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Apud GR, Kristof I, Ledesma SC, Stivala MG, Aredes Fernandez PA. Health-promoting peptides in fermented beverages. Rev Argent Microbiol 2024:S0325-7541(24)00022-1. [PMID: 38599912 DOI: 10.1016/j.ram.2024.02.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 11/15/2023] [Accepted: 02/03/2024] [Indexed: 04/12/2024] Open
Abstract
Since ancient times, the consumption of fermented low-alcoholic beverages has enjoyed widespread popularity in various countries, because of their distinct flavors and health benefits. Several studies have demonstrated that light to moderate alcohol consumption is associated with beneficial effects on human health, mainly in cardiovascular disease prevention. Fermented beverages have different non-ethanol components that confer beneficial health effects. These bioactive compounds are mainly peptides that have often been overlooked or poorly explored in numerous fermented beverages. The aim of this review is to provide knowledge and generate interest in the biological activities of peptides that are present and/or released during the fermentation process of widely consumed traditional fermented beverages. Additionally, a brief description of the microorganisms involved in these beverages is provided. Furthermore, this review also explores topics related to the detection, isolation, and identification of peptides, addressing the structure-activity relationships of both antioxidant and angiotensin-converting enzyme inhibitory (ACE-I) activities.
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Affiliation(s)
- Gisselle Raquel Apud
- Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 491, 4000 San Miguel de Tucumán, Argentina
| | - Irina Kristof
- Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 491, 4000 San Miguel de Tucumán, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Silvana Cecilia Ledesma
- Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 491, 4000 San Miguel de Tucumán, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Maria Gilda Stivala
- Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 491, 4000 San Miguel de Tucumán, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina
| | - Pedro Adrian Aredes Fernandez
- Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 491, 4000 San Miguel de Tucumán, Argentina; Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Argentina.
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Saini S, Rathore A, Sharma S, Saini A. Exploratory data analysis of physicochemical parameters of natural antimicrobial and anticancer peptides: Unraveling the patterns and trends for the rational design of novel peptides. BIOIMPACTS : BI 2023; 14:26438. [PMID: 38327633 PMCID: PMC10844588 DOI: 10.34172/bi.2023.26438] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 11/04/2022] [Accepted: 12/04/2022] [Indexed: 02/09/2024]
Abstract
Introduction Peptide-based research has attained new avenues in the antibiotics and cancer drug resistance era. The basis of peptide design research lies in playing with or altering physicochemical parameters. Here in this work, we have done exploratory data analysis (EDA) of physicochemical parameters of antimicrobial peptides (AMPs) and anticancer peptides (ACPs), two promising therapeutics for microbial and cancer drug resistance to deduce patterns and trends. Methods Briefly, we have captured the natural AMPs and ACPs data from the APD3 database. After cleaning the data manually and by CD-HIT web server, further data analysis has been done using Python-based packages, modlAMP and Pandas. We have extracted the descriptive statistics of 10 physicochemical parameters of AMPs and ACPs to build a comprehensive dataset containing all major parameters. The global analysis of datasets has been done using modlAMP to find the initial patterns in global data. The subsets of AMPs and ACPs were curated based on the length of the peptides and were analyzed by Pandas package to deduce the graphical profile of AMPs and ACPs. Results EDA of AMPs and ACPs shows selectivity in the length and amino acid compositions. The distribution of physicochemical parameters in defined quartile ranges was observed in the descriptive statistical and graphical analysis. The preferred length range of AMPs and ACPs was found to be 21-30 amino acids, whereas few outliers in each parameter were evident after EDA analysis. Conclusion The derived patterns from natural AMPs and ACPs can be used for the rational design of novel peptides. The statistical and graphical data distribution findings will help in combining the different parameters for potent design of novel AMPs and ACPs.
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Affiliation(s)
- Sandeep Saini
- Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India
- Department of Bioinformatics, Goswami Ganesh Dutta Sanatan Dharma College, Sector 32-C, Chandigarh 160030, India
| | - Aayushi Rathore
- Institute of Bioinformatics and Applied Biotechnology, Biotech Park, Bengaluru 560100, India
| | - Sheetal Sharma
- Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India
| | - Avneet Saini
- Department of Biophysics, Panjab University, Sector 25, Chandigarh 160014, India
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van Dijk A, Guabiraba R, Bailleul G, Schouler C, Haagsman HP, Lalmanach AC. Evolutionary diversification of defensins and cathelicidins in birds and primates. Mol Immunol 2023; 157:53-69. [PMID: 36996595 DOI: 10.1016/j.molimm.2023.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 03/09/2023] [Accepted: 03/14/2023] [Indexed: 03/30/2023]
Abstract
Divergent evolution for more than 310 million years has resulted in an avian immune system that is complex and more compact than that of primates, sharing much of its structure and functions. Not surprisingly, well conserved ancient host defense molecules, such as defensins and cathelicidins, have diversified over time. In this review, we describe how evolution influenced the host defense peptides repertoire, its distribution, and the relationship between structure and biological functions. Marked features of primate and avian HDPs are linked to species-specific characteristics, biological requirements, and environmental challenge.
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El-Beltagi HS, El-Sayed SM, Abdelhamid AN, Hassan KM, Elshalakany WA, Nossier MI, Alabdallah NM, Al-Harbi NA, Al-Qahtani SM, Darwish DBE, Abbas ZK, Ibrahim HA. Potentiating Biosynthesis of Alkaloids and Polyphenolic Substances in Catharanthus roseus Plant Using ĸ-Carrageenan. Molecules 2023; 28:molecules28083642. [PMID: 37110876 PMCID: PMC10143362 DOI: 10.3390/molecules28083642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/17/2023] [Accepted: 04/19/2023] [Indexed: 04/29/2023] Open
Abstract
Catharanthus roseus is a medicinal plant that produces indole alkaloids, which are utilized in anticancer therapy. Vinblastine and vincristine, two commercially important antineoplastic alkaloids, are mostly found in the leaves of Catharanthus roseus. ĸ-carrageenan has been proven as plant growth promoting substance for a number of medicinal and agricultural plants. Considering the importance of ĸ-carrageenan as a promoter of plant growth and phytochemical constituents, especially alkaloids production in Catharanthus roseus, an experiment was carried out to explore the effect of ĸ-carrageenan on the plant growth, phytochemicals content, pigments content, and production of antitumor alkaloids in Catharanthus roseus after planting. Foliar application of ĸ-carrageenan (at 0, 400, 600 and 800 ppm) significantly improved the performance of Catharanthus roseus. Phytochemical analysis involved determining the amount of total phenolics (TP), flavonoids (F), free amino acids (FAA), alkaloids (TAC) and pigments contents by spectrophotometer, minerals by ICP, amino acids, phenolic compounds and alkaloids (Vincamine, Catharanthine, Vincracine (Vincristine), and vinblastine) analysis uses HPLC. The results indicated that all examined ĸ-carrageenan treatments led to a significant (p ≤ 0.05) increase in growth parameters compared to the untreated plants. Phytochemical examination indicates that the spray of ĸ-carrageenan at 800 mg L-1 increased the yield of alkaloids (Vincamine, Catharanthine and Vincracine (Vincristine)) by 41.85 μg/g DW, total phenolic compounds by 3948.6 μg gallic/g FW, the content of flavonoids 951.3 μg quercetin /g FW and carotenoids content 32.97 mg/g FW as compared to the control. An amount of 400 ppm ĸ-carrageenan treatment gave the best contents of FAA, Chl a, Chl b and anthocyanin. The element content of K, Ca, Cu, Zn and Se increased by treatments. Amino acids constituents and phenolics compounds contents were altered by ĸ-carrageenan.
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Affiliation(s)
- Hossam S El-Beltagi
- Agricultural Biotechnology Department, College of Agriculture and Food Sciences, King Faisal University, Al-Ahsa 31982, Saudi Arabia
- Biochemistry Department, Faculty of Agriculture, Cairo University, Giza 12613, Egypt
| | - Salwa M El-Sayed
- Department of Biochemistry, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt
| | - Ahmed N Abdelhamid
- Department of Horticulture, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt
| | - Karim M Hassan
- Department of Horticulture, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt
| | - Walaa A Elshalakany
- Department of Biochemistry, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt
| | - Mona Ibrahim Nossier
- Soil and Water Department, Faculty of Agriculture 11241, Ain Shams University, Cairo 11566, Egypt
| | - Nadiyah M Alabdallah
- Department of Biology, College of Science, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
- Basic & Applied Scientific Research Centre, Imam Abdulrahman Bin Faisal University, P.O. Box 1982, Dammam 31441, Saudi Arabia
| | - Nadi Awad Al-Harbi
- Biology Department, University College of Tayma, University of Tabuk, Tabuk 47512, Saudi Arabia
| | - Salem Mesfir Al-Qahtani
- Biology Department, University College of Tayma, University of Tabuk, Tabuk 47512, Saudi Arabia
| | - Doaa Bahaa Eldin Darwish
- Biology department, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
- Botany Department, Faculty of Science, Mansoura University, Mansoura 35511, Egypt
| | - Zahid Khorshid Abbas
- Biology department, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Hemmat A Ibrahim
- Department of Biochemistry, Faculty of Agriculture, Ain Shams University, Cairo 11566, Egypt
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Sheehan FK, Wang H, Podbevšek D, Naranjo E, Rivera-Cancel J, Moran C, Ulijn RV, Chen X. Aromatic Zipper Topology Dictates Water-Responsive Actuation in Phenylalanine-Based Crystals. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023:e2207773. [PMID: 36971275 DOI: 10.1002/smll.202207773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/28/2023] [Indexed: 06/18/2023]
Abstract
Water-responsive (WR) materials that reversibly deform in response to relative humidity (RH) changes are gaining increasing interest for their potential in energy harvesting and soft robotics applications. Despite progress, there are significant gaps in the understanding of how supramolecular structure underpins the reconfiguration and performance of WR materials. Here, three crystals are compared based on the amino acid phenylalanine (F) that contain water channels and F packing domains that are either layered (F), continuously connected (phenylalanyl-phenylalanine, FF), or isolated (histidyl-tyrosyl-phenylalanine, HYF). Hydration-induced reconfiguration is analyzed through changes in hydrogen-bond interactions and aromatic zipper topology. F crystals show the greatest WR deformation (WR energy density of 19.8 MJ m-3 ) followed by HYF (6.5 MJ m-3 ), while FF exhibits no observable response. The difference in water-responsiveness strongly correlates to the deformability of aromatic regions, with FF crystals being too stiff to deform, whereas HYF is too soft to efficiently transfer water tension to external loads. These findings reveal aromatic topology design rules for WR crystals and provide insight into general mechanisms of high-performance WR actuation. Moreover, the best-performing crystal, F emerges as an efficient WR material for applications at scale and low cost.
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Affiliation(s)
- Fahmeed K Sheehan
- Advanced Science Research Center (ASRC) at the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave, New York, NY, 10016, USA
- Department of Chemistry, Hunter College, 695 Park Ave, New York, NY, 10065, USA
| | - Haozhen Wang
- Advanced Science Research Center (ASRC) at the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, 365 5th Ave, New York, NY, 10016, USA
| | - Darjan Podbevšek
- Advanced Science Research Center (ASRC) at the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA
| | - Elma Naranjo
- Advanced Science Research Center (ASRC) at the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA
- Department of Chemical Engineering, The City College of New York, 275 Convent Ave, New York, NY, 10031, USA
| | - Janel Rivera-Cancel
- Advanced Science Research Center (ASRC) at the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave, New York, NY, 10016, USA
| | - Cooper Moran
- Department of Chemistry, Hunter College, 695 Park Ave, New York, NY, 10065, USA
| | - Rein V Ulijn
- Advanced Science Research Center (ASRC) at the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave, New York, NY, 10016, USA
- Department of Chemistry, Hunter College, 695 Park Ave, New York, NY, 10065, USA
| | - Xi Chen
- Advanced Science Research Center (ASRC) at the Graduate Center of the City University of New York, 85 St. Nicholas Terrace, New York, NY, 10031, USA
- Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave, New York, NY, 10016, USA
- Ph.D. Program in Physics, The Graduate Center of the City University of New York, 365 5th Ave, New York, NY, 10016, USA
- Department of Chemical Engineering, The City College of New York, 275 Convent Ave, New York, NY, 10031, USA
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Integrated Transcriptome and Metabolome Analysis of Rice Leaves Response to High Saline-Alkali Stress. Int J Mol Sci 2023; 24:ijms24044062. [PMID: 36835473 PMCID: PMC9960601 DOI: 10.3390/ijms24044062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 02/11/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
Rice (Oryza sativa) is one of the most important crops grown worldwide, and saline-alkali stress seriously affects the yield and quality of rice. It is imperative to elucidate the molecular mechanisms underlying rice response to saline-alkali stress. In this study, we conducted an integrated analysis of the transcriptome and metabolome to elucidate the effects of long-term saline-alkali stress on rice. High saline-alkali stress (pH > 9.5) induced significant changes in gene expression and metabolites, including 9347 differentially expressed genes (DEGs) and 693 differentially accumulated metabolites (DAMs). Among the DAMs, lipids and amino acids accumulation were greatly enhanced. The pathways of the ABC transporter, amino acid biosynthesis and metabolism, glyoxylate and dicarboxylate metabolism, glutathione metabolism, TCA cycle, and linoleic acid metabolism, etc., were significantly enriched with DEGs and DAMs. These results suggest that the metabolites and pathways play important roles in rice's response to high saline-alkali stress. Our study deepens the understanding of mechanisms response to saline-alkali stress and provides references for molecular design breeding of saline-alkali resistant rice.
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Zhao Y, Yuan Z, Wang S, Wang H, Chao Y, Sederoff RR, Sederoff H, Yan H, Pan J, Peng M, Wu D, Borriss R, Niu B. Gene sdaB Is Involved in the Nematocidal Activity of Enterobacter ludwigii AA4 Against the Pine Wood Nematode Bursaphelenchus xylophilus. Front Microbiol 2022; 13:870519. [PMID: 35602027 PMCID: PMC9121001 DOI: 10.3389/fmicb.2022.870519] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 03/25/2022] [Indexed: 11/13/2022] Open
Abstract
Bursaphelenchus xylophilus, a plant parasitic nematode, is the causal agent of pine wilt, a devastating forest tree disease. Essentially, no efficient methods for controlling B. xylophilus and pine wilt disease have yet been developed. Enterobacter ludwigii AA4, isolated from the root of maize, has powerful nematocidal activity against B. xylophilus in a new in vitro dye exclusion test. The corrected mortality of the B. xylophilus treated by E. ludwigii AA4 or its cell extract reached 98.3 and 98.6%, respectively. Morphological changes in B. xylophilus treated with a cell extract from strain AA4 suggested that the death of B. xylophilus might be caused by an increased number of vacuoles in non-apoptotic cell death and the damage to tissues of the nematodes. In a greenhouse test, the disease index of the seedlings of Scots pine (Pinus sylvestris) treated with the cells of strain AA4 plus B. xylophilus or those treated by AA4 cell extract plus B. xylophilus was 38.2 and 30.3, respectively, was significantly lower than 92.5 in the control plants treated with distilled water and B. xylophilus. We created a sdaB gene knockout in strain AA4 by deleting the gene that was putatively encoding the beta-subunit of L-serine dehydratase through Red homologous recombination. The nematocidal and disease-suppressing activities of the knockout strain were remarkably impaired. Finally, we revealed a robust colonization of P. sylvestris seedling needles by E. ludwigii AA4, which is supposed to contribute to the disease-controlling efficacy of strain AA4. Therefore, E. ludwigii AA4 has significant potential to serve as an agent for the biological control of pine wilt disease caused by B. xylophilus.
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Affiliation(s)
- Yu Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zhibo Yuan
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Shuang Wang
- Administrative Office of the Summer Palace, Beijing Municipal Administration Center of Parks, Beijing, China
| | - Haoyu Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Yanjie Chao
- The Center for Microbes, Development and Health (CMDH), Institut Pasteur of Shanghai, Chinese Academy of Sciences, Shanghai, China
| | - Ronald R. Sederoff
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Heike Sederoff
- Department of Plant and Microbial Biology, North Carolina State University, Raleigh, NC, United States
| | - He Yan
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang, China
| | - Jialiang Pan
- Center for Biological Disaster Prevention and Control, National Forestry and Grassland Administration, Shenyang, China
| | - Mu Peng
- College of Biological Science and Technology, Hubei Minzu University, Enshi, China
| | - Di Wu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Rainer Borriss
- Nord Reet UG, Greifswald, Germany
- Institute of Marine Biotechnology e.V. (IMaB), Greifswald, Germany
- *Correspondence: Rainer Borriss,
| | - Ben Niu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
- Ben Niu,
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Guo J, Lu X, Tao Y, Guo H, Min W. Comparative Ionomics and Metabolic Responses and Adaptive Strategies of Cotton to Salt and Alkali Stress. FRONTIERS IN PLANT SCIENCE 2022; 13:871387. [PMID: 35548284 PMCID: PMC9084190 DOI: 10.3389/fpls.2022.871387] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 03/30/2022] [Indexed: 05/27/2023]
Abstract
Soil salinization and alkalization severely inhibit agriculture. However, the response mechanisms of cotton to salt stress or alkali stress are unclear. Ionomics and metabolomics were used to investigate salt and alkali stresses in cotton roots and leaves. Compared with the control, salt-treated and alkali-treated cotton plants showed 51.8 and 53.0% decreases in biomass, respectively. Under salt stress, the concentration of N decreased in roots but increased in leaves, and the concentrations of P and K increased in roots but decreased in leaves. Salt stress inhibited Ca, B, N, and Fe uptake and Mg, K, P, S, and Cu transport, but promoted Mo, Mn, Zn, Mg, K, P, S, and Cu uptake and Mo, Mn, Zn, B, N, and Fe transport. Under alkali stress, the concentrations of N and P in roots and leaves decreased, while the concentrations of K in roots and leaves increased. Alkali stress inhibited P, Ca, S, N, Fe, and Zn uptake and N, P, Mg and B transport, but promoted K, Mn, Cu, Mo, Mg, and B uptake and K, Mn, Cu, Mo, Fe, and Zn transport. Under salt stress in the leaves, 93 metabolites increased, mainly organic acids, amino acids, and sugars, increased in abundance, while 6 decreased. In the roots, 72 metabolites increased, mainly amino acids, organic acids, and sugars, while 18 decreased. Under alkali stress, in the leaves, 96 metabolites increased, including organic acids, amino acids, and sugars, 83 metabolites decreased, including organic acids, amino acids, and sugars; In the roots, 108 metabolites increased, including organic acids, amino acids, and sugars. 83 metabolites decreased, including organic acids and amino acids. Under salt stress, cotton adapts to osmotic stress through the accumulation of organic acids, amino acids and sugars, while under alkali stress, osmoregulation was achieved via inorganic ion accumulation. Under salt stress, significant metabolic pathways in the leaves and roots were associated with amino acid and organic acid metabolism, sugar metabolism was mainly used as a source of energy, while under alkali stress, the pathways in the leaves were related to amino acid and linoleic acid metabolism, β-Oxidation, TCA cycle, and glycolysis were enhanced to provide the energy needed for life activities. Enhancing organic acid accumulation and metabolism in the roots is the key response mechanism of cotton to alkalinity.
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Affiliation(s)
| | | | | | | | - Wei Min
- Department of Resources and Environmental Science, Shihezi University, Shihezi, China
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Atomic-Resolution Structures and Mode of Action of Clinically Relevant Antimicrobial Peptides. Int J Mol Sci 2022; 23:ijms23094558. [PMID: 35562950 PMCID: PMC9100274 DOI: 10.3390/ijms23094558] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/18/2022] [Accepted: 04/18/2022] [Indexed: 02/01/2023] Open
Abstract
Global rise of infections and deaths caused by drug-resistant bacterial pathogens are among the unmet medical needs. In an age of drying pipeline of novel antibiotics to treat bacterial infections, antimicrobial peptides (AMPs) are proven to be valid therapeutics modalities. Direct in vivo applications of many AMPs could be challenging; however, works are demonstrating encouraging results for some of them. In this review article, we discussed 3-D structures of potent AMPs e.g., polymyxin, thanatin, MSI, protegrin, OMPTA in complex with bacterial targets and their mode of actions. Studies on human peptide LL37 and de novo-designed peptides are also discussed. We have focused on AMPs which are effective against drug-resistant Gram-negative bacteria. Since treatment options for the infections caused by super bugs of Gram-negative bacteria are now extremely limited. We also summarize some of the pertinent challenges in the field of clinical trials of AMPs.
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Mohid SA, Sharma P, Alghalayini A, Saini T, Datta D, Willcox MD, Ali H, Raha S, Singha A, Lee D, Sahoo N, Cranfield CG, Roy S, Bhunia A. A rationally designed synthetic antimicrobial peptide against Pseudomonas-associated corneal keratitis: Structure-function correlation. Biophys Chem 2022; 286:106802. [DOI: 10.1016/j.bpc.2022.106802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/10/2022] [Accepted: 03/15/2022] [Indexed: 11/02/2022]
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Sinha S, Dhanabal VB, Sperandeo P, Polissi A, Bhattacharjya S. Linking dual mode of action of host defense antimicrobial peptide thanatin: Structures, lipopolysaccharide and LptA m binding of designed analogs. BIOCHIMICA ET BIOPHYSICA ACTA. BIOMEMBRANES 2022; 1864:183839. [PMID: 34915021 DOI: 10.1016/j.bbamem.2021.183839] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 12/02/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
At present, antibiotics options to cure infections caused by drug resistant Gram-negative pathogens are highly inadequate. LPS outer membrane, proteins involved in LPS transport and biosynthesis pathways are vital targets. Thanatin, an insect derived 21-residue long antimicrobial peptide may be exploited for the development of effective antibiotics against Gram-negative bacteria. As a mode of bacterial cell killing, thanatin disrupts LPS outer membrane and inhibits LPS transport by binding to the periplasmic protein LptAm. Here, we report structure-activity correlation of thanatin and analogs for the purpose of rational design. These analogs of thanatin are investigated, by NMR, ITC and fluorescence, to correlate structure, antibacterial activity and binding with LPS and LptAm, a truncated monomeric variant. Our results demonstrate that an analog thanatin M21F exhibits superior antibacterial activity. In LPS interaction analyses, thanatin M21F demonstrate high affinity binding to outer membrane LPS. The atomic resolution structure of thanatin M21F in LPS micelle reveals four stranded β-sheet structure in a dimeric topology whereby the sidechain of aromatic residues Y10, F21 sustained mutual packing at the interface. Strikingly, LptAm binding affinity of thanatin M21F has been significantly increased with an estimated Kd ~ 0.73 nM vs 13 nM for thanatin. Further, atomic resolution structures and interactions of Ala based thanatin analogs define plausible correlations with antibacterial activity and LPS, LptAm interactions. Taken together, the current work provides a frame-work for the designing of thanatin based potent antimicrobial peptides for the treatment of drug resistance Gram-negative bacteria.
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Affiliation(s)
- Sheetal Sinha
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore; Interdisciplinary Graduate School, Nanyang Technological University, 50 Nanyang Avenue, Singapore 639798, Singapore; Advanced Environmental Biotechnology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, 1 Cleantech Loop, Singapore 637141, Singapore
| | - Vidhya Bharathi Dhanabal
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore
| | - Paola Sperandeo
- Dept. of Pharmacological and Biomolecular Sciences, University of Milano, Via Balzaretti 9, 20133 Milano, Italy
| | - Alessandra Polissi
- Dept. of Pharmacological and Biomolecular Sciences, University of Milano, Via Balzaretti 9, 20133 Milano, Italy
| | - Surajit Bhattacharjya
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551, Singapore.
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12
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Biswas K, Bhunia A. Probing the Functional Interaction Interface of Lipopolysaccharide and Antimicrobial Peptides: A Solution-State NMR Perspective. Methods Mol Biol 2022; 2548:211-231. [PMID: 36151500 DOI: 10.1007/978-1-0716-2581-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Antimicrobial peptides (AMPs) have been a topic of substantial research as the next-generation antibiotics. They have been extensively studied for the selectivity and action against microbial membrane lipids in imparting their targeted functioning. To determine the effectivity of the peptides against the Gram-negative pathogens, it is imperative to elucidate their role in interacting with the lipopolysaccharide moieties. Lipopolysaccharide is a major component of the outer membrane of the Gram-negative bacteria. It serves to protect the bacteria as well as govern the functionality of several antibacterial agents. It can prevent the access of the agents into the inner membrane of the bacteria, thus rendering them inactive. Several techniques have been employed to study the interaction for better designing of peptides; NMR spectroscopy is one of the most widely used techniques in determining the interactive properties of peptides with LPS as it can provide the details in atomistic level. NMR spectroscopy provides information about the structural and conformational changes as well as the dynamics of the interactions.
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Affiliation(s)
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, Kolkata, India.
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13
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Erdem Büyükkiraz M, Kesmen Z. Antimicrobial peptides (AMPs): A promising class of antimicrobial compounds. J Appl Microbiol 2021; 132:1573-1596. [PMID: 34606679 DOI: 10.1111/jam.15314] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 08/26/2021] [Accepted: 09/17/2021] [Indexed: 12/13/2022]
Abstract
Antimicrobial peptides (AMPs) are compounds, which have inhibitory activity against microorganisms. In the last decades, AMPs have become powerful alternative agents that have met the need for novel anti-infectives to overcome increasing antibiotic resistance problems. Moreover, recent epidemics and pandemics are increasing the popularity of AMPs, due to the urgent necessity for effective antimicrobial agents in combating the new emergence of microbial diseases. AMPs inhibit a wide range of microorganisms through diverse and special mechanisms by targeting mainly cell membranes or specific intracellular components. In addition to extraction from natural sources, AMPs are produced in various hosts using recombinant methods. More recently, the synthetic analogues of AMPs, designed with some modifications, are predicted to overcome the limitations of stability, toxicity and activity associated with natural AMPs. AMPs have potential applications as antimicrobial agents in food, agriculture, environment, animal husbandry and pharmaceutical industries. In this review, we have provided an overview of the structure, classification and mechanism of action of AMPs, as well as discussed opportunities for their current and potential applications.
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Affiliation(s)
- Mine Erdem Büyükkiraz
- School of Health Sciences, Department of Nutrition and Dietetics, Cappadocia University, Nevsehir, Turkey
| | - Zülal Kesmen
- Engineering Faculty, Department of Food Engineering, Erciyes University, Kayseri, Turkey
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14
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Santos‐Filho NA, Righetto GM, Pereira MR, Piccoli JP, Almeida LMT, Leal TC, Camargo ILBC, Cilli EM. Effect of C‐terminal and N‐terminal dimerization and alanine scanning on antibacterial activity of the analogs of the peptide
p‐BthTX‐I. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
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15
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Creane SE, Carlile SR, Downey D, Weldon S, Dalton JP, Taggart CC. The Impact of Lung Proteases on Snake-Derived Antimicrobial Peptides. Biomolecules 2021; 11:biom11081106. [PMID: 34439773 PMCID: PMC8394243 DOI: 10.3390/biom11081106] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/16/2022] Open
Abstract
Respiratory infections are a leading cause of global morbidity and mortality and are of significant concern for individuals with chronic inflammatory lung diseases. There is an urgent need for novel antimicrobials. Antimicrobial peptides (AMPs) are naturally occurring innate immune response peptides with therapeutic potential. However, therapeutic development has been hindered by issues with stability and cytotoxicity. Availing of direct drug delivery to the affected site, for example the lung, can reduce unwanted systemic side effects and lower the required dose. As cystic fibrosis (CF) and chronic obstructive pulmonary disease (COPD) lungs typically exhibit elevated protease levels, the aim of this study was to assess their impact on snake-derived AMPs. Peptide cleavage was determined using SDS-PAGE and antimicrobial and anti-inflammatory activities of neutrophil elastase (NE)-incubated peptides were assessed using a radial diffusion assay (RDA) and an in vitro LPS-induced inflammation model, respectively. Although the snake-derived AMPs were found to be susceptible to cleavage by lung proteases including NE, several retained their function following NE-incubation. This facilitated the design of novel truncated derivatives that retained functionality following NE incubation. Snake-derived AMPs are tractable candidate treatments for use in environments that feature elevated NE levels, such as the CF airways.
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Affiliation(s)
- Shannice E. Creane
- Airway Innate Immunity Research (AiiR) Group, Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (S.E.C.); (S.R.C.); (S.W.)
| | - Simon R. Carlile
- Airway Innate Immunity Research (AiiR) Group, Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (S.E.C.); (S.R.C.); (S.W.)
| | - Damian Downey
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK;
| | - Sinéad Weldon
- Airway Innate Immunity Research (AiiR) Group, Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (S.E.C.); (S.R.C.); (S.W.)
| | - John P. Dalton
- Zoology Department, School of Natural Sciences, Centre for One Health, Ryan Institute, National University of Ireland Galway, H91 TK33 Galway, Ireland;
- School of Biological Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK
| | - Clifford C. Taggart
- Airway Innate Immunity Research (AiiR) Group, Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen’s University Belfast, 97 Lisburn Road, Belfast BT9 7BL, UK; (S.E.C.); (S.R.C.); (S.W.)
- Correspondence:
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16
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Ilyas H, van der Plas MJA, Agnoletti M, Kumar S, Mandal AK, Atreya HS, Bhunia A, Malmsten M. Effect of PEGylation on Host Defense Peptide Complexation with Bacterial Lipopolysaccharide. Bioconjug Chem 2021; 32:1729-1741. [PMID: 34282895 DOI: 10.1021/acs.bioconjchem.1c00259] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Conjugation with poly(ethylene glycol) ("PEGylation") is a widely used approach for improving the therapeutic propensities of peptide and protein drugs through prolonging bloodstream circulation, reducing toxicity and immunogenicity, and improving proteolytic stability. In the present study, we investigate how PEGylation affects the interaction of host defense peptides (HDPs) with bacterial lipopolysaccharide (LPS) as well as HDP suppression of LPS-induced cell activation. In particular, we investigate the effects of PEGylation site for KYE28 (KYEITTIHNLFRKLTHRLFRRNFGYTLR), a peptide displaying potent anti-inflammatory effects, primarily provided by its N-terminal part. PEGylation was performed either in the N-terminus, the C-terminus, or in both termini, keeping the total number of ethylene groups (n = 48) constant. Ellipsometry showed KYE28 to exhibit pronounced affinity to both LPS and its hydrophobic lipid A moiety. The PEGylated peptide variants displayed lower, but comparable, affinity for both LPS and lipid A, irrespective of the PEGylation site. Furthermore, both KYE28 and its PEGylated variants triggered LPS aggregate disruption. To investigate the peptide structure in such LPS complexes, a battery of nuclear magnetic resonance (NMR) methods was employed. From this, it was found that KYE28 formed a well-folded structure after LPS binding, stabilized by hydrophobic domains involving aromatic amino acids as well as by electrostatic interactions. In contrast, the PEGylated peptide variants displayed a less well-defined secondary structure, suggesting weaker LPS interactions in line with the ellipsometry findings. Nevertheless, the N-terminal part of KYE28 retained helix formation after PEGylation, irrespective of the conjugation site. For THP1-Xblue-CD14 reporter cells, KYE28 displayed potent suppression of LPS activation at simultaneously low cell toxicity. Interestingly, the PEGylated KYE28 variants displayed similar or improved suppression of LPS-induced cell activation, implying the underlying key role of the largely retained helical structure close to the N-terminus, irrespective of PEGylation site. Taken together, the results show that PEGylation of HDPs can be done insensitively to the conjugation site without losing anti-inflammatory effects, even for peptides inducing such effects through one of its termini.
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Affiliation(s)
- Humaira Ilyas
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Mariena J A van der Plas
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark.,Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University, SE-221 84 Lund, Sweden
| | - Monica Agnoletti
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark
| | - Sourav Kumar
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Atin Kumar Mandal
- Division of Molecular Medicine, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Hanudatta S Atreya
- NMR Research Center, Indian Institute of Science, Bangalore 560012, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Martin Malmsten
- Department of Pharmacy, University of Copenhagen, DK-2100 Copenhagen, Denmark.,Department of Physical Chemistry 1, University of Lund, SE-22100 Lund, Sweden
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17
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Comparative study of antimicrobial activity between some medicine plants and recombinant Lactoferrin peptide against some pathogens of cultivated button mushroom. Arch Microbiol 2020; 202:2525-2532. [PMID: 32653933 DOI: 10.1007/s00203-020-01964-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 06/19/2020] [Accepted: 06/24/2020] [Indexed: 12/16/2022]
Abstract
The adverse effects of chemical pesticides on human health and environment cannot be ignored, hence it seems that novel alternative compounds should be applied to control plant pathogens. Among various alternative sources, natural compounds such as plant essential oils, plant extracts and recombinant antimicrobial peptides are of significance. The aim of the present study was to investigate antimicrobial activity of plants essential oils and plant extracts of six medicinal plants (Lippia citriodora, Ferula gummosa, Bunium persicum, Mentha piperita, Plantago major and Salvadora persica) along with a chimera peptide of camel lactoferrin, which is the most important antimicrobial component of camel milk, against Pseudomonas tolaasii and Trichoderma harzianum as pathogens of white button mushroom. The antibacterial activity test was conducted under in vitro conditions through disc diffusion method. The results showed that chimera camel lactoferrin peptide, with the highest amount of inhibitory zone (14.63 mm in 20 μg/mL concentration), has a significant difference in antibacterial activity compared to other treatments. Ferula gummosa conferred no antibacterial activity. Also, the results of antifungal effects indicated that plant essential oils and extracts have more antifungal activity than recombinant peptide. Generally, L. citriodora, B. persicum, M. piperita treatments could completely prevent growth of fungal in in vitro conditions. Therefore, using the mentioned plants can be a good replacement for reducing the chemical pesticides against pathogenic agents of button mushroom, without any adverse effects on environment and human health.
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18
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Porto WF, Irazazabal LN, Humblot V, Haney EF, Ribeiro SM, Hancock REW, Ladram A, Franco OL. EcDBS1R6: A novel cationic antimicrobial peptide derived from a signal peptide sequence. Biochim Biophys Acta Gen Subj 2020; 1864:129633. [PMID: 32416198 DOI: 10.1016/j.bbagen.2020.129633] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2019] [Revised: 04/10/2020] [Accepted: 05/08/2020] [Indexed: 12/23/2022]
Abstract
BACKGROUND Bacterial infections represent a major worldwide health problem the antimicrobial peptides (AMPs) have been considered as potential alternative agents for treating these infections. Here we demonstrated the antimicrobial activity of EcDBS1R6, a peptide derived from a signal peptide sequence of Escherichia coli that we previously turned into an AMP by making changes through the Joker algorithm. METHODS Antimicrobial activity was measured by broth microdilution method. Membrane integrity was measured using fluorescent probes and through scanning electron microscopy imaging. A sliding window of truncated peptides was used to determine the EcDBS1R6 active core. Molecular dynamics in TFE/water environment was used to assess the EcDBS1R6 structure. RESULTS Signal peptides are known to naturally interact with membranes; however, the modifications introduced by Joker transformed this peptide into a membrane-active agent capable of killing bacteria. The C-terminus was unable to fold into an α-helix whereas its fragments showed poor or no antimicrobial activity, suggesting that the EcDBS1R6 antibacterial core was located at the helical N-terminus, corresponding to the signal peptide portion of the parent peptide. CONCLUSION The strategy of transforming signal peptides into AMPs appears to be promising and could be used to produce novel antimicrobial agents. GENERAL SIGNIFICANCE The process of transforming an inactive signal peptide into an antimicrobial peptide could open a new venue for creating new AMPs derived from signal peptides.
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Affiliation(s)
- William F Porto
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil; Porto Reports, Brasília, DF, Brazil
| | - Luz N Irazazabal
- Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília, DF, Brazil; Molecular Pathology Post-graduate Program, University of Brasília, Brasília, Distrito Federal, Brazil
| | - Vincent Humblot
- Sorbonne Université, CNRS, Laboratoire de Réactivité de Surface, LRS, F-75252 Paris, France
| | - Evan F Haney
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, 2259 Lower Mall Research Station, Vancouver, British Columbia V6T 1Z4, Canada
| | - Suzana M Ribeiro
- Programa de Pós-Graduação em Ciências da Saúde, Universidade Federal da Grande Dourados, Dourados, MS, Brazil
| | - Robert E W Hancock
- Centre for Microbial Diseases and Immunity Research, University of British Columbia, 2259 Lower Mall Research Station, Vancouver, British Columbia V6T 1Z4, Canada
| | - Ali Ladram
- Sorbonne Université, CNRS, Institut de Biologie Paris-Seine, IBPS, BIOSIPE, F-75252 Paris, France
| | - Octavio L Franco
- S-Inova Biotech, Pós-graduação em Biotecnologia, Universidade Católica Dom Bosco, Campo Grande, MS, Brazil; Centro de Análises Proteômicas e Bioquímicas, Pós-Graduação em Ciências Genômicas e Biotecnologia Universidade Católica de Brasília, Brasília, DF, Brazil; Molecular Pathology Post-graduate Program, University of Brasília, Brasília, Distrito Federal, Brazil.
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19
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Biswas K, Ilyas H, Datta A, Bhunia A. NMR Assisted Antimicrobial Peptide Designing: Structure Based Modifications and Functional Correlation of a Designed Peptide VG16KRKP. Curr Med Chem 2020; 27:1387-1404. [PMID: 31232231 DOI: 10.2174/0929867326666190624090817] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 05/16/2019] [Accepted: 05/29/2019] [Indexed: 01/08/2023]
Abstract
Antimicrobial Peptides (AMPs), within their realm incorporate a diverse group of structurally and functionally varied peptides, playing crucial roles in innate immunity. Over the last few decades, the field of AMP has seen a huge upsurge, mainly owing to the generation of the so-called drug resistant 'superbugs' as well as limitations associated with the existing antimicrobial agents. Due to their resilient biological properties, AMPs can very well form the sustainable alternative for nextgeneration therapeutic agents. Certain drawbacks associated with existing AMPs are, however, issues of major concern, circumventing which are imperative. These limitations mainly include proteolytic cleavage and hence poor stability inside the biological systems, reduced activity due to inadequate interaction with the microbial membrane, and ineffectiveness because of inappropriate delivery among others. In this context, the application of naturally occurring AMPs as an efficient prototype for generating various synthetic and designed counterparts has evolved as a new avenue in peptide-based therapy. Such designing approaches help to overcome the drawbacks of the parent AMPs while retaining the inherent activity. In this review, we summarize some of the basic NMR structure based approaches and techniques which aid in improving the activity of AMPs, using the example of a 16-residue dengue virus fusion protein derived peptide, VG16KRKP. Using first principle based designing technique and high resolution NMR-based structure characterization we validate different types of modifications of VG16KRKP, highlighting key motifs, which optimize its activity. The approaches and designing techniques presented can support our peers in their drug development work.
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Affiliation(s)
- Karishma Biswas
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII(M), Kolkata 700054, India
| | - Humaira Ilyas
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII(M), Kolkata 700054, India
| | - Aritreyee Datta
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII(M), Kolkata 700054, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII(M), Kolkata 700054, India
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20
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Yang Q, Zhao D, Liu Q. Connections Between Amino Acid Metabolisms in Plants: Lysine as an Example. FRONTIERS IN PLANT SCIENCE 2020; 11:928. [PMID: 32636870 PMCID: PMC7317030 DOI: 10.3389/fpls.2020.00928] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 06/08/2020] [Indexed: 05/19/2023]
Abstract
Extensive efforts have been made to fortify essential amino acids and boost nutrition in plants, but unintended effects on growth and physiology are also observed. Understanding how different amino acid metabolisms are connected with other biological pathways is therefore important. In addition to protein synthesis, amino acid metabolism is also tightly linked to energy and carbohydrate metabolism, the carbon-nitrogen budget, hormone and secondary metabolism, stress responses, and so on. Here, we update the currently available information on the connections between amino acid metabolisms, which tend to be overlooked in higher plants. Particular emphasis was placed on the connections between lysine metabolism and other pathways, such as tryptophan metabolism, the tricarboxylic acid cycle, abiotic and biotic stress responses, starch metabolism, and the unfolded protein response. Interestingly, regulation of lysine metabolism was found to differ between plant species, as is the case between dicots and monocots. Determining the metabolic connection between amino acid metabolisms will help improve our understanding of the metabolic flux, supporting studies on crop nutrition.
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Affiliation(s)
- Qingqing Yang
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Dongsheng Zhao
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
| | - Qiaoquan Liu
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou, China
- Key Laboratory of Crop Genetics and Physiology of Jiangsu Province, Jiangsu Co-Innovation Center for Modern Production Technology of Grain Crops, Yangzhou University, Yangzhou, China
- *Correspondence: Qiaoquan Liu,
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21
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Fields FR, Freed SD, Carothers KE, Hamid MN, Hammers DE, Ross JN, Kalwajtys VR, Gonzalez AJ, Hildreth AD, Friedberg I, Lee SW. Novel antimicrobial peptide discovery using machine learning and biophysical selection of minimal bacteriocin domains. Drug Dev Res 2019; 81:43-51. [PMID: 31483516 DOI: 10.1002/ddr.21601] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 05/17/2019] [Accepted: 08/20/2019] [Indexed: 02/06/2023]
Abstract
Bacteriocins, the ribosomally produced antimicrobial peptides of bacteria, represent an untapped source of promising antibiotic alternatives. However, bacteriocins display diverse mechanisms of action, a narrow spectrum of activity, and inherent challenges in natural product isolation making in vitro verification of putative bacteriocins difficult. A subset of bacteriocins exert their antimicrobial effects through favorable biophysical interactions with the bacterial membrane mediated by the charge, hydrophobicity, and conformation of the peptide. We have developed a pipeline for bacteriocin-derived compound design and testing that combines sequence-free prediction of bacteriocins using machine learning and a simple biophysical trait filter to generate 20 amino acid peptides that can be synthesized and evaluated for activity. We generated 28,895 total 20-mer candidate peptides and scored them for charge, α-helicity, and hydrophobic moment. Of those, we selected 16 sequences for synthesis and evaluated their antimicrobial, cytotoxicity, and hemolytic activities. Peptides with the overall highest scores for our biophysical parameters exhibited significant antimicrobial activity against Escherichia coli and Pseudomonas aeruginosa. Our combined method incorporates machine learning and biophysical-based minimal region determination to create an original approach to swiftly discover bacteriocin candidates amenable to rapid synthesis and evaluation for therapeutic use.
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Affiliation(s)
- Francisco R Fields
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana.,Chemistry-Biochemistry-Biology Interface Program, University of Notre Dame, Notre Dame, Indiana
| | - Stefan D Freed
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana.,Chemistry-Biochemistry-Biology Interface Program, University of Notre Dame, Notre Dame, Indiana
| | - Katelyn E Carothers
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana
| | - Md Nafiz Hamid
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa
| | - Daniel E Hammers
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana
| | - Jessica N Ross
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana
| | - Veronica R Kalwajtys
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Alejandro J Gonzalez
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Andrew D Hildreth
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana
| | - Iddo Friedberg
- Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, Iowa.,Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa
| | - Shaun W Lee
- Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana.,Eck Institute for Global Health, University of Notre Dame, Notre Dame, Indiana.,Chemistry-Biochemistry-Biology Interface Program, University of Notre Dame, Notre Dame, Indiana
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22
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Ilyas H, Kim J, Lee D, Malmsten M, Bhunia A. Structural insights into the combinatorial effects of antimicrobial peptides reveal a role of aromatic-aromatic interactions in antibacterial synergism. J Biol Chem 2019; 294:14615-14633. [PMID: 31383740 DOI: 10.1074/jbc.ra119.009955] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 08/02/2019] [Indexed: 01/10/2023] Open
Abstract
The recent development of plants that overexpress antimicrobial peptides (AMPs) provides opportunities for controlling plant diseases. Because plants employ a broad-spectrum antimicrobial defense, including those based on AMPs, transgenic modification for AMP overexpression represents a potential way to utilize a defense system already present in plants. Herein, using an array of techniques and approaches, we report on VG16KRKP and KYE28, two antimicrobial peptides, which in combination exhibit synergistic antimicrobial effects against plant pathogens and are resistant against plant proteases. Investigating the structural origin of these synergistic antimicrobial effects with NMR spectroscopy of the complex formed between these two peptides and their mutated analogs, we demonstrate the formation of an unusual peptide complex, characterized by the formation of a bulky hydrophobic hub, stabilized by aromatic zippers. Using three-dimensional structure analyses of the complex in bacterial outer and inner membrane components and when bound to lipopolysaccharide (LPS) or bacterial membrane mimics, we found that this structure is key for elevating antimicrobial potency of the peptide combination. We conclude that the synergistic antimicrobial effects of VG16KRKP and KYE28 arise from the formation of a well-defined amphiphilic dimer in the presence of LPS and also in the cytoplasmic bacterial membrane environment. Together, these findings highlight a new application of solution NMR spectroscopy to solve complex structures to study peptide-peptide interactions, and they underscore the importance of structural insights for elucidating the antimicrobial effects of AMP mixtures.
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Affiliation(s)
- Humaira Ilyas
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - JaeWoong Kim
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 139743, Korea
| | - DongKuk Lee
- Department of Fine Chemistry, Seoul National University of Science and Technology, Seoul 139743, Korea
| | - Martin Malmsten
- Department of Pharmacy, Uppsala University, SE-75123 Uppsala, Sweden .,Department of Pharmacy, University of Copenhagen, DK 2100, Copenhagen, Denmark
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
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23
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Talandashti R, Mahdiuni H, Jafari M, Mehrnejad F. Molecular Basis for Membrane Selectivity of Antimicrobial Peptide Pleurocidin in the Presence of Different Eukaryotic and Prokaryotic Model Membranes. J Chem Inf Model 2019; 59:3262-3276. [DOI: 10.1021/acs.jcim.9b00245] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Reza Talandashti
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, P.O. Box 14395-1561, Tehran, Iran
| | - Hamid Mahdiuni
- Bioinformatics Lab., Department of Biology, School of Sciences, Razi University, P.O. Box 67149-67346, Kermanshah, Iran
| | - Majid Jafari
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, P.O. Box 14395-1561, Tehran, Iran
| | - Faramarz Mehrnejad
- Department of Life Science Engineering, Faculty of New Sciences and Technologies, University of Tehran, P.O. Box 14395-1561, Tehran, Iran
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24
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Varnava KG, Mohid SA, Calligari P, Stella L, Reynison J, Bhunia A, Sarojini V. Design, Synthesis, Antibacterial Potential, and Structural Characterization of N-Acylated Derivatives of the Human Autophagy 16 Polypeptide. Bioconjug Chem 2019; 30:1998-2010. [PMID: 31145591 DOI: 10.1021/acs.bioconjchem.9b00290] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
A synthetic antimicrobial peptide library based on the human autophagy 16 polypeptide has been developed. Designed acetylated peptides bearing lipids of different chain lengths resulted in peptides with enhanced potency compared to the parent Atg16. A 21-residue fragment of Atg16 conjugated to 4-methylhexanoic acid (K30) emerged as the most potent antibacterial, with negligible hemolysis. Several studies, including microscopy, dye leakage, and ITC, were conducted to gain insight into the antibacterial mechanism of action of the peptide. Visual inspection using both SEM and TEM revealed the membranolytic effect of the peptide on bacterial cells. The selectivity of the peptide against bacterial cell membranes was also proven using dye leakage assays. ITC analysis revealed the exothermic nature of the binding interaction of the peptide to D8PG micelles. The three-dimensional solution NMR structure of K30 in complex with dioctanoylphosphatidylglycerol (D8PG) micelles revealed that the peptide adopts a helix-loop-helix structure in the presence of anionic membrane lipids mimicking bacterial membranes. Intermolecular NOEs between the peptide and lipid deciphered the location of the peptide in the bound state, which was subsequently supported by the paramagnetic relaxation enhancement (PRE) NMR experiment. Collectively, these results describe the structure-function relationship of the peptide in the bacterial membrane.
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Affiliation(s)
- Kyriakos Gabriel Varnava
- School of Chemical Sciences , The University of Auckland , Private Bag 92019 , Auckland , New Zealand
| | - Sk Abdul Mohid
- Department of Biophysics , Bose Institute , P-1/12 CIT Scheme VII (M) , Kolkata 700054 , India
| | - Paolo Calligari
- Department of Chemical Science and Technologies , University of Rome Tor Vergata , 00133 Rome , Italy
| | - Lorenzo Stella
- Department of Chemical Science and Technologies , University of Rome Tor Vergata , 00133 Rome , Italy
| | - Jóhannes Reynison
- School of Chemical Sciences , The University of Auckland , Private Bag 92019 , Auckland , New Zealand.,School of Pharmacy, Hornbeam Building , Keele University , Staffordshire ST5 5BG , United Kingdom
| | - Anirban Bhunia
- Department of Biophysics , Bose Institute , P-1/12 CIT Scheme VII (M) , Kolkata 700054 , India
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences , The University of Auckland , Private Bag 92019 , Auckland , New Zealand.,The MacDiarmid Institute for Advanced Materials and Nanotechnology , Wellington 6140 , New Zealand
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25
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Auwal SM, Zainal Abidin N, Zarei M, Tan CP, Saari N. Identification, structure-activity relationship and in silico molecular docking analyses of five novel angiotensin I-converting enzyme (ACE)-inhibitory peptides from stone fish (Actinopyga lecanora) hydrolysates. PLoS One 2019; 14:e0197644. [PMID: 31145747 PMCID: PMC6542528 DOI: 10.1371/journal.pone.0197644] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Accepted: 05/03/2019] [Indexed: 12/29/2022] Open
Abstract
Stone fish is an under-utilized sea cucumber with many health benefits. Hydrolysates with strong ACE-inhibitory effects were generated from stone fish protein under the optimum conditions of hydrolysis using bromelain and fractionated based on hydrophobicity and isoelectric properties of the constituent peptides. Five novel peptide sequences with molecular weight (mw) < 1000 daltons (Da) were identified using LC-MS/MS. The peptides including Ala-Leu-Gly-Pro-Gln-Phe-Tyr (794.44 Da), Lys-Val-Pro-Pro-Lys-Ala (638.88 Da), Leu-Ala-Pro-Pro-Thr-Met (628.85 Da), Glu-Val-Leu-Ile-Gln (600.77 Da) and Glu-His-Pro-Val-Leu (593.74 Da) were evaluated for ACE-inhibitory activity and showed IC50 values of 0.012 mM, 0.980 mM, 1.310 mM, 1.440 mM and 1.680 mM, respectively. The ACE-inhibitory effects of the peptides were further verified using molecular docking study. The docking results demonstrated that the peptides exhibit their effect mainly via hydrogen and electrostatic bond interactions with ACE. These findings provide evidence about stone fish as a valuable source of raw materials for the manufacture of antihypertensive peptides that can be incorporated to enhance therapeutic relevance and commercial significance of formulated functional foods.
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Affiliation(s)
- Shehu Muhammad Auwal
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Department of Biochemistry, Faculty of Basic Medical Sciences, Bayero University, Kano, Nigeria
| | - Najib Zainal Abidin
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Mohammad Zarei
- Department of Food Science and Technology, School of Industrial Technology, Faculty of Applied Sciences, Universiti Teknologi MARA, Shah Alam, Selangor, Malaysia
| | - Chin Ping Tan
- Department of Food Technology, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Nazamid Saari
- Department of Food Science, Faculty of Food Science and Technology, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
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26
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Ganguly A, Sharma K, Majumder K. Food-derived bioactive peptides and their role in ameliorating hypertension and associated cardiovascular diseases. ADVANCES IN FOOD AND NUTRITION RESEARCH 2019; 89:165-207. [PMID: 31351525 DOI: 10.1016/bs.afnr.2019.04.001] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Non-communicable diseases including cardiovascular diseases (CVDs) and associated metabolic disorders are responsible for nearly 40 million deaths globally per year. Hypertension or high blood pressure (BP) is one of the primary reasons for the development of CVDs. A healthy nutritional strategy complementing with physical activity can substantially reduce high BP and prevent the occurrence of CVD-associated morbidity and mortality. Bioactive peptides currently are the next wave of the promising bench to clinic options for potential targeting chronic and acute health issues including hypertension. Peptides demonstrating anti-inflammatory, anti-oxidant, and angiotensin-converting enzyme-I inhibitory activity are widely studied for the amelioration of hypertension and associated CVDs. Isolating these potent bioactive peptides from different food sources is a promising endeavor toward nutraceutical based dietary management and prevention of hypertension. Understanding the pathophysiology of hypertension and the action mechanisms of the bioactive peptides would complement in designing and characterizing more potent peptides and suitable comprehensive dietary plans for the prevention of hypertension and associated CVDs.
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Affiliation(s)
- Advaita Ganguly
- Comprehensive Tissue Centre, UAH Transplant Services, Alberta Health Services, Edmonton, AB, Canada
| | - Kumakshi Sharma
- Health, Safety and Environment Branch, National Research Council Canada, Edmonton, AB, Canada
| | - Kaustav Majumder
- Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, United States.
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27
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Boutin JA, Tartar AL, van Dorsselaer A, Vaudry H. General lack of structural characterization of chemically synthesized long peptides. Protein Sci 2019; 28:857-867. [PMID: 30851143 PMCID: PMC6459998 DOI: 10.1002/pro.3601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/07/2019] [Accepted: 03/07/2019] [Indexed: 01/01/2023]
Abstract
Many peptide chemistry scientists have been reporting extremely interesting work on the basis of chemical peptides for which the only characterization was their purity, mass, and biological activity. It seems slightly overenthusiastic, as many of these structures should be thoroughly characterized first to demonstrate the uniqueness of the structure, as opposed to the uniqueness of the sequence. Among the peptides of identical sequences in the final chemical preparation, what amount of well-folded peptide supports the measured activity? The activity of a peptide preparation cannot prove the purity of the desired peptide. Therefore, greater care should be taken in characterizing peptides, particularly those coming from chemical synthesis. At a time when the pharmaceutical industry is changing its paradigm by moving substantially from small molecules to biologics to better serve patients' needs, it is important to understand the limitations of the descriptions of these products and to start to apply the same "good laboratory practices" to our peptide research. Here, we attempt to delineate how synthetic peptides are described and characterized and what will be needed to describe them in regards to how they are well-folded and homogeneous in their tertiary structure. Older studies were done when the tools were not yet discovered, but more recent publications are still lacking proper descriptions of these peptides. Modern tools of analysis are capable of segregating folded and unfolded peptides, even if the preparation is biologically active.
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Affiliation(s)
- Jean A. Boutin
- Institut de Recherches Internationales Servier50 rue Carnot, 92284, Suresnes‐CedexFrance
| | - André L. Tartar
- Faculté de Pharmacie 3rue du Professeur Laguesse, BP83 ‐ 59006, Lille‐CedexFrance
| | - Alain van Dorsselaer
- Laboratoire de Spectrométrie de Masse Bio‐Organique, Département des Sciences AnalytiquesInstitut Pluridisciplinaire Hubert CurienUMR 7178 (CNRS‐UdS), ECPM, 25 rue Becquerel, F67087, Strasbourg‐Cedex 2France
| | - Hubert Vaudry
- Plate‐Forme de Recherche en Imagerie Cellulaire de Normandie (PRIMACEN)Institut de Recherche et d'Innovation Biomédicales (IRIB), Université de Rouen76821, Mont‐Saint‐Aignan CedexFrance
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28
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Saporito P, Biljana M, Løbner Olesen A, Jenssen H. Antibacterial mechanisms of GN-2 derived peptides and peptoids against Escherichia coli. Biopolymers 2019; 110:e23275. [PMID: 30951211 DOI: 10.1002/bip.23275] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/08/2019] [Accepted: 03/12/2019] [Indexed: 12/30/2022]
Abstract
Escherichia coli is the main etiological agent of urinary trait infections, able to form biofilms in indwelling devices, resulting in chronic infections which are refractory to antibiotics treatment. In this study, we investigated the antimicrobial and anti-biofilm properties exerted against E. coli ATCC 25922, by a set of peptoids and peptides modeled upon the peptide GN-2, previously reported as a valid antimicrobial agent. The putative antimicrobials were designed to evaluate the effect of cationicity, hydrophobicity and their partitioning on the overall properties against planktonic cells and biofilms as well as on LPS binding, permeabilization of Gram-negative bacteria membranes and hemolysis. The data demonstrated that peptides are stronger antimicrobials than the analogue peptoids which in return have superior anti-biofilm properties. In this study, we present evidence that peptides antimicrobial activity correlates with enhanced LPS binding and hydrophobicity but is not affected by partitioning. The data demonstrated that the enhanced anti-biofilm properties of the peptoids are associated with decreased hydrophobicity and increased penetration of the inner membrane, compared to that of their peptide counterpart, suggesting that the characteristic flexibility of peptoids or their lack of H-bonding donors in their backbone, would play a role in their ability to penetrate bacterial membranes.
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Affiliation(s)
- Paola Saporito
- Department of Science and Environment, Roskilde University, Roskilde, Denmark.,Section for Functional Genomics and Center for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Mojsoska Biljana
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Anders Løbner Olesen
- Section for Functional Genomics and Center for Bacterial Stress Response and Persistence, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Håvard Jenssen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
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29
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Microgels as carriers of antimicrobial peptides – Effects of peptide PEGylation. Colloids Surf A Physicochem Eng Asp 2019. [DOI: 10.1016/j.colsurfa.2018.12.049] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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30
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The C-Terminal Domain of the Bacillus thuringiensis Cry4Ba Mosquito-Specific Toxin Serves as a Potential Membrane Anchor. Toxins (Basel) 2019; 11:toxins11020062. [PMID: 30678087 PMCID: PMC6410236 DOI: 10.3390/toxins11020062] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 01/15/2019] [Accepted: 01/18/2019] [Indexed: 11/16/2022] Open
Abstract
Although the C-terminal domain (DIII) of three-domain Cry insecticidal toxins from Bacillus thuringiensis has been implicated in various biological functions, its exact role still remains to be elucidated. Here, the 21-kDa isolated DIII fragment of the 65-kDa Cry4Ba mosquito-specific toxin was analyzed for its binding characteristics toward lipid-bilayer membranes. When the highly-purified Cry4Ba-DIII protein was structurally verified by attenuated total reflection Fourier transform infrared (ATR-FTIR) spectroscopy, it revealed the presence of a distinct β-sheet structure, corresponding to its structure embodied in the Cry4Ba crystal structure. Binding analysis via surface plasmon resonance (SPR) spectroscopy revealed that the 21-kDa Cry4Ba-DIII truncate displayed tight binding to immobilized liposome membranes in a two-step manner, exhibiting a dissociation rate constant (kd) comparable to the 65-kDa full-length toxin. Also similar to the Cry4Ba full-length toxin, its isolated DIII truncate was able to anchor a part of its molecule into the immobilized membrane as the SPR signal was still detected after prolonged treatment with proteinase K. However, unlike the full-length active toxin, the DIII truncate was unable to induce membrane permeability of calcein-loaded liposomes or ion-channel formation in planar lipid bilayers. Together, our present data have disclosed a pivotal role of C-terminal DIII in serving as a membrane anchor rather than a pore-forming moiety of the Cry4Ba mosquito-active toxin, highlighting its potential mechanistic contribution to the interaction of the full-length toxin with lipid membranes in mediating toxicity.
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31
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Bao K, Yuan W, Ma C, Yu X, Wang L, Hong M, Xi X, Zhou M, Chen T. Modification Targeting the "Rana Box" Motif of a Novel Nigrocin Peptide From Hylarana latouchii Enhances and Broadens Its Potency Against Multiple Bacteria. Front Microbiol 2018; 9:2846. [PMID: 30555431 PMCID: PMC6280737 DOI: 10.3389/fmicb.2018.02846] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Accepted: 11/05/2018] [Indexed: 11/15/2022] Open
Abstract
Public health is confronting the threat caused by antibiotic resistance and this means new antibacterial strategies must be developed urgently. Antimicrobial peptides (AMPs) have been considered as promising therapeutic candidates against infection in the post-antibiotic era. In this paper, we dismissed the significance of “Rana box” in the natural nigrocin-HL identified from skin secretion of Hylarana latouchii by comparing its activity with nigrocin-HLD without the motif. By substituting the “Rana box” sequence with an amidated phenylalanine residue, the natural peptide was modified into a shorter AMP nigrocin-HLM. Activities and toxicities of these two peptides in vitro and in vivo were compared. As a result, nigrocin-HLM not only displayed significantly increased potency against several representative microbes, but also high activity against the antibiotic-resistant methicillin-resistant S. aureus (MRSA, NCTC 12493 and ATCC43300 and several clinical isolates) as evidenced by markedly reduced minimal inhibitory concentration (MIC), minimal bactericidal concentration (MBC), and minimum biofilm eradication concentration (MBEC). More strikingly, nigrocin-HLM exhibited prominent inhibition against MRSA infection in a pneumonia mice model. In addition, the substitution attenuated the toxicity of nigrocin-HLM as evidenced by precipitously decreased hemolytic and cytotoxic activities in vitro, and acute toxicity to mice in vivo. Taken these results into consideration, nigrocin-HLM should be a promising therapeutic candidate for anti-infection. And in addition to dismiss an indispensable role of “Rana box” in maintaining antimicrobial activity of nigrocin-HL, our data provided an inspired strategy for peptide optimization.
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Affiliation(s)
- Kaifan Bao
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China.,Natural Drug Discovery Group, School of Pharmacy, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Weiyuan Yuan
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Chengbang Ma
- Natural Drug Discovery Group, School of Pharmacy, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Xi Yu
- Nanjing Pharmaceutical Co., Ltd., Nanjing, China
| | - Lei Wang
- Natural Drug Discovery Group, School of Pharmacy, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Min Hong
- Jiangsu Key Laboratory for Pharmacology and Safety Evaluation of Chinese Materia Medica, Nanjing University of Chinese Medicine, Nanjing, China
| | - Xinping Xi
- Natural Drug Discovery Group, School of Pharmacy, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Mei Zhou
- Natural Drug Discovery Group, School of Pharmacy, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, United Kingdom
| | - Tianbao Chen
- Natural Drug Discovery Group, School of Pharmacy, Faculty of Medicine, Health and Life Sciences, Queen's University Belfast, Belfast, United Kingdom
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32
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Structural basis for endotoxin neutralisation and anti-inflammatory activity of thrombin-derived C-terminal peptides. Nat Commun 2018; 9:2762. [PMID: 30018388 PMCID: PMC6050251 DOI: 10.1038/s41467-018-05242-0] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 06/18/2018] [Indexed: 01/22/2023] Open
Abstract
Thrombin-derived C-terminal peptides (TCPs) of about 2 kDa are present in wounds, where they exert anti-endotoxic functions. Employing a combination of nuclear magnetic resonance spectroscopy (NMR), biophysical, mass spectrometry and cellular studies combined with in silico multiscale modelling, we here determine the bound conformation of HVF18 (HVFRLKKWIQKVIDQFGE), a TCP generated by neutrophil elastase, in complex with bacterial lipopolysaccharide (LPS) and define a previously undisclosed interaction between TCPs and human CD14. Further, we show that TCPs bind to the LPS-binding hydrophobic pocket of CD14 and identify the peptide region crucial for TCP interaction with LPS and CD14. Taken together, our results demonstrate the role of structural transitions in LPS complex formation and CD14 interaction, providing a molecular explanation for the previously observed therapeutic effects of TCPs in experimental models of bacterial sepsis and endotoxin shock. Thrombin-derived C-terminal peptides (TCPs) have anti-endotoxic functions in wounds by binding to bacterial lipopolysaccharide (LPS) and Gram-negative bacteria. Here authors use a spectrum of biophysical techniques to determine the conformation of a TCP in complex with LPS and define the interaction between TCPs and CD14.
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33
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Passarini I, Rossiter S, Malkinson J, Zloh M. In Silico Structural Evaluation of Short Cationic Antimicrobial Peptides. Pharmaceutics 2018; 10:E72. [PMID: 29933540 PMCID: PMC6160961 DOI: 10.3390/pharmaceutics10030072] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 06/11/2018] [Accepted: 06/12/2018] [Indexed: 12/26/2022] Open
Abstract
Cationic peptides with antimicrobial properties are ubiquitous in nature and have been studied for many years in an attempt to design novel antibiotics. However, very few molecules are used in the clinic so far, sometimes due to their complexity but, mostly, as a consequence of the unfavorable pharmacokinetic profile associated with peptides. The aim of this work is to investigate cationic peptides in order to identify common structural features which could be useful for the design of small peptides or peptido-mimetics with improved drug-like properties and activity against Gram negative bacteria. Two sets of cationic peptides (AMPs) with known antimicrobial activity have been investigated. The first reference set comprised molecules with experimentally-known conformations available in the protein databank (PDB), and the second one was composed of short peptides active against Gram negative bacteria but with no significant structural information available. The predicted structures of the peptides from the first set were in excellent agreement with those experimentally-observed, which allowed analysis of the structural features of the second group using computationally-derived conformations. The peptide conformations, either experimentally available or predicted, were clustered in an “all vs. all” fashion and the most populated clusters were then analyzed. It was confirmed that these peptides tend to assume an amphipathic conformation regardless of the environment. It was also observed that positively-charged amino acid residues can often be found next to aromatic residues. Finally, a protocol was evaluated for the investigation of the behavior of short cationic peptides in the presence of a membrane-like environment such as dodecylphosphocholine (DPC) micelles. The results presented herein introduce a promising approach to inform the design of novel short peptides with a potential antimicrobial activity.
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Affiliation(s)
- Ilaria Passarini
- School of Life and Medical Sciences, University of Hertfordshire, College Lane, Hatfield AL10 9AB, UK.
| | - Sharon Rossiter
- School of Life and Medical Sciences, University of Hertfordshire, College Lane, Hatfield AL10 9AB, UK.
| | - John Malkinson
- UCL School of Pharmacy, University College London, 29/39 Brunswick Square, London WC1N 1AX, UK.
| | - Mire Zloh
- School of Life and Medical Sciences, University of Hertfordshire, College Lane, Hatfield AL10 9AB, UK.
- Faculty of Pharmacy, University Business Academy, Trg mladenaca 5, 21000 Novi Sad, Serbia.
- NanoPuzzle Medicines Design, Business & Technology Centre, Bessemer Drive, Stevenage SG1 2DX, UK.
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34
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Structure and Interactions of A Host Defense Antimicrobial Peptide Thanatin in Lipopolysaccharide Micelles Reveal Mechanism of Bacterial Cell Agglutination. Sci Rep 2017; 7:17795. [PMID: 29259246 PMCID: PMC5736615 DOI: 10.1038/s41598-017-18102-6] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 12/05/2017] [Indexed: 12/15/2022] Open
Abstract
Host defense cationic Antimicrobial Peptides (AMPs) can kill microorganisms including bacteria, viruses and fungi using various modes of action. The negatively charged bacterial membranes serve as a key target for many AMPs. Bacterial cell death by membrane permeabilization has been well perceived. A number of cationic AMPs kill bacteria by cell agglutination which is a distinctly different mode of action compared to membrane pore formation. However, mechanism of cell agglutinating AMPs is poorly understood. The outer membrane lipopolysaccharide (LPS) or the cell-wall peptidoglycans are targeted by AMPs as a key step in agglutination process. Here, we report the first atomic-resolution structure of thanatin, a cell agglutinating AMP, in complex with LPS micelle by solution NMR. The structure of thanatin in complex with LPS, revealed four stranded antiparallel β-sheet in a ‘head-tail’ dimeric topology. By contrast, thanatin in free solution assumed an antiparallel β-hairpin conformation. Dimeric structure of thanatin displayed higher hydrophobicity and cationicity with sites of LPS interactions. MD simulations and biophysical interactions analyses provided mode of LPS recognition and perturbation of LPS micelle structures. Mechanistic insights of bacterial cell agglutination obtained in this study can be utilized to develop antibiotics of alternative mode of action.
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35
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Singh S, Datta A, Borro BC, Davoudi M, Schmidtchen A, Bhunia A, Malmsten M. Conformational Aspects of High Content Packing of Antimicrobial Peptides in Polymer Microgels. ACS APPLIED MATERIALS & INTERFACES 2017; 9:40094-40106. [PMID: 29087182 DOI: 10.1021/acsami.7b13714] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Successful use of microgels as delivery systems of antimicrobial peptides (AMPs) requires control of factors determining peptide loading and release to/from the microgels as well as of membrane interactions of both microgel particles and released peptides. Addressing these, we here investigate effects of microgel charge density and conformationally induced peptide amphiphilicity on AMP loading and release using detailed nuclear magnetic resonance (NMR) structural studies combined with ellipsometry, isothermal titration calorimetry, circular dichroism, and light scattering. In parallel, consequences of peptide loading and release for membrane interactions and antimicrobial effects were investigated. In doing so, poly(ethyl acrylate-co-methacrylic acid) microgels were found to incorporate the cationic AMPs EFK17a (EFKRIVQRIKDFLRNLV) and its partially d-amino acid-substituted variant EFK17da (E(dF)KR(dI)VQR(dI)KD(dF)LRNLV). Peptide incorporation was found to increase with increasing with microgel charge density and peptide amphiphilicity. After microgel incorporation, which appeared to occur preferentially in the microgel core, NMR showed EFK17a to form a helix with pronounced amphiphilicity, while EFK17da displayed a folded conformation, stabilized by a hydrophobic hub consisting of aromatic/aromatic and aliphatic/aromatic interactions, resulting in much lower amphiphilicity. Under wide ranges of peptide loading, the microgels displayed net negative z-potential. Such negatively charged microgels do not bind to, nor lyse, bacteria-mimicking membranes. Instead, membrane disruption in these systems is mediated largely by peptide release, which in turn is promoted at higher ionic strength and lower peptide amphiphilicity. Analogously, antimicrobial effects against Escherichia coli were found to be dictated by peptide release. Taken together, the findings show that peptide loading, packing, and release strongly affect the performance of microgels as AMP delivery systems, effects that can be tuned by (conformationally induced) peptide amphiphilicity and by microgel charge density.
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Affiliation(s)
- Shalini Singh
- Department of Pharmacy, Uppsala University , SE-75232 Uppsala, Sweden
| | - Aritreyee Datta
- Department of Biophysics, Bose Institute , P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Bruno C Borro
- Department of Pharmacy, University of Copenhagen , DK-2100 Copenhagen, Denmark
| | - Mina Davoudi
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University , SE-221 84 Lund, Sweden
| | - Artur Schmidtchen
- Division of Dermatology and Venereology, Department of Clinical Sciences, Lund University , SE-221 84 Lund, Sweden
- Lee Kong Chian School of Medicine, Nanyang Technological University , 11 Mandalay Road, Singapore 308232, Singapore
- Wound Healing Centre, Bispebjerg University Hospital , DK-2100 Copenhagen, Denmark
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute , P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Martin Malmsten
- Department of Pharmacy, Uppsala University , SE-75232 Uppsala, Sweden
- Department of Pharmacy, University of Copenhagen , DK-2100 Copenhagen, Denmark
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36
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Jeon D, Jacob B, Kwak C, Kim Y. Short Antimicrobial Peptides Exhibiting Antibacterial and Anti-Inflammatory Activities Derived from the N-Terminal Helix of Papiliocin. B KOREAN CHEM SOC 2017. [DOI: 10.1002/bkcs.11277] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Dasom Jeon
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 143-701 Korea
| | - Binu Jacob
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 143-701 Korea
| | - Chulhee Kwak
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 143-701 Korea
| | - Yangmee Kim
- Department of Bioscience and Biotechnology; Konkuk University; Seoul 143-701 Korea
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37
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Ghosh A, Bhattacharyya D, Bhunia A. Structural insights of a self-assembling 9-residue peptide from the C-terminal tail of the SARS corona virus E-protein in DPC and SDS micelles: A combined high and low resolution spectroscopic study. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1860:335-346. [PMID: 29038024 PMCID: PMC7094419 DOI: 10.1016/j.bbamem.2017.10.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Revised: 10/09/2017] [Accepted: 10/11/2017] [Indexed: 12/25/2022]
Abstract
In recent years, several studies based on the interaction of self-assembling short peptides derived from viroporins with model membranes, have improved our understanding of the molecular mechanism of corona virus (CoV) infection under physiological conditions. In this study, we have characterized the mechanism of membrane interaction of a short, 9-residue peptide TK9 (T55VYVYSRVK63) that had been derived from the carboxyl terminal of the Severe Acute Respiratory Syndrome (SARS) corona virus (SARS CoV) envelope (E) protein. The peptide has been studied for its physical changes in the presence of both zwitterionic DPC and negatively charged SDS model membrane micelles, respectively, with the help of a battery of biophysical techniques including two-dimensional solution state NMR spectroscopy. Interestingly, in both micellar environments, TK9 adopted an alpha helical conformation; however, the helical propensities were much higher in the case of DPC compared to those of SDS micelle, suggesting that TK9 has more specificity towards eukaryotic cell membrane than the bacterial cell membrane. The orientation of the peptide TK9 also varies in the different micellar environments. The peptide's affinity was further manifested by its pronounced membrane disruption ability towards the mammalian compared to the bacterial membrane mimic. Collectively, the in-depth structural information on the interaction of TK9 with different membrane environments explains the host specificity and membrane orientation owing to subsequent membrane disruption implicated in the viral pathogenesis.
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Affiliation(s)
- Anirban Ghosh
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Dipita Bhattacharyya
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India
| | - Anirban Bhunia
- Department of Biophysics, Bose Institute, P-1/12 CIT Scheme VII (M), Kolkata 700054, India.
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38
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van der Weide H, Brunetti J, Pini A, Bracci L, Ambrosini C, Lupetti P, Paccagnini E, Gentile M, Bernini A, Niccolai N, Jongh DVD, Bakker-Woudenberg IAJM, Goessens WHF, Hays JP, Falciani C. Investigations into the killing activity of an antimicrobial peptide active against extensively antibiotic-resistant K. pneumon iae and P. aeruginosa. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2017; 1859:1796-1804. [PMID: 28583831 DOI: 10.1016/j.bbamem.2017.06.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/10/2017] [Accepted: 06/01/2017] [Indexed: 10/19/2022]
Abstract
SET-M33 is a multimeric antimicrobial peptide active against Gram-negative bacteria in vitro and in vivo. Insights into its killing mechanism could elucidate correlations with selectivity. SET-M33 showed concentration-dependent bactericidal activity against colistin-susceptible and resistant isolates of P. aeruginosa and K. pneumoniae. Scanning and transmission microscopy studies showed that SET-M33 generated cell blisters, blebs, membrane stacks and deep craters in K. pneumoniae and P. aeruginosa cells. NMR analysis and CD spectra in the presence of sodium dodecyl sulfate micelles showed a transition from an unstructured state to a stable α-helix, driving the peptide to arrange itself on the surface of micelles. SET-M33 kills Gram-negative bacteria after an initial interaction with bacterial LPS. The molecule becomes then embedded in the outer membrane surface, thereby impairing cell function. This activity of SET-M33, in contrast to other similar antimicrobial peptides such as colistin, does not generate resistant mutants after 24h of exposure, non-specific interactions or toxicity against eukaryotic cell membranes, suggesting that SET-M33 is a promising new option for the treatment of Gram-negative antibiotic-resistant infections.
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Affiliation(s)
- Hessel van der Weide
- Department of Medical Microbiology & Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jlenia Brunetti
- Department of Medical Biotechnology, University of Siena, Italy
| | - Alessandro Pini
- Department of Medical Biotechnology, University of Siena, Italy
| | - Luisa Bracci
- Department of Medical Biotechnology, University of Siena, Italy
| | | | | | | | | | - Andrea Bernini
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy
| | - Neri Niccolai
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Italy
| | - Denise Vermeulen-de Jongh
- Department of Medical Microbiology & Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Irma A J M Bakker-Woudenberg
- Department of Medical Microbiology & Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wil H F Goessens
- Department of Medical Microbiology & Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John P Hays
- Department of Medical Microbiology & Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Chiara Falciani
- Department of Medical Biotechnology, University of Siena, Italy; Setlance srl, Research and Development Department, Siena, Italy.
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39
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Datta A, Jaiswal N, Ilyas H, Debnath S, Biswas K, Kumar D, Bhunia A. Structural and Dynamic Insights into a Glycine-Mediated Short Analogue of a Designed Peptide in Lipopolysaccharide Micelles: Correlation Between Compact Structure and Anti-Endotoxin Activity. Biochemistry 2017; 56:1348-1362. [PMID: 28168875 DOI: 10.1021/acs.biochem.6b01229] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In this study, we report an interaction study of a 13-residue analogue peptide VG13P (VARGWGRKCPLFG), derived from a designed VG16KRKP peptide (VARGWKRKCPLFGKGG), with a Lys6Gly mutation and removal of the last three residues Lys14-Gly15-Gly16, in lipopolysaccharide (LPS), a major component of the outer membrane of Gram-negative bacteria and responsible for sepsis or septic shock. VG13P displays an enhanced anti-endotoxin property as evident from significant reduction in LPS-induced TNF-α gene expression levels in a monocytic cell line, while it retains almost unchanged antimicrobial activity as its parent VG16KRKP against Gram-negative bacterial as well as fungal pathogens. In addition, in vitro LPS binding properties of VG13P in comparison to its parent VG16KRKP also remained unhindered, suggesting that the flexible C-terminal end of VG16KRKP may not play a major role in its observed antibacterial and LPS binding properties. An NMR-resolved solution structure of VG13P in LPS reveals two consecutive β-turns: one at the N-terminus, followed by another at the central region, closely resembling a rocking chair. The crucial Lys6Gly mutation along with C-terminal truncation from VG16KRKP reorients the hydrophobic hub in VG13P in a unique way so as to fold the N-terminal end back on itself, forming a turn and allowing Val1 and Ala2 to interact with Leu11 and Phe12 to bring the hydrophobic residues closer together to form a more compact hub compared to its parent. The hub is further strengthened via CH-π interaction between Gly4 and Phe12. This accounts for its improved anti-endotoxin activity as well as to its uninterrupted antimicrobial activity.
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Affiliation(s)
| | - Nancy Jaiswal
- Center of Biomedical Research , SGPGIMS Campus, Lucknow 226014, India
| | | | | | | | - Dinesh Kumar
- Center of Biomedical Research , SGPGIMS Campus, Lucknow 226014, India
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40
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Li W, Sun Z, O'Brien-Simpson NM, Otvos L, Reynolds EC, Hossain MA, Separovic F, Wade JD. The Effect of Selective D- or N α-Methyl Arginine Substitution on the Activity of the Proline-Rich Antimicrobial Peptide, Chex1-Arg20. Front Chem 2017; 5:1. [PMID: 28154813 PMCID: PMC5243837 DOI: 10.3389/fchem.2017.00001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Accepted: 01/04/2017] [Indexed: 01/21/2023] Open
Abstract
In vivo pharmacokinetics studies have shown that the proline-rich antimicrobial peptide, A3-APO, which is a discontinuous dimer of the peptide, Chex1-Arg20, undergoes degradation to small fragments at positions Pro6-Arg7 and Val19-Arg20. With the aim of minimizing or abolishing this degradation, a series of Chex1-Arg20 analogs were prepared via Fmoc/tBu solid phase peptide synthesis with D-arginine or, in some cases, peptide backbone Nα-methylated arginine, substitution at these sites. All the peptides were tested for antibacterial activity against the Gram-negative bacterium Klebsiella pneumoniae. The resulting activity of position-7 substitution of Chex1-Arg20 analogs showed that arginine-7 is a crucial residue for maintaining activity against K. pneumoniae. However, arginine-20 substitution had a much less deleterious effect on the antibacterial activity of the peptide. Moreover, none of these peptides displayed any cytotoxicity to HEK and H-4-II-E mammalian cells. These results will aid the development of more effective and stable PrAMPs via judicious amino acid substitutions.
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Affiliation(s)
- Wenyi Li
- Florey Institute of Neuroscience and Mental Health, University of MelbourneParkville, VIC, Australia; School of Chemistry, University of MelbourneParkville, VIC, Australia
| | - Zhe Sun
- Oral Health Cooperative Research Centre, Melbourne Dental School, University of MelbourneParkville, VIC, Australia; Bio21 Institute, University of MelbourneParkville, VIC, Australia
| | - Neil M O'Brien-Simpson
- Oral Health Cooperative Research Centre, Melbourne Dental School, University of MelbourneParkville, VIC, Australia; Bio21 Institute, University of MelbourneParkville, VIC, Australia
| | - Laszlo Otvos
- Department of Biology, Temple University Philadelphia, PA, USA
| | - Eric C Reynolds
- Oral Health Cooperative Research Centre, Melbourne Dental School, University of MelbourneParkville, VIC, Australia; Bio21 Institute, University of MelbourneParkville, VIC, Australia
| | - Mohammed A Hossain
- Florey Institute of Neuroscience and Mental Health, University of MelbourneParkville, VIC, Australia; School of Chemistry, University of MelbourneParkville, VIC, Australia
| | - Frances Separovic
- School of Chemistry, University of MelbourneParkville, VIC, Australia; Bio21 Institute, University of MelbourneParkville, VIC, Australia
| | - John D Wade
- Florey Institute of Neuroscience and Mental Health, University of MelbourneParkville, VIC, Australia; School of Chemistry, University of MelbourneParkville, VIC, Australia
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41
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Zhang W, He J, Wu J, Schmuck C. In Vivo Detoxification of Lipopolysaccharide by Antimicrobial Peptides. Bioconjug Chem 2016; 28:319-324. [DOI: 10.1021/acs.bioconjchem.6b00664] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wenxu Zhang
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Jiangcheng He
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Junchen Wu
- Key Laboratory for Advanced Materials & Institute of Fine Chemicals, School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai 200237, China
| | - Carsten Schmuck
- Institute
for Organic Chemistry University of Duisburg-Essen, 47057 Essen, Germany
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