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Bergman M, Xiao X, Hall CK. In Silico Design and Analysis of Plastic-Binding Peptides. J Phys Chem B 2023; 127:8370-8381. [PMID: 37735840 PMCID: PMC10591858 DOI: 10.1021/acs.jpcb.3c04319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
Peptides that bind to inorganic materials can be used to functionalize surfaces, control crystallization, or assist in interfacial self-assembly. In the past, inorganic-binding peptides have been found predominantly through peptide library screening. While this method has successfully identified peptides that bind to a variety of materials, an alternative design approach that can intelligently search for peptides and provide physical insight for peptide affinity would be desirable. In this work, we develop a computational, physics-based approach to design inorganic-binding peptides, focusing on peptides that bind to the common plastics polyethylene, polypropylene, polystyrene, and poly(ethylene terephthalate). The PepBD algorithm, a Monte Carlo method that samples peptide sequence and conformational space, was modified to include simulated annealing, relax hydration constraints, and an ensemble of conformations to initiate design. These modifications led to the discovery of peptides with significantly better scores compared to those obtained using the original PepBD. PepBD scores were found to improve with increasing van der Waals interactions, although strengthening the intermolecular van der Waals interactions comes at the cost of introducing unfavorable electrostatic interactions. The best designs are enriched in amino acids with bulky side chains and possess hydrophobic and hydrophilic patches whose location depends on the adsorbed conformation. Future work will evaluate the top peptide designs in molecular dynamics simulations and experiment, enabling their application in microplastic pollution remediation and plastic-based biosensors.
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Affiliation(s)
- Michael Bergman
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27606, USA
| | - Xingqing Xiao
- Department of Chemistry, School of Science, Hainan University, Longhua District, Haikou, Hainan, 571101, China
| | - Carol K. Hall
- Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27606, USA
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Punginelli D, Catania V, Abruscato G, Luparello C, Vazzana M, Mauro M, Cunsolo V, Saletti R, Di Francesco A, Arizza V, Schillaci D. New Bioactive Peptides from the Mediterranean Seagrass Posidonia oceanica (L.) Delile and Their Impact on Antimicrobial Activity and Apoptosis of Human Cancer Cells. Int J Mol Sci 2023; 24:5650. [PMID: 36982723 PMCID: PMC10056643 DOI: 10.3390/ijms24065650] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 03/18/2023] Open
Abstract
The demand for new molecules to counter bacterial resistance to antibiotics and tumor cell resistance is increasingly pressing. The Mediterranean seagrass Posidonia oceanica is considered a promising source of new bioactive molecules. Polypeptide-enriched fractions of rhizomes and green leaves of the seagrass were tested against Gram-positive (e.g., Staphylococcus aureus, Enterococcus faecalis) and Gram-negative bacteria (e.g., Pseudomonas aeruginosa, Escherichia coli), as well as towards the yeast Candida albicans. The aforementioned extracts showed indicative MIC values, ranging from 1.61 μg/mL to 7.5 μg/mL, against the selected pathogens. Peptide fractions were further analyzed through a high-resolution mass spectrometry and database search, which identified nine novel peptides. Some discovered peptides and their derivatives were chemically synthesized and tested in vitro. The assays identified two synthetic peptides, derived from green leaves and rhizomes of P. oceanica, which revealed interesting antibiofilm activity towards S. aureus, E. coli, and P. aeruginosa (BIC50 equal to 17.7 μg/mL and 70.7 μg/mL). In addition, the natural and derivative peptides were also tested for potential cytotoxic and apoptosis-promoting effects on HepG2 cells, derived from human hepatocellular carcinomas. One natural and two synthetic peptides were proven to be effective against the "in vitro" liver cancer cell model. These novel peptides could be considered a good chemical platform for developing potential therapeutics.
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Affiliation(s)
- Diletta Punginelli
- Section of Pharmaceutical Chemistry, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy
| | - Valentina Catania
- Department of Earth and Sea Science (DiSTeM), University of Palermo, Viale delle Scienze Blg. 16, 90128 Palermo, Italy
| | - Giulia Abruscato
- Section of Cell Biology, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Blg. 16, 90128 Palermo, Italy
| | - Claudio Luparello
- Section of Cell Biology, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze Blg. 16, 90128 Palermo, Italy
| | - Mirella Vazzana
- Section of Animal Biology and Anthropology, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 18, 90123 Palermo, Italy
| | - Manuela Mauro
- Section of Animal Biology and Anthropology, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 18, 90123 Palermo, Italy
| | - Vincenzo Cunsolo
- Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Rosaria Saletti
- Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Antonella Di Francesco
- Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy
| | - Vincenzo Arizza
- Section of Animal Biology and Anthropology, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 18, 90123 Palermo, Italy
| | - Domenico Schillaci
- Section of Pharmaceutical Chemistry, Department of Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Via Archirafi 32, 90123 Palermo, Italy
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Davidoff Aguas E, Azizogli AR, Kashyap J, Dodd-o J, Siddiqui Z, Sy J, Kumar V. Rational Design of de novo CCL2 Binding Peptides. Adv Theory Simul 2023; 6:2200810. [PMID: 37122440 PMCID: PMC10139756 DOI: 10.1002/adts.202200810] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Indexed: 12/23/2022]
Abstract
Chronic levels of inflammation lead to autoimmune diseases such as rheumatoid arthritis and atherosclerosis. A key molecular mediator responsible for the progression of these diseases is Chemokine C-C motif ligand 2 (CCL2), a homodimerized cytokine that dissociates into monomeric form and binds to the CCR2 receptor. CCL2, also known as monocyte chemoattractant protein-1 (MCP-1), attracts monocytes to migrate to areas of injury and mature into macrophages, leading to positive feedback inflammation with further release of proinflammatory molecules such as IL-1β and TNF-α. Sequestering CCL2 to prevent its binding to CCR2 may prevent this inflammatory activity. Prior work adapted an α-helical CCL2-binding peptide (WKNFQTI) from murine CCR2 through extracellular loop analysis. Here, higher-affinity peptide binders were computationally designed through homology modeling and energy calculations, yielding an 11-amino acid peptide with high binding affinity. In addition, Rosetta mutations improved binding affinity in silico with blockage of the CCL2 dimerization site. Future work in analyzing binding kinetics and in vivo inflammation abrogation will confirm the accuracy of computational modeling techniques in de novo rational design of CCL2 cytokine binders.
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Affiliation(s)
| | - Abdul-Rahman Azizogli
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102
| | - Jatin Kashyap
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102
| | - Joseph Dodd-o
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102
| | - Zain Siddiqui
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102
| | - Jay Sy
- Department of Biomedical Engineering, Rutgers University, Piscataway, NJ, 08544
| | - Vivek Kumar
- Department of Biological Sciences, New Jersey Institute of Technology, Newark, NJ, 07102
- Department of Biomedical Engineering, New Jersey Institute of Technology, Newark, NJ, 07102
- Department of Chemical and Materials Engineering, New Jersey Institute of Technology, Newark, NJ, 07102
- Department of Endodontics, Rutgers School of Dental Medicine, Newark, NJ, 07103
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