1
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Zhao M, Lopes LJS, Sahni H, Yadav A, Do HN, Reddy T, López CA, Neale C, Gnanakaran S. Insertion and Anchoring of HIV-1 Fusion Peptide into Complex Membrane Mimicking Human T-cell. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.02.606381. [PMID: 39131401 PMCID: PMC11312619 DOI: 10.1101/2024.08.02.606381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/13/2024]
Abstract
A fundamental understanding of how HIV-1 envelope (Env) protein facilitates fusion is still lacking. The HIV-1 fusion peptide, consisting of 15 to 22 residues, is the N-terminus of the gp41 subunit of the Env protein. Further, this peptide, a promising vaccine candidate, initiates viral entry into target cells by inserting and anchoring into human immune cells. The influence of membrane lipid reorganization and the conformational changes of the fusion peptide during the membrane insertion and anchoring processes, which can significantly affect HIV-1 cell entry, remains largely unexplored due to the limitations of experimental measurements. In this work, we investigate the insertion of the fusion peptide into an immune cell membrane mimic through multiscale molecular dynamics simulations. We mimic the native T-cell by constructing a 9-lipid asymmetric membrane, along with geometrical restraints accounting for insertion in the context of gp41. To account for the slow timescale of lipid mixing while enabling conformational changes, we implement a protocol to go back and forth between atomistic and coarse-grained simulations. Our study provides a molecular understanding of the interactions between the HIV-1 fusion peptide and the T-cell membrane, highlighting the importance of conformational flexibility of fusion peptides and local lipid reorganization in stabilizing the anchoring of gp41 into the targeted host membrane during the early events of HIV-1 cell entry. Importantly, we identify a motif within the fusion peptide critical for fusion that can be further manipulated in future immunological studies.
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Affiliation(s)
- Mingfei Zhao
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
| | | | - Harshita Sahni
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
- Department of Computer Science, University of New Mexico, Albuquerque NM, USA
| | - Anju Yadav
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
- Department of Chemistry and Biochemistry, University of Texas at El Paso, El Paso TX, USA
| | - Hung N Do
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
| | - Tyler Reddy
- CCS-7 Applied Computer Science Group, Los Alamos National Laboratory, Los Alamos NM USA
| | - Cesar A López
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
| | - Chris Neale
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
| | - S Gnanakaran
- T-6 Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos NM USA
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2
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Park S, Kim J, Oh SS, Choi SQ. Arginine-Rich Cell-Penetrating Peptides Induce Lipid Rearrangements for Their Active Translocation across Laterally Heterogeneous Membranes. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024:e2404563. [PMID: 38932459 DOI: 10.1002/advs.202404563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 06/01/2024] [Indexed: 06/28/2024]
Abstract
Arginine-rich cell-penetrating peptides (CPPs) have emerged as valuable tools for the intracellular delivery of bioactive molecules, but their membrane perturbation during cell penetration is not fully understood. Here, nona-arginine (R9)-mediated membrane reorganization that facilitates the translocation of peptides across laterally heterogeneous membranes is directly visualized. The electrostatic binding of cationic R9 to anionic phosphatidylserine (PS)-enriched domains on a freestanding lipid bilayer induces lateral lipid rearrangements; in particular, in real-time it is observed that R9 fluidizes PS-rich liquid-ordered (Lo) domains into liquid-disordered (Ld) domains, resulting in the membrane permeabilization. The experiments with giant unilamellar vesicles (GUVs) confirm the preferential translocation of R9 through Ld domains without pore formation, even when Lo domains are more negatively charged. Indeed, whenever R9 comes into contact with negatively charged Lo domains, it dissolves the Lo domains first, promoting translocation across phase-separated membranes. Collectively, the findings imply that arginine-rich CPPs modulate lateral membrane heterogeneity, including membrane fluidization, as one of the fundamental processes for their effective cell penetration across densely packed lipid bilayers.
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Affiliation(s)
- Sujin Park
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
| | - Jinmin Kim
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
| | - Seung Soo Oh
- Department of Materials Science and Engineering, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea
- Institute for Convergence Research and Education in Advanced Technology (I-CREATE), Yonsei University, Incheon, 21983, Republic of Korea
| | - Siyoung Q Choi
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea
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3
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Ghaemi B, Tanwar S, Singh A, Arifin DR, McMahon MT, Barman I, Bulte JWM. Cell-Penetrating and Enzyme-Responsive Peptides for Targeted Cancer Therapy: Role of Arginine Residue Length on Cell Penetration and In Vivo Systemic Toxicity. ACS APPLIED MATERIALS & INTERFACES 2024; 16:11159-11171. [PMID: 38385360 DOI: 10.1021/acsami.3c14908] [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] [Indexed: 02/23/2024]
Abstract
For the improved delivery of cancer therapeutics and imaging agents, the conjugation of cell-penetrating peptides (CPPs) increases the cellular uptake and water solubility of agents. Among the various CPPs, arginine-rich peptides have been the most widely used. Combining CPPs with enzyme-responsive peptides presents an innovative strategy to target specific intracellular enzymes in cancer cells and when combined with the appropriate click chemistry can enhance theranostic drug delivery through the formation of intracellular self-assembled nanostructures. However, one drawback of CPPs is their high positive charge which can cause nonspecific binding, leading to off-target accumulation and potential toxicity. Hence, balancing cell-specific penetration, toxicity, and biocompatibility is essential for future clinical efficacy. We synthesized six cancer-specific, legumain-responsive RnAANCK peptides containing one to six arginine residues, with legumain being an asparaginyl endopeptidase that is overexpressed in aggressive prostate tumors. When conjugated to Alexa Fluor 488, R1-R6AANCK peptides exhibited a concentration- and time-dependent cell penetration in prostate cancer cells, which was higher for peptides with higher R values, reaching a plateau after approximately 120 min. Highly aggressive DU145 prostate tumor cells, but not less aggressive LNCaP cells, self-assembled nanoparticles in the cytosol after the cleavage of the legumain-specific peptide. The in vivo biocompatibility was assessed in mice after the intravenous injection of R1-R6AANCK peptides, with concentrations ranging from 0.0125 to 0.4 mmol/kg. The higher arginine content in R4-6 peptides showed blood and urine indicators for the impairment of bone marrow, liver, and kidney function in a dose-dependent manner, with instant hemolysis and morbidity in extreme cases. These findings underscore the importance of designing peptides with the optimal arginine residue length for a proper balance of cell-specific penetration, toxicity, and in vivo biocompatibility.
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Affiliation(s)
- Behnaz Ghaemi
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Swati Tanwar
- Department of Mechanical Engineering, The Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland 21218, United States
| | - Aruna Singh
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Inc., Baltimore, Maryland 21205, United States
| | - Dian R Arifin
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Michael T McMahon
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Inc., Baltimore, Maryland 21205, United States
| | - Ishan Barman
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Mechanical Engineering, The Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland 21218, United States
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
| | - Jeff W M Bulte
- Russell H. Morgan Department of Radiology and Radiological Science, Division of MR Research, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Cellular Imaging Section and Vascular Biology Program, Institute for Cell Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- F.M. Kirby Research Center for Functional Brain Imaging, Kennedy Krieger Inc., Baltimore, Maryland 21205, United States
- Department of Biomedical Engineering, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Oncology, The Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, United States
- Department of Chemical and Biomolecular Engineering, The Johns Hopkins University Whiting School of Engineering, Baltimore, Maryland 21218, United States
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4
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Ren J, Wang S, Zong Z, Pan T, Liu S, Mao W, Huang H, Yan X, Yang B, He X, Zhou F, Zhang L. TRIM28-mediated nucleocapsid protein SUMOylation enhances SARS-CoV-2 virulence. Nat Commun 2024; 15:244. [PMID: 38172120 PMCID: PMC10764958 DOI: 10.1038/s41467-023-44502-6] [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: 06/15/2023] [Accepted: 12/15/2023] [Indexed: 01/05/2024] Open
Abstract
Viruses, as opportunistic intracellular parasites, hijack the cellular machinery of host cells to support their survival and propagation. Numerous viral proteins are subjected to host-mediated post-translational modifications. Here, we demonstrate that the SARS-CoV-2 nucleocapsid protein (SARS2-NP) is SUMOylated on the lysine 65 residue, which efficiently mediates SARS2-NP's ability in homo-oligomerization, RNA association, liquid-liquid phase separation (LLPS). Thereby the innate antiviral immune response is suppressed robustly. These roles can be achieved through intermolecular association between SUMO conjugation and a newly identified SUMO-interacting motif in SARS2-NP. Importantly, the widespread SARS2-NP R203K mutation gains a novel site of SUMOylation which further increases SARS2-NP's LLPS and immunosuppression. Notably, the SUMO E3 ligase TRIM28 is responsible for catalyzing SARS2-NP SUMOylation. An interfering peptide targeting the TRIM28 and SARS2-NP interaction was screened out to block SARS2-NP SUMOylation and LLPS, and consequently inhibit SARS-CoV-2 replication and rescue innate antiviral immunity. Collectively, these data support SARS2-NP SUMOylation is critical for SARS-CoV-2 virulence, and therefore provide a strategy to antagonize SARS-CoV-2.
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Affiliation(s)
- Jiang Ren
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China
| | - Shuai Wang
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, 215123, China
| | - Zhi Zong
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
| | - Ting Pan
- Shenzhen Key Laboratory of Systems Medicine for Inflammatory Diseases, School of Medicine, Shenzhen Campus of Sun Yat-sen University, Shenzhen, 518107, China
| | - Sijia Liu
- International Biomed-X Research Center, Second Affiliated Hospital of Zhejiang University, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Wei Mao
- Zhejiang Hospital, Zhejiang University School of Medicine, Hangzhou, 310058, China
| | - Huizhe Huang
- Faculty of Basic Medical Sciences, Chongqing Medical University, Chongqing, 400016, China
| | - Xiaohua Yan
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Nanchang University, Nanchang, 330031, China
| | - Bing Yang
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China
- Department of Pharmaceutical Chemistry and the Cardiovascular Research Institute, University of California, San Francisco, CA, 94158, USA
| | - Xin He
- Institute of Human Virology, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510080, China.
| | - Fangfang Zhou
- Institutes of Biology and Medical Sciences, Soochow University, Suzhou, 215123, China.
| | - Long Zhang
- The Eighth Affiliated Hospital, Sun Yat-sen University, Shenzhen, 518033, China.
- MOE Key Laboratory of Biosystems Homeostasis & Protection and Innovation Center for Cell Signaling Network, Life Sciences Institute, Zhejiang University, Hangzhou, 310058, China.
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5
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Tsylents U, Siekierska I, Trylska J. Peptide nucleic acid conjugates and their antimicrobial applications-a mini-review. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:533-544. [PMID: 37610696 PMCID: PMC10618302 DOI: 10.1007/s00249-023-01673-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 08/24/2023]
Abstract
Peptide nucleic acid (PNA) is a nucleic acid mimic with high specificity and binding affinity to natural DNA or RNA, as well as resistance to enzymatic degradation. PNA sequences can be designed to selectively silence gene expression, which makes PNA a promising tool for antimicrobial applications. However, the poor membrane permeability of PNA remains the main limiting factor for its applications in cells. To overcome this obstacle, PNA conjugates with different molecules have been developed. This mini-review focuses on covalently linked conjugates of PNA with cell-penetrating peptides, aminosugars, aminoglycoside antibiotics, and non-peptidic molecules that were tested, primarily as PNA carriers, in antibacterial and antiviral applications. The chemistries of the conjugation and the applied linkers are also discussed.
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Affiliation(s)
- Uladzislava Tsylents
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Izabela Siekierska
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Banacha 2C, 02-097, Warsaw, Poland.
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6
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Lunde PK, Manfra O, Støle TP, Lunde M, Martinsen M, Carlson CR, Louch WE. Polyarginine Cell-Penetrating Peptides Bind and Inhibit SERCA2. Cells 2023; 12:2358. [PMID: 37830576 PMCID: PMC10571751 DOI: 10.3390/cells12192358] [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: 08/15/2023] [Revised: 09/19/2023] [Accepted: 09/21/2023] [Indexed: 10/14/2023] Open
Abstract
Cell-penetrating peptides (CPPs) are short peptide sequences that have the ability to cross the cell membrane and deliver cargo. Although it is critical that CPPs accomplish this task with minimal off-target effects, such actions have in many cases not been robustly screened. We presently investigated whether the commonly used CPPs TAT and the polyarginines Arg9 and Arg11 exert off-target effects on cellular Ca2+ homeostasis. In experiments employing myocytes and homogenates from the cardiac left ventricle or soleus muscle, we observed marked inhibition of Ca2+ recycling into the sarcoplasmic reticulum (SR) following incubation with polyarginine CPPs. In both tissues, the rate of SR Ca2+ leak remained unchanged, indicating that protracted Ca2+ removal from the cytosol stemmed from inhibition of the SR Ca2+ ATPase 2 (SERCA2). No such inhibition occurred following treatment with TAT, or in preparations from the SERCA1-expressing extensor digitorum longus muscle. Experiments in HEK cells overexpressing individual SERCA isoforms confirmed that polyarginine incubation specifically inhibited the activity of SERCA2a and 2b, but not SERCA1 or 3. The attenuation of SERCA2 activity was not dependent on the presence of phospholamban, and ELISA-based analyses rather revealed direct interaction between the polyarginines and the actuator domain of the protein. Surface plasmon resonance experiments confirmed strong binding within this region of SERCA2, and slow dissociation between the two species. Based on these observations, we urge caution when employing polyarginine CPPs. Indeed, as SERCA2 is expressed in diverse cell types, the wide-ranging consequences of SERCA2 binding and inhibition should be anticipated in both experimental and therapeutic settings.
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Affiliation(s)
| | | | | | | | | | - Cathrine Rein Carlson
- Institute for Experimental Medical Research, Oslo University Hospital and University of Oslo, 0450 Oslo, Norway; (P.K.L.); (O.M.); (T.P.S.); (M.L.); (M.M.); (W.E.L.)
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7
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Abstract
Cell penetrating peptides (CPPs) are natural agents that efficiently permeate biological membranes. They are frequently positively charged, which is surprising since membranes pose hydrophobic barriers. In this Perspective, I discuss computations and experiments of a permeation model that couples permeant displacement with a membrane defect. We call the proposed mechanism Defect Assisted by Charge (DAC) and illustrate that it reduces the free energy barrier for translocation. A metastable state at the center of the membrane may be observed due to the charge interactions with the phospholipid head groups at the two leaflets. The combination of experiments and simulations sheds light on the mechanisms of a charged peptide translocation across phospholipid membranes.
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Affiliation(s)
- Ron Elber
- The Department of Chemistry, The Oden Institute, The University of Texas at Austin, Austin, Texas 78712, United States
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8
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Ivánczi M, Balogh B, Kis L, Mándity I. Molecular Dynamics Simulations of Drug-Conjugated Cell-Penetrating Peptides. Pharmaceuticals (Basel) 2023; 16:1251. [PMID: 37765059 PMCID: PMC10535489 DOI: 10.3390/ph16091251] [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: 06/16/2023] [Revised: 08/08/2023] [Accepted: 08/11/2023] [Indexed: 09/29/2023] Open
Abstract
Cell-penetrating peptides (CPPs) are small peptides capable of translocating through biological membranes carrying various attached cargo into cells and even into the nucleus. They may also participate in transcellular transport. Our in silico study intends to model several peptides and their conjugates. We have selected three CPPs with a linear backbone, including penetratin, a naturally occurring oligopeptide; two of its modified sequence analogues (6,14-Phe-penetratin and dodeca-penetratin); and three natural CPPs with a cyclic backbone: Kalata B1, the Sunflower trypsin inhibitor 1 (SFT1), and Momordica cochinchinensis trypsin inhibitor II (MCoTI-II). We have also built conjugates with the small-molecule drug compounds doxorubicin, zidovudine, and rasagiline for each peptide. Molecular dynamics (MD) simulations were carried out with explicit membrane models. The analysis of the trajectories showed that the interaction of penetratin with the membrane led to spectacular rearrangements in the secondary structure of the peptide, while cyclic peptides remained unchanged due to their high conformational stability. Membrane-peptide and membrane-conjugate interactions have been identified and compared. Taking into account well-known examples from the literature, our simulations demonstrated the utility of computational methods for CPP complexes, and they may contribute to a better understanding of the mechanism of penetration, which could serve as the basis for delivering conjugated drug molecules to their intracellular targets.
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Affiliation(s)
- Márton Ivánczi
- Institute of Organic Chemistry, Semmelweis University, Hőgyes Endre Utca 7., H-1092 Budapest, Hungary (L.K.)
| | - Balázs Balogh
- Institute of Organic Chemistry, Semmelweis University, Hőgyes Endre Utca 7., H-1092 Budapest, Hungary (L.K.)
| | - Loretta Kis
- Institute of Organic Chemistry, Semmelweis University, Hőgyes Endre Utca 7., H-1092 Budapest, Hungary (L.K.)
| | - István Mándity
- Institute of Organic Chemistry, Semmelweis University, Hőgyes Endre Utca 7., H-1092 Budapest, Hungary (L.K.)
- Artificial Transporters Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, Magyar Tudósok Körútja 2., H-1117 Budapest, Hungary
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9
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Neumann E, Sohn YS, Povilaitis SC, Cardenas AE, Mittler R, Friedler A, Webb LJ, Nechushtai R, Elber R. Visualization of Molecular Permeation into a Multi-compartment Phospholipid Vesicle. J Phys Chem Lett 2023; 14:6349-6354. [PMID: 37418426 DOI: 10.1021/acs.jpclett.3c01286] [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: 07/09/2023]
Abstract
Passive permeation of small molecules into vesicles with multiple compartments is a critical event in many chemical and biological processes. We consider the translocation of the peptide NAF-144-67 labeled with a fluorescent fluorescein dye across membranes of rhodamine-labeled 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) into liposomes with internal vesicles. Time-resolved microscopy revealed a sequential absorbance of the peptide in both the outer and inner micrometer vesicles that developed over a time period of minutes to hours, illustrating the spatial and temporal progress of the permeation. There is minimal perturbation of the membrane structure and no evidence for pore formation. On the basis of molecular dynamics simulations of NAF-144-67, we extended a local defect model to migration processes that include multiple compartments. The model captures the long residence time of the peptide within the membrane and the rate of permeation through the liposome and its internal compartments. Imaging experiments confirm the semi-quantitative description of the permeation of the model by activated diffusion and open the way for studies of more complex systems.
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Affiliation(s)
- Ehud Neumann
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Yang Sung Sohn
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Sydney C Povilaitis
- Department of Chemistry, The University of Texas at Austin, 2506 Speedway, Stop A5300, Austin, Texas 78712, United States
| | - Alfredo E Cardenas
- Oden Institute for Computational Engineering and Science, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Ron Mittler
- Department of Surgery, University of Missouri School of Medicine, Christopher S. Bond Life Sciences Center, University of Missouri, 1201 Rollins Street, Columbia, Missouri 65201, United States
| | - Assaf Friedler
- Institute of Chemistry, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Lauren J Webb
- Department of Chemistry, The University of Texas at Austin, 2506 Speedway, Stop A5300, Austin, Texas 78712, United States
| | - Rachel Nechushtai
- The Alexander Silberman Institute of Life Science, The Hebrew University of Jerusalem, Edmond J. Safra Campus at Givat Ram, Jerusalem 9190401, Israel
| | - Ron Elber
- Department of Chemistry, The University of Texas at Austin, 2506 Speedway, Stop A5300, Austin, Texas 78712, United States
- Oden Institute for Computational Engineering and Science, The University of Texas at Austin, Austin, Texas 78712, United States
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10
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Vogel E, Santos D, Huygens C, Peeters P, Van den Brande S, Wynant N, Vanden Broeck J. The Study of Cell-Penetrating Peptides to Deliver dsRNA and siRNA by Feeding in the Desert Locust, Schistocerca gregaria. INSECTS 2023; 14:597. [PMID: 37504603 PMCID: PMC10380834 DOI: 10.3390/insects14070597] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 06/23/2023] [Accepted: 06/25/2023] [Indexed: 07/29/2023]
Abstract
RNA(i) interference is a gene silencing mechanism triggered by double-stranded (ds)RNA, which promises to contribute to species-specific insect pest control strategies. The first step toward the application of RNAi as an insecticide is to enable efficient gene silencing upon dsRNA oral delivery. The desert locust, Schistocerca gregaria is a devastating agricultural pest. While this species is responsive to dsRNA delivered by intra-hemocoelic injection, it is refractory to orally delivered dsRNA. In this study, we evaluated the capacity of five cell-penetrating peptides (CPPs) to bind long dsRNA and protect it from the locust midgut environment. We then selected the CPP EB1 for further in vivo studies. EB1:dsRNA complexes failed to induce RNAi by feeding. Interestingly, we observed that intra-hemocoelic injection of small-interfering (si)RNAs does not result in a silencing response, but that this response can be obtained by injecting EB1:siRNA complexes. EB1 also protected siRNAs from midgut degradation activity. However, EB1:siRNA complexes failed as well in triggering RNAi when fed. Our findings highlight the complexity of the dsRNA/siRNA-triggered RNAi in this species and emphasize the multifactorial nature of the RNAi response in insects. Our study also stresses the importance of in vivo studies when it comes to dsRNA/siRNA delivery systems.
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Affiliation(s)
- Elise Vogel
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Dulce Santos
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Cissy Huygens
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, 3000 Leuven, Belgium
- Laboratory of Behavioral and Developmental Genetics, Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Paulien Peeters
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Stijn Van den Brande
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Niels Wynant
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, 3000 Leuven, Belgium
| | - Jozef Vanden Broeck
- Research Group of Molecular Developmental Physiology and Signal Transduction, Division of Animal Physiology and Neurobiology, Department of Biology, KU Leuven, 3000 Leuven, Belgium
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11
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Zakany F, Mándity IM, Varga Z, Panyi G, Nagy P, Kovacs T. Effect of the Lipid Landscape on the Efficacy of Cell-Penetrating Peptides. Cells 2023; 12:1700. [PMID: 37443733 PMCID: PMC10340183 DOI: 10.3390/cells12131700] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2023] [Revised: 06/16/2023] [Accepted: 06/20/2023] [Indexed: 07/15/2023] Open
Abstract
Every cell biological textbook teaches us that the main role of the plasma membrane is to separate cells from their neighborhood to allow for a controlled composition of the intracellular space. The mostly hydrophobic nature of the cell membrane presents an impenetrable barrier for most hydrophilic molecules larger than 1 kDa. On the other hand, cell-penetrating peptides (CPPs) are capable of traversing this barrier without compromising membrane integrity, and they can do so on their own or coupled to cargos. Coupling biologically and medically relevant cargos to CPPs holds great promise of delivering membrane-impermeable drugs into cells. If the cargo is able to interact with certain cell types, uptake of the CPP-drug complex can be tailored to be cell-type-specific. Besides outlining the major membrane penetration pathways of CPPs, this review is aimed at deciphering how properties of the membrane influence the uptake mechanisms of CPPs. By summarizing an extensive body of experimental evidence, we argue that a more ordered, less flexible membrane structure, often present in the very diseases planned to be treated with CPPs, decreases their cellular uptake. These correlations are not only relevant for understanding the cellular biology of CPPs, but also for rationally improving their value in translational or clinical applications.
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Affiliation(s)
- Florina Zakany
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (F.Z.); (Z.V.); (G.P.)
| | - István M. Mándity
- Department of Organic Chemistry, Faculty of Pharmacy, Semmelweis University, 1085 Budapest, Hungary;
- TTK Lendület Artificial Transporter Research Group, Institute of Materials and Environmental Chemistry, Research Centre for Natural Sciences, 1117 Budapest, Hungary
| | - Zoltan Varga
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (F.Z.); (Z.V.); (G.P.)
| | - Gyorgy Panyi
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (F.Z.); (Z.V.); (G.P.)
| | - Peter Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (F.Z.); (Z.V.); (G.P.)
| | - Tamas Kovacs
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, 4032 Debrecen, Hungary; (F.Z.); (Z.V.); (G.P.)
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12
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Liu BR, Chen CW, Huang YW, Lee HJ. Cell-Penetrating Peptides for Use in Development of Transgenic Plants. Molecules 2023; 28:molecules28083367. [PMID: 37110602 PMCID: PMC10142301 DOI: 10.3390/molecules28083367] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2023] [Revised: 03/24/2023] [Accepted: 04/07/2023] [Indexed: 04/29/2023] Open
Abstract
Genetically modified plants and crops can contribute to remarkable increase in global food supply, with improved yield and resistance to plant diseases or insect pests. The development of biotechnology introducing exogenous nucleic acids in transgenic plants is important for plant health management. Different genetic engineering methods for DNA delivery, such as biolistic methods, Agrobacterium tumefaciens-mediated transformation, and other physicochemical methods have been developed to improve translocation across the plasma membrane and cell wall in plants. Recently, the peptide-based gene delivery system, mediated by cell-penetrating peptides (CPPs), has been regarded as a promising non-viral tool for efficient and stable gene transfection into both animal and plant cells. CPPs are short peptides with diverse sequences and functionalities, capable of agitating plasma membrane and entering cells. Here, we highlight recent research and ideas on diverse types of CPPs, which have been applied in DNA delivery in plants. Various basic, amphipathic, cyclic, and branched CPPs were designed, and modifications of functional groups were performed to enhance DNA interaction and stabilization in transgenesis. CPPs were able to carry cargoes in either a covalent or noncovalent manner and to internalize CPP/cargo complexes into cells by either direct membrane translocation or endocytosis. Importantly, subcellular targets of CPP-mediated nucleic acid delivery were reviewed. CPPs offer transfection strategies and influence transgene expression at subcellular localizations, such as in plastids, mitochondria, and the nucleus. In summary, the technology of CPP-mediated gene delivery provides a potent and useful tool to genetically modified plants and crops of the future.
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Affiliation(s)
- Betty Revon Liu
- Department of Laboratory Medicine and Biotechnology, College of Medicine, Tzu Chi University, Hualien 970374, Taiwan
| | - Chi-Wei Chen
- Department of Life Science, College of Science and Engineering, National Dong Hwa University, Hualien 974301, Taiwan
| | - Yue-Wern Huang
- Department of Biological Sciences, College of Arts, Sciences, and Education, Missouri University of Science and Technology, Rolla, MO 65409, USA
| | - Han-Jung Lee
- Department of Natural Resources and Environmental Studies, College of Environmental Studies and Oceanography, National Dong Hwa University, Hualien 974301, Taiwan
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13
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Goyal P, Malviya R. Advances in nuclei targeted delivery of nanoparticles for the management of cancer. Biochim Biophys Acta Rev Cancer 2023; 1878:188881. [PMID: 36965678 DOI: 10.1016/j.bbcan.2023.188881] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 02/16/2023] [Accepted: 03/21/2023] [Indexed: 03/27/2023]
Abstract
A carrier is inserted into the appropriate organelles (nucleus) in successful medication transport, crucial to achieving very effective illness treatment. Cell-membrane targeting is the major focus of using nuclei to localize delivery. It has been demonstrated that high quantities of anticancer drugs can be injected directly into the nuclei of cancer cells, causing the cancer cells to die and increasing the effectiveness of chemotherapy. There are several effective ways to functionalize Nanoparticles (NPs), including changing their chemical makeup or attaching functional groups to their surface to increase their ability to target organelles. To cause tumor cells to apoptosis, released medicines must engage with molecular targets on particular organelles when their concentration is high enough. Targeted medication delivery studies will increasingly focus on organelle-specific delivery.
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Affiliation(s)
- Priyanshi Goyal
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, Uttar Pradesh, India
| | - Rishabha Malviya
- Department of Pharmacy, School of Medical and Allied Sciences, Galgotias University, Greater Noida, Uttar Pradesh, India.
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14
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Gareev K, Tagaeva R, Bobkov D, Yudintceva N, Goncharova D, Combs SE, Ten A, Samochernych K, Shevtsov M. Passing of Nanocarriers across the Histohematic Barriers: Current Approaches for Tumor Theranostics. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:1140. [PMID: 37049234 PMCID: PMC10096980 DOI: 10.3390/nano13071140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 03/19/2023] [Accepted: 03/20/2023] [Indexed: 06/19/2023]
Abstract
Over the past several decades, nanocarriers have demonstrated diagnostic and therapeutic (i.e., theranostic) potencies in translational oncology, and some agents have been further translated into clinical trials. However, the practical application of nanoparticle-based medicine in living organisms is limited by physiological barriers (blood-tissue barriers), which significantly hampers the transport of nanoparticles from the blood into the tumor tissue. This review focuses on several approaches that facilitate the translocation of nanoparticles across blood-tissue barriers (BTBs) to efficiently accumulate in the tumor. To overcome the challenge of BTBs, several methods have been proposed, including the functionalization of particle surfaces with cell-penetrating peptides (e.g., TAT, SynB1, penetratin, R8, RGD, angiopep-2), which increases the passing of particles across tissue barriers. Another promising strategy could be based either on the application of various chemical agents (e.g., efflux pump inhibitors, disruptors of tight junctions, etc.) or physical methods (e.g., magnetic field, electroporation, photoacoustic cavitation, etc.), which have been shown to further increase the permeability of barriers.
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Affiliation(s)
- Kamil Gareev
- Institute of Cytology of the Russian Academy of Sciences (RAS), 194064 Saint Petersburg, Russia
- Department of Micro and Nanoelectronics, Saint Petersburg Electrotechnical University “LETI”, 197022 Saint Petersburg, Russia
| | - Ruslana Tagaeva
- Institute of Cytology of the Russian Academy of Sciences (RAS), 194064 Saint Petersburg, Russia
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 Saint Petersburg, Russia
| | - Danila Bobkov
- Institute of Cytology of the Russian Academy of Sciences (RAS), 194064 Saint Petersburg, Russia
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 Saint Petersburg, Russia
| | - Natalia Yudintceva
- Institute of Cytology of the Russian Academy of Sciences (RAS), 194064 Saint Petersburg, Russia
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 Saint Petersburg, Russia
| | - Daria Goncharova
- Institute of Cytology of the Russian Academy of Sciences (RAS), 194064 Saint Petersburg, Russia
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 Saint Petersburg, Russia
| | - Stephanie E. Combs
- Department of Radiation Oncology, Technishe Universität München (TUM), Klinikum rechts der Isar, Ismaningerstr. 22, 81675 Munich, Germany
| | - Artem Ten
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia
| | - Konstantin Samochernych
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 Saint Petersburg, Russia
| | - Maxim Shevtsov
- Institute of Cytology of the Russian Academy of Sciences (RAS), 194064 Saint Petersburg, Russia
- Personalized Medicine Centre, Almazov National Medical Research Centre, 2 Akkuratova Str., 197341 Saint Petersburg, Russia
- Department of Radiation Oncology, Technishe Universität München (TUM), Klinikum rechts der Isar, Ismaningerstr. 22, 81675 Munich, Germany
- Institute of Life Sciences and Biomedicine, Far Eastern Federal University, 690922 Vladivostok, Russia
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15
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Izumi K, Saito C, Kawano R. Liposome Deformation Induced by Membrane-Binding Peptides. MICROMACHINES 2023; 14:373. [PMID: 36838073 PMCID: PMC9967443 DOI: 10.3390/mi14020373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/25/2023] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
This paper presents an investigation of liposome deformation and shape distortion using four membrane-binding peptides: TAT and C105Y as cell-penetrating peptides (CPPs), and melittin and ovispirin as antimicrobial peptides (AMPs). Liposome deformation was monitored utilizing fluorescent microscopy, while the binding of peptides to the DOPC membrane was estimated through capacitance measurements. The degree of liposome deformation and shape distortion was found to be higher for the CPPs compared to the AMPs. Additionally, it was observed that C105Y did not induce liposome rupture, unlike the other three peptides. We propose that these variations in liposome distortion may be attributed to differences in secondary structure, specifically the presence of an α-helix or random coil. Our studies offer insight into the use of peptides to elicit control of liposome architecture and may offer a promising approach for regulating the bodies of liposomal molecular robots.
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16
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Perkins MV, Joseph S, Dittmer DP, Mackman N. Cardiovascular Disease and Thrombosis in HIV Infection. Arterioscler Thromb Vasc Biol 2023; 43:175-191. [PMID: 36453273 PMCID: PMC10165851 DOI: 10.1161/atvbaha.122.318232] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Accepted: 11/18/2022] [Indexed: 12/03/2022]
Abstract
HIV infection has transitioned from an acute, fatal disease to a chronic one managed by antiretroviral therapy. Thus, the aging population of people living with HIV (PLWH) continues to expand. HIV infection results in a dysregulated immune system, wherein CD4+ T cells are depleted, particularly in the gastrointestinal tract, disrupting the gut epithelial barrier. Long-term HIV infection is associated with chronic inflammation through potentially direct mechanisms caused by viral replication or exposure to viral proteins and indirect mechanisms resulting from increased translocation of microbial products from the intestine or exposure to antiretroviral therapy. Chronic inflammation (as marked by IL [interleukin]-6 and CRP [C-reactive protein]) in PLWH promotes endothelial cell dysfunction and atherosclerosis. PLWH show significantly increased rates of cardiovascular disease, such as myocardial infarction (risk ratio, 1.79 [95% CI, 1.54-2.08]) and stroke (risk ratio, 2.56 [95% CI, 1.43-4.61]). In addition, PLWH have increased levels of the coagulation biomarker D-dimer and have a two to ten-fold increased risk of venous thromboembolism compared with the general population. Several small clinical trials analyzed the effect of different antithrombotic agents on platelet activation, coagulation, inflammation, and immune cell activation. Although some markers for coagulation were reduced, most agents failed to reduce inflammatory markers in PLWH. More studies are needed to understand the underlying mechanisms driving inflammation in PLWH to create better therapies for lowering chronic inflammation in PLWH. Such therapies can potentially reduce atherosclerosis, cardiovascular disease, and thrombosis rates in PLWH and thus overall mortality in this population.
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Affiliation(s)
- Megan V. Perkins
- UNC Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sarah Joseph
- UNC Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Dirk P. Dittmer
- UNC Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Nigel Mackman
- UNC Blood Research Center, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Division of Hematology, Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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17
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Ghanam RH, Eastep GN, Saad JS. Structural Insights into the Mechanism of HIV-1 Tat Secretion from the Plasma Membrane. J Mol Biol 2023; 435:167880. [PMID: 36370804 PMCID: PMC9822876 DOI: 10.1016/j.jmb.2022.167880] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/27/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022]
Abstract
Human immunodeficiency virus type 1 (HIV-1) trans-activator of transcription (Tat) is a small, intrinsically disordered basic protein that plays diverse roles in the HIV-1 replication cycle, including promotion of efficient viral RNA transcription. Tat is released by infected cells and subsequently absorbed by healthy cells, thereby contributing to HIV-1 pathogenesis including HIV-associated neurocognitive disorder. It has been shown that, in HIV-1-infected primary CD4 T-cells, Tat accumulates at the plasma membrane (PM) for secretion, a mechanism mediated by phosphatidylinositol 4,5-bisphosphate (PI(4,5)P2). However, the structural basis for Tat interaction with the PM and thereby secretion is lacking. Herein, we employed NMR and biophysical methods to characterize Tat86 (86 amino acids) interactions with PI(4,5)P2 and lipid nanodiscs (NDs). Our data revealed that Arg49, Lys50 and Lys51 (RKK motif) constitute the PI(4,5)P2 binding site, that Tat86 interaction with lipid NDs is dependent on PI(4,5)P2 and phosphatidylserine (PS), and that the arginine-rich motif (RRQRRR) preferentially interacts with PS. Furthermore, we show that Trp11, previously implicated in Tat secretion, penetrates deeply in the membrane; substitution of Trp11 severely reduced Tat86 interaction with membranes. Deletion of the entire highly basic region and Trp11 completely abolished Tat86 binding to lipid NDs. Our data support a mechanism by which HIV-1 Tat secretion from the PM is mediated by a tripartite signal consisting of binding of the RKK motif to PI(4,5)P2, arginine-rich motif to PS, and penetration of Trp11 in the membrane. Altogether, these findings provide new insights into the molecular requirements for Tat binding to membranes during secretion.
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Affiliation(s)
- Ruba H Ghanam
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Gunnar N Eastep
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States
| | - Jamil S Saad
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, United States.
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18
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Choe S. Translocation of a single Arg[Formula: see text] peptide across a DOPC/DOPG(4:1) model membrane using the weighted ensemble method. Sci Rep 2023; 13:1168. [PMID: 36670187 PMCID: PMC9860060 DOI: 10.1038/s41598-023-28493-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/19/2023] [Indexed: 01/21/2023] Open
Abstract
It is difficult to observe a spontaneous translocation of cell-penetrating peptides(CPPs) within a short time scale (e.g., a few hundred ns) in all-atom molecular dynamics(MD) simulations because the time required for the translocation of usual CPPs is on the order of minutes or so. In this work, we report a spontaneous translocation of a single Arg[Formula: see text](R9) across a DOPC/DOPG(4:1) model membrane within an order of a few tens ns scale by using the weighted ensemble(WE) method. We identify how water molecules and the orientation of Arg[Formula: see text] play a role in translocation. We also show how lipid molecules are transported along with Arg[Formula: see text]. In addition, we present free energy profiles of the translocation across the membrane using umbrella sampling and show that a single Arg[Formula: see text] translocation is energetically unfavorable. We expect that the WE method can help study interactions of CPPs with various model membranes within MD simulation approaches.
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Affiliation(s)
- Seungho Choe
- Department of Energy Science & Engineering, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, 42988 South Korea
- Energy Science & Engineering Research Center, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu, 42988 South Korea
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19
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Rajapaksha SP, Nawagamuwage SU. Anticorrelated position fluctuation of lipids in forming membrane water pores: molecular dynamics simulations study with dengue virus capsid protein. J Biomol Struct Dyn 2022; 40:11395-11404. [PMID: 34343444 DOI: 10.1080/07391102.2021.1958698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
The traffic of molecules into or out of cells is regulated by many membrane-associated mechanisms. Membrane pores are considered as one of the major passage mechanisms, although molecular-level understanding of pore formation is still vague. The opening of a membrane pore depends on many factors, including the influence of some proteins. The ability of the cell-penetrating peptides and supercharged proteins to form membrane pores has been reported. We studied pore formation through dipalmitoylphosphatidylcholine (DPPC) lipid bilayers by supercharged dengue virus capsid (C) protein. Atomistic molecular dynamics simulations confirmed the formation of membrane pores by a combined effect of the C protein and the membrane electric field. Analyses of simulated trajectories showed highly correlated vertical position fluctuations between the Cα atom of the membrane-anchored arginine residues and the phosphorus atoms of the surrounding DPPC lipids. Certain regions of the bilayer were negatively correlated while the others were positively correlated with respect to the fluctuations of the Cα atom of the anchored arginine residues. When positively correlated lipids in one leaflet vertically aligned with the negatively correlated lipids in the other leaflet, a local anticorrelated region was generated by weakening the bilayer. The membrane pore was always formed close to this anticorrelated region. Once formed, the C protein followed the hydrated pathway provided by the water-filled pores to cross the membrane.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Suneth P Rajapaksha
- Department of Chemistry, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
| | - Sithara U Nawagamuwage
- Department of Chemistry, Faculty of Applied Sciences, University of Sri Jayewardenepura, Nugegoda, Sri Lanka
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20
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Ouyang J, Sheng Y, Wang W. Recent Advances of Studies on Cell-Penetrating Peptides Based on Molecular Dynamics Simulations. Cells 2022; 11:cells11244016. [PMID: 36552778 PMCID: PMC9776715 DOI: 10.3390/cells11244016] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 12/14/2022] Open
Abstract
With the ability to transport cargo molecules across cell membranes with low toxicity, cell-penetrating peptides (CPPs) have become promising candidates for next generation peptide-based drug delivery vectors. Over the past three decades since the first CPP was discovered, a great deal of work has been done on the cellular uptake mechanisms and the applications for the delivery of therapeutic molecules, and significant advances have been made. But so far, we still do not have a precise and unified understanding of the structure-activity relationship of the CPPs. Molecular dynamics (MD) simulations provide a method to reveal peptide-membrane interactions at the atomistic level and have become an effective complement to experiments. In this paper, we review the progress of the MD simulations on CPP-membrane interactions, including the computational methods and technical improvements in the MD simulations, the research achievements in the CPP internalization mechanism, CPP decoration and coupling, and the peptide-induced membrane reactions during the penetration process, as well as the comparison of simulated and experimental results.
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Affiliation(s)
- Jun Ouyang
- School of Public Courses, Bengbu Medical College, Bengbu 233030, China
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
| | - Yuebiao Sheng
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- High Performance Computing Center, Nanjing University, Nanjing 210093, China
- Correspondence: (Y.S.); (W.W.)
| | - Wei Wang
- Collaborative Innovation Center of Advanced Microstructures, National Laboratory of Solid State Microstructure, Department of Physics, Nanjing University, Nanjing 210093, China
- Correspondence: (Y.S.); (W.W.)
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21
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Insights into the equilibrium structure and translocation mechanism of TP1, a spontaneous membrane-translocating peptide. Sci Rep 2022; 12:19880. [PMID: 36400938 PMCID: PMC9674684 DOI: 10.1038/s41598-022-23631-w] [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: 08/25/2022] [Accepted: 11/02/2022] [Indexed: 11/19/2022] Open
Abstract
Crossing the cellular membrane is one of the main barriers during drug discovery; many potential drugs are rejected for their inability to integrate into the intracell fluid. Although many solutions have been proposed to overcome this barrier, arguably the most promising solution is the use of cell-penetrating peptides. Recently, an array of hydrophobic penetrating peptides was discovered via high throughput screening which proved to be able to cross the membrane passively, and although these peptides proved to be effective at penetrating the cell, the details behind the underlying mechanism of this process remain unknown. In this study, we developed a method to find the equilibrium structure at the transmembrane domain of TP1, a hydrophobic penetrating peptide. In this method, we selectively deuterium-label amino acids in the peptidic chain, and employ results of [Formula: see text]H-NMR spectroscopy to find a molecular dynamics simulation of the peptide that reproduces the experimental results. Effectively finding the equilibrium orientation and dynamics of the peptide in the membrane. We employed this equilibrium structure to simulate the entire translocation mechanism and found that after the peptide reaches its equilibrium structure, it must undergo a two-step mechanism in order to completely translocate the membrane, each step involving the flip-flop of each arginine residue in the peptide. This leads us to conclude that the RLLR motif is essential for the translocating activity of the peptide.
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22
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Wu H, Zhang K, Zhang Z, Wang J, Jia P, Cong L, Li J, Duan Y, Ke F, Zhang F, Liu Z, Lu F, Wang Y, Li Z, Chang M, Zou J, Zhu K. Cell-penetrating peptide: A powerful delivery tool for DNA-free crop genome editing. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 324:111436. [PMID: 36037982 DOI: 10.1016/j.plantsci.2022.111436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/24/2022] [Accepted: 08/23/2022] [Indexed: 06/15/2023]
Abstract
Genome editing system based on the CRISPR/Cas (clustered regularly interspaced short palindromic repeats) technology is a milestone for biology. However, public concerns regarding genetically modified organisms (GMOs) and recalcitrance in the crop of choice for regeneration have limited its application. Cell-penetrating peptides (CPPs) are derived from protein transduction domains (PTDs) that can take on various cargoes across the plant wall, and membrane of target cells. Selected CPPs show mild cytotoxicity and are a suitable delivery tool for DNA-free genome editing. Moreover, CPPs may also be applied for the transient delivery of morphogenic transcription factors, also known as developmental regulators (DRs), to overcome the bottleneck of the crop of choice regeneration. In this review, we introduce a brief history of cell-penetrating peptides and discuss the practice of CPP-mediated DNA-free transfection and the prospects of this potential delivery tool for improving crop genome editing.
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Affiliation(s)
- Han Wu
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China.
| | - Kuangye Zhang
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Zhipeng Zhang
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Jiaxu Wang
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Pengxiang Jia
- Zhejiang Wanli University, 315100 Ningbo, Zhejiang Province, China
| | - Ling Cong
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Jia Li
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Youhou Duan
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Fulai Ke
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Fei Zhang
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Zhiqiang Liu
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Feng Lu
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Yanqiu Wang
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Zhihua Li
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China
| | - Ming Chang
- The Key Laboratory of Bio-interactions and Plant Health, College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu 210095, China
| | - Jianqiu Zou
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China.
| | - Kai Zhu
- Sorghum Research Institute, Liaoning Academy of Agricultural Sciences, Shenyang 110161, Liaoning Province, China.
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23
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Yang Y, Distaffen H, Jalali S, Nieuwkoop AJ, Nilsson BL, Dias CL. Atomic Insights into Amyloid-Induced Membrane Damage. ACS Chem Neurosci 2022; 13:2766-2777. [PMID: 36095304 DOI: 10.1021/acschemneuro.2c00446] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Amphipathic peptides can cause biological membranes to leak either by dissolving their lipid content via a detergent-like mechanism or by forming pores on the membrane surface. These modes of membrane damage have been related to the toxicity of amyloid peptides and to the activity of antimicrobial peptides. Here, we perform the first all-atom simulations in which membrane-bound amphipathic peptides self-assemble into β-sheets that subsequently either form stable pores inside the bilayer or drag lipids out of the membrane surface. An analysis of these simulations shows that the acyl tail of lipids interact strongly with non-polar side chains of peptides deposited on the membrane. These strong interactions enable lipids to be dragged out of the bilayer by oligomeric structures accounting for detergent-like damage. They also disturb the orientation of lipid tails in the vicinity of peptides. These distortions are minimized around pore structures. We also show that membrane-bound β-sheets become twisted with one of their extremities partially penetrating the lipid bilayer. This allows peptides on opposite leaflets to interact and form a long transmembrane β-sheet, which initiates poration. In simulations, where peptides are deposited on a single leaflet, the twist in β-sheets allows them to penetrate the membrane and form pores. In addition, our simulations show that fibril-like structures produce little damage to lipid membranes, as non-polar side chains in these structures are unavailable to interact with the acyl tail of lipids.
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Affiliation(s)
- Yanxing Yang
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Hannah Distaffen
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Sharareh Jalali
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
| | - Andrew J Nieuwkoop
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, United States
| | - Bradley L Nilsson
- Department of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Cristiano L Dias
- Department of Physics, New Jersey Institute of Technology, Newark, New Jersey 07102-1982, United States
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24
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Son B, Yoon H, Ryu J, Lee H, Joo J, Park HH, Park TH. Enhanced efficiency of generating human-induced pluripotent stem cells using Lin28-30Kc19 fusion protein. Front Bioeng Biotechnol 2022; 10:911614. [PMID: 35935494 PMCID: PMC9354855 DOI: 10.3389/fbioe.2022.911614] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 06/28/2022] [Indexed: 11/13/2022] Open
Abstract
Induced pluripotent stem cells (iPSCs) have intrinsic properties, such as self-renewal ability and pluripotency, which are also shown in embryonic stem cells (ESCs). The challenge of improving the iPSC generation efficiency has been an important issue and there have been many attempts to develop iPSC generation methods. In this research, we added Lin28, known as one of the reprogramming factors, in the form of a soluble recombinant protein from E. coli to improve the efficiency of human iPSC (hiPSC) generation, in respect of alkaline phosphatase (AP)-positive colonies. To deliver Lin28 inside the cells, we generated a soluble Lin28-30Kc19 fusion protein, with 30Kc19 at the C-terminal domain of Lin28. 30Kc19, a silkworm hemolymph-derived protein, was fused due to its cell-penetrating and protein-stabilizing properties. The Lin28-30Kc19 was treated to human dermal fibroblasts (HDFs), in combination with four defined reprogramming factors (Oct4, Sox2, c-Myc, and Klf4). After 14 days of cell culture, we confirmed the generated hiPSCs through AP staining. According to the results, the addition of Lin28-30Kc19 increased the number and size of generated AP-positive hiPSC colonies. Through this research, we anticipate that this recombinant protein would be a valuable material for increasing the efficiency of hiPSC generation and for enhancing the possibility as a substitute of the conventional method.
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Affiliation(s)
- Boram Son
- Department of Bioengineering, Hanyang University, Seoul, South Korea
| | - Hyungro Yoon
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Jina Ryu
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
| | - Haein Lee
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul, South Korea
| | - Jinmyoung Joo
- Department of Biomedical Engineering, Ulsan National Institute of Science and Technology (UNIST), Ulsan, South Korea
| | - Hee Ho Park
- Department of Bioengineering, Hanyang University, Seoul, South Korea
- Education and Research Group for Biopharmaceutical Innovation Leader, Hanyang University, Seoul, South Korea
- *Correspondence: Hee Ho Park, ; Tai Hyun Park,
| | - Tai Hyun Park
- Interdisciplinary Program in Bioengineering, Seoul National University, Seoul, South Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul, South Korea
- BioMAX/N-Bio Institute, Institute of Bioengineering, Seoul National University, Seoul, South Korea
- *Correspondence: Hee Ho Park, ; Tai Hyun Park,
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25
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Jerath G, Darvin P, Christian Y, Trivedi V, Kumar TRS, Ramakrishnan V. Delivery of Small Molecules by Syndiotactic Peptides for Breast Cancer Therapy. Mol Pharm 2022; 19:2877-2887. [PMID: 35839086 DOI: 10.1021/acs.molpharmaceut.2c00238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The utilization of peptide-based drug delivery systems has been suboptimal due to their poor proteolytic susceptibility, poor cell permeability, and limited tumor homing capabilities. Earlier attempts in using d-enantiomers in peptide sequences increased proteolytic stability but have compromised the overall penetration capability. We designed a series of peptides (STRAPs) with a syndiotactic polypeptide backbone that can potentially form a spatial array of cationic groups, an important feature that facilitates cellular uptake. The peptides penetrate cell membranes through a combination of active and passive modes. Furthermore, the cellular uptake of the peptides was unaffected by the presence of or treatment with bovine serum and human plasma. The designed peptides successfully delivered methotrexate, an anticancer drug, to the in vitro and in vivo models of breast cancer, with the best performing peptide STRAP-4-MTX conjugate having an EC50 value of 1.34 μM. Peptide drug delivery in mouse xenograft models showed a greater reduction of primary tumor and metastasis of breast cancer, in comparison to methotrexate of the same dose. The in vivo biodistribution assay of the STRAP-4 peptide suggests that the peptide accumulates at the tumor site after 2 h of treatment, and in the absence of tumors, the peptide gets metabolized and excreted from the system.
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Affiliation(s)
- Gaurav Jerath
- Molecular Informatics and Design Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Pramod Darvin
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - Yvonne Christian
- Molecular Informatics and Design Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - Vishal Trivedi
- Malaria Research Group, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
| | - T R Santhosh Kumar
- Cancer Research Program-1, Rajiv Gandhi Centre for Biotechnology, Thiruvananthapuram, Kerala 695014, India
| | - Vibin Ramakrishnan
- Molecular Informatics and Design Laboratory, Indian Institute of Technology Guwahati, Guwahati, Assam 781039, India
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26
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Zhuang Y, Thota N, Quirk S, Hernandez R. Implementation of Telescoping Boxes in Adaptive Steered Molecular Dynamics. J Chem Theory Comput 2022; 18:4649-4659. [PMID: 35830368 DOI: 10.1021/acs.jctc.2c00498] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Long-time dynamical processes, such as those involving protein unfolding and ligand interactions, can be accelerated and realized through steered molecular dynamics (SMD). The challenge has been the extraction of information from such simulations that generalize for complex nonequilibrium processes. The use of Jarzynski's equality opened the possibility of determining the free energy along the steered coordinate, but sampling over the nonequilibrium trajectories is slow to converge. Adaptive steered molecular dynamics (ASMD) and other related techniques have been introduced to overcome this challenge through the use of stages. Here, we take advantage of these stages to address the numerical cost that arises from the required use of very large solvent boxes. We introduce telescoping box schemes within adaptive steered molecular dynamics (ASMD) in which we adjust the solvent box between stages and thereby vary (and optimize) the required number of solvent molecules. We have benchmarked the method on a relatively long α-helical peptide, Ala30, with respect to the potential of mean force and hydrogen bonds. We show that the use of telescoping boxes introduces little numerical error while significantly reducing the computational cost.
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Affiliation(s)
- Yi Zhuang
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Nikhil Thota
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Stephen Quirk
- Kimberly-Clark Corporation, Atlanta, Georgia 30076-2199, United States
| | - Rigoberto Hernandez
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States.,Department of Materials Science and Engineering, Johns Hopkins University, Baltimore, Maryland 21218, United States
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27
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Singh S, Murillo G, Richner J, Singh SP, Berleth E, Kumar V, Mehta R, Ramiya V, Parihar AS. A Broad-Based Characterization of a Cell-Penetrating, Single Domain Camelid Bi-Specific Antibody Monomer That Targets STAT3 and KRAS Dependent Cancers. Int J Mol Sci 2022; 23:ijms23147565. [PMID: 35886918 PMCID: PMC9323098 DOI: 10.3390/ijms23147565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/01/2022] [Accepted: 07/04/2022] [Indexed: 12/07/2022] Open
Abstract
STAT3 and KRAS regulate cell proliferation, survival, apoptosis, cell migration, and angiogenesis. Aberrant expression of STAT3 and mutant active forms of KRAS have been well-established in the induction and maintenance of multiple cancers. STAT3 and KRAS mutant proteins have been considered anti-cancer targets; however, they are also considered to be clinically “undruggable” intracellular molecules, except for KRAS(G12C). Here we report a first-in-class molecule, a novel, single domain camelid VHH antibody (15 kDa), SBT-100, that binds to both STAT3 and KRAS and can penetrate the tumor cell membrane, and significantly inhibit cancer cell growth. Additionally, SBT-100 inhibits KRAS GTPase activity and downstream phosphorylation of ERK in vitro. In addition, SBT-100 inhibits the growth of multiple human cancers in vitro and in vivo. These results demonstrate the feasibility of targeting hard-to-reach aberrant intracellular transcription factors and signaling proteins simultaneously with one VHH to improve cancer therapies.
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Affiliation(s)
- Sunanda Singh
- Singh Biotechnology, 1547 Fox Grape Loop, Lutz, FL 33558, USA;
- Correspondence: (S.S.); (A.S.P.)
| | - Genoveva Murillo
- IIT Research Institute, 10 W. 35th Street, Chicago, IL 60616, USA; (G.M.); (R.M.)
| | - Justin Richner
- Department of Microbiology & Immunology, University of Illinois Chicago, E829 Medical Sciences Building, Chicago, IL 60612, USA;
| | - Samara P. Singh
- Division of Surgical Oncology, Department of Surgery, University of Miami Miller School of Medicine, Miami, FL 33136, USA;
| | - Erica Berleth
- Acudex, Inc., 701 Ellicott Street, CBLS, Buffalo, NY 14203, USA; (E.B.); (V.K.)
| | - Vijay Kumar
- Acudex, Inc., 701 Ellicott Street, CBLS, Buffalo, NY 14203, USA; (E.B.); (V.K.)
| | - Rajendra Mehta
- IIT Research Institute, 10 W. 35th Street, Chicago, IL 60616, USA; (G.M.); (R.M.)
| | - Vijay Ramiya
- Singh Biotechnology, 1547 Fox Grape Loop, Lutz, FL 33558, USA;
| | - Ashutosh S. Parihar
- Singh Biotechnology, 1547 Fox Grape Loop, Lutz, FL 33558, USA;
- Correspondence: (S.S.); (A.S.P.)
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28
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Amphiphilic Gold Nanoparticles: A Biomimetic Tool to Gain Mechanistic Insights into Peptide-Lipid Interactions. MEMBRANES 2022; 12:membranes12070673. [PMID: 35877876 PMCID: PMC9324301 DOI: 10.3390/membranes12070673] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/20/2022] [Accepted: 06/22/2022] [Indexed: 02/04/2023]
Abstract
Functional peptides are now widely used in a myriad of biomedical and clinical contexts, from cancer therapy and tumor targeting to the treatment of bacterial and viral infections. Underlying this diverse range of applications are the non-specific interactions that can occur between peptides and cell membranes, which, in many contexts, result in spontaneous internalization of the peptide within cells by avoiding energy-driven endocytosis. For this to occur, the amphipathicity and surface structural flexibility of the peptides play a crucial role and can be regulated by the presence of specific molecular residues that give rise to precise molecular events. Nevertheless, most of the mechanistic details regulating the encounter between peptides and the membranes of bacterial or animal cells are still poorly understood, thus greatly limiting the biomimetic potential of these therapeutic molecules. In this arena, finely engineered nanomaterials—such as small amphiphilic gold nanoparticles (AuNPs) protected by a mixed thiol monolayer—can provide a powerful tool for mimicking and investigating the physicochemical processes underlying peptide-lipid interactions. Within this perspective, we present here a critical review of membrane effects induced by both amphiphilic AuNPs and well-known amphiphilic peptide families, such as cell-penetrating peptides and antimicrobial peptides. Our discussion is focused particularly on the effects provoked on widely studied model cell membranes, such as supported lipid bilayers and lipid vesicles. Remarkable similarities in the peptide or nanoparticle membrane behavior are critically analyzed. Overall, our work provides an overview of the use of amphiphilic AuNPs as a highly promising tailor-made model to decipher the molecular events behind non-specific peptide-lipid interactions and highlights the main affinities observed both theoretically and experimentally. The knowledge resulting from this biomimetic approach could pave the way for the design of synthetic peptides with tailored functionalities for next-generation biomedical applications, such as highly efficient intracellular delivery systems.
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29
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Zhou Z, Maxeiner K, Moscariello P, Xiang S, Wu Y, Ren Y, Whitfield CJ, Xu L, Kaltbeitzel A, Han S, Mücke D, Qi H, Wagner M, Kaiser U, Landfester K, Lieberwirth I, Ng DYW, Weil T. In Situ Assembly of Platinum(II)-Metallopeptide Nanostructures Disrupts Energy Homeostasis and Cellular Metabolism. J Am Chem Soc 2022; 144:12219-12228. [PMID: 35729777 PMCID: PMC9284552 DOI: 10.1021/jacs.2c03215] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Nanostructure-based functions are omnipresent in nature and essential for the diversity of life. Unlike small molecules, which are often inhibitors of enzymes or biomimetics with established methods of elucidation, we show that functions of nanoscale structures in cells are complex and can implicate system-level effects such as the regulation of energy and redox homeostasis. Herein, we design a platinum(II)-containing tripeptide that assembles into intracellular fibrillar nanostructures upon molecular rearrangement in the presence of endogenous H2O2. The formed nanostructures blocked metabolic functions, including aerobic glycolysis and oxidative phosphorylation, thereby shutting down ATP production. As a consequence, ATP-dependent actin formation and glucose metabolite-dependent histone deacetylase activity are downregulated. We demonstrate that assembly-driven nanomaterials offer a rich avenue to achieve broad-spectrum bioactivities that could provide new opportunities in drug discovery.
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Affiliation(s)
- Zhixuan Zhou
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Konrad Maxeiner
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | | | - Siyuan Xiang
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Yingke Wu
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Yong Ren
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | | | - Lujuan Xu
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | | | - Shen Han
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - David Mücke
- Central Facility of Materials Science Electron Microscopy, Universität Ulm, 89081 Ulm, Germany
| | - Haoyuan Qi
- Central Facility of Materials Science Electron Microscopy, Universität Ulm, 89081 Ulm, Germany.,Faculty of Chemistry and Food Chemistry & Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062 Dresden, Germany
| | - Manfred Wagner
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Ute Kaiser
- Central Facility of Materials Science Electron Microscopy, Universität Ulm, 89081 Ulm, Germany
| | | | | | - David Y W Ng
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Tanja Weil
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
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30
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Wang L, Wang H, Chen X, Zhou S, Wang Y, Guan X. Chemistry solutions to facilitate nanopore detection and analysis. Biosens Bioelectron 2022; 213:114448. [PMID: 35716643 DOI: 10.1016/j.bios.2022.114448] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/24/2022] [Accepted: 05/30/2022] [Indexed: 11/29/2022]
Abstract
Characteristic ionic current modulations will be produced in a single molecule manner during the communication of individual molecules with a nanopore. Hence, the information regarding the length, composition, and structure of a molecule can be extracted from deciphering the electrical message. However, until now, achieving a satisfactory resolution for observation and quantification of a target analyte in a complex system remains a nontrivial task. In this review, we summarize the progress and especially the recent advance in utilizing chemistry solutions to facilitate nanopore detection and analysis. The discussed chemistry solutions are classified into several major categories, including covalent/non-covalent chemistry, redox chemistry, displacement chemistry, back titration chemistry, chelation chemistry, hydrolysis-chemistry, and click chemistry. Considering the significant success of using chemical reaction-assisted nanopore sensing strategies to improve sensor sensitivity & selectivity and to study various topics, other non-chemistry based methodologies can undoubtedly be employed by nanopore sensors to explore new applications in the interdisciplinary area of chemistry, biology, materials, and nanotechnology.
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Affiliation(s)
- Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Han Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Xiaohan Chen
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Shuo Zhou
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing, 400714, China; Chongqing School, University of Chinese Academy of Sciences, Chongqing, 400714, China.
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, IL, 60616, USA.
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31
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Patra P, Banerjee R, Chakrabarti J. Effect of biphosphate salt on dipalmitoylphosphatidylcholine bilayer deformation by Tat polypeptide. Biopolymers 2022; 113:e23518. [PMID: 35621373 DOI: 10.1002/bip.23518] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/06/2022]
Abstract
Translocation of positively charged cell penetrating peptides (CPP) through cell membrane is important in drug delivery. Here we report all-atom molecular dynamics simulations to investigate how a biphosphate salt in a solvent affects the interaction of a CPP, HIV-1 Tat peptide with model dipalmitoylphosphatidylcholine (DPPC) lipid bilayer. Tat peptide has a large number of basic arginines and a couple of polar glutamines. We observe that in absence of salt, the basic residues of the polypeptide get localized in the vicinity of the membrane without altering the bilayer properties much; polypeptide induce local thinning of the bilayer membrane at the area of localization. In presence of biphosphate salt, the basic residues, dressed by the biphosphate ions, are repelled by the phosphate head groups of the lipid molecules. However, polar glutamine prefers to stay in the vicinity of the bilayer. This leads to larger local bilayer thickness at the contact point by the polar residue and non-uniform bilayer thickness profile. The thickness deformation of bilayer structure disappears upon mutating the polar residue, suggesting importance of the polar residue in bilayer deformation. Our studies point to control bilayer deformation by appropriate peptide sequence and solvent conditions.
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Affiliation(s)
- Piya Patra
- Maulana Abul Kalam Azad University of Technology, West Bengal, Haringhata, Nadia, West Bengal, India
| | - Raja Banerjee
- Maulana Abul Kalam Azad University of Technology, West Bengal, Haringhata, Nadia, West Bengal, India
| | - Jaydeb Chakrabarti
- Department of Chemical, Biological and Macro-Molecular Sciences, Thematic Unit of Excellence on Computational Materials Science and Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Salt Lake, Kolkata, West Bengal, India
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32
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Sun S, Yang Y, Niu H, Luo M, Wu ZS. Design and application of DNA nanostructures for organelle-targeted delivery of anticancer drugs. Expert Opin Drug Deliv 2022; 19:707-723. [PMID: 35618266 DOI: 10.1080/17425247.2022.2083603] [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] [Indexed: 11/04/2022]
Abstract
INTRODUCTION DNA nanostructures targeting organelles are of great significance for the early diagnosis and precise therapy of human cancers. This review is expected to promote the development of DNA nanostructure-based cancer treatment with organelle-level precision in the future. AREAS COVERED In this review, we introduce the different principles for targeting organelles, summarize the progresses in the development of organelle-targeting DNA nanostructures, highlight their advantages and applications in disease treatment, and discuss current challenges and future prospects. EXPERT OPINION Accurate targeting is a basic problem for effective cancer treatment. However, current DNA nanostructures cannot meet the actual needs. Targeting specific organelles is expected to further improve the therapeutic effect and overcome tumor cell resistance, thereby holding great practical significance for tumor treatment in the clinic. With the deepening of the research on the molecular mechanism of disease development, especially on tumorigenesis and tumor progression, and increasing understanding of the behavior of biological materials in living cells, more versatile DNA nanostructures will be constructed to target subcellular organelles for drug delivery, essentially promoting the early diagnosis of cancers, classification, precise therapy and the estimation of prognosis in the future.
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Affiliation(s)
- Shujuan Sun
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China.,Collaborative Innovation Center of Tumor Marker Detection Technology, Equipment and Diagnosis-Therapy Integration in Universities of Shandong, Shandong Provincial Key Laboratory of Detection Technology for Tumor Markers, College of Chemistry and Chemical Engineering, Linyi University, Linyi 276000, China
| | - Ya Yang
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
| | - Huimin Niu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China.,Fujian Key Laboratory of Aptamers Technology, The 900th Hospital of Joint Logistics Support Force, Fuzhou 350025, China
| | - Mengxue Luo
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
| | - Zai-Sheng Wu
- Cancer Metastasis Alert and Prevention Center, Fujian Provincial Key Laboratory of Cancer Metastasis Chemoprevention and Chemotherapy, National & Local Joint Biomedical Engineering Research Center on Photodynamic Technologies, State Key Laboratory of Photocatalysis on Energy and Environment, College of Chemistry, Fuzhou University, Fuzhou 305108, China
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33
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Kang Z, Liu Q, Zhang Z, Zheng Y, Wang C, Pan Z, Li Q, Liu Y, Shi L. Arginine-Rich Polymers with Pore-Forming Capability Enable Efficient Intracellular Delivery via Direct Translocation Across Cell Membrane. Adv Healthc Mater 2022; 11:e2200371. [PMID: 35460333 DOI: 10.1002/adhm.202200371] [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: 02/15/2022] [Revised: 04/06/2022] [Indexed: 11/07/2022]
Abstract
Efficient delivery of biomacromolecules or drugs across the cell membrane via endocytosis usually encounters inevitable entrapment in endosomes and subsequent degradation in lyso-endosomes. To address this issue, a series of arginine-rich cell penetrating polymers is designed and synthesized, which internalize into cells by inducing the formation of pores on the cell membrane, thereby crossing the cell membrane via direct translocation that fundamentally avoids endo/lysosomal entrapment. The structure-activity relationship studies show that PTn-R2-C6, which is a type of polymer that has two arginine residues and a flexible hexanoic acid linker in each side chain, exhibits excellent pore-formation ability on the cell membrane. Further investigations indicate that PTn-R2-C6 rapidly transports plasmid DNAs into cytosol through a similar endocytosis-independent pathway, thereby achieving significantly higher transfection efficiency and lower cytotoxicity than the gold-standard transfection reagent PEI 25K. These results suggest the great potential of PTn-R2-C6 as a safe and efficient gene transfection reagent for wide applications including disease treatments, vaccine development, and biomedical research purposes.
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Affiliation(s)
- Ziyao Kang
- State Key Laboratory of Medicinal Chemical Biology Key Laboratory of Functional Polymer Materials of Ministry of Education College of Chemistry Frontiers Science Center for New Organic Matter Nankai University Tianjin 300071 P. R. China
| | - Qi Liu
- State Key Laboratory of Medicinal Chemical Biology Key Laboratory of Functional Polymer Materials of Ministry of Education College of Chemistry Frontiers Science Center for New Organic Matter Nankai University Tianjin 300071 P. R. China
| | - Zhanzhan Zhang
- State Key Laboratory of Medicinal Chemical Biology Key Laboratory of Functional Polymer Materials of Ministry of Education College of Chemistry Frontiers Science Center for New Organic Matter Nankai University Tianjin 300071 P. R. China
| | - Yadan Zheng
- State Key Laboratory of Medicinal Chemical Biology Key Laboratory of Functional Polymer Materials of Ministry of Education College of Chemistry Frontiers Science Center for New Organic Matter Nankai University Tianjin 300071 P. R. China
| | - Chun Wang
- State Key Laboratory of Medicinal Chemical Biology Key Laboratory of Functional Polymer Materials of Ministry of Education College of Chemistry Frontiers Science Center for New Organic Matter Nankai University Tianjin 300071 P. R. China
| | - Zheng Pan
- State Key Laboratory of Medicinal Chemical Biology Key Laboratory of Functional Polymer Materials of Ministry of Education College of Chemistry Frontiers Science Center for New Organic Matter Nankai University Tianjin 300071 P. R. China
| | - Qiushi Li
- State Key Laboratory of Medicinal Chemical Biology Key Laboratory of Functional Polymer Materials of Ministry of Education College of Chemistry Frontiers Science Center for New Organic Matter Nankai University Tianjin 300071 P. R. China
| | - Yang Liu
- State Key Laboratory of Medicinal Chemical Biology Key Laboratory of Functional Polymer Materials of Ministry of Education College of Chemistry Frontiers Science Center for New Organic Matter Nankai University Tianjin 300071 P. R. China
| | - Linqi Shi
- State Key Laboratory of Medicinal Chemical Biology Key Laboratory of Functional Polymer Materials of Ministry of Education College of Chemistry Frontiers Science Center for New Organic Matter Nankai University Tianjin 300071 P. R. China
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34
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Szabó I, Yousef M, Soltész D, Bató C, Mező G, Bánóczi Z. Redesigning of Cell-Penetrating Peptides to Improve Their Efficacy as a Drug Delivery System. Pharmaceutics 2022; 14:pharmaceutics14050907. [PMID: 35631493 PMCID: PMC9146218 DOI: 10.3390/pharmaceutics14050907] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 12/29/2022] Open
Abstract
Cell-penetrating peptides (CPP) are promising tools for the transport of a broad range of compounds into cells. Since the discovery of the first members of this peptide family, many other peptides have been identified; nowadays, dozens of these peptides are known. These peptides sometimes have very different chemical–physical properties, but they have similar drawbacks; e.g., non-specific internalization, fast elimination from the body, intracellular/vesicular entrapment. Although our knowledge regarding the mechanism and structure–activity relationship of internalization is growing, the prediction and design of the cell-penetrating properties are challenging. In this review, we focus on the different modifications of well-known CPPs to avoid their drawbacks, as well as how these modifications may increase their internalization and/or change the mechanism of penetration.
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Affiliation(s)
- Ildikó Szabó
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd Research Network (ELKH), Eötvös Loránd University, 1117 Budapest, Hungary;
- Correspondence: (I.S.); (Z.B.)
| | - Mo’ath Yousef
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary; (M.Y.); (D.S.); (C.B.)
| | - Dóra Soltész
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary; (M.Y.); (D.S.); (C.B.)
| | - Csaba Bató
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary; (M.Y.); (D.S.); (C.B.)
| | - Gábor Mező
- MTA-ELTE Research Group of Peptide Chemistry, Eötvös Loránd Research Network (ELKH), Eötvös Loránd University, 1117 Budapest, Hungary;
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary; (M.Y.); (D.S.); (C.B.)
| | - Zoltán Bánóczi
- Department of Organic Chemistry, Institute of Chemistry, Eötvös Loránd University, 1117 Budapest, Hungary; (M.Y.); (D.S.); (C.B.)
- Correspondence: (I.S.); (Z.B.)
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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] [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, Texas 78712, United States
| | - Chad I Drexler
- Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
| | - 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 Street, Columbia, Missouri 65201, United States
| | - 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, Texas 78712, United States
| | - Ron Elber
- Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas 78712, United States.,Department of Chemistry, The University of Texas at Austin, Austin, Texas 78712, United States
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36
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Paul R, Bera S, Devi M, Paul S. Inhibition of Aβ 16–22 Peptide Aggregation by Small Molecules and Their Permeation through POPC Lipid Bilayer: Insight from Molecular Dynamics Simulation Study. J Chem Inf Model 2022; 62:5193-5207. [DOI: 10.1021/acs.jcim.1c01366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Rabindranath Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India 781039
| | - Siddhartha Bera
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India 781039
| | - Madhusmita Devi
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India 781039
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India 781039
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37
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Tietz O, Cortezon-Tamarit F, Chalk R, Able S, Vallis KA. Tricyclic cell-penetrating peptides for efficient delivery of functional antibodies into cancer cells. Nat Chem 2022; 14:284-293. [PMID: 35145246 DOI: 10.1038/s41557-021-00866-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 11/19/2021] [Indexed: 12/13/2022]
Abstract
The intracellular environment hosts a large number of cancer- and other disease-relevant human proteins. Targeting these with internalized antibodies would allow therapeutic modulation of hitherto undruggable pathways, such as those mediated by protein-protein interactions. However, one of the major obstacles in intracellular targeting is the entrapment of biomacromolecules in the endosome. Here we report an approach to delivering antibodies and antibody fragments into the cytosol and nucleus of cells using trimeric cell-penetrating peptides (CPPs). Four trimers, based on linear and cyclic sequences of the archetypal CPP Tat, are significantly more potent than monomers and can be tuned to function by direct interaction with the plasma membrane or escape from vesicle-like bodies. These studies identify a tricyclic Tat construct that enables intracellular delivery of functional immunoglobulin-G antibodies and Fab fragments that bind intracellular targets in the cytosol and nuclei of live cells at effective concentrations as low as 1 μM.
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Affiliation(s)
- Ole Tietz
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | | | - Rod Chalk
- Centre for Medicines Discovery, University of Oxford, Oxford, UK
| | - Sarah Able
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK
| | - Katherine A Vallis
- Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, UK.
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38
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Choe S. Free Energy Analyses of Cell-Penetrating Peptides Using the Weighted Ensemble Method. MEMBRANES 2021; 11:membranes11120974. [PMID: 34940475 PMCID: PMC8706838 DOI: 10.3390/membranes11120974] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/27/2021] [Accepted: 12/01/2021] [Indexed: 12/22/2022]
Abstract
Cell-penetrating peptides (CPPs) have been widely used for drug-delivery agents; however, it has not been fully understood how they translocate across cell membranes. The Weighted Ensemble (WE) method, one of the most powerful and flexible path sampling techniques, can be helpful to reveal translocation paths and free energy barriers along those paths. Within the WE approach we show how Arg9 (nona-arginine) and Tat interact with a DOPC/DOPG(4:1) model membrane, and we present free energy (or potential mean of forces, PMFs) profiles of penetration, although a translocation across the membrane has not been observed in the current simulations. Two different compositions of lipid molecules were also tried and compared. Our approach can be applied to any CPPs interacting with various model membranes, and it will provide useful information regarding the transport mechanisms of CPPs.
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Affiliation(s)
- Seungho Choe
- Department of Energy Science & Engineering, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 42988, Korea;
- Energy Science & Engineering Research Center, Daegu Gyeongbuk Institute of Science & Technology (DGIST), Daegu 42988, Korea
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39
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Kalathingal M, Sumikama T, Oiki S, Saito S. Vectorial insertion of a β-helical peptide into membrane: a theoretical study on polytheonamide B. Biophys J 2021; 120:4786-4797. [PMID: 34555359 DOI: 10.1016/j.bpj.2021.09.028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Revised: 09/07/2021] [Accepted: 09/15/2021] [Indexed: 10/20/2022] Open
Abstract
Spontaneous unidirectional, or vectorial, insertion of transmembrane peptides is a fundamental biophysical process for toxin and viral actions. Polytheonamide B (pTB) is a potent cytotoxic peptide with a β6.3-helical structure. Previous experimental studies revealed that the pTB inserts into the membrane in a vectorial fashion and forms a channel with its single molecular length long enough to span the membrane. Also, molecular dynamics simulation studies demonstrated that the pTB is prefolded in aqueous solution. These are unique features of pTB because most of the peptide toxins form channels through oligomerization of transmembrane helices. Here, we performed all-atom molecular dynamics simulations to examine the dynamic mechanism of the vectorial insertion of pTB, providing underlying elementary processes of the membrane insertion of a prefolded single transmembrane peptide. We find that the insertion of pTB proceeds with only the local lateral compression of the membrane in three successive phases: "landing," "penetration," and "equilibration" phases. The free energy calculations using the replica-exchange umbrella sampling simulations present an energy cost of 4.3 kcal/mol at the membrane surface for the membrane insertion of pTB from bulk water. The trajectories of membrane insertion revealed that the insertion process can occur in two possible pathways, namely "trapped" and "untrapped" insertions; in some cases, pTB is trapped in the upper leaflet during the penetration phase. Our simulations demonstrated the importance of membrane anchoring by the hydrophobic N-terminal blocking group in the landing phase, leading to subsequent vectorial insertion.
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Affiliation(s)
- Mahroof Kalathingal
- School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Japan
| | - Takashi Sumikama
- PRESTO, JST, Kawaguchi, Japan; Nano Life Science Institute (WPI-NanoLSI), Kanazawa University, Kanazawa, Japan
| | - Shigetoshi Oiki
- Biomedical Imaging Research Center, University of Fukui, Fukui, Japan.
| | - Shinji Saito
- School of Physical Sciences, The Graduate University for Advanced Studies, Okazaki, Japan; Institute for Molecular Science, Okazaki, Japan.
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40
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Trofimenko E, Grasso G, Heulot M, Chevalier N, Deriu MA, Dubuis G, Arribat Y, Serulla M, Michel S, Vantomme G, Ory F, Dam LC, Puyal J, Amati F, Lüthi A, Danani A, Widmann C. Genetic, cellular, and structural characterization of the membrane potential-dependent cell-penetrating peptide translocation pore. eLife 2021; 10:69832. [PMID: 34713805 PMCID: PMC8639150 DOI: 10.7554/elife.69832] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 10/28/2021] [Indexed: 12/11/2022] Open
Abstract
Cell-penetrating peptides (CPPs) allow intracellular delivery of bioactive cargo molecules. The mechanisms allowing CPPs to enter cells are ill-defined. Using a CRISPR/Cas9-based screening, we discovered that KCNQ5, KCNN4, and KCNK5 potassium channels positively modulate cationic CPP direct translocation into cells by decreasing the transmembrane potential (Vm). These findings provide the first unbiased genetic validation of the role of Vm in CPP translocation in cells. In silico modeling and live cell experiments indicate that CPPs, by bringing positive charges on the outer surface of the plasma membrane, decrease the Vm to very low values (–150 mV or less), a situation we have coined megapolarization that then triggers formation of water pores used by CPPs to enter cells. Megapolarization lowers the free energy barrier associated with CPP membrane translocation. Using dyes of varying dimensions in CPP co-entry experiments, the diameter of the water pores in living cells was estimated to be 2 (–5) nm, in accordance with the structural characteristics of the pores predicted by in silico modeling. Pharmacological manipulation to lower transmembrane potential boosted CPP cellular internalization in zebrafish and mouse models. Besides identifying the first proteins that regulate CPP translocation, this work characterized key mechanistic steps used by CPPs to cross cellular membranes. This opens the ground for strategies aimed at improving the ability of cells to capture CPP-linked cargos in vitro and in vivo. Before a drug can have its desired effect, it must reach its target tissue or organ, and enter its cells. This is not easy because cells are surrounded by the plasma membrane, a fat-based barrier that separates the cell from its external environment. The plasma membrane contains proteins that act as channels, shuttling specific molecules in and out of the cell, and it also holds charge, with its inside surface being more negatively charged than its outside surface. Cell-penetrating peptides are short sequences of amino acids (the building blocks that form proteins) that carry positive charges. These positive charges allow them to cross the membrane easily, but it is not well understood how. To find out how cell-penetrating peptides cross the membrane, Trofimenko et al. attached them to dyes of different sizes. This revealed that the cell-penetrating peptides enter the cell through temporary holes called water pores, which measure about two nanometres across. The water pores form when the membrane becomes ‘megapolarized’, this is, when the difference in charge between the inside and the outside of the membrane becomes greater than normal. This can happen when the negative charge on the inside surface or the positive charge on the outer surface of the membrane increase. Megapolarization depends on potassium channels, which transport positive potassium ions outside the cell, making the outside of the membrane positive. When cell-penetrating peptides arrive at the outer surface of the cell near potassium channels, they make it even more positive. This increases the charge difference between the inside and the outside of the cell, allowing water pores to form. Once the peptides pass through the pores, the charge difference between the inside and the outside of the cell membrane dissipates, and the pores collapse. Drug developers are experimenting with attaching cell-penetrating peptides to drugs to help them get inside their target cells. Currently there are several experimental medications of this kind in clinical trials. Understanding how these peptides gain entry, and what size of molecule they could carry with them, provides solid ground for further drug development.
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Affiliation(s)
- Evgeniya Trofimenko
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Gianvito Grasso
- Dalle Molle Institute for Artificial Intelligence Research, Università della Svizzera italiana, Scuola Universitaria Professionale della Svizzera Italiana, Lugano, Switzerland
| | - Mathieu Heulot
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Nadja Chevalier
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Marco A Deriu
- PolitoBIOMed Lab Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy
| | - Gilles Dubuis
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Yoan Arribat
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Marc Serulla
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Sebastien Michel
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Gil Vantomme
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Florine Ory
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Linh Chi Dam
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Julien Puyal
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland.,CURML (University Center of Legal Medicine), Lausanne University Hospital, Lausanne, Switzerland
| | - Francesca Amati
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
| | - Anita Lüthi
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Andrea Danani
- Dalle Molle Institute for Artificial Intelligence Research, Università della Svizzera italiana, Scuola Universitaria Professionale della Svizzera Italiana, Lugano, Switzerland
| | - Christian Widmann
- Department of Biomedical Sciences, University of Lausanne, Lausanne, Switzerland
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Diederichs T, Ahmad K, Burns JR, Nguyen QH, Siwy ZS, Tornow M, Coveney PV, Tampé R, Howorka S. Principles of Small-Molecule Transport through Synthetic Nanopores. ACS NANO 2021; 15:16194-16206. [PMID: 34596387 DOI: 10.1021/acsnano.1c05139] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Synthetic nanopores made from DNA replicate the key biological processes of transporting molecular cargo across lipid bilayers. Understanding transport across the confined lumen of the nanopores is of fundamental interest and of relevance to their rational design for biotechnological applications. Here we reveal the transport principles of organic molecules through DNA nanopores by synergistically combining experiments and computer simulations. Using a highly parallel nanostructured platform, we synchronously measure the kinetic flux across hundreds of individual pores to obtain rate constants. The single-channel transport kinetics are close to the theoretical maximum, while selectivity is determined by the interplay of cargo charge and size, the pores' sterics and electrostatics, and the composition of the surrounding lipid bilayer. The narrow distribution of transport rates implies a high structural homogeneity of DNA nanopores. The molecular passageway through the nanopore is elucidated via coarse-grained constant-velocity steered molecular dynamics simulations. The ensemble simulations pinpoint with high resolution and statistical validity the selectivity filter within the channel lumen and determine the energetic factors governing transport. Our findings on these synthetic pores' structure-function relationship will serve to guide their rational engineering to tailor transport selectivity for cell biological research, sensing, and drug delivery.
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Affiliation(s)
- Tim Diederichs
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/M., 60438, Germany
| | - Katya Ahmad
- Centre for Computational Science, University College London, London, WC1H0AJ, England, U.K
| | - Jonathan R Burns
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H0AJ, England, U.K
| | - Quoc Hung Nguyen
- Molecular Electronics, Technical University of Munich, Munich, 80333, Germany
| | - Zuzanna S Siwy
- School of Physical Sciences, University of California, Irvine, California 92697, United States
| | - Marc Tornow
- Molecular Electronics, Technical University of Munich, Munich, 80333, Germany
- Fraunhofer Research Institution for Microsystems and Solid State Technologies (EMFT), Munich, 80686, Germany
- Center of NanoScience (CeNS), Ludwig-Maximilian-University, Munich, 80539, Germany
| | - Peter V Coveney
- Centre for Computational Science, University College London, London, WC1H0AJ, England, U.K
- Informatics Institute, University of Amsterdam, Amsterdam, 1090 GH, The Netherlands
| | - Robert Tampé
- Institute of Biochemistry, Biocenter, Goethe University Frankfurt, Frankfurt/M., 60438, Germany
| | - Stefan Howorka
- Department of Chemistry, Institute for Structural and Molecular Biology, University College London, London, WC1H0AJ, England, U.K
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42
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A Re-evaluation of the Free Energy Profiles for Cell-Penetrating Peptides Across DOPC Membranes. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10301-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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43
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Sadiq IZ, Muhammad A, Mada SB, Ibrahim B, Umar UA. Biotherapeutic effect of cell-penetrating peptides against microbial agents: a review. Tissue Barriers 2021; 10:1995285. [PMID: 34694961 DOI: 10.1080/21688370.2021.1995285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022] Open
Abstract
Selective permeability of biological membranes represents a significant barrier to the delivery of therapeutic substances into both microorganisms and mammalian cells, restricting the access of drugs into intracellular pathogens. Cell-penetrating peptides usually 5-30 amino acids with the characteristic ability to penetrate biological membranes have emerged as promising antimicrobial agents for treating infections as well as an effective delivery modality for biological conjugates such as nucleic acids, drugs, vaccines, nanoparticles, and therapeutic antibodies. However, several factors such as antimicrobial resistance and poor drug delivery of the existing medications justify the urgent need for developing a new class of antimicrobials. Herein, we review cell-penetrating peptides (CPPs) used to treat microbial infections. Although these peptides are biologically active for infections, effective transduction into membranes and cargo transport, serum stability, and half-life must be improved for optimum functions and development of next-generation antimicrobial agents.
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Affiliation(s)
- Idris Zubairu Sadiq
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Aliyu Muhammad
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Sanusi Bello Mada
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Bashiru Ibrahim
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
| | - Umar Aliyu Umar
- Department of Biochemistry, Faculty of Life Sciences, Ahmadu Bello University, Zaria, Nigeria
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44
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Wang H, Huang W, Wang Y, Li W, Liu Q, Yin B, Liang L, Wang D, Guan X, Wang L. Enzyme Hinders HIV-1 Tat Viral Transport and Real-Time Measured with Nanopores. ACS Sens 2021; 6:3781-3788. [PMID: 34528798 DOI: 10.1021/acssensors.1c01717] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
HIV-1 Tat protein, an intercellular transporter with a determinant function of delivering "information-rich" molecules in viral multiplication, was tryptic-hydrolyzed and real-time single molecule-monitored in a transmembrane pore. The electrokinetic studies revealed the catalytic and inhibitory effects on enzymatic digestion associated with Ca2+ and Cu2+ ions, respectively, in response to binding interactions with trypsin. Our strategy permits accurate and distinguishable sensing of Ca2+ and Cu2+ via an enzyme assay. In addition, considering the closer mimic of the real situation of HIV spread, measurements in the serum and on cells were also investigated. Transmembrane current measurements together with fluorescence microscopy imaging indicated the potential to perturb the Tat transport in the serum environment and on cells. Because the involved Tat proteolysis should prevent the occurrence of viral delivery, the presented method probably enables efficient hindrance to HIV-1 infection, in complementary to current traditional treatments.
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Affiliation(s)
- Han Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, Chongqing 401147, China
| | - Wenli Huang
- Biotechnology and Nuclear Technology Research Institute, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China
| | - Yunjiao Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Wei Li
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Qianshan Liu
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Bohua Yin
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
| | - Liyuan Liang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Deqiang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, Chicago, Illinois 60616, United States
| | - Liang Wang
- Chongqing Institute of Green and Intelligent Technology, Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing School, University of Chinese Academy of Sciences, Chongqing 400714, China
- Chongqing Key Laboratory of Intelligent Medicine Engineering for Hepatopancreatobiliary Diseases, Chongqing 401147, China
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Zhang S, Ma M, Shao Z, Zhang J, Fu L, Li X, Fang W, Gao L. Structure and Formation Mechanism of Antimicrobial Peptides Temporin B- and L-Induced Tubular Membrane Protrusion. Int J Mol Sci 2021; 22:ijms222011015. [PMID: 34681675 PMCID: PMC8537239 DOI: 10.3390/ijms222011015] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 10/08/2021] [Accepted: 10/08/2021] [Indexed: 12/17/2022] Open
Abstract
Temporins are a family of antimicrobial peptides (AMPs) isolated from frog skin, which are very short, weakly charged, and highly hydrophobic. They execute bactericidal activities in different ways from many other AMPs. This work investigated morphological changes of planar bilayer membranes composed of mixed zwitterionic and anionic phospholipids induced by temporin B and L (TB and TL) using all-atom and coarse-grained molecular dynamics simulations. We found that TB and TL fold to α-helices at the membrane surface and penetrate shallowly into the bilayer. These short AMPs have low propensity to induce membrane pore formation but possess high ability to extract lipids out. At relatively high peptide concentrations, the strong hydrophobicity of TB and TL promotes them to aggregate into clusters on the membrane surface. These aggregates attract a large amount of lipids out of the membrane to release compression induced by other dispersed peptides binding to the membrane. The extruded lipids mix evenly with the peptides in the cluster and form tubule-like protrusions. Certain water molecules follow the movement of lipids, which not only fill the cavities of the protrusion but also assist in maintaining the tubular structures. In contrast, the peptide-free leaflet remains intact. The present results unravel distinctive antimicrobial mechanisms of temporins disturbing membranes.
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46
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Ni SD, Chen YL, Chen YQ, Zhou K, Ding HM. Molecular Simulation Studies on the Interactions of Bilirubin at Different States with a Lipid Bilayer. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:11707-11715. [PMID: 34570511 DOI: 10.1021/acs.langmuir.1c01613] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The unconjugated bilirubin (BR) may penetrate through the cell membrane and cause a severe cytotoxicity. However, the molecular mechanism underlying the penetration of BR into the cell membrane is still largely unknown. In this work, we systematically investigate the interaction of BR and a lipid bilayer under different conditions by using all-atom molecular dynamics simulations. It is found that BR at the Z,Z conformation can easily enter into the interior of the lipid bilayer due to its hydrophobicity. However, when BR transforms from the Z,Z conformation to the E,E conformation (after the blue-light emission), its penetration ability is greatly reduced (especially at its ionized state). This study may offer useful physical insights into the effect of phototherapy on the penetration behavior and the cytotoxicity of the unconjugated BR.
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Affiliation(s)
- Song-Di Ni
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Ya-Li Chen
- Rugao Guangci Hospital, Nantong 226500, China
| | - Yuan-Qiang Chen
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Kun Zhou
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
| | - Hong-Ming Ding
- Center for Soft Condensed Matter Physics and Interdisciplinary Research, School of Physical Science and Technology, Soochow University, Suzhou 215006, China
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Herrera R, Rosbe K, Tugizov SM. Inactivation of HIV-1 in Polarized Infant Tonsil Epithelial Cells by Human Beta-Defensins 2 and 3 Tagged with the Protein Transduction Domain of HIV-1 Tat. Viruses 2021; 13:v13102043. [PMID: 34696473 PMCID: PMC8538026 DOI: 10.3390/v13102043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Revised: 10/04/2021] [Accepted: 10/06/2021] [Indexed: 11/16/2022] Open
Abstract
Mother-to-child transmission (MTCT) of HIV-1 may occur during pregnancy, labor, and breastfeeding; however, the molecular mechanism of MTCT of virus remains poorly understood. Infant tonsil mucosal epithelium may sequester HIV-1, serving as a transient reservoir, and may play a critical role in MTCT. Innate immune proteins human beta-defensins 2 (hBD-2) and -3 may inactivate intravesicular virions. To establish delivery of hBD-2 and -3 into vesicles containing HIV-1, we tagged hBDs with the protein transduction domain (PTD) of HIV-1 Tat, which facilitates an efficient translocation of proteins across cell membranes. Our new findings showed that hBD-2 and -3 proteins tagged with PTD efficiently penetrated polarized tonsil epithelial cells by endocytosis and direct penetration. PTD-initiated internalization of hBD-2 and -3 proteins into epithelial cells led to their subsequent penetration of multivesicular bodies (MVB) and vacuoles containing HIV-1. Furthermore, PTD played a role in the fusion of vesicles containing HIV-1 with lysosomes, where virus was inactivated. PTD-initiated internalization of hBD-2 and -3 proteins into ex vivo tonsil tissue explants reduced the spread of virus from epithelial cells to CD4+ T lymphocytes, CD68+ macrophages, and CD1c+ dendritic cells, suggesting that this approach may serve as an antiviral strategy for inactivating intraepithelial HIV-1 and reducing viral MTCT.
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Affiliation(s)
- Rossana Herrera
- Department of Medicine, University of California–San Francisco, 513 Parnassus Ave., San Francisco, CA 94143, USA;
| | - Kristina Rosbe
- Department of Otolaryngology, University of California–San Francisco, San Francisco, CA 94115, USA;
| | - Sharof M. Tugizov
- Department of Medicine, University of California–San Francisco, 513 Parnassus Ave., San Francisco, CA 94143, USA;
- Correspondence: ; Tel.: +1-(415)-514-3177; Fax: +1-(415)-476-9364
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Klabenkova K, Fokina A, Stetsenko D. Chemistry of Peptide-Oligonucleotide Conjugates: A Review. Molecules 2021; 26:5420. [PMID: 34500849 PMCID: PMC8434111 DOI: 10.3390/molecules26175420] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Revised: 08/30/2021] [Accepted: 09/01/2021] [Indexed: 12/25/2022] Open
Abstract
Peptide-oligonucleotide conjugates (POCs) represent one of the increasingly successful albeit costly approaches to increasing the cellular uptake, tissue delivery, bioavailability, and, thus, overall efficiency of therapeutic nucleic acids, such as, antisense oligonucleotides and small interfering RNAs. This review puts the subject of chemical synthesis of POCs into the wider context of therapeutic oligonucleotides and the problem of nucleic acid drug delivery, cell-penetrating peptide structural types, the mechanisms of their intracellular transport, and the ways of application, which include the formation of non-covalent complexes with oligonucleotides (peptide additives) or covalent conjugation. The main strategies for the synthesis of POCs are viewed in detail, which are conceptually divided into (a) the stepwise solid-phase synthesis approach and (b) post-synthetic conjugation either in solution or on the solid phase, especially by means of various click chemistries. The relative advantages and disadvantages of both strategies are discussed and compared.
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Affiliation(s)
- Kristina Klabenkova
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Alesya Fokina
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Dmitry Stetsenko
- Faculty of Physics, Novosibirsk State University, 630090 Novosibirsk, Russia; (K.K.); (D.S.)
- Institute of Cytology and Genetics, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
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Paul R, Paul S. Translocation of Endo-Functionalized Molecular Tubes across Different Lipid Bilayers: Atomistic Molecular Dynamics Simulation Study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:10376-10387. [PMID: 34415773 DOI: 10.1021/acs.langmuir.1c01594] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Various artificial receptors, such as calixarenes, cyclodextrins, cucurbit[n]urils, and their acyclic compounds, pliiar[n]arenes, deep cavitands, and molecular tweezers, can permeate the lipid membranes and they are used as drug carriers to improve the drug solubility, stability, and bioavailability. Inspired by these, we have employed atomistic molecular dynamics simulation to examine the effects of endo-functionalized molecular tubes or naphthotubes (host-1a and host-1b) on seven different types of model lipid bilayers and the permeation properties of these receptors through these model lipid bilayers. Lipid types include six model lipid bilayers (POPC, POPE, DOPC, POPG, DPPE, POPE/POPG) and one realistic membrane (Yeast). We observe that these receptors are spontaneously translocated toward these model lipid bilayer head regions and do not proceed further into these lipid bilayer tail regions (reside at the interface between lipid head and lipid tail region), except for the DPPE-containing systems. In the DPPE model lipid bilayer-containing systems (1a-dppe and 1b-dppe), receptor molecules are only adsorbed on the bilayer surface and reside at the interface between lipid head and water. This finding is also supported by the biased free-energy profiles of these translocation processes. Passive transport of these receptors may be possible through these model lipid bilayers (due to low barrier height), except for DPPE bilayer-containing systems (that have a very high energy barrier at the center). The results from these simulations provide insight into the biocompatibility of host-1a or host-1b in microscopic detail. Based on this work, more research is needed to fully comprehend the role of these synthesized receptors as a prospective drug carrier.
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Affiliation(s)
- Rabindranath Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam 781039, India
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Zhang X, Lei T, Du H. Prospect of cell penetrating peptides in stem cell tracking. Stem Cell Res Ther 2021; 12:457. [PMID: 34391472 PMCID: PMC8364034 DOI: 10.1186/s13287-021-02522-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 07/12/2021] [Indexed: 01/19/2023] Open
Abstract
Stem cell therapy has shown great efficacy in many diseases. However, the treatment mechanism is still unclear, which is a big obstacle for promoting clinical research. Therefore, it is particularly important to track transplanted stem cells in vivo, find out the distribution and condition of the stem cells, and furthermore reveal the treatment mechanism. Many tracking methods have been developed, including magnetic resonance imaging (MRI), fluorescence imaging, and ultrasound imaging (UI). Among them, MRI and UI techniques have been used in clinical. In stem cell tracking, a major drawback of these technologies is that the imaging signal is not strong enough, mainly due to the low cell penetration efficiency of imaging particles. Cell penetrating peptides (CPPs) have been widely used for cargo delivery due to its high efficacy, good safety properties, and wide delivery of various cargoes. However, there are few reports on the application of CPPs in current stem cell tracking methods. In this review, we systematically introduced the mechanism of CPPs into cell membranes and their advantages in stem cell tracking, discussed the clinical applications and limitations of CPPs, and finally we summarized several commonly used CPPs and their specific applications in stem cell tracking. Although it is not an innovation of tracer materials, CPPs as a powerful tool have broad prospects in stem cell tracking. ![]()
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Affiliation(s)
- Xiaoshuang Zhang
- Daxing Research Institute, University of Science and Technology Beijing, Beijing, 100083, China.,School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Tong Lei
- Daxing Research Institute, University of Science and Technology Beijing, Beijing, 100083, China.,School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China
| | - Hongwu Du
- Daxing Research Institute, University of Science and Technology Beijing, Beijing, 100083, China. .,School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, 100083, China.
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