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Nematian M, Noormohammadi Z, Rahimi P, Irani S, Arefian E. Exploring the potential of structural modeling and molecular docking for efficient siRNA screening: A promising approach to Combat viral mutants, with a focus on HIV-1. Biochem Biophys Res Commun 2024; 708:149769. [PMID: 38518723 DOI: 10.1016/j.bbrc.2024.149769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 03/03/2024] [Accepted: 03/10/2024] [Indexed: 03/24/2024]
Abstract
RNA interference (RNAi) holds immense potential for sequence-specific downregulation of disease-related genes. Small interfering RNA (siRNA) therapy has made remarkable strides, with FDA approval for treating specific human diseases, showcasing its promising future in disease treatment. Designing highly efficient siRNAs is a critical step in this process. Previous studies have introduced various algorithms and parameters for siRNA design and scoring. However, these attempts have often fallen short of meeting all essential criteria or required modifications, resulting in variable and unclear effectiveness of screened siRNAs, particularly against viral mutants with non-conserved short sequences. In this study, we present a fully optimized siRNA screening system considering all necessary parameters. Notably, we highlight the critical role of molecular docking simulations between siRNA and two functional domains of the Argonaute protein (PAZ and PIWI) in identifying the most efficient siRNAs, since the appropriate interaction between the guide siRNA strand and the RISC complex is crucial. Through our stringent method, we designed approximately 50 potential siRNAs targeting the HIV-1 vpr gene. Evaluation through XTT, qRT-PCR, and flow cytometry analysis on RAW 264.7 macrophage stable cells revealed negligible cytotoxicity and exceptional gene-silencing efficiency at both the transcriptional and translational levels for the top-ranked screened siRNAs. Given the growing interest in siRNA-based therapeutics, we anticipate that the insights from this study will contribute to improving treatment strategies against mutant viruses, particularly HIV-1.
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Affiliation(s)
- Mohammad Nematian
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Zahra Noormohammadi
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Pooneh Rahimi
- Department of Hepatitis and AIDS, Pasteur Institute of Iran, Tehran, Iran; Viral Vaccine Research Center (VVRC), Pasteur Institute of Iran, Tehran, Iran.
| | - Shiva Irani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Ehsan Arefian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
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2
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El-Mowafi SA, Konshina AG, Mohammed EHM, Krylov NA, Efremov RG, Parang K. Structural Analysis and Activity Correlation of Amphiphilic Cyclic Antimicrobial Peptides Derived from the [W 4R 4] Scaffold. Molecules 2023; 28:8049. [PMID: 38138539 PMCID: PMC10745345 DOI: 10.3390/molecules28248049] [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: 11/21/2023] [Revised: 12/08/2023] [Accepted: 12/10/2023] [Indexed: 12/24/2023] Open
Abstract
In our ongoing quest to design effective antimicrobial peptides (AMPs), this study aimed to elucidate the mechanisms governing cyclic amphiphilic AMPs and their interactions with membranes. The objective was to discern the nature of these interactions and understand how peptide sequence and structure influence antimicrobial activity. We introduced modifications into the established cyclic AMP peptide, [W4R4], incorporating an extra aromatic hydrophobic residue (W), a positively charged residue (R), or the unique 2,5-diketopiperazine (DKP). This study systematically explored the structure-activity relationships (SARs) of a series of cyclic peptides derived from the [W4R4] scaffold, including the first synthesis and evaluation of [W4R4(DKP)]. Structural, dynamic, hydrophobic, and membrane-binding properties of four cyclic peptides ([W4R4], [W5R4], [W4R5], [W4R4(DKP)]) were explored using molecular dynamics simulations within a DOPC/DOPG lipid bilayer that mimics the bacterial membrane. The results revealed distinct SARs linking antimicrobial activity to parameters such as conformational plasticity, immersion depth in the bilayer, and population of the membrane binding mode. Notably, [W4R5] exhibited an optimal "activity/binding to the bacterial membrane" pattern. This multidisciplinary approach efficiently decoded finely regulated SAR profiles, laying a foundation for the rational design of novel antimicrobial peptides.
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Affiliation(s)
- Shaima A. El-Mowafi
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618, USA; (S.A.E.-M.); (E.H.M.M.)
- Peptide Chemistry Department, National Research Centre, Dokki, Cairo 12622, Egypt
| | - Anastasia G. Konshina
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia; (A.G.K.); (N.A.K.)
| | - Eman H. M. Mohammed
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618, USA; (S.A.E.-M.); (E.H.M.M.)
- Department of Chemistry, Faculty of Science, Menoufia University, Shebin El-Koam 51132, Egypt
| | - Nikolay A. Krylov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia; (A.G.K.); (N.A.K.)
| | - Roman G. Efremov
- M.M. Shemyakin & Yu.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street, 16/10, 117997 Moscow, Russia; (A.G.K.); (N.A.K.)
- Department of Applied Mathematics, National Research University Higher School of Economics, Myasnitskaya ul. 20, 101000 Moscow, Russia
| | - Keykavous Parang
- Center for Targeted Drug Delivery, Department of Biomedical and Pharmaceutical Sciences, Chapman University School of Pharmacy, Harry and Diane Rinker Health Science Campus, Irvine, CA 92618, USA; (S.A.E.-M.); (E.H.M.M.)
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3
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Algayer B, O'Brien A, Momose A, Murphy DJ, Procopio W, Tellers DM, Tucker TJ. Novel pH Selective, Highly Lytic Peptides Based on a Chimeric Influenza Hemagglutinin Peptide/Cell Penetrating Peptide Motif. Molecules 2019; 24:E2079. [PMID: 31159194 PMCID: PMC6600388 DOI: 10.3390/molecules24112079] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Revised: 05/22/2019] [Accepted: 05/24/2019] [Indexed: 11/17/2022] Open
Abstract
Delivery of macromolecular cargos such as siRNA to the cytosol after endocytosis remains a critical challenge. Numerous approaches including viruses, lipid nanoparticles, polymeric constructs, and various peptide-based approaches have yet to yield a general solution to this delivery issue. In this manuscript, we describe our efforts to design novel endosomolytic peptides that could be used to facilitate the release of cargos from a late endosomal compartment. These amphiphilic peptides, based on a chimeric influenza hemagglutinin peptide/cell-penetrating peptide (CPP) template, utilize a pH-triggering mechanism in which the peptides are protonated after acidification of the endosome, and thereby adopt an alpha-helical conformation. The helical forms of the peptides are lytically active, while the non-protonated forms are much less or non-lytically active at physiological pH. Starting from an initial lead peptide (INF7-Tat), we systematically modified the sequence of the chimeric peptides to obtain peptides with greatly enhanced lytic activity that maintain good pH selectivity in a red blood cell hemolysis assay.
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Affiliation(s)
- Bethany Algayer
- Merck Research Laboratories, Merck and Co, Inc., West Point, PA 19486, USA.
| | - Ann O'Brien
- Merck Research Laboratories, Merck and Co, Inc., West Point, PA 19486, USA.
| | - Aaron Momose
- Merck Research Laboratories, Merck and Co, Inc., West Point, PA 19486, USA.
| | - Dennis J Murphy
- Merck Research Laboratories, Merck and Co, Inc., West Point, PA 19486, USA.
| | - William Procopio
- Merck Research Laboratories, Merck and Co, Inc., West Point, PA 19486, USA.
| | - David M Tellers
- Merck Research Laboratories, Merck and Co, Inc., West Point, PA 19486, USA.
| | - Thomas J Tucker
- Merck Research Laboratories, Merck and Co, Inc., West Point, PA 19486, USA.
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4
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Feiner-Gracia N, Olea RA, Fitzner R, El Boujnouni N, van Asbeck AH, Brock R, Albertazzi L. Super-resolution Imaging of Structure, Molecular Composition, and Stability of Single Oligonucleotide Polyplexes. NANO LETTERS 2019; 19:2784-2792. [PMID: 31001985 PMCID: PMC6509642 DOI: 10.1021/acs.nanolett.8b04407] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 04/11/2019] [Indexed: 05/20/2023]
Abstract
The successful application of gene therapy relies on the development of safe and efficient delivery vectors. Cationic polymers such as cell-penetrating peptides (CPPs) can condense genetic material into nanoscale particles, called polyplexes, and induce cellular uptake. With respect to this point, several aspects of the nanoscale structure of polyplexes have remained elusive because of the difficulty in visualizing the molecular arrangement of the two components with nanometer resolution. This limitation has hampered the rational design of polyplexes based on direct structural information. Here, we used super-resolution imaging to study the structure and molecular composition of individual CPP-mRNA polyplexes with nanometer accuracy. We use two-color direct stochastic optical reconstruction microscopy (dSTORM) to unveil the impact of peptide stoichiometry on polyplex structure and composition and to assess their destabilization in blood serum. Our method provides information about the size and composition of individual polyplexes, allowing the study of such properties on a single polyplex basis. Furthermore, the differences in stoichiometry readily explain the differences in cellular uptake behavior. Thus, quantitative dSTORM of polyplexes is complementary to the currently used characterization techniques for understanding the determinants of polyplex activity in vitro and inside cells.
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Affiliation(s)
- Natalia Feiner-Gracia
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering of Catalonia
(IBEC), The Barcelona Institute of Science
and Technology (BIST), Carrer Baldiri
Reixac 15-21, 08024 Barcelona, Spain
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
| | - R. Alis Olea
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering of Catalonia
(IBEC), The Barcelona Institute of Science
and Technology (BIST), Carrer Baldiri
Reixac 15-21, 08024 Barcelona, Spain
- Department
of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Robert Fitzner
- Department
of Mathematics and Computer Science, Eindhoven
University of Technology, Post Office
Box 513, 5600 MD Eindhoven, The Netherlands
| | - Najoua El Boujnouni
- Department
of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Alexander H. van Asbeck
- Department
of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Roland Brock
- Department
of Biochemistry, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Lorenzo Albertazzi
- Nanoscopy
for Nanomedicine Group, Institute for Bioengineering of Catalonia
(IBEC), The Barcelona Institute of Science
and Technology (BIST), Carrer Baldiri
Reixac 15-21, 08024 Barcelona, Spain
- Department
of Biomedical Engineering, Institute for Complex Molecular Systems
(ICMS), Eindhoven University of Technology, 5612AZ Eindhoven, The Netherlands
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Ivanova L, Tammiku-Taul J, García-Sosa AT, Sidorova Y, Saarma M, Karelson M. Molecular Dynamics Simulations of the Interactions between Glial Cell Line-Derived Neurotrophic Factor Family Receptor GFRα1 and Small-Molecule Ligands. ACS OMEGA 2018; 3:11407-11414. [PMID: 30320260 PMCID: PMC6173496 DOI: 10.1021/acsomega.8b01524] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 09/06/2018] [Indexed: 06/01/2023]
Abstract
The glial cell line-derived neurotrophic factor (GDNF) family ligands (GFLs) support the survival and functioning of various neuronal populations. Thus, they could be attractive therapeutic agents against a multitude of neurodegenerative diseases caused by progressive death of GFLs responsive neurons. Small-molecule ligands BT13 and BT18 show an effect on GDNF family receptor GFRα1 and RET receptor tyrosine kinase RetA function. Thus, their potential binding sites and interactions were explored in the GDNF-GFRα1-RetA complex using molecular docking calculations as well as molecular dynamics (MD) simulations. Three possible regions were examined: the interface between GDNF and GFRα1 (region A), the RetA interface with GFRα1 (region B), and a possible allosteric site in GFRα1 (region C). The results obtained by the docking calculations and the MD simulations indicate that the preferable binding occurs at the allosteric site. A less preferable binding site was detected on the RetA surface interfacing GFRα1. In the membrane-bound state of RetA this can enable compounds BT13 and BT18 to act as direct RetA agonists. The analysis of the MD simulations shows hydrogen bonds for BT13 and significant hydrophobic interactions with GFRα1 for BT13 and BT18 at the allosteric site.
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Affiliation(s)
- Larisa Ivanova
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411 Tartu, Estonia
| | - Jaana Tammiku-Taul
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411 Tartu, Estonia
| | | | - Yulia Sidorova
- Laboratory of Molecular
Neuroscience, Institute of Biotechnology, HiLIFE, University of Helsinki, Viikinkaari 5D, 00014 Helsinki, Finland
| | - Mart Saarma
- Laboratory of Molecular
Neuroscience, Institute of Biotechnology, HiLIFE, University of Helsinki, Viikinkaari 5D, 00014 Helsinki, Finland
| | - Mati Karelson
- Institute of Chemistry, University of Tartu, Ravila 14A, 50411 Tartu, Estonia
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Pärnaste L, Arukuusk P, Langel K, Tenson T, Langel Ü. The Formation of Nanoparticles between Small Interfering RNA and Amphipathic Cell-Penetrating Peptides. MOLECULAR THERAPY. NUCLEIC ACIDS 2017. [PMID: 28624185 PMCID: PMC5363680 DOI: 10.1016/j.omtn.2017.02.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Cell-penetrating peptides (CPPs) are delivery vectors widely used to aid the transport of biologically active cargoes to intracellular targets. These cargoes include small interfering RNAs (siRNA) that are not naturally internalized by cells. Elucidating the complexities behind the formation of CPP and cargo complexes is crucial for understanding the processes related to their delivery. In this study, we used modified analogs of the CPP transportan10 and investigated the binding properties of these CPPs to siRNA, the formation parameters of the CPP/siRNA complexes, and their stabiliy to enzymatic degradation. We conclude that the pH dependent change of the net charge of the CPP may very well be the key factor leading to the high delivery efficiency and the optimal binding strength between CPPs to siRNAs, while the hydrophobicity, secondary structure of the CPP, and the positions of the positive charges are responsible for the stability of the CPP/siRNA particles. Also, CPPs with distinct hydrophobic and hydrophilic regions may assemble into nanoparticles that could be described as core-shell formulations.
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Affiliation(s)
- Ly Pärnaste
- Institute of Technology, University of Tartu, Nooruse 1-517, 50411 Tartu, Estonia.
| | - Piret Arukuusk
- Institute of Technology, University of Tartu, Nooruse 1-517, 50411 Tartu, Estonia
| | - Kent Langel
- Institute of Technology, University of Tartu, Nooruse 1-517, 50411 Tartu, Estonia
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Nooruse 1-517, 50411 Tartu, Estonia
| | - Ülo Langel
- Institute of Technology, University of Tartu, Nooruse 1-517, 50411 Tartu, Estonia; Department of Neurochemistry, Stockholm University, Stockholm 106 91, Sweden
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7
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Abstract
The in silico methods for the prediction of the cell-penetrating peptides are reviewed. Those include the multivariate statistical methods, machine-learning methods such as the artificial neural networks and support vector machines, and molecular modeling techniques including molecular docking and molecular dynamics.The applicability of the methods is demonstrated on the basis of the exemplary cases from the literature.
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8
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Chen B, Xu W, Pan R, Chen P. Design and characterization of a new peptide vector for short interfering RNA delivery. J Nanobiotechnology 2015; 13:39. [PMID: 26054932 PMCID: PMC4459685 DOI: 10.1186/s12951-015-0098-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 05/13/2015] [Indexed: 11/10/2022] Open
Abstract
RNA interference holds tremendous potential as one of the most powerful therapeutic strategies. However, the properties of short interfering RNA (siRNA), such as hydrophilicity, negative charge, and instability in serum have limited its applications; therefore, significant efforts have been undertaken to improve its cellular uptake. Cell penetrating peptides have been utilized to deliver various biologically active molecules, such as proteins, liposomes, nanoparticles, peptide nucleic acids, and recently small interfering RNAs. Here, we introduce a new cell penetrating peptide GL1(Ac-GLWRAWLWKAFLASNWRRLLRLLR-NH2) to improve the intracellular uptake of siRNA. This peptide consists of four tryptophan residues that facilitated its binding with the cell membrane, five arginine residues and one lysine residue which are positively charged at physiological pH, which induced the formation of peptide-siRNA complexes and enhanced the affinity of the peptide and cell membrane. Moreover, GL1 adopted helical secondary structure due to the altered distribution of polar and nonpolar residues in the sequence. In this study, we investigated the effect of peptide/siRNA molar ratio on the particle size, surface charge, secondary structure, and uptake efficiency. The results showed that GL1 formed stable complexes with siRNA mainly through electrostatic interaction and hydrophobic interaction, and the complexes displayed a spherical shape with the size of ~100 nm and positive surface charge. Utilizing the techniques of fluorescence microscopy and flow cytometry, the intracellular localization of Cy3-labeled GAPDH siRNA was visualized and the cellular uptake was quantified. It is worth noting that in the serum free environment, compared to Lipofectamine 2000, GL1 achieved higher cellular uptake of siRNA (~95%); in the presence of serum, GL1 retained the same level of siRNA cellular uptake (~84%) as Lipofectamine 2000. In addition, the viability of cells treated by GL1 in all studied molar ratios was >85%, which was significantly higher than that treated by Lipofectamine 2000 (~70%). Taken together, the peptide GL1 demonstrated promise as a siRNA delivery system.
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Affiliation(s)
- Baoling Chen
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
| | - Wen Xu
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
| | - Ran Pan
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
| | - P Chen
- Department of Chemical Engineering, University of Waterloo, 200 University Avenue West, Waterloo, ON, N2L 3G1, Canada.
- Waterloo Institute for Nanotechnology, University of Waterloo, Waterloo, ON, N2L 3G1, Canada.
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