1
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Zhang F, Li J, Wen Z, Fang C. FusPB-ESM2: Fusion model of ProtBERT and ESM-2 for cell-penetrating peptide prediction. Comput Biol Chem 2024; 111:108098. [PMID: 38820799 DOI: 10.1016/j.compbiolchem.2024.108098] [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: 02/02/2024] [Revised: 04/18/2024] [Accepted: 05/16/2024] [Indexed: 06/02/2024]
Abstract
Cell-penetrating peptides have attracted much attention for their ability to break through cell membrane barriers, which can improve drug bioavailability, reduce side effects, and promote the development of gene therapy. Traditional wet-lab prediction methods are time-consuming and costly, and computational methods provide a short-time and low-cost alternative. Still, the accuracy and reliability need to be further improved. To solve this problem, this study proposes a feature fusion-based prediction model, where the protein pre-trained language models ProtBERT and ESM-2 are used as feature extractors, and the extracted features from both are fused to obtain a more comprehensive and effective feature representation, which is then predicted by linear mapping. Validated by many experiments on public datasets, the method has an AUC value as high as 0.983 and shows high accuracy and reliability in cell-penetrating peptide prediction.
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Affiliation(s)
- Fan Zhang
- Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Jinfeng Li
- Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Zhenguo Wen
- Beijing Institute of Petrochemical Technology, Beijing 102617, China
| | - Chun Fang
- Beijing Institute of Petrochemical Technology, Beijing 102617, China.
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2
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Serebrennikova M, Grafskaia E, Maltsev D, Ivanova K, Bashkirov P, Kornilov F, Volynsky P, Efremov R, Bocharov E, Lazarev V. TriplEP-CPP: Algorithm for Predicting the Properties of Peptide Sequences. Int J Mol Sci 2024; 25:6869. [PMID: 38999985 PMCID: PMC11241344 DOI: 10.3390/ijms25136869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 07/14/2024] Open
Abstract
Advancements in medicine and pharmacology have led to the development of systems that deliver biologically active molecules inside cells, increasing drug concentrations at target sites. This improves effectiveness and duration of action and reduces side effects on healthy tissues. Cell-penetrating peptides (CPPs) show promise in this area. While traditional medicinal chemistry methods have been used to develop CPPs, machine learning techniques can speed up and reduce costs in the search for new peptides. A predictive algorithm based on machine learning models was created to identify novel CPP sequences using molecular descriptors using a combination of algorithms like k-nearest neighbors, gradient boosting, and random forest. Some potential CPPs were found and tested for cytotoxicity and penetrating ability. A new low-toxicity CPP was discovered from the Rhopilema esculentum venom proteome through this study.
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Affiliation(s)
- Maria Serebrennikova
- Laboratory of Genetic Engineering, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (M.S.); (K.I.); (V.L.)
- Moscow Center for Advanced Studies 20, Kulakova Str., Moscow 123592, Russia; (P.B.); (F.K.); (R.E.); (E.B.)
| | - Ekaterina Grafskaia
- Laboratory of Genetic Engineering, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (M.S.); (K.I.); (V.L.)
| | - Dmitriy Maltsev
- Federal Center of Brain Research and Neurotechnologies, Federal Medical Biological Agency, Moscow 117997, Russia;
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
- Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Moscow 117997, Russia
| | - Kseniya Ivanova
- Laboratory of Genetic Engineering, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (M.S.); (K.I.); (V.L.)
- Moscow Center for Advanced Studies 20, Kulakova Str., Moscow 123592, Russia; (P.B.); (F.K.); (R.E.); (E.B.)
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
| | - Pavel Bashkirov
- Moscow Center for Advanced Studies 20, Kulakova Str., Moscow 123592, Russia; (P.B.); (F.K.); (R.E.); (E.B.)
- Research Institute for Systems Biology and Medicine, Moscow 117246, Russia
| | - Fedor Kornilov
- Moscow Center for Advanced Studies 20, Kulakova Str., Moscow 123592, Russia; (P.B.); (F.K.); (R.E.); (E.B.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
| | - Pavel Volynsky
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
- Institute of Cytology, Russian Academy of Sciences, St. Petersburg 194064, Russia
| | - Roman Efremov
- Moscow Center for Advanced Studies 20, Kulakova Str., Moscow 123592, Russia; (P.B.); (F.K.); (R.E.); (E.B.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
| | - Eduard Bocharov
- Moscow Center for Advanced Studies 20, Kulakova Str., Moscow 123592, Russia; (P.B.); (F.K.); (R.E.); (E.B.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117997, Russia;
| | - Vassili Lazarev
- Laboratory of Genetic Engineering, Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, Moscow 119435, Russia; (M.S.); (K.I.); (V.L.)
- Moscow Center for Advanced Studies 20, Kulakova Str., Moscow 123592, Russia; (P.B.); (F.K.); (R.E.); (E.B.)
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3
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Liu J, Heddleston J, Perkins DR, Chen JJH, Ghanbarpour A, Smith BW, Miles R, Aihara E, Afshar S. Discovery of a new class of cell-penetrating peptides by novel phage display platform. Sci Rep 2024; 14:13437. [PMID: 38862601 PMCID: PMC11167021 DOI: 10.1038/s41598-024-64405-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/07/2024] [Indexed: 06/13/2024] Open
Abstract
The primary hurdles for small interference RNA (siRNA) in clinical use are targeted and cytosolic delivery. To overcome both challenges, we have established a novel platform based on phage display, called NNJA. In this approach, a lysosomal cathepsin substrate is engineered within the flexible loops of PIII, that is displaying a unique random sequence at its N-terminus. NNJA library selection targeting cell-expressed targets should yield specific peptides localized in the cytoplasm. That is because phage internalization and subsequent localization to lysosome, upon peptide binding to the cell expressed target, will result in cleavage of PIII, rendering phage non-infective. Such phage will be eliminated from the selected pool and only peptide-phage that escapes lysosomes will advance to the next round. Proof of concept studies with the NNJA library demonstrated cytosolic localization of selected peptide-phage and peptide-siRNA, confirmed through confocal microscopy. More importantly, conjugation of siHPRT to monomeric or multimeric NNJA peptides resulted in significant reduction in HPRT mRNA in various cell types without significant cytotoxicity. Sequence similarity and clustering analysis from NGS dataset provide insights into sequence composition facilitating cell penetration. NNJA platform offers a highly efficient peptide discovery engine for targeted delivery of oligonucleotides to cytosol.
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Affiliation(s)
- Jinsha Liu
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - John Heddleston
- Biotechnology Research, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN, 46221, USA
| | - Douglas Raymond Perkins
- Genetic Medicine, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN, 46221, USA
| | - Jack Jia Hua Chen
- Biotechnology Research, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN, 46221, USA
| | - Ahmadreza Ghanbarpour
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Bill William Smith
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA
| | - Rebecca Miles
- Genetic Medicine, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN, 46221, USA
| | - Eitaro Aihara
- Biotechnology Research, Lilly Corporate Center, Eli Lilly and Company, Indianapolis, IN, 46221, USA
| | - Sepideh Afshar
- Protein Engineering, Lilly Biotechnology Center, Eli Lilly and Company, San Diego, CA, 92121, USA.
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4
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Bae DH, Bae H, Yu HS, Dorjsembe B, No YH, Kim T, Kim NH, Kim JW, Kim J, Lee BS, Kim YJ, Park S, Khaleel ZH, Sa DH, Lee EC, Lee J, Ham J, Kim JC, Kim YH. Peptide-Drug Conjugate with Statistically Designed Transcellular Peptide for Psoriasis-Like Inflammation. Adv Healthc Mater 2024; 13:e2303480. [PMID: 38421096 DOI: 10.1002/adhm.202303480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 02/26/2024] [Indexed: 03/02/2024]
Abstract
Peptide-drug conjugates (PDCs) are a promising class of drug delivery systems that utilize covalently conjugated carrier peptides with therapeutic agents. PDCs offer several advantages over traditional drug delivery systems including enhanced target engagement, improved bioavailability, and increased cell permeability. However, the development of efficient transcellular peptides capable of effectively transporting drugs across biological barriers remains an unmet need. In this study, physicochemical criteria based on cell-penetrating peptides are employed to design transcellular peptides derived from an antimicrobial peptides library. Among the statistically designed transcellular peptides (SDTs), SDT7 exhibits higher skin permeability, faster kinetics, and improved cell permeability in human keratinocyte cells compared to the control peptide. Subsequently, it is found that 6-Paradol (PAR) exhibits inhibitory activity against phosphodiesterase 4, which can be utilized for an anti-inflammatory PDC. The transcellular PDC (SDT7-conjugated with PAR, named TM5) is evaluated in mouse models of psoriasis, exhibiting superior therapeutic efficacy compared to PAR alone. These findings highlight the potential of transcellular PDCs (TDCs) as a promising approach for the treatment of inflammatory skin disorders.
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Affiliation(s)
- Do Hyun Bae
- Department of Biomedical Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Center for Neuroscience Imaging Research (CNIR), Institute for Basic Science (IBS), Suwon, 16419, Republic of Korea
| | - Hayeon Bae
- SKKU Advanced Institute of Nano Technology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Department of Nano Science and Technology, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Hyung-Seok Yu
- Natural Products Research Institute, Korea Institute of Science and Technology (KIST), Gangneung, 25451, Republic of Korea
| | - Banzragch Dorjsembe
- Natural Products Research Institute, Korea Institute of Science and Technology (KIST), Gangneung, 25451, Republic of Korea
- Division of Bio-Medical Science & Technology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Young Hyun No
- SKKU Advanced Institute of Nano Technology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Department of Nano Science and Technology, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Taejung Kim
- Natural Products Research Institute, Korea Institute of Science and Technology (KIST), Gangneung, 25451, Republic of Korea
- Division of Bio-Medical Science & Technology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Nam Hyeong Kim
- SKKU Advanced Institute of Nano Technology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Department of Nano Science and Technology, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Jin-Woo Kim
- Natural Products Research Institute, Korea Institute of Science and Technology (KIST), Gangneung, 25451, Republic of Korea
| | - Jiyool Kim
- Natural Products Research Institute, Korea Institute of Science and Technology (KIST), Gangneung, 25451, Republic of Korea
- Division of Bio-Medical Science & Technology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Bok-Soo Lee
- SKKU Advanced Institute of Nano Technology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Ye Ji Kim
- Center for Neuroscience Imaging Research (CNIR), Institute for Basic Science (IBS), Suwon, 16419, Republic of Korea
- SKKU Advanced Institute of Nano Technology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Department of Nano Science and Technology, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Seongchan Park
- SKKU Advanced Institute of Nano Technology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Department of Nano Science and Technology, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Zinah Hilal Khaleel
- Center for Neuroscience Imaging Research (CNIR), Institute for Basic Science (IBS), Suwon, 16419, Republic of Korea
- SKKU Advanced Institute of Nano Technology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Department of Nano Science and Technology, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Deok Hyang Sa
- SKKU Advanced Institute of Nano Technology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Department of Nano Science and Technology, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Eui-Chul Lee
- SKKU Advanced Institute of Nano Technology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Department of Nano Science and Technology, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
| | - Jaecheol Lee
- School of Pharmacy, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Biomedical Institute for Convergence at SKKU (BICS), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Department of Biopharmaceutical Convergence, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- IMNEWRUN Inc., Suwon, 16419, Republic of Korea
| | - Jungyeob Ham
- Natural Products Research Institute, Korea Institute of Science and Technology (KIST), Gangneung, 25451, Republic of Korea
- Division of Bio-Medical Science & Technology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Jin-Chul Kim
- Natural Products Research Institute, Korea Institute of Science and Technology (KIST), Gangneung, 25451, Republic of Korea
- Division of Bio-Medical Science & Technology, University of Science and Technology (UST), Daejeon, 34113, Republic of Korea
| | - Yong Ho Kim
- Department of Biomedical Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Center for Neuroscience Imaging Research (CNIR), Institute for Basic Science (IBS), Suwon, 16419, Republic of Korea
- SKKU Advanced Institute of Nano Technology (SAINT), Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- Department of Nano Science and Technology, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
- IMNEWRUN Inc., Suwon, 16419, Republic of Korea
- Department of Nano Engineering, Sungkyunkwan University (SKKU), Suwon, 16419, Republic of Korea
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5
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Wang N, Mcneer NA, Eton E, Fass J, Kentsis A. Proteomic Barcoding Platform for Macromolecular Screening and Delivery. J Proteome Res 2024. [PMID: 38776430 DOI: 10.1021/acs.jproteome.4c00068] [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: 05/25/2024]
Abstract
Engineered macromolecules offer compelling means for the therapy of conventionally undruggable interactions in human disease. However, their efficacy is limited by barriers to tissue and intracellular delivery. Inspired by recent advances in molecular barcoding and evolution, we developed BarcodeBabel, a generalized method for the design of libraries of peptide barcodes suitable for high-throughput mass spectrometry proteomics. Combined with PeptideBabel, a Monte Carlo sampling algorithm for the design of peptides with evolvable physicochemical properties and sequence complexity, we developed a barcoded library of cell penetrating peptides (CPPs) with distinct physicochemical features. Using quantitative targeted mass spectrometry, we identified CPPS with improved nuclear and cytoplasmic delivery exceeding hundreds of millions of molecules per human cell while maintaining minimal membrane disruption and negligible toxicity in vitro. These studies provide a proof of concept for peptide barcoding as a homogeneous high-throughput method for macromolecular screening and delivery. BarcodeBabel and PeptideBabel are available open-source from https://github.com/kentsisresearchgroup/.
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Affiliation(s)
- Ning Wang
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Nicole A Mcneer
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Elliot Eton
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Josh Fass
- Tri-I PhD Program in Computational Biology and Medicine, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Tow Center for Developmental Oncology, Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Medical College, Cornell University, New York, New York 10065, United States
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6
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Toshchakov VY. Peptide-Based Inhibitors of the Induced Signaling Protein Interactions: Current State and Prospects. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:784-798. [PMID: 38880642 DOI: 10.1134/s000629792405002x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/29/2024] [Accepted: 03/12/2024] [Indexed: 06/18/2024]
Abstract
Formation of the transient protein complexes in response to activation of cellular receptors is a common mechanism by which cells respond to external stimuli. This article presents the concept of blocking interactions of signaling proteins by the peptide inhibitors, and describes the progress achieved to date in the development of signaling inhibitors that act by blocking the signal-dependent protein interactions.
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Affiliation(s)
- Vladimir Y Toshchakov
- Sirius University of Science and Technology, Sirius Federal Territory, Krasnodar Region, 354340, Russia.
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7
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Fukunaga I, Matsukiyo Y, Kaitoh K, Yamanishi Y. Automatic generation of functional peptides with desired bioactivity and membrane permeability using Bayesian optimization. Mol Inform 2024; 43:e202300148. [PMID: 38182544 DOI: 10.1002/minf.202300148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 02/03/2024] [Accepted: 02/03/2024] [Indexed: 01/07/2024]
Abstract
Peptides are potentially useful modalities of drugs; however, cell membrane permeability is an obstacle in peptide drug discovery. The identification of bioactive peptides for a therapeutic target is also challenging because of the huge amino acid sequence patterns of peptides. In this study, we propose a novel computational method, PEptide generation system using Neural network Trained on Amino acid sequence data and Gaussian process-based optimizatiON (PENTAGON), to automatically generate new peptides with desired bioactivity and cell membrane permeability. In the algorithm, we mapped peptide amino acid sequences onto the latent space constructed using a variational autoencoder and searched for peptides with desired bioactivity and cell membrane permeability using Bayesian optimization. We used our proposed method to generate peptides with cell membrane permeability and bioactivity for each of the nine therapeutic targets, such as the estrogen receptor (ER). Our proposed method outperformed a previously developed peptide generator in terms of similarity to known active peptide sequences and the length of generated peptide sequences.
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Affiliation(s)
- Itsuki Fukunaga
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Yuki Matsukiyo
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
| | - Kazuma Kaitoh
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, Aichi, 464-8601, Japan
| | - Yoshihiro Yamanishi
- Department of Bioscience and Bioinformatics, Faculty of Computer Science and Systems Engineering, Kyushu Institute of Technology, 680-4 Kawazu, Iizuka, Fukuoka, 820-8502, Japan
- Department of Complex Systems Science, Graduate School of Informatics, Nagoya University, Chikusa, Nagoya, Aichi, 464-8601, Japan
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8
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Lifshits LA, Breuer Y, Sova M, Gupta S, Kadosh D, Weinberg E, Hayouka Z, Bar DZ, Gal M. Nature-inspired peptide of MtDef4 C-terminus tail enables protein delivery in mammalian cells. Sci Rep 2024; 14:4604. [PMID: 38409451 PMCID: PMC10897151 DOI: 10.1038/s41598-024-55274-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 02/21/2024] [Indexed: 02/28/2024] Open
Abstract
Cell-penetrating peptides show promise as versatile tools for intracellular delivery of therapeutic agents. Various peptides have originated from natural proteins with antimicrobial activity. We investigated the mammalian cell-penetrating properties of a 16-residue peptide with the sequence GRCRGFRRRCFCTTHC from the C-terminus tail of the Medicago truncatula defensin MtDef4. We evaluated the peptide's ability to penetrate multiple cell types. Our results demonstrate that the peptide efficiently penetrates mammalian cells within minutes and at a micromolar concentration. Moreover, upon N-terminal fusion to the fluorescent protein GFP, the peptide efficiently delivers GFP into the cells. Despite its remarkable cellular permeability, the peptide has only a minor effect on cellular viability, making it a promising candidate for developing a cell-penetrating peptide with potential therapeutic applications.
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Affiliation(s)
- Lucia Adriana Lifshits
- Department of Oral Biology, Faculty of Medicine, The Goldschleger School of Dental Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Yoav Breuer
- Department of Oral Biology, Faculty of Medicine, The Goldschleger School of Dental Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Marina Sova
- Department of Oral Biology, Faculty of Medicine, The Goldschleger School of Dental Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Sumit Gupta
- BLAVATNIK CENTER for Drug Discovery, Tel-Aviv University, 6997801, Tel Aviv, Israel
| | - Dar Kadosh
- Department of Oral Biology, Faculty of Medicine, The Goldschleger School of Dental Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Evgeny Weinberg
- Department of Oral Biology, Faculty of Medicine, The Goldschleger School of Dental Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Zvi Hayouka
- Institute of Biochemistry, Food Science and Nutrition, The Robert H. Smith Faculty of Agricultural, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
| | - Daniel Z Bar
- Department of Oral Biology, Faculty of Medicine, The Goldschleger School of Dental Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel
| | - Maayan Gal
- Department of Oral Biology, Faculty of Medicine, The Goldschleger School of Dental Medicine, Tel Aviv University, 6997801, Tel Aviv, Israel.
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9
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Iwaniak A, Minkiewicz P, Darewicz M. Bioinformatics and bioactive peptides from foods: Do they work together? ADVANCES IN FOOD AND NUTRITION RESEARCH 2024; 108:35-111. [PMID: 38461003 DOI: 10.1016/bs.afnr.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/11/2024]
Abstract
We live in the Big Data Era which affects many aspects of science, including research on bioactive peptides derived from foods, which during the last few decades have been a focus of interest for scientists. These two issues, i.e., the development of computer technologies and progress in the discovery of novel peptides with health-beneficial properties, are closely interrelated. This Chapter presents the example applications of bioinformatics for studying biopeptides, focusing on main aspects of peptide analysis as the starting point, including: (i) the role of peptide databases; (ii) aspects of bioactivity prediction; (iii) simulation of peptide release from proteins. Bioinformatics can also be used for predicting other features of peptides, including ADMET, QSAR, structure, and taste. To answer the question asked "bioinformatics and bioactive peptides from foods: do they work together?", currently it is almost impossible to find examples of peptide research with no bioinformatics involved. However, theoretical predictions are not equivalent to experimental work and always require critical scrutiny. The aspects of compatibility of in silico and in vitro results are also summarized herein.
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Affiliation(s)
- Anna Iwaniak
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland.
| | - Piotr Minkiewicz
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland
| | - Małgorzata Darewicz
- Chair of Food Biochemistry, Faculty of Food Science, University of Warmia and Mazury in Olsztyn, Olsztyn-Kortowo, Poland
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10
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Shi K, Xiong Y, Wang Y, Deng Y, Wang W, Jing B, Gao X. PractiCPP: a deep learning approach tailored for extremely imbalanced datasets in cell-penetrating peptide prediction. Bioinformatics 2024; 40:btae058. [PMID: 38305405 PMCID: PMC11212486 DOI: 10.1093/bioinformatics/btae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 01/25/2024] [Accepted: 01/30/2024] [Indexed: 02/03/2024] Open
Abstract
MOTIVATION Effective drug delivery systems are paramount in enhancing pharmaceutical outcomes, particularly through the use of cell-penetrating peptides (CPPs). These peptides are gaining prominence due to their ability to penetrate eukaryotic cells efficiently without inflicting significant damage to the cellular membrane, thereby ensuring optimal drug delivery. However, the identification and characterization of CPPs remain a challenge due to the laborious and time-consuming nature of conventional methods, despite advances in proteomics. Current computational models, however, are predominantly tailored for balanced datasets, an approach that falls short in real-world applications characterized by a scarcity of known positive CPP instances. RESULTS To navigate this shortfall, we introduce PractiCPP, a novel deep-learning framework tailored for CPP prediction in highly imbalanced data scenarios. Uniquely designed with the integration of hard negative sampling and a sophisticated feature extraction and prediction module, PractiCPP facilitates an intricate understanding and learning from imbalanced data. Our extensive computational validations highlight PractiCPP's exceptional ability to outperform existing state-of-the-art methods, demonstrating remarkable accuracy, even in datasets with an extreme positive-to-negative ratio of 1:1000. Furthermore, through methodical embedding visualizations, we have established that models trained on balanced datasets are not conducive to practical, large-scale CPP identification, as they do not accurately reflect real-world complexities. In summary, PractiCPP potentially offers new perspectives in CPP prediction methodologies. Its design and validation, informed by real-world dataset constraints, suggest its utility as a valuable tool in supporting the acceleration of drug delivery advancements. AVAILABILITY AND IMPLEMENTATION The source code of PractiCPP is available on Figshare at https://doi.org/10.6084/m9.figshare.25053878.v1.
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Affiliation(s)
- Kexin Shi
- Syneron Technology, Guangzhou 510000, China
- Individualized Interdisciplinary Program (Data Science and Analytics), The Hong Kong University of Science and Technology, Hong Kong SAR, China
| | | | - Yu Wang
- Syneron Technology, Guangzhou 510000, China
| | - Yifan Deng
- Syneron Technology, Guangzhou 510000, China
| | - Wenjia Wang
- Data Science and Analytics Thrust, The Hong Kong University of Science and Technology (Guangzhou), Nansha, Guangzhou, 511400, Guangdong, China
| | - Bingyi Jing
- Department of Statistics and Data Science, Southern University of Science and Technology, Shenzhen 518000, China
| | - Xin Gao
- Syneron Technology, Guangzhou 510000, China
- Computer Science Program, Computer, Electrical and Mathematical Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
- Computational Bioscience Research Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955, Saudi Arabia
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11
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Shin HJ, Lee BK, Kang HA. Transdermal Properties of Cell-Penetrating Peptides: Applications and Skin Penetration Mechanisms. ACS APPLIED BIO MATERIALS 2024; 7:1-16. [PMID: 38079575 DOI: 10.1021/acsabm.3c00659] [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] [Indexed: 01/16/2024]
Abstract
Cell-penetrating peptides (CPPs) consist of 5-30 amino acids with intracellular transduction abilities and diverse physicochemical properties, origins, and sequences. Although recent developments in bioinformatics have facilitated the prediction of CPP candidates with the potential for transduction into cells, the mechanisms by which CPPs penetrate cells and various tissues have not yet been elucidated at the molecular interaction level. Recently, the skin-penetrating ability of CPPs has gained wide attention and emerged as a simple and effective strategy for the delivery of macromolecules into the skin. Studies on the skin structure have suggested that the penetration potential of CPPs is based on the molecular interactions and characteristics of the lipid lamellar structure between corneocytes in the stratum corneum. This review provides a brief overview of the general properties, transduction mechanisms, applications, and safety issues of CPPs, focusing on CPPs with transdermal properties, that are currently being used to develop therapeutics and cosmetics.
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Affiliation(s)
- Hee Je Shin
- ProCell R&D Center, ProCell Therapeutics, Inc., #1009 Ace-Twin Tower II, 273, Digital-ro, Guro-gu, Seoul 08381, Republic of Korea
- Department of Life Science, College of Natural Science, Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
| | - Byung Kyu Lee
- ProCell R&D Center, ProCell Therapeutics, Inc., #1009 Ace-Twin Tower II, 273, Digital-ro, Guro-gu, Seoul 08381, Republic of Korea
| | - Hyun Ah Kang
- Department of Life Science, College of Natural Science, Chung-Ang University, 84, Heukseok-ro, Dongjak-gu, Seoul 06974, Republic of Korea
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12
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Agoni C, Stavropoulos I, Kirwan A, Mysior MM, Holton T, Kranjc T, Simpson JC, Roche HM, Shields DC. Cell-Penetrating Milk-Derived Peptides with a Non-Inflammatory Profile. Molecules 2023; 28:6999. [PMID: 37836842 PMCID: PMC10574647 DOI: 10.3390/molecules28196999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 09/24/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023] Open
Abstract
Milk-derived peptides are known to confer anti-inflammatory effects. We hypothesised that milk-derived cell-penetrating peptides might modulate inflammation in useful ways. Using computational techniques, we identified and synthesised peptides from the milk protein Alpha-S1-casein that were predicted to be cell-penetrating using a machine learning predictor. We modified the interpretation of the prediction results to consider the effects of histidine. Peptides were then selected for testing to determine their cell penetrability and anti-inflammatory effects using HeLa cells and J774.2 mouse macrophage cell lines. The selected peptides all showed cell penetrating behaviour, as judged using confocal microscopy of fluorescently labelled peptides. None of the peptides had an effect on either the NF-κB transcription factor or TNFα and IL-1β secretion. Thus, the identified milk-derived sequences have the ability to be internalised into the cell without affecting cell homeostatic mechanisms such as NF-κB activation. These peptides are worthy of further investigation for other potential bioactivities or as a naturally derived carrier to promote the cellular internalisation of other active peptides.
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Affiliation(s)
- Clement Agoni
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin 4, Ireland (M.M.M.); (J.C.S.)
- School of Medicine, University College Dublin, Belfield, D04 W6F6 Dublin 4, Ireland
- Discipline of Pharmaceutical Sciences, University of KwaZulu Natal, Durban 4041, South Africa
| | - Ilias Stavropoulos
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin 4, Ireland (M.M.M.); (J.C.S.)
- School of Medicine, University College Dublin, Belfield, D04 W6F6 Dublin 4, Ireland
| | - Anna Kirwan
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin 4, Ireland (M.M.M.); (J.C.S.)
- School of Biology and Environmental Science, University College Dublin, Belfield, D04 N2E5 Dublin 4, Ireland
| | - Margharitha M. Mysior
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin 4, Ireland (M.M.M.); (J.C.S.)
- Institute of Food and Health, University College Dublin, Belfield, D04 V1W8 Dublin 4, Ireland
| | - Therese Holton
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin 4, Ireland (M.M.M.); (J.C.S.)
- Institute of Food and Health, University College Dublin, Belfield, D04 V1W8 Dublin 4, Ireland
| | - Tilen Kranjc
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin 4, Ireland (M.M.M.); (J.C.S.)
- Institute of Food and Health, University College Dublin, Belfield, D04 V1W8 Dublin 4, Ireland
| | - Jeremy C. Simpson
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin 4, Ireland (M.M.M.); (J.C.S.)
- School of Biology and Environmental Science, University College Dublin, Belfield, D04 N2E5 Dublin 4, Ireland
| | - Helen M. Roche
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin 4, Ireland (M.M.M.); (J.C.S.)
- Institute for Global Food Security, Queens University Belfast, Belfast BT9 5DL, UK
| | - Denis C. Shields
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, D04 V1W8 Dublin 4, Ireland (M.M.M.); (J.C.S.)
- School of Medicine, University College Dublin, Belfield, D04 W6F6 Dublin 4, Ireland
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13
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Robledo SM, Pérez-Silanes S, Fernández-Rubio C, Poveda A, Monzote L, González VM, Alonso-Collado P, Carrión J. Neglected Zoonotic Diseases: Advances in the Development of Cell-Penetrating and Antimicrobial Peptides against Leishmaniosis and Chagas Disease. Pathogens 2023; 12:939. [PMID: 37513786 PMCID: PMC10383258 DOI: 10.3390/pathogens12070939] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/12/2023] [Accepted: 07/12/2023] [Indexed: 07/30/2023] Open
Abstract
In 2020, the WHO established the road map for neglected tropical diseases 2021-2030, which aims to control and eradicate 20 diseases, including leishmaniosis and Chagas disease. In addition, since 2015, the WHO has been developing a Global Action Plan on Antimicrobial Resistance. In this context, the achievement of innovative strategies as an alternative to replace conventional therapies is a first-order socio-sanitary priority, especially regarding endemic zoonoses in poor regions, such as those caused by Trypanosoma cruzi and Leishmania spp. infections. In this scenario, it is worth highlighting a group of natural peptide molecules (AMPs and CPPs) that are promising strategies for improving therapeutic efficacy against these neglected zoonoses, as they avoid the development of toxicity and resistance of conventional treatments. This review presents the novelties of these peptide molecules and their ability to cross a whole system of cell membranes as well as stimulate host immune defenses or even serve as vectors of molecules. The efforts of the biotechnological sector will make it possible to overcome the limitations of antimicrobial peptides through encapsulation and functionalization methods to obtain approval for these treatments to be used in clinical programs for the eradication of leishmaniosis and Chagas disease.
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Affiliation(s)
- Sara M Robledo
- Programa de Estudio y Control de Enfermedades Tropicales PECET, Facultad de Medicina, Universidad de Antioquia, Medellín 050010, Colombia
| | - Silvia Pérez-Silanes
- Department of Pharmaceutical Technology and Chemistry, ISTUN Instituto de Salud Tropical, IdiSNA, Universidad de Navarra, 31008 Pamplona, Spain
| | - Celia Fernández-Rubio
- Department of Microbiology and Parasitology, ISTUN Instituto de Salud Tropical, IdiSNA, Universidad de Navarra, 31008 Pamplona, Spain
| | - Ana Poveda
- DNA Replication and Genome Instability Unit, Grupo de Investigación en Biodiversidad, Zoonosis y Salud Pública (GIBCIZ), Instituto de Investigación en Zoonosis-CIZ, Facultad de Ciencias Químicas, Universidad Central del Ecuador, Quito 170521, Ecuador
| | - Lianet Monzote
- Department of Parasitology, Institute of Tropical Medicine "Pedro Kourí", Apartado Postal No. 601, Marianao 13, La Habana 10400, Cuba
| | - Víctor M González
- Grupo de Aptámeros, Departamento de Bioquímica-Investigación, IRYCIS-Hospital Universitario Ramón y Cajal, Carretera de Colmenar Viejo Km. 9.100, 28034 Madrid, Spain
| | - Paloma Alonso-Collado
- Department of Animal Health, Faculty of Veterinary Science, Complutense University of Madrid, 28040 Madrid, Spain
| | - Javier Carrión
- Department of Animal Health, Faculty of Veterinary Science, Complutense University of Madrid, 28040 Madrid, Spain
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14
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Sun Z, Huang J, Fishelson Z, Wang C, Zhang S. Cell-Penetrating Peptide-Based Delivery of Macromolecular Drugs: Development, Strategies, and Progress. Biomedicines 2023; 11:1971. [PMID: 37509610 PMCID: PMC10377493 DOI: 10.3390/biomedicines11071971] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 07/11/2023] [Accepted: 07/11/2023] [Indexed: 07/30/2023] Open
Abstract
Cell-penetrating peptides (CPPs), developed for more than 30 years, are still being extensively studied due to their excellent delivery performance. Compared with other delivery vehicles, CPPs hold promise for delivering different types of drugs. Here, we review the development process of CPPs and summarize the composition and classification of the CPP-based delivery systems, cellular uptake mechanisms, influencing factors, and biological barriers. We also summarize the optimization routes of CPP-based macromolecular drug delivery from stability and targeting perspectives. Strategies for enhanced endosomal escape, which prolong its half-life in blood, improved targeting efficiency and stimuli-responsive design are comprehensively summarized for CPP-based macromolecule delivery. Finally, after concluding the clinical trials of CPP-based drug delivery systems, we extracted the necessary conditions for a successful CPP-based delivery system. This review provides the latest framework for the CPP-based delivery of macromolecular drugs and summarizes the optimized strategies to improve delivery efficiency.
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Affiliation(s)
- Zhe Sun
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, Tianjin 300072, China
| | - Zvi Fishelson
- Department of Cell and Developmental Biology, Faculty of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Chenhui Wang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
| | - Sihe Zhang
- Department of Cell Biology, School of Medicine, Nankai University, Tianjin 300071, China
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15
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Ejazi SA, Louisthelmy R, Maisel K. Mechanisms of Nanoparticle Transport across Intestinal Tissue: An Oral Delivery Perspective. ACS NANO 2023. [PMID: 37410891 DOI: 10.1021/acsnano.3c02403] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Oral drug administration has been a popular choice due to patient compliance and limited clinical resources. Orally delivered drugs must circumvent the harsh gastrointestinal (GI) environment to effectively enter the systemic circulation. The GI tract has a number of structural and physiological barriers that limit drug bioavailability including mucus, the tightly regulated epithelial layer, immune cells, and associated vasculature. Nanoparticles have been used to enhance oral bioavailability of drugs, as they can act as a shield to the harsh GI environment and prevent early degradation while also increasing uptake and transport of drugs across the intestinal epithelium. Evidence suggests that different nanoparticle formulations may be transported via different intracellular mechanisms to cross the intestinal epithelium. Despite the existence of a significant body of work on intestinal transport of nanoparticles, many key questions remain: What causes the poor bioavailability of the oral drugs? What factors contribute to the ability of a nanoparticle to cross different intestinal barriers? Do nanoparticle properties such as size and charge influence the type of endocytic pathways taken? In this Review, we summarize the different components of intestinal barriers and the types of nanoparticles developed for oral delivery. In particular, we focus on the various intracellular pathways used in nanoparticle internalization and nanoparticle or cargo translocation across the epithelium. Understanding the gut barrier, nanoparticle characteristics, and transport pathways may lead to the development of more therapeutically useful nanoparticles as drug carriers.
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Affiliation(s)
- Sarfaraz Ahmad Ejazi
- Fischell Department of Bioengineering, University of Maryland, 3120 A. James Clark Hall, College Park, Maryland 20742, United States
| | - Rebecca Louisthelmy
- Fischell Department of Bioengineering, University of Maryland, 3120 A. James Clark Hall, College Park, Maryland 20742, United States
| | - Katharina Maisel
- Fischell Department of Bioengineering, University of Maryland, 3120 A. James Clark Hall, College Park, Maryland 20742, United States
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16
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Todaro B, Ottalagana E, Luin S, Santi M. Targeting Peptides: The New Generation of Targeted Drug Delivery Systems. Pharmaceutics 2023; 15:1648. [PMID: 37376097 DOI: 10.3390/pharmaceutics15061648] [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: 04/29/2023] [Revised: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
Peptides can act as targeting molecules, analogously to oligonucleotide aptamers and antibodies. They are particularly efficient in terms of production and stability in physiological environments; in recent years, they have been increasingly studied as targeting agents for several diseases, from tumors to central nervous system disorders, also thanks to the ability of some of them to cross the blood-brain barrier. In this review, we will describe the techniques employed for their experimental and in silico design, as well as their possible applications. We will also discuss advancements in their formulation and chemical modifications that make them even more stable and effective. Finally, we will discuss how their use could effectively help to overcome various physiological problems and improve existing treatments.
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Affiliation(s)
- Biagio Todaro
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Elisa Ottalagana
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
- Fondazione Pisana per la Scienza, Via Ferruccio Giovannini 13, San Giuliano Terme, 56017 Pisa, Italy
| | - Stefano Luin
- NEST Laboratory, Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
| | - Melissa Santi
- NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore, Piazza San Silvestro 12, 56127 Pisa, Italy
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17
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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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18
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Nuclear localization signal peptides enhance genetic transformation of Dunaliella salina. Mol Biol Rep 2023; 50:1459-1467. [PMID: 36482029 DOI: 10.1007/s11033-022-08159-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 11/24/2022] [Indexed: 12/13/2022]
Abstract
BACKGROUND Dunaliella salina (D. salina) expression system shows a very attractive application prospect, but it currently has a technical bottleneck, namely the low or unstable expression of recombinant proteins. Given the characteristics of cell-penetrating peptides or/and nuclear localization signal (NLS) peptides, this study is the first attempt to improve the transformation rate of foreign gene with trans-activating transcriptional (TAT) protein or/and NLS peptides. METHODS AND RESULTS Using salt gradient method, exogenous plasmids were transferred into D. salina cells with TAT or TAT/NLS complexes simultaneously. The β-glucuronidase gene expression was identified by means of histochemical stain and RT-qPCR detection. Through observation with light microscope, TAT-mediating cells exhibit an apparent cytotoxicity even at ratios of 0.5, no significant toxicity was noted in the TAT/plasmid/NLS complex group. It is obvious that with the addition of peptides the toxicity decreases significantly. Histochemical staining showed that the transformants presented blue color under light microscope, but the negative control and blank control are not. Furthermore, based on a TAT/plasmids ratio of 4 with 10 µg NLS peptides mediation, RT-qPCR results demonstrated that the transcripts of target gene were increased by 269 times than that of control group. CONCLUSIONS This study demonstrated that combination of TAT and NLS peptides can significantly improve the transformation rate and expression level of foreign gene in D. salina system. It offers a promising way for promoting the application and development of D. salina bioreactor.
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19
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Parrasia S, Szabò I, Zoratti M, Biasutto L. Peptides as Pharmacological Carriers to the Brain: Promises, Shortcomings and Challenges. Mol Pharm 2022; 19:3700-3729. [PMID: 36174227 DOI: 10.1021/acs.molpharmaceut.2c00523] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Central nervous system (CNS) diseases are among the most difficult to treat, mainly because the vast majority of the drugs fail to cross the blood-brain barrier (BBB) or to reach the brain at concentrations adequate to exert a pharmacological activity. The obstacle posed by the BBB has led to the in-depth study of strategies allowing the brain delivery of CNS-active drugs. Among the most promising strategies is the use of peptides addressed to the BBB. Peptides are versatile molecules that can be used to decorate nanoparticles or can be conjugated to drugs, with either a stable link or as pro-drugs. They have been used to deliver to the brain both small molecules and proteins, with applications in diverse therapeutic areas such as brain cancers, neurodegenerative diseases and imaging. Peptides can be generally classified as receptor-targeted, recognizing membrane proteins expressed by the BBB microvessels (e.g., Angiopep2, CDX, and iRGD), "cell-penetrating peptides" (CPPs; e.g. TAT47-57, SynB1/3, and Penetratin), undergoing transcytosis through unspecific mechanisms, or those exploiting a mixed approach. The advantages of peptides have been extensively pointed out, but so far few studies have focused on the potential negative aspects. Indeed, despite having a generally good safety profile, some peptide conjugates may display toxicological characteristics distinct from those of the peptide itself, causing for instance antigenicity, cardiovascular alterations or hemolysis. Other shortcomings are the often brief lifetime in vivo, caused by the presence of peptidases, the vulnerability to endosomal/lysosomal degradation, and the frequently still insufficient attainable increase of brain drug levels, which remain below the therapeutically useful concentrations. The aim of this review is to analyze not only the successful and promising aspects of the use of peptides in brain targeting but also the problems posed by this strategy for drug delivery.
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Affiliation(s)
- Sofia Parrasia
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
| | - Ildikò Szabò
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
| | - Mario Zoratti
- CNR Neuroscience Institute, Viale G. Colombo 3, 35131 Padova, Italy.,Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
| | - Lucia Biasutto
- CNR Neuroscience Institute, Viale G. Colombo 3, 35131 Padova, Italy.,Department of Biomedical Sciences, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy
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20
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MLCPP 2.0: An updated cell-penetrating peptides and their uptake efficiency predictor. J Mol Biol 2022; 434:167604. [DOI: 10.1016/j.jmb.2022.167604] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 04/03/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022]
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21
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de Oliveira ECL, da Costa KS, Taube PS, Lima AH, Junior CDSDS. Biological Membrane-Penetrating Peptides: Computational Prediction and Applications. Front Cell Infect Microbiol 2022; 12:838259. [PMID: 35402305 PMCID: PMC8992797 DOI: 10.3389/fcimb.2022.838259] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/21/2022] [Indexed: 12/14/2022] Open
Abstract
Peptides comprise a versatile class of biomolecules that present a unique chemical space with diverse physicochemical and structural properties. Some classes of peptides are able to naturally cross the biological membranes, such as cell membrane and blood-brain barrier (BBB). Cell-penetrating peptides (CPPs) and blood-brain barrier-penetrating peptides (B3PPs) have been explored by the biotechnological and pharmaceutical industries to develop new therapeutic molecules and carrier systems. The computational prediction of peptides’ penetration into biological membranes has been emerged as an interesting strategy due to their high throughput and low-cost screening of large chemical libraries. Structure- and sequence-based information of peptides, as well as atomistic biophysical models, have been explored in computer-assisted discovery strategies to classify and identify new structures with pharmacokinetic properties related to the translocation through biomembranes. Computational strategies to predict the permeability into biomembranes include cheminformatic filters, molecular dynamics simulations, artificial intelligence algorithms, and statistical models, and the choice of the most adequate method depends on the purposes of the computational investigation. Here, we exhibit and discuss some principles and applications of these computational methods widely used to predict the permeability of peptides into biomembranes, exhibiting some of their pharmaceutical and biotechnological applications.
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Affiliation(s)
- Ewerton Cristhian Lima de Oliveira
- Institute of Technology, Federal University of Pará, Belém, Brazil
- *Correspondence: Kauê Santana da Costa, ; Ewerton Cristhian Lima de Oliveira,
| | - Kauê Santana da Costa
- Laboratory of Computational Simulation, Institute of Biodiversity, Federal University of Western Pará, Santarém, Brazil
- *Correspondence: Kauê Santana da Costa, ; Ewerton Cristhian Lima de Oliveira,
| | - Paulo Sérgio Taube
- Laboratory of Computational Simulation, Institute of Biodiversity, Federal University of Western Pará, Santarém, Brazil
| | - Anderson H. Lima
- Laboratório de Planejamento e Desenvolvimento de Fármacos, Instituto de Ciências Exatas e Naturais, Universidade Federal do Pará, Belém, Brazil
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22
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Design of Membrane Active Peptides Considering Multi-Objective Optimization for Biomedical Application. MEMBRANES 2022; 12:membranes12020180. [PMID: 35207101 PMCID: PMC8880019 DOI: 10.3390/membranes12020180] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/21/2022] [Accepted: 01/26/2022] [Indexed: 02/04/2023]
Abstract
A multitude of membrane active peptides exists that divides into subclasses, such as cell penetrating peptides (CPPs) capable to enter eukaryotic cells or antimicrobial peptides (AMPs) able to interact with prokaryotic cell envelops. Peptide membrane interactions arise from unique sequence motifs of the peptides that account for particular physicochemical properties. Membrane active peptides are mainly cationic, often primary or secondary amphipathic, and they interact with membranes depending on the composition of the bilayer lipids. Sequences of these peptides consist of short 5–30 amino acid sections derived from natural proteins or synthetic sources. Membrane active peptides can be designed using computational methods or can be identified in screenings of combinatorial libraries. This review focuses on strategies that were successfully applied to the design and optimization of membrane active peptides with respect to the fact that diverse features of successful peptide candidates are prerequisites for biomedical application. Not only membrane activity but also degradation stability in biological environments, propensity to induce resistances, and advantageous toxicological properties are crucial parameters that have to be considered in attempts to design useful membrane active peptides. Reliable assay systems to access the different biological characteristics of numerous membrane active peptides are essential tools for multi-objective peptide optimization.
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23
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Bio-Membrane Internalization Mechanisms of Arginine-Rich Cell-Penetrating Peptides in Various Species. MEMBRANES 2022; 12:membranes12010088. [PMID: 35054614 PMCID: PMC8778423 DOI: 10.3390/membranes12010088] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Revised: 01/06/2022] [Accepted: 01/10/2022] [Indexed: 02/04/2023]
Abstract
Recently, membrane-active peptides or proteins that include antimicrobial peptides (AMPs), cytolytic proteins, and cell-penetrating peptides (CPPs) have attracted attention due to their potential applications in the biomedical field. Among them, CPPs have been regarded as a potent drug/molecules delivery system. Various cargoes, such as DNAs, RNAs, bioactive proteins/peptides, nanoparticles and drugs, can be carried by CPPs and delivered into cells in either covalent or noncovalent manners. Here, we focused on four arginine-rich CPPs and reviewed the mechanisms that these CPPs used for intracellular uptake across cellular plasma membranes. The varying transduction efficiencies of them alone or with cargoes were discussed, and the membrane permeability was also expounded for CPP/cargoes delivery in various species. Direct membrane translocation (penetration) and endocytosis are two principal mechanisms for arginine-rich CPPs mediated cargo delivery. Furthermore, the amino acid sequence is the primary key factor that determines the cellular internalization mechanism. Importantly, the non-cytotoxic nature and the wide applicability make CPPs a trending tool for cellular delivery.
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In Silico Design of Chemically Modified Cell-Penetrating Peptides. Methods Mol Biol 2021; 2383:63-71. [PMID: 34766282 DOI: 10.1007/978-1-0716-1752-6_4] [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: 03/03/2023]
Abstract
In the past few decades, a large number of cell-penetrating peptides (CPPs) have been discovered. These CPPs have a wide range of applications including drug delivery vehicles. Numerous in silico tools have been developed over the years to design and predict the cell-penetrating peptides that contain natural amino acids. The majority of natural cell-penetrating peptides have several limitations including stability, immunogenicity as well as got entrapped in the cell's endosomes. The chemical modification is commonly used to most of these limitations. An in silico tool called CellPPDMod have been developed by our group to predict cell-penetration potential of chemically modified peptides. This chapter is dedicated for designing therapeutically important cell-penetrating peptides using CellPPDMod ( http://webs.iiitd.edu.in/raghava/cellppdmod/ ).
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Fasiku V, Omolo CA, Devnarain N, Ibrahim UH, Rambharose S, Faya M, Mocktar C, Singh SD, Govender T. Chitosan-Based Hydrogel for the Dual Delivery of Antimicrobial Agents Against Bacterial Methicillin-Resistant Staphylococcus aureus Biofilm-Infected Wounds. ACS OMEGA 2021; 6:21994-22010. [PMID: 34497894 PMCID: PMC8412894 DOI: 10.1021/acsomega.1c02547] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
Chronic wound infections caused by antibiotic-resistant bacteria have become a global health concern. This is attributed to the biofilm-forming ability of bacteria on wound surfaces, thus enabling their persistent growth. In most cases, it leads to morbidity and in severe cases mortality. Current conventional approaches used in the treatment of biofilm wounds are proving to be ineffective due to limitations such as the inability to penetrate the biofilm matrix; hence, biofilm-related wounds remain a challenge. Therefore, there is a need for more efficient alternate therapeutic interventions. Hydrogen peroxide (HP) is a known antibacterial/antibiofilm agent; however, prolonged delivery has been challenging due to its short half-life. In this study, we developed a hydrogel for the codelivery of HP and antimicrobial peptides (Ps) against bacteria, biofilms, and wound infection associated with biofilms. The hydrogel was prepared via the Michael addition technique, and the physiochemical properties were characterized. The safety, in vitro, and in vivo antibacterial/antibiofilm activity of the hydrogel was also investigated. Results showed that the hydrogel is biosafe. A greater antibacterial effect was observed with HP-loaded hydrogels (CS-HP; hydrogel loaded with HP and CS-HP-P; hydrogel loaded with HP and peptide) when compared to HP as seen in an approximately twofold and threefold decrease in minimum inhibitory concentration values against methicillin-resistant Staphylococcus aureus (MRSA) bacteria, respectively. Similarly, both the HP-releasing hydrogels showed enhanced antibiofilm activity in the in vivo study in mice models as seen in greater wound closure and enhanced wound healing in histomorphological analysis. Interestingly, the results revealed a synergistic antibacterial/antibiofilm effect between HP and P in both in vitro and in vivo studies. The successfully prepared HP-releasing hydrogels showed the potential to combat bacterial biofilm-related infections and enhance wound healing in mice models. These results suggest that the HP-releasing hydrogels may be a superior platform for eliminating bacterial biofilms without using antibiotics in the treatment of chronic MRSA wound infections, thus improving the quality of human health.
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Affiliation(s)
- Victoria
O. Fasiku
- Discipline
of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South
Africa
| | - Calvin A. Omolo
- Discipline
of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South
Africa
- School
of Pharmacy and Health Sciences, Department of Pharmaceutics, United States International University-Africa, P.O. Box 14634, Nairobi 00800, Kenya
| | - Nikita Devnarain
- Discipline
of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South
Africa
| | - Usri H. Ibrahim
- Discipline
of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South
Africa
| | - Sanjeev Rambharose
- Department
of Physiological Sciences, Faculty of Science, Stellenbosch University, Private Bag X1 Matieland, Stellenbosch 7602, South Africa
| | - Mbuso Faya
- Discipline
of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South
Africa
| | - Chunderika Mocktar
- Discipline
of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South
Africa
| | - Sanil D. Singh
- Biomedical
Research Unit, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South
Africa
| | - Thirumala Govender
- Discipline
of Pharmaceutical Sciences, College of Health Sciences, University of KwaZulu-Natal, Private Bag X54001, Durban 4000, South
Africa
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Chen L, Guo X, Wang L, Geng J, Wu J, Hu B, Wang T, Li J, Liu C, Wang H. In silico identification and experimental validation of cellular uptake by a new cell penetrating peptide P1 derived from MARCKS. Drug Deliv 2021; 28:1637-1648. [PMID: 34338123 PMCID: PMC8330795 DOI: 10.1080/10717544.2021.1960922] [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] [Indexed: 12/28/2022] Open
Abstract
Viral vectors for vaccine delivery are challenged by recently reported safety issues like immunogenicity and risk for cancer development, and thus there is a growing need for the development of non-viral vectors. Cell penetrating peptides (CPPs) are non-viral vectors that can enter plasma membranes efficiently and deliver a broad range of cargoes. Our bioinformatic prediction and wet-lab validation data suggested that peptide P1 derived from MARCKS protein phosphorylation site domain is a new potential CPP candidate. We found that peptide P1 can efficiently internalize into various cell lines in a concentration-dependent manner. Receptor-mediated endocytosis pathway is the major mechanism of P1 penetration, although P1 also directly penetrates the plasma membrane. We also found that peptide P1 has low cytotoxicity in cultured cell lines as well as mouse red blood cells. Furthermore, peptide P1 not only can enter into cultured cells itself, but it also can interact with plasmid DNA and mediate the functional delivery of plasmid DNA into cultured cells, even in hard-to-transfect cells. Combined, these findings indicate that P1 may be a promising vector for efficient intracellular delivery of bioactive cargos.
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Affiliation(s)
- Linlin Chen
- Department of Pathology and Immunology, Medical School, China Three Gorges University, Yichang, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China.,Affiliated Ren He Hospital of China Three Gorges University, Yichang, China
| | - Xiangli Guo
- Department of Pathology and Immunology, Medical School, China Three Gorges University, Yichang, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
| | - Lidan Wang
- Department of Pathology and Immunology, Medical School, China Three Gorges University, Yichang, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
| | - Jingping Geng
- Department of Pathology and Immunology, Medical School, China Three Gorges University, Yichang, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
| | - Jiao Wu
- Affiliated Ren He Hospital of China Three Gorges University, Yichang, China
| | - Bin Hu
- Affiliated Ren He Hospital of China Three Gorges University, Yichang, China
| | - Tao Wang
- The First Clinical Medical College of China Three Gorges University, Yichang, China
| | - Jason Li
- Department of Biology, Johns Hopkins University, Baltimore, MD, USA
| | - Changbai Liu
- Department of Pathology and Immunology, Medical School, China Three Gorges University, Yichang, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, Yichang, China
| | - Hu Wang
- Department of Pathology and Immunology, Medical School, China Three Gorges University, Yichang, China
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Sanchez-Martos M, Martinez-Navarrete G, Bernabeu-Zornoza A, Humphreys L, Fernandez E. Evaluation and Optimization of Poly-d-Lysine as a Non-Natural Cationic Polypeptide for Gene Transfer in Neuroblastoma Cells. NANOMATERIALS 2021; 11:nano11071756. [PMID: 34361142 PMCID: PMC8308159 DOI: 10.3390/nano11071756] [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: 06/06/2021] [Revised: 06/26/2021] [Accepted: 06/29/2021] [Indexed: 11/17/2022]
Abstract
Cationic polypeptides and cationic polymers have cell-penetrating capacities and have been used in gene transfer studies. In this study, we investigate the capability of a polymer of d-lysine (PDL), a chiral form of α–Poly-lysine, as a possible nonviral vector for releasing genetic materials to neuroblastoma cells and evaluate its stability against proteases. We tested and compared its transfection effectiveness in vitro as a vehicle for the EGFP plasmid DNA (pDNA) reporter in the SH-SY5Y human neuroblastoma, HeLa, and 3T3 cell lines. Using fluorescent microscopy and flow cytometry, we demonstrated high transfection efficiencies based on EGFP fluorescence in SH-SY5Y cells, compared with HeLa and 3T3. Our results reveal PDL as an efficient vector for gene delivery specifically in the SH-SY5Y cell line and suggest that PDL can be used as a synthetic cell-penetrating polypeptide for gene therapy in neuroblastoma cells.
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Affiliation(s)
- Miguel Sanchez-Martos
- Neuroprothesis and Neuroengineering Research Group, Miguel Hernández University, 03201 Elche, Spain; (M.S.-M.); (G.M.-N.); (A.B.-Z.); (L.H.)
| | - Gema Martinez-Navarrete
- Neuroprothesis and Neuroengineering Research Group, Miguel Hernández University, 03201 Elche, Spain; (M.S.-M.); (G.M.-N.); (A.B.-Z.); (L.H.)
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
| | - Adela Bernabeu-Zornoza
- Neuroprothesis and Neuroengineering Research Group, Miguel Hernández University, 03201 Elche, Spain; (M.S.-M.); (G.M.-N.); (A.B.-Z.); (L.H.)
| | - Lawrence Humphreys
- Neuroprothesis and Neuroengineering Research Group, Miguel Hernández University, 03201 Elche, Spain; (M.S.-M.); (G.M.-N.); (A.B.-Z.); (L.H.)
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
| | - Eduardo Fernandez
- Neuroprothesis and Neuroengineering Research Group, Miguel Hernández University, 03201 Elche, Spain; (M.S.-M.); (G.M.-N.); (A.B.-Z.); (L.H.)
- Biomedical Research Networking Center in Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), 28029 Madrid, Spain
- Correspondence: ; Tel.: +34-965222001
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Casadio R, Lenhard B, Sternberg MJE. Computational Resources for Molecular Biology 2021. J Mol Biol 2021; 433:166962. [PMID: 33774035 DOI: 10.1016/j.jmb.2021.166962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Rita Casadio
- Biocomputing Group, FABIT-University of Bologna, Italy
| | - Boris Lenhard
- Institute of Clinical Sciences, Faculty of Medicine. Imperial College London, Hammersmith Campus, Du Cane Road, London W12 0NN, UK; Computational Regulatory Genomics, MRC London Institute of Medical Sciences, Du Cane Road, London W12 0NN, UK
| | - Michael J E Sternberg
- Structural Bioinformatics Group, Centre for Integrative Systems Biology and Bioinformatics, Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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Design, Synthesis and Evaluation of Antimicrobial Database-Derived Peptides Against Drug-Resistant Gram-Positive and Gram-Negative Pathogens. Int J Pept Res Ther 2021. [DOI: 10.1007/s10989-021-10183-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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30
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Kardani K, Bolhassani A. Exploring novel and potent cell penetrating peptides in the proteome of SARS-COV-2 using bioinformatics approaches. PLoS One 2021; 16:e0247396. [PMID: 33606823 PMCID: PMC7894964 DOI: 10.1371/journal.pone.0247396] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 02/06/2021] [Indexed: 02/08/2023] Open
Abstract
Among various delivery systems for vaccine and drug delivery, cell-penetrating peptides (CPPs) have been known as a potent delivery system because of their capability to penetrate cell membranes and deliver some types of cargoes into cells. Several CPPs were found in the proteome of viruses such as Tat originated from human immunodeficiency virus-1 (HIV-1), and VP22 derived from herpes simplex virus-1 (HSV-1). In the current study, a wide-range of CPPs was identified in the proteome of SARS-CoV-2, a new member of coronaviruses family, using in silico analyses. These CPPs may play a main role for high penetration of virus into cells and infection of host. At first, we submitted the proteome of SARS-CoV-2 to CellPPD web server that resulted in a huge number of CPPs with ten residues in length. Afterward, we submitted the predicted CPPs to C2Pred web server for evaluation of the probability of each peptide. Then, the uptake efficiency of each peptide was investigated using CPPred-RF and MLCPP web servers. Next, the physicochemical properties of the predicted CPPs including net charge, theoretical isoelectric point (pI), amphipathicity, molecular weight, and water solubility were calculated using protparam and pepcalc tools. In addition, the probability of membrane binding potential and cellular localization of each CPP were estimated by Boman index using APD3 web server, D factor, and TMHMM web server. On the other hand, the immunogenicity, toxicity, allergenicity, hemolytic potency, and half-life of CPPs were predicted using various web servers. Finally, the tertiary structure and the helical wheel projection of some CPPs were predicted by PEP-FOLD3 and Heliquest web servers, respectively. These CPPs were divided into: a) CPP containing tumor homing motif (RGD) and/or tumor penetrating motif (RXXR); b) CPP with the highest Boman index; c) CPP with high half-life (~100 hour) in mammalian cells, and d) CPP with +5.00 net charge. Based on the results, we found a large number of novel CPPs with various features. Some of these CPPs possess tumor-specific motifs which can be evaluated in cancer therapy. Furthermore, the novel and potent CPPs derived from SARS-CoV-2 may be used alone or conjugated to some sequences such as nuclear localization sequence (NLS) for vaccine and drug delivery.
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Affiliation(s)
- Kimia Kardani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
| | - Azam Bolhassani
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran
- * E-mail: ,
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31
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Rádis-Baptista G. Cell-Penetrating Peptides Derived from Animal Venoms and Toxins. Toxins (Basel) 2021; 13:147. [PMID: 33671927 PMCID: PMC7919042 DOI: 10.3390/toxins13020147] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 01/31/2021] [Accepted: 02/09/2021] [Indexed: 12/18/2022] Open
Abstract
Cell-penetrating peptides (CPPs) comprise a class of short polypeptides that possess the ability to selectively interact with the cytoplasmic membrane of certain cell types, translocate across plasma membranes and accumulate in the cell cytoplasm, organelles (e.g., the nucleus and mitochondria) and other subcellular compartments. CPPs are either of natural origin or de novo designed and synthesized from segments and patches of larger proteins or designed by algorithms. With such intrinsic properties, along with membrane permeation, translocation and cellular uptake properties, CPPs can intracellularly convey diverse substances and nanomaterials, such as hydrophilic organic compounds and drugs, macromolecules (nucleic acids and proteins), nanoparticles (nanocrystals and polyplexes), metals and radionuclides, which can be covalently attached via CPP N- and C-terminals or through preparation of CPP complexes. A cumulative number of studies on animal toxins, primarily isolated from the venom of arthropods and snakes, have revealed the cell-penetrating activities of venom peptides and toxins, which can be harnessed for application in biomedicine and pharmaceutical biotechnology. In this review, I aimed to collate examples of peptides from animal venoms and toxic secretions that possess the ability to penetrate diverse types of cells. These venom CPPs have been chemically or structurally modified to enhance cell selectivity, bioavailability and a range of target applications. Herein, examples are listed and discussed, including cysteine-stabilized and linear, α-helical peptides, with cationic and amphipathic character, from the venom of insects (e.g., melittin, anoplin, mastoparans), arachnids (latarcin, lycosin, chlorotoxin, maurocalcine/imperatoxin homologs and wasabi receptor toxin), fish (pardaxins), amphibian (bombesin) and snakes (crotamine and cathelicidins).
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Affiliation(s)
- Gandhi Rádis-Baptista
- Laboratory of Biochemistry and Biotechnology, Institute for Marine Sciences, Federal University of Ceara, Fortaleza 60165-081, Brazil
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