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Abdullah SJ, Yan BTS, Palanivelu N, Dhanabal VB, Bifani JP, Bhattacharjya S. Outer-Membrane Permeabilization, LPS Transport Inhibition: Activity, Interactions, and Structures of Thanatin Derived Antimicrobial Peptides. Int J Mol Sci 2024; 25:2122. [PMID: 38396798 PMCID: PMC10888688 DOI: 10.3390/ijms25042122] [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: 01/11/2024] [Revised: 01/30/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Currently, viable antibiotics available to mitigate infections caused by drug-resistant Gram-negative bacteria are highly limited. Thanatin, a 21-residue-long insect-derived antimicrobial peptide (AMP), is a promising lead molecule for the potential development of novel antibiotics. Thanatin is extremely potent, particularly against the Enterobacter group of Gram-negative pathogens, e.g., E. coli and K. pneumoniae. As a mode of action, cationic thanatin efficiently permeabilizes the LPS-outer membrane and binds to the periplasmic protein LptAm to inhibit outer membrane biogenesis. Here, we have utilized N-terminal truncated 16- and 14-residue peptide fragments of thanatin and investigated structure, activity, and selectivity with correlating modes of action. A designed 16-residue peptide containing D-Lys (dk) named VF16 (V1PIIYCNRRT-dk-KCQRF16) demonstrated killing activity in Gram-negative bacteria. The VF16 peptide did not show any detectable toxicity to the HEK 293T cell line and kidney cell line Hep G2. As a mode of action, VF16 interacted with LPS, permeabilizing the outer membrane and binding to LptAm with high affinity. Atomic-resolution structures of VF16 in complex with LPS revealed cationic and aromatic surfaces involved in outer membrane interactions and permeabilization. Further, analyses of an inactive 14-residue native thanatin peptide (IM14: IIYCNRRTGKCQRM) delineated the requirement of the β-sheet structure in activity and target interactions. Taken together, this work would pave the way for the designing of short analogs of thanatin-based antimicrobials.
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Affiliation(s)
- Swaleeha Jaan Abdullah
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (S.J.A.); (N.P.)
| | - Bernice Tan Siu Yan
- A*Star Infectious Diseases Labs, 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
| | - Nithya Palanivelu
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (S.J.A.); (N.P.)
| | - Vidhya Bharathi Dhanabal
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (S.J.A.); (N.P.)
| | - Juan Pablo Bifani
- A*Star Infectious Diseases Labs, 8A Biomedical Grove, Immunos, Singapore 138648, Singapore
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore; (S.J.A.); (N.P.)
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Prediction of anti-inflammatory peptides by a sequence-based stacking ensemble model named AIPStack. iScience 2022; 25:104967. [PMID: 36093066 PMCID: PMC9449674 DOI: 10.1016/j.isci.2022.104967] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 08/09/2022] [Accepted: 08/12/2022] [Indexed: 11/23/2022] Open
Abstract
Accurate and efficient identification of anti-inflammatory peptides (AIPs) is crucial for the treatment of inflammation. Here, we proposed a two-layer stacking ensemble model, AIPStack, to effectively predict AIPs. At first, we constructed a new dataset for model building and validation. Then, peptide sequences were represented by hybrid features, which were fused by two amino acid composition descriptors. Next, the stacking ensemble model was constructed by random forest and extremely randomized tree as the base-classifiers and logistic regression as the meta-classifier to receive the outputs from the base-classifiers. AIPStack achieved an AUC of 0.819, accuracy of 0.755, and MCC of 0.510 on the independent set 3, which were higher than other AIP predictors. Furthermore, the essential sequence features were highlighted by the Shapley Additive exPlanation (SHAP) method. It is anticipated that AIPStack could be used for AIP prediction in a high-throughput manner and facilitate the hypothesis-driven experimental design. AIPStack model was developed for the prediction of anti-inflammatory peptides The hybrid features were used to describe the peptide sequences The proposed model AIPStack outperformed existing ones SHAP was used to highlight the essential features required for AIP prediction
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Synthetic Antimicrobial Immunomodulatory Peptides: Ongoing Studies and Clinical Trials. Antibiotics (Basel) 2022; 11:antibiotics11081062. [PMID: 36009931 PMCID: PMC9405281 DOI: 10.3390/antibiotics11081062] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 07/30/2022] [Accepted: 08/03/2022] [Indexed: 11/25/2022] Open
Abstract
The increasingly widespread antimicrobial resistance forces the search for new antimicrobial substances capable of fighting infection. Antimicrobial peptides (AMPs) and their synthetic analogs form an extensive group of compounds of great structural diversity and multifunctionality, different modes of antimicrobial action, and considerable market potential. Some AMPs, in addition to their proven antibacterial, antifungal, and antiviral activity, also demonstrate anti-inflammatory and immunomodulatory capabilities; these are called innate defense regulator (IDR) peptides. IDR peptides stimulate or inhibit the body’s immune system, e.g., by stimulating leukocyte migration to the site of infection, driving macrophage differentiation and activation, providing chemotactic action for neutrophils, degranulation and activation of mast cells, altering chemokine and cytokine production, and even induction of angiogenesis and wound healing. Such multifunctional immunomodulatory peptide molecules are currently being investigated and developed. Exploring and utilizing IDR peptides as an indirect weapon against infectious diseases could represent a completely new strategy to cope with the issue of antimicrobial resistance.
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Qin X, Zou H. The role of lipopolysaccharides in diabetic retinopathy. BMC Ophthalmol 2022; 22:86. [PMID: 35193549 PMCID: PMC8862382 DOI: 10.1186/s12886-022-02296-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Accepted: 02/03/2022] [Indexed: 11/29/2022] Open
Abstract
Diabetes mellitus (DM) is a complex metabolic syndrome characterized by hyperglycemia. Diabetic retinopathy (DR) is the most common complication of DM and the leading cause of blindness in the working-age population of the Western world. Lipopolysaccharides (LPS) is an essential ingredient of the outer membrane of gram-negative bacteria, which induces systemic inflammatory responses and cellular apoptotic changes in the host. High-level serum LPS has been found in diabetic patients at the advanced stages, which is mainly due to gut leakage and dysbiosis. In this light, increasing evidence points to a strong correlation between systemic LPS challenge and the progression of DR. Although the underlying molecular mechanisms have not been fully elucidated yet, LPS-related pathobiological events in the retina may contribute to the exacerbation of vasculopathy and neurodegeneration in DR. In this review, we focus on the involvement of LPS in the progression of DR, with emphasis on the blood-retina barrier dysfunction and dysregulated glial activation. Eventually, we summarize the recent advances in the therapeutic strategies for antagonising LPS activity, which may be introduced to DR treatment with promising clinical value.
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Affiliation(s)
- Xinran Qin
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Haidong Zou
- Department of Ophthalmology, Shanghai General Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China. .,Shanghai Eye Diseases Prevention & Treatment Center, Shanghai Eye Hospital, Shanghai, China. .,Shanghai Engineering Center for Precise Diagnosis and Treatment of Eye Diseases, Shanghai, China. .,National Clinical Research Center for Eye Diseases, Shanghai, China. .,Shanghai Key Laboratory of Fundus Diseases, Shanghai, China.
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Pape T, Hunkemöller AM, Kümpers P, Haller H, David S, Stahl K. Targeting the "sweet spot" in septic shock - A perspective on the endothelial glycocalyx regulating proteins Heparanase-1 and -2. Matrix Biol Plus 2021; 12:100095. [PMID: 34917926 PMCID: PMC8669377 DOI: 10.1016/j.mbplus.2021.100095] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 11/20/2021] [Accepted: 11/23/2021] [Indexed: 12/23/2022] Open
Abstract
Sepsis is a life-threatening syndrome caused by a pathological host response to an infection that eventually, if uncontrolled, leads to septic shock and ultimately, death. In sepsis, a massive aggregation of pathogen-associated molecular patterns (PAMPs) and damage-associated molecular patterns (DAMPs) cause a cytokine storm. The endothelial glycocalyx (eGC) is a gel like layer on the luminal side of the endothelium that consists of proteoglycans, glycosaminoglycans (GAG) and plasma proteins. It is synthesized by endothelial cells and plays an active role in the regulation of inflammation, permeability, and coagulation. In sepsis, early and profound injury of the eGC is observed and circulating eGC components correlate directly with clinical severity and outcome. The activity of the heparan sulfate (HS) specific glucuronidase Heparanase-1 (Hpa-1) is elevated in sepsis, resulting in shedding of heparan sulfate (HS), a main GAG of the eGC. HS induces endothelial barrier breakdown and accelerates systemic inflammation. Lipopolysaccharide (LPS), a PAMP mainly found on the surface of gram-negative bacteria, activates TLR-4, which results in cytokine production and further activation of Hpa-1. Hpa-1 shed HS fragments act as DAMPs themselves, leading to a vicious cycle of inflammation and end-organ dysfunction such as septic cardiomyopathy and encephalopathy. Recently, Hpa-1's natural antagonist, Heparanase-2 (Hpa-2) has been identified. It has no intrinsic enzymatic activity but instead acts by reducing inflammation. Hpa-2 levels are reduced in septic mice and patients, leading to an acquired imbalance of Hpa-1 and Hpa-2 paving the road towards a therapeutic intervention. Recently, the synthetic antimicrobial peptide 19-2.5 was described as a promising therapy protecting the eGC by inhibition of Hpa-1 activity and HS shed fragments in animal studies. However, a recombinant Hpa-2 therapy does not exist to the present time. Therapeutic plasma exchange (TPE), a modality already tested in clinical practice, effectively removes injurious mediators, e.g., Hpa-1, while replacing depleted protective molecules, e.g., Hpa-2. In critically ill patients with septic shock, TPE restores the physiological Hpa-1/Hpa-2 ratio and attenuates eGC breakdown. TPE results in a significant improvement in hemodynamic instability including reduced vasopressor requirement. Although promising, further studies are needed to determine the therapeutic impact of TPE in septic shock.
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Affiliation(s)
- Thorben Pape
- Division of Nephrology and Hypertension, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Anna Maria Hunkemöller
- Department of Medicine, Division of General Internal and Emergency Medicine, Nephrology, and Rheumatology, University Hospital Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Philipp Kümpers
- Department of Medicine, Division of General Internal and Emergency Medicine, Nephrology, and Rheumatology, University Hospital Münster, Albert-Schweitzer-Campus 1, 48149 Münster, Germany
| | - Hermann Haller
- Division of Nephrology and Hypertension, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
| | - Sascha David
- Institute of Intensive Care Medicine, University Hospital Zurich, Rämistrasse 100, 8091 Zurich, Switzerland
| | - Klaus Stahl
- Division of Nephrology and Hypertension, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany.,Division of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625 Hannover, Germany
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Luo Y, Song Y. Mechanism of Antimicrobial Peptides: Antimicrobial, Anti-Inflammatory and Antibiofilm Activities. Int J Mol Sci 2021; 22:ijms222111401. [PMID: 34768832 PMCID: PMC8584040 DOI: 10.3390/ijms222111401] [Citation(s) in RCA: 129] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/08/2021] [Accepted: 10/20/2021] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial peptides (AMPs) are regarded as a new generation of antibiotics. Besides antimicrobial activity, AMPs also have antibiofilm, immune-regulatory, and other activities. Exploring the mechanism of action of AMPs may help in the modification and development of AMPs. Many studies were conducted on the mechanism of AMPs. The present review mainly summarizes the research status on the antimicrobial, anti-inflammatory, and antibiofilm properties of AMPs. This study not only describes the mechanism of cell wall action and membrane-targeting action but also includes the transmembrane mechanism of intracellular action and intracellular action targets. It also discusses the dual mechanism of action reported by a large number of investigations. Antibiofilm and anti-inflammatory mechanisms were described based on the formation of biofilms and inflammation. This study aims to provide a comprehensive review of the multiple activities and coordination of AMPs in vivo, and to fully understand AMPs to realize their therapeutic prospect.
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Affiliation(s)
- Ying Luo
- College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
| | - Yuzhu Song
- College of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China;
- Medical College, Kunming University of Science and Technology, Kunming 650500, China
- Correspondence: ; Tel.: +86-871-65939528
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