51
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Cabalteja CC, Mihalko DS, Seth Horne W. Heterogeneous-Backbone Foldamer Mimics of a Computationally Designed, Disulfide-Rich Miniprotein. Chembiochem 2019; 20:103-110. [PMID: 30326175 PMCID: PMC6314896 DOI: 10.1002/cbic.201800558] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Indexed: 12/29/2022]
Abstract
Disulfide-rich peptides have found widespread use in the development of bioactive agents; however, low proteolytic stability and the difficulty of exerting synthetic control over chain topology present barriers to their application in some systems. Herein, we report a method that enables the creation of artificial backbone ("foldamer") mimics of compact, disulfide-rich tertiary folds. Systematic replacement of a subset of natural α-residues with various artificial building blocks in the context of a computationally designed prototype sequence leads to "heterogeneous-backbone" variants that undergo clean oxidative folding, adopt tertiary structures indistinguishable from that of the prototype, and enjoy proteolytic protection beyond that inherent to the topologically constrained scaffold. Collectively, these results demonstrate systematic backbone substitution to be a viable method to engineer the properties of disulfide-rich sequences and expands the repertoire of protein mimicry by foldamers to an exciting new structural class.
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Affiliation(s)
- Chino C. Cabalteja
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260 (USA)
| | - Daniel S. Mihalko
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260 (USA)
| | - W. Seth Horne
- Department of Chemistry, University of Pittsburgh, 219 Parkman Ave., Pittsburgh, PA 15260 (USA)
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52
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Bai Z, Cai C, Yu Z, Wang H. Backbone‐Enabled Directional Peptide Macrocyclization through Late‐Stage Palladium‐Catalyzed δ‐C(sp
2
)−H Olefination. Angew Chem Int Ed Engl 2018; 57:13912-13916. [DOI: 10.1002/anie.201807953] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Zengbing Bai
- State Key Laboratory of Coordination ChemistryJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Chuangxu Cai
- State Key Laboratory of Coordination ChemistryJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Zonglun Yu
- State Key Laboratory of Coordination ChemistryJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Huan Wang
- State Key Laboratory of Coordination ChemistryJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing University No. 163 Xianlin Ave Nanjing 210093 China
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53
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Bai Z, Cai C, Yu Z, Wang H. Backbone‐Enabled Directional Peptide Macrocyclization through Late‐Stage Palladium‐Catalyzed δ‐C(sp
2
)−H Olefination. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201807953] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Affiliation(s)
- Zengbing Bai
- State Key Laboratory of Coordination ChemistryJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Chuangxu Cai
- State Key Laboratory of Coordination ChemistryJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Zonglun Yu
- State Key Laboratory of Coordination ChemistryJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing University No. 163 Xianlin Ave Nanjing 210093 China
| | - Huan Wang
- State Key Laboratory of Coordination ChemistryJiangsu Key Laboratory of Advanced Organic MaterialsSchool of Chemistry and Chemical EngineeringNanjing University No. 163 Xianlin Ave Nanjing 210093 China
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54
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Cis/trans isomerization of proline peptide bonds in the backbone of cyclic disulfide‐bridged peptides. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24088] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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55
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Synthesis, biophysical and functional studies of two BP100 analogues modified by a hydrophobic chain and a cyclic peptide. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1502-1516. [PMID: 29750913 DOI: 10.1016/j.bbamem.2018.05.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Revised: 05/02/2018] [Accepted: 05/07/2018] [Indexed: 12/22/2022]
Abstract
Antimicrobial peptides (AMPs) work as a primary defense against pathogenic microorganisms. BP100, (KKLFKKILKYL-NH2), a rationally designed short, highly cationic AMP, acts against many bacteria, displaying low toxicity to eukaryotic cells. Previously we found that its mechanism of action depends on membrane surface charge and on peptide-to-lipid ratio. Here we present the synthesis of two BP100 analogs: BP100‑alanyl‑hexadecyl‑1‑amine (BP100-Ala-NH-C16H33) and cyclo(1‑4)‑d‑Cys1, Ile2, Leu3, Cys4-BP100 (Cyclo(1‑4)‑cILC-BP100). We examined their binding to large unilamellar vesicles (LUV), conformational and functional properties, and compared with those of BP100. The analogs bound to membranes with higher affinity and a lesser dependence on electrostatic forces than BP100. In the presence of LUV, BP100 and BP100-Ala-NH-C16H33 acquired α-helical conformation, while Cyclo(1‑4)‑cILC-BP100) was partly α-helical and partly β-turn. Taking in conjunction: 1. particle sizes and zeta potential, 2. effects on lipid flip-flop, 3. leakage of LUVs internal contents, and 4. optical microscopy of giant unilamellar vesicles, we concluded that at high concentrations, all three peptides acted by a carpet mechanism, while at low concentrations the peptides acted by disorganizing the lipid bilayer, probably causing membrane thinning. The higher activity and lesser membrane surface charge dependence of the analogs was probably due to their greater hydrophobicity. The MIC values of both analogs towards Gram-positive and Gram-negative bacteria were similar to those of BP100 but both analogues were more hemolytic. Confocal microscopy showed Gram-positive B. subtilis killing with concomitant extensive membrane damage suggestive of lipid clustering, or peptide-lipid aggregation. These results were in agreement with those found in model membranes.
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56
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Hegemann JD, van der Donk WA. Investigation of Substrate Recognition and Biosynthesis in Class IV Lanthipeptide Systems. J Am Chem Soc 2018; 140:5743-5754. [PMID: 29633842 PMCID: PMC5932250 DOI: 10.1021/jacs.8b01323] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Lanthipeptides belong to the family of ribosomally synthesized and post-translationally modified peptides (RiPPs) and are subdivided into four classes. The first two classes have been heavily studied, but less is known about classes III and IV. The lanthipeptide synthetases of classes III and IV share a similar organization of protein domains: A lyase domain at the N-terminus, a central kinase domain, and a C-terminal cyclase domain. Here, we provide deeper insight into class IV enzymes (LanLs). A series of putative producer strains was screened to identify production conditions of four new venezuelin-like lanthipeptides, and an Escherichia coli based heterologous production system was established for a fifth. The latter not only allowed production of fully modified core peptide but was also employed as the basis for mutational analysis of the precursor peptide to identify regions important for enzyme recognition. These experiments were complemented by in vitro binding studies aimed at identifying the region of the leader peptide recognized by the LanL enzymes as well as determining which domain of the enzyme is recognizing the substrate peptide. Combined, these studies revealed that the kinase domain is mediating the interaction with the precursor peptide and that a putatively α-helical stretch of residues at the center to N-terminal region of the leader peptide is important for enzyme recognition. In addition, a combination of in vitro assays and tandem mass spectrometry was used to elucidate the order of dehydration events in these systems.
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Affiliation(s)
- Julian D Hegemann
- Howard Hughes Medical Institute and Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana, Illinois 61801 , United States
| | - Wilfred A van der Donk
- Howard Hughes Medical Institute and Department of Chemistry , University of Illinois at Urbana-Champaign , 600 South Mathews Avenue , Urbana, Illinois 61801 , United States
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57
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Saikhedkar NS, Joshi RS, Bhoite AS, Mohandasan R, Yadav AK, Fernandes M, Kulkarni KA, Giri AP. Tripeptides derived from reactive centre loop of potato type II protease inhibitors preferentially inhibit midgut proteases of Helicoverpa armigera. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 95:17-25. [PMID: 29486250 DOI: 10.1016/j.ibmb.2018.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 02/07/2018] [Indexed: 06/08/2023]
Abstract
Potato type II protease inhibitors (Pin-II PIs) impede the growth of lepidopteran insects by inhibiting serine protease-like enzymes in the larval gut. The three amino acid reactive centre loop (RCL) of these proteinaceous inhibitors is crucial for protease binding and is conserved across the Pin-II family. However, the molecular mechanism and inhibitory potential of the RCL tripeptides in isolation of the native protein has remained elusive. In this study, six peptides corresponding to the RCLs of the predominant Pin-II PIs were identified, synthesized and evaluated for in vitro and in vivo inhibitory activity against serine proteases of the polyphagous insect, Helicoverpa armigera. RCL peptides with sequences PRN, PRY and TRE were found to be potent inhibitors that adversely affected the growth and development of H. armigera. The binding mechanism and differential affinity of the RCL peptides with serine proteases was delineated by crystal structures of complexes of the RCL peptides with trypsin. Residues P1 and P2 of the inhibitors play a crucial role in the interaction and specificity of these inhibitors. Important features of RCL peptides like higher inhibition of insect proteases, enhanced efficacy at alkaline gut pH, longer retention and high stability in insect gut make them suitable molecules for the development of sustainable pest management strategies for crop protection.
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Affiliation(s)
- Nidhi S Saikhedkar
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| | - Rakesh S Joshi
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India; Institute of Bioinformatics and Biotechnology, Savitribai Phule Pune University, Ganeshkhind, Pune, 411007, India
| | - Ashiwini S Bhoite
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| | - Radhika Mohandasan
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India
| | - Amit Kumar Yadav
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune 411 008, India
| | - Moneesha Fernandes
- Division of Organic Chemistry, CSIR-National Chemical Laboratory, Pune 411 008, India
| | - Kiran A Kulkarni
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India.
| | - Ashok P Giri
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411 008, India.
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58
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Zhang P, Wu J, Xiao F, Zhao D, Luan Y. Disulfide bond based polymeric drug carriers for cancer chemotherapy and relevant redox environments in mammals. Med Res Rev 2018; 38:1485-1510. [PMID: 29341223 DOI: 10.1002/med.21485] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2017] [Revised: 12/14/2017] [Accepted: 12/26/2017] [Indexed: 12/14/2022]
Abstract
Increasing numbers of disulfide linkage-employing polymeric drug carriers that utilize the reversible peculiarity of this unique covalent bond have been reported. The reduction-sensitive disulfide bond is usually employed as a linkage between hydrophilic and hydrophobic polymers, polymers and drugs, or as cross-linkers in polymeric drug carriers. These polymeric drug carriers are designed to exploit the significant redox potential difference between the reducing intracellular environments and relatively oxidizing extracellular spaces. In addition, these drug carriers can release a considerable amount of anticancer drug in response to the reducing environment when they reach tumor tissues, effectively improving antitumor efficacy. This review focuses on various disulfide linkage-employing polymeric drug carriers. Important redox thiol pools, including GSH/GSSG, Cys/CySS, and Trx1, as well as redox environments in mammals, will be introduced.
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Affiliation(s)
- Pei Zhang
- School of Pharmaceutical Science, Shandong University, Jinan, P. R. China
| | - Jilian Wu
- School of Pharmaceutical Science, Shandong University, Jinan, P. R. China
| | - Fengmei Xiao
- Binzhou Tuberculosis Prevention and Treatment Hospital, Binzhou, P. R. China
| | - Dujuan Zhao
- School of Pharmaceutical Science, Shandong University, Jinan, P. R. China
| | - Yuxia Luan
- School of Pharmaceutical Science, Shandong University, Jinan, P. R. China
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59
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Zaretsky S, Yudin AK. Recent advances in the synthesis of cyclic pseudopeptides. DRUG DISCOVERY TODAY. TECHNOLOGIES 2017; 26:3-10. [PMID: 29249240 DOI: 10.1016/j.ddtec.2017.11.004] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 06/07/2023]
Abstract
Constrained peptides pose tremendous value in drug discovery. For example, owing to their large surface areas, they offer novel ways at inhibiting protein-protein interactions. As this field has grown, it has become desirable to introduce non-peptidic functionality into these rings to enable differentiated structure activity relationships and improved pharmacokinetic properties. Recent advances in the synthesis of cyclic pseudopeptides include macrocyclization through cysteine alkylation, multicomponent reactions, decarboxylative couplings, and novel stapling chemistry.
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Affiliation(s)
- Serge Zaretsky
- University of Toronto, Lash Miller Chemical Labs, 80 St. George Street, Toronto, ON M5S 3H6, Canada.
| | - Andrei K Yudin
- University of Toronto, Lash Miller Chemical Labs, 80 St. George Street, Toronto, ON M5S 3H6, Canada.
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60
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Silva AF, Torres MDT, Silva LS, Alves FL, de Sá Pinheiro AA, Miranda A, Capurro ML, de la Fuente-Nunez C, Oliveira VX. Angiotensin II-derived constrained peptides with antiplasmodial activity and suppressed vasoconstriction. Sci Rep 2017; 7:14326. [PMID: 29085013 PMCID: PMC5662717 DOI: 10.1038/s41598-017-14642-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 10/05/2017] [Indexed: 12/19/2022] Open
Abstract
Angiotensin II (Ang II) is a natural mammalian hormone that has been described to exhibit antiplasmodial activity therefore constituting a promising alternative for the treatment of malaria. Despite its promise, the development of Ang II as an antimalarial is limited by its potent induction of vasoconstriction and its rapid degradation within minutes. Here, we used peptide design to perform targeted chemical modifications to Ang II to generate conformationally restricted (disulfide-crosslinked) peptide derivatives with suppressed vasoconstrictor activity and increased stability. Designed constrained peptides were synthesized chemically and then tested for antiplasmodial activity. Two lead constrained peptides were identified (i.e., peptides 1 and 2), each composed of 10 amino acid residues. These peptides exhibited very promising activity in both our Plasmodium gallinaceum (>80%) and Plasmodium falciparum (>40%) models, an activity that was equivalent to that of Ang II, and led to complete suppression of vasoconstriction. In addition, peptide 5 exhibited selective activity towards the pre-erythrocytic stage (98% of activity against P. gallinaceum), thus suggesting that it may be possible to design peptides that target specific stages of the malaria life cycle. The Ang II derived stable scaffolds presented here may provide the basis for development of a new generation of peptide-based drugs for the treatment of malaria.
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Affiliation(s)
- Adriana Farias Silva
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil
| | - Marcelo Der Torossian Torres
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil.,Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.,The Center for Microbiome Informatics and Therapeutics, Cambridge, Massachusetts, USA
| | - Leandro Souza Silva
- Instituto de Biofísica Carlos Chagas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Flavio Lopes Alves
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana Acácia de Sá Pinheiro
- Instituto de Biofísica Carlos Chagas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Antonio Miranda
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Margareth Lara Capurro
- Departamento de Parasitologia, Instituto de Ciências Biomédicas II, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Cesar de la Fuente-Nunez
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. .,Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. .,Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA. .,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA. .,The Center for Microbiome Informatics and Therapeutics, Cambridge, Massachusetts, USA.
| | - Vani Xavier Oliveira
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André, SP, Brazil.
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61
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Schmidt M, Toplak A, Quaedflieg PJLM, Ippel H, Richelle GJJ, Hackeng TM, van Maarseveen JH, Nuijens T. Omniligase-1: A Powerful Tool for Peptide Head-to-Tail Cyclization. Adv Synth Catal 2017. [DOI: 10.1002/adsc.201700314] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Marcel Schmidt
- EnzyPep B.V.; Brightlands Campus; Urmonderbaan 22 6167 RD Geleen The Netherlands
- Van 't Hoff Institute of Molecular Sciences; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | - Ana Toplak
- EnzyPep B.V.; Brightlands Campus; Urmonderbaan 22 6167 RD Geleen The Netherlands
| | | | - Hans Ippel
- Department of Biochemistry; CARIM; University of Maastricht; Universiteitsingel 50 6229 ER Maastricht The Netherlands
| | - Gaston J. J. Richelle
- Van 't Hoff Institute of Molecular Sciences; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | - Tilman M. Hackeng
- Department of Biochemistry; CARIM; University of Maastricht; Universiteitsingel 50 6229 ER Maastricht The Netherlands
| | - Jan H. van Maarseveen
- Van 't Hoff Institute of Molecular Sciences; University of Amsterdam; Science Park 904 1098 XH Amsterdam The Netherlands
| | - Timo Nuijens
- EnzyPep B.V.; Brightlands Campus; Urmonderbaan 22 6167 RD Geleen The Netherlands
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62
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Macrocycles as protein-protein interaction inhibitors. Biochem J 2017; 474:1109-1125. [PMID: 28298556 DOI: 10.1042/bcj20160619] [Citation(s) in RCA: 116] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Revised: 01/12/2017] [Accepted: 01/18/2017] [Indexed: 12/13/2022]
Abstract
Macrocyclic compounds such as cyclic peptides have emerged as a new and exciting class of drug candidates for inhibition of intracellular protein-protein interactions, which are challenging targets for conventional drug modalities (i.e. small molecules and proteins). Over the past decade, several complementary technologies have been developed to synthesize macrocycle libraries and screen them for binding to therapeutically relevant targets. Two different approaches have also been explored to increase the membrane permeability of cyclic peptides. In this review, we discuss these methods and their applications in the discovery of macrocyclic compounds against protein-protein interactions.
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63
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Johnson AM, Anslyn EV. Reversible Macrocyclization of Peptides with a Conjugate Acceptor. Org Lett 2017; 19:1654-1657. [DOI: 10.1021/acs.orglett.7b00451] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amber M. Johnson
- Department of Chemistry, University of Texas, 1 University Station A1590, Austin, Texas 78712, United States
| | - Eric V. Anslyn
- Department of Chemistry, University of Texas, 1 University Station A1590, Austin, Texas 78712, United States
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64
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Synthesis of Reusable Silica Nanosphere-Supported Pt(IV) Complex for Formation of Disulfide Bonds in Peptides. Molecules 2017; 22:molecules22020338. [PMID: 28241453 PMCID: PMC6155793 DOI: 10.3390/molecules22020338] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2016] [Revised: 02/10/2017] [Accepted: 02/16/2017] [Indexed: 11/17/2022] Open
Abstract
Some peptide-based drugs, including oxytocin, vasopressin, ziconotide, pramlintide, nesiritide, and octreotide, contain one intramolecular disulfide bond. A novel and reusable monodispersed silica nanosphere-supported Pt(IV) complex (SiO₂@TPEA@Pt(IV)); TPEA: N-[3-(trimethoxysilyl)propyl]ethylenediamine) was synthesized via a four-step procedure and was used for the formation of intramolecular disulfide bonds in peptides. Transmission electron microscopy (TEM) and chemical mapping results for the Pt(II) intermediates and for SiO₂@TPEA@Pt(IV) show that the silica nanospheres possess a monodisperse spherical structure and contain uniformly-distributed Si, O, C, N, Cl, and Pt. The valence state of Pt on the silica nanospheres was characterized by X-ray photoelectron spectroscopy (XPS). The Pt(IV) loaded on SiO₂@TPEA@Pt(IV) was 0.15 mmol/g, as determined by UV-VIS spectrometry. The formation of intramolecular disulfides in six dithiol-containing peptides of variable lengths by the use of SiO₂@TPEA@Pt(IV) was investigated, and the relative oxidation yields were determined by high-performance liquid chromatography (HPLC). In addition, peptide 1 (Ac-CPFC-NH₂) was utilized to study the reusability of SiO₂@TPEA@Pt(IV). No significant decrease in the relative oxidation yield was observed after ten reaction cycles. Moreover, the structure of SiO₂@TPEA@Pt(IV) after being used for ten cycles was determined to be similar to its initial one, demonstrating the cycling stability of the complex.
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65
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Hanold LE, Fulton MD, Kennedy EJ. Targeting kinase signaling pathways with constrained peptide scaffolds. Pharmacol Ther 2017; 173:159-170. [PMID: 28185915 DOI: 10.1016/j.pharmthera.2017.02.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Kinases are amongst the largest families in the human proteome and serve as critical mediators of a myriad of cell signaling pathways. Since altered kinase activity is implicated in a variety of pathological diseases, kinases have become a prominent class of proteins for targeted inhibition. Although numerous small molecule and antibody-based inhibitors have already received clinical approval, several challenges may still exist with these strategies including resistance, target selection, inhibitor potency and in vivo activity profiles. Constrained peptide inhibitors have emerged as an alternative strategy for kinase inhibition. Distinct from small molecule inhibitors, peptides can provide a large binding surface area that allows them to bind shallow protein surfaces rather than defined pockets within the target protein structure. By including chemical constraints within the peptide sequence, additional benefits can be bestowed onto the peptide scaffold such as improved target affinity and target selectivity, cell permeability and proteolytic resistance. In this review, we highlight examples of diverse chemistries that are being employed to constrain kinase-targeting peptide scaffolds and highlight their application to modulate kinase signaling as well as their potential clinical implications.
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Affiliation(s)
- Laura E Hanold
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States
| | - Melody D Fulton
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, College of Pharmacy, University of Georgia, Athens, GA 30602, United States.
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66
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Porto WF, Miranda VJ, Pinto MFS, Dohms SM, Franco OL. High-performance computational analysis and peptide screening from databases of cyclotides from poaceae. Biopolymers 2017; 106:109-18. [PMID: 26572696 DOI: 10.1002/bip.22771] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Revised: 10/21/2015] [Accepted: 11/09/2015] [Indexed: 12/22/2022]
Abstract
Cyclotides are a family of head-to-tail cyclized peptides containing three conserved disulfide bonds, in a structural scaffold also known as a cyclic cysteine knot. Due to the high degree of cysteine conservation, novel members from this peptide family can be identified in protein databases through a search through regular expression (REGEX). In this work, six novel cyclotide-like precursors from the Poaceae were identified from NCBI's non-redundant protein database by the use of REGEX. Two out of six sequences (named Zea mays L and M) showed an Asp residue in the C-terminal, which indicated that they could be cyclic. Gene expression in maize tissues was investigated, showing that the previously described cyclotide-like Z. mays J is expressed in the roots. According to molecular dynamics, the structure of Z. mays J seems to be stable, despite the putative absence of cyclization. As regards cyclotide evolution, it was hypothesized that this is an outcome from convergent evolution and/or horizontal gene transfer. The results showed that peptide screening from databases should be performed periodically in order to include novel sequences, which are deposited as the databases grow. Indeed, the advances in computational and experimental methods will together help to answer key questions and reach new horizons in defense-related peptide identification.
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Affiliation(s)
- William F Porto
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia Universidade Católica De Brasília, Brasília-DF, Brazil
| | - Vivian J Miranda
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia Universidade Católica De Brasília, Brasília-DF, Brazil
| | - Michelle F S Pinto
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia Universidade Católica De Brasília, Brasília-DF, Brazil
| | - Stephan M Dohms
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia Universidade Católica De Brasília, Brasília-DF, Brazil
| | - Octavio L Franco
- Centro De Análises Proteômicas E Bioquímicas, Pós-Graduação Em Ciências Genômicas E Biotecnologia Universidade Católica De Brasília, Brasília-DF, Brazil.,S-Inova Biotech, Pos Graduação em Biotecnologia, Universidade Catolica Dom Bosco, Campo Grande MS, Brazil
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67
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Schrimpf A, Linne U, Geyer A. Eight at one stroke – a synthetic tetra-disulfide peptide epitope. Org Biomol Chem 2017; 15:2512-2521. [DOI: 10.1039/c6ob02746f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
A tetra-disulfide peptide dimer, representing an antiparallel hinge, is synthesised without the need for orthogonal cysteine protecting groups.
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Affiliation(s)
- Andreas Schrimpf
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Uwe Linne
- Mass spectrometry facility of the Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
| | - Armin Geyer
- Department of Chemistry
- Philipps-Universität Marburg
- 35032 Marburg
- Germany
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68
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Park S, Yoo KO, Marcussen T, Backlund A, Jacobsson E, Rosengren KJ, Doo I, Göransson U. Cyclotide Evolution: Insights from the Analyses of Their Precursor Sequences, Structures and Distribution in Violets ( Viola). FRONTIERS IN PLANT SCIENCE 2017; 8:2058. [PMID: 29326730 PMCID: PMC5741643 DOI: 10.3389/fpls.2017.02058] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 11/17/2017] [Indexed: 05/20/2023]
Abstract
Cyclotides are a family of plant proteins that are characterized by a cyclic backbone and a knotted disulfide topology. Their cyclic cystine knot (CCK) motif makes them exceptionally resistant to thermal, chemical, and enzymatic degradation. By disrupting cell membranes, the cyclotides function as host defense peptides by exhibiting insecticidal, anthelmintic, antifouling, and molluscicidal activities. In this work, we provide the first insight into the evolution of this family of plant proteins by studying the Violaceae, in particular species of the genus Viola. We discovered 157 novel precursor sequences by the transcriptomic analysis of six Viola species: V. albida var. takahashii, V. mandshurica, V. orientalis, V. verecunda, V. acuminata, and V. canadensis. By combining these precursor sequences with the phylogenetic classification of Viola, we infer the distribution of cyclotides across 63% of the species in the genus (i.e., ~380 species). Using full precursor sequences from transcriptomes, we show an evolutionary link to the structural diversity of the cyclotides, and further classify the cyclotides by sequence signatures from the non-cyclotide domain. Also, transcriptomes were compared to cyclotide expression on a peptide level determined using liquid chromatography-mass spectrometry. Furthermore, the novel cyclotides discovered were associated with the emergence of new biological functions.
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Affiliation(s)
- Sungkyu Park
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Ki-Oug Yoo
- Department of Biological Sciences, Kangwon National University, Chuncheon, South Korea
| | - Thomas Marcussen
- Department of Biosciences, Centre for Ecological and Evolutionary Synthesis, University of Oslo, Oslo, Norway
| | - Anders Backlund
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - Erik Jacobsson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
| | - K. Johan Rosengren
- School of Biomedical Sciences, The University of Queensland, Brisbane, QLD, Australia
| | - Inseok Doo
- Biotech Research Team, Biotech Research Center of Dong-A Pharm Co Ltd., Seoul, South Korea
| | - Ulf Göransson
- Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Uppsala, Sweden
- *Correspondence: Ulf Göransson
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69
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Qiu Y, Taichi M, Wei N, Yang H, Luo KQ, Tam JP. An Orally Active Bradykinin B1 Receptor Antagonist Engineered as a Bifunctional Chimera of Sunflower Trypsin Inhibitor. J Med Chem 2016; 60:504-510. [DOI: 10.1021/acs.jmedchem.6b01011] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Yibo Qiu
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, 637551, Singapore
| | - Misako Taichi
- Biofunctional Synthetic Chemistry Laboratory, RIKEN 2-1 Hirosawa, Wako-shi, Saitama, 351-0198, Japan
| | - Na Wei
- School
of Chemical and Biomedical Engineering, Nanyang Technological University, 62 Nanyang Drive, 637459, Singapore
| | - Huan Yang
- School
of Pharmacy, Jiangsu University, 301 Xuefu Road, Zhenjiang, Jiangsu 212013, P. R. China
| | - Kathy Qian Luo
- Faculty
of Health Sciences, University of Macau, Taipa, Macau, P. R. China
| | - James P. Tam
- School
of Biological Sciences, Nanyang Technological University, 60 Nanyang
Drive, 637551, Singapore
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70
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Niyomploy P, Chan LY, Poth AG, Colgrave ML, Sangvanich P, Craik DJ. Discovery, isolation, and structural characterization of cyclotides from
Viola sumatrana
Miq. Pept Sci (Hoboken) 2016; 106:796-805. [DOI: 10.1002/bip.22914] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Revised: 06/21/2016] [Accepted: 06/29/2016] [Indexed: 01/18/2023]
Affiliation(s)
- Ploypat Niyomploy
- Institute for Molecular Bioscience, The University of QueenslandBrisbane QLD4072 Australia
- Department of Chemistry, Faculty of ScienceChulalongkorn UniversityBangkok10330 Thailand
| | - Lai Yue Chan
- Institute for Molecular Bioscience, The University of QueenslandBrisbane QLD4072 Australia
| | - Aaron G. Poth
- Institute for Molecular Bioscience, The University of QueenslandBrisbane QLD4072 Australia
| | | | - Polkit Sangvanich
- Department of Chemistry, Faculty of ScienceChulalongkorn UniversityBangkok10330 Thailand
| | - David J. Craik
- Institute for Molecular Bioscience, The University of QueenslandBrisbane QLD4072 Australia
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71
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Leenheer D, ten Dijke P, Hipolito CJ. A current perspective on applications of macrocyclic-peptide-based high-affinity ligands. Biopolymers 2016; 106:889-900. [PMID: 27352774 PMCID: PMC5132055 DOI: 10.1002/bip.22900] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2016] [Revised: 05/24/2016] [Accepted: 05/31/2016] [Indexed: 01/05/2023]
Abstract
Monoclonal antibodies can bind with high affinity and high selectivity to their targets. As a tool in therapeutics or diagnostics, however, their large size (∼150 kDa) reduces penetration into tissue and prevents passive cellular uptake. To overcome these and other problems, minimized protein scaffolds have been chosen or engineered, with care taken to not compromise binding affinity or specificity. An alternate approach is to begin with a minimal non-antibody scaffold and select functional ligands from a de novo library. We will discuss the structure, production, applications, strengths, and weaknesses of several classes of antibody-derived ligands, that is, antibodies, intrabodies, and nanobodies, and nonantibody-derived ligands, that is, monobodies, affibodies, and macrocyclic peptides. In particular, this review is focussed on macrocyclic peptides produced by the Random non-standard Peptides Integrated Discovery (RaPID) system that are small in size (typically ∼2 kDa), but are able to perform tasks typically handled by larger proteinaceous ligands.
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Affiliation(s)
- Daniël Leenheer
- Ph.D. Program in Human Biology, School of Integrative and Global MajorsUniversity of TsukubaTsukubaIbarakiJapan
| | - Peter ten Dijke
- Leiden University Medical Center, Department of Molecular Cell BiologyLeidenSouth HollandThe Netherlands
- Cancer Signaling, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of TsukubaTsukubaIbarakiJapan
| | - Christopher John Hipolito
- Cancer Signaling, Graduate School of Comprehensive Human Sciences and Faculty of Medicine, University of TsukubaTsukubaIbarakiJapan
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72
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73
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Chan LY, Craik DJ, Daly NL. Dual-targeting anti-angiogenic cyclic peptides as potential drug leads for cancer therapy. Sci Rep 2016; 6:35347. [PMID: 27734947 PMCID: PMC5062114 DOI: 10.1038/srep35347] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 09/28/2016] [Indexed: 12/29/2022] Open
Abstract
Peptide analogues derived from bioactive hormones such as somatostatin or certain growth factors have great potential as angiogenesis inhibitors for cancer applications. In an attempt to combat emerging drug resistance many FDA-approved anti-angiogenesis therapies are co-administered with cytotoxic drugs as a combination therapy to target multiple signaling pathways of cancers. However, cancer therapies often encounter limiting factors such as high toxicities and side effects. Here, we combined two anti-angiogenic epitopes that act on different pathways of angiogenesis into a single non-toxic cyclic peptide framework, namely MCoTI-II (Momordica cochinchinensis trypsin inhibitor-II), and subsequently assessed the anti-angiogenic activity of the novel compound. We hypothesized that the combination of these two epitopes would elicit a synergistic effect by targeting different angiogenesis pathways and result in improved potency, compared to that of a single epitope. This novel approach has resulted in the development of a potent, non-toxic, stable and cyclic analogue with nanomolar potency inhibition in in vitro endothelial cell migration and in vivo chorioallantoic membrane angiogenesis assays. This is the first report to use the MCoTI-II framework to develop a 2-in-1 anti-angiogenic peptide, which has the potential to be used as a form of combination therapy for targeting a wide range of cancers.
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Affiliation(s)
- Lai Yue Chan
- The University of Queensland, Institute for Molecular Bioscience, 4072 Brisbane, Australia
| | - David J Craik
- The University of Queensland, Institute for Molecular Bioscience, 4072 Brisbane, Australia
| | - Norelle L Daly
- Centre for Biodiscovery and Molecular Development of Therapeutics, Australian Institute of Tropical Health and Medicine, James Cook University, 4870 Cairns, Australia
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74
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Li Y, Tang C, Zhang E, Yang L. Colistin-entrapped liposomes driven by the electrostatic interaction: Mechanism of drug loading and in vivo characterization. Int J Pharm 2016; 515:20-29. [PMID: 27713028 DOI: 10.1016/j.ijpharm.2016.10.001] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/16/2016] [Accepted: 10/03/2016] [Indexed: 11/19/2022]
Abstract
The potential in vivo application of liposome for polycationic colistin has been hindered by the poor entrapment efficiency (EE) due to their phospholipid membrane permeability. The objective of this study is to investigate the loading mechanism and validity of applying electrostatic attraction for the colistin entrapment and delivery in liposomes. Anionic lipids with various structures were used for colistin entrapment, and the properties of resulting liposomes (i.e. zeta-potential, EE and release rate) were highly dependent on the structure of anionic lipids. Based on consideration of intermolecular interactions, the retention of electrostatically entrapped colistin is essentially determined by the balance of interfacial hydrophobic attraction and electrostatic repulsion. The liposomal colistin showed the reduced bacterial killing rate, but did not compromise the in vitro antibacterial activity. Specially, the PEGylated liposomal colistin of sodium cholesteryl sulfate (Chol-SO4-) showed the best drug retention, resulting in the significantly increased maximum-tolerated dose, prolonged blood circulation and decreased colistin distribution in kidney after intravenous administration in mice. These results highlight the potential utility of electrostatically entrapped liposome for polycationic colistin delivery.
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Affiliation(s)
- Yang Li
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Chengcheng Tang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Enbo Zhang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China
| | - Li Yang
- School of Pharmacy, Shenyang Pharmaceutical University, Shenyang, China.
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75
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Albert A, Eksteen JJ, Isaksson J, Sengee M, Hansen T, Vasskog T. General Approach To Determine Disulfide Connectivity in Cysteine-Rich Peptides by Sequential Alkylation on Solid Phase and Mass Spectrometry. Anal Chem 2016; 88:9539-9546. [DOI: 10.1021/acs.analchem.6b02115] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
| | | | - Johan Isaksson
- Department
of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | | | - Terkel Hansen
- Department
of Pharmacy, Faculty of Health Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Terje Vasskog
- Norut Northern Research Institute, 9294 Tromsø, Norway
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76
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77
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Kilbane JJ. Biodesulfurization: How to Make it Work? ARABIAN JOURNAL FOR SCIENCE AND ENGINEERING 2016. [DOI: 10.1007/s13369-016-2269-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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78
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Kilbane JJ, Stark B. Biodesulfurization: a model system for microbial physiology research. World J Microbiol Biotechnol 2016; 32:137. [DOI: 10.1007/s11274-016-2084-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Accepted: 05/11/2016] [Indexed: 10/21/2022]
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79
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Cromm PM, Schaubach S, Spiegel J, Fürstner A, Grossmann TN, Waldmann H. Orthogonal ring-closing alkyne and olefin metathesis for the synthesis of small GTPase-targeting bicyclic peptides. Nat Commun 2016; 7:11300. [PMID: 27075966 PMCID: PMC4834642 DOI: 10.1038/ncomms11300] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Accepted: 03/11/2016] [Indexed: 02/06/2023] Open
Abstract
Bicyclic peptides are promising scaffolds for the development of inhibitors of biological targets that proved intractable by typical small molecules. So far, access to bioactive bicyclic peptide architectures is limited due to a lack of appropriate orthogonal ring-closing reactions. Here, we report chemically orthogonal ring-closing olefin (RCM) and alkyne metathesis (RCAM), which enable an efficient chemo- and regioselective synthesis of complex bicyclic peptide scaffolds with variable macrocycle geometries. We also demonstrate that the formed alkyne macrocycle can be functionalized subsequently. The orthogonal RCM/RCAM system was successfully used to evolve a monocyclic peptide inhibitor of the small GTPase Rab8 into a bicyclic ligand. This modified peptide shows the highest affinity for an activated Rab GTPase that has been reported so far. The RCM/RCAM-based formation of bicyclic peptides provides novel opportunities for the design of bioactive scaffolds suitable for the modulation of challenging protein targets. Bicyclic peptides can inhibit biological targets hard to address with small molecules. Here, the authors combine two orthogonal ring-closing reactions to produce bicyclic peptides with improved bioactivity thereby providing a strategy that can greatly improve the structural diversity of such peptides.
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Affiliation(s)
- Philipp M Cromm
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.,Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Sebastian Schaubach
- Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany.,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim/Ruhr, Germany
| | - Jochen Spiegel
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.,Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
| | - Alois Fürstner
- Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany.,Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim/Ruhr, Germany
| | - Tom N Grossmann
- Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany.,Chemical Genomics Centre of the Max Planck Society, Otto-Hahn-Strasse 15, D-44227 Dortmund, Germany.,Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Herbert Waldmann
- Department of Chemical Biology, Max-Planck-Institute of Molecular Physiology, Otto-Hahn-Strasse 11, D-44227 Dortmund, Germany.,Technische Universität Dortmund, Fakultät für Chemie and Chemische Biologie, Otto-Hahn-Strasse 6, D-44227 Dortmund, Germany
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80
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Zaretsky S, Rai V, Gish G, Forbes MW, Kofler M, Yu JCY, Tan J, Hickey JL, Pawson T, Yudin AK. Twisted amide electrophiles enable cyclic peptide sequencing. Org Biomol Chem 2016; 13:7384-8. [PMID: 26077966 DOI: 10.1039/c5ob01050k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There is an ever-increasing interest in synthetic methods that not only enable peptide macrocyclization, but also facilitate downstream application of the synthesized molecules. We have found that aziridine amides are stereoelectronically attenuated in a macrocyclic environment such that non-specific interactions with biological nucleophiles are reduced or even shut down. The electrophilic reactivity, revealed at high pH, enables peptide sequencing by mass spectrometry, which will further broaden the utility of aziridine amide-containing libraries of macrocycles.
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Affiliation(s)
- Serge Zaretsky
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George St., Toronto, ON M5S 3H6, Canada.
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81
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Wang CK, Stalmans S, De Spiegeleer B, Craik DJ. Biodistribution of the cyclotide MCoTI-II, a cyclic disulfide-rich peptide drug scaffold. J Pept Sci 2016; 22:305-10. [PMID: 26929247 DOI: 10.1002/psc.2862] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 01/13/2016] [Accepted: 01/14/2016] [Indexed: 12/28/2022]
Abstract
Disulfide-rich macrocyclic peptides are promising templates for drug design because of their unique topology and remarkable stability. However, little is known about their pharmacokinetics. In this study, we characterize the biodistribution in mice of Momordica cochinchinensis trypsin inhibitor-II (MCoTI-II), a cyclic three-disulfide-containing peptide that has been used in a number of studies as a drug scaffold. The distribution of MCoTI-II was compared with that of chlorotoxin, which is a four-disulfide-containing peptide that has been used to develop brain tumor imaging agents; dermorphin, which is a disulfide-less peptide; and bovine serum albumin, a large protein. Both MCoTI-II and chlorotoxin distributed predominantly to the serum and kidneys, confirming that they are stable in serum and suggesting that they are eliminated from the blood through renal clearance. Although cell-penetrating peptides have been reported to be able to transport across the blood-brain barrier, MCoTI-II, which is a cell-penetrating peptide, showed no uptake into the brain. The uptake of chlorotoxin was higher than that of MCoTI-II but lower than that of dermorphin, which is considered to have low uptake into the brain. This study provides insight into the behavior of disulfide-rich peptides in vivo. Copyright © 2016 European Peptide Society and John Wiley & Sons, Ltd.
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Affiliation(s)
- Conan K Wang
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
| | - Sofie Stalmans
- Drug Quality and Registration (DruQuaR) Group, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - Bart De Spiegeleer
- Drug Quality and Registration (DruQuaR) Group, Ottergemsesteenweg 460, 9000, Ghent, Belgium
| | - David J Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland, 4072, Australia
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82
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Inhibition of tau aggregation using a naturally-occurring cyclic peptide scaffold. Eur J Med Chem 2016; 109:342-9. [DOI: 10.1016/j.ejmech.2016.01.006] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 11/24/2022]
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83
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Conibear AC, Chaousis S, Durek T, Johan Rosengren K, Craik DJ, Schroeder CI. Approaches to the stabilization of bioactive epitopes by grafting and peptide cyclization. Biopolymers 2016; 106:89-100. [DOI: 10.1002/bip.22767] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Accepted: 11/02/2015] [Indexed: 02/06/2023]
Affiliation(s)
- Anne C. Conibear
- Institute for Molecular Bioscience, The University of Queensland; Brisbane QLD 4072 Australia
| | - Stephanie Chaousis
- Institute for Molecular Bioscience, The University of Queensland; Brisbane QLD 4072 Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, The University of Queensland; Brisbane QLD 4072 Australia
| | - K. Johan Rosengren
- Institute for Molecular Bioscience, The University of Queensland; Brisbane QLD 4072 Australia
- School of Biomedical Sciences; The University of Queensland; Brisbane QLD 4072 Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland; Brisbane QLD 4072 Australia
| | - Christina I. Schroeder
- Institute for Molecular Bioscience, The University of Queensland; Brisbane QLD 4072 Australia
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84
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Shafee TMA, Robinson AJ, van der Weerden N, Anderson MA. Structural homology guided alignment of cysteine rich proteins. SPRINGERPLUS 2016; 5:27. [PMID: 26788439 PMCID: PMC4709342 DOI: 10.1186/s40064-015-1609-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Accepted: 12/13/2015] [Indexed: 11/14/2022]
Abstract
Background Cysteine rich protein families are notoriously difficult to align due to low sequence identity and frequent insertions and deletions. Results Here we present an alignment method that ensures homologous cysteines align by assigning a unique 10 amino acid barcode to those identified as structurally homologous by the DALI webserver. The free inter-cysteine regions of the barcoded sequences can then be aligned using any standard algorithm. Finally the barcodes are replaced with the original columns to yield an alignment which requires the minimum of manual refinement. Conclusions Using structural homology information to constrain sequence alignments allows the alignment of highly divergent, repetitive sequences that are poorly dealt with by existing algorithms. Tools are provided to perform this method online using the CysBar web-tool (http://CysBar.science.latrobe.edu.au) and offline (python script available from http://github.com/ts404/CysBar). Electronic supplementary material The online version of this article (doi:10.1186/s40064-015-1609-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Thomas M A Shafee
- Department of Biochemistry, La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, 3086 Australia
| | - Andrew J Robinson
- College of Science, Health and Engineering, La Trobe University, Melbourne, 3086 Australia ; Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Melbourne, 3053 Australia
| | - Nicole van der Weerden
- Department of Biochemistry, La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, 3086 Australia
| | - Marilyn A Anderson
- Department of Biochemistry, La Trobe Institute of Molecular Sciences, La Trobe University, Melbourne, 3086 Australia
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85
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The Structure-Activity Relationship of the Antioxidant Peptides from Natural Proteins. Molecules 2016; 21:72. [PMID: 26771594 PMCID: PMC6273900 DOI: 10.3390/molecules21010072] [Citation(s) in RCA: 466] [Impact Index Per Article: 51.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 12/31/2015] [Accepted: 01/05/2016] [Indexed: 12/27/2022] Open
Abstract
Peptides derived from dietary proteins, have been reported to display significant antioxidant activity, which may exert notably beneficial effects in promoting human health and in food processing. Recently, much research has focused on the generation, separation, purification and identification of novel peptides from various protein sources. Some researchers have tried to discover the structural characteristics of antioxidant peptides in order to lessen or avoid the tedious and aimless work involving the ongoing generated peptide preparation schemes. This review aims to summarize the current knowledge on the relationship between the structural features of peptides and their antioxidant activities. The relationship between the structure of the precursor proteins and their abilities to release antioxidant fragments will also be summarized and inferred. The preparation methods and antioxidant capacity evaluation assays of peptides and a prediction scheme of quantitative structure–activity relationship (QSAR) will also be pointed out and discussed.
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86
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Wang CK, Swedberg JE, Northfield SE, Craik DJ. Effects of Cyclization on Peptide Backbone Dynamics. J Phys Chem B 2015; 119:15821-30. [DOI: 10.1021/acs.jpcb.5b11085] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Conan K. Wang
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Joakim E. Swedberg
- Institute
for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Susan E. Northfield
- 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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87
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Ranganath S, Bhandari A, Avitahl-Curtis N, McMahon J, Wachtel D, Zhang J, Leitheiser C, Bernier SG, Liu G, Tran TT, Celino H, Tobin J, Jung J, Zhao H, Glen KE, Graul C, Griffin A, Schairer WC, Higgins C, Reza TL, Mowe E, Rivers S, Scott S, Monreal A, Shea C, Bourne G, Coons C, Smith A, Tang K, Mandyam RA, Masferrer J, Liu D, Patel DV, Fretzen A, Murphy CA, Milne GT, Smythe ML, Carlson KE. Discovery and Characterization of a Potent Interleukin-6 Binding Peptide with Neutralizing Activity In Vivo. PLoS One 2015; 10:e0141330. [PMID: 26555695 PMCID: PMC4640888 DOI: 10.1371/journal.pone.0141330] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 10/06/2015] [Indexed: 12/23/2022] Open
Abstract
Interleukin-6 (IL-6) is an important member of the cytokine superfamily, exerting pleiotropic actions on many physiological processes. Over-production of IL-6 is a hallmark of immune-mediated inflammatory diseases such as Castleman's Disease (CD) and rheumatoid arthritis (RA). Antagonism of the interleukin IL-6/IL-6 receptor (IL-6R)/gp130 signaling complex continues to show promise as a therapeutic target. Monoclonal antibodies (mAbs) directed against components of this complex have been approved as therapeutics for both CD and RA. To potentially provide an additional modality to antagonize IL-6 induced pathophysiology, a peptide-based antagonist approach was undertaken. Using a combination of molecular design, phage-display, and medicinal chemistry, disulfide-rich peptides (DRPs) directed against IL-6 were developed with low nanomolar potency in inhibiting IL-6-induced pSTAT3 in U937 monocytic cells. Targeted PEGylation of IL-6 binding peptides resulted in molecules that retained their potency against IL-6 and had a prolongation of their pharmacokinetic (PK) profiles in rodents and monkeys. One such peptide, PN-2921, contained a 40 kDa polyethylene glycol (PEG) moiety and inhibited IL-6-induced pSTAT3 in U937 cells with sub-nM potency and possessed 23, 36, and 59 h PK half-life values in mice, rats, and cynomolgus monkeys, respectively. Parenteral administration of PN-2921 to mice and cynomolgus monkeys potently inhibited IL-6-induced biomarker responses, with significant reductions in the acute inflammatory phase proteins, serum amyloid A (SAA) and C-reactive protein (CRP). This potent, PEGylated IL-6 binding peptide offers a new approach to antagonize IL-6-induced signaling and associated pathophysiology.
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Affiliation(s)
- Sheila Ranganath
- Discovery Biology, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Ashok Bhandari
- Chemistry, Protagonist Therapeutics, Milpitas, CA, United States of America
| | - Nicole Avitahl-Curtis
- Discovery Pharmacology, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Jaimee McMahon
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Derek Wachtel
- DMPK, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Jenny Zhang
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Christopher Leitheiser
- Pharmaceutical Development, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Sylvie G. Bernier
- Discovery Biology, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Guang Liu
- Discovery Biology, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Tran T. Tran
- Protagonist Pty Ltd, Therapeutics Pty Ltd, Brisbane, Australia
| | - Herodion Celino
- Chemistry, Protagonist Therapeutics, Milpitas, CA, United States of America
| | - Jenny Tobin
- Discovery Pharmacology, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Joon Jung
- Chemistry, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Hong Zhao
- Pharmaceutical Development, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Katie E. Glen
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Chris Graul
- Discovery Pharmacology, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Aliesha Griffin
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Wayne C. Schairer
- Pharmaceutical Development, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Carolyn Higgins
- DMPK, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Tammi L. Reza
- Discovery Toxicology, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Eva Mowe
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Sam Rivers
- Discovery Pharmacology, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Sonya Scott
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Alex Monreal
- Discovery Biology, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Courtney Shea
- Discovery Pharmacology, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Greg Bourne
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Protagonist Pty Ltd, Therapeutics Pty Ltd, Brisbane, Australia
| | - Casey Coons
- Pharmaceutical Development, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Adaline Smith
- Discovery Toxicology, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Kim Tang
- Discovery Pharmacology, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Ramya A. Mandyam
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
| | - Jaime Masferrer
- Discovery Pharmacology, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - David Liu
- Biology, Protagonist Therapeutics, Milpitas, CA, United States of America
| | - Dinesh V. Patel
- Chemistry, Protagonist Therapeutics, Milpitas, CA, United States of America
| | - Angelika Fretzen
- Pharmaceutical Development, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Craig A. Murphy
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Protagonist Pty Ltd, Therapeutics Pty Ltd, Brisbane, Australia
| | - G. Todd Milne
- Discovery Biology, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
| | - Mark L. Smythe
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Australia
- Protagonist Pty Ltd, Therapeutics Pty Ltd, Brisbane, Australia
| | - Kenneth E. Carlson
- Discovery Biology, Ironwood Pharmaceuticals, Cambridge, MA, United States of America
- * E-mail:
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88
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Hellinger R, Koehbach J, Soltis DE, Carpenter EJ, Wong GKS, Gruber CW. Peptidomics of Circular Cysteine-Rich Plant Peptides: Analysis of the Diversity of Cyclotides from Viola tricolor by Transcriptome and Proteome Mining. J Proteome Res 2015; 14:4851-62. [PMID: 26399495 PMCID: PMC4642221 DOI: 10.1021/acs.jproteome.5b00681] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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Cyclotides are plant-derived mini proteins. They are genetically
encoded as precursor proteins that become post-translationally modified
to yield circular cystine-knotted molecules. Because of this structural
topology cyclotides resist enzymatic degradation in biological fluids,
and hence they are considered as promising lead molecules for pharmaceutical
applications. Despite ongoing efforts to discover novel cyclotides
and analyze their biodiversity, it is not clear how many individual
peptides a single plant specimen can express. Therefore, we investigated
the transcriptome and cyclotide peptidome of Viola tricolor. Transcriptome mining enabled the characterization of cyclotide
precursor architecture and processing sites important for biosynthesis
of mature peptides. The cyclotide peptidome was explored by mass spectrometry
and bottom-up proteomics using the extracted peptide sequences as
queries for database searching. In total 164 cyclotides were discovered
by nucleic acid and peptide analysis in V. tricolor. Therefore, violaceous plants at a global scale may be the source
to as many as 150 000 individual cyclotides. Encompassing the
diversity of V. tricolor as a combinatorial library
of bioactive peptides, this commercially available medicinal herb
may be a suitable starting point for future bioactivity-guided screening
studies.
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Affiliation(s)
- Roland Hellinger
- Center for Physiology and Pharmacology, Medical University of Vienna , Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Johannes Koehbach
- Center for Physiology and Pharmacology, Medical University of Vienna , Schwarzspanierstrasse 17, 1090 Vienna, Austria.,School of Biomedical Sciences, The University of Queensland , St. Lucia, Queensland 4072, Australia
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida , Gainesville, Florida 32611, United States
| | - Eric J Carpenter
- Department of Biological Sciences, University of Alberta , Edmonton, Alberta T6G 2E9, Canada
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of Alberta , Edmonton, Alberta T6G 2E9, Canada.,Department of Medicine, University of Alberta , Edmonton, Alberta T6G 2E1, Canada.,BGI-Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen 518083, China
| | - Christian W Gruber
- Center for Physiology and Pharmacology, Medical University of Vienna , Schwarzspanierstrasse 17, 1090 Vienna, Austria.,School of Biomedical Sciences, The University of Queensland , St. Lucia, Queensland 4072, Australia
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89
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Carbonaro M, Maselli P, Nucara A. Structural aspects of legume proteins and nutraceutical properties. Food Res Int 2015. [DOI: 10.1016/j.foodres.2014.11.007] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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90
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Treder AP, Hickey JL, Tremblay MCJ, Zaretsky S, Scully CCG, Mancuso J, Doucet A, Yudin AK, Marsault E. Solid-Phase Parallel Synthesis of Functionalised Medium-to-Large Cyclic Peptidomimetics through Three-Component Coupling Driven by Aziridine Aldehyde Dimers. Chemistry 2015; 21:9249-55. [PMID: 26014974 DOI: 10.1002/chem.201500068] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Indexed: 11/06/2022]
Abstract
The first solid-phase parallel synthesis of macrocyclic peptides using three-component coupling driven by aziridine aldehyde dimers is described. The method supports the synthesis of 9- to 18-membered aziridine-containing macrocycles, which are then functionalized by nucleophilic opening of the aziridine ring. This constitutes a robust approach for the rapid parallel synthesis of macrocyclic peptides.
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Affiliation(s)
- Adam P Treder
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord Sherbrooke (QC) J1H 5N4 (Canada)
| | - Jennifer L Hickey
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto (ON) M5S 3H6 (Canada)
| | - Marie-Claude J Tremblay
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord Sherbrooke (QC) J1H 5N4 (Canada)
| | - Serge Zaretsky
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto (ON) M5S 3H6 (Canada)
| | - Conor C G Scully
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto (ON) M5S 3H6 (Canada)
| | - John Mancuso
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord Sherbrooke (QC) J1H 5N4 (Canada)
| | - Annie Doucet
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord Sherbrooke (QC) J1H 5N4 (Canada)
| | - Andrei K Yudin
- Davenport Research Laboratories, Department of Chemistry, University of Toronto, 80 St. George Street, Toronto (ON) M5S 3H6 (Canada)
| | - Eric Marsault
- Institut de Pharmacologie de Sherbrooke, Université de Sherbrooke, 3001, 12e av nord Sherbrooke (QC) J1H 5N4 (Canada).
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91
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Hellinger R, Koehbach J, Puigpinós A, Clark RJ, Tarragó T, Giralt E, Gruber CW. Inhibition of Human Prolyl Oligopeptidase Activity by the Cyclotide Psysol 2 Isolated from Psychotria solitudinum. JOURNAL OF NATURAL PRODUCTS 2015; 78:1073-82. [PMID: 25894999 PMCID: PMC4444998 DOI: 10.1021/np501061t] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Indexed: 05/21/2023]
Abstract
Cyclotides are head-to-tail cyclized peptides comprising a stabilizing cystine-knot motif. To date, they are well known for their diverse bioactivities such as anti-HIV and immunosuppressive properties. Yet little is known about specific molecular mechanisms, in particular the interaction of cyclotides with cellular protein targets. Native and synthetic cyclotide-like peptides from Momordica plants are potent and selective inhibitors of different serine-type proteinases such as trypsin, chymotrypsin, matriptase, and tryptase-beta. This study describes the bioactivity-guided isolation of a cyclotide from Psychotria solitudinum as an inhibitor of another serine-type protease, namely, the human prolyl oligopeptidase (POP). Analysis of the inhibitory potency of Psychotria extracts and subsequent fractionation by liquid chromatography yielded the isolated peptide psysol 2 (1), which exhibited an IC50 of 25 μM. In addition the prototypical cyclotide kalata B1 inhibited POP activity with an IC50 of 5.6 μM. The inhibitory activity appeared to be selective for POP, since neither psysol 2 nor kalata B1 were able to inhibit the proteolytic activity of trypsin or chymotrypsin. The enzyme POP is well known for its role in memory and learning processes, and it is currently being considered as a promising therapeutic target for the cognitive deficits associated with several psychiatric and neurodegenerative diseases, such as schizophrenia and Parkinson's disease. In the context of discovery and development of POP inhibitors with beneficial ADME properties, cyclotides may be suitable starting points considering their stability in biological fluids and possible oral bioavailability.
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Affiliation(s)
- Roland Hellinger
- Center
for Physiology and Pharmacology, Medical
University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Johannes Koehbach
- Center
for Physiology and Pharmacology, Medical
University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
| | - Albert Puigpinós
- Institute
for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
| | - Richard J. Clark
- School
of Biomedical Sciences, The University of
Queensland, Brisbane, QLD 4072, Australia
| | - Teresa Tarragó
- Institute
for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
| | - Ernest Giralt
- Institute
for Research in Biomedicine (IRB Barcelona), 08028 Barcelona, Spain
- Department
of Organic Chemistry, University of Barcelona
(UB), 08028 Barcelona, Spain
| | - Christian W. Gruber
- Center
for Physiology and Pharmacology, Medical
University of Vienna, Schwarzspanierstrasse 17, 1090 Vienna, Austria
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92
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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: 3.0] [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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93
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Rational design and synthesis of an orally bioavailable peptide guided by NMR amide temperature coefficients. Proc Natl Acad Sci U S A 2015; 111:17504-9. [PMID: 25416591 DOI: 10.1073/pnas.1417611111] [Citation(s) in RCA: 126] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Enhancing the oral bioavailability of peptide drug leads is a major challenge in drug design. As such, methods to address this challenge are highly sought after by the pharmaceutical industry. Here, we propose a strategy to identify appropriate amides for N-methylation using temperature coefficients measured by NMR to identify exposed amides in cyclic peptides. N-methylation effectively caps these amides, modifying the overall solvation properties of the peptides and making them more membrane permeable. The approach for identifying sites for N-methylation is a rapid alternative to the elucidation of 3D structures of peptide drug leads, which has been a commonly used structure-guided approach in the past. Five leucine-rich peptide scaffolds are reported with selectively designed N-methylated derivatives. In vitro membrane permeability was assessed by parallel artificial membrane permeability assay and Caco-2 assay. The most promising N-methylated peptide was then tested in vivo. Here we report a novel peptide (15), which displayed an oral bioavailability of 33% in a rat model, thus validating the design approach. We show that this approach can also be used to explain the notable increase in oral bioavailability of a somatostatin analog.
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94
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Tsomaia N. Peptide therapeutics: Targeting the undruggable space. Eur J Med Chem 2015; 94:459-70. [DOI: 10.1016/j.ejmech.2015.01.014] [Citation(s) in RCA: 256] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 01/07/2015] [Accepted: 01/08/2015] [Indexed: 01/04/2023]
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95
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Hanold LE, Watkins CP, Ton NT, Liaw P, Beedle AM, Kennedy EJ. Design of a selenylsulfide-bridged EGFR dimerization arm mimic. Bioorg Med Chem 2015; 23:2761-6. [PMID: 25840798 DOI: 10.1016/j.bmc.2015.03.040] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Revised: 03/11/2015] [Accepted: 03/13/2015] [Indexed: 01/25/2023]
Abstract
The epidermal growth factor receptor (EGFR) dimerization arm is a key feature that stabilizes dimerization of the extracellular receptor, thereby mediating activation of the tyrosine kinase domain. Peptides mimicking this β-loop feature can disrupt dimer formation and kinase activation, yet these peptides lack structural constraints or contain redox sensitive disulfide bonds which may limit their stability in physiological environments. Selenylsulfide bonds are a promising alternative to disulfide bonds as they maintain much of the same structural and chemical behavior, yet they are inherently less prone to reduction. Herein, we describe the synthesis, stability and activity of selenylsulfide-bridged dimerization arm mimics. The synthesis was accomplished using an Fmoc-based strategy along with C-terminal labeling for improved overall yield. This selenylsulfide-bridged peptide displayed both proteolytic stability and structural stability even under reducing conditions, demonstrating the potential application of the selenylsulfide bond to generate redox stable β-loop peptides for disruption of protein-protein interactions.
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Affiliation(s)
- Laura E Hanold
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy, 240 W. Green St., Athens, GA 30602, USA
| | - Christopher P Watkins
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy, 240 W. Green St., Athens, GA 30602, USA
| | - Norman T Ton
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy, 240 W. Green St., Athens, GA 30602, USA
| | - Peter Liaw
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy, 240 W. Green St., Athens, GA 30602, USA
| | - Aaron M Beedle
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy, 240 W. Green St., Athens, GA 30602, USA
| | - Eileen J Kennedy
- Department of Pharmaceutical and Biomedical Sciences, University of Georgia College of Pharmacy, 240 W. Green St., Athens, GA 30602, USA.
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96
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Li C, Blencke HM, Haug T, Stensvåg K. Antimicrobial peptides in echinoderm host defense. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2015; 49:190-197. [PMID: 25445901 DOI: 10.1016/j.dci.2014.11.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2014] [Revised: 10/02/2014] [Accepted: 11/03/2014] [Indexed: 06/04/2023]
Abstract
Antimicrobial peptides (AMPs) are important effector molecules in innate immunity. Here we briefly summarize characteristic traits of AMPs and their mechanisms of antimicrobial activity. Echinoderms live in a microbe-rich marine environment and are known to express a wide range of AMPs. We address two novel AMP families from coelomocytes of sea urchins: cysteine-rich AMPs (strongylocins) and heterodimeric AMPs (centrocins). These peptide families have conserved preprosequences, are present in both adults and pluteus stage larvae, have potent antimicrobial properties, and therefore appear to be important innate immune effectors. Strongylocins have a unique cysteine pattern compared to other cysteine-rich peptides, which suggests a novel AMP folding pattern. Centrocins and SdStrongylocin 2 contain brominated tryptophan residues in their native form. This review also includes AMPs isolated from other echinoderms, such as holothuroidins, fragments of beta-thymosin, and fragments of lectin (CEL-III). Echinoderm AMPs are crucial molecules for the understanding of echinoderm immunity, and their potent antimicrobial activity makes them potential precursors of novel drug leads.
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Affiliation(s)
- Chun Li
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway.
| | - Hans-Matti Blencke
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway; Centre for Research-based Innovation on Marine Bioactives and Drug Discovery (MabCent-SFI), UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Tor Haug
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway; Centre for Research-based Innovation on Marine Bioactives and Drug Discovery (MabCent-SFI), UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Klara Stensvåg
- Norwegian College of Fishery Science, Faculty of Biosciences, Fisheries and Economics, UiT The Arctic University of Norway, Breivika, N-9037 Tromsø, Norway; Centre for Research-based Innovation on Marine Bioactives and Drug Discovery (MabCent-SFI), UiT The Arctic University of Norway, N-9037 Tromsø, Norway.
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97
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Körling M, Geyer A. Stabilization of a Natural β-Hairpin by a Twist-Compatible β-Turn Mimetic. European J Org Chem 2015. [DOI: 10.1002/ejoc.201500048] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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98
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Li Q, Yu H, Zhao X, Huang X. Insight into the impact of environments on structure of chimera C3 of human β-defensins 2 and 3 from molecular dynamics simulations. J Biomol Struct Dyn 2014; 33:1989-2002. [DOI: 10.1080/07391102.2014.985255] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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99
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Structural parameters modulating the cellular uptake of disulfide-rich cyclic cell-penetrating peptides: MCoTI-II and SFTI-1. Eur J Med Chem 2014; 88:10-8. [DOI: 10.1016/j.ejmech.2014.06.047] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 06/17/2014] [Accepted: 06/18/2014] [Indexed: 01/13/2023]
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100
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Ciccimaro E, Ranasinghe A, D’Arienzo C, Xu C, Onorato J, Drexler DM, Josephs JL, Poss M, Olah T. Strategy to Improve the Quantitative LC-MS Analysis of Molecular Ions Resistant to Gas-Phase Collision Induced Dissociation: Application to Disulfide-Rich Cyclic Peptides. Anal Chem 2014; 86:11523-7. [DOI: 10.1021/ac502678y] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Eugene Ciccimaro
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Asoka Ranasinghe
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Celia D’Arienzo
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Carrie Xu
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Joelle Onorato
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | | | - Jonathan L. Josephs
- ThermoFisher Scientific, 355 River
Oaks Parkway, San Jose, California 95134, United States
| | - Michael Poss
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
| | - Timothy Olah
- Bristol-Myers Squibb, Princeton, New Jersey 08543, United States
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