stanford, CA, 94305, USA
| | - James R Kintzing
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA
| | - Mark Smith
- Stanford ChEM-H Medicinal Chemistry Knowledge Center, Stanford University, Stanford, CA, 94305, USA
| | - Gerald A Grant
- Department of Neurosurgery, Stanford University, Stanford, CA, 94305, USA
| | - Jennifer R Cochran
- Department of Bioengineering, Stanford University, Stanford, CA, 94305, USA.
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16
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Su M, Li H, Wang H, Kim EL, Kim HS, Kim EH, Lee J, Jung JH. Stable and biocompatible cystine knot peptides from the marine sponge Asteropus sp. Bioorg Med Chem 2016; 24:2979-2987. [PMID: 27189887 DOI: 10.1016/j.bmc.2016.05.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2016] [Revised: 05/05/2016] [Accepted: 05/05/2016] [Indexed: 11/16/2022]
Abstract
Two new cystine knot peptides, asteropsins F (ASPF) and G (ASPG), were isolated from the marine sponge Asteropus sp. ASPF and ASPG are composed of 33 and 32 amino acids, respectively, and contain six cysteines which are involved in three disulfide bonds. They shared the characteristic features of the asteropsin family, such as, N-terminal pyroglutamate modification, incorporation of cis prolines, and the unique anionic profile, which distinguish them from other knottin families. Tertiary structures of the peptides were determined by high resolution NMR. ASPF and ASPG were found to be remarkably resistant not only to digestive enzymes (chymotrypsin, pepsin, elastase, and trypsin) but also to thermal degradation. In addition, these peptides were pharmacologically inert; non-hemolytic to human and fish red blood cells, non-stimulatory to murine macrophage cells, and nontoxic in vitro or in vivo. These observations support their stability and biocompatibility as suitable carrier scaffolds for the design of oral peptide drug.
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Affiliation(s)
- Mingzhi Su
- College of Pharmacy, Pusan National University, Busan 609-735, Republic of Korea
| | - Huayue Li
- School of Medicine and Pharmacy, Ocean University of China, Qingdao 266003, China
| | - Haibo Wang
- College of Pharmacy, Pusan National University, Busan 609-735, Republic of Korea
| | - Eun La Kim
- College of Pharmacy, Pusan National University, Busan 609-735, Republic of Korea
| | - Hyung Sik Kim
- College of Pharmacy, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Eun-Hee Kim
- Division of Magnetic Resonance, Korea Basic Science Institute, Ochang 363-883, Republic of Korea
| | - Jaewon Lee
- College of Pharmacy, Pusan National University, Busan 609-735, Republic of Korea
| | - Jee H Jung
- College of Pharmacy, Pusan National University, Busan 609-735, Republic of Korea.
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17
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Poth AG, Chan LY, Craik DJ. Cyclotides as grafting frameworks for protein engineering and drug design applications. Biopolymers 2016; 100:480-91. [PMID: 23893608 DOI: 10.1002/bip.22284] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2013] [Revised: 04/30/2013] [Accepted: 05/07/2013] [Indexed: 11/08/2022]
Abstract
Cyclotides are a family of naturally occurring backbone-cyclized macrocyclic mini-proteins from plants that have a knotted trio of intramolecular disulfide bonds. Their structural features imbue cyclotides with extraordinary stability against degradation at elevated temperatures or in the presence of proteolytic enzymes. The plasticity of their intracysteine loop sequences is exemplified by the more than 250 natural cyclotides sequenced to date, and this tolerance to sequence variation, along with their diverse bioactivities, underpins the suitability of the cyclic cystine knot motif as a valuable drug design scaffold and research tool for protein engineering studies. Here, we review the recent literature on applications of cyclotides for the stabilization of peptide epitopes and related protein engineering studies. Possible future directions in this field are also described.
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Affiliation(s)
- Aaron G Poth
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
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18
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Jones PM, George AM. Computational analysis of the MCoTI-II plant defence knottin reveals a novel intermediate conformation that facilitates trypsin binding. Sci Rep 2016; 6:23174. [PMID: 26975976 PMCID: PMC4791599 DOI: 10.1038/srep23174] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 02/25/2016] [Indexed: 11/09/2022] Open
Abstract
MCoTI-I and II are plant defence proteins, potent trypsin inhibitors from the bitter gourd Momordica cochinchinensis. They are members of the Knottin Family, which display exceptional stability due to unique topology comprising three interlocked disulfide bridges. Knottins show promise as scaffolds for new drug development. A crystal structure of trypsin-bound MCoTI-II suggested that loop 1, which engages the trypsin active site, would show decreased dynamics in the bound state, an inference at odds with an NMR analysis of MCoTI-I, which revealed increased dynamics of loop 1 in the presence of trypsin. To investigate this question, we performed unrestrained MD simulations of trypsin-bound and free MCoTI-II. This analysis found that loop 1 of MCoTI-II is not more dynamic in the trypsin-bound state than in the free state. However, it revealed an intermediate conformation, transitional between the free and bound MCoTI-II states. The data suggest that MCoTI-II binding involves a process in which initial interaction with trypsin induces transitions between the free and intermediate conformations, and fluctuations between these states account for the increase in dynamics of loop 1 observed for trypsin-bound MCoTI-I. The MD analysis thus revealed new aspects of the inhibitors’ dynamics that may be of utility in drug design.
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Affiliation(s)
- Peter M Jones
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, NSW 2007 Australia
| | - Anthony M George
- School of Life Sciences, University of Technology Sydney, PO Box 123, Broadway, NSW 2007 Australia
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19
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Synthetic Cystine-Knot Miniproteins - Valuable Scaffolds for Polypeptide Engineering. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 917:121-44. [PMID: 27236555 DOI: 10.1007/978-3-319-32805-8_7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Peptides with the cystine-knot architecture, often termed knottins, are promising scaffolds for biomolecular engineering. These unique molecules combine diverse bioactivities with excellent structural, thermal, and proteolytical stability. Being different in the composition and structure of their amino acid backbone, knottins share the same core element, namely cystine knot, which is built by six cysteine residues forming three disulfides upon oxidative folding. This motif ensures a notably rigid framework that highly tolerates both rational and combinatorial changes in the primary structure. Being accessible through recombinant production and total chemical synthesis, cystine-knot miniproteins can be endowed with novel bioactivities by variation of surface-exposed loops and incorporation of non-natural elements within their non-conserved regions towards the generation of tailor-made peptidic compounds. In this chapter the topology of cystine-knot peptides, their synthesis and applications for diagnostics and therapy is discussed.
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20
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High Proteolytic Resistance of Spider-Derived Inhibitor Cystine Knots. INTERNATIONAL JOURNAL OF PEPTIDES 2015; 2015:537508. [PMID: 26843868 PMCID: PMC4710912 DOI: 10.1155/2015/537508] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 11/30/2015] [Accepted: 12/09/2015] [Indexed: 12/21/2022]
Abstract
Proteolytic stability in gastrointestinal tract and blood plasma is the major obstacle for oral peptide drug development. Inhibitor cystine knots (ICKs) are linear cystine knot peptides which have multifunctional properties and could become promising drug scaffolds. ProTx-I, ProTx-II, GTx1-15, and GsMTx-4 were spider-derived ICKs and incubated with pepsin, trypsin, chymotrypsin, and elastase in physiological conditions to find that all tested peptides were resistant to pepsin, and ProTx-II, GsMTx-4, and GTx1-15 showed resistance to all tested proteases. Also, no ProTx-II degradation was observed in rat blood plasma for 24 hours in vitro and ProTx-II concentration in circulation decreased to half in 40 min, indicating absolute stability in plasma and fast clearance from the system. So far, linear peptides are generally thought to be unsuitable in vivo, but all tested ICKs were not degraded by pepsin and stomach could be selected for the alternative site of drug absorption for fast onset of the drug action. Since spider ICKs are selective inhibitors of various ion channels which are related to the pathology of many diseases, engineered ICKs will make a novel class of peptide medicines which can treat variety of bothering symptoms.
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21
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Tam JP, Wang S, Wong KH, Tan WL. Antimicrobial Peptides from Plants. Pharmaceuticals (Basel) 2015; 8:711-57. [PMID: 26580629 PMCID: PMC4695807 DOI: 10.3390/ph8040711] [Citation(s) in RCA: 283] [Impact Index Per Article: 31.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/06/2015] [Accepted: 09/01/2015] [Indexed: 12/25/2022] Open
Abstract
Plant antimicrobial peptides (AMPs) have evolved differently from AMPs from other life forms. They are generally rich in cysteine residues which form multiple disulfides. In turn, the disulfides cross-braced plant AMPs as cystine-rich peptides to confer them with extraordinary high chemical, thermal and proteolytic stability. The cystine-rich or commonly known as cysteine-rich peptides (CRPs) of plant AMPs are classified into families based on their sequence similarity, cysteine motifs that determine their distinctive disulfide bond patterns and tertiary structure fold. Cystine-rich plant AMP families include thionins, defensins, hevein-like peptides, knottin-type peptides (linear and cyclic), lipid transfer proteins, α-hairpinin and snakins family. In addition, there are AMPs which are rich in other amino acids. The ability of plant AMPs to organize into specific families with conserved structural folds that enable sequence variation of non-Cys residues encased in the same scaffold within a particular family to play multiple functions. Furthermore, the ability of plant AMPs to tolerate hypervariable sequences using a conserved scaffold provides diversity to recognize different targets by varying the sequence of the non-cysteine residues. These properties bode well for developing plant AMPs as potential therapeutics and for protection of crops through transgenic methods. This review provides an overview of the major families of plant AMPs, including their structures, functions, and putative mechanisms.
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Affiliation(s)
- James P Tam
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Shujing Wang
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
- Department of Pharmacology and Pharmaceutical Sciences, School of Medicine, Tsinghua University, Beijing 100084, China.
| | - Ka H Wong
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
| | - Wei Liang Tan
- School of Biological Sciences, Nanyang Technological University, Singapore, Singapore.
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22
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Herzig V, King GF. The Cystine Knot Is Responsible for the Exceptional Stability of the Insecticidal Spider Toxin ω-Hexatoxin-Hv1a. Toxins (Basel) 2015; 7:4366-80. [PMID: 26516914 PMCID: PMC4626739 DOI: 10.3390/toxins7104366] [Citation(s) in RCA: 79] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/14/2015] [Accepted: 10/21/2015] [Indexed: 12/27/2022] Open
Abstract
The inhibitor cystine knot (ICK) is an unusual three-disulfide architecture in which one of the disulfide bonds bisects a loop formed by the two other disulfide bridges and the intervening sections of the protein backbone. Peptides containing an ICK motif are frequently considered to have high levels of thermal, chemical and enzymatic stability due to cross-bracing provided by the disulfide bonds. Experimental studies supporting this contention are rare, in particular for spider-venom toxins, which represent the largest diversity of ICK peptides. We used ω-hexatoxin-Hv1a (Hv1a), an insecticidal toxin from the deadly Australian funnel-web spider, as a model system to examine the contribution of the cystine knot to the stability of ICK peptides. We show that Hv1a is highly stable when subjected to temperatures up to 75 °C, pH values as low as 1, and various organic solvents. Moreover, Hv1a was highly resistant to digestion by proteinase K and when incubated in insect hemolymph and human plasma. We demonstrate that the ICK motif is essential for the remarkable stability of Hv1a, with the peptide’s stability being dramatically reduced when the disulfide bonds are eliminated. Thus, this study demonstrates that the ICK motif significantly enhances the chemical and thermal stability of spider-venom peptides and provides them with a high level of protease resistance. This study also provides guidance to the conditions under which Hv1a could be stored and deployed as a bioinsecticide.
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Affiliation(s)
- Volker Herzig
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia.
| | - Glenn F King
- Institute for Molecular Bioscience, The University of Queensland, St. Lucia QLD 4072, Australia.
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23
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Zhan C, Li C, Wei X, Lu W, Lu W. Toxins and derivatives in molecular pharmaceutics: Drug delivery and targeted therapy. Adv Drug Deliv Rev 2015; 90:101-18. [PMID: 25959429 DOI: 10.1016/j.addr.2015.04.025] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2015] [Revised: 04/20/2015] [Accepted: 04/29/2015] [Indexed: 01/13/2023]
Abstract
Protein and peptide toxins offer an invaluable source for the development of actively targeted drug delivery systems. They avidly bind to a variety of cognate receptors, some of which are expressed or even up-regulated in diseased tissues and biological barriers. Protein and peptide toxins or their derivatives can act as ligands to facilitate tissue- or organ-specific accumulation of therapeutics. Some toxins have evolved from a relatively small number of structural frameworks that are particularly suitable for addressing the crucial issues of potency and stability, making them an instrumental source of leads and templates for targeted therapy. The focus of this review is on protein and peptide toxins for the development of targeted drug delivery systems and molecular therapies. We summarize disease- and biological barrier-related toxin receptors, as well as targeted drug delivery strategies inspired by those receptors. The design of new therapeutics based on protein and peptide toxins is also discussed.
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Affiliation(s)
- Changyou Zhan
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education, Shanghai 201203, PR China
| | - Chong Li
- College of Pharmaceutical Sciences, Southwest University & Chongqing Engineering Research Center for Pharmaceutical Process and Quality Control, Chongqing 400716, PR China
| | - Xiaoli Wei
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education, Shanghai 201203, PR China; State Key Laboratory of Medical Neurobiology and the Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, PR China
| | - Wuyuan Lu
- Institute of Human Virology and Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Weiyue Lu
- Department of Pharmaceutics, School of Pharmacy, Fudan University & Key Laboratory of Smart Drug Delivery (Fudan University), Ministry of Education, Shanghai 201203, PR China; State Key Laboratory of Medical Neurobiology and the Collaborative Innovation Center for Brain Science, Fudan University, Shanghai 200032, PR China; State Key Laboratory of Molecular Engineering of Polymers, Fudan University, Shanghai 200433, PR China.
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24
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Gilmore SA, Voorhies M, Gebhart D, Sil A. Genome-Wide Reprogramming of Transcript Architecture by Temperature Specifies the Developmental States of the Human Pathogen Histoplasma. PLoS Genet 2015; 11:e1005395. [PMID: 26177267 PMCID: PMC4503680 DOI: 10.1371/journal.pgen.1005395] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2015] [Accepted: 06/26/2015] [Indexed: 11/28/2022] Open
Abstract
Eukaryotic cells integrate layers of gene regulation to coordinate complex cellular processes; however, mechanisms of post-transcriptional gene regulation remain poorly studied. The human fungal pathogen Histoplasma capsulatum (Hc) responds to environmental or host temperature by initiating unique transcriptional programs to specify multicellular (hyphae) or unicellular (yeast) developmental states that function in infectivity or pathogenesis, respectively. Here we used recent advances in next-generation sequencing to uncover a novel re-programming of transcript length between Hc developmental cell types. We found that ~2% percent of Hc transcripts exhibit 5’ leader sequences that differ markedly in length between morphogenetic states. Ribosome density and mRNA abundance measurements of differential leader transcripts revealed nuanced transcriptional and translational regulation. One such class of regulated longer leader transcripts exhibited tight transcriptional and translational repression. Further examination of these dually repressed genes revealed that some control Hc morphology and that their strict regulation is necessary for the pathogen to make appropriate developmental decisions in response to temperature. Eukaryotic cells alter their developmental programs in response to environmental signals. Histoplasma capsulatum (Hc), a ubiquitous fungal pathogen of humans, establishes unique transcriptional programs to specify growth in either a multicellular hyphal form or unicellular yeast form in response to temperature. Since hyphae and yeast are specialized to function in infectivity or pathogenesis, respectively, Hc provides a clinically relevant system in which to query eukaryotic regulatory processes. Here we used next-generation sequencing approaches to annotate the transcriptomes of four distinct Hc strains in response to temperature. We found that a fraction of Hc transcripts have differential transcript architecture in hyphae and yeast, exhibiting 5’ leader sequences that differ markedly in length between morphogenetic states. To begin to understand the effect of these differential leader sequences on expression, we performed the first ribosome density and mRNA abundance measurements in Hc, thereby uncovering transcriptional and translational control that contribute to cell-type regulation.
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Affiliation(s)
- Sarah A. Gilmore
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Mark Voorhies
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Dana Gebhart
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America
| | - Anita Sil
- Department of Microbiology and Immunology, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, California, United States of America
- * E-mail:
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25
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Maaß F, Wüstehube-Lausch J, Dickgießer S, Valldorf B, Reinwarth M, Schmoldt HU, Daneschdar M, Avrutina O, Sahin U, Kolmar H. Cystine-knot peptides targeting cancer-relevant human cytotoxic T lymphocyte-associated antigen 4 (CTLA-4). J Pept Sci 2015; 21:651-60. [PMID: 25964162 DOI: 10.1002/psc.2782] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Revised: 03/15/2015] [Accepted: 03/16/2015] [Indexed: 11/09/2022]
Abstract
Cystine-knot peptides sharing a common fold but displaying a notably large diversity within the primary structure of flanking loops have shown great potential as scaffolds for the development of therapeutic and diagnostic agents. In this study, we demonstrated that the cystine-knot peptide MCoTI-II, a trypsin inhibitor from Momordica cochinchinensis, can be engineered to bind to cytotoxic T lymphocyte-associated antigen 4 (CTLA-4), an inhibitory receptor expressed by T lymphocytes, that has emerged as a target for the treatment of metastatic melanoma. Directed evolution was used to convert a cystine-knot trypsin inhibitor into a CTLA-4 binder by screening a library of variants using yeast surface display. A set of cystine-knot peptides possessing dissociation constants in the micromolar range was obtained; the most potent variant was synthesized chemically. Successive conjugation with neutravidin, fusion to antibody Fc domain or the oligomerization domain of C4b binding protein resulted in oligovalent variants that possessed enhanced (up to 400-fold) dissociation constants in the nanomolar range. Our data indicate that display of multiple knottin peptides on an oligomeric scaffold protein is a valid strategy to improve their functional affinity with ramifications for applications in diagnostics and therapy.
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Affiliation(s)
- Franziska Maaß
- Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | | | - Stephan Dickgießer
- Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Bernhard Valldorf
- Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Michael Reinwarth
- Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | | | | | - Olga Avrutina
- Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | | | - Harald Kolmar
- Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
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26
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Kim JW, Cochran FV, Cochran JR. A chemically cross-linked knottin dimer binds integrins with picomolar affinity and inhibits tumor cell migration and proliferation. J Am Chem Soc 2014; 137:6-9. [PMID: 25486381 PMCID: PMC4304478 DOI: 10.1021/ja508416e] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
![]()
Molecules that target and inhibit
αvβ3, αvβ5, and α5β1 integrins have
generated great interest
because of the role of these receptors in mediating angiogenesis and
metastasis. Attempts to increase the binding affinity and hence the
efficacy of integrin inhibitors by dimerization have been marginally
effective. In the present work, we achieved this goal by using oxime-based
chemical conjugation to synthesize dimers of integrin-binding cystine
knot (knottin) miniproteins with low-picomolar binding affinity to
tumor cells. A non-natural amino acid containing an aminooxy side
chain was introduced at different locations within a knottin monomer
and reacted with dialdehyde-containing cross-linkers of different
lengths to create knottin dimers with varying molecular topologies.
Dimers cross-linked through an aminooxy functional group located near
the middle of the protein exhibited higher apparent binding affinity
to integrin-expressing tumor cells compared with dimers cross-linked
through an aminooxy group near the C-terminus. In contrast, the cross-linker
length had no effect on the integrin binding affinity. A chemical-based
dimerization strategy was critical, as knottin dimers created through
genetic fusion to a bivalent antibody domain exhibited only modest
improvement (less than 5-fold) in tumor cell binding relative to the
knottin monomer. The best oxime-conjugated knottin dimer achieved
an unprecedented 150-fold increase in apparent binding affinity over
the knottin monomer. Also, this dimer bound 3650-fold stronger and
inhibited tumor cell migration and proliferation compared with cilengitide,
an integrin-targeting peptidomimetic that performed poorly in recent
clinical trials, suggesting promise for further therapeutic development.
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Affiliation(s)
- Jun W Kim
- Departments of †Bioengineering and ‡Chemical Engineering, Stanford University , Stanford, California 94305, United States
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27
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Reinwarth M, Avrutina O, Fabritz S, Kolmar H. Fragmentation follows structure: top-down mass spectrometry elucidates the topology of engineered cystine-knot miniproteins. PLoS One 2014; 9:e108626. [PMID: 25303319 PMCID: PMC4193770 DOI: 10.1371/journal.pone.0108626] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Accepted: 09/02/2014] [Indexed: 12/21/2022] Open
Abstract
Over the last decades the field of pharmaceutically relevant peptides has enormously expanded. Among them, several peptide families exist that contain three or more disulfide bonds. In this context, elucidation of the disulfide patterns is extremely important as these motifs are often prerequisites for folding, stability, and activity. An example of this structure-determining pattern is a cystine knot which comprises three constrained disulfide bonds and represents a core element in a vast number of mechanically interlocked peptidic structures possessing different biological activities. Herein, we present our studies on disulfide pattern determination and structure elucidation of cystine-knot miniproteins derived from Momordica cochinchinensis peptide MCoTI-II, which act as potent inhibitors of human matriptase-1. A top-down mass spectrometric analysis of the oxidised and bioactive peptides is described. Following the detailed sequencing of the peptide backbone, interpretation of the MS(3) spectra allowed for the verification of the knotted topology of the examined miniproteins. Moreover, we found that the fragmentation pattern depends on the knottin's folding state, hence, tertiary structure, which to our knowledge has not been described for a top-down MS approach before.
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Affiliation(s)
- Michael Reinwarth
- Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | - Olga Avrutina
- Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
| | | | - Harald Kolmar
- Institute of Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Darmstadt, Germany
- * E-mail: (SF); (HK)
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28
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Ackerman SE, Wilson CM, Kahn SA, Kintzing JR, Jindal DA, Cheshier SH, Grant GA, Cochran JR. A Bioengineered Peptide that Localizes to and Illuminates Medulloblastoma: A New Tool with Potential for Fluorescence-Guided Surgical Resection. Cureus 2014; 6:e207. [PMID: 28729960 PMCID: PMC5515084 DOI: 10.7759/cureus.207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Tumors of the central nervous system are challenging to treat due to the limited effectiveness and associated toxicities of chemotherapy and radiation therapy. For tumors that can be removed surgically, extent of malignant tissue resection has been shown to correlate with disease progression, recurrence, and survival. Thus, improved technologies for real-time brain tumor imaging are critically needed as tools for guided surgical resection. We previously engineered a novel peptide that binds with high affinity and unique specificity to αVβ3, αVβ5, and α5β1 integrins, which are present on tumor cells, and the vasculature of many cancers, including brain tumors. In the current study, we conjugated this engineered peptide to a near infrared fluorescent dye (Alexa Fluor 680), and used the resulting molecular probe for non-invasive whole body imaging of patient-derived medulloblastoma xenograft tumors implanted in the cerebellum of mice. The engineered peptide exhibited robust targeting and illumination of intracranial medulloblastoma following both intravenous and intraperitoneal injection routes. In contrast, a variant of the engineered peptide containing a scrambled integrin-binding sequence did not localize to brain tumors, demonstrating that tumor-targeting is driven by specific integrin interactions. Ex vivo imaging was used to confirm the presence of tumor and molecular probe localization to the cerebellar region. These results warrant further clinical development of the engineered peptide as a tool for image-guided resection of central nervous system tumors.
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Affiliation(s)
| | | | - Suzana A. Kahn
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305
| | | | | | - Samuel H. Cheshier
- Department of Neurosurgery and Neurology, Stanford University School of Medicine & Lucile Packard Children’s Hospital, Department of Neurosurgery and Neurology, Stanford University School of Medicine & Lucile Packard Children’s Hospital at Stanford
| | - Gerald A. Grant
- Department of Neurosurgery, Stanford University School of Medicine
| | - Jennifer R. Cochran
- Department of Bioengineering and (by courtesy) Chemical Engineering, Stanford University
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29
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Lindgren J, Eriksson Karlström A. Intramolecular thioether crosslinking of therapeutic proteins to increase proteolytic stability. Chembiochem 2014; 15:2132-8. [PMID: 25204725 DOI: 10.1002/cbic.201400002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Indexed: 11/10/2022]
Abstract
Protein-based pharmaceuticals typically display high selectivity and low toxicity, but are also characterized by low oral availability, mainly because of enzymatic degradation in the gastrointestinal tract and poor permeability across the intestinal wall. One way to increase the proteolytic stability of peptides and proteins is by intramolecular crosslinking, such as the introduction of disulfide bridges. However, disulfide bridges are at risk of thiol-disulfide exchange or reduction during production, purification, and/or therapeutic use, whereas thioether bridges are expected to be stable under the same conditions. In this study, thioether crosslinking was investigated for a 46 aa albumin-binding domain (ABD) derived from streptococcal protein G. ABD binds with high affinity to human serum albumin (HSA) and has been proposed as a fusion partner to increase the in vivo half-lives of therapeutic proteins. In the study, five ABD variants with single or double intramolecular thioether bridges were designed and synthesized. The binding affinity, secondary structure, and thermal stability of each protein was investigated by SPR-based biosensor analysis and CD spectroscopy. The proteolytic stability in the presence of the major intestinal proteases pepsin (found in the stomach) and trypsin in combination with chymotrypsin (found in pancreatin secreted to the duodenum by the pancreas) was also investigated. The most promising crosslinked variant, ABD_CL1, showed high thermal stability, retained high affinity in binding to HSA, and showed dramatically increased stability in the presence of pepsin and trypsin/chymotrypsin, compared to the ABD reference protein. This suggests that the intramolecular thioether crosslinking strategy can be used to increase the stability towards gastrointestinal enzymes.
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Affiliation(s)
- Joel Lindgren
- KTH Royal Institute of Technology, School of Biotechnology, Division of Protein Technology, AlbaNova University Center, 106 91 Stockholm (Sweden)
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30
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Ackerman SE, Currier NV, Bergen JM, Cochran JR. Cystine-knot peptides: emerging tools for cancer imaging and therapy. Expert Rev Proteomics 2014; 11:561-72. [DOI: 10.1586/14789450.2014.932251] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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31
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Li H, Su M, Hamann MT, Bowling JJ, Kim HS, Jung JH. Solution structure of a sponge-derived cystine knot peptide and its notable stability. JOURNAL OF NATURAL PRODUCTS 2014; 77:304-310. [PMID: 24499386 PMCID: PMC4128683 DOI: 10.1021/np400899a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A novel cystine knot peptide, asteropsin E (ASPE), was isolated from an Asteropus sp. marine sponge. The primary, secondary, and tertiary structures of ASPE were determined by high-resolution 2D NMR spectroscopy (900 MHz). With the exception of an N-terminal modification, ASPE shares properties with the previously reported asteropsins A-D, that is, the absence of basic residues, a highly acidic nature, conserved structurally important residues (including two cis-prolines), and a highly conserved tertiary structural framework. ASPE was found to be remarkably stable to gastrointestinal tract enzymes (chymotrypsin, elastase, pepsin, and trypsin) and to human plasma.
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Affiliation(s)
- Huayue Li
- College of Pharmacy, Pusan National University, Busan 609-735, Republic of Korea
| | - Mingzhi Su
- College of Pharmacy, Pusan National University, Busan 609-735, Republic of Korea
| | - Mark T. Hamann
- Department of Pharmacognosy, School of Pharmacy, The University of Mississippi, Oxford, Mississippi 38677, United States
| | - John J. Bowling
- Department of Pharmacognosy, School of Pharmacy, The University of Mississippi, Oxford, Mississippi 38677, United States
| | - Hyung Sik Kim
- College of Pharmacy, Sungkyunkwan University, Suwon 440-746, Republic of Korea
| | - Jee H. Jung
- College of Pharmacy, Pusan National University, Busan 609-735, Republic of Korea
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32
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Zhu X, Li J, Hong Y, Kimura RH, Ma X, Liu H, Qin C, Hu X, Hayes TR, Benny P, Gambhir SS, Cheng Z. 99mTc-labeled cystine knot peptide targeting integrin αvβ6 for tumor SPECT imaging. Mol Pharm 2014; 11:1208-17. [PMID: 24524409 PMCID: PMC3993876 DOI: 10.1021/mp400683q] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Integrin
αvβ6 is overexpressed
in a variety of cancers, and its expression is often associated with
poor prognosis. Therefore, there is a need to develop affinity reagents
for noninvasive imaging of integrin αvβ6 expression since it may provide early cancer diagnosis, more
accurate prognosis, and better treatment planning. We recently engineered
and validated highly stable cystine knot peptides that selectively
bind integrin αvβ6 with no cross-reactivity
to integrins αvβ5, α5β1, or αvβ3, also
known to be overexpressed in many cancers. Here, we developed a single
photon emission computed tomography (SPECT) probe for imaging integrin
αvβ6 positive tumors. Cystine knot
peptide, S02, was first conjugated with a single amino
acid chelate (SAAC) and labeled with [99mTc(H2O)3(CO)3]+. The resulting probe, 99mTc-SAAC-S02, was then evaluated by in
vitro cell uptake studies using two αvβ6 positive cell lines (human lung adenocarcinoma cell line
HCC4006 and pancreatic cancer cell line BxPC-3) and two αvβ6 negative cell lines (human lung adenocarcinoma
cell line H838 and human embryonic kidney cell line 293T). Next, SPECT/CT
and biodistribution studies were performed in nude mice bearing HCC4006
and H838 tumor xenografts to evaluate the in vivo performance of 99mTc-SAAC-S02. Significant
differences in the uptake of 99mTc-SAAC-S02
were observed in αvβ6 positive vs
negative cells (P < 0.05). Biodistribution and
small animal SPECT/CT studies revealed that 99mTc-SAAC-S02 accumulated to moderate levels in antigen positive tumors
(∼2% ID/g at 1 and 6 h postinjection, n =
3 or 4/group). Moreover, the probe demonstrated tumor-to-background
tissue ratios of 6.81 ± 2.32 (tumor-to-muscle) and 1.63 ±
0.18 (tumor-to-blood) at 6 h postinjection in αvβ6 positive tumor xenografts. Co-incubation of the probe with
excess amount of unlabeled S02 as a blocking agent demonstrated
significantly reduced tumor uptake, which is consistent with specific
binding to the target. Renal filtration was the main route of clearance.
In conclusion, knottin peptides are excellent scaffolds for which
to develop highly stable imaging probes for a variety of oncological
targets. 99mTc-SAAC-S02 demonstrates promise
for use as a SPECT agent to image integrin αvβ6 expression in living systems.
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Affiliation(s)
- Xiaohua Zhu
- Molecular Imaging Program at Stanford (MIPS), Department of Radiology, and Bio-X Program, Canary Center at Stanford for Cancer Early Detection, Stanford University , Stanford, California 94305-5344, United States
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Asteropsins B-D, sponge-derived knottins with potential utility as a novel scaffold for oral peptide drugs. Biochim Biophys Acta Gen Subj 2013; 1840:977-84. [PMID: 24225326 DOI: 10.1016/j.bbagen.2013.11.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2013] [Revised: 10/19/2013] [Accepted: 11/05/2013] [Indexed: 01/19/2023]
Abstract
BACKGROUND Known linear knottins are unsuitable as scaffolds for oral peptide drug due to their gastrointestinal instability. Herein, a new subclass of knottin peptides from Porifera is structurally described and characterized regarding their potential for oral peptide drug development. METHODS Asteropsins B-D (ASPB, ASPC, and ASPD) were isolated from the marine sponge Asteropus sp. The tertiary structures of ASPB and ASPC were determined by solution NMR spectroscopy and that of ASPD by homology modeling. RESULTS The isolated asteropsins B-D, together with the previously reported asteropsin A (ASPA), compose a new subclass of knottins that share a highly conserved structural framework and remarkable stability against the enzymes in gastrointestinal tract (chymotrypsin, elastase, pepsin, and trypsin) and human plasma. CONCLUSION Asteropsins can be considered as promising peptide scaffolds for oral bioavailability. GENERAL SIGNIFICANCE The structural details of asteropsins provide essential information for the engineering of orally bioavailable peptides.
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Knottins: disulfide-bonded therapeutic and diagnostic peptides. DRUG DISCOVERY TODAY. TECHNOLOGIES 2013; 9:e1-e70. [PMID: 24064239 DOI: 10.1016/j.ddtec.2011.07.003] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Glotzbach B, Reinwarth M, Weber N, Fabritz S, Tomaszowski M, Fittler H, Christmann A, Avrutina O, Kolmar H. Combinatorial optimization of cystine-knot peptides towards high-affinity inhibitors of human matriptase-1. PLoS One 2013; 8:e76956. [PMID: 24146945 PMCID: PMC3795654 DOI: 10.1371/journal.pone.0076956] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 08/27/2013] [Indexed: 12/02/2022] Open
Abstract
Cystine-knot miniproteins define a class of bioactive molecules with several thousand natural members. Their eponymous motif comprises a rigid structured core formed by six disulfide-connected cysteine residues, which accounts for its exceptional stability towards thermic or proteolytic degradation. Since they display a remarkable sequence tolerance within their disulfide-connected loops, these molecules are considered promising frameworks for peptide-based pharmaceuticals. Natural open-chain cystine-knot trypsin inhibitors of the MCoTI (Momordica cochinchinensis trypsin inhibitor) and SOTI (Spinacia oleracea trypsin inhibitor) families served as starting points for the generation of inhibitors of matriptase-1, a type II transmembrane serine protease with possible clinical relevance in cancer and arthritic therapy. Yeast surface-displayed libraries of miniproteins were used to select unique and potent matriptase-1 inhibitors. To this end, a knowledge-based library design was applied that makes use of detailed information on binding and folding behavior of cystine-knot peptides. Five inhibitor variants, four of the MCoTI family and one of the SOTI family, were identified, chemically synthesized and oxidatively folded towards the bioactive conformation. Enzyme assays revealed inhibition constants in the low nanomolar range for all candidates. One subnanomolar binder (Ki = 0.83 nM) with an inverted selectivity towards trypsin and matriptase-1 was identified.
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Affiliation(s)
- Bernhard Glotzbach
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
| | - Michael Reinwarth
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
| | - Niklas Weber
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
| | | | - Michael Tomaszowski
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
| | - Heiko Fittler
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
| | - Andreas Christmann
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
| | - Olga Avrutina
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
| | - Harald Kolmar
- Clemens-Schöpf-Institut für Organische Chemie und Biochemie, Technische Universität Darmstadt, Darmstadt, Germany
- * E-mail:
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Moore SJ, Leung CL, Norton HK, Cochran JR. Engineering agatoxin, a cystine-knot peptide from spider venom, as a molecular probe for in vivo tumor imaging. PLoS One 2013; 8:e60498. [PMID: 23573262 PMCID: PMC3616073 DOI: 10.1371/journal.pone.0060498] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2012] [Accepted: 02/26/2013] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Cystine-knot miniproteins, also known as knottins, have shown great potential as molecular scaffolds for the development of targeted therapeutics and diagnostic agents. For this purpose, previous protein engineering efforts have focused on knottins based on the Ecballium elaterium trypsin inhibitor (EETI) from squash seeds, the Agouti-related protein (AgRP) neuropeptide from mammals, or the Kalata B1 uterotonic peptide from plants. Here, we demonstrate that Agatoxin (AgTx), an ion channel inhibitor found in spider venom, can be used as a molecular scaffold to engineer knottins that bind with high-affinity to a tumor-associated integrin receptor. METHODOLOGY/PRINCIPAL FINDINGS We used a rational loop-grafting approach to engineer AgTx variants that bound to αvβ3 integrin with affinities in the low nM range. We showed that a disulfide-constrained loop from AgRP, a structurally-related knottin, can be substituted into AgTx to confer its high affinity binding properties. In parallel, we identified amino acid mutations required for efficient in vitro folding of engineered integrin-binding AgTx variants. Molecular imaging was used to evaluate in vivo tumor targeting and biodistribution of an engineered AgTx knottin compared to integrin-binding knottins based on AgRP and EETI. Knottin peptides were chemically synthesized and conjugated to a near-infrared fluorescent dye. Integrin-binding AgTx, AgRP, and EETI knottins all generated high tumor imaging contrast in U87MG glioblastoma xenograft models. Interestingly, EETI-based knottins generated significantly lower non-specific kidney imaging signals compared to AgTx and AgRP-based knottins. CONCLUSIONS/SIGNIFICANCE In this study, we demonstrate that AgTx, a knottin from spider venom, can be engineered to bind with high affinity to a tumor-associated receptor target. This work validates AgTx as a viable molecular scaffold for protein engineering, and further demonstrates the promise of using tumor-targeting knottins as probes for in vivo molecular imaging.
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Affiliation(s)
- Sarah J. Moore
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Cheuk Lun Leung
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
| | - Heidi K. Norton
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
| | - Jennifer R. Cochran
- Department of Bioengineering, Stanford University, Stanford, California, United States of America
- Department of Chemical Engineering, Stanford University, Stanford, California, United States of America
- Stanford Cancer Institute and Bio-X Program, Stanford, California, United States of America
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Reinwarth M, Glotzbach B, Tomaszowski M, Fabritz S, Avrutina O, Kolmar H. Oxidative folding of peptides with cystine-knot architectures: kinetic studies and optimization of folding conditions. Chembiochem 2012; 14:137-46. [PMID: 23229141 DOI: 10.1002/cbic.201200604] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Indexed: 11/07/2022]
Abstract
Bioactive peptides often contain several disulfide bonds that provide the main contribution to conformational rigidity and structural, thermal, or biological stability. Among them, cystine-knot peptides-commonly named "knottins"-make up a subclass with several thousand natural members. Hence, they are considered promising frameworks for peptide-based pharmaceuticals. Although cystine-knot peptides are available through chemical and recombinant synthetic routes, oxidative folding to afford the bioactive isomers still remains a crucial step. We therefore investigated the oxidative folding of ten protease-inhibiting peptides from two knottin families, as well as that of an HIV entry inhibitor and of aprotinin, under two conventional sets of folding conditions and by a newly developed procedure. Kinetic studies identified folding conditions that resulted in correctly folded miniproteins with high rates of conversion even for highly hydrophobic and aggregation-prone peptides in concentrated solutions.
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Affiliation(s)
- Michael Reinwarth
- Institute for Organic Chemistry and Biochemistry, Technische Universität Darmstadt, Petersenstr. 22, 64287 Darmstadt, Germany
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Eliasen R, Daly NL, Wulff BS, Andresen TL, Conde-Frieboes KW, Craik DJ. Design, synthesis, structural and functional characterization of novel melanocortin agonists based on the cyclotide kalata B1. J Biol Chem 2012; 287:40493-501. [PMID: 23012369 DOI: 10.1074/jbc.m112.395442] [Citation(s) in RCA: 82] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
BACKGROUND Cyclotides are useful scaffolds to stabilize bioactive peptides. RESULTS Four melanocortin analogues of kalata B1 were synthesized. One is a selective MC4R agonist. CONCLUSION The analogues retain the native kalata B1 scaffold and introduce a designed pharmacological activity, validating cyclotides as protein engineering scaffolds. SIGNIFICANCE A novel type of melanocortin agonist has been developed, with potential as a drug lead for treating obesity. Obesity is an increasingly important global health problem that lacks current treatment options. The melanocortin receptor 4 (MC4R) is a target for obesity therapies because its activation triggers appetite suppression and increases energy expenditure. Cyclotides have been suggested as scaffolds for the insertion and stabilization of pharmaceutically active peptides. In this study, we explored the development of appetite-reducing peptides by synthesizing MC4R agonists based on the insertion of the His-Phe-Arg-Trp sequence into the cyclotide kalata B1. The ability of the analogues to fold similarly to kalata B1 but display MC4R activity were investigated. Four peptides were synthesized using t-butoxycarbonyl peptide chemistry with a C-terminal thioester to facilitate backbone cyclization. The structures of the peptides were found to be similar to kalata B1, evaluated by Hα NMR chemical shifts. KB1(GHFRWG;23-28) had a K(i) of 29 nm at the MC4R and was 107 or 314 times more selective over this receptor than MC1R or MC5R, respectively, and had no detectable binding to MC3R. The peptide had higher affinity for the MC4R than the endogenous agonist, α-melanocyte stimulation hormone, but it was less potent at the MC4R, with an EC(50) of 580 nm for activation of the MC4R. In conclusion, we synthesized melanocortin analogues of kalata B1 that preserve the structural scaffold and display receptor binding and functional activity. KB1(GHFRWG;23-28) is potent and selective for the MC4R. This compound validates the use of cyclotides as scaffolds and has the potential to be a new lead for the treatment of obesity.
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Eliasen R, Andresen TL, Conde-Frieboes KW. Handling a tricycle: orthogonal versus random oxidation of the tricyclic inhibitor cystine knotted peptide gurmarin. Peptides 2012; 37:144-9. [PMID: 22771618 DOI: 10.1016/j.peptides.2012.06.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/22/2012] [Revised: 06/26/2012] [Accepted: 06/26/2012] [Indexed: 11/22/2022]
Abstract
Gurmarin is a 35 amino acid peptide with three disulfide bridges in an inhibitor cystine knot. It is found in the plant Gymnema sylvestre, and has been identified as a sweet taste inhibitor in rodents. In this article we provide an efficient route for the synthesis of gurmarin by a controlled random oxidation strategy. We compared two oxidation procedures to form the three disulfide bridges. In the first, based on random oxidation, reduced gurmarin was synthesized using trityl for cysteine protection, and oxidized for 48 h in a Tris-HCl buffer containing cystamine and reduced glutathione to facilitate disulfide scrambling. The second was based on step-wise deprotection followed by oxidation in which the cysteine pairs are orthogonally protected with tert-Butylthio, trityl and acetamidomethyl. To verify that the native gurmarin oxidation product was obtained, thermolysin cleavage was used. Cleavage of random oxidized gurmarin showed two possible disulfide combinations; the native and a non-native gurmarin disulfide isomer. The non-native isomer was therefore synthesized using the orthogonal deprotection-oxidation strategy and the native and the non-native gurmarin isomers were analyzed using UPLC. It was found that the random oxidation procedure leads to native gurmarin in high yield. Thus, the synthetic route was simple and significantly more efficient than previously reported syntheses of gurmarin and other cysteine rich peptides. Importantly, native gurmarin was obtained by random oxidation, which was confirmed by a synthetic approach for the first time.
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Affiliation(s)
- Rasmus Eliasen
- Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
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Abstract
Cystine-knot miniproteins, also known as knottins, contain a conserved core of three tightly woven disulfide bonds which impart extraordinary thermal and proteolytic stability. Interspersed between their conserved cysteine residues are constrained loops that possess high levels of sequence diversity among knottin family members. Together these attributes make knottins promising molecular scaffolds for protein engineering and translational applications. While naturally occurring knottins have shown potential as both diagnostic agents and therapeutics, protein engineering is playing an important and increasing role in creating designer molecules that bind to a myriad of biomedical targets. Toward this goal, rational and combinatorial approaches have been used to engineer knottins with novel molecular recognition properties. Here, methods are described for creating and screening knottin libraries using yeast surface display and fluorescence-activated cell sorting. Protocols are also provided for producing knottins by synthetic and recombinant methods, and for measuring the binding affinity of knottins to target proteins expressed on the cell surface.
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Affiliation(s)
- Sarah J Moore
- Department of Bioengineering, Cancer Institute, and Bio-X Program, Stanford University, Stanford, California, USA
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Getz JA, Rice JJ, Daugherty PS. Protease-resistant peptide ligands from a knottin scaffold library. ACS Chem Biol 2011; 6:837-44. [PMID: 21615106 PMCID: PMC3158827 DOI: 10.1021/cb200039s] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Peptides within the knottin family have been shown to possess inherent stability, making them attractive scaffolds for the development of therapeutic and diagnostic agents. Given its remarkable stability to proteases, the cyclic peptide kalata B1 was employed as a scaffold to create a large knottin library displayed on the surface of E. coli. A library exceeding 10(9) variants was constructed by randomizing seven amino acids within a loop of the kalata B1 scaffold and screened using fluorescence-activated cell sorting to identify peptide ligands specific for the active site of human thrombin. Refolded thrombin binders exhibited high nanomolar affinities in solution and slow dissociation rates and were able to inhibit thrombin's enzymatic activity. Importantly, 80% of a knottin-based thrombin inhibitor remained intact after a 2 h incubation both with trypsin and with chymotrypsin, demonstrating that modifying the kalata B1 sequence did not compromise its stability properties. In addition, the knottin variant mediated 20-fold enhanced affinity for thrombin, when compared to the same seven residue binding epitope constrained by a single disulfide bond. Our results indicate that peptide libraries derived from the kalata B1 scaffold can yield high-affinity protein ligands that retain the remarkable protease resistance associated with the parent scaffold. More generally, this strategy may prove useful in the development of stable peptide ligands suitable for in vivo applications.
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Affiliation(s)
- Jennifer A. Getz
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106
| | - Jeffrey J. Rice
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106
| | - Patrick S. Daugherty
- Department of Chemical Engineering, University of California, Santa Barbara, CA 93106
- Institute for Collaborative Biotechnologies, University of California, Santa Barbara, CA 93106
- Biomolecular Science and Engineering, University of California, Santa Barbara, CA 93106
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Makhlof A, Tozuka Y, Takeuchi H. Design and evaluation of novel pH-sensitive chitosan nanoparticles for oral insulin delivery. Eur J Pharm Sci 2011; 42:445-51. [DOI: 10.1016/j.ejps.2010.12.007] [Citation(s) in RCA: 204] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2010] [Revised: 11/30/2010] [Accepted: 12/11/2010] [Indexed: 11/16/2022]
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Kolmar H. Engineered cystine-knot miniproteins for diagnostic applications. Expert Rev Mol Diagn 2010; 10:361-8. [PMID: 20370592 DOI: 10.1586/erm.10.15] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Owing to their extraordinary thermal and biological stability, cystine-knot miniproteins provide an attractive scaffold for the development of peptide-based diagnostics. One of the major advantages of this scaffold lies in the fact that the disulfide-constrained structural core can be functionalized by decoration with bioactive-loop residues. Methods have been developed to generate miniproteins with prescribed binding characteristics to a broad spectrum of different target proteins. They combine structural, biophysical and functional features that are beneficial for applications in molecular diagnostics in vivo (i.e., high affinity and selectivity, small size, high biological stability and fast renal clearance). Promising candidates for tumor imaging have been generated recently and evaluated in animal models, and more applications are expected in the near future.
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Affiliation(s)
- Harald Kolmar
- Clemens-Schöpf-Institut für Biochemie und Organische Chemie, Technische Universität Darmstadt, Petersenstrasse 22, Darmstadt, Germany.
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Silverman AP, Kariolis MS, Cochran JR. Cystine-knot peptides engineered with specificities for αIIbβ3 or αIIbβ3 and αvβ3 integrins are potent inhibitors of platelet aggregation. J Mol Recognit 2010; 24:127-35. [DOI: 10.1002/jmr.1036] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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46
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Jiang L, Kimura RH, Miao Z, Silverman AP, Ren G, Liu H, Li P, Gambhir SS, Cochran JR, Cheng Z. Evaluation of a (64)Cu-labeled cystine-knot peptide based on agouti-related protein for PET of tumors expressing alphavbeta3 integrin. J Nucl Med 2010; 51:251-258. [PMID: 20124048 DOI: 10.2967/jnumed.109.069831] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
UNLABELLED Recently, a truncated form of the agouti-related protein (AgRP), a 4-kDa cystine-knot peptide of human origin, was used as a scaffold to engineer mutants that bound to alpha(v)beta(3) integrin with high affinity and specificity. In this study, we evaluated the potential of engineered integrin-binding AgRP peptides for use as cancer imaging agents in living subjects. METHODS Engineered AgRP peptides were prepared by solid-phase peptide synthesis and were folded in vitro and purified by reversed-phase high-performance liquid chromatography. Competition assays were used to measure the relative binding affinities of engineered AgRP peptides for integrin receptors expressed on the surface of U87MG glioblastoma cells. The highest-affinity mutant, AgRP clone 7C, was site-specifically conjugated with 1,4,7,10-tetra-azacyclododecane-N,N',N''N'''-tetraacetic acid (DOTA). The resulting bioconjugate, DOTA-AgRP-7C, was radiolabeled with (64)Cu for biodistribution analysis and small-animal PET studies in mice bearing U87MG tumor xenografts. In addition to serum stability, the in vivo metabolic stability of (64)Cu-DOTA-AgRP-7C was assessed after injection and probe recovery from mouse kidney, liver, tumor, and urine. RESULTS AgRP-7C and DOTA-AgRP-7C bound with high affinity to integrin receptors expressed on U87MG cells (half maximal inhibitory concentration values, 20 +/- 4 and 14 +/- 2 nM, respectively). DOTA-AgRP-7C was labeled with (64)Cu with high radiochemical purity (>99%). In biodistribution and small-animal PET studies, (64)Cu-DOTA-AgRP-7C displayed rapid blood clearance, good tumor uptake and retention (2.70 +/- 0.93 percentage injected dose per gram [%ID/g] and 2.37 +/- 1.04 %ID/g at 2 and 24 h, respectively), and high tumor-to-background tissue ratios. The integrin-binding specificity of (64)Cu-DOTA-AgRP-7C was confirmed in vitro and in vivo by showing that a large molar excess of the unlabeled peptidomimetic c(RGDyK) could block probe binding and tumor uptake. Serum stability and in vivo metabolite assays demonstrated that engineered AgRP peptides are sufficiently stable for in vivo molecular imaging applications. CONCLUSION A radiolabeled version of the engineered AgRP peptide 7C showed promise as a PET agent for tumors that express the alpha(v)beta(3) integrin. Collectively, these results validate AgRP-based cystine-knot peptides for use in vivo as molecular imaging agents and provide support for the general use of AgRP as a scaffold to develop targeting peptides, and hence diagnostics, against other tumor receptors.
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Affiliation(s)
- Lei Jiang
- Department of Nuclear Medicine, Ruijin Hospital, Shanghai Jiaotong University, Shanghai, China.,Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Cancer Center, Bio-X Program, Stanford University, Stanford, California
| | - Richard H Kimura
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Cancer Center, Bio-X Program, Stanford University, Stanford, California
| | - Zheng Miao
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Cancer Center, Bio-X Program, Stanford University, Stanford, California
| | - Adam P Silverman
- Department of Bioengineering, Cancer Center, Bio-X Program, Stanford University, Stanford, California
| | - Gang Ren
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Cancer Center, Bio-X Program, Stanford University, Stanford, California
| | - Hongguang Liu
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Cancer Center, Bio-X Program, Stanford University, Stanford, California
| | - Peiyong Li
- Department of Nuclear Medicine, Ruijin Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Sanjiv Sam Gambhir
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Cancer Center, Bio-X Program, Stanford University, Stanford, California.,Department of Bioengineering, Cancer Center, Bio-X Program, Stanford University, Stanford, California
| | - Jennifer R Cochran
- Department of Bioengineering, Cancer Center, Bio-X Program, Stanford University, Stanford, California
| | - Zhen Cheng
- Department of Radiology, Molecular Imaging Program at Stanford (MIPS), Cancer Center, Bio-X Program, Stanford University, Stanford, California
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Craik DJ, Mylne JS, Daly NL. Cyclotides: macrocyclic peptides with applications in drug design and agriculture. Cell Mol Life Sci 2010; 67:9-16. [PMID: 19795188 PMCID: PMC11115554 DOI: 10.1007/s00018-009-0159-3] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2009] [Revised: 08/20/2009] [Accepted: 09/16/2009] [Indexed: 11/29/2022]
Abstract
Cyclotides are disulfide-rich peptides from plants that are exceptionally stable as a result of their unique cyclic cystine knot structural motif. Their natural role is thought to be as plant defence agents, most notably against insect pests, but they also have potential applications in drug design and agriculture. This article identifies gaps in current knowledge on cyclotides and suggests future directions for research into this fascinating family of ultra-stable mini-proteins.
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Affiliation(s)
- David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, 4072, Australia.
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Jagadish K, Camarero JA. Cyclotides, a promising molecular scaffold for peptide-based therapeutics. Biopolymers 2010; 94:611-6. [PMID: 20564025 PMCID: PMC3000894 DOI: 10.1002/bip.21433] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Cyclotides are a new emerging family of large plant-derived backbone-cyclized polypeptides (approximately 30 amino acids long) that share a disulfide-stabilized core (three disulfide bonds) characterized by an unusual knotted structure. Their unique circular backbone topology and knotted arrangement of three disulfide bonds make them exceptionally stable to thermal, chemical, and enzymatic degradation compared to other peptides of similar size. Currently, more than 100 sequences of different cyclotides have been characterized, and the number is expected to increase dramatically in the coming years. Considering their stability and biological activities like anti-HIV, uterotonic, and insecticidal, and also their abilities to cross the cell membrane, cyclotides can be exploited to develop new stable peptide-based drugs. We have recently demonstrated the intriguing possibility of producing libraries of cyclotides inside living bacterial cells. This opens the possibility to generate large genetically encoded libraries of cyclotides that can then be screened inside the cell for selecting particular biological activities in a high-throughput fashion. The present minireview reports the efforts carried out toward the selection of cyclotide-based compounds with specific biological activities for drug design.
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Affiliation(s)
- Krishnappa Jagadish
- 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
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Kimura RH, Levin AM, Cochran FV, Cochran JR. Engineered cystine knot peptides that bind alphavbeta3, alphavbeta5, and alpha5beta1 integrins with low-nanomolar affinity. Proteins 2009; 77:359-69. [PMID: 19452550 DOI: 10.1002/prot.22441] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
There is a critical need for compounds that target cell surface integrin receptors for applications in cancer therapy and diagnosis. We used directed evolution to engineer the Ecballium elaterium trypsin inhibitor (EETI-II), a knottin peptide from the squash family of protease inhibitors, as a new class of integrin-binding agents. We generated yeast-displayed libraries of EETI-II by substituting its 6-amino acid trypsin binding loop with 11-amino acid loops containing the Arg-Gly-Asp integrin binding motif and randomized flanking residues. These libraries were screened in a high-throughput manner by fluorescence-activated cell sorting to identify mutants that bound to alpha(v)beta(3) integrin. Select peptides were synthesized and were shown to compete for natural ligand binding to integrin receptors expressed on the surface of U87MG glioblastoma cells with half-maximal inhibitory concentration values of 10-30 nM. Receptor specificity assays demonstrated that engineered knottin peptides bind to both alpha(v)beta(3) and alpha(v)beta(5) integrins with high affinity. Interestingly, we also discovered a peptide that binds with high affinity to alpha(v)beta(3), alpha(v)beta(5), and alpha(5)beta(1) integrins. This finding has important clinical implications because all three of these receptors can be coexpressed on tumors. In addition, we showed that engineered knottin peptides inhibit tumor cell adhesion to the extracellular matrix protein vitronectin, and in some cases fibronectin, depending on their integrin binding specificity. Collectively, these data validate EETI-II as a scaffold for protein engineering, and highlight the development of unique integrin-binding peptides with potential for translational applications in cancer.
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Affiliation(s)
- Richard H Kimura
- Department of Bioengineering, Cancer Center, Bio-X Program, Stanford University, Stanford, California 94305, USA
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Heitz A, Avrutina O, Le-Nguyen D, Diederichsen U, Hernandez JF, Gracy J, Kolmar H, Chiche L. Knottin cyclization: impact on structure and dynamics. BMC STRUCTURAL BIOLOGY 2008; 8:54. [PMID: 19077275 PMCID: PMC2659701 DOI: 10.1186/1472-6807-8-54] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Accepted: 12/12/2008] [Indexed: 01/30/2023]
Abstract
Background Present in various species, the knottins (also referred to as inhibitor cystine knots) constitute a group of extremely stable miniproteins with a plethora of biological activities. Owing to their small size and their high stability, knottins are considered as excellent leads or scaffolds in drug design. Two knottin families contain macrocyclic compounds, namely the cyclotides and the squash inhibitors. The cyclotide family nearly exclusively contains head-to-tail cyclized members. On the other hand, the squash family predominantly contains linear members. Head-to-tail cyclization is intuitively expected to improve bioactivities by increasing stability and lowering flexibility as well as sensitivity to proteolytic attack. Results In this paper, we report data on solution structure, thermal stability, and flexibility as inferred from NMR experiments and molecular dynamics simulations of a linear squash inhibitor EETI-II, a circular squash inhibitor MCoTI-II, and a linear analog lin-MCoTI. Strikingly, the head-to-tail linker in cyclic MCoTI-II is by far the most flexible region of all three compounds. Moreover, we show that cyclic and linear squash inhibitors do not display large differences in structure or flexibility in standard conditions, raising the question as to why few squash inhibitors have evolved into cyclic compounds. The simulations revealed however that the cyclization increases resistance to high temperatures by limiting structure unfolding. Conclusion In this work, we show that, in contrast to what could have been intuitively expected, cyclization of squash inhibitors does not provide clear stability or flexibility modification. Overall, our results suggest that, for squash inhibitors in standard conditions, the circularization impact might come from incorporation of an additional loop sequence, that can contribute to the miniprotein specificity and affinity, rather than from an increase in conformational rigidity or protein stability. Unfolding simulations showed however that cyclization is a stabilizing factor in strongly denaturing conditions. This information should be useful if one wants to use the squash inhibitor scaffold in drug design.
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Affiliation(s)
- Annie Heitz
- CNRS, UMR5048, Université Montpellier 1 et 2, Centre de Biochimie Structurale, 34090 Montpellier, France.
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