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Jian T, Wang M, Hettige J, Li Y, Wang L, Gao R, Yang W, Zheng R, Zhong S, Baer MD, Noy A, De Yoreo JJ, Cai J, Chen CL. Self-Assembling and Pore-Forming Peptoids as Antimicrobial Biomaterials. ACS NANO 2024; 18:23077-23089. [PMID: 39146502 DOI: 10.1021/acsnano.4c05250] [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: 08/17/2024]
Abstract
Bacterial infections have been a serious threat to mankind throughout history. Natural antimicrobial peptides (AMPs) and their membrane disruption mechanism have generated immense interest in the design and development of synthetic mimetics that could overcome the intrinsic drawbacks of AMPs, such as their susceptibility to proteolytic degradation and low bioavailability. Herein, by exploiting the self-assembly and pore-forming capabilities of sequence-defined peptoids, we discovered a family of low-molecular weight peptoid antibiotics that exhibit excellent broad-spectrum activity and high selectivity toward a panel of clinically significant Gram-positive and Gram-negative bacterial strains, including vancomycin-resistant Enterococcus faecalis (VREF), methicillin-resistant Staphylococcus aureus (MRSA), methicillin-resistant Staphylococcus epidermidis (MRSE), Escherichia coli, Pseudomonas aeruginosa, and Klebsiella pneumoniae. Tuning the peptoid side chain chemistry and structure enabled us to tune the efficacy of antimicrobial activity. Mechanistic studies using transmission electron microscopy (TEM), bacterial membrane depolarization and lysis, and time-kill kinetics assays along with molecular dynamics simulations reveal that these peptoids kill both Gram-positive and Gram-negative bacteria through a membrane disruption mechanism. These robust and biocompatible peptoid-based antibiotics can provide a valuable tool for combating emerging drug resistance.
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Affiliation(s)
- Tengyue Jian
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Minghui Wang
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Jeevapani Hettige
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Yuhao Li
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Lei Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, China
| | - Ruixuan Gao
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Wenchao Yang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Renyu Zheng
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Shengliang Zhong
- College of Chemistry and Chemical Engineering, Jiangxi Normal University, Nanchang 330022, Jiangxi, China
| | - Marcel D Baer
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Aleksandr Noy
- Materials Science Division, Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
- School of Natural Sciences, University of California, Merced, Merced, California 95343, United States
| | - James J De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department of Materials Science and Engineering, University of Washington, Seattle, Washington 98195, United States
| | - Jianfeng Cai
- Department of Chemistry, University of South Florida, Tampa, Florida 33620, United States
| | - Chun-Long Chen
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
- Department of Chemical Engineering, University of Washington, Seattle, Washington 98195, United States
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Khavani M, Mehranfar A, Mofrad MRK. Antimicrobial peptide interactions with bacterial cell membranes. J Biomol Struct Dyn 2024:1-14. [PMID: 38263741 DOI: 10.1080/07391102.2024.2304683] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 01/06/2024] [Indexed: 01/25/2024]
Abstract
Antimicrobial peptides (AMPs) are potential alternatives for common antibiotics because of their greater activity and efficiency against a broad range of viruses, bacteria, fungi, and parasites. In this project, two antimicrobial peptides including magainin 2 and protegrin 1 with α-helix and β-sheet secondary structures were selected to investigate their interactions with different lipid bilayers such as 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoserine (POPS), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoglycerol (POPG), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphoethanolamine (POPE), POPC/POPG (7:3), POPC/POPS (7:3), POPG/POPE(1:3), and POPG/POPE(3:1). The obtained structures of the AMPs illustrated that protegrin 1 cannot maintain its secondary structure in the solution phase in contrast to magainin 2. The head groups of the lipid units play a key role in the stability of the lipid bilayers. The head parts of the lipid membranes by increasing the internal H-bond contribute to membrane compactness. The POPG and POPS units inside the POPC/POPG and POPC/POPS membranes increase the order of the POPC units. The cationic residues of the AMPs form remarkable electrostatic interactions with the negatively charged membrane surfaces, which play a key role in the stabilization process of the peptide secondary structures. The Arg residues of protegrin 1 and the Gly1, Lys4, Lys10, Lys11, Lys14, and Glu19 of the magainin 2 have the most important roles in the complexation process. The values of Gibbs binding energies (ΔG) indicate that the complexation process between AMPs and different bacterial membranes is favorable from the thermodynamic viewpoint and AMPs could form stable complexes with the lipid bilayers. As a result of ΔG values, protegrin 1 forms a more stable complex with POPG/POPE(3:1), while the α-helix has more affinity to the POPG/POPE(1:3) bacterial membranes. Therefore, it can be considered that β-sheet and α-helix AMPs are more effective against gram-positive and gram-negative bacteria, respectively. The results of this study can provide useful details about the antimicrobial peptide interactions with the bacterial cell, which can be employed for designing new antimicrobial materials with greater efficiency.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Mohammad Khavani
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California, USA
| | - Aliyeh Mehranfar
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California, USA
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California Berkeley, Berkeley, California, USA
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Konakbayeva D, Karlsson AJ. Strategies and opportunities for engineering antifungal peptides for therapeutic applications. Curr Opin Biotechnol 2023; 81:102926. [PMID: 37028003 PMCID: PMC10229436 DOI: 10.1016/j.copbio.2023.102926] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Revised: 03/01/2023] [Accepted: 03/03/2023] [Indexed: 04/09/2023]
Abstract
Antifungal peptides (AFPs) are widely described as promising prospects to treat and prevent fungal infections, though they are far less studied than their antibacterial counterparts. Although promising, AFPs have practical limitations that have hindered their use as therapeutics. Rational design and combinatorial engineering are powerful protein engineering strategies with much potential to address the limitations of AFPs by designing peptides with improved physiochemical and biological characteristics. We examine how rational design and combinatorial engineering approaches have already been used to improve the properties of AFPs and propose key opportunities for applying these strategies to push the design and application of AFPs forward.
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Affiliation(s)
- Dinara Konakbayeva
- Department of Chemical and Biomolecular Engineering, University of Maryland, 2113 Chemical and Nuclear Engineering Building (#090), 4418 Stadium Drive, College Park, MD 20742, USA
| | - Amy J Karlsson
- Department of Chemical and Biomolecular Engineering, University of Maryland, 2113 Chemical and Nuclear Engineering Building (#090), 4418 Stadium Drive, College Park, MD 20742, USA.
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Mitra S, Coopershlyak M, Li Y, Chandersekhar B, Koenig R, Chen MT, Evans B, Heinrich F, Deslouches B, Tristram-Nagle S. Novel Helical Trp- and Arg-Rich Antimicrobial Peptides Locate Near Membrane Surfaces and Rigidify Lipid Model Membranes. ADVANCED NANOBIOMED RESEARCH 2023; 3:2300013. [PMID: 37476397 PMCID: PMC10358585 DOI: 10.1002/anbr.202300013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/22/2023] Open
Abstract
Antibiotics are losing effectiveness as bacteria become resistant to conventional drugs. To find new alternatives, antimicrobial peptides (AMPs) are rationally designed with different lengths, charges, hydrophobicities (H ), and hydrophobic moments (μH ), containing only three types of amino acids: arginine, tryptophan, and valine. Six AMPs with low minimum inhibitory concentrations (MICs) and <25% toxicity to mammalian cells are selected for biophysical studies. Their secondary structures are determined using circular dichroism (CD), which finds that the % α -helicity of AMPs depends on composition of the lipid model membranes (LMMs): gram-negative (G ( - ) ) inner membrane (IM) >gram-positive (G ( + ) ) > Euk33 (eukaryotic with 33 mol% cholesterol). The two most effective peptides, E2-35 (16 amino acid [AA] residues) and E2-05 (22 AAs), are predominantly helical in G ( - ) IM and G ( + ) LMMs. AMP/membrane interactions such as membrane elasticity, chain order parameter, and location of the peptides in the membrane are investigated by low-angle and wide-angle X-ray diffuse scattering (XDS). It is found that headgroup location correlates with efficacy and toxicity. The membrane bending modulus K C displays nonmonotonic changes due to increasing concentrations of E2-35 and E2-05 in G ( - ) and G ( + ) LMMs, suggesting a bacterial killing mechanism where domain formation causes ion and water leakage.
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Affiliation(s)
- Saheli Mitra
- Biological Physics Group Physics Department Carnegie Mellon University Pittsburgh, PA 15213, USA
| | - Mark Coopershlyak
- Biological Physics Group Physics Department Carnegie Mellon University Pittsburgh, PA 15213, USA
| | - Yunshu Li
- Biological Physics Group Physics Department Carnegie Mellon University Pittsburgh, PA 15213, USA
| | - Bhairavi Chandersekhar
- Biological Physics Group Physics Department Carnegie Mellon University Pittsburgh, PA 15213, USA
| | - Rachel Koenig
- Biological Physics Group Physics Department Carnegie Mellon University Pittsburgh, PA 15213, USA
| | - Mei-Tung Chen
- Biological Physics Group Physics Department Carnegie Mellon University Pittsburgh, PA 15213, USA
| | - Brandt Evans
- Biological Physics Group Physics Department Carnegie Mellon University Pittsburgh, PA 15213, USA
| | - Frank Heinrich
- Biological Physics Group Physics Department Carnegie Mellon University Pittsburgh, PA 15213, USA
- Center for Neutron Research National Institute of Standards and Technology Gaithersburg, MD 20878, USA
| | - Berthony Deslouches
- Department of Environmental and Occupational Health University of Pittsburgh Pittsburgh, PA 15261, USA
| | - Stephanie Tristram-Nagle
- Biological Physics Group Physics Department Carnegie Mellon University Pittsburgh, PA 15213, USA
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Feng S, Park S, Choi YK, Im W. CHARMM-GUI Membrane Builder: Past, Current, and Future Developments and Applications. J Chem Theory Comput 2023; 19:2161-2185. [PMID: 37014931 PMCID: PMC10174225 DOI: 10.1021/acs.jctc.2c01246] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Indexed: 04/06/2023]
Abstract
Molecular dynamics simulations of membranes and membrane proteins serve as computational microscopes, revealing coordinated events at the membrane interface. As G protein-coupled receptors, ion channels, transporters, and membrane-bound enzymes are important drug targets, understanding their drug binding and action mechanisms in a realistic membrane becomes critical. Advances in materials science and physical chemistry further demand an atomistic understanding of lipid domains and interactions between materials and membranes. Despite a wide range of membrane simulation studies, generating a complex membrane assembly remains challenging. Here, we review the capability of CHARMM-GUI Membrane Builder in the context of emerging research demands, as well as the application examples from the CHARMM-GUI user community, including membrane biophysics, membrane protein drug-binding and dynamics, protein-lipid interactions, and nano-bio interface. We also provide our perspective on future Membrane Builder development.
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Affiliation(s)
- Shasha Feng
- Departments of Biological
Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Soohyung Park
- Departments of Biological
Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Yeol Kyo Choi
- Departments of Biological
Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
| | - Wonpil Im
- Departments of Biological
Sciences and Chemistry, Lehigh University, Bethlehem, Pennsylvania 18015, United States
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