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Kravchenko SV, Domnin PA, Grishin SY, Zakhareva AP, Zakharova AA, Mustaeva LG, Gorbunova EY, Kobyakova MI, Surin AK, Poshvina DV, Fadeev RS, Azev VN, Ostroumova OS, Ermolaeva SA, Galzitskaya OV. Optimizing Antimicrobial Peptide Design: Integration of Cell-Penetrating Peptides, Amyloidogenic Fragments, and Amino Acid Residue Modifications. Int J Mol Sci 2024; 25:6030. [PMID: 38892216 PMCID: PMC11173194 DOI: 10.3390/ijms25116030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 05/27/2024] [Accepted: 05/29/2024] [Indexed: 06/21/2024] Open
Abstract
The escalating threat of multidrug-resistant pathogens necessitates innovative approaches to combat infectious diseases. In this study, we examined peptides R23FS*, V31KS*, and R44KS*, which were engineered to include an amyloidogenic fragment sourced from the S1 protein of S. aureus, along with one or two cell-penetrating peptide (CPP) components. We assessed the antimicrobial efficacy of these peptides in a liquid medium against various strains of both Gram-positive bacteria, including S. aureus (209P and 129B strains), MRSA (SA 180 and ATCC 43300 strains), and B. cereus (strain IP 5832), and Gram-negative bacteria such as P. aeruginosa (ATCC 28753 and 2943 strains) and E. coli (MG1655 and K12 strains). Peptides R23FS*, V31KS*, and R44KS* exhibited antimicrobial activity comparable to gentamicin and meropenem against all tested bacteria at concentrations ranging from 24 to 48 μM. The peptides showed a stronger antimicrobial effect against B. cereus. Notably, peptide R44KS* displayed high efficacy compared to peptides R23FS* and V31KS*, particularly evident at lower concentrations, resulting in significant inhibition of bacterial growth. Furthermore, modified peptides V31KS* and R44KS* demonstrated enhanced inhibitory effects on bacterial growth across different strains compared to their unmodified counterparts V31KS and R44KS. These results highlight the potential of integrating cell-penetrating peptides, amyloidogenic fragments, and amino acid residue modifications to advance the innovation in the field of antimicrobial peptides, thereby increasing their effectiveness against a broad spectrum of pathogens.
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Affiliation(s)
- Sergey V. Kravchenko
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (S.V.K.); (A.P.Z.); (D.V.P.)
| | - Pavel A. Domnin
- Biology Faculty, Lomonosov Moscow State University, 119991 Moscow, Russia;
- Gamaleya Research Centre of Epidemiology and Microbiology, 123098 Moscow, Russia;
| | - Sergei Y. Grishin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.Y.G.); (A.K.S.)
| | - Alena P. Zakhareva
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (S.V.K.); (A.P.Z.); (D.V.P.)
| | - Anastasiia A. Zakharova
- Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia; (A.A.Z.); (O.S.O.)
| | - Leila G. Mustaeva
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (L.G.M.); (E.Y.G.); (V.N.A.)
| | - Elena Y. Gorbunova
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (L.G.M.); (E.Y.G.); (V.N.A.)
| | - Margarita I. Kobyakova
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia; (M.I.K.); (R.S.F.)
- Research Institute of Clinical and Experimental Lymphology—Branch of the Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, 630060 Novosibirsk, Russia
| | - Alexey K. Surin
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.Y.G.); (A.K.S.)
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (L.G.M.); (E.Y.G.); (V.N.A.)
- State Research Center for Applied Microbiology and Biotechnology, 142279 Obolensk, Russia
| | - Darya V. Poshvina
- Institute of Environmental and Agricultural Biology (X-BIO), Tyumen State University, 625003 Tyumen, Russia; (S.V.K.); (A.P.Z.); (D.V.P.)
| | - Roman S. Fadeev
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia; (M.I.K.); (R.S.F.)
| | - Viacheslav N. Azev
- The Branch of the Institute of Bioorganic Chemistry, Russian Academy of Sciences, 142290 Pushchino, Russia; (L.G.M.); (E.Y.G.); (V.N.A.)
| | - Olga S. Ostroumova
- Institute of Cytology of the Russian Academy of Sciences, Tikhoretsky Ave. 4, 194064 St. Petersburg, Russia; (A.A.Z.); (O.S.O.)
| | | | - Oxana V. Galzitskaya
- Gamaleya Research Centre of Epidemiology and Microbiology, 123098 Moscow, Russia;
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia; (S.Y.G.); (A.K.S.)
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia; (M.I.K.); (R.S.F.)
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Xiang K, Li Y, Cong H, Yu B, Shen Y. Peptide-based non-viral gene delivery: A comprehensive review of the advances and challenges. Int J Biol Macromol 2024; 266:131194. [PMID: 38554914 DOI: 10.1016/j.ijbiomac.2024.131194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 03/14/2024] [Accepted: 03/26/2024] [Indexed: 04/02/2024]
Abstract
Gene therapy is the most effective treatment option for diseases, but its effectiveness is affected by the choice and design of gene carriers. The genes themselves have to pass through multiple barriers in order to enter the cell and therefore require additional vectors to carry them inside the cell. In gene therapy, peptides have unique properties and potential as gene carriers, which can effectively deliver genes into specific cells or tissues, protect genes from degradation, improve gene transfection efficiency, and enhance gene targeting and biological responsiveness. This paper reviews the research progress of peptides and their derivatives in the field of gene delivery recently, describes the obstacles encountered by foreign materials to enter the interior of the cell, and introduces the following classes of functional peptides that can carry materials into the interior of the cell, and assist in transmembrane translocation of carriers, thus breaking through endosomal traps to enable successful entry of genetic materials into the nucleus of the cell. The paper also discusses the combined application of peptide vectors with other vectors to enhance its transfection ability, explores current challenges encountered by peptide vectors, and looks forward to future developments in the field.
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Affiliation(s)
- Kai Xiang
- College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao 266071, China
| | - Yanan Li
- College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao 266071, China
| | - Hailin Cong
- College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao 266071, China; State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao 266071, China; School of Materials Science and Engineering, Shandong University of Technology, Zibo 255000, China.
| | - Bing Yu
- College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao 266071, China; State Key Laboratory of Bio-Fibers and Eco-Textiles, Qingdao University, Qingdao 266071, China.
| | - Youqing Shen
- College of Chemistry and Chemical Engineering, College of Materials Science and Engineering, Institute of Biomedical Materials and Engineering, Qingdao University, Qingdao 266071, China; Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Center for Bio nanoengineering, and Department of Chemical and Biological Engineering, Zhejiang University, Hangzhou 310027, China
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3
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Eweje F, Walsh ML, Ahmad K, Ibrahim V, Alrefai A, Chen J, Chaikof EL. Protein-based nanoparticles for therapeutic nucleic acid delivery. Biomaterials 2024; 305:122464. [PMID: 38181574 PMCID: PMC10872380 DOI: 10.1016/j.biomaterials.2023.122464] [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: 09/23/2023] [Revised: 12/25/2023] [Accepted: 12/31/2023] [Indexed: 01/07/2024]
Abstract
To realize the full potential of emerging nucleic acid therapies, there is a need for effective delivery agents to transport cargo to cells of interest. Protein materials exhibit several unique properties, including biodegradability, biocompatibility, ease of functionalization via recombinant and chemical modifications, among other features, which establish a promising basis for therapeutic nucleic acid delivery systems. In this review, we highlight progress made in the use of non-viral protein-based nanoparticles for nucleic acid delivery in vitro and in vivo, while elaborating on key physicochemical properties that have enabled the use of these materials for nanoparticle formulation and drug delivery. To conclude, we comment on the prospects and unresolved challenges associated with the translation of protein-based nucleic acid delivery systems for therapeutic applications.
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Affiliation(s)
- Feyisayo Eweje
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA; Harvard and MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Harvard/MIT MD-PhD Program, Boston, MA, USA, 02115; Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA
| | - Michelle L Walsh
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA; Harvard and MIT Division of Health Sciences and Technology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA; Harvard/MIT MD-PhD Program, Boston, MA, USA, 02115
| | - Kiran Ahmad
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Vanessa Ibrahim
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Assma Alrefai
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Jiaxuan Chen
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA; Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
| | - Elliot L Chaikof
- Department of Surgery, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA; Wyss Institute of Biologically Inspired Engineering, Harvard University, Boston, MA, 02115, USA.
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Kharga K, Jha S, Vishwakarma T, Kumar L. Current developments and prospects of the antibiotic delivery systems. Crit Rev Microbiol 2024:1-40. [PMID: 38425122 DOI: 10.1080/1040841x.2024.2321480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 02/16/2024] [Indexed: 03/02/2024]
Abstract
Antibiotics have remained the cornerstone for the treatment of bacterial infections ever since their discovery in the twentieth century. The uproar over antibiotic resistance among bacteria arising from genome plasticity and biofilm development has rendered current antibiotic therapies ineffective, urging the development of innovative therapeutic approaches. The development of antibiotic resistance among bacteria has further heightened the clinical failure of antibiotic therapy, which is often linked to its low bioavailability, side effects, and poor penetration and accumulation at the site of infection. In this review, we highlight the potential use of siderophores, antibodies, cell-penetrating peptides, antimicrobial peptides, bacteriophages, and nanoparticles to smuggle antibiotics across impermeable biological membranes to achieve therapeutically relevant concentrations of antibiotics and combat antimicrobial resistance (AMR). We will discuss the general mechanisms via which each delivery system functions and how it can be tailored to deliver antibiotics against the paradigm of mechanisms underlying antibiotic resistance.
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Affiliation(s)
- Kusum Kharga
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Himachal Pradesh, India
| | - Shubhang Jha
- School of Bioengineering and Food Technology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Himachal Pradesh, India
| | - Tanvi Vishwakarma
- School of Bioengineering and Food Technology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Himachal Pradesh, India
| | - Lokender Kumar
- School of Biotechnology, Faculty of Applied Sciences and Biotechnology, Shoolini University, Himachal Pradesh, India
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Hu W, Cai W, Wu Y, Ren C, Yu D, Li T, Shen T, Xu D, Yu J. Topical Application of Cell-Penetrating Peptide Modified Anti-VEGF Drug Alleviated Choroidal Neovascularization in Mice. Int J Nanomedicine 2024; 19:35-51. [PMID: 38187905 PMCID: PMC10771783 DOI: 10.2147/ijn.s428684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Accepted: 12/19/2023] [Indexed: 01/09/2024] Open
Abstract
Background Age-related macular degeneration (AMD) stands as the foremost cause of irreversible central vision impairment, marked by choroidal neovascularization (CNV). The prevailing clinical approach to AMD treatment relies on intravitreal injections of anti-vascular endothelial growth factor (VEGF) drugs. However, this method is encumbered by diverse complications, prompting exploration of non-invasive alternatives such as ocular administration via eye drops for anti-VEGF therapy. Methods Two complexes, 5-FITC-CPP-Ranibizumab (5-FCR) and 5-FITC-CPP-Conbercept (5-FCC), were synthesized by incorporating the anti-VEGF drugs Ranibizumab (RBZ) or Conbercept (CBC) with cell-penetrating peptide (CPP). Circular dichroism spectrum (CD) facilitated complexes characterization. Eye drops was utilized to address laser-induced CNV in mice. Fluorescein fundus angiography (FFA) observe the CNV lesion, while FITC-dextran and IB4 dual fluorescent staining, along with hematoxylin-eosin (HE) staining, assessed in lesion size. Tissue immunofluorescence examined CD31 and VEGF expression in choroidal/retinal pigment epithelial (RPE) tissues. Biocompatibility and biosafety of 5-FCR and 5-FCC was evaluated through histological examination of various organs or cell experiments. Results Both 5-FCR and 5-FCC exhibited favorable biocompatibility and safety profiles. VEGF-induced migration of Human umbilical vein endothelial cells (HUVECs) significantly decreased post-5-FCR/5-FCC treatment. Additionally, both complexes suppressed VEGF-induced tube formation in HUVECs. FFA results revealed a significant improvement in retinal exudation in mice. Histological examination unveiled the lesion areas in the 5-FCR and 5-FCC groups showed a significant reduction compared to the control group. Similar outcomes were observed in histological sections of the RPE-choroid-sclera flat mounts. Conclusion In this study, utilizing the properties of CPP and two anti-VEGF drugs, we successfully synthesized two complexes, 5-FCR and 5-FCC, through a straightforward approach. Effectively delivering the anti-VEGF drugs to the target area in a non-invasive manner, suppressing the progression of laser-induced CNV. This offers a novel approach for the treatment of wet AMD.
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Affiliation(s)
- Weinan Hu
- Department of Ophthalmology, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, People’s Republic of China
| | - Wenting Cai
- Department of Ophthalmology, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, People’s Republic of China
| | - Yan Wu
- Department of Ophthalmology, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, People’s Republic of China
| | - Chengda Ren
- Department of Ophthalmology, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, People’s Republic of China
| | - Donghui Yu
- Department of Ophthalmology, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, People’s Republic of China
| | - Tingting Li
- Department of Ophthalmology, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, People’s Republic of China
| | - Tianyi Shen
- Department of Ophthalmology, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, People’s Republic of China
| | - Ding Xu
- Department of Ophthalmology, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, People’s Republic of China
| | - Jing Yu
- Department of Ophthalmology, Shanghai Tenth People’s Hospital, Tongji University, Shanghai, People’s Republic of China
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Wang K, Wei Y, Xie X, Li Q, Liu X, Wang L, Li J, Wu J, Fan C. DNA-Programmed Stem Cell Niches via Orthogonal Extracellular Vesicle-Cell Communications. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2302323. [PMID: 37463346 DOI: 10.1002/adma.202302323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 07/13/2023] [Accepted: 07/17/2023] [Indexed: 07/20/2023]
Abstract
Extracellular vesicles (EVs) are natural carriers for intercellular transfer of bioactive molecules, which are harnessed for wide biomedical applications. However, a facile yet general approach to engineering interspecies EV-cell communications is still lacking. Here, the use of DNA to encode the heterogeneous interfaces of EVs and cells in a manner free of covalent or genetic modifications is reported, which enables orthogonal EV-cell interkingdom interactions in complex environments. Cholesterol-modified DNA strands and tetrahedral DNA frameworks are employed with complementary sequences to serve as artificial ligands and receptors docking on EVs and living cells, respectively, which can mediate specific yet efficient cellular internalization of EVs via Watson-Crick base pairing. It is shown that based on this system, human cells can adopt EVs derived from the mouse, watermelon, and Escherichia coli. By implementing several EV-cell circuits, it shows that this DNA-programmed system allows orthogonal EV-cell communications in complex environments. This study further demonstrates efficient delivery of EVs with bioactive contents derived from feeder cells toward monkey female germline stem cells (FGSCs), which enables self-renewal and stemness maintenance of the FGSCs without feeder cells. This system may provide a universal platform to customize intercellular exchanges of materials and signals across species and kingdoms.
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Affiliation(s)
- Kaizhe Wang
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- Ningbo Key Laboratory of Biomedical Imaging Probe Materials and Technology, Ningbo Cixi Institute of BioMedical Engineering, Ningbo Institute of Materials Technology and Engineering, Chinese Academy of Sciences, Ningbo, 315300, China
| | - Yuhan Wei
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaodong Xie
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Qian Li
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Xiaoguo Liu
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Lihua Wang
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai, 200444, China
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Jiang Li
- Institute of Materiobiology, Department of Chemistry, College of Science, Shanghai University, Shanghai, 200444, China
- The Interdisciplinary Research Center, Shanghai Synchrotron Radiation Facility, Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Ji Wu
- Key Laboratory for the Genetics of Developmental & Neuropsychiatric Disorders (Ministry of Education), Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Chunhai Fan
- School of Chemistry and Chemical Engineering, New Cornerstone Science Laboratory, Frontiers Science Center for Transformative Molecules, Zhangjiang Institute for Advanced Study and National Center for Translational Medicine, Shanghai Jiao Tong University, Shanghai, 200240, China
- Institute of Molecular Medicine, Shanghai Key Laboratory for Nucleic Acids Chemistry and Nanomedicine, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, Shanghai, 200127, China
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Carrera-Aubesart A, Gallo M, Defaus S, Todorovski T, Andreu D. Topoisomeric Membrane-Active Peptides: A Review of the Last Two Decades. Pharmaceutics 2023; 15:2451. [PMID: 37896211 PMCID: PMC10610229 DOI: 10.3390/pharmaceutics15102451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 10/29/2023] Open
Abstract
In recent decades, bioactive peptides have been gaining recognition in various biomedical areas, such as intracellular drug delivery (cell-penetrating peptides, CPPs) or anti-infective action (antimicrobial peptides, AMPs), closely associated to their distinct mode of interaction with biological membranes. Exploiting the interaction of membrane-active peptides with diverse targets (healthy, tumoral, bacterial or parasitic cell membranes) is opening encouraging prospects for peptides in therapeutics. However, ordinary peptides formed by L-amino acids are easily decomposed by proteases in biological fluids. One way to sidestep this limitation is to use topoisomers, namely versions of the peptide made up of D-amino acids in either canonic (enantio) or inverted (retroenantio) sequence. Rearranging peptide sequences in this fashion provides a certain degree of native structure mimicry that, in appropriate contexts, may deliver desirable biological activity while avoiding protease degradation. In this review, we will focus on recent accounts of membrane-active topoisomeric peptides with therapeutic applications as CPP drug delivery vectors, or as antimicrobial and anticancer candidates. We will also discuss the most common modes of interaction of these peptides with their membrane targets.
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Affiliation(s)
- Adam Carrera-Aubesart
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.C.-A.); (M.G.); (S.D.); (T.T.)
| | - Maria Gallo
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.C.-A.); (M.G.); (S.D.); (T.T.)
| | - Sira Defaus
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.C.-A.); (M.G.); (S.D.); (T.T.)
| | - Toni Todorovski
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.C.-A.); (M.G.); (S.D.); (T.T.)
- Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
| | - David Andreu
- Department of Medicine and Life Sciences, Universitat Pompeu Fabra, 08003 Barcelona, Spain; (A.C.-A.); (M.G.); (S.D.); (T.T.)
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Zhang H, Zhang Y, Zhang C, Yu H, Ma Y, Li Z, Shi N. Recent Advances of Cell-Penetrating Peptides and Their Application as Vectors for Delivery of Peptide and Protein-Based Cargo Molecules. Pharmaceutics 2023; 15:2093. [PMID: 37631307 PMCID: PMC10459450 DOI: 10.3390/pharmaceutics15082093] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 07/31/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Peptides and proteins, two important classes of biomacromolecules, play important roles in the biopharmaceuticals field. As compared with traditional drugs based on small molecules, peptide- and protein-based drugs offer several advantages, although most cannot traverse the cell membrane, a natural barrier that prevents biomacromolecules from directly entering cells. However, drug delivery via cell-penetrating peptides (CPPs) is increasingly replacing traditional approaches that mediate biomacromolecular cellular uptake, due to CPPs' superior safety and efficiency as drug delivery vehicles. In this review, we describe the discovery of CPPs, recent developments in CPP design, and recent advances in CPP applications for enhanced cellular delivery of peptide- and protein-based drugs. First, we discuss the discovery of natural CPPs in snake, bee, and spider venom. Second, we describe several synthetic types of CPPs, such as cyclic CPPs, glycosylated CPPs, and D-form CPPs. Finally, we summarize and discuss cell membrane permeability characteristics and therapeutic applications of different CPPs when used as vehicles to deliver peptides and proteins to cells, as assessed using various preclinical disease models. Ultimately, this review provides an overview of recent advances in CPP development with relevance to applications related to the therapeutic delivery of biomacromolecular drugs to alleviate diverse diseases.
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Affiliation(s)
- Huifeng Zhang
- School of Pharmacy, Jilin Medical University, Jilin 132013, China; (H.Z.); (Y.Z.); (C.Z.); (H.Y.); (Y.M.)
| | - Yanfei Zhang
- School of Pharmacy, Jilin Medical University, Jilin 132013, China; (H.Z.); (Y.Z.); (C.Z.); (H.Y.); (Y.M.)
| | - Chuang Zhang
- School of Pharmacy, Jilin Medical University, Jilin 132013, China; (H.Z.); (Y.Z.); (C.Z.); (H.Y.); (Y.M.)
| | - Huan Yu
- School of Pharmacy, Jilin Medical University, Jilin 132013, China; (H.Z.); (Y.Z.); (C.Z.); (H.Y.); (Y.M.)
| | - Yinghui Ma
- School of Pharmacy, Jilin Medical University, Jilin 132013, China; (H.Z.); (Y.Z.); (C.Z.); (H.Y.); (Y.M.)
| | - Zhengqiang Li
- Key Laboratory for Molecular Enzymology and Engineering of the Ministry of Education, College of Life Sciences, Jilin University, Changchun 130012, China;
| | - Nianqiu Shi
- School of Pharmacy, Jilin Medical University, Jilin 132013, China; (H.Z.); (Y.Z.); (C.Z.); (H.Y.); (Y.M.)
- College of Pharmaceutical Sciences, Yanbian University, Yanji 133002, China
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9
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Schissel CK, Farquhar CE, Loas A, Malmberg AB, Pentelute BL. In-Cell Penetration Selection-Mass Spectrometry Produces Noncanonical Peptides for Antisense Delivery. ACS Chem Biol 2023; 18:615-628. [PMID: 36857503 PMCID: PMC10460143 DOI: 10.1021/acschembio.2c00920] [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] [Indexed: 03/03/2023]
Abstract
Peptide-mediated delivery of macromolecules in cells has significant potential therapeutic benefits, but no therapy employing cell-penetrating peptides (CPPs) has reached the market after 30 years of investigation due to challenges in the discovery of new, more efficient sequences. Here, we demonstrate a method for in-cell penetration selection-mass spectrometry (in-cell PS-MS) to discover peptides from a synthetic library capable of delivering macromolecule cargo to the cytosol. This method was inspired by recent in vivo selection approaches for cell-surface screening, with an added spatial dimension resulting from subcellular fractionation. A representative peptide discovered in the cytosolic extract, Cyto1a, is nearly 100-fold more active toward antisense phosphorodiamidate morpholino oligomer (PMO) delivery compared to a sequence identified from a whole cell extract, which includes endosomes. Cyto1a is composed of d-residues and two non-α-amino acids, is more stable than its all-l isoform, and is less toxic than known CPPs with comparable activity. Pulse-chase and microscopy experiments revealed that while the PMO-Cyto1a conjugate is likely taken up by endosomes, it can escape to localize to the nucleus without nonspecifically releasing other endosomal components. In-cell PS-MS introduces a means to empirically discover unnatural synthetic peptides for subcellular delivery of therapeutically relevant cargo.
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Affiliation(s)
- Carly K Schissel
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Charlotte E Farquhar
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Andrei Loas
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
| | - Annika B Malmberg
- Sarepta Therapeutics, 215 First Street, Cambridge, Massachusetts 02142, United States
| | - Bradley L Pentelute
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- Center for Environmental Health Sciences, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, United States
- The Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, 500 Main Street, Cambridge, Massachusetts 02142, United States
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, Massachusetts 02142, United States
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10
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In Silico Screening and Optimization of Cell-Penetrating Peptides Using Deep Learning Methods. Biomolecules 2023; 13:biom13030522. [PMID: 36979457 PMCID: PMC10046020 DOI: 10.3390/biom13030522] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Revised: 03/03/2023] [Accepted: 03/09/2023] [Indexed: 03/16/2023] Open
Abstract
Cell-penetrating peptides (CPPs) have great potential to deliver bioactive agents into cells. Although there have been many recent advances in CPP-related research, it is still important to develop more efficient CPPs. The development of CPPs by in silico methods is a very useful addition to experimental methods, but in many cases it can lead to a large number of false-positive results. In this study, we developed a deep-learning-based CPP prediction method, AiCPP, to develop novel CPPs. AiCPP uses a large number of peptide sequences derived from human-reference proteins as a negative set to reduce false-positive predictions and adopts a method to learn small-length peptide sequence motifs that may have CPP tendencies. Using AiCPP, we found that short peptide sequences derived from amyloid precursor proteins are efficient new CPPs, and experimentally confirmed that these CPP sequences can be further optimized.
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11
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Protein Transduction Domain-Mediated Delivery of Recombinant Proteins and In Vitro Transcribed mRNAs for Protein Replacement Therapy of Human Severe Genetic Mitochondrial Disorders: The Case of Sco2 Deficiency. Pharmaceutics 2023; 15:pharmaceutics15010286. [PMID: 36678915 PMCID: PMC9861957 DOI: 10.3390/pharmaceutics15010286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/31/2022] [Accepted: 01/09/2023] [Indexed: 01/19/2023] Open
Abstract
Mitochondrial disorders represent a heterogeneous group of genetic disorders with variations in severity and clinical outcomes, mostly characterized by respiratory chain dysfunction and abnormal mitochondrial function. More specifically, mutations in the human SCO2 gene, encoding the mitochondrial inner membrane Sco2 cytochrome c oxidase (COX) assembly protein, have been implicated in the mitochondrial disorder fatal infantile cardioencephalomyopathy with COX deficiency. Since an effective treatment is still missing, a protein replacement therapy (PRT) was explored using protein transduction domain (PTD) technology. Therefore, the human recombinant full-length mitochondrial protein Sco2, fused to TAT peptide (a common PTD), was produced (fusion Sco2 protein) and successfully transduced into fibroblasts derived from a SCO2/COX-deficient patient. This PRT contributed to effective COX assembly and partial recovery of COX activity. In mice, radiolabeled fusion Sco2 protein was biodistributed in the peripheral tissues of mice and successfully delivered into their mitochondria. Complementary to that, an mRNA-based therapeutic approach has been more recently considered as an innovative treatment option. In particular, a patented, novel PTD-mediated IVT-mRNA delivery platform was developed and applied in recent research efforts. PTD-IVT-mRNA of full-length SCO2 was successfully transduced into the fibroblasts derived from a SCO2/COX-deficient patient, translated in host ribosomes into a nascent chain of human Sco2, imported into mitochondria, and processed to the mature protein. Consequently, the recovery of reduced COX activity was achieved, thus suggesting the potential of this mRNA-based technology for clinical translation as a PRT for metabolic/genetic disorders. In this review, such research efforts will be comprehensibly presented and discussed to elaborate their potential in clinical application and therapeutic usefulness.
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12
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Hemmati S, Rasekhi Kazerooni H. Polypharmacological Cell-Penetrating Peptides from Venomous Marine Animals Based on Immunomodulating, Antimicrobial, and Anticancer Properties. Mar Drugs 2022; 20:md20120763. [PMID: 36547910 PMCID: PMC9787916 DOI: 10.3390/md20120763] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Revised: 11/25/2022] [Accepted: 11/30/2022] [Indexed: 12/09/2022] Open
Abstract
Complex pathological diseases, such as cancer, infection, and Alzheimer's, need to be targeted by multipronged curative. Various omics technologies, with a high rate of data generation, demand artificial intelligence to translate these data into druggable targets. In this study, 82 marine venomous animal species were retrieved, and 3505 cryptic cell-penetrating peptides (CPPs) were identified in their toxins. A total of 279 safe peptides were further analyzed for antimicrobial, anticancer, and immunomodulatory characteristics. Protease-resistant CPPs with endosomal-escape ability in Hydrophis hardwickii, nuclear-localizing peptides in Scorpaena plumieri, and mitochondrial-targeting peptides from Synanceia horrida were suitable for compartmental drug delivery. A broad-spectrum S. horrida-derived antimicrobial peptide with a high binding-affinity to bacterial membranes was an antigen-presenting cell (APC) stimulator that primes cytokine release and naïve T-cell maturation simultaneously. While antibiofilm and wound-healing peptides were detected in Synanceia verrucosa, APC epitopes as universal adjuvants for antiviral vaccination were in Pterois volitans and Conus monile. Conus pennaceus-derived anticancer peptides showed antiangiogenic and IL-2-inducing properties with moderate BBB-permeation and were defined to be a tumor-homing peptide (THP) with the ability to inhibit programmed death ligand-1 (PDL-1). Isoforms of RGD-containing peptides with innate antiangiogenic characteristics were in Conus tessulatus for tumor targeting. Inhibitors of neuropilin-1 in C. pennaceus are proposed for imaging probes or therapeutic delivery. A Conus betulinus cryptic peptide, with BBB-permeation, mitochondrial-targeting, and antioxidant capacity, was a stimulator of anti-inflammatory cytokines and non-inducer of proinflammation proposed for Alzheimer's. Conclusively, we have considered the dynamic interaction of cells, their microenvironment, and proportional-orchestrating-host- immune pathways by multi-target-directed CPPs resembling single-molecule polypharmacology. This strategy might fill the therapeutic gap in complex resistant disorders and increase the candidates' clinical-translation chance.
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Affiliation(s)
- Shiva Hemmati
- Department of Pharmaceutical Biotechnology, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz 71345-1583, Iran
- Department of Pharmaceutical Biology, Faculty of Pharmaceutical Sciences, UCSI University, Cheras, Kuala Lumpur 56000, Malaysia
- Biotechnology Research Center, Shiraz University of Medical Sciences, Shiraz 71345-1583, Iran
- Correspondence: ; Tel.: +98-7132-424-128
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13
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Porosk L, Langel Ü. Approaches for evaluation of novel CPP-based cargo delivery systems. Front Pharmacol 2022; 13:1056467. [PMID: 36339538 PMCID: PMC9634181 DOI: 10.3389/fphar.2022.1056467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 10/10/2022] [Indexed: 08/05/2023] Open
Abstract
Cell penetrating peptides (CPPs) can be broadly defined as relatively short synthetic, protein derived or chimeric peptides. Their most remarkable property is their ability to cross cell barriers and facilitate the translocation of cargo, such as drugs, nucleic acids, peptides, small molecules, dyes, and many others across the plasma membrane. Over the years there have been several approaches used, adapted, and developed for the evaluation of CPP efficacies as delivery systems, with the fluorophore attachment as the most widely used approach. It has become progressively evident, that the evaluation method, in order to lead to successful outcome, should concede with the specialties of the delivery. For characterization and assessment of CPP-cargo a combination of research tools of chemistry, physics, molecular biology, engineering, and other fields have been applied. In this review, we summarize the diverse, in silico, in vitro and in vivo approaches used for evaluation and characterization of CPP-based cargo delivery systems.
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Affiliation(s)
- Ly Porosk
- Laboratory of Drug Delivery, Institute of Technology, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
| | - Ülo Langel
- Laboratory of Drug Delivery, Institute of Technology, Faculty of Science and Technology, University of Tartu, Tartu, Estonia
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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14
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In Silico Prediction of Anti-Infective and Cell-Penetrating Peptides from Thalassophryne nattereri Natterin Toxins. Pharmaceuticals (Basel) 2022; 15:ph15091141. [PMID: 36145362 PMCID: PMC9501638 DOI: 10.3390/ph15091141] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2022] [Revised: 09/01/2022] [Accepted: 09/06/2022] [Indexed: 12/14/2022] Open
Abstract
The therapeutic potential of venom-derived peptides, such as bioactive peptides (BAPs), is determined by specificity, stability, and pharmacokinetics properties. BAPs, including anti-infective or antimicrobial peptides (AMPs) and cell-penetrating peptides (CPPs), share several physicochemical characteristics and are potential alternatives to antibiotic-based therapies and drug delivery systems, respectively. This study used in silico methods to predict AMPs and CPPs derived from natterins from the venomous fish Thalassophryne nattereri. Fifty-seven BAPs (19 AMPs, 8 CPPs, and 30 AMPs/CPPs) were identified using the web servers CAMP, AMPA, AmpGram, C2Pred, and CellPPD. The physicochemical properties were analyzed using ProtParam, PepCalc, and DispHred tools. The membrane-binding potential and cellular location of each peptide were analyzed using the Boman index by APD3, and TMHMM web servers. All CPPs and two AMPs showed high membrane-binding potential. Fifty-four peptides were located in the plasma membrane. Peptide immunogenicity, toxicity, allergenicity, and ADMET parameters were evaluated using several web servers. Sixteen antiviral peptides and 37 anticancer peptides were predicted using the web servers Meta-iAVP and ACPred. Secondary structures and helical wheel projections were predicted using the PEP-FOLD3 and Heliquest web servers. Fifteen peptides are potential lead compounds and were selected to be further synthesized and tested experimentally in vitro to validate the in silico screening. The use of computer-aided design for predicting peptide structure and activity is fast and cost-effective and facilitates the design of potent therapeutic peptides. The results demonstrate that toxins form a natural biotechnological platform in drug discovery, and the presence of CPP and AMP sequences in toxin families opens new possibilities in toxin biochemistry research.
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15
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Okano S, Kawaguchi Y, Kawano K, Hirose H, Imanishi M, Futaki S. Split luciferase-based estimation of cytosolic cargo concentration delivered intracellularly via attenuated cationic amphiphilic lytic peptides. Bioorg Med Chem Lett 2022; 72:128875. [DOI: 10.1016/j.bmcl.2022.128875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 11/02/2022]
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16
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Shinga K, Iwata T, Murata K, Daitoku Y, Michibata J, Arafiles JVV, Sakamoto K, Akishiba M, Takatani-Nakase T, Mizuno S, Sugiyama F, Imanishi M, Futaki S. L17ER4: A cell-permeable attenuated cationic amphiphilic lytic peptide. Bioorg Med Chem 2022; 61:116728. [PMID: 35395514 DOI: 10.1016/j.bmc.2022.116728] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/25/2022] [Accepted: 03/27/2022] [Indexed: 11/29/2022]
Abstract
We have developed a series of attenuated cationic amphiphilic lytic (ACAL) peptides that can efficiently bring immunoglobulin G (IgG) and other functional proteins into cells. Delivery is generally achieved through the coadministration of ACAL peptides with cargo proteins. However, conjugation of ACAL peptides with cargos may be a promising approach for in vivo application to link in vivo outcomes of ACAL peptides and cargos. This study describes the creation of a new cell-permeable ACAL peptide, L17ER4. L17E is an optimized prototype of ACAL peptides previously developed in our laboratory for efficient delivery of IgGs into cells. Delivery was improved by functionalizing L17E with a tetra-arginine (R4) tag. Compared to the use of R8, a representative cell-penetrating peptide with high intracellular delivery efficacy, conjugation with L17ER4 afforded approximately four-fold higher cellular uptake of model small-molecule cargos (fluorescein isothiocyanate and HiBiT peptide). L17ER4 was also able to deliver proteins to cells. Fused with L17ER4, Cre recombinase was delivered into cells. Intracerebroventricular injection of Cre-L17ER4 into green red reporter mice, R26GRR, led to significant in vivo gene recombination in ependymal cells, suggesting that L17ER4 may be used as a cell-penetrating peptide for delivering protein therapeutics into cells in vivo.
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Affiliation(s)
- Kenta Shinga
- Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto 611-0011, Japan
| | - Takahiro Iwata
- Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto 611-0011, Japan
| | - Kazuya Murata
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8575, Japan
| | - Yoko Daitoku
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8575, Japan
| | - Junya Michibata
- Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto 611-0011, Japan
| | | | - Kentarou Sakamoto
- Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto 611-0011, Japan
| | - Misao Akishiba
- Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto 611-0011, Japan
| | - Tomoka Takatani-Nakase
- School of Pharmacy and Pharmaceutical Sciences, Mukogawa Women's University, Nishinomiya, Hyogo 663-8179, Japan; Institute for Bioscience, Mukogawa Women's University, Nishinomiya, Hyogo 663-8179, Japan
| | - Seiya Mizuno
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8575, Japan
| | - Fumihiro Sugiyama
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8575, Japan
| | - Miki Imanishi
- Institute for Chemical Research, Kyoto University Gokasho, Uji, Kyoto 611-0011, Japan
| | - Shiroh Futaki
- Laboratory Animal Resource Center, Transborder Medical Research Center, Faculty of Medicine, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki 305-8575, Japan.
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17
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Cardenas AE, Drexler CI, Nechushtai R, Mittler R, Friedler A, Webb LJ, Elber R. Peptide Permeation across a Phosphocholine Membrane: An Atomically Detailed Mechanism Determined through Simulations and Supported by Experimentation. J Phys Chem B 2022; 126:2834-2849. [PMID: 35388695 PMCID: PMC9074375 DOI: 10.1021/acs.jpcb.1c10966] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell-penetrating peptides (CPPs) facilitate translocation across biological membranes and are of significant biological and medical interest. Several CPPs can permeate into specific cells and organelles. We examine the incorporation and translocation of a novel anticancer CPP in a dioleoylphosphatidylcholine (DOPC) lipid bilayer membrane. The peptide, NAF-144-67, is a short fragment of a transmembrane protein, consisting of hydrophobic N-terminal and charged C-terminal segments. Experiments using fluorescently labeled NAF-144-67 in ∼100 nm DOPC vesicles and atomically detailed simulations conducted with Milestoning support a model in which a significant barrier for peptide-membrane entry is found at the interface between the aqueous solution and membrane. The initial step is the insertion of the N-terminal segment and the hydrophobic helix into the membrane, passing the hydrophilic head groups. Both experiments and simulations suggest that the free energy difference in the first step of the permeation mechanism in which the hydrophobic helix crosses the phospholipid head groups is -0.4 kcal mol-1 slightly favoring motion into the membrane. Milestoning calculations of the mean first passage time and the committor function underscore the existence of an early polar barrier followed by a diffusive barrierless motion in the lipid tail region. Permeation events are coupled to membrane fluctuations that are examined in detail. Our study opens the way to investigate in atomistic resolution the molecular mechanism, kinetics, and thermodynamics of CPP permeation to diverse membranes.
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Affiliation(s)
- Alfredo E. Cardenas
- Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chad I. Drexler
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Rachel Nechushtai
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 91904, Israel
| | - Ron Mittler
- The Department of Surgery, University of Missouri School of Medicine. Christopher S. Bond Life Sciences Center, University of Missouri. 1201 Rollins St, Columbia, MO 65201, USA
| | - Assaf Friedler
- The Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat-Ram, Jerusalem 91904, Israel
| | - Lauren J. Webb
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
| | - Ron Elber
- Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, TX 78712, USA
- Department of Chemistry, The University of Texas at Austin, Austin, TX 78712, USA
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18
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Lessons from a Single Amino Acid Substitution: Anticancer and Antibacterial Properties of Two Phospholipase A2-Derived Peptides. Curr Issues Mol Biol 2021; 44:46-62. [PMID: 35723383 PMCID: PMC8929095 DOI: 10.3390/cimb44010004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 12/13/2021] [Accepted: 12/15/2021] [Indexed: 12/15/2022] Open
Abstract
The membrane-active nature of phospholipase A2-derived peptides makes them potential candidates for antineoplastic and antibacterial therapies. Two short 13-mer C-terminal fragments taken from snake venom Lys49-PLA2 toxins (p-AppK and p-Acl), differing by a leucine/phenylalanine substitution, were synthesized and their bioactivity was evaluated. Their capacity to interfere with the survival of Gram-positive and Gram-negative bacteria as well as with solid and liquid tumors was assessed in vitro. Toxicity to red blood cells was investigated via in silico and in vitro techniques. The mode of action was mainly studied by molecular dynamics simulations and membrane permeabilization assays. Briefly, both peptides have dual activity, i.e., they act against both bacteria, including multidrug-resistant strains and tumor cells. All tested bacteria were susceptible to both peptides, Pseudomonas aeruginosa being the most affected. RAMOS, K562, NB4, and CEM cells were the main leukemic targets of the peptides. In general, p-Acl showed more significant activity, suggesting that phenylalanine confers advantages to the antibacterial and antitumor mechanism, particularly for osteosarcoma lines (HOS and MG63). Peptide-based treatment increased the uptake of a DNA-intercalating dye by bacteria, suggesting membrane damage. Indeed, p-AppK and p-Acl did not disrupt erythrocyte membranes, in agreement with in silico predictions. The latter revealed that the peptides deform the membrane and increase its permeability by facilitating solvent penetration. This phenomenon is expected to catalyze the permeation of solutes that otherwise could not cross the hydrophobic membrane core. In conclusion, the present study highlights the role of a single amino acid substitution present in natural sequences towards the development of dual-action agents. In other words, dissecting and fine-tuning biomembrane remodeling proteins, such as snake venom phospholipase A2 isoforms, is again demonstrated as a valuable source of therapeutic peptides.
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19
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Sinha NJ, Langenstein MG, Pochan DJ, Kloxin CJ, Saven JG. Peptide Design and Self-assembly into Targeted Nanostructure and Functional Materials. Chem Rev 2021; 121:13915-13935. [PMID: 34709798 DOI: 10.1021/acs.chemrev.1c00712] [Citation(s) in RCA: 93] [Impact Index Per Article: 31.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Peptides have been extensively utilized to construct nanomaterials that display targeted structure through hierarchical assembly. The self-assembly of both rationally designed peptides derived from naturally occurring domains in proteins as well as intuitively or computationally designed peptides that form β-sheets and helical secondary structures have been widely successful in constructing nanoscale morphologies with well-defined 1-d, 2-d, and 3-d architectures. In this review, we discuss these successes of peptide self-assembly, especially in the context of designing hierarchical materials. In particular, we emphasize the differences in the level of peptide design as an indicator of complexity within the targeted self-assembled materials and highlight future avenues for scientific and technological advances in this field.
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Affiliation(s)
- Nairiti J Sinha
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Matthew G Langenstein
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Darrin J Pochan
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Christopher J Kloxin
- Department of Materials Science and Engineering, University of Delaware, Newark, Delaware 19716, United States.,Department of Chemical and Biomolecular Engineering, University of Delaware, Newark, Delaware 19716, United States
| | - Jeffery G Saven
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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20
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Porosk L, Põhako K, Arukuusk P, Langel Ü. Cell-Penetrating Peptides Predicted From CASC3, AKIP1, and AHRR Proteins. Front Pharmacol 2021; 12:716226. [PMID: 34504427 PMCID: PMC8421526 DOI: 10.3389/fphar.2021.716226] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Peptides can be used as research tools and for diagnostic or therapeutic applications. Peptides, alongside small molecules and antibodies, are used and are gaining further interest as protein-protein interaction (PPI) modulators. Peptides have high target specificity and high affinity, but, unlike small molecule modulators, they are not able to cross the cell membranes to reach their intracellular targets. To overcome this limitation, the special property of the cell-penetrating peptides (CPPs) could benefit their cause. CPPs are a class of peptides that can enter the cells and with them also deliver the attached cargoes. Today, with the advancement of in silico prediction tools and the availability of protein databases, designing new and multifunctional peptides that are able to reach intracellular targets and inhibit certain cellular processes in a very specific manner is reachable. Although there are several efficient CPP sequences already known, the discovery of new CPPs is crucial for the development of efficient delivery methods for both biotechnological and therapeutic applications. In this work, we chose 10 human nuclear proteins from which we predicted new potential CPP sequences by using three different CPP predictors: cell-penetrating peptide prediction tool, CellPPD, and SkipCPP-Pred. From each protein, one predicted CPP sequence was synthesized and its internalization into cells was assessed. Out of the tested sequences, three peptides displayed features characteristic to CPPs. These peptides and also the predicted peptide sequences could be used to design and modify new CPPs. In this work, we show that we can use protein sequences as input for generating new peptides with cell internalization properties. Three new CPPs, AHRR8-24, CASC3251-264, and AKIP127-37, can be further used for the delivery of other cargoes or designed into multifunctional peptides with capability of internalizing cells.
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Affiliation(s)
- Ly Porosk
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Kaisa Põhako
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Piret Arukuusk
- Institute of Technology, University of Tartu, Tartu, Estonia
| | - Ülo Langel
- Institute of Technology, University of Tartu, Tartu, Estonia.,Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
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21
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de Mello LR, Porosk L, Lourenço TC, Garcia BBM, Costa CAR, Han SW, de Souza JS, Langel Ü, da Silva ER. Amyloid-like Self-Assembly of a Hydrophobic Cell-Penetrating Peptide and Its Use as a Carrier for Nucleic Acids. ACS APPLIED BIO MATERIALS 2021; 4:6404-6416. [PMID: 35006917 DOI: 10.1021/acsabm.1c00601] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cell-penetrating peptides (CPPs) are a topical subject potentially exploitable for creating nanotherapeutics for the delivery of bioactive loads. These compounds are often classified into three major categories according to their physicochemical characteristics: cationic, amphiphilic, and hydrophobic. Among them, the group of hydrophobic CPPs has received increasing attention in recent years due to toxicity concerns posed by highly cationic CPPs. The hexapeptide PFVYLI (P, proline; F, phenylalanine; V, valine; Y, tyrosine; L, leucine; and I, isoleucine), a fragment derived from the C-terminal portion of α1-antitrypsin, is a prototypal example of hydrophobic CPP. This sequence shows reduced cytotoxicity and a capacity of nuclear localization, and its small size readily hints at its suitability as a building block to construct nanostructured materials. In this study, we examine the self-assembling properties of PFVYLI and investigate its ability to form noncovalent complexes with nucleic acids. By using a combination of biophysical tools including synchrotron small-angle X-ray scattering and atomic force microscopy-based infrared spectroscopy, we discovered that this CPP self-assembles into discrete nanofibrils with remarkable amyloidogenic features. Over the course of days, these fibrils coalesce into rodlike crystals that easily reach the micrometer range. Despite lacking cationic residues in the composition, PFVYLI forms noncovalent complexes with nucleic acids that retain β-sheet pairing found in amyloid aggregates. In vitro vectorization experiments performed with double-stranded DNA fragments indicate that complexes promote the internalization of nucleic acids, revealing that tropism toward cell membranes is preserved upon complexation. On the other hand, transfection assays with splice-correction oligonucleotides (SCOs) for luciferase expression show limited bioactivity across a narrow concentration window, suggesting that the propensity to form amyloidogenic aggregates may trigger endosomal entrapment. We anticipate that the findings presented here open perspectives for using this archetypical hydrophobic CPP in the fabrication of nanostructured scaffolds, which potentially integrate properties of amyloids and translocation capabilities of CPPs.
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Affiliation(s)
- Lucas R de Mello
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | - Ly Porosk
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
| | - Thiago C Lourenço
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | - Bianca B M Garcia
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | - Carlos A R Costa
- Laboratório Nacional de Nanotecnologia (LNNano), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas 13083-861, Brazil
| | - Sang W Han
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
| | - Juliana S de Souza
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, Santo André 09210580, Brazil
| | - Ülo Langel
- Institute of Technology, University of Tartu, Tartu 50411, Estonia
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-10691, Sweden
| | - Emerson R da Silva
- Departamento de Biofísica, Universidade Federal de São Paulo, São Paulo 04023-062, Brazil
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