1
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Song D, Kim B, Kim M, Lee JK, Choi J, Lee H, Shin S, Shin D, Nam HY, Lee Y, Lee S, Kim Y, Seo J. Impact of Conjugation of the Reactive Oxygen Species (ROS)-Generating Catalytic Moiety with Membrane-Active Antimicrobial Peptoids: Promoting Multitarget Mechanism and Enhancing Selectivity. J Med Chem 2024. [PMID: 39207209 DOI: 10.1021/acs.jmedchem.4c00775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/04/2024]
Abstract
Antimicrobial peptides (AMPs) represent promising therapeutic modalities against multidrug-resistant bacterial infections. As a mimic of natural AMPs, peptidomimetic oligomers like peptoids (i.e., oligo-N-substituted glycines) have been utilized for antimicrobials with resistance against proteolytic degradation. Here, we explore the conjugation of catalytic metal-binding motifs─the amino terminal Cu(II) and Ni(II) binding (ATCUN) motif─with cationic amphipathic antimicrobial peptoids to enhance their efficacy. Upon complexation with Cu(II) or Ni(II), the conjugates catalyzed hydroxyl radical generation, and 22 and 22-Cu exhibited over 10-fold improved selectivity compared to the parent peptoid, likely due to reduced hydrophobicity. Cu-ATCUN-peptoids caused bacterial membrane disruption, aggregation of intracellular biomolecules, DNA oxidation, and lipid peroxidation, promoting multiple killing mechanisms. In a mouse sepsis model, 22 demonstrated antimicrobial and anti-inflammatory efficacy with low toxicity. This study suggests a strategy to improve the potency of membrane-acting antimicrobial peptoids by incorporating ROS-generating motifs, thereby adding oxidative damage as a killing mechanism.
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Affiliation(s)
- Dasom Song
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Byeongkwon Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Minsang Kim
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Jin Kyeong Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Jieun Choi
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Hyeju Lee
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Sujin Shin
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Dongmin Shin
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Ho Yeon Nam
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Yunho Lee
- School of Earth Sciences and Environmental Engineering, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Seongsoo Lee
- Gwangju Center, Korea Basic Science Institute (KBSI), Gwangju 61751, Republic of Korea
- Department of Systems Biotechnology, Chung-Ang University, Anseong, Gyeonggi 17546, Republic of Korea
- Department of Bio-Analysis Science, University of Science & Technology, Daejeon 34113, Republic of Korea
| | - Yangmee Kim
- Department of Bioscience and Biotechnology, Konkuk University, Seoul 05029, Republic of Korea
| | - Jiwon Seo
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
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2
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Jordan O, Gan BH, Alwan S, Perron K, Sublet E, Ducret V, Ye H, Borchard G, Reymond JL, Patrulea V. Highly Potent Cationic Chitosan Derivatives Coupled to Antimicrobial Peptide Dendrimers to Combat Pseudomonas aeruginosa. Adv Healthc Mater 2024; 13:e2304118. [PMID: 38412457 DOI: 10.1002/adhm.202304118] [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: 11/22/2023] [Indexed: 02/29/2024]
Abstract
The burden of bacterial wound infections has considerably increased due to antibiotic resistance to most of the currently available antimicrobial drugs. Herein, for the first time, a chemical coupling of two cationic N-aryl (pyridyl and aminocinnamyl) chitosan derivatives to antimicrobial peptide dendrimers (AMPDs) of different generations (first, second, and third) via thioether-haloacetyl reaction is reported. The new chitosan-AMPD conjugates show high selectivity by killing Pseudomonas aeruginosa and very low toxicity toward mammalian cells, as well as extremely low hemolysis to red blood cells. Electron microscopy reveals that the new chitosan derivatives coupled to AMPD destroy both the inner and outer membranes of Gram-negative P. aeruginosa. Moreover, chitosan-AMPD conjugates show synergetic effects within extremely low concentrations. The new chitosan-AMPD conjugates can be used as potent antimicrobial therapeutic agents, to eradicate pathogens such as those present in acute and chronic infected wounds.
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Affiliation(s)
- Olivier Jordan
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1 Rue Michel Servet, Geneva, 1211, Switzerland
- Section of Pharmaceutical Sciences, University of Geneva, 1 Rue Michel Servet, Geneva, 1211, Switzerland
| | - Bee Ha Gan
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, 3012, Switzerland
| | - Sari Alwan
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1 Rue Michel Servet, Geneva, 1211, Switzerland
- Section of Pharmaceutical Sciences, University of Geneva, 1 Rue Michel Servet, Geneva, 1211, Switzerland
| | - Karl Perron
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1 Rue Michel Servet, Geneva, 1211, Switzerland
- Section of Pharmaceutical Sciences, University of Geneva, 1 Rue Michel Servet, Geneva, 1211, Switzerland
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, 30 Quai Ernest-Ansermet, Geneva, 1211, Switzerland
| | - Emmanuelle Sublet
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1 Rue Michel Servet, Geneva, 1211, Switzerland
- Section of Pharmaceutical Sciences, University of Geneva, 1 Rue Michel Servet, Geneva, 1211, Switzerland
| | - Verena Ducret
- Microbiology Unit, Department of Botany and Plant Biology, University of Geneva, 30 Quai Ernest-Ansermet, Geneva, 1211, Switzerland
| | - Hua Ye
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, OX3 7DQ, Oxford, UK
| | - Gerrit Borchard
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1 Rue Michel Servet, Geneva, 1211, Switzerland
- Section of Pharmaceutical Sciences, University of Geneva, 1 Rue Michel Servet, Geneva, 1211, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, Bern, 3012, Switzerland
| | - Viorica Patrulea
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, 1 Rue Michel Servet, Geneva, 1211, Switzerland
- Section of Pharmaceutical Sciences, University of Geneva, 1 Rue Michel Servet, Geneva, 1211, Switzerland
- Institute of Biomedical Engineering, Department of Engineering Science, University of Oxford, OX3 7DQ, Oxford, UK
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3
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Cai X, Orsi M, Capecchi A, Köhler T, van Delden C, Javor S, Reymond JL. An intrinsically disordered antimicrobial peptide dendrimer from stereorandomized virtual screening. CELL REPORTS. PHYSICAL SCIENCE 2022; 3:101161. [PMID: 36632208 PMCID: PMC9780108 DOI: 10.1016/j.xcrp.2022.101161] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 10/21/2022] [Accepted: 11/02/2022] [Indexed: 06/17/2023]
Abstract
Membrane-disruptive amphiphilic antimicrobial peptides behave as intrinsically disordered proteins by being unordered in water and becoming α-helical in contact with biological membranes. We recently discovered that synthesizing the α-helical antimicrobial peptide dendrimer L-T25 ((KL)8(KKL)4(KLL)2 KKLL) using racemic amino acids to form stereorandomized sr-T25, an analytically pure mixture of all possible diastereoisomers of L-T25, preserved antibacterial activity but abolished hemolysis and cytotoxicity, pointing to an intrinsically disordered antibacterial conformation and an α-helical cytotoxic conformation. In this study, to identify non-toxic intrinsically disordered homochiral antimicrobial peptide dendrimers (AMPDs), we surveyed sixty-three sr-analogs of sr-T25 selected by virtual screening. One of the analogs, sr-X18 ((KL)8(KLK)4(KLL)2 KLLL), lost antibacterial activity as L-enantiomer and became hemolytic due to α-helical folding. By contrast, the L- and D-enantiomers of sr-X22 ((KL)8(KL)4(KKLL)2 KLKK) were equally antibacterial, non-hemolytic, and non-toxic, implying an intrinsically disordered bioactive conformation. Screening stereorandomized libraries may be generally useful to identify or optimize intrinsically disordered bioactive peptides.
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Affiliation(s)
- Xingguang Cai
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Markus Orsi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Alice Capecchi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Thilo Köhler
- Department of Microbiology and Molecular Medicine, University of Geneva, Service of Infectious Diseases, University Hospital of Geneva, Geneva, Switzerland
| | - Christian van Delden
- Department of Microbiology and Molecular Medicine, University of Geneva, Service of Infectious Diseases, University Hospital of Geneva, Geneva, Switzerland
| | - Sacha Javor
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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4
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Synergistic effects of antimicrobial peptide dendrimer-chitosan polymer conjugates against Pseudomonas aeruginosa. Carbohydr Polym 2022; 280:119025. [PMID: 35027127 DOI: 10.1016/j.carbpol.2021.119025] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 11/19/2021] [Accepted: 12/14/2021] [Indexed: 12/20/2022]
Abstract
We report herein a new chemical platform for coupling chitosan derivatives to antimicrobial peptide dendrimers (AMPDs) with different degrees of ramification and molecular weights via thiol-maleimide reactions. Previous studies showed that simple incorporation of AMPDs to polymeric hydrogels resulted in a loss of antibacterial activity and augmented cytotoxicity to mammalian cells. We have shown that coupling AMPDs to chitosan derivatives enabled the two compounds to act synergistically. We showed that the antimicrobial activity was preserved when incorporating AMPD conjugates into various biopolymer formulations, including nanoparticles, gels, and foams. Investigating their mechanism of action using electron and time-lapse microscopy, we showed that the AMPD-chitosan conjugates were internalized after damaging outer and inner Gram-negative bacterial membranes. We also showed the absence of AMPD conjugates toxicity to mammalian cells. This chemical technological platform could be used for the development of new membrane disruptive therapeutics to eradicate pathogens present in acute and chronic wounds.
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5
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Lin L, Chi J, Yan Y, Luo R, Feng X, Zheng Y, Xian D, Li X, Quan G, Liu D, Wu C, Lu C, Pan X. Membrane-disruptive peptides/peptidomimetics-based therapeutics: Promising systems to combat bacteria and cancer in the drug-resistant era. Acta Pharm Sin B 2021; 11:2609-2644. [PMID: 34589385 PMCID: PMC8463292 DOI: 10.1016/j.apsb.2021.07.014] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 02/05/2023] Open
Abstract
Membrane-disruptive peptides/peptidomimetics (MDPs) are antimicrobials or anticarcinogens that present a general killing mechanism through the physical disruption of cell membranes, in contrast to conventional chemotherapeutic drugs, which act on precise targets such as DNA or specific enzymes. Owing to their rapid action, broad-spectrum activity, and mechanisms of action that potentially hinder the development of resistance, MDPs have been increasingly considered as future therapeutics in the drug-resistant era. Recently, growing experimental evidence has demonstrated that MDPs can also be utilized as adjuvants to enhance the therapeutic effects of other agents. In this review, we evaluate the literature around the broad-spectrum antimicrobial properties and anticancer activity of MDPs, and summarize the current development and mechanisms of MDPs alone or in combination with other agents. Notably, this review highlights recent advances in the design of various MDP-based drug delivery systems that can improve the therapeutic effect of MDPs, minimize side effects, and promote the co-delivery of multiple chemotherapeutics, for more efficient antimicrobial and anticancer therapy.
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Affiliation(s)
- Liming Lin
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- College of Pharmacy, Jinan University, Guangzhou 511443, China
| | - Jiaying Chi
- College of Pharmacy, Jinan University, Guangzhou 511443, China
| | - Yilang Yan
- College of Pharmacy, Jinan University, Guangzhou 511443, China
| | - Rui Luo
- College of Pharmacy, Jinan University, Guangzhou 511443, China
| | - Xiaoqian Feng
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
- College of Pharmacy, Jinan University, Guangzhou 511443, China
| | - Yuwei Zheng
- College of Pharmacy, Jinan University, Guangzhou 511443, China
| | - Dongyi Xian
- College of Pharmacy, Jinan University, Guangzhou 511443, China
| | - Xin Li
- The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Guilan Quan
- College of Pharmacy, Jinan University, Guangzhou 511443, China
| | - Daojun Liu
- Shantou University Medical College, Shantou 515041, China
| | - Chuanbin Wu
- College of Pharmacy, Jinan University, Guangzhou 511443, China
| | - Chao Lu
- College of Pharmacy, Jinan University, Guangzhou 511443, China
| | - Xin Pan
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou 510006, China
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6
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Li W, Separovic F, O'Brien-Simpson NM, Wade JD. Chemically modified and conjugated antimicrobial peptides against superbugs. Chem Soc Rev 2021; 50:4932-4973. [PMID: 33710195 DOI: 10.1039/d0cs01026j] [Citation(s) in RCA: 210] [Impact Index Per Article: 70.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Antimicrobial resistance (AMR) is one of the greatest threats to human health that, by 2050, will lead to more deaths from bacterial infections than cancer. New antimicrobial agents, both broad-spectrum and selective, that do not induce AMR are urgently required. Antimicrobial peptides (AMPs) are a novel class of alternatives that possess potent activity against a wide range of Gram-negative and positive bacteria with little or no capacity to induce AMR. This has stimulated substantial chemical development of novel peptide-based antibiotics possessing improved therapeutic index. This review summarises recent synthetic efforts and their impact on analogue design as well as their various applications in AMP development. It includes modifications that have been reported to enhance antimicrobial activity including lipidation, glycosylation and multimerization through to the broad application of novel bio-orthogonal chemistry, as well as perspectives on the direction of future research. The subject area is primarily the development of next-generation antimicrobial agents through selective, rational chemical modification of AMPs. The review further serves as a guide toward the most promising directions in this field to stimulate broad scientific attention, and will lead to new, effective and selective solutions for the several biomedical challenges to which antimicrobial peptidomimetics are being applied.
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Affiliation(s)
- Wenyi Li
- Melbourne Dental School, Centre for Oral Health Research, University of Melbourne, VIC 3010, Australia. and Bio21 Institute, University of Melbourne, VIC 3010, Australia
| | - Frances Separovic
- Bio21 Institute, University of Melbourne, VIC 3010, Australia and School of Chemistry, University of Melbourne, VIC 3010, Australia
| | - Neil M O'Brien-Simpson
- Melbourne Dental School, Centre for Oral Health Research, University of Melbourne, VIC 3010, Australia. and Bio21 Institute, University of Melbourne, VIC 3010, Australia
| | - John D Wade
- School of Chemistry, University of Melbourne, VIC 3010, Australia and The Florey Institute of Neuroscience and Mental Health, University of Melbourne, VIC 3010, Australia.
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7
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Gan BH, Gaynord J, Rowe SM, Deingruber T, Spring DR. The multifaceted nature of antimicrobial peptides: current synthetic chemistry approaches and future directions. Chem Soc Rev 2021; 50:7820-7880. [PMID: 34042120 PMCID: PMC8689412 DOI: 10.1039/d0cs00729c] [Citation(s) in RCA: 175] [Impact Index Per Article: 58.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Indexed: 12/13/2022]
Abstract
Bacterial infections caused by 'superbugs' are increasing globally, and conventional antibiotics are becoming less effective against these bacteria, such that we risk entering a post-antibiotic era. In recent years, antimicrobial peptides (AMPs) have gained significant attention for their clinical potential as a new class of antibiotics to combat antimicrobial resistance. In this review, we discuss several facets of AMPs including their diversity, physicochemical properties, mechanisms of action, and effects of environmental factors on these features. This review outlines various chemical synthetic strategies that have been applied to develop novel AMPs, including chemical modifications of existing peptides, semi-synthesis, and computer-aided design. We will also highlight novel AMP structures, including hybrids, antimicrobial dendrimers and polypeptides, peptidomimetics, and AMP-drug conjugates and consider recent developments in their chemical synthesis.
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Affiliation(s)
- Bee Ha Gan
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Josephine Gaynord
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Sam M Rowe
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - Tomas Deingruber
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
| | - David R Spring
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
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8
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Jafari P, Luscher A, Siriwardena T, Michetti M, Que YA, Rahme LG, Reymond JL, Raffoul W, Van Delden C, Applegate LA, Köhler T. Antimicrobial Peptide Dendrimers and Quorum-Sensing Inhibitors in Formulating Next-Generation Anti-Infection Cell Therapy Dressings for Burns. Molecules 2021; 26:molecules26133839. [PMID: 34202446 PMCID: PMC8270311 DOI: 10.3390/molecules26133839] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 06/02/2021] [Accepted: 06/12/2021] [Indexed: 12/21/2022] Open
Abstract
Multidrug resistance infections are the main cause of failure in the pro-regenerative cell-mediated therapy of burn wounds. The collagen-based matrices for delivery of cells could be potential substrates to support bacterial growth and subsequent lysis of the collagen leading to a cell therapy loss. In this article, we report the development of a new generation of cell therapy formulations with the capacity to resist infections through the bactericidal effect of antimicrobial peptide dendrimers and the anti-virulence effect of anti-quorum sensing MvfR (PqsR) system compounds, which are incorporated into their formulation. Anti-quorum sensing compounds limit the pathogenicity and antibiotic tolerance of pathogenic bacteria involved in the burn wound infections, by inhibiting their virulence pathways. For the first time, we report a biological cell therapy dressing incorporating live progenitor cells, antimicrobial peptide dendrimers, and anti-MvfR compounds, which exhibit bactericidal and anti-virulence properties without compromising the viability of the progenitor cells.
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Affiliation(s)
- Paris Jafari
- Regenerative Therapy Unit (UTR), Department of Musculoskeletal Medicine DAL, Lausanne University Hospital, 1011 Lausanne, Switzerland; (P.J.); (M.M.)
- Service of Plastic, Reconstructive & Hand Surgery, Lausanne University Hospital, 1011 Lausanne, Switzerland;
- Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, UT 84112, USA
| | - Alexandre Luscher
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland; (A.L.); (C.V.D.)
| | - Thissa Siriwardena
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland; (T.S.); (J.-L.R.)
| | - Murielle Michetti
- Regenerative Therapy Unit (UTR), Department of Musculoskeletal Medicine DAL, Lausanne University Hospital, 1011 Lausanne, Switzerland; (P.J.); (M.M.)
- Service of Plastic, Reconstructive & Hand Surgery, Lausanne University Hospital, 1011 Lausanne, Switzerland;
| | - Yok-Ai Que
- Department of Intensive Care Medicine, Inselspital, Bern University Hospital, University of Bern, 3010 Bern, Switzerland;
| | - Laurence G. Rahme
- Department of Surgery, Harvard Medical School and Massachusetts General Hospital, Boston, MA 02114, USA;
- Shriners Hospitals for Children Boston, Boston, MA 02114, USA
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, 3012 Bern, Switzerland; (T.S.); (J.-L.R.)
| | - Wassim Raffoul
- Service of Plastic, Reconstructive & Hand Surgery, Lausanne University Hospital, 1011 Lausanne, Switzerland;
| | - Christian Van Delden
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland; (A.L.); (C.V.D.)
- Division on Infectious Disease and Transplantation, University Hospital of Geneva, 1205 Geneva, Switzerland
| | - Lee Ann Applegate
- Regenerative Therapy Unit (UTR), Department of Musculoskeletal Medicine DAL, Lausanne University Hospital, 1011 Lausanne, Switzerland; (P.J.); (M.M.)
- Service of Plastic, Reconstructive & Hand Surgery, Lausanne University Hospital, 1011 Lausanne, Switzerland;
- Center for Applied Biotechnology and Molecular Medicine, University of Zurich, Winterthurerstrasse 260, 8057 Zurich, Switzerland
- Oxford OSCAR Suzhou Center, Oxford University, Suzhou 215028, China
- Correspondence: (L.A.A.); (T.K.); Tel.: +41-21-314-3510 (L.A.A.); +41-22-379-5571 (T.K.)
| | - Thilo Köhler
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland; (A.L.); (C.V.D.)
- Division on Infectious Disease and Transplantation, University Hospital of Geneva, 1205 Geneva, Switzerland
- Correspondence: (L.A.A.); (T.K.); Tel.: +41-21-314-3510 (L.A.A.); +41-22-379-5571 (T.K.)
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9
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Cai X, Javor S, Gan BH, Köhler T, Reymond JL. The antibacterial activity of peptide dendrimers and polymyxin B increases sharply above pH 7.4. Chem Commun (Camb) 2021; 57:5654-5657. [PMID: 33972964 PMCID: PMC8186529 DOI: 10.1039/d1cc01838h] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/04/2021] [Indexed: 12/25/2022]
Abstract
pH-activity profiling reveals that antimicrobial peptide dendrimers (AMPDs) kill Klebsiella pneumoniae and Methicillin-resistant Staphylococcus aureus (MRSA) at pH = 8.0, against which they are inactive at pH = 7.4, due to stronger electrostatic binding to bacterial cells at higher pH. A similar effect occurs with polymyxin B and might be general for polycationic antimicrobials.
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Affiliation(s)
- Xingguang Cai
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| | - Sacha Javor
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| | - Bee Ha Gan
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
| | - Thilo Köhler
- Department of Microbiology and Molecular Medicine, University of Geneva, Geneva, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland.
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10
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Chen S, Huang S, Li Y, Zhou C. Recent Advances in Epsilon-Poly-L-Lysine and L-Lysine-Based Dendrimer Synthesis, Modification, and Biomedical Applications. Front Chem 2021; 9:659304. [PMID: 33869146 PMCID: PMC8044885 DOI: 10.3389/fchem.2021.659304] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/02/2021] [Indexed: 12/17/2022] Open
Abstract
With the advantages in biocompatibility, antimicrobial ability, and comparative facile synthesis technology, poly-L-lysine (PLL) has received considerable attention in recent years. Different arrangement forms and structures of the backbone endow lysine-based polymers with versatile applications, especially for ε-poly-L-lysine (EPL) and lysine-based dendrimer (LBD) compounds. This review summarized the advanced development of the synthesis and modification strategies of EPL and LBD, focus on the modification of bio-synthesis and artificial synthesis, respectively. Meanwhile, biomedical fields, where EPL and LBD are mainly utilized, such as agents, adjuvants, or carriers to anti-pathogen or used in tumor or gene therapies, are also introduced. With the deeper of knowledge of pharmacodynamics and pharmacokinetics of the drug system, the design and synthesis of these drugs can be further optimized. Furthermore, the performances of combination with other advanced methodologies and technologies demonstrated that challenges, such as scale production and high expenses, will not hinder the prospective future of lysine-based polymers.
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Affiliation(s)
| | | | - Yan Li
- School of Material Science and Engineering, Tongji University, Shanghai, China
| | - Chuncai Zhou
- School of Material Science and Engineering, Tongji University, Shanghai, China
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12
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Siriwardena T, Gan BH, Köhler T, van Delden C, Javor S, Reymond JL. Stereorandomization as a Method to Probe Peptide Bioactivity. ACS CENTRAL SCIENCE 2021; 7:126-134. [PMID: 33532575 PMCID: PMC7845017 DOI: 10.1021/acscentsci.0c01135] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/24/2020] [Indexed: 06/01/2023]
Abstract
Solid-phase peptide synthesis (SPPS) is usually performed with optically pure building blocks to prepare peptides as single enantiomers. Herein we report that SPPS using racemic amino acids provides stereorandomized (sr) peptides, containing up to billions of different stereoisomers, as well-defined single HPLC peaks, single mass products with high yield, which can be used to investigate peptide bioactivity. To exemplify our method, we show that stereorandomization abolishes the membrane-disruptive effect of α-helical amphiphilic antimicrobial peptides but preserves their antibiofilm effect, implying different mechanisms involving folded versus disordered conformations. For antimicrobial peptide dendrimers by contrast, stereorandomization preserves antibacterial, membrane-disruptive, and antibiofilm effects but reduces hemolysis and cytotoxicity, thereby increasing their therapeutic index. Finally, we identify partially stereorandomized analogues of the last resort cyclic peptide antibiotic polymyxin B with preserved antibacterial activity but lacking membrane-disruptive and lipopolysaccharide-neutralizing activity, pointing to the existence of additional targets.
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Affiliation(s)
- Thissa
N. Siriwardena
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Bee-Ha Gan
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Thilo Köhler
- Department
of Microbiology and Molecular Medicine, University of Geneva, Service
of Infectious Diseases, University Hospital
of Geneva, 1211 Geneva, Switzerland
| | - Christian van Delden
- Department
of Microbiology and Molecular Medicine, University of Geneva, Service
of Infectious Diseases, University Hospital
of Geneva, 1211 Geneva, Switzerland
| | - Sacha Javor
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jean-Louis Reymond
- Department
of Chemistry and Biochemistry, University
of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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13
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Falanga A, Del Genio V, Galdiero S. Peptides and Dendrimers: How to Combat Viral and Bacterial Infections. Pharmaceutics 2021; 13:101. [PMID: 33466852 PMCID: PMC7830367 DOI: 10.3390/pharmaceutics13010101] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 01/08/2021] [Accepted: 01/12/2021] [Indexed: 12/15/2022] Open
Abstract
The alarming growth of antimicrobial resistance and recent viral pandemic events have enhanced the need for novel approaches through innovative agents that are mainly able to attach to the external layers of bacteria and viruses, causing permanent damage. Antimicrobial molecules are potent broad-spectrum agents with a high potential as novel therapeutics. In this context, antimicrobial peptides, cell penetrating peptides, and antiviral peptides play a major role, and have been suggested as promising solutions. Furthermore, dendrimers are to be considered as suitable macromolecules for the development of advanced nanosystems that are able to complement the typical properties of dendrimers with those of peptides. This review focuses on the description of nanoplatforms constructed with peptides and dendrimers, and their applications.
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Affiliation(s)
- Annarita Falanga
- Department of Agricultural Science, University of Naples “Federico II”, Via dell’Università 100, 80100 Portici, Italy
| | - Valentina Del Genio
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano 49, 80131 Naples, Italy;
| | - Stefania Galdiero
- Department of Pharmacy, University of Naples “Federico II”, Via Domenico Montesano 49, 80131 Naples, Italy;
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14
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Meng F, Liang Z, Zhao K, Luo C. Drug design targeting active posttranslational modification protein isoforms. Med Res Rev 2020; 41:1701-1750. [PMID: 33355944 DOI: 10.1002/med.21774] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/29/2020] [Accepted: 12/03/2020] [Indexed: 12/11/2022]
Abstract
Modern drug design aims to discover novel lead compounds with attractable chemical profiles to enable further exploration of the intersection of chemical space and biological space. Identification of small molecules with good ligand efficiency, high activity, and selectivity is crucial toward developing effective and safe drugs. However, the intersection is one of the most challenging tasks in the pharmaceutical industry, as chemical space is almost infinity and continuous, whereas the biological space is very limited and discrete. This bottleneck potentially limits the discovery of molecules with desirable properties for lead optimization. Herein, we present a new direction leveraging posttranslational modification (PTM) protein isoforms target space to inspire drug design termed as "Post-translational Modification Inspired Drug Design (PTMI-DD)." PTMI-DD aims to extend the intersections of chemical space and biological space. We further rationalized and highlighted the importance of PTM protein isoforms and their roles in various diseases and biological functions. We then laid out a few directions to elaborate the PTMI-DD in drug design including discovering covalent binding inhibitors mimicking PTMs, targeting PTM protein isoforms with distinctive binding sites from that of wild-type counterpart, targeting protein-protein interactions involving PTMs, and hijacking protein degeneration by ubiquitination for PTM protein isoforms. These directions will lead to a significant expansion of the biological space and/or increase the tractability of compounds, primarily due to precisely targeting PTM protein isoforms or complexes which are highly relevant to biological functions. Importantly, this new avenue will further enrich the personalized treatment opportunity through precision medicine targeting PTM isoforms.
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Affiliation(s)
- Fanwang Meng
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China.,Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Zhongjie Liang
- Center for Systems Biology, Department of Bioinformatics, School of Biology and Basic Medical Sciences, Soochow University, Suzhou, China
| | - Kehao Zhao
- School of Pharmacy, Key Laboratory of Molecular Pharmacology and Drug Evaluation (Yantai University), Ministry of Education, Collaborative Innovation Center of Advanced Drug Delivery System and Biotech Drugs in Universities of Shandong, Yantai University, Yantai, China
| | - Cheng Luo
- Drug Discovery and Design Center, the Center for Chemical Biology, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China
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15
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Gan BH, Cai X, Javor S, Köhler T, Reymond JL. Synergistic Effect of Propidium Iodide and Small Molecule Antibiotics with the Antimicrobial Peptide Dendrimer G3KL against Gram-Negative Bacteria. Molecules 2020; 25:E5643. [PMID: 33266085 PMCID: PMC7730455 DOI: 10.3390/molecules25235643] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 11/24/2020] [Accepted: 11/26/2020] [Indexed: 12/22/2022] Open
Abstract
There is an urgent need to develop new antibiotics against multidrug-resistant bacteria. Many antimicrobial peptides (AMPs) are active against such bacteria and often act by destabilizing membranes, a mechanism that can also be used to permeabilize bacteria to other antibiotics, resulting in synergistic effects. We recently showed that G3KL, an AMP with a multibranched dendritic topology of the peptide chain, permeabilizes the inner and outer membranes of Gram-negative bacteria including multidrug-resistant strains, leading to efficient bacterial killing. Here, we show that permeabilization of the outer and inner membranes of Pseudomonas aeruginosa by G3KL, initially detected using the DNA-binding fluorogenic dye propidium iodide (PI), also leads to a synergistic effect between G3KL and PI in this bacterium. We also identify a synergistic effect between G3KL and six different antibiotics against the Gram-negative Klebsiella pneumoniae, against which G3KL is inactive.
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Affiliation(s)
- Bee-Ha Gan
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (B.-H.G.); (X.C.); (S.J.)
| | - Xingguang Cai
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (B.-H.G.); (X.C.); (S.J.)
| | - Sacha Javor
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (B.-H.G.); (X.C.); (S.J.)
| | - Thilo Köhler
- Department of Microbiology and Molecular Medicine, University of Geneva, 1211 Geneva, Switzerland;
- Service of Infectious Diseases, Geneva University Hospitals, 1211 Geneva, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland; (B.-H.G.); (X.C.); (S.J.)
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16
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Alfei S, Schito AM. From Nanobiotechnology, Positively Charged Biomimetic Dendrimers as Novel Antibacterial Agents: A Review. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2022. [PMID: 33066468 PMCID: PMC7602242 DOI: 10.3390/nano10102022] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 10/07/2020] [Accepted: 10/09/2020] [Indexed: 01/27/2023]
Abstract
The alarming increase in antimicrobial resistance, based on the built-in abilities of bacteria to nullify the activity of current antibiotics, leaves a growing number of bacterial infections untreatable. An appealing approach, advanced in recent decades, concerns the development of novel agents able to interact with the external layers of bacteria, causing irreparable damage. Regarding this, some natural cationic antimicrobial peptides (CAMPs) have been reconsidered, and synthetic cationic polymers, mimicking CAMPs and able to kill bacteria by non-specific detrimental interaction with the negative bacterial membranes, have been proposed as promising solutions. Lately, also dendrimers were considered suitable macromolecules for the preparation of more advanced cationic biomimetic nanoparticles, able to harmonize the typical properties of dendrimers, including nanosize, mono-dispersion, long-term stability, high functionality, and the non-specific mechanism of action of CAMPs. Although cationic dendrimers are extensively applied in nanomedicine for drug or gene delivery, their application as antimicrobial agents is still in its infancy. The state of the art of their potential applications in this important field has therefore been reviewed here, with particular attention to the innovative case studies in the literature including also amino acid-modified polyester-based dendrimers, practically unexplored as membrane-active antimicrobials and able to kill bacteria on contact.
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Affiliation(s)
- Silvana Alfei
- Department of Pharmacy (DiFAR), University of Genoa, Viale Cembrano 4, I-16148 Genova, Italy
| | - Anna Maria Schito
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Viale Benedetto XV, 6, I-16132 Genova, Italy;
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17
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Schito AM, Alfei S. Antibacterial Activity of Non-Cytotoxic, Amino Acid-Modified Polycationic Dendrimers against Pseudomonas aeruginosa and Other Non-Fermenting Gram-Negative Bacteria. Polymers (Basel) 2020; 12:E1818. [PMID: 32823557 PMCID: PMC7464783 DOI: 10.3390/polym12081818] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/02/2020] [Accepted: 08/10/2020] [Indexed: 01/08/2023] Open
Abstract
Due to the rapid increase of antimicrobial resistance with ensuring therapeutic failures, the purpose of this study was to identify novel synthetic molecules as alternatives to conventional available, but presently ineffective antibiotics. Variously structured cationic dendrimers previously reported have provided promising outcomes. However, the problem of their cytotoxicity towards eukaryotic cells has not been completely overcome. We have now investigated the antibacterial activities of three not cytotoxic cationic dendrimers (G5Ds: G5H, G5K, and G5HK) against several multidrug-resistant (MDR) clinical strains. All G5Ds displayed remarkable activity against MDR non-fermenting Gram-negative species such as P. aeruginosa, S. maltophilia, and A. baumannii (MICs = 0.5-33.2 µM). In particular, very low MIC values (0.5-2.1 µM) were observed for G5K, which proved to be more active than the potent colistin (2.1 versus 3.19 µM) against P. aeruginosa. Concerning its mechanism of action, in time-killing and turbidimetric studies, G5K displayed a rapid non-lytic bactericidal activity. Considering the absence of cytotoxicity of these new compounds and their potency, comparable or even higher than that provided by the dendrimers previously reported, G5Ds may be proposed as promising novel antibacterial agents capable of overcoming the alarming resistance rates of several nosocomial non-fermenting Gram-negative pathogens.
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Affiliation(s)
- Anna Maria Schito
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Viale Benedetto XV, 6, I-16132 Genova, Italy;
| | - Silvana Alfei
- Department of Pharmacy (DiFAR), University of Genoa, Viale Cembrano 4, I-16148 Genova, Italy
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18
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Lin S, Liu J, Li H, Liu Y, Chen Y, Luo J, Liu S. Development of Highly Potent Carbazole Amphiphiles as Membrane-Targeting Antimicrobials for Treating Gram-Positive Bacterial Infections. J Med Chem 2020; 63:9284-9299. [DOI: 10.1021/acs.jmedchem.0c00433] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Shuimu Lin
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, P. R. China
| | - Jiayong Liu
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, P. R. China
| | - Hongxia Li
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, P. R. China
| | - Ying Liu
- Guangdong Key Laboratory of Optical Fiber Sensing and Communications, Institute of Photonics Technology, Jinan University, Guangzhou 510632, Guangdong, P. R. China
| | - Yongzhi Chen
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, P. R. China
| | - Jiachun Luo
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, P. R. China
| | - Shouping Liu
- Key Laboratory of Molecular Target & Clinical Pharmacology and the State Key Laboratory of Respiratory Disease, School of Pharmaceutical Sciences & the Fifth Affiliated Hospital, Guangzhou Medical University, Guangzhou 511436, P. R. China
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19
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Mukhopadhyay S, Bharath Prasad AS, Mehta CH, Nayak UY. Antimicrobial peptide polymers: no escape to ESKAPE pathogens-a review. World J Microbiol Biotechnol 2020; 36:131. [PMID: 32737599 PMCID: PMC7395033 DOI: 10.1007/s11274-020-02907-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 07/26/2020] [Indexed: 01/01/2023]
Abstract
Antimicrobial resistance (AMR) is one of the significant clinical challenges and also an emerging area of concern arising from nosocomial infections of ESKAPE pathogens, which has been on the rise in both the developed and developing countries alike. These pathogens/superbugs can undergo rapid mutagenesis, which helps them to generate resistance against antimicrobials in addition to the patient's non-adherence to the antibiotic regimen. Sticking to the idea of a 'one-size-fits-all' approach has led to the inappropriate administration of antibiotics resulting in augmentation of antimicrobial resistance. Antimicrobial peptides (AMPs) are the natural host defense peptides that have gained attention in the field of AMR, and recently, synthetic AMPs are well studied to overcome the drawbacks of natural counterparts. This review deals with the novel techniques utilizing the bacteriolytic activity of natural AMPs. The effective localization of these peptides onto the negatively charged bacterial surface by using nanocarriers and structurally nanoengineered antimicrobial peptide polymers (SNAPPs) owing to its smaller size and better antimicrobial activity is also described here.
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Affiliation(s)
- Songhita Mukhopadhyay
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - A S Bharath Prasad
- Department of Ageing Research, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Chetan H Mehta
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India
| | - Usha Y Nayak
- Department of Pharmaceutics, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, Karnataka, 576104, India.
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20
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Drayton M, Kizhakkedathu JN, Straus SK. Towards Robust Delivery of Antimicrobial Peptides to Combat Bacterial Resistance. Molecules 2020; 25:molecules25133048. [PMID: 32635310 PMCID: PMC7412191 DOI: 10.3390/molecules25133048] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/24/2020] [Accepted: 06/30/2020] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial peptides (AMPs), otherwise known as host defence peptides (HDPs), are naturally occurring biomolecules expressed by a large array of species across the phylogenetic kingdoms. They have great potential to combat microbial infections by directly killing or inhibiting bacterial activity and/or by modulating the immune response of the host. Due to their multimodal properties, broad spectrum activity, and minimal resistance generation, these peptides have emerged as a promising response to the rapidly concerning problem of multidrug resistance (MDR). However, their therapeutic efficacy is limited by a number of factors, including rapid degradation, systemic toxicity, and low bioavailability. As such, many strategies have been developed to mitigate these limitations, such as peptide modification and delivery vehicle conjugation/encapsulation. Oftentimes, however, particularly in the case of the latter, this can hinder the activity of the parent AMP. Here, we review current delivery strategies used for AMP formulation, focusing on methodologies utilized for targeted infection site release of AMPs. This specificity unites the improved biocompatibility of the delivery vehicle with the unhindered activity of the free AMP, providing a promising means to effectively translate AMP therapy into clinical practice.
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Affiliation(s)
- Matthew Drayton
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada;
| | - Jayachandran N. Kizhakkedathu
- Department of Pathology and Laboratory Medicine, and Centre for Blood Research, University of British Columbia, 2350 Health Sciences Mall, Life Sciences Centre, Vancouver, BC V6T 1Z3, Canada;
| | - Suzana K. Straus
- Department of Chemistry, University of British Columbia, 2036 Main Mall, Vancouver, BC V6T 1Z1, Canada;
- Correspondence: ; Tel.: +1-604-822-2537
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21
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Capecchi A, Probst D, Reymond JL. One molecular fingerprint to rule them all: drugs, biomolecules, and the metabolome. J Cheminform 2020; 12:43. [PMID: 33431010 PMCID: PMC7291580 DOI: 10.1186/s13321-020-00445-4] [Citation(s) in RCA: 127] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 06/04/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Molecular fingerprints are essential cheminformatics tools for virtual screening and mapping chemical space. Among the different types of fingerprints, substructure fingerprints perform best for small molecules such as drugs, while atom-pair fingerprints are preferable for large molecules such as peptides. However, no available fingerprint achieves good performance on both classes of molecules. RESULTS Here we set out to design a new fingerprint suitable for both small and large molecules by combining substructure and atom-pair concepts. Our quest resulted in a new fingerprint called MinHashed atom-pair fingerprint up to a diameter of four bonds (MAP4). In this fingerprint the circular substructures with radii of r = 1 and r = 2 bonds around each atom in an atom-pair are written as two pairs of SMILES, each pair being combined with the topological distance separating the two central atoms. These so-called atom-pair molecular shingles are hashed, and the resulting set of hashes is MinHashed to form the MAP4 fingerprint. MAP4 significantly outperforms all other fingerprints on an extended benchmark that combines the Riniker and Landrum small molecule benchmark with a peptide benchmark recovering BLAST analogs from either scrambled or point mutation analogs. MAP4 furthermore produces well-organized chemical space tree-maps (TMAPs) for databases as diverse as DrugBank, ChEMBL, SwissProt and the Human Metabolome Database (HMBD), and differentiates between all metabolites in HMBD, over 70% of which are indistinguishable from their nearest neighbor using substructure fingerprints. CONCLUSION MAP4 is a new molecular fingerprint suitable for drugs, biomolecules, and the metabolome and can be adopted as a universal fingerprint to describe and search chemical space. The source code is available at https://github.com/reymond-group/map4 and interactive MAP4 similarity search tools and TMAPs for various databases are accessible at http://map-search.gdb.tools/ and http://tm.gdb.tools/map4/.
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Affiliation(s)
- Alice Capecchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Daniel Probst
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland.
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22
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Adaptive and Mutational Responses to Peptide Dendrimer Antimicrobials in Pseudomonas aeruginosa. Antimicrob Agents Chemother 2020; 64:AAC.02040-19. [PMID: 32015046 PMCID: PMC7179292 DOI: 10.1128/aac.02040-19] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 01/24/2020] [Indexed: 01/15/2023] Open
Abstract
Colistin (polymyxin E) is a last-resort antibiotic against multidrug-resistant isolates of Pseudomonas aeruginosa. However, the nephro-toxicity of colistin limits its use, spurring the interest in novel antimicrobial peptides (AMP). Here, we show that the synthetic AMP-dendrimer G3KL (MW 4,531.38 Da, 15 positive charges, MIC = 8 mg/liter) showed faster killing than polymyxin B (Pmx-B) with no detectable resistance selection in P. aeruginosa strain PA14. Colistin (polymyxin E) is a last-resort antibiotic against multidrug-resistant isolates of Pseudomonas aeruginosa. However, the nephro-toxicity of colistin limits its use, spurring the interest in novel antimicrobial peptides (AMP). Here, we show that the synthetic AMP-dendrimer G3KL (MW 4,531.38 Da, 15 positive charges, MIC = 8 mg/liter) showed faster killing than polymyxin B (Pmx-B) with no detectable resistance selection in P. aeruginosa strain PA14. Spontaneous mutants selected on Pmx-B, harboring loss of function mutations in the PhoQ sensor kinase gene, showed increased Pmx-B MICs and arnB operon expression (4-amino-l-arabinose addition to lipid A), but remained susceptible to dendrimers. Two mutants carrying a missense mutation in the periplasmic loop of the PmrB sensor kinase showed increased MICs for Pmx-B (8-fold) and G3KL (4-fold) but not for the dendrimer T7 (MW 4,885.64 Da, 16 positive charges, MIC = 8 mg/liter). The pmrB mutants showed increased expression of the arnB operon as well as of the speD2-speE2-PA4775 operon, located upstream of pmrAB, and involved in polyamine biosynthesis. Exogenous supplementation with the polyamines spermine and norspermine increased G3KL and T7 MICs in a phoQ mutant background but not in the PA14 wild type. This suggests that both addition of 4-amino-l-arabinose and secretion of polyamines are required to reduce susceptibility to dendrimers, probably neutralizing the negative charges present on the lipid A and the 2-keto-3-deoxyoctulosonic acid (KDO) sugars of the lipopolysaccharide (LPS), respectively. We further show by transcriptome analysis that the dendrimers G3KL and T7 induce adaptive responses through the CprRS two-component system in PA14.
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23
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Singla P, Kaur M, Kumari A, Kumari L, Pawar SV, Singh R, Salunke DB. Facially Amphiphilic Cholic Acid-Lysine Conjugates as Promising Antimicrobials. ACS OMEGA 2020; 5:3952-3963. [PMID: 32149222 PMCID: PMC7057326 DOI: 10.1021/acsomega.9b03425] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 01/15/2020] [Indexed: 06/10/2023]
Abstract
The emergence of multidrug-resistant microbes is a significant health concern posing a constant need for new antimicrobials. Membrane-targeting antibiotics are promising candidates with reduced ability of microbes to develop resistance. In the present investigation, the principal reason behind choosing cholic acid as the crucial scaffold lies in the fact that it has a facially amphiphilic nature, which provides ample opportunity to refine the amphiphilicity by linking the amino acid lysine. A total of 16 novel amphipathic cholic acid derivatives were synthesized by sequentially linking lysine to C3-β-amino cholic acid methyl ester to maintain the hydrophobic/hydrophilic balance, which could be the essential requirement for the antimicrobial activity. Among the synthesized conjugates, a series with fluorenyl-9-methoxycarbonyl moiety attached to cholic acid via lysine linker showed promising antimicrobial activity against Staphylococcus aureus, Escherichia coli, and Candida albicans. A pronounced effect of increase in lysine residues was noted on the observed activity. The lead compounds were found to be active against drug-resistant bacterial and fungal clinical isolates and also improved the efficacy of antifungal agents amphotericin B and voriconazole. Membrane-permeability studies demonstrated the ability of these compounds to induce membrane damage in the tested microbes. The active conjugates did not show any hemolytic activity and were also found to be nontoxic to the normal cells as well as the examined cancer cell lines. The observed antimicrobial activity was attributed to the facial amphiphilic conformations, hydrophobic/hydrophilic balance, and the overall charge on the molecules.
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Affiliation(s)
- Poonam Singla
- Department
of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
| | - Mahaldeep Kaur
- Department
of Microbial Biotechnology, Panjab University, Chandigarh 160014, India
| | - Anjna Kumari
- Department
of Microbial Biotechnology, Panjab University, Chandigarh 160014, India
| | - Laxmi Kumari
- University
Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh 160014, India
| | - Sandip V. Pawar
- University
Institute of Pharmaceutical Sciences (UIPS), Panjab University, Chandigarh 160014, India
| | - Rachna Singh
- Department
of Microbial Biotechnology, Panjab University, Chandigarh 160014, India
| | - Deepak B. Salunke
- Department
of Chemistry and Centre for Advanced Studies in Chemistry, Panjab University, Chandigarh 160014, India
- National
Interdisciplinary Centre of Vaccine, Immunotherapeutics and Antimicrobials, Panjab University, Chandigarh 160014, India
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24
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Capecchi A, Zhang A, Reymond JL. Populating Chemical Space with Peptides Using a Genetic Algorithm. J Chem Inf Model 2020; 60:121-132. [PMID: 31868369 DOI: 10.1021/acs.jcim.9b01014] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In drug discovery, one uses chemical space as a concept to organize molecules according to their structures and properties. One often would like to generate new possible molecules at a specific location in the chemical space marked by a molecule of interest. Herein, we report the peptide design genetic algorithm (PDGA, code available at https://github.com/reymond-group/PeptideDesignGA ), a computational tool capable of producing peptide sequences of various topologies (linear, cyclic/polycyclic, or dendritic) in proximity of any molecule of interest in a chemical space defined by macromolecule extended atom-pair fingerprint (MXFP), an atom-pair fingerprint describing molecular shape and pharmacophores. We show that the PDGA generates high-similarity analogues of bioactive peptides with diverse peptide chain topologies and of nonpeptide target molecules. We illustrate the chemical space accessible by the PDGA with an interactive 3D map of the MXFP property space available at http://faerun.gdb.tools/ . The PDGA should be generally useful to generate peptides at any location in the chemical space.
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Affiliation(s)
- Alice Capecchi
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Alain Zhang
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland
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25
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Kozhikhova KV, Shilovskiy IP, Shatilov AA, Timofeeva AV, Turetskiy EA, Vishniakova LI, Nikolskii AA, Barvinskaya ED, Karthikeyan S, Smirnov VV, Kudlay DA, Andreev SM, Khaitov MR. Linear and dendrimeric antiviral peptides: design, chemical synthesis and activity against human respiratory syncytial virus. J Mater Chem B 2020; 8:2607-2617. [DOI: 10.1039/c9tb02485a] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Novel artificial peptides possess anti-RSV activity through a combination of two mechanisms: direct nonspecific destabilization of the viral envelope and competitive interaction with the RSV cellular receptor.
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Affiliation(s)
| | | | - Artem A. Shatilov
- NRC Institute Immunology FMBA
- Moscow
- Russian Federation
- Sechenov First Moscow State Medical University
- Moscow
| | - Anastasiia V. Timofeeva
- NRC Institute Immunology FMBA
- Moscow
- Russian Federation
- Sechenov First Moscow State Medical University
- Moscow
| | - Evgeny A. Turetskiy
- NRC Institute Immunology FMBA
- Moscow
- Russian Federation
- Sechenov First Moscow State Medical University
- Moscow
| | | | | | | | | | - Valeriy V. Smirnov
- NRC Institute Immunology FMBA
- Moscow
- Russian Federation
- Sechenov First Moscow State Medical University
- Moscow
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Zamolo SJ, Darbre T, Reymond JL. Transfecting tissue models with CRISPR/Cas9 plasmid DNA using peptide dendrimers. Chem Commun (Camb) 2020; 56:11981-11984. [DOI: 10.1039/d0cc04750c] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
A peptide dendrimer vector is shown to transfect a large CRISPR/Cas9 plasmid into 3D-tumor spheroids with exceptionally high efficiency.
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Affiliation(s)
- Susanna J. Zamolo
- Department of Chemistry and Biochemistry
- University of Bern
- Freiestrasse 3
- 3012 Bern
- Switzerland
| | - Tamis Darbre
- Department of Chemistry and Biochemistry
- University of Bern
- Freiestrasse 3
- 3012 Bern
- Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry
- University of Bern
- Freiestrasse 3
- 3012 Bern
- Switzerland
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27
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Gan BH, Siriwardena TN, Javor S, Darbre T, Reymond JL. Fluorescence Imaging of Bacterial Killing by Antimicrobial Peptide Dendrimer G3KL. ACS Infect Dis 2019; 5:2164-2173. [PMID: 31618574 DOI: 10.1021/acsinfecdis.9b00299] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
We recently discovered that peptide dendrimers such as G3KL ((KL)8(KKL)4(KKL)2KKL, K = branching l-lysine) exert strong activity against Gram-negative bacteria including Pseudomonas aeruginosa, Acinetobacter baumannii, and Escherichia coli. Herein, we report a detailed mechanistic study using fluorescence labeled analogs bearing fluorescein (G3KL-Fluo) or dansyl (G3KL-Dansyl), which show a similar bioactivity profile as G3KL. Imaging bacterial killing by super-resolution stimulated emission depletion (STED) microscopy, time-lapse imaging, and transmission electron microscopy (TEM) reveals that the dendrimer localizes at the bacterial membrane, induces membrane depolarization and permeabilization, and destroys the outer leaflet and the inner membrane. G3KL accumulates in bacteria against which it is active; however, it only weakly penetrates into eukaryotic cells without inducing significant toxicity. G3KL furthermore binds to lipopolysaccharide (LPS) and inhibits the LPS induced release of TNF-α by macrophages, similarly to polymyxin B. Taken together, these experiments show that G3KL behaves as a potent membrane disruptive antimicrobial peptide.
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Affiliation(s)
- Bee-Ha Gan
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Thissa N. Siriwardena
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Sacha Javor
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Tamis Darbre
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012 Bern, Switzerland
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Dias AP, da Silva Santos S, da Silva JV, Parise-Filho R, Igne Ferreira E, Seoud OE, Giarolla J. Dendrimers in the context of nanomedicine. Int J Pharm 2019; 573:118814. [PMID: 31759101 DOI: 10.1016/j.ijpharm.2019.118814] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/17/2019] [Accepted: 10/18/2019] [Indexed: 01/23/2023]
Abstract
Dendrimers are globular structures, presenting an initiator core, repetitive layers starting radially from the core and terminal groups on the surface, resembling tree architecture. These structures have been studied in many biological applications, as drug, DNA, RNA and proteins delivery, as well as imaging and radiocontrast agents. With reference to that, this review focused in providing examples of dendrimers used in nanomedicine. Although most studies emphasize cancer, there are others which reveal action in the neurosystem, reducing either neuroinflammation or protein aggregation. Dendrimers can carry bioactive compounds by covalent bond (dendrimer prodrug), or by ionic interaction or adsortion in the internal space of the nanostructure. Additionally, dendrimers can be associated with other polymers, as PEG (polyethylene glycol), and with targeting structures as aptamers, antibodies, folic acid and carbohydrates. Their products in preclinical/clinical trial and those in the market are also discussed, with a total of six derivatives in clinical trials and seven products available in the market.
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Affiliation(s)
- Ana Paula Dias
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo - USP, São Paulo, SP 05508-900, Brazil
| | - Soraya da Silva Santos
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo - USP, São Paulo, SP 05508-900, Brazil
| | - João Vitor da Silva
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo - USP, São Paulo, SP 05508-900, Brazil
| | - Roberto Parise-Filho
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo - USP, São Paulo, SP 05508-900, Brazil
| | - Elizabeth Igne Ferreira
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo - USP, São Paulo, SP 05508-900, Brazil
| | - Omar El Seoud
- Department of Organic Chemistry, Institute of Chemistry, University of São Paulo - USP, São Paulo, SP, Brazil
| | - Jeanine Giarolla
- Department of Pharmacy, Faculty of Pharmaceutical Sciences, University of São Paulo - USP, São Paulo, SP 05508-900, Brazil.
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29
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Bazan EL, Ruan L, Zhou C. Improving the antimicrobial efficacy against resistant Staphylococcus aureus by a combined use of conjugated oligoelectrolytes. PLoS One 2019; 14:e0224816. [PMID: 31730663 PMCID: PMC6857938 DOI: 10.1371/journal.pone.0224816] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/22/2019] [Indexed: 01/01/2023] Open
Abstract
Two membrane-intercalating conjugated oligoelectrolytes (COEs), namely COE-D8 and COE-S6, were combined to achieve enhanced antimicrobial efficacy. COE-D8 has a shorter molecular length than COE-S6 and is typical of effective antimicrobial COE molecules, presumably due to its prominent membrane disrupting function. In contrast, COE-D6 exhibits lower efficacy against bacteria and lower toxicity toward mammalian cells. Surprisingly, after supplementing 8 μM COE-S6, the minimum inhibitory concentration (MIC) of COE-D8 against methicillin-resistant Staphylococcus aureus (MRSA) was improved 8-fold, from 0.5 μM to 0.063 μM (0.050 μg mL-1). No increased toxicity toward mammalian cells was observed by the combination of COEs, as indicated by cytotoxicity measurements using the 3T3 cell line. Indeed, there is an extended ratio between the half maximal inhibitory concentration based on 3T3 cells to MIC against MRSA from 12 to greater than 256. Biophysical experiments using liposome models suggest that COE-S6 promotes the interactions between COE-D8 and lipid bilayers, which is in agreement with damages of cellular permeability and morphology, as observed by confocal microscopy and scanning electron microscopy. The application of a combined mixture of COEs further demonstrates their promising potential as a new class of antimicrobial agents with high efficacy and selectivity.
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Affiliation(s)
- Elias L. Bazan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore
| | - Lin Ruan
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore
| | - Cheng Zhou
- School of Chemical and Biomedical Engineering, Nanyang Technological University, Singapore
- Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Nanyang Technological University, Singapore
- * E-mail:
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30
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Sapra R, Verma RP, Maurya GP, Dhawan S, Babu J, Haridas V. Designer Peptide and Protein Dendrimers: A Cross-Sectional Analysis. Chem Rev 2019; 119:11391-11441. [PMID: 31556597 DOI: 10.1021/acs.chemrev.9b00153] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Dendrimers have attracted immense interest in science and technology due to their unique chemical structure that offers a myriad of opportunities for researchers. Dendritic design allows us to present peptides in a branched three-dimensional fashion that eventually leads to a globular shape, thus mimicking globular proteins. Peptide dendrimers, unlike other classes of dendrimers, have immense applications in biomedical research due to their biological origin. The diversity of potential building blocks and innumerable possibilities for design, along with the fact that the area is relatively underexplored, make peptide dendrimers sought-after candidates for various applications. This review summarizes the stepwise evolution of peptidic dendrimers along with their multifaceted applications in various fields. Further, the introduction of biomacromolecules such as proteins to a dendritic scaffold, resulting in complex macromolecules with discrete molecular weights, is an altogether new addition to the area of organic chemistry. The synthesis of highly complex and fully folded biomacromolecules on a dendritic scaffold requires expertise in synthetic organic chemistry and biology. Presently, there are only a handful of examples of protein dendrimers; we believe that these limited examples will fuel further research in this area.
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Affiliation(s)
- Rachit Sapra
- Department of Chemistry , Indian Institute of Technology Delhi , Hauz Khas , New Delhi 110016 , India
| | - Ram P Verma
- Department of Chemistry , Indian Institute of Technology Delhi , Hauz Khas , New Delhi 110016 , India
| | - Govind P Maurya
- Department of Chemistry , Indian Institute of Technology Delhi , Hauz Khas , New Delhi 110016 , India
| | - Sameer Dhawan
- Department of Chemistry , Indian Institute of Technology Delhi , Hauz Khas , New Delhi 110016 , India
| | - Jisha Babu
- Department of Chemistry , Indian Institute of Technology Delhi , Hauz Khas , New Delhi 110016 , India
| | - V Haridas
- Department of Chemistry , Indian Institute of Technology Delhi , Hauz Khas , New Delhi 110016 , India
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31
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Baeriswyl S, Javor S, Stocker A, Darbre T, Reymond J. X‐Ray Crystal Structure of a Second‐Generation Peptide Dendrimer in Complex with
Pseudomonas aeruginosa
Lectin LecB. Helv Chim Acta 2019. [DOI: 10.1002/hlca.201900178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Stéphane Baeriswyl
- Department of Chemistry and BiochemistryUniversity of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Sacha Javor
- Department of Chemistry and BiochemistryUniversity of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Achim Stocker
- Department of Chemistry and BiochemistryUniversity of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Tamis Darbre
- Department of Chemistry and BiochemistryUniversity of Bern Freiestrasse 3 3012 Bern Switzerland
| | - Jean‐Louis Reymond
- Department of Chemistry and BiochemistryUniversity of Bern Freiestrasse 3 3012 Bern Switzerland
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32
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Heitz M, Javor S, Darbre T, Reymond JL. Stereoselective pH Responsive Peptide Dendrimers for siRNA Transfection. Bioconjug Chem 2019; 30:2165-2182. [PMID: 31398014 DOI: 10.1021/acs.bioconjchem.9b00403] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Transfecting nucleic acids into cells is an essential procedure in biological research usually performed using nonviral transfection reagents. Unfortunately, most transfection reagents have polymeric or undisclosed structures and require nonstandard synthetic procedures. Herein we report peptide dendrimers accessible as pure products from standard building blocks by solid-phase peptide synthesis and acting as nontoxic single component siRNA transfection reagents for a variety of cell lines with equal or better performance than the gold standard lipofectamine L2000. Structure-activity relationships and mechanistic studies illuminate their transfection mechanism in unprecedented detail. Stereoselective dendrimer aggregation via intermolecular β-sheets at neutral pH enables siRNA complexation to form nanoparticles which enter cells by endocytosis. Endosome acidification triggers protonation of amino termini and rearrangement to an α-helical conformation forming smaller dendrimer/siRNA nanoparticles, which escape the endosome and release their siRNA cargo in the cytosol. Two particularly efficient d-enantiomeric dendrimers are proposed as new reference reagents for siRNA transfection.
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Affiliation(s)
- Marc Heitz
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Sacha Javor
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Tamis Darbre
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry , University of Bern , Freiestrasse 3 , 3012 Bern , Switzerland
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33
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Siriwardena TN, Lüscher A, Köhler T, van Delden C, Javor S, Reymond J. Antimicrobial Peptide Dendrimer Chimera. Helv Chim Acta 2019. [DOI: 10.1002/hlca.201900034] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Thissa N. Siriwardena
- Department of Chemistry and BiochemistryUniversity of Bern, Freiestrasse 3 CH-3012 Bern Switzerland
| | - Alexandre Lüscher
- Department of Microbiology and Molecular Medicine, University of Geneva, Service of Infectious DiseasesUniversity Hospital of Geneva, 4 rue Gabrielle-Perret-Gentil CH-1211 Geneva Switzerland
| | - Thilo Köhler
- Department of Microbiology and Molecular Medicine, University of Geneva, Service of Infectious DiseasesUniversity Hospital of Geneva, 4 rue Gabrielle-Perret-Gentil CH-1211 Geneva Switzerland
| | - Christian van Delden
- Department of Microbiology and Molecular Medicine, University of Geneva, Service of Infectious DiseasesUniversity Hospital of Geneva, 4 rue Gabrielle-Perret-Gentil CH-1211 Geneva Switzerland
| | - Sacha Javor
- Department of Chemistry and BiochemistryUniversity of Bern, Freiestrasse 3 CH-3012 Bern Switzerland
| | - Jean‐Louis Reymond
- Department of Chemistry and BiochemistryUniversity of Bern, Freiestrasse 3 CH-3012 Bern Switzerland
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34
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Capecchi A, Awale M, Probst D, Reymond JL. PubChem and ChEMBL beyond Lipinski. Mol Inform 2019; 38:e1900016. [PMID: 30844149 DOI: 10.1002/minf.201900016] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 02/18/2019] [Indexed: 12/13/2022]
Abstract
Seven million of the currently 94 million entries in the PubChem database break at least one of the four Lipinski constraints for oral bioavailability, 183,185 of which are also found in the ChEMBL database. These non-Lipinski PubChem (NLP) and ChEMBL (NLC) subsets are interesting because they contain new modalities that can display biological properties not accessible to small molecule drugs. Unfortunately, the current search tools in PubChem and ChEMBL are designed for small molecules and are not well suited to explore these subsets, which therefore remain poorly appreciated. Herein we report MXFP (macromolecule extended atom-pair fingerprint), a 217-D fingerprint tailored to analyze large molecules in terms of molecular shape and pharmacophores. We implement MXFP in two web-based applications, the first one to visualize NLP and NLC interactively using Faerun (http://faerun.gdb.tools/), the second one to perform MXFP nearest neighbor searches in NLP and NLC (http://similaritysearch.gdb.tools/). We show that these tools provide a meaningful insight into the diversity of large molecules in NLP and NLC. The interactive tools presented here are publicly available at http://gdb.unibe.ch and can be used freely to explore and better understand the diversity of non-Lipinski molecules in PubChem and ChEMBL.
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Affiliation(s)
- Alice Capecchi
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Mahendra Awale
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Daniel Probst
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
| | - Jean-Louis Reymond
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, 3012, Bern, Switzerland
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35
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Yadav K, Kumar S, Mishra D, Asad M, Mitra M, Yavvari PS, Gupta S, Vedantham M, Ranga P, Komalla V, Pal S, Sharma P, Kapil A, Singh A, Singh N, Srivastava A, Thukral L, Bajaj A. Deciphering the Role of Intramolecular Networking in Cholic Acid–Peptide Conjugates on the Lipopolysaccharide Surface in Combating Gram-Negative Bacterial Infections. J Med Chem 2019; 62:1875-1886. [DOI: 10.1021/acs.jmedchem.8b01357] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Kavita Yadav
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Sandeep Kumar
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
- Manipal Academy of Higher Education, Manipal 576104, Karnataka, India
| | - Deepakkumar Mishra
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Mohammad Asad
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Madhurima Mitra
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Prabhu S. Yavvari
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal 462030, Madhya Pradesh, India
| | - Siddhi Gupta
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Madhukar Vedantham
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Pavit Ranga
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Varsha Komalla
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Sanjay Pal
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
- Kalinga Institute of Industrial Technology, Bhubaneswar 751024, Odisha, India
| | - Priyanka Sharma
- Department of Microbiology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Arti Kapil
- Department of Microbiology, All India Institute of Medical Sciences, Ansari Nagar, New Delhi 110029, India
| | - Archana Singh
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Nirpendra Singh
- Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
| | - Aasheesh Srivastava
- Department of Chemistry, Indian Institute of Science Education and Research, Bhopal 462030, Madhya Pradesh, India
| | - Lipi Thukral
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, New Delhi 110025, India
| | - Avinash Bajaj
- Laboratory of Nanotechnology and Chemical Biology, Regional Centre for Biotechnology, 3rd Milestone Faridabad-Gurgaon Expressway, NCR Biotech Science Cluster, Faridabad 121001, Haryana, India
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