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Ulmschneider JP, Ulmschneider MB. Melittin can permeabilize membranes via large transient pores. Nat Commun 2024; 15:7281. [PMID: 39179607 PMCID: PMC11343860 DOI: 10.1038/s41467-024-51691-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 08/15/2024] [Indexed: 08/26/2024] Open
Abstract
Membrane active peptides are known to porate lipid bilayers, but their exact permeabilization mechanism and the structure of the nanoaggregates they form in membranes have often been difficult to determine experimentally. For many sequences at lower peptide concentrations, transient leakage is observed in experiments, suggesting the existence of transient pores. For two well-know peptides, alamethicin and melittin, we show here that molecular mechanics simulations i) can directly distinguish equilibrium poration and non-equilibrium transient leakage processes, and ii) can be used to observe the detailed pore structures and mechanism of permeabilization in both cases. Our results are in very high agreement with numerous experimental evidence for these two peptides. This suggests that molecular simulations can capture key membrane poration phenomena directly and in the future may develop to be a useful tool that can assist experimental peptide design.
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Affiliation(s)
- Jakob P Ulmschneider
- Institute of Natural Sciences and School of Physics and Astronomy, Shanghai Jiao Tong University, Shanghai, China.
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2
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Deb R, Torres MDT, Boudný M, Koběrská M, Cappiello F, Popper M, Dvořáková
Bendová K, Drabinová M, Hanáčková A, Jeannot K, Petřík M, Mangoni ML, Balíková Novotná G, Mráz M, de la Fuente-Nunez C, Vácha R. Computational Design of Pore-Forming Peptides with Potent Antimicrobial and Anticancer Activities. J Med Chem 2024; 67:14040-14061. [PMID: 39116273 PMCID: PMC11345766 DOI: 10.1021/acs.jmedchem.4c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/05/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024]
Abstract
Peptides that form transmembrane barrel-stave pores are potential alternative therapeutics for bacterial infections and cancer. However, their optimization for clinical translation is hampered by a lack of sequence-function understanding. Recently, we have de novo designed the first synthetic barrel-stave pore-forming antimicrobial peptide with an identified function of all residues. Here, we systematically mutate the peptide to improve pore-forming ability in anticipation of enhanced activity. Using computer simulations, supported by liposome leakage and atomic force microscopy experiments, we find that pore-forming ability, while critical, is not the limiting factor for improving activity in the submicromolar range. Affinity for bacterial and cancer cell membranes needs to be optimized simultaneously. Optimized peptides more effectively killed antibiotic-resistant ESKAPEE bacteria at submicromolar concentrations, showing low cytotoxicity to human cells and skin model. Peptides showed systemic anti-infective activity in a preclinical mouse model of Acinetobacter baumannii infection. We also demonstrate peptide optimization for pH-dependent antimicrobial and anticancer activity.
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Affiliation(s)
- Rahul Deb
- CEITEC
− Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
| | - Marcelo D. T. Torres
- Machine
Biology Group, Departments of Psychiatry and Microbiology, Institute
for Biomedical Informatics, Institute for Translational Medicine and
Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments
of Bioengineering and Chemical and Biomolecular Engineering, School
of Engineering and Applied Science, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn
Institute for Computational Science, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department
of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Miroslav Boudný
- CEITEC
− Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- Department
of Internal Medicine, Hematology and Oncology, University Hospital
Brno and Faculty of Medicine, Masaryk University, Brno 625 00, Czech Republic
| | - Markéta Koběrská
- Institute
of Microbiology, Czech Academy of Sciences,
BIOCEV, Vestec 252 50, Czech Republic
| | - Floriana Cappiello
- Department
of Biochemical Sciences, Laboratory Affiliated to Istituto Pasteur
Italia-Fondazione Cenci Bolognetti, Sapienza
University of Rome, Rome 00185, Italy
| | - Miroslav Popper
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc 779 00, Czech Republic
| | - Kateřina Dvořáková
Bendová
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc 779 00, Czech Republic
| | - Martina Drabinová
- CEITEC
− Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Adelheid Hanáčková
- CEITEC
− Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
| | - Katy Jeannot
- University
of Franche-Comté, CNRS, Chrono-environment, Besançon 25030, France
- National Reference Centre for Antibiotic
Resistance, Besançon 25030, France
| | - Miloš Petřík
- Institute
of Molecular and Translational Medicine, Faculty of Medicine and Dentistry, Palacký University, Olomouc 779 00, Czech Republic
- Czech
Advanced Technology and Research Institute, Palacký University, Olomouc 779 00, Czech Republic
| | - Maria Luisa Mangoni
- Department
of Biochemical Sciences, Laboratory Affiliated to Istituto Pasteur
Italia-Fondazione Cenci Bolognetti, Sapienza
University of Rome, Rome 00185, Italy
| | | | - Marek Mráz
- CEITEC
− Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- Department
of Internal Medicine, Hematology and Oncology, University Hospital
Brno and Faculty of Medicine, Masaryk University, Brno 625 00, Czech Republic
| | - Cesar de la Fuente-Nunez
- Machine
Biology Group, Departments of Psychiatry and Microbiology, Institute
for Biomedical Informatics, Institute for Translational Medicine and
Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Departments
of Bioengineering and Chemical and Biomolecular Engineering, School
of Engineering and Applied Science, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Penn
Institute for Computational Science, University
of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
- Department
of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Robert Vácha
- CEITEC
− Central European Institute of Technology, Masaryk University, Brno 625 00, Czech Republic
- National
Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno 625 00, Czech Republic
- Department
of Condensed Matter Physics, Faculty of Science, Masaryk University, Brno 611 37, Czech Republic
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Maffeis V, Hürlimann D, Krywko-Cendrowska A, Schoenenberger CA, Housecroft CE, Palivan CG. A DNA-Micropatterned Surface for Propagating Biomolecular Signals by Positional on-off Assembly of Catalytic Nanocompartments. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2202818. [PMID: 35869606 DOI: 10.1002/smll.202202818] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/17/2022] [Indexed: 06/15/2023]
Abstract
Signal transduction is pivotal for the transfer of information between and within living cells. The composition and spatial organization of specified compartments are key to propagating soluble signals. Here, a high-throughput platform mimicking multistep signal transduction which is based on a geometrically defined array of immobilized catalytic nanocompartments (CNCs) that consist of distinct polymeric nanoassemblies encapsulating enzymes and DNA or enzymes alone is presented. The dual role of single entities or tandem CNCs in providing confined but communicating spaces for complex metabolic reactions and in protecting encapsulated compounds from denaturation is explored. To support a controlled spatial organization of CNCs, CNCs are patterned by means of DNA hybridization to a microprinted glass surface. Specifically, CNC-functionalized DNA microarrays are produced where individual reaction compartments are kept in close proximity by a distinct geometrical arrangement to promote effective communication. Besides a remarkable versatility and robustness, the most prominent feature of this platform is the reversibility of DNA-mediated CNC-anchoring which renders it reusable. Micropatterns of polymer-based nanocompartment assemblies offer an ideal scaffold for the development of the next generation responsive and communicative soft-matter analytical devices for applications in catalysis and medicine.
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Affiliation(s)
- Viviana Maffeis
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4058, Switzerland
- NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
| | - Dimitri Hürlimann
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4058, Switzerland
- NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
| | - Agata Krywko-Cendrowska
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4058, Switzerland
| | - Cora-Ann Schoenenberger
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4058, Switzerland
- NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
| | - Catherine E Housecroft
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4058, Switzerland
- NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
| | - Cornelia G Palivan
- Department of Chemistry, University of Basel, Mattenstrasse 24a, BPR 1096, Basel, 4058, Switzerland
- NCCR-Molecular Systems Engineering, BPR 1095, Mattenstrasse 24a, Basel, CH-4058, Switzerland
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Abstract
Perturbation of cell membranes by amyloid β (Ab) peptide oligomers is one possible mechanism of cytotoxicity in Alzheimer's disease, but the structure of such Ab-membrane complexes is unknown. Here we examine the stability of several putative structures by implicit membrane and all-atom molecular dynamics simulations. The structures include (a) a variety of models proposed by other researchers in the past, (b) a heptameric β barrel determined by grafting the Ab sequence onto α-hemolysin, (c) a similar structure with modified strand orientation and turn location based on an experimental β-hairpin structure, (d) oligomers inserting C-terminal β hairpins into one leaflet of the bilayer, (e) oligomers forming parallel C-terminal β barrels, and (f) a helical hexamer made of C-terminal fragments. The α-hemolysin-grafted structure and its alternately oriented variant are stable in the membrane and form an aqueous pore. In contrast, the C-terminal parallel barrels are not stable, presumably due to excessive hydrophobicity of their inner surface. The helical hexamer also failed to stabilize an aqueous pore for the same reason. The C-terminal hairpin-inserting structures remain stably inserted but, again, do not form an aqueous pore. Our results suggest that only β-barrels inserting a combination of C-terminal and other residues can form stable aqueous pores.
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Affiliation(s)
- Aliasghar Sepehri
- Department of Chemistry, City College of New York, CUNY, 160 Convent Avenue, New York, New York10031, United States
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, CUNY, 160 Convent Avenue, New York, New York10031, United States.,Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, 365 Fifth Avenue, New York, New York10016, United States
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5
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Xie YL, Wang JY, He Y, Yu XM, Zheng QY, Ling C, Feng XL, Zhu LQ. The use of melittin to enhance transgene expression mediated by recombinant adeno-associated virus serotype 2 vectors both in vitro and in vivo. JOURNAL OF INTEGRATIVE MEDICINE 2023; 21:106-115. [PMID: 36333178 DOI: 10.1016/j.joim.2022.10.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 06/26/2022] [Indexed: 11/13/2022]
Abstract
OBJECTIVE Melittin, a cell-penetrating peptide, improves the efficiency of many non-viral gene delivery vectors, yet its application in viral vectors has not been well studied. The non-pathogenic recombinant adeno-associated virus (rAAV) vector is an ideal in vivo gene delivery vector. However, its full potential will only be achieved after improvement of its transduction efficiency. To improve the transduction efficiency of rAAV2 vectors, we attempted to develop a melittin-based rAAV2 vector delivery strategy. METHODS The melittin peptide was inserted into the rAAV2 capsid either in the loop VIII of all viral proteins (VPs) or at the N terminus of VP2. Various rAAV2-gfp or -fluc vectors were subjected to quantitative real-time polymerase chain reaction and Western blot assays to determine their titers and integrity of capsid proteins, respectively. Alternatively, the vectors based on wild-type capsid were pre-incubated with melittin, followed by transduction of cultured cells or tail vein administration of the mixture to C57BL/6 and BALB/c nude mice. In vivo bioluminescence imaging was performed to evaluate the transgene expression. RESULTS rAAV2 vectors with melittin peptide inserted in the loop VIII of VPs had low transduction efficiency, probably due to dramatically reduced ability to bind to the target cells. Fusing the melittin peptide at the N-terminus of VP2 produced vectors without the VP2 subunit. Interestingly, among the commonly used rAAV vectors, pre-incubation of rAAV2 and rAAV6 vectors with melittin significantly enhanced their transduction efficiency in HEK293 and Huh7 cells in vitro. Melittin also had the ability to increase the rAAV2-mediated transgene expression in mouse liver in vivo. Mechanistically, melittin did not change the vector-receptor interaction. Moreover, cell counting kit-8 assays of cultured cells and serum transaminase levels indicated melittin had little cytotoxicity. CONCLUSION Pre-incubation with melittin, but not insertion of melittin into the rAAV2 capsid, significantly enhanced rAAV2-mediated transgene expression. Although further in vivo evaluations are required, this research not only expands the pharmacological potential of melittin, but also provides a new strategy to improve gene therapy mediated by rAAV vectors.
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Affiliation(s)
- Yi-Lin Xie
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Ji-Yao Wang
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Department of Clinical Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China; Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou 325000, Zhejiang Province, China
| | - Yun He
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Xiao-Min Yu
- Department of Clinical Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China; Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou 325000, Zhejiang Province, China
| | - Qing-Yun Zheng
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China
| | - Chen Ling
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Department of Clinical Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China; Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou 325000, Zhejiang Province, China
| | - Xi-Lin Feng
- State Key Laboratory of Genetic Engineering and Engineering Research Center of Gene Technology (Ministry of Education), School of Life Sciences, Zhongshan Hospital, Fudan University, Shanghai 200438, China; Yantai Fuheng Biological Technology Co., Ltd., Yantai 264006, Shandong Province, China.
| | - Li-Qing Zhu
- Department of Clinical Laboratory, the First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, Zhejiang Province, China; Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou 325000, Zhejiang Province, China.
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Takahashi H, Sovadinova I, Yasuhara K, Vemparala S, Caputo GA, Kuroda K. Biomimetic antimicrobial polymers—Design, characterization, antimicrobial, and novel applications. WIRES NANOMEDICINE AND NANOBIOTECHNOLOGY 2022; 15:e1866. [PMID: 36300561 DOI: 10.1002/wnan.1866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Revised: 09/15/2022] [Accepted: 09/27/2022] [Indexed: 11/05/2022]
Abstract
Biomimetic antimicrobial polymers have been an area of great interest as the need for novel antimicrobial compounds grows due to the development of resistance. These polymers were designed and developed to mimic naturally occurring antimicrobial peptides in both physicochemical composition and mechanism of action. These antimicrobial peptide mimetic polymers have been extensively investigated using chemical, biophysical, microbiological, and computational approaches to gain a deeper understanding of the molecular interactions that drive function. These studies have helped inform SARs, mechanism of action, and general physicochemical factors that influence the activity and properties of antimicrobial polymers. However, there are still lingering questions in this field regarding 3D structural patterning, bioavailability, and applicability to alternative targets. In this review, we present a perspective on the development and characterization of several antimicrobial polymers and discuss novel applications of these molecules emerging in the field. This article is categorized under: Therapeutic Approaches and Drug Discovery > Emerging Technologies Therapeutic Approaches and Drug Discovery > Nanomedicine for Infectious Disease.
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Affiliation(s)
- Haruko Takahashi
- Graduate School of Integrated Sciences for Life Hiroshima University Higashi‐Hiroshima Hiroshima Japan
| | - Iva Sovadinova
- RECETOX, Faculty of Science Masaryk University Brno Czech Republic
| | - Kazuma Yasuhara
- Division of Materials Science, Graduate School of Science and Technology Nara Institute of Science and Technology Nara Japan
- Center for Digital Green‐Innovation Nara Institute of Science and Technology Nara Japan
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences CIT Campus Chennai India
- Homi Bhabha National Institute Training School Complex Mumbai India
| | - Gregory A. Caputo
- Department of Chemistry & Biochemistry Rowan University Glassboro New Jersey USA
| | - Kenichi Kuroda
- Department of Biologic and Materials Sciences & Prosthodontics, School of Dentistry University of Michigan Ann Arbor Michigan USA
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Stapling of Peptides Potentiates: The Antibiotic Treatment of Acinetobacter baumannii In Vivo. Antibiotics (Basel) 2022; 11:antibiotics11020273. [PMID: 35203875 PMCID: PMC8868297 DOI: 10.3390/antibiotics11020273] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 02/15/2022] [Accepted: 02/18/2022] [Indexed: 11/21/2022] Open
Abstract
The rising incidence of multidrug resistance in Gram-negative bacteria underlines the urgency for novel treatment options. One promising new approach is the synergistic combination of antibiotics with antimicrobial peptides. However, the use of such peptides is not straightforward; they are often sensitive to proteolytic degradation, which greatly limits their clinical potential. One approach to increase stability is to apply a hydrocarbon staple to the antimicrobial peptide, thereby fixing them in an α-helical conformation, which renders them less exposed to proteolytic activity. In this work we applied several different hydrocarbon staples to two previously described peptides shown to act on the outer membrane, L6 and L8, and tested their activity in a zebrafish embryo infection model using a clinical isolate of Acinetobacter baumannii as a pathogen. We show that the introduction of such a hydrocarbon staple to the peptide L8 improves its in vivo potentiating activity on antibiotic treatment, without increasing its in vivo antimicrobial activity, toxicity or hemolytic activity.
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8
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Natural Peptides Inducing Cancer Cell Death: Mechanisms and Properties of Specific Candidates for Cancer Therapeutics. Molecules 2021; 26:molecules26247453. [PMID: 34946535 PMCID: PMC8708364 DOI: 10.3390/molecules26247453] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/05/2021] [Accepted: 12/07/2021] [Indexed: 01/10/2023] Open
Abstract
Nowadays, cancer has become the second highest leading cause of death, and it is expected to continue to affect the population in forthcoming years. Additionally, treatment options will become less accessible to the public as cases continue to grow and disease mechanisms expand. Hence, specific candidates with confirmed anticancer effects are required to develop new drugs. Among the novel therapeutic options, proteins are considered a relevant source, given that they have bioactive peptides encrypted within their sequences. These bioactive peptides, which are molecules consisting of 2–50 amino acids, have specific activities when administered, producing anticancer effects. Current databases report the effects of peptides. However, uncertainty is found when their molecular mechanisms are investigated. Furthermore, analyses addressing their interaction networks or their directly implicated mechanisms are needed to elucidate their effects on cancer cells entirely. Therefore, relevant peptides considered as candidates for cancer therapeutics with specific sequences and known anticancer mechanisms were accurately reviewed. Likewise, those features which turn certain peptides into candidates and the mechanisms by which peptides mediate tumor cell death were highlighted. This information will make robust the knowledge of these candidate peptides with recognized mechanisms and enhance their non-toxic capacity in relation to healthy cells and further avoid cell resistance.
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9
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Trinidad-Calderón PA, Varela-Chinchilla CD, García-Lara S. Natural Peptides Inducing Cancer Cell Death: Mechanisms and Properties of Specific Candidates for Cancer Therapeutics. Molecules 2021. [DOI: https://doi.org/10.3390/molecules26247453] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Nowadays, cancer has become the second highest leading cause of death, and it is expected to continue to affect the population in forthcoming years. Additionally, treatment options will become less accessible to the public as cases continue to grow and disease mechanisms expand. Hence, specific candidates with confirmed anticancer effects are required to develop new drugs. Among the novel therapeutic options, proteins are considered a relevant source, given that they have bioactive peptides encrypted within their sequences. These bioactive peptides, which are molecules consisting of 2–50 amino acids, have specific activities when administered, producing anticancer effects. Current databases report the effects of peptides. However, uncertainty is found when their molecular mechanisms are investigated. Furthermore, analyses addressing their interaction networks or their directly implicated mechanisms are needed to elucidate their effects on cancer cells entirely. Therefore, relevant peptides considered as candidates for cancer therapeutics with specific sequences and known anticancer mechanisms were accurately reviewed. Likewise, those features which turn certain peptides into candidates and the mechanisms by which peptides mediate tumor cell death were highlighted. This information will make robust the knowledge of these candidate peptides with recognized mechanisms and enhance their non-toxic capacity in relation to healthy cells and further avoid cell resistance.
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10
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Sepehri A, Nepal B, Lazaridis T. Distinct Modes of Action of IAPP Oligomers on Membranes. J Chem Inf Model 2021; 61:4645-4655. [PMID: 34499498 DOI: 10.1021/acs.jcim.1c00767] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Islet amyloid polypeptide (IAPP, also known as amylin) is a peptide hormone that is co-secreted with insulin by pancreatic β-cells and forms amyloid aggregates in type II diabetes. Various lines of evidence indicate that oligomers of this peptide may induce toxicity by disrupting or forming pores in cell membranes, but the structure of these pores is unknown. Here, we create models of pores for both helical and β-structured peptides using implicit membrane modeling and test their stability using multimicrosecond all-atom simulations. We find that the helical peptides behave similarly to antimicrobial peptides; they remain stably inserted in a highly tilted or partially unfolded configuration creating a narrow water channel. Parallel helix orientation creates a somewhat larger pore. An octameric β barrel of parallel β-hairpins is highly stable in the membrane, whereas the corresponding barrel made of antiparallel hairpins is not. We propose that certain experiments probe the helical pore state while others probe the β-structured pore state; this provides a possible explanation for lack of correlation that is sometimes observed between in vivo toxicity and in vitro liposome permeabilization experiments.
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Affiliation(s)
- Aliasghar Sepehri
- Department of Chemistry, City College of New York, New York, New York 10031, United States
| | - Binod Nepal
- Department of Chemistry, City College of New York, New York, New York 10031, United States
| | - Themis Lazaridis
- Department of Chemistry, City College of New York, New York, New York 10031, United States.,Graduate Programs in Chemistry, Biochemistry, and Physics, The Graduate Center, City University of New York, New York, New York, New York 10016, United States
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11
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Schistocins: Novel antimicrobial peptides encrypted in the Schistosoma mansoni Kunitz Inhibitor SmKI-1. Biochim Biophys Acta Gen Subj 2021; 1865:129989. [PMID: 34389467 DOI: 10.1016/j.bbagen.2021.129989] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 07/30/2021] [Accepted: 08/06/2021] [Indexed: 02/06/2023]
Abstract
BACKGROUND Here we describe a new class of cryptides (peptides encrypted within a larger protein) with antimicrobial properties, named schistocins, derived from SmKI-1, a key protein in Shistosoma mansoni survival. This is a multi-functional protein with biotechnological potential usage as a therapeutic molecule in inflammatory diseases and to control schistosomiasis. METHODS We used our algorithm enCrypted, to perform an in silico proteolysis of SmKI-1 and a screening for potential antimicrobial activity. The selected peptides were chemically synthesized, tested in vitro and evaluated by both structural (CD, NMR) and biophysical (ITC) studies to access their structure-function relationship. RESULTS EnCrypted was capable of predicting AMPs in SmKI-1. Our biophysical analyses described a membrane-induced conformational change from random coil-to-α-helix and a peptide-membrane equilibrium for all schistocins. Our structural data allowed us to suggest a well-known mode of peptide-membrane interaction in which electrostatic attraction between the cationic peptides and anionic membranes results in the bilayer disordering. Moreover, the NMR exchange H/D data with the higher entropic contribution observed for the peptide-membrane interaction showed that shistocins have different orientations upon the membrane. CONCLUSIONS This work demonstrate the robustness for using the physicochemical features of predicted peptides in the identification of new bioactive cryptides besides the relevance of combining these analyses with biophysical methods to understand the peptide-membrane affinity and improve further algorithms. GENERAL SIGNIFICANCE Bioprospecting cryptides can be conducted through data mining of protein databases demonstrating the success of our strategy. The peptides-based agents derived from SmKI-1 might have high impact for system-biology and biotechnology.
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12
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Lipid interactions of an actinoporin pore-forming oligomer. Biophys J 2021; 120:1357-1366. [PMID: 33617834 DOI: 10.1016/j.bpj.2021.02.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 01/16/2021] [Accepted: 02/11/2021] [Indexed: 12/16/2022] Open
Abstract
The actinoporins are cytolytic toxins produced by sea anemones. Upon encountering a membrane, preferably containing sphingomyelin, they oligomerize and insert their N-terminal helix into the membrane, forming a pore. Whether sphingomyelin is specifically recognized by the protein or simply induces phase coexistence in the membrane has been debated. Here, we perform multi-microsecond molecular dynamics simulations of an octamer of fragaceatoxin C, a member of the actinoporin family, in lipid bilayers containing either pure 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) or a 1:1 mixture of DOPC and palmitoyl sphingomyelin (PSM). The complex is highly stable in both environments, with only slight fraying of the inserted helices near their N-termini. Analyzing the structural parameters of the mixed membrane in the course of the simulation, we see signs of a phase transition for PSM in the inner leaflet of the bilayer. In both leaflets, cross-interactions between lipids of different type decrease over time. Surprisingly, the aromatic loop thought to be responsible for sphingomyelin recognition interacts more with DOPC than PSM by the end of the simulation. These results support the notion that the key membrane property that actinoporins recognize is lipid phase coexistence.
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Tuning of a Membrane-Perforating Antimicrobial Peptide to Selectively Target Membranes of Different Lipid Composition. J Membr Biol 2021; 254:75-96. [PMID: 33564914 DOI: 10.1007/s00232-021-00174-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/21/2021] [Indexed: 12/16/2022]
Abstract
The use of designed antimicrobial peptides as drugs has been impeded by the absence of simple sequence-structure-function relationships and design rules. The likely cause is that many of these peptides permeabilize membranes via highly disordered, heterogeneous mechanisms, forming aggregates without well-defined tertiary or secondary structure. We suggest that the combination of high-throughput library screening with atomistic computer simulations can successfully address this challenge by tuning a previously developed general pore-forming peptide into a selective pore-former for different lipid types. A library of 2916 peptides was designed based on the LDKA template. The library peptides were synthesized and screened using a high-throughput orthogonal vesicle leakage assay. Dyes of different sizes were entrapped inside vesicles with varying lipid composition to simultaneously screen for both pore size and affinity for negatively charged and neutral lipid membranes. From this screen, nine different LDKA variants that have unique activity were selected, sequenced, synthesized, and characterized. Despite the minor sequence changes, each of these peptides has unique functional properties, forming either small or large pores and being selective for either neutral or anionic lipid bilayers. Long-scale, unbiased atomistic molecular dynamics (MD) simulations directly reveal that rather than rigid, well-defined pores, these peptides can form a large repertoire of functional dynamic and heterogeneous aggregates, strongly affected by single mutations. Predicting the propensity to aggregate and assemble in a given environment from sequence alone holds the key to functional prediction of membrane permeabilization.
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