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Bahlool AZ, Cavanagh B, Sullivan AO, MacLoughlin R, Keane J, Sullivan MPO, Cryan SA. Microfluidics produced ATRA-loaded PLGA NPs reduced tuberculosis burden in alveolar epithelial cells and enabled high delivered dose under simulated human breathing pattern in 3D printed head models. Eur J Pharm Sci 2024; 196:106734. [PMID: 38417586 DOI: 10.1016/j.ejps.2024.106734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 02/15/2024] [Accepted: 02/24/2024] [Indexed: 03/01/2024]
Abstract
Tuberculosis, caused by Mycobacterium tuberculosis (Mtb), is second only to COVID-19 as the top infectious disease killer worldwide. Multi-drug resistant TB (MDR-TB) may arise because of poor patient adherence to medications due to lengthy treatment duration and side effects. Delivering novel host directed therapies (HDT), like all trans retinoic acid (ATRA) may help to improve drug regimens and reduce the incidence of MDR-TB. Local delivery of ATRA to the site of infection leads to higher bioavailability and reduced systemic side effects. ATRA is poorly soluble in water and has a short half-life in plasma. Therefore, it requires a formulation step before it can be administered in vivo. ATRA loaded PLGA nanoparticles suitable for nebulization were manufactured and optimized using a scalable nanomanufacturing microfluidics (MF) mixing approach (MF-ATRA-PLGA NPs). MF-ATRA-PLGA NPs demonstrated a dose dependent inhibition of Mtb growth in TB-infected A549 alveolar epithelial cell model while preserving cell viability. The MF-ATRA-PLGA NPs were nebulized with the Aerogen Solo vibrating mesh nebulizer, with aerosol droplet size characterized using laser diffraction and the estimated delivered dose was determined. The volume median diameter (VMD) of the MF-ATRA-PLGA NPs was 3.00 ± 0.18 μm. The inhaled dose delivered in adult and paediatric 3D printed head models under a simulated normal adult and paediatric breathing pattern was found to be 47.05 ± 3 % and 20.15 ± 3.46 % respectively. These aerosol characteristics of MF-ATRA-PLGA NPs supports its suitability for delivery to the lungs via inhalation. The data generated on the efficacy of an inhalable, scalable and regulatory friendly ATRA-PLGA NPs formulation provides a foundation on which further pre-clinical testing can be built. Overall, the results of this project are promising for future research into ATRA loaded NPs formulations as inhaled host directed therapies for TB.
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Affiliation(s)
- Ahmad Z Bahlool
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland (RCSI), 123 St Stephens Green, Dublin 2, D02 YN77, Dublin, Ireland; Tissue Engineering Research Group, Royal College of Surgeons in Ireland (RCSI), 123 St Stephens Green, Dublin, Ireland; Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Trinity College Dublin, The University of Dublin, Dublin 8, Ireland
| | - Brenton Cavanagh
- Cellular and Molecular Imaging Core, Royal College of Surgeons in Ireland RCSI, Dublin 2, Ireland
| | - Andrew O' Sullivan
- Research and Development, Science and Emerging Technologies, Aerogen Ltd, Galway Business Park, Dangan, Galway, Ireland
| | - Ronan MacLoughlin
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland (RCSI), 123 St Stephens Green, Dublin 2, D02 YN77, Dublin, Ireland; Research and Development, Science and Emerging Technologies, Aerogen Ltd, Galway Business Park, Dangan, Galway, Ireland; School of Pharmacy and Pharmaceutical Sciences, Trinity College, D02 PN40 Dublin, Ireland
| | - Joseph Keane
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Trinity College Dublin, The University of Dublin, Dublin 8, Ireland
| | - Mary P O' Sullivan
- Department of Clinical Medicine, Trinity Translational Medicine Institute, St. James's Hospital, Trinity College Dublin, The University of Dublin, Dublin 8, Ireland
| | - Sally-Ann Cryan
- School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland (RCSI), 123 St Stephens Green, Dublin 2, D02 YN77, Dublin, Ireland; Tissue Engineering Research Group, Royal College of Surgeons in Ireland (RCSI), 123 St Stephens Green, Dublin, Ireland; SFI Advanced Materials and Bioengineering Research (AMBER) Centre, RCSI and Trinity College Dublin, Dublin, Ireland; SFI Centre for Research in Medical Devices (CÚRAM), NUIG & RCSI, Dublin, Ireland.
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Painter H, Harriss E, Fletcher HA, McShane H, Tanner R. Development and application of the direct mycobacterial growth inhibition assay: a systematic review. Front Immunol 2024; 15:1355983. [PMID: 38380319 PMCID: PMC10877019 DOI: 10.3389/fimmu.2024.1355983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 01/17/2024] [Indexed: 02/22/2024] Open
Abstract
Introduction First described by Wallis et al. in 2001 for the assessment of TB drugs, the direct mycobacterial growth inhibition assay (MGIA) offers a tractable ex vivo tool measuring the combined influences of host immunity, strain virulence and intervention effects. Over the past 13 years, we have led efforts to adapt the direct MGIA for the assessment of TB vaccines including optimisation, harmonisation and validation of BCG vaccine-induced responses as a benchmark, as well as assay transfer to institutes worldwide. Methods We have performed a systematic review on the primary published literature describing the development and applications of the direct MGIA from 2001 to June 2023 in accordance with the PRISMA reporting guidelines. Results We describe 63 studies in which the direct MGIA has been applied across species for the evaluation of TB drugs and novel TB vaccine candidates, the study of clinical cohorts including those with comorbidities, and to further understanding of potential immune correlates of protection from TB. We provide a comprehensive update on progress of the assay since its conception and critically evaluate current findings and evidence supporting its utility, highlighting priorities for future directions. Discussion While further standardisation and validation work is required, significant advancements have been made in the past two decades. The direct MGIA provides a potentially valuable tool for the early evaluation of TB drug and vaccine candidates, clinical cohorts, and immune mechanisms of mycobacterial control. Systematic review registration https://www.crd.york.ac.uk/prospero/, identifier CRD42023423491.
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Affiliation(s)
- Hannah Painter
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Eli Harriss
- Bodleian Health Care Libraries, University of Oxford, Oxford, United Kingdom
| | - Helen A. Fletcher
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Helen McShane
- Nuffield Department of Medicine, Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Rachel Tanner
- Department of Biology, University of Oxford, Oxford, United Kingdom
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R PA, Anbarasu A. Antimicrobial Peptides as Immunomodulators and Antimycobacterial Agents to Combat Mycobacterium tuberculosis: a Critical Review. Probiotics Antimicrob Proteins 2023; 15:1539-1566. [PMID: 36576687 DOI: 10.1007/s12602-022-10018-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2022] [Indexed: 12/29/2022]
Abstract
Tuberculosis (TB) is a devastating disease foisting a significantly high morbidity, prepotent in low- and middle-income developing countries. Evolution of drug resistance among Mycobacterium tuberculosis (Mtb), the causative agent of tuberculosis, has made the TB treatment more complicated. The protracted nature of present TB treatment, persistent and tolerant Mtb populations, interaction with antiretroviral therapy and existing toxicity concerned with conventional anti-TB drugs are the four major challenges inflicted with emergence of drug-resistant mycobacterial strains, and the standard medications are unable to combat these strains. These factors emphasize an exigency to develop new drugs to overcome these barriers in current TB therapy. With this regard, antimycobacterial peptides derived from various sources such as human cells, bacterial sources, mycobacteriophages, fungal, plant and animal sources could be considered as antituberculosis leads as most of these peptides are associated with dual advantages of having both bactericidal activity towards Mtb as well as immuno-regulatory property. Some of the peptides possess the additional advantage of interacting synergistically with antituberculosis medications too, thereby increasing their efficiency, underscoring the vigour of antimicrobial peptides (AMPs) as best possible alternative therapeutic candidates or adjuvants in TB treatment. Albeit the beneficiary features of these peptides, few obstacles allied with them like cytotoxicity and proteolytic degradation are matter of concerns too. In this review, we have focused on structural hallmarks, targeting mechanisms and specific structural aspects contributing to antimycobacterial activity and discovered natural and synthetic antimycobacterial peptides along with their sources, anti-TB, immuno-regulatory properties, merits and demerits and possible delivery methods of AMPs.
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Affiliation(s)
- Preethi A R
- Medical & Biological Computing Laboratory, School of Bio-Sciences & Technology, Vellore Institute of Technology, Vellore-632014, India
- Department of Biotechnology, SBST, VIT, Vellore-632014, Tamil Nadu, India
| | - Anand Anbarasu
- Medical & Biological Computing Laboratory, School of Bio-Sciences & Technology, Vellore Institute of Technology, Vellore-632014, India.
- Department of Biotechnology, SBST, VIT, Vellore-632014, Tamil Nadu, India.
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Jacobo-Delgado YM, Rodríguez-Carlos A, Serrano CJ, Rivas-Santiago B. Mycobacterium tuberculosis cell-wall and antimicrobial peptides: a mission impossible? Front Immunol 2023; 14:1194923. [PMID: 37266428 PMCID: PMC10230078 DOI: 10.3389/fimmu.2023.1194923] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Accepted: 04/25/2023] [Indexed: 06/03/2023] Open
Abstract
Mycobacterium tuberculosis (Mtb) is one of the most important infectious agents worldwide and causes more than 1.5 million deaths annually. To make matters worse, the drug resistance among Mtb strains has risen substantially in the last few decades. Nowadays, it is not uncommon to find patients infected with Mtb strains that are virtually resistant to all antibiotics, which has led to the urgent search for new molecules and therapies. Over previous decades, several studies have demonstrated the efficiency of antimicrobial peptides to eliminate even multidrug-resistant bacteria, making them outstanding candidates to counterattack this growing health problem. Nevertheless, the complexity of the Mtb cell wall makes us wonder whether antimicrobial peptides can effectively kill this persistent Mycobacterium. In the present review, we explore the complexity of the Mtb cell wall and analyze the effectiveness of antimicrobial peptides to eliminate the bacilli.
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Miranda-Velez M, Sarker GS, Ramisetty P, Geden S, Bartolomeu Halicki PC, Annamalai T, Tse-Dinh YC, Rohde KH, Moon JH. Proton Motive Force-Disrupting Antimycobacterial Guanylurea Polymer. Biomacromolecules 2022; 23:4668-4677. [DOI: 10.1021/acs.biomac.2c00902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Michelle Miranda-Velez
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
| | - Golam Sabbir Sarker
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
| | - Priya Ramisetty
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
| | - Sandra Geden
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, Florida 32827, United States
| | - Priscila Cristina Bartolomeu Halicki
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, Florida 32827, United States
| | - Thirunavukkarasu Annamalai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
| | - Yuk-Ching Tse-Dinh
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
| | - Kyle H. Rohde
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, Florida 32827, United States
| | - Joong Ho Moon
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
- Biomolecular Sciences Institute, Florida International University, 11200 SW 8th St., Miami, Florida 33199, United States
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Abstract
The ribonuclease A (RNase A) family is one of the best-characterized vertebrate-specific proteins. In humans, eight catalytically active RNases (numbered 1–8) have been identified and have unique tissue distributions. Apart from the digestion of dietary RNA, a broad range of biological actions, including the regulation of intra- or extra-cellular RNA metabolism as well as antiviral, antibacterial, and antifungal activities, neurotoxicity, promotion of cell proliferation, anti-apoptosis, and immunomodulatory abilities, have been recently reported for the members of this family. Based on multiple biological roles, RNases are found to participate in the pathogenic processes of many diseases, such as infection, immune dysfunction, neurodegeneration, cancer, and cardiovascular disorders. This review summarizes the available data on the human RNase A family and illustrates the significant roles of the eight canonical RNases in health and disease, for stimulating further basic research and development of ideas on the potential solutions for disease diagnosis and treatment.
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Affiliation(s)
- Desen Sun
- Department of Gastroenterology, The Affiliated Hospital of Medical School, Ningbo University, Ningbo, Zhejiang 315020, China,Department of Biochemistry and Molecular Biology, and Zhejiang Key Laboratory of Pathophysiology, School of Medicine, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Chenjie Han
- Institute of Environmental Medicine and Affiliated Hangzhou First People’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China,Undergraduate Program in Public Health, School of Public Health, Zhejiang University, Hangzhou, Zhejiang 310058, China
| | - Jinghao Sheng
- Institute of Environmental Medicine and Affiliated Hangzhou First People’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang 310058, China,Corresponding author
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Jadhav K, Singh R, Ray E, Singh AK, Verma RK. Taming the Devil: Antimicrobial Peptides for Safer TB Therapeutics. Curr Protein Pept Sci 2022; 23:643-656. [PMID: 35619262 DOI: 10.2174/1389203723666220526161109] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 12/29/2022]
Abstract
Tuberculosis (TB) is a highly contagious infection with extensive mortality and morbidity. The rise of TB-superbugs (drug-resistant strains) with the increase of their resistance to conventional antibiotics has prompted a further search for new anti-mycobacterial agents. It is difficult to breach the barriers around TB bacteria, including mycolic cell wall, granuloma, biofilm and mucus, by conventional antibiotics in a short span of time. Hence, there is an essential need for molecules with an unconventional mode of action and structure that can efficiently break the barriers around mycobacterium. Antimicrobial peptides (AMP) are essential components of innate immunity having cationic and amphipathic characteristics. Lines of evidence show that AMPs have good myco-bactericidal and antibiofilm activity against normal as well as antibiotic-resistant TB bacteria. These peptides have shown direct killing of bacteria by membrane lysis and indirect killing by activation of innate immune response in host cells by interacting with the component of the bacterial membrane and intracellular targets through diverse mechanisms. Despite a good anti-mycobacterial activity, some undesirable characteristics are also associated with AMP, including hemolysis, cytotoxicity, susceptibility to proteolysis and poor pharmacokinetic profile, and hence only a few clinical studies have been conducted with these biomolecules. The design of new combinatorial therapies, including AMPs and particulate drug delivery systems, could be new potential alternatives to conventional antibiotics to fight MDR- and XDRTB. This review outlined the array of AMP roles in TB therapy, possible mechanisms of actions, activities, and current advances in pragmatic strategies to improve challenges accompanying the delivery of AMP for tuberculosis therapeutics.
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Affiliation(s)
- Krishna Jadhav
- Institute of Nano Science and Technology (INST), Habitat Centre, Phase-10, Sector-64, Mohali, Punjab-160062, India
| | - Raghuraj Singh
- Institute of Nano Science and Technology (INST), Habitat Centre, Phase-10, Sector-64, Mohali, Punjab-160062, India
| | - Eupa Ray
- Institute of Nano Science and Technology (INST), Habitat Centre, Phase-10, Sector-64, Mohali, Punjab-160062, India
| | - Amit Kumar Singh
- National JALMA Institute for Leprosy and Other Mycobacterial Diseases (ICMR), Tajganj, Agra-282001, India
| | - Rahul Kumar Verma
- Institute of Nano Science and Technology (INST), Habitat Centre, Phase-10, Sector-64, Mohali, Punjab-160062, India
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Role of Antimicrobial Peptides in Treatment and Prevention of Mycobacterium Tuberculosis: A Review. Int J Pept Res Ther 2022; 28:132. [PMID: 35891800 PMCID: PMC9305673 DOI: 10.1007/s10989-022-10435-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/16/2022] [Indexed: 11/01/2022]
Abstract
Tuberculosis (TB) is one of the leading cause of death worldwide, and the world is fighting with this global health emergency from the past 25 year. The current clinical interventions for the management of TB face a number of inherent challenges which includes low patient compliance due to the long therapy regimen, and emerging antimicrobial resistance. Therefore, there is an unmet need of new anti-TB therapeutic agent with enhanced safety profile, which can reduce the duration of therapy, enhanced bioavailability and efficacy against drug resistant forms of TB. Bacteriocins or anti microbial peptides (AMPs) occurring in microbes, human beings and other life forms have been investigated as host defense peptides. Structurally AMPs are short and ionized and play crucial role in innate immunity of host. Some AMPs can kill microbial infections directly while others function indirectly by altering the host defense mechanisms. Amidst rising issue of antibiotic resistance, AMPs are being tested in clinical research as potential antibiotics and novel therapeutics to fight against infections and non-infectious diseases. Studies have also highlighted the ability of AMPs to act against the bacteria spreading tuberculosis. The present review provides information on antimicrobial peptides, highlights their biological role, classification and mode of action in treatment and prevention of tuberculosis. It further mentions the prospects and challenges of developing peptides for their therapeutic applications against mycobacterium tuberculosis.
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Sudadech P, Roytrakul S, Kaewprasert O, Sirichoat A, Chetchotisakd P, Kanthawong S, Faksri K. Assessment of in vitro activities of novel modified antimicrobial peptides against clarithromycin resistant Mycobacterium abscessus. PLoS One 2021; 16:e0260003. [PMID: 34780520 PMCID: PMC8592419 DOI: 10.1371/journal.pone.0260003] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Accepted: 11/01/2021] [Indexed: 01/21/2023] Open
Abstract
Mycobacterium abscessus (Mab) is one of the most drug resistant bacteria with a high treatment failure rate. Antimicrobial peptides (AMPs) are alternative therapeutic agents against this infection. This study was aimed to assess the in vitro activities of thirteen AMPs (S5, S52, S6, S61, S62, S63, KLK, KLK1, KLK2, Pug-1, Pug-2, Pug-3 and Pug-4) that have never been investigated against drug resistant Mab isolates. Only four novel modified AMPs (S61, S62, S63 and KLK1) provided the lowest minimum inhibitory concentration (MIC) values ranging from 200–400 μg/ml against the Mab ATCC19977 strain. These four potential AMPs were further tested with 16 clinical isolates of clarithromycin resistant Mab. The majority of the tested strains (10/16 isolates, 62.5%) showed ~99% kill by all four AMPs within 24 hours with an MIC <50 μg/ml. Only two isolates (12.5%) with acquired clarithromycin resistance, however, exhibited values <50 μg/ml of four potential AMPs, S61, S62, S63 and KLK1 after 3-days-incubation. At the MICs level, S63 showed the lowest toxicity with 1.50% hemolysis and 100% PBMC viability whereas KLK1 showed the highest hemolysis (10.21%) and lowest PBMC viability (93.52%). S61, S62 and S63 were further tested with clarithromycin-AMP interaction assays and found that 5/10 (50%) of selected isolates exhibited a synergistic interaction with 0.02–0.41 FICI values. This present study demonstrated the potential application of novel AMPs as an adjunctive treatment with clarithromycin against drug resistant Mab infection.
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Affiliation(s)
- Phantitra Sudadech
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Sittiruk Roytrakul
- Genome Institute, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Orawee Kaewprasert
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Auttawit Sirichoat
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Ploenchan Chetchotisakd
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
- Department of Medicine, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
| | - Sakawrat Kanthawong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
| | - Kiatichai Faksri
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Khon Kaen, Thailand
- Research and Diagnostic Center for Emerging Infectious Diseases (RCEID), Khon Kaen University, Khon Kaen, Thailand
- * E-mail:
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Jacobo-Delgado YM, Torres-Juarez F, Rodríguez-Carlos A, Santos-Mena A, Enciso-Moreno JE, Rivas-Santiago C, Diamond G, Rivas-Santiago B. Retinoic acid induces antimicrobial peptides and cytokines leading to Mycobacterium tuberculosis elimination in airway epithelial cells. Peptides 2021; 142:170580. [PMID: 34033876 DOI: 10.1016/j.peptides.2021.170580] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 05/07/2021] [Accepted: 05/19/2021] [Indexed: 10/21/2022]
Abstract
Tuberculosis (TB) is the leading cause of death by a single infectious agent, Mycobacterium tuberculosis (Mtb). Alveolar macrophages and respiratory epithelial cells are the first cells exposed to Mtb during the primary infection, once these cells are activated, secrete cytokines and antimicrobial peptides that are associated with the Mtb contention and elimination. Vitamins are micronutrients that function as boosters on the innate immune system, however, is unclear whether they have any protective activity during Mtb infection. Thus, we investigated the role of vitamin A (retinoic acid), vitamin C (ascorbic acid), vitamin D (calcitriol), and vitamin E (alfa-tocopherol) as inductors of molecules related to mycobacterial infection in macrophages and epithelial cells. Our results showed that retinoic acid promotes the expression of pro- and anti-inflammatory molecules such as Thymic stromal lymphopoietin (TSLP), β-defensin-2, IL-1β, CCL20, β-defensin-3, Cathelicidin LL-37, TGF-β, and RNase 7, whereas calcitriol, ascorbic acid, and α-tocopherol lead to an anti-inflammatory response. Treatment of Mtb-infected epithelial cells and macrophage-like cells with the vitamins showed a differential response, where calcitriol reduced Mtb in macrophages, while retinoic acid reduced infection in epithelial cells. Thereby, we propose that a combination of calcitriol and retinoic acid supplementation can drive the immune response, and promotes the Mtb elimination by increasing the expression of antimicrobial peptides and cytokines, while simultaneously modulating inflammation.
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Affiliation(s)
| | | | | | | | | | - Cesar Rivas-Santiago
- CONACYT-Academic Unit of Chemical Sciences, University Autonomous of Zacatecas, Zacatecas, Mexico
| | - Gill Diamond
- Department of Oral Immunology and Infectious Diseases, University of Louisville School of Dentistry, Louisville, KY, 40202, USA
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Raj S, Venugopal U, Pant G, Kalyan M, Arockiaraj J, Krishnan MY, Pasupuleti M. Anti-mycobacterial activity evaluation of designed peptides: cryptic and database filtering based approach. Arch Microbiol 2021; 203:4891-4899. [PMID: 34244831 DOI: 10.1007/s00203-021-02474-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Revised: 06/30/2021] [Accepted: 07/01/2021] [Indexed: 01/21/2023]
Abstract
Worldwide, TB is one of the deadly airborne diseases, which accounts for 10.4 million deaths annually. Serious toxicity issue, prolonged treatment regimens of the current drugs, rise in multidrug-resistant strains, and the unique defensive mechanism makes the development of novel therapeutic molecules against Mycobacterium tuberculosis (MT) an urgent need. As MT has a lengthy latent phase and unique cell wall architecture, a reasonable approach is needed to find molecules having a different killing mechanism rather than traditional approaches. Host defence peptides (HDPs) will be the most promising alternative, potential therapeutic candidates as they target the microbial membrane in particular and are an essential part of the innate immunity of humans. This works demonstrates the utility of "Database filtering" and three-dimensional (3D) modelling approach in finding novel AMPs with appreciable activity towards MT. Results of this study indicate that peptides with 70% hydrophobicity, but without hydrophobicity patches (> 4 hydrophobic amino acids in series) and charge of + 4 or + 5 are most likely to be good anti-tubercular candidates.
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Affiliation(s)
- Sneha Raj
- Microbiology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Umamageswaran Venugopal
- Microbiology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Garima Pant
- Electron Microscopy Unit, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Mitra Kalyan
- Electron Microscopy Unit, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Jesu Arockiaraj
- SRM Research Institute, SRM Institute of Science and Technology, Kattankulathur, Chennai, Tamil Nadu, 603 203, India
| | - Manju Y Krishnan
- Microbiology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India
| | - Mukesh Pasupuleti
- Microbiology Division, CSIR-Central Drug Research Institute, Sector 10, Jankipuram Extension, Sitapur Road, Lucknow, 226031, India.
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Sarkar T, Chetia M, Chatterjee S. Antimicrobial Peptides and Proteins: From Nature's Reservoir to the Laboratory and Beyond. Front Chem 2021; 9:691532. [PMID: 34222199 PMCID: PMC8249576 DOI: 10.3389/fchem.2021.691532] [Citation(s) in RCA: 79] [Impact Index Per Article: 26.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Rapid rise of antimicrobial resistance against conventional antimicrobials, resurgence of multidrug resistant microbes and the slowdown in the development of new classes of antimicrobials, necessitates the urgent development of alternate classes of therapeutic molecules. Antimicrobial peptides (AMPs) are small proteins present in different lifeforms in nature that provide defense against microbial infections. They have been effective components of the host defense system for a very long time. The fact that the development of resistance by the microbes against the AMPs is relatively slower or delayed compared to that against the conventional antibiotics, makes them prospective alternative therapeutics of the future. Several thousands of AMPs have been isolated from various natural sources like microorganisms, plants, insects, crustaceans, animals, humans, etc. to date. However, only a few of them have been translated commercially to the market so far. This is because of some inherent drawbacks of the naturally obtained AMPs like 1) short half-life owing to the susceptibility to protease degradation, 2) inactivity at physiological salt concentrations, 3) cytotoxicity to host cells, 4) lack of appropriate strategies for sustained and targeted delivery of the AMPs. This has led to a surge of interest in the development of synthetic AMPs which would retain or improve the antimicrobial potency along with circumventing the disadvantages of the natural analogs. The development of synthetic AMPs is inspired by natural designs and sequences and strengthened by the fusion with various synthetic elements. Generation of the synthetic designs are based on various strategies like sequence truncation, mutation, cyclization and introduction of unnatural amino acids and synthons. In this review, we have described some of the AMPs isolated from the vast repertoire of natural sources, and subsequently described the various synthetic designs that have been developed based on the templates of natural AMPs or from de novo design to make commercially viable therapeutics of the future. This review entails the journey of the AMPs from their natural sources to the laboratory.
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Affiliation(s)
| | | | - Sunanda Chatterjee
- Department of Chemistry, Indian Institute of Technology, Guwahati, India
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13
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Nucera F, Lo Bello F, Shen SS, Ruggeri P, Coppolino I, Di Stefano A, Stellato C, Casolaro V, Hansbro PM, Adcock IM, Caramori G. Role of Atypical Chemokines and Chemokine Receptors Pathways in the Pathogenesis of COPD. Curr Med Chem 2021; 28:2577-2653. [PMID: 32819230 DOI: 10.2174/0929867327999200819145327] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 06/11/2020] [Accepted: 06/18/2020] [Indexed: 11/22/2022]
Abstract
Chronic obstructive pulmonary disease (COPD) represents a heightened inflammatory response in the lung generally resulting from tobacco smoking-induced recruitment and activation of inflammatory cells and/or activation of lower airway structural cells. Several mediators can modulate activation and recruitment of these cells, particularly those belonging to the chemokines (conventional and atypical) family. There is emerging evidence for complex roles of atypical chemokines and their receptors (such as high mobility group box 1 (HMGB1), antimicrobial peptides, receptor for advanced glycosylation end products (RAGE) or toll-like receptors (TLRs)) in the pathogenesis of COPD, both in the stable disease and during exacerbations. Modulators of these pathways represent potential novel therapies for COPD and many are now in preclinical development. Inhibition of only a single atypical chemokine or receptor may not block inflammatory processes because there is redundancy in this network. However, there are many animal studies that encourage studies for modulating the atypical chemokine network in COPD. Thus, few pharmaceutical companies maintain a significant interest in developing agents that target these molecules as potential antiinflammatory drugs. Antibody-based (biological) and small molecule drug (SMD)-based therapies targeting atypical chemokines and/or their receptors are mostly at the preclinical stage and their progression to clinical trials is eagerly awaited. These agents will most likely enhance our knowledge about the role of atypical chemokines in COPD pathophysiology and thereby improve COPD management.
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Affiliation(s)
- Francesco Nucera
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences (BIOMORF), University of Messina, Pugliatti Square 1, 98122 Messina, Italy
| | - Federica Lo Bello
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences (BIOMORF), University of Messina, Pugliatti Square 1, 98122 Messina, Italy
| | - Sj S Shen
- Faculty of Science, Centre for Inflammation, Centenary Institute, University of Technology, Ultimo, Sydney, Australia
| | - Paolo Ruggeri
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences (BIOMORF), University of Messina, Pugliatti Square 1, 98122 Messina, Italy
| | - Irene Coppolino
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences (BIOMORF), University of Messina, Pugliatti Square 1, 98122 Messina, Italy
| | - Antonino Di Stefano
- Division of Pneumology, Cyto- Immunopathology Laboratory of the Cardio-Respiratory System, Clinical Scientific Institutes Maugeri IRCCS, Veruno, Italy
| | - Cristiana Stellato
- Department of Medicine, Surgery and Dentistry, Salerno Medical School, University of Salerno, Salerno, Italy
| | - Vincenzo Casolaro
- Department of Medicine, Surgery and Dentistry, Salerno Medical School, University of Salerno, Salerno, Italy
| | - Phil M Hansbro
- Faculty of Science, Centre for Inflammation, Centenary Institute, University of Technology, Ultimo, Sydney, Australia
| | - Ian M Adcock
- Airway Disease Section, National Heart and Lung Institute, Imperial College, London, United Kingdom
| | - Gaetano Caramori
- Department of Biomedical, Dental, Morphological and Functional Imaging Sciences (BIOMORF), University of Messina, Pugliatti Square 1, 98122 Messina, Italy
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14
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Lu L, Wei R, Prats-Ejarque G, Goetz M, Wang G, Torrent M, Boix E. Human RNase3 immune modulation by catalytic-dependent and independent modes in a macrophage-cell line infection model. Cell Mol Life Sci 2021; 78:2963-2985. [PMID: 33226440 PMCID: PMC8004517 DOI: 10.1007/s00018-020-03695-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 09/21/2020] [Accepted: 10/31/2020] [Indexed: 02/06/2023]
Abstract
The human RNase3 is a member of the RNaseA superfamily involved in host immunity. RNase3 is expressed by leukocytes and shows broad-spectrum antimicrobial activity. Together with a direct antimicrobial action, RNase3 exhibits immunomodulatory properties. Here, we have analysed the transcriptome of macrophages exposed to the wild-type protein and a catalytic-defective mutant (RNase3-H15A). The analysis of differently expressed genes (DEGs) in treated THP1-derived macrophages highlighted a common pro-inflammatory "core-response" independent of the protein ribonucleolytic activity. Network analysis identified the epidermal growth factor receptor (EGFR) as the main central regulatory protein. Expression of selected DEGs and MAPK phosphorylation were inhibited by an anti-EGFR antibody. Structural analysis suggested that RNase3 activates the EGFR pathway by direct interaction with the receptor. Besides, we identified a subset of DEGs related to the protein ribonucleolytic activity, characteristic of virus infection response. Transcriptome analysis revealed an early pro-inflammatory response, not associated to the protein catalytic activity, followed by a late activation in a ribonucleolytic-dependent manner. Next, we demonstrated that overexpression of macrophage endogenous RNase3 protects the cells against infection by Mycobacterium aurum and the human respiratory syncytial virus. Comparison of cell infection profiles in the presence of Erlotinib, an EGFR inhibitor, revealed that the receptor activation is required for the antibacterial but not for the antiviral protein action. Moreover, the DEGs related and unrelated to the protein catalytic activity are associated to the immune response to bacterial and viral infection, respectively. We conclude that RNase3 modulates the macrophage defence against infection in both catalytic-dependent and independent manners.
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Affiliation(s)
- Lu Lu
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autonoma de Barcelona, Cerdanyola del Vallès, Spain
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - RanLei Wei
- Center of Precision Medicine and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, China
| | - Guillem Prats-Ejarque
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autonoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Maria Goetz
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autonoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Gang Wang
- Center of Precision Medicine and Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, China
| | - Marc Torrent
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autonoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autonoma de Barcelona, Cerdanyola del Vallès, Spain.
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15
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Bosso A, Di Maro A, Cafaro V, Di Donato A, Notomista E, Pizzo E. Enzymes as a Reservoir of Host Defence Peptides. Curr Top Med Chem 2021; 20:1310-1323. [PMID: 32223733 DOI: 10.2174/1568026620666200327173815] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 02/21/2020] [Accepted: 03/11/2020] [Indexed: 12/16/2022]
Abstract
Host defence peptides (HDPs) are powerful modulators of cellular responses to various types of insults caused by pathogen agents. To date, a wide range of HDPs, from species of different kingdoms including bacteria, plant and animal with extreme diversity in structure and biological activity, have been described. Apart from a limited number of peptides ribosomally synthesized, a large number of promising and multifunctional HDPs have been identified within protein precursors, with properties not necessarily related to innate immunity, consolidating the fascinating hypothesis that proteins have a second or even multiple biological mission in the form of one or more bio-active peptides. Among these precursors, enzymes constitute certainly an interesting group, because most of them are mainly globular and characterized by a fine specific internal structure closely related to their catalytic properties and also because they are yet little considered as potential HDP releasing proteins. In this regard, the main aim of the present review is to describe a panel of HDPs, identified in all canonical classes of enzymes, and to provide a detailed description on hydrolases and their corresponding HDPs, as there seems to exist a striking link between these structurally sophisticated catalysts and their high content in cationic and amphipathic cryptic peptides.
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Affiliation(s)
- Andrea Bosso
- Department of Biology, University of Naples 'Federico II', Naples, Italy
| | - Antimo Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies (DiSTABiF), University of Campania 'Luigi Vanvitelli', Caserta, Italy
| | - Valeria Cafaro
- Department of Biology, University of Naples 'Federico II', Naples, Italy
| | - Alberto Di Donato
- Department of Biology, University of Naples 'Federico II', Naples, Italy
| | - Eugenio Notomista
- Department of Biology, University of Naples 'Federico II', Naples, Italy
| | - Elio Pizzo
- Department of Biology, University of Naples 'Federico II', Naples, Italy
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16
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Di Natale C, De Benedictis I, De Benedictis A, Marasco D. Metal-Peptide Complexes as Promising Antibiotics to Fight Emerging Drug Resistance: New Perspectives in Tuberculosis. Antibiotics (Basel) 2020; 9:antibiotics9060337. [PMID: 32570779 PMCID: PMC7344629 DOI: 10.3390/antibiotics9060337] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 06/14/2020] [Accepted: 06/16/2020] [Indexed: 12/21/2022] Open
Abstract
In metal-peptide interactions, cations form stable complexes through bonds with coordinating groups as side chains of amino acids. These compounds, among other things, exert a wide variety of antimicrobial activities through structural changes of peptides upon metal binding and redox chemistry. They exhibit different mechanisms of action (MOA), including the modification of DNA/RNA, protein and cell wall synthesis, permeabilization and modulation of gradients of cellular membranes. Nowadays, the large increase in antibiotic resistance represents a crucial problem to limit progression at the pandemic level of the diseases that seemed nearly eradicated, such as tuberculosis (Tb). Mycobacterium tuberculosis (Mtb) is intrinsically resistant to many antibiotics due to chromosomal mutations which can lead to the onset of novel strains. Consequently, the maximum pharmaceutical effort should be focused on the development of new therapeutic agents and antimicrobial peptides can represent a valuable option as a copious source of potential bioactive compounds. The introduction of a metal center can improve chemical diversity and hence specificity and bioavailability while, in turn, the coordination to peptides of metal complexes can protect them and enhance their poor water solubility and air stability: the optimization of these parameters is strictly required for drug prioritization and to obtain potent inhibitors of Mtb infections with novel MOAs. Here, we present a panoramic review of the most recent findings in the field of metal complex-peptide conjugates and their delivery systems with the potential pharmaceutical application as novel antibiotics in Mtb infections.
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Affiliation(s)
- Concetta Di Natale
- Department of Pharmacy, University of Naples “Federico II”, 80134 Napoli NA, Italy; (C.D.N.); (I.D.B.); (A.D.B.)
- Center for Advanced Biomaterial for Health Care (CABHC), Istituto Italiano di Tecnologia, 80125 Naples, Italy
- Interdisciplinary Research Centre on Biomaterials (CRIB) and Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale, University of Naples Federico II, Piazzale Tecchio 80, 80125 Naples, Italy
| | - Ilaria De Benedictis
- Department of Pharmacy, University of Naples “Federico II”, 80134 Napoli NA, Italy; (C.D.N.); (I.D.B.); (A.D.B.)
| | - Arianna De Benedictis
- Department of Pharmacy, University of Naples “Federico II”, 80134 Napoli NA, Italy; (C.D.N.); (I.D.B.); (A.D.B.)
| | - Daniela Marasco
- Department of Pharmacy, University of Naples “Federico II”, 80134 Napoli NA, Italy; (C.D.N.); (I.D.B.); (A.D.B.)
- Correspondence:
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17
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Chessa C, Bodet C, Jousselin C, Wehbe M, Lévêque N, Garcia M. Antiviral and Immunomodulatory Properties of Antimicrobial Peptides Produced by Human Keratinocytes. Front Microbiol 2020; 11:1155. [PMID: 32582097 PMCID: PMC7283518 DOI: 10.3389/fmicb.2020.01155] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 05/06/2020] [Indexed: 12/15/2022] Open
Abstract
Keratinocytes, the main cells of the epidermis, are the first site of replication as well as the first line of defense against many viruses such as arboviruses, enteroviruses, herpes viruses, human papillomaviruses, or vaccinia virus. During viral replication, these cells can sense virus associated molecular patterns leading to the initiation of an innate immune response composed of pro-inflammatory cytokines, chemokines, and antimicrobial peptides. Human keratinocytes produce and secrete at least nine antimicrobial peptides: human cathelicidin LL-37, types 1–4 human β-defensins, S100 peptides such as psoriasin (S100A7), calprotectin (S100A8/9) and koebnerisin (S100A15), and RNase 7. These peptides can exert direct antiviral effects on the viral particle or its replication cycle, and indirect antiviral activity, by modulating the host immune response. The purpose of this review is to summarize current knowledge of antiviral and immunomodulatory properties of human keratinocyte antimicrobial peptides.
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Affiliation(s)
- Céline Chessa
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, Poitiers, France.,Laboratoire Inflammation, Tissus Epithéliaux et Cytokines, LITEC EA 4331, Université de Poitiers, Poitiers, France
| | - Charles Bodet
- Laboratoire Inflammation, Tissus Epithéliaux et Cytokines, LITEC EA 4331, Université de Poitiers, Poitiers, France
| | - Clément Jousselin
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, Poitiers, France.,Laboratoire Inflammation, Tissus Epithéliaux et Cytokines, LITEC EA 4331, Université de Poitiers, Poitiers, France
| | - Michel Wehbe
- Laboratoire Inflammation, Tissus Epithéliaux et Cytokines, LITEC EA 4331, Université de Poitiers, Poitiers, France
| | - Nicolas Lévêque
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, Poitiers, France.,Laboratoire Inflammation, Tissus Epithéliaux et Cytokines, LITEC EA 4331, Université de Poitiers, Poitiers, France
| | - Magali Garcia
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, Poitiers, France.,Laboratoire Inflammation, Tissus Epithéliaux et Cytokines, LITEC EA 4331, Université de Poitiers, Poitiers, France
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18
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Kosgey JC, Jia L, Nyamao RM, Zhao Y, Xue T, Yang J, Fang Y, Zhang F. RNase 1, 2, 5 & 8 role in innate immunity: Strain specific antimicrobial activity. Int J Biol Macromol 2020; 160:1042-1049. [PMID: 32504708 DOI: 10.1016/j.ijbiomac.2020.06.001] [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: 04/14/2020] [Revised: 05/31/2020] [Accepted: 06/01/2020] [Indexed: 01/26/2023]
Abstract
The increase in microbial resistance to conventional antimicrobial agents is driving research for the discovery of new antibiotics and antifungal agents. The greatest challenge in this endeavor is to find antimicrobial agents with broad antimicrobial activity and low toxicity. Antimicrobial peptides, for example, RNases, are one of the promising areas. The production of RNases increases during infection, but their role is still being explored. Whereas the enzymatic activity of RNases is well documented, their physiological function is still being investigated. This study aimed to evaluate the antimicrobial activity of RNase 1, 2, 5, and 8 against E. coli strains, S. aureus, Streptococcus thermophilus, P. aeruginosa, Candida albicans, and Candida glabrata. The results demonstrated that RNases have a strain-specific antimicrobial activity. RNase 1 had the highest antimicrobial activity compared to other RNases. All the microorganisms screened had varying levels of susceptibility to RNases, except P. aeruginosa and E. coli DR115. RNase 1 showed dose-dependent activity against C. albicans. The RNase killed Candida albicans by lowering the mitochondrial membrane potential but did not damage the cell membrane. We concluded that strain-specific antimicrobial activity is one of the physiological roles of RNases.
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Affiliation(s)
- Janet Cheruiyot Kosgey
- School of Biological and Life Sciences, The Technical University of Kenya, 52428-00200, Kenya; Department of Microbiology, WU Lien-Teh Institute, Harbin Medical University, Harbin 150086, China
| | - Lina Jia
- Department of Microbiology, WU Lien-Teh Institute, Harbin Medical University, Harbin 150086, China
| | - Rose Magoma Nyamao
- Department of Microbiology, WU Lien-Teh Institute, Harbin Medical University, Harbin 150086, China; School of Medicine, Kenyatta University, 43844, 00100, Kenya
| | - Yi Zhao
- Department of Microbiology, WU Lien-Teh Institute, Harbin Medical University, Harbin 150086, China
| | - Teng Xue
- Department of Microbiology, WU Lien-Teh Institute, Harbin Medical University, Harbin 150086, China
| | - Jianxun Yang
- Department of Microbiology, WU Lien-Teh Institute, Harbin Medical University, Harbin 150086, China; Department of Dermatology, The 2nd Hospital of Harbin Medical University, Harbin 150086, China
| | - Yong Fang
- Department of Microbiology, WU Lien-Teh Institute, Harbin Medical University, Harbin 150086, China
| | - Fengmin Zhang
- Department of Microbiology, WU Lien-Teh Institute, Harbin Medical University, Harbin 150086, China.
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19
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Srinivasan S, Waghu FH, Idicula-Thomas S, Venkatesh KV. A steady-state modeling approach for simulation of antimicrobial peptide-cell membrane interaction. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2020; 1862:183242. [DOI: 10.1016/j.bbamem.2020.183242] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Revised: 02/08/2020] [Accepted: 02/12/2020] [Indexed: 01/17/2023]
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20
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Rademacher F, Dreyer S, Kopfnagel V, Gläser R, Werfel T, Harder J. The Antimicrobial and Immunomodulatory Function of RNase 7 in Skin. Front Immunol 2019; 10:2553. [PMID: 31749808 PMCID: PMC6848066 DOI: 10.3389/fimmu.2019.02553] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 10/15/2019] [Indexed: 11/13/2022] Open
Abstract
The human ribonuclease RNase 7 has been originally isolated from human skin and is a member of the human RNase A superfamily. RNase 7 is constantly released by keratinocytes and accumulates on the skin surface. The expression of RNase 7 in keratinocytes can be induced by diverse stimuli such as cytokines, growth factors, and microbial factors. RNase 7 exhibits a potent broad spectrum of antimicrobial activity against various microorganisms and contributes to control bacterial growth on the skin surface. The ribonuclease and antimicrobial activity of RNase 7 can be blocked by the endogenous ribonuclease inhibitor. There is also increasing evidence that RNase 7 exerts immunomodulatory activities and may participate in antiviral defense. In this review, we discuss how these characteristics of RNase 7 contribute to innate cutaneous defense and highlight its role in skin infection and inflammation. We also speculate how a potential dysregulation of RNase 7 promotes inflammatory skin diseases and if RNase 7 may have therapeutic potential.
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Affiliation(s)
| | - Sylvia Dreyer
- Division of Immunodermatology and Allergy Research, Department of Dermatology and Allergy, Hannover Medical School, Hanover, Germany
| | - Verena Kopfnagel
- Division of Immunodermatology and Allergy Research, Department of Dermatology and Allergy, Hannover Medical School, Hanover, Germany
- Hannover Unified Biobank, Hannover Medical School, Hanover, Germany
| | - Regine Gläser
- Department of Dermatology, University of Kiel, Kiel, Germany
| | - Thomas Werfel
- Division of Immunodermatology and Allergy Research, Department of Dermatology and Allergy, Hannover Medical School, Hanover, Germany
- Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hanover, Germany
| | - Jürgen Harder
- Department of Dermatology, University of Kiel, Kiel, Germany
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21
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Salazar VA, Arranz-Trullén J, Prats-Ejarque G, Torrent M, Andreu D, Pulido D, Boix E. Insight into the Antifungal Mechanism of Action of Human RNase N-terminus Derived Peptides. Int J Mol Sci 2019; 20:ijms20184558. [PMID: 31540052 PMCID: PMC6770517 DOI: 10.3390/ijms20184558] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 09/13/2019] [Indexed: 02/06/2023] Open
Abstract
Candida albicans is a polymorphic fungus responsible for mucosal and skin infections. Candida cells establish themselves into biofilm communities resistant to most currently available antifungal agents. An increase of severe infections ensuing in fungal septic shock in elderly or immunosuppressed patients, along with the emergence of drug-resistant strains, urge the need for the development of alternative antifungal agents. In the search for novel antifungal drugs our laboratory demonstrated that two human ribonucleases from the vertebrate-specific RNaseA superfamily, hRNase3 and hRNase7, display a high anticandidal activity. In a previous work, we proved that the N-terminal region of the RNases was sufficient to reproduce most of the parental protein bactericidal activity. Next, we explored their potency against a fungal pathogen. Here, we have tested the N-terminal derived peptides that correspond to the eight human canonical RNases (RN1-8) against planktonic cells and biofilms of C. albicans. RN3 and RN7 peptides displayed the most potent inhibitory effect with a mechanism of action characterized by cell-wall binding, membrane permeabilization and biofilm eradication activities. Both peptides are able to eradicate planktonic and sessile cells, and to alter their gene expression, reinforcing its role as a lead candidate to develop novel antifungal and antibiofilm therapies.
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Affiliation(s)
- Vivian A Salazar
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - Javier Arranz-Trullén
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - Guillem Prats-Ejarque
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - Marc Torrent
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - David Andreu
- Department of Experimental and Health Sciences, Universitat Pompeu Fabra, Dr. Aiguader 88, 08003 Barcelona, Spain.
| | - David Pulido
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain.
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22
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Yathursan S, Wiles S, Read H, Sarojini V. A review on anti-tuberculosis peptides: Impact of peptide structure on anti-tuberculosis activity. J Pept Sci 2019; 25:e3213. [PMID: 31515916 DOI: 10.1002/psc.3213] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2019] [Revised: 08/03/2019] [Accepted: 08/07/2019] [Indexed: 12/18/2022]
Abstract
Antibiotic resistance is a major public health problem globally. Particularly concerning amongst drug-resistant human pathogens is Mycobacterium tuberculosis that causes the deadly infectious tuberculosis (TB) disease. Significant issues associated with current treatment options for drug-resistant TB and the high rate of mortality from the disease makes the development of novel treatment options against this pathogen an urgent need. Antimicrobial peptides are part of innate immunity in all forms of life and could provide a potential solution against drug-resistant TB. This review is a critical analysis of antimicrobial peptides that are reported to be active against the M tuberculosis complex exclusively. However, activity on non-TB strains such as Mycobacterium avium and Mycobacterium intracellulare, whenever available, have been included at appropriate sections for these anti-TB peptides. Natural and synthetic antimicrobial peptides of diverse sequences, along with their chemical structures, are presented, discussed, and correlated to their observed antimycobacterial activities. Critical analyses of the structure allied to the anti-mycobacterial activity have allowed us to draw important conclusions and ideas for research and development on these promising molecules to realise their full potential. Even though the review is focussed on peptides, we have briefly summarised the structures and potency of the various small molecule drugs that are available and under development, for TB treatment.
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Affiliation(s)
- Sutharsana Yathursan
- School of Chemical Sciences, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Siouxsie Wiles
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Hannah Read
- Bioluminescent Superbugs Lab, Department of Molecular Medicine and Pathology, University of Auckland, Private Bag, 92019, Auckland, New Zealand
| | - Vijayalekshmi Sarojini
- School of Chemical Sciences, 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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23
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Lu L, Arranz-Trullén J, Prats-Ejarque G, Pulido D, Bhakta S, Boix E. Human Antimicrobial RNases Inhibit Intracellular Bacterial Growth and Induce Autophagy in Mycobacteria-Infected Macrophages. Front Immunol 2019; 10:1500. [PMID: 31312205 PMCID: PMC6614385 DOI: 10.3389/fimmu.2019.01500] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 06/14/2019] [Indexed: 12/11/2022] Open
Abstract
The development of novel treatment against tuberculosis is a priority global health challenge. Antimicrobial proteins and peptides offer a multifaceted mechanism suitable to fight bacterial resistance. Within the RNaseA superfamily there is a group of highly cationic proteins secreted by innate immune cells with anti-infective and immune-regulatory properties. In this work, we have tested the human canonical members of the RNase family using a spot-culture growth inhibition assay based mycobacteria-infected macrophage model for evaluating their anti-tubercular properties. Out of the seven tested recombinant human RNases, we have identified two members, RNase3 and RNase6, which were highly effective against Mycobacterium aurum extra- and intracellularly and induced an autophagy process. We observed the proteins internalization within macrophages and their capacity to eradicate the intracellular mycobacterial infection at a low micro-molar range. Contribution of the enzymatic activity was discarded by site-directed mutagenesis at the RNase catalytic site. The protein induction of autophagy was analyzed by RT-qPCR, western blot, immunofluorescence, and electron microscopy. Specific blockage of auto-phagosome formation and maturation reduced the protein's ability to eradicate the infection. In addition, we found that the M. aurum infection of human THP1 macrophages modulates the expression of endogenous RNase3 and RNase6, suggesting a function in vivo. Overall, our data anticipate a biological role for human antimicrobial RNases in host response to mycobacterial infections and set the basis for the design of novel anti-tubercular drugs.
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Affiliation(s)
- Lu Lu
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Javier Arranz-Trullén
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Guillem Prats-Ejarque
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - David Pulido
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck, University of London, London, United Kingdom
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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Prats-Ejarque G, Li J, Ait-Ichou F, Lorente H, Boix E. Testing a Human Antimicrobial RNase Chimera Against Bacterial Resistance. Front Microbiol 2019; 10:1357. [PMID: 31275278 PMCID: PMC6594349 DOI: 10.3389/fmicb.2019.01357] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 05/31/2019] [Indexed: 12/11/2022] Open
Abstract
The emergence of bacterial resistance to the most commonly used antibiotics encourages the design of novel antimicrobial drugs. Antimicrobial proteins and peptides (AMPs) are the key players in host innate immunity. They exert a rapid and multifaceted action that reduces the development of bacterial adaptation mechanisms. Human antimicrobial RNases belonging to the vertebrate specific RNase A superfamily participate in the maintenance of tissue and body fluid sterility. Among the eight human canonical RNases, RNase 3 stands out as the most cationic and effective bactericidal protein against Gram-negative species. Its enhanced ability to disrupt the bacterial cell wall has evolved in detriment of its catalytic activity. Based on structure-functional studies we have designed an RNase 3/1 hybrid construct that combines the high catalytic activity of RNase 1 with RNase 3 bactericidal properties. Next, we have explored the ability of this hybrid RNase to target the development of bacterial resistance on an Acinetobacter baumannii cell culture. Synergy assays were performed in combination with colistin, a standard antimicrobial peptide used as an antibiotic to treat severe infections. Positive synergism was observed between colistin and the RNase 3/1 hybrid protein. Subsequently, using an in vitro experimental evolution assay, by exposure of a bacterial culture to colistin at incremental doses, we demonstrated the ability of the RNase 3/1 construct to reduce the emergence of bacterial antimicrobial resistance. The results advance the potential applicability of RNase-based drugs as antibiotic adjuvants.
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Affiliation(s)
| | | | | | | | - Ester Boix
- Faculty of Biosciences, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Barcelona, Spain
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O'Shea MK, Fletcher TE, Muller J, Tanner R, Matsumiya M, Bailey JW, Jones J, Smith SG, Koh G, Horsnell WG, Beeching NJ, Dunbar J, Wilson D, Cunningham AF, McShane H. Human Hookworm Infection Enhances Mycobacterial Growth Inhibition and Associates With Reduced Risk of Tuberculosis Infection. Front Immunol 2018; 9:2893. [PMID: 30619265 PMCID: PMC6302045 DOI: 10.3389/fimmu.2018.02893] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 11/26/2018] [Indexed: 12/22/2022] Open
Abstract
Soil-transmitted helminths and Mycobacterium tuberculosis frequently coincide geographically and it is hypothesized that gastrointestinal helminth infection may exacerbate tuberculosis (TB) disease by suppression of Th1 and Th17 responses. However, few studies have focused on latent TB infection (LTBI), which predominates globally. We performed a large observational study of healthy adults migrating from Nepal to the UK (n = 645). Individuals were screened for LTBI and gastrointestinal parasite infections. A significant negative association between hookworm and LTBI-positivity was seen (OR = 0.221; p = 0.039). Hookworm infection treatment did not affect LTBI conversions. Blood from individuals with hookworm had a significantly greater ability to control virulent mycobacterial growth in vitro than from those without, which was lost following hookworm treatment. There was a significant negative relationship between mycobacterial growth and eosinophil counts. Eosinophil-associated differential gene expression characterized the whole blood transcriptome of hookworm infection and correlated with improved mycobacterial control. These data provide a potential alternative explanation for the reduced prevalence of LTBI among individuals with hookworm infection, and possibly an anti-mycobacterial role for helminth-induced eosinophils.
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Affiliation(s)
- Matthew K. O'Shea
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
- Royal Centre for Defence Medicine, Joint Medical Command, Birmingham, United Kingdom
| | - Thomas E. Fletcher
- Royal Centre for Defence Medicine, Joint Medical Command, Birmingham, United Kingdom
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Julius Muller
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Rachel Tanner
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - Magali Matsumiya
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
| | - J. Wendi Bailey
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Jayne Jones
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Steven G. Smith
- Department of Immunology and Infection, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Gavin Koh
- Department of Infectious Diseases, Northwick Park Hospital, London, United Kingdom
| | - William G. Horsnell
- Institute of Microbiology and Infection, University of Birmingham, Birmingham, United Kingdom
- Institute of Infectious Disease and Molecular Medicine and Division of Immunology, University of Cape Town, Cape Town, South Africa
| | - Nicholas J. Beeching
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - James Dunbar
- Royal Centre for Defence Medicine, Joint Medical Command, Birmingham, United Kingdom
- Department of Infectious Diseases, The Friarage Hospital, Northallerton, United Kingdom
| | - Duncan Wilson
- Royal Centre for Defence Medicine, Joint Medical Command, Birmingham, United Kingdom
| | - Adam F. Cunningham
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Helen McShane
- Nuffield Department of Medicine, The Jenner Institute, University of Oxford, Oxford, United Kingdom
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Baranzini N, Monti L, Vanotti M, Orlandi VT, Bolognese F, Scaldaferri D, Girardello R, Tettamanti G, de Eguileor M, Vizioli J, Taramelli R, Acquati F, Grimaldi A. AIF-1 and RNASET2 Play Complementary Roles in the Innate Immune Response of Medicinal Leech. J Innate Immun 2018; 11:150-167. [PMID: 30368505 DOI: 10.1159/000493804] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 09/12/2018] [Indexed: 12/13/2022] Open
Abstract
Recent studies demonstrated that allograft inflammatory factor-1 (AIF-1) and RNASET2 act as chemoattractants for macrophages and modulate the inflammatory processes in both vertebrates and invertebrates. The expression of these proteins significantly increases after bacterial infection; however, the mechanisms by which they regulate the innate immune response are still poorly defined. Here, we evaluate the effect of bacterial lipopolysaccharide injection on the expression pattern of these genes and the interrelation between them during innate immune response in the medicinal leech, an invertebrate model with a simple anatomy and a marked similarity with vertebrates in inflammatory processes. Collectively, prokaryotic-eukaryotic co-cultures and in vivo infection assays suggest that RNASET2 and AIF-1 play a crucial role in orchestrating a functional cross-talk between granulocytes and macrophages in leeches, resulting in the activation of an effective response against pathogen infection. RNASET2, firstly released by granulocytes, likely plays an early antibacterial role. Subsequently, AIF-1+ RNASET2-recruited macrophages further recruit other macrophages to potentiate the antibacterial inflammatory response. These experimental data are in keeping with the notion of RNA-SET2 acting as an alarmin-like molecule whose role is to locally transmit a "danger" signal (such as a bacterial infection) to the innate immune system in order to trigger an appropriate host response.
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Affiliation(s)
- Nicolò Baranzini
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Laura Monti
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Marta Vanotti
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Viviana T Orlandi
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Fabrizio Bolognese
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Debora Scaldaferri
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Rossana Girardello
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Gianluca Tettamanti
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Magda de Eguileor
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Jacopo Vizioli
- Protéomique Réponse Inflammatoire Spectrométrie de Masse - PRISM, University of Lille, Lille, France
| | - Roberto Taramelli
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Francesco Acquati
- Department of Biotechnology and Life Science, University of Insubria, Varese, Italy
| | - Annalisa Grimaldi
- Department of Biotechnology and Life Science, University of Insubria, Varese,
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Usmani SS, Kumar R, Kumar V, Singh S, Raghava GPS. AntiTbPdb: a knowledgebase of anti-tubercular peptides. DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION 2018; 2018:4915494. [PMID: 29688365 PMCID: PMC5829563 DOI: 10.1093/database/bay025] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 02/09/2018] [Indexed: 12/28/2022]
Abstract
Tuberculosis is a global menace, caused by Mycobacterium tuberculosis, responsible for millions of premature deaths every year. In the era of drug-resistant tuberculosis, peptide-based therapeutics may provide alternate to small molecule based drugs. In order to create knowledgebase, AntiTbPdb (http://webs.iiitd.edu.in/raghava/antitbpdb/), experimentally validated anti-tubercular and anti-mycobacterial peptides were compiled from literature. We curate 10 652 research articles and 35 patents to extract anti-tubercular peptides and annotate these peptides manually. This knowledgebase has 1010 entries, each entry provides extensive information about an anti-tubercular peptide such as sequence, chemical modification, chirality, nature and source of origin. The tertiary structure of these anti-tubercular peptides containing natural as well as chemically modified residues was predicted using PEPstrMOD and I-TASSER. In addition to structural information, database maintains other properties of peptides like physiochemical properties. Numerous web-based tools have been integrated for data retrieval, browsing, sequence similarity search and peptide mapping. In order to assist wide range of user, we developed a responsive website suitable for smartphone, tablet and desktop. Database URL: http://webs.iiitd.edu.in/raghava/antitbpdb/
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Affiliation(s)
- Salman Sadullah Usmani
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh - 160036, India
| | - Rajesh Kumar
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh - 160036, India
| | - Vinod Kumar
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh - 160036, India
| | - Sandeep Singh
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh - 160036, India
| | - Gajendra P S Raghava
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh - 160036, India.,Centre for Computational Biology, Indraprastha Institute of Information Technology, Okhla, New Delhi - 110020, India
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Yii AC, Soh AZ, Chee CBE, Wang YT, Yuan JM, Koh WP. Asthma, Sinonasal Disease, and the Risk of Active Tuberculosis. THE JOURNAL OF ALLERGY AND CLINICAL IMMUNOLOGY-IN PRACTICE 2018; 7:641-648.e1. [PMID: 30130591 DOI: 10.1016/j.jaip.2018.07.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 07/22/2018] [Accepted: 07/26/2018] [Indexed: 01/07/2023]
Abstract
BACKGROUND Although asthma is associated with impaired lung immunity, it is unclear whether asthma affects the risk of active tuberculosis (TB). Because the upper and lower airways are immunologically related, sinonasal disease may also modify susceptibility to TB disease. OBJECTIVES To evaluate whether asthma and sinonasal disease prospectively modulate the risk of active TB in the Singapore Chinese Health Study. METHODS In this population-based prospective cohort, we recruited 63,257 Chinese adults aged 45 to 74 years from 1993 to 1998 in Singapore, and conducted follow-up I interviews among 52,325 surviving participants from 1999 to 2004. Data on self-reported history of physician-diagnosed sinonasal disease were collected at baseline, and data on asthma and chronic bronchitis were collected at follow-up I interviews. Active TB cases were identified by linkage with the National TB Notification Registry through December 2014. Multivariable Cox proportional hazards regression models were used to estimate the risk of active TB. RESULTS During a mean follow-up of 17 years from recruitment, there were 1249 cases of active TB, and among them, 678 cases were diagnosed in the 12-year period from follow-up I interviews. We observed reduced risk of active TB in those with a history of asthma at follow-up I (hazard ratio [HR], 0.55; 95% CI, 0.32-0.93) or sinonasal disease at baseline (HR, 0.59; 95% CI, 0.36-0.95). Conversely, history of chronic bronchitis was not associated with risk of TB (HR, 0.95; 95% CI, 0.68-1.31). CONCLUSIONS Asthma or sinonasal disease may modulate immunological response to reduce the incidence of active TB in the adult population.
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Affiliation(s)
- Anthony C Yii
- Department of Respiratory and Critical Care Medicine, Changi General Hospital, Singapore, Singapore; Health Services and Systems Research, Duke-NUS Medical School Singapore, Singapore
| | - Avril Z Soh
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Cynthia B E Chee
- Singapore Tuberculosis Control Unit, Tan Tock Seng Hospital, Singapore, Singapore
| | - Yee T Wang
- Singapore Tuberculosis Control Unit, Tan Tock Seng Hospital, Singapore, Singapore
| | - Jian-Min Yuan
- UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pa; Department of Epidemiology, University of Pittsburgh Graduate School of Public Health, Pittsburgh, Pa
| | - Woon-Puay Koh
- Health Services and Systems Research, Duke-NUS Medical School Singapore, Singapore; Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.
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Unveiling the Multifaceted Mechanisms of Antibacterial Activity of Buforin II and Frenatin 2.3S Peptides from Skin Micro-Organs of the Orinoco Lime Treefrog ( Sphaenorhynchus lacteus). Int J Mol Sci 2018; 19:ijms19082170. [PMID: 30044391 PMCID: PMC6121439 DOI: 10.3390/ijms19082170] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Accepted: 07/19/2018] [Indexed: 12/15/2022] Open
Abstract
Amphibian skin is a rich source of natural compounds with diverse antimicrobial and immune defense properties. Our previous studies showed that the frog skin secretions obtained by skin micro-organs from various species of Colombian anurans have antimicrobial activities against bacteria and viruses. We purified for the first time two antimicrobial peptides from the skin micro-organs of the Orinoco lime treefrog (Sphaenorhynchus lacteus) that correspond to Buforin II (BF2) and Frenatin 2.3S (F2.3S). Here, we have synthesized the two peptides and tested them against Gram-negative and Gram-positive bacteria, observing an effective bactericidal activity at micromolar concentrations. Evaluation of BF2 and F2.3S membrane destabilization activity on bacterial cell cultures and synthetic lipid bilayers reveals a distinct membrane interaction mechanism. BF2 agglutinates E. coli cells and synthetic vesicles, whereas F2.3S shows a high depolarization and membrane destabilization activities. Interestingly, we found that F2.3S is able to internalize within bacterial cells and can bind nucleic acids, as previously reported for BF2. Moreover, bacterial exposure to both peptides alters the expression profile of genes related to stress and resistance response. Overall, these results show the multifaceted mechanism of action of both antimicrobial peptides that can provide alternative tools in the fight against bacterial resistance.
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30
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Lee MW, Lee EY, Wong GCL. What Can Pleiotropic Proteins in Innate Immunity Teach Us about Bioconjugation and Molecular Design? Bioconjug Chem 2018; 29:2127-2139. [PMID: 29771496 DOI: 10.1021/acs.bioconjchem.8b00176] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A common bioengineering strategy to add function to a given molecule is by conjugation of a new moiety onto that molecule. Adding multiple functions in this way becomes increasingly challenging and leads to composite molecules with larger molecular weights. In this review, we attempt to gain a new perspective by looking at this problem in reverse, by examining nature's strategies of multiplexing different functions into the same pleiotropic molecule using emerging analysis techniques such as machine learning. We concentrate on examples from the innate immune system, which employs a finite repertoire of molecules for a broad range of tasks. An improved understanding of how diverse functions are multiplexed into a single molecule can inspire new approaches for the deterministic design of multifunctional molecules.
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31
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Lu L, Li J, Moussaoui M, Boix E. Immune Modulation by Human Secreted RNases at the Extracellular Space. Front Immunol 2018; 9:1012. [PMID: 29867984 PMCID: PMC5964141 DOI: 10.3389/fimmu.2018.01012] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/23/2018] [Indexed: 12/23/2022] Open
Abstract
The ribonuclease A superfamily is a vertebrate-specific family of proteins that encompasses eight functional members in humans. The proteins are secreted by diverse innate immune cells, from blood cells to epithelial cells and their levels in our body fluids correlate with infection and inflammation processes. Recent studies ascribe a prominent role to secretory RNases in the extracellular space. Extracellular RNases endowed with immuno-modulatory and antimicrobial properties can participate in a wide variety of host defense tasks, from performing cellular housekeeping to maintaining body fluid sterility. Their expression and secretion are induced in response to a variety of injury stimuli. The secreted proteins can target damaged cells and facilitate their removal from the focus of infection or inflammation. Following tissue damage, RNases can participate in clearing RNA from cellular debris or work as signaling molecules to regulate the host response and contribute to tissue remodeling and repair. We provide here an overall perspective on the current knowledge of human RNases’ biological properties and their role in health and disease. The review also includes a brief description of other vertebrate family members and unrelated extracellular RNases that share common mechanisms of action. A better knowledge of RNase mechanism of actions and an understanding of their physiological roles should facilitate the development of novel therapeutics.
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Affiliation(s)
- Lu Lu
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Jiarui Li
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Mohammed Moussaoui
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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32
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Pulido D, Prats-Ejarque G, Villalba C, Albacar M, Moussaoui M, Andreu D, Volkmer R, Torrent M, Boix E. Positional scanning library applied to the human eosinophil cationic protein/RNase3 N-terminus reveals novel and potent anti-biofilm peptides. Eur J Med Chem 2018; 152:590-599. [DOI: 10.1016/j.ejmech.2018.05.012] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 04/20/2018] [Accepted: 05/07/2018] [Indexed: 01/14/2023]
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Verapamil Targets Membrane Energetics in Mycobacterium tuberculosis. Antimicrob Agents Chemother 2018; 62:AAC.02107-17. [PMID: 29463541 PMCID: PMC5923092 DOI: 10.1128/aac.02107-17] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Accepted: 02/13/2018] [Indexed: 01/19/2023] Open
Abstract
Mycobacterium tuberculosis kills more people than any other bacterial pathogen and is becoming increasingly untreatable due to the emergence of resistance. Verapamil, an FDA-approved calcium channel blocker, potentiates the effect of several antituberculosis (anti-TB) drugs in vitro and in vivo. This potentiation is widely attributed to inhibition of the efflux pumps of M. tuberculosis, resulting in intrabacterial drug accumulation. Here, we confirmed and quantified verapamil's synergy with several anti-TB drugs, including bedaquiline (BDQ) and clofazimine (CFZ), but found that the effect is not due to increased intrabacterial drug accumulation. We show that, consistent with its in vitro potentiating effects on anti-TB drugs that target or require oxidative phosphorylation, the cationic amphiphile verapamil disrupts membrane function and induces a membrane stress response similar to those seen with other membrane-active agents. We recapitulated these activities in vitro using inverted mycobacterial membrane vesicles, indicating a direct effect of verapamil on membrane energetics. We observed bactericidal activity against nonreplicating “persister” M. tuberculosis that was consistent with such a mechanism of action. In addition, we demonstrated a pharmacokinetic interaction whereby human-equivalent doses of verapamil caused a boost of rifampin exposure in mice, providing a potential explanation for the observed treatment-shortening effect of verapamil in mice receiving first-line drugs. Our findings thus elucidate the mechanistic basis for verapamil's potentiation of anti-TB drugs in vitro and in vivo and highlight a previously unrecognized role for the membrane of M. tuberculosis as a pharmacologic target.
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Geng R, Liu H, Wang W. Differential Expression of Six Rnase2 and Three Rnase3 Paralogs Identified in Blunt Snout Bream in Response to Aeromonas hydrophila Infection. Genes (Basel) 2018; 9:E95. [PMID: 29443944 PMCID: PMC5852591 DOI: 10.3390/genes9020095] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/05/2018] [Accepted: 02/06/2018] [Indexed: 12/12/2022] Open
Abstract
Ribonucleases (Rnases)2 and Rnase3 belong to the ribonuclease A (RnaseA) superfamily. Apart from their role in molecular evolutionary and functional biological studies, these genes have also been studied in the context of defense against pathogen infection in mammals. However, expression patterns, structures and response to bacterial infection of the two genes in blunt snout bream (Megalobrama amblycephala) remain unknown. In this study, we identified multiple copies of Rnase2 (six) and Rnase3 (three) in the M. amblycephala genome. The nine genes all possess characteristics typical of the RnaseA superfamily. No expression was detected in the early developmental stages, while a weak expression was observed at 120 and 140 h post-fertilization (hpf) for Rnase2b, Rnase2c, Rnase2e and Rnase3a, suggesting that only three copies of Rnase2 and one of Rnase3 are expressed. Interestingly, only Rnase2e was up-regulated in the kidney of M. amblycephala after Aeromonas hydrophila infection, while Rnase3a was significantly up-regulated in liver, gut and blood after the infection. We conclude that the paralogs of Rnase3 are more susceptible to A. hydrophila infection than Rnase2. These results indicate that different Rnase2 and Rnase3 paralogs suggest a role in the innate immune response of M. amblycephala to bacterial infection.
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Affiliation(s)
- Ruijing Geng
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
| | - Han Liu
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Chinese Academy of Fishery Sciences, Wuxi 214081, China.
| | - Weimin Wang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education/Key Lab of Freshwater Animal Breeding, College of Fisheries, Huazhong Agricultural University, Wuhan 430070, China.
- Collaborative Innovation Center for Efficient and Health Production of Fisheries in Hunan Province, Changde 415000, China.
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Kettles GJ, Bayon C, Sparks CA, Canning G, Kanyuka K, Rudd JJ. Characterization of an antimicrobial and phytotoxic ribonuclease secreted by the fungal wheat pathogen Zymoseptoria tritici. THE NEW PHYTOLOGIST 2018; 217:320-331. [PMID: 28895153 PMCID: PMC5724701 DOI: 10.1111/nph.14786] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 08/11/2017] [Indexed: 05/19/2023]
Abstract
The fungus Zymoseptoria tritici is the causal agent of Septoria Tritici Blotch (STB) disease of wheat leaves. Zymoseptoria tritici secretes many functionally uncharacterized effector proteins during infection. Here, we characterized a secreted ribonuclease (Zt6) with an unusual biphasic expression pattern. Transient expression systems were used to characterize Zt6, and mutants thereof, in both host and non-host plants. Cell-free protein expression systems monitored the impact of Zt6 protein on functional ribosomes, and in vitro assays of cells treated with recombinant Zt6 determined toxicity against bacteria, yeasts and filamentous fungi. We demonstrated that Zt6 is a functional ribonuclease and that phytotoxicity is dependent on both the presence of a 22-amino-acid N-terminal 'loop' region and its catalytic activity. Zt6 selectively cleaves both plant and animal rRNA species, and is toxic to wheat, tobacco, bacterial and yeast cells, but not to Z. tritici itself. Zt6 is the first Z. tritici effector demonstrated to have a likely dual functionality. The expression pattern of Zt6 and potent toxicity towards microorganisms suggest that, although it may contribute to the execution of wheat cell death, it is also likely to have an important secondary function in antimicrobial competition and niche protection.
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Affiliation(s)
- Graeme J. Kettles
- Biointeractions & Crop ProtectionRothamsted ResearchHarpendenAL5 2JQUK
| | - Carlos Bayon
- Biointeractions & Crop ProtectionRothamsted ResearchHarpendenAL5 2JQUK
| | | | - Gail Canning
- Biointeractions & Crop ProtectionRothamsted ResearchHarpendenAL5 2JQUK
| | - Kostya Kanyuka
- Biointeractions & Crop ProtectionRothamsted ResearchHarpendenAL5 2JQUK
| | - Jason J. Rudd
- Biointeractions & Crop ProtectionRothamsted ResearchHarpendenAL5 2JQUK
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Arranz-Trullén J, Lu L, Pulido D, Bhakta S, Boix E. Host Antimicrobial Peptides: The Promise of New Treatment Strategies against Tuberculosis. Front Immunol 2017; 8:1499. [PMID: 29163551 PMCID: PMC5681943 DOI: 10.3389/fimmu.2017.01499] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Accepted: 10/24/2017] [Indexed: 12/11/2022] Open
Abstract
Tuberculosis (TB) continues to be a devastating infectious disease and remerges as a global health emergency due to an alarming rise of antimicrobial resistance to its treatment. Despite of the serious effort that has been applied to develop effective antitubercular chemotherapies, the potential of antimicrobial peptides (AMPs) remains underexploited. A large amount of literature is now accessible on the AMP mechanisms of action against a diversity of pathogens; nevertheless, research on their activity on mycobacteria is still scarce. In particular, there is an urgent need to integrate all available interdisciplinary strategies to eradicate extensively drug-resistant Mycobacterium tuberculosis strains. In this context, we should not underestimate our endogenous antimicrobial proteins and peptides as ancient players of the human host defense system. We are confident that novel antibiotics based on human AMPs displaying a rapid and multifaceted mechanism, with reduced toxicity, should significantly contribute to reverse the tide of antimycobacterial drug resistance. In this review, we have provided an up to date perspective of the current research on AMPs to be applied in the fight against TB. A better understanding on the mechanisms of action of human endogenous peptides should ensure the basis for the best guided design of novel antitubercular chemotherapeutics.
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Affiliation(s)
- Javier Arranz-Trullén
- Faculty of Biosciences, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain.,Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck University of London, London, United Kingdom
| | - Lu Lu
- Faculty of Biosciences, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - David Pulido
- Faculty of Biosciences, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Sanjib Bhakta
- Mycobacteria Research Laboratory, Department of Biological Sciences, Institute of Structural and Molecular Biology, Birkbeck University of London, London, United Kingdom
| | - Ester Boix
- Faculty of Biosciences, Department of Biochemistry and Molecular Biology, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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Mohammed I, Said DG, Dua HS. Human antimicrobial peptides in ocular surface defense. Prog Retin Eye Res 2017; 61:1-22. [DOI: 10.1016/j.preteyeres.2017.03.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2016] [Revised: 03/22/2017] [Accepted: 03/27/2017] [Indexed: 01/17/2023]
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Nguyen TV, Osipov AV. A study of ribonuclease activity in venom of vietnam cobra. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2017; 59:20. [PMID: 29021904 PMCID: PMC5611641 DOI: 10.1186/s40781-017-0145-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 06/22/2017] [Indexed: 11/10/2022]
Abstract
BACKGROUND Ribonuclease (RNase) is one of the few toxic proteins that are present constantly in snake venoms of all types. However, to date this RNase is still poorly studied in comparison not only with other toxic proteins of snake venom, but also with the enzymes of RNase group. The objective of this paper was to investigate some properties of RNase from venom of Vietnam cobra Naja atra. METHODS Kinetic methods and gel filtration chromatography were used to investigate RNase from venom of Vietnam cobra. RESULTS RNase from venom of Vietnam cobra Naja atra has some characteristic properties. This RNase is a thermostable enzyme and has high conformational stability. This is the only acidic enzyme of the RNase A superfamily exhibiting a high catalytic activity in the pH range of 1-4, with pHopt = 2.58 ± 0.35. Its activity is considerably reduced with increasing ionic strength of reaction mixture. Venom proteins are separated by gel filtration into four peaks with ribonucleolytic activity, which is abnormally distributed among the isoforms: only a small part of the RNase activity is present in fractions of proteins with molecular weights of 12-15 kDa and more than 30 kDa, but most of the enzyme activity is detected in fractions of polypeptides, having molecular weights of less than 9 kDa, that is unexpected. CONCLUSIONS RNase from the venom of Vietnam cobra is a unique member of RNase A superfamily according to its acidic optimum pH (pHopt = 2.58 ± 0.35) and extremely low molecular weights of its major isoforms (approximately 8.95 kDa for RNase III and 5.93 kDa for RNase IV).
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Affiliation(s)
- Thiet Van Nguyen
- Institute of Biotechnology, Vietnam Academy of Science and Technology (VAST), Hanoi, Vietnam
| | - A. V. Osipov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences (RAS), Moscow, Russia
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Asfaw H, Laqua K, Walkowska AM, Cunningham F, Martinez-Martinez MS, Cuevas-Zurita JC, Ballell-Pages L, Imming P. Design, synthesis and structure-activity relationship study of wollamide B; a new potential anti TB agent. PLoS One 2017; 12:e0176088. [PMID: 28423019 PMCID: PMC5397059 DOI: 10.1371/journal.pone.0176088] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 04/05/2017] [Indexed: 11/26/2022] Open
Abstract
Wollamide B is a cationic antimycobacterial cyclohexapeptide that exhibits activity against Mycobacterium bovis (M. bovis) (IC50 of 3.1 μM). Aiming to define its structural activity relationship (SAR), optimizing potency and pharmacokinetic properties, libraries of analogues were synthesized following a standard Fmoc-based solid phase peptide synthesis approach. The antimycobacterial activities of wollamide B and all the synthesized analogues were tested against Mycobacterium tuberculosis (Mtb) H37Rv. Parallely, in vitro drug metabolism and pharmacokinetic (ADME) profiling was done for the synthesized compounds to evaluate their drug likeness. Among the 25 synthesized wollamides five of them showed potent activities with MICs ≤ 3.1 μM and found to be nontoxic against human HepG2 cells up to 100 μM. The results of the in vitro ADME profiling revealed the remarkable plasma stability and very good aqueous solubility of the class in general while the metabolic stability was found to be moderate to low. Of particular note, compounds 7c (MIC = 1.1 μM) and 13c (0.6 μM) that exhibited good balance of antimycobacterial activity vs. optimal pharmacokinetic properties could be used as a new lead for further development.
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Affiliation(s)
- Henok Asfaw
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Katja Laqua
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Anna Maria Walkowska
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
| | - Fraser Cunningham
- Diseases of the Developing World, Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | | | - Juan Carlos Cuevas-Zurita
- Diseases of the Developing World, Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - Lluís Ballell-Pages
- Diseases of the Developing World, Medicines Development Campus, GlaxoSmithKline, Tres Cantos, Madrid, Spain
| | - Peter Imming
- Institut für Pharmazie, Martin-Luther-Universität Halle-Wittenberg, Halle (Saale), Germany
- * E-mail:
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Wang B. Human Skin RNases Offer Dual Protection against Invading Bacteria. Front Microbiol 2017; 8:624. [PMID: 28443087 PMCID: PMC5386971 DOI: 10.3389/fmicb.2017.00624] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Accepted: 03/27/2017] [Indexed: 12/25/2022] Open
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le Roex N, Jolles A, Beechler B, van Helden P, Hoal E. Toll-like receptor (TLR) diversity influences mycobacterial growth in African buffalo. Tuberculosis (Edinb) 2017; 104:87-94. [PMID: 28454655 DOI: 10.1016/j.tube.2017.03.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 03/21/2017] [Accepted: 03/28/2017] [Indexed: 01/04/2023]
Abstract
Understanding the role of wildlife in the maintenance or spread of emerging infectious diseases is a growing priority across the world. Bovine tuberculosis (BTB) is a chronic, infectious disease caused by Mycobacterium bovis (M. bovis). BTB is widespread within game reserves in southern Africa, and within these ecosystems the primary wildlife host of this disease is the African buffalo. We used a modified bacterial killing assay for mycobacteria to investigate the effect of Toll-like receptor (TLR) genetic diversity and demographic parameters on the ability of African buffalo to restrict mycobacterial growth. Eosinophil count, time delay, bovine PPD response and avian PPD response were negatively correlated with mycobacterial growth. TLR6 diversity and the interaction of age group and sex were positively correlated with mycobacterial growth. Our results suggest that both demographic and individual immune parameters influence the ability to control mycobacterial infection in African buffalo. TLR6 diversity is particularly interesting as this locus has also shown associations with BTB in cattle, suggesting that further research into the effects, selection and role of TLR6 variants in bovine tuberculosis will be productive.
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Affiliation(s)
- Nikki le Roex
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ Medical Research Council (MRC) Centre for TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
| | - Anna Jolles
- College of Veterinary Medicine, Oregon State University, Corvallis, OR, 97331, USA; Department of Integrative Biology, Oregon State University, Corvallis, OR, 97331, USA.
| | - Brianna Beechler
- College of Veterinary Medicine, Oregon State University, Corvallis, OR, 97331, USA.
| | - Paul van Helden
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ Medical Research Council (MRC) Centre for TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
| | - Eileen Hoal
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research/ Medical Research Council (MRC) Centre for TB Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Tygerberg, South Africa.
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Pulido D, Garcia-Mayoral MF, Moussaoui M, Velázquez D, Torrent M, Bruix M, Boix E. Structural basis for endotoxin neutralization by the eosinophil cationic protein. FEBS J 2016; 283:4176-4191. [PMID: 27696685 DOI: 10.1111/febs.13915] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Revised: 09/07/2016] [Accepted: 09/29/2016] [Indexed: 12/13/2022]
Abstract
Acute infection by Gram-negative pathogens can induce an exacerbated immune response that leads to lethal septic shock syndrome. Bacterial lipopolysaccharide (LPS) is a major pathogen-associated molecular pattern molecule that can initiate massive and lethal immune system stimulation. Therefore, the development of new and effective LPS-neutralizing agents is a top priority. The eosinophil cationic protein (ECP) is an antimicrobial protein secreted in response to infection, with a remarkable affinity for LPS. In the present study, we demonstrate that ECP is able to neutralize bacterial LPS and inhibit tumor necrosis factor-α production in human macrophages. We also characterized ECP neutralizing activity using progressively truncated LPS mutants, and conclude that the polysaccharide moiety and lipid A portions are required for LPS-mediated neutralization. In addition, we mapped the structural determinants required for the ECP-LPS interaction by nuclear magnetic resonance. Our results show that ECP is able to neutralize LPS and therefore opens a new route for developing novel therapeutic agents based on the ECP structural scaffolding.
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Affiliation(s)
- David Pulido
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | | | - Mohammed Moussaoui
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Diego Velázquez
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Marc Torrent
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Marta Bruix
- Departamento de Química Biológica, Instituto de Química-Física Rocasolano, CSIC, Madrid, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Biosciences Faculty, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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A Novel RNase 3/ECP Peptide for Pseudomonas aeruginosa Biofilm Eradication That Combines Antimicrobial, Lipopolysaccharide Binding, and Cell-Agglutinating Activities. Antimicrob Agents Chemother 2016; 60:6313-25. [PMID: 27527084 DOI: 10.1128/aac.00830-16] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Accepted: 07/22/2016] [Indexed: 12/19/2022] Open
Abstract
Eradication of established biofilm communities of pathogenic Gram-negative species is one of the pending challenges for the development of new antimicrobial agents. In particular, Pseudomonas aeruginosa is one of the main dreaded nosocomial species, with a tendency to form organized microbial communities that offer an enhanced resistance to conventional antibiotics. We describe here an engineered antimicrobial peptide (AMP) which combines bactericidal activity with a high bacterial cell agglutination and lipopolysaccharide (LPS) affinity. The RN3(5-17P22-36) peptide is a 30-mer derived from the eosinophil cationic protein (ECP), a host defense RNase secreted by eosinophils upon infection, with a wide spectrum of antipathogen activity. The protein displays high biofilm eradication activity that is not dependent on its RNase catalytic activity, as evaluated by using an active site-defective mutant. On the other hand, the peptide encompasses both the LPS-binding and aggregation-prone regions from the parental protein, which provide the appropriate structural features for the peptide's attachment to the bacterial exopolysaccharide layer and further improved removal of established biofilms. Moreover, the peptide's high cationicity and amphipathicity promote the cell membrane destabilization action. The results are also compared side by side with other reported AMPs effective against either planktonic and/or biofilm forms of Pseudomonas aeruginosa strain PAO1. The ECP and its derived peptide are unique in combining high bactericidal potency and cell agglutination activity, achieving effective biofilm eradication at a low micromolar range. We conclude that the designed RN3(5-17P22-36) peptide is a promising lead candidate against Gram-negative biofilms.
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Koczera P, Martin L, Marx G, Schuerholz T. The Ribonuclease A Superfamily in Humans: Canonical RNases as the Buttress of Innate Immunity. Int J Mol Sci 2016; 17:ijms17081278. [PMID: 27527162 PMCID: PMC5000675 DOI: 10.3390/ijms17081278] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Revised: 07/29/2016] [Accepted: 08/01/2016] [Indexed: 12/18/2022] Open
Abstract
In humans, the ribonuclease A (RNase A) superfamily contains eight different members that have RNase activities, and all of these members are encoded on chromosome 14. The proteins are secreted by a large variety of different tissues and cells; however, a comprehensive understanding of these proteins’ physiological roles is lacking. Different biological effects can be attributed to each protein, including antiviral, antibacterial and antifungal activities as well as cytotoxic effects against host cells and parasites. Different immunomodulatory effects have also been demonstrated. This review summarizes the available data on the human RNase A superfamily and illustrates the significant role of the eight canonical RNases in inflammation and the host defence system against infections.
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Affiliation(s)
- Patrick Koczera
- Department of Intensive Care and Intermediate Care, University Hospital Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen, Aachen 52074, Germany.
- Department for Experimental Molecular Imaging, University Hospital RWTH Aachen and Helmholtz Institute for Biomedical Engineering, RWTH Aachen University, Aachen 52074, Germany.
| | - Lukas Martin
- Department of Intensive Care and Intermediate Care, University Hospital Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen, Aachen 52074, Germany.
| | - Gernot Marx
- Department of Intensive Care and Intermediate Care, University Hospital Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen, Aachen 52074, Germany.
| | - Tobias Schuerholz
- Department of Intensive Care and Intermediate Care, University Hospital Rheinisch-Westfälische Technische Hochschule (RWTH) Aachen, Aachen 52074, Germany.
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Salazar VA, Arranz-Trullén J, Navarro S, Blanco JA, Sánchez D, Moussaoui M, Boix E. Exploring the mechanisms of action of human secretory RNase 3 and RNase 7 against Candida albicans. Microbiologyopen 2016; 5:830-845. [PMID: 27277554 PMCID: PMC5061719 DOI: 10.1002/mbo3.373] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 03/30/2016] [Accepted: 04/04/2016] [Indexed: 12/17/2022] Open
Abstract
Human antimicrobial RNases, which belong to the vertebrate RNase A superfamily and are secreted upon infection, display a wide spectrum of antipathogen activities. In this work, we examined the antifungal activity of the eosinophil RNase 3 and the skin-derived RNase 7, two proteins expressed by innate cell types that are directly involved in the host defense against fungal infection. Candida albicans has been selected as a suitable working model for testing RNase activities toward a eukaryotic pathogen. We explored the distinct levels of action of both RNases on yeast by combining cell viability and membrane model assays together with protein labeling and confocal microscopy. Site-directed mutagenesis was applied to ablate either the protein active site or the key anchoring region for cell binding. This is the first integrated study that highlights the RNases' dual mechanism of action. Along with an overall membrane-destabilization process, the RNases could internalize and target cellular RNA. The data support the contribution of the enzymatic activity for the antipathogen action of both antimicrobial proteins, which can be envisaged as suitable templates for the development of novel antifungal drugs. We suggest that both human RNases work as multitasking antimicrobial proteins that provide a first line immune barrier.
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Affiliation(s)
- Vivian A Salazar
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, E-08193, Spain
| | - Javier Arranz-Trullén
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, E-08193, Spain
| | - Susanna Navarro
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, E-08193, Spain.,Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, E-08193, Spain
| | - Jose A Blanco
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, E-08193, Spain
| | - Daniel Sánchez
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, E-08193, Spain
| | - Mohammed Moussaoui
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, E-08193, Spain
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, E-08193, Spain.
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Rademacher F, Simanski M, Harder J. RNase 7 in Cutaneous Defense. Int J Mol Sci 2016; 17:560. [PMID: 27089327 PMCID: PMC4849016 DOI: 10.3390/ijms17040560] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 04/07/2016] [Accepted: 04/08/2016] [Indexed: 02/07/2023] Open
Abstract
RNase 7 belongs to the RNase A superfamily and exhibits a broad spectrum of antimicrobial activity against various microorganisms. RNase 7 is expressed in human skin, and expression in keratinocytes can be induced by cytokines and microbes. These properties suggest that RNase 7 participates in innate cutaneous defense. In this review, we provide an overview about the role of RNase 7 in cutaneous defense with focus on the molecular mechanism of the antimicrobial activity of RNase 7, the regulation of RNase 7 expression, and the role of RNase 7 in skin diseases.
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Affiliation(s)
| | - Maren Simanski
- Department of Dermatology, University of Kiel, 24105 Kiel, Germany.
| | - Jürgen Harder
- Department of Dermatology, University of Kiel, 24105 Kiel, Germany.
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Insights into the Antimicrobial Mechanism of Action of Human RNase6: Structural Determinants for Bacterial Cell Agglutination and Membrane Permeation. Int J Mol Sci 2016; 17:552. [PMID: 27089320 PMCID: PMC4849008 DOI: 10.3390/ijms17040552] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 03/18/2016] [Accepted: 04/05/2016] [Indexed: 12/26/2022] Open
Abstract
Human Ribonuclease 6 is a secreted protein belonging to the ribonuclease A (RNaseA) superfamily, a vertebrate specific family suggested to arise with an ancestral host defense role. Tissue distribution analysis revealed its expression in innate cell types, showing abundance in monocytes and neutrophils. Recent evidence of induction of the protein expression by bacterial infection suggested an antipathogen function in vivo. In our laboratory, the antimicrobial properties of the protein have been evaluated against Gram-negative and Gram-positive species and its mechanism of action was characterized using a membrane model. Interestingly, our results indicate that RNase6, as previously reported for RNase3, is able to specifically agglutinate Gram-negative bacteria as a main trait of its antimicrobial activity. Moreover, a side by side comparative analysis with the RN6(1-45) derived peptide highlights that the antimicrobial activity is mostly retained at the protein N-terminus. Further work by site directed mutagenesis and structural analysis has identified two residues involved in the protein antimicrobial action (Trp1 and Ile13) that are essential for the cell agglutination properties. This is the first structure-functional characterization of RNase6 antimicrobial properties, supporting its contribution to the infection focus clearance.
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Gutsmann T. Interaction between antimicrobial peptides and mycobacteria. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1034-43. [PMID: 26851776 DOI: 10.1016/j.bbamem.2016.01.031] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2015] [Revised: 01/29/2016] [Accepted: 01/31/2016] [Indexed: 01/21/2023]
Abstract
Mycobacteria can cause different severe health problems, including tuberculosis (TB). The treatment of TB with conventional antibiotics is successful, however, the number of multi-drug and extensively-drug resistant Mycobacterium tuberculosis strains increases. Moreover, many classical antimycobacterial antibiotics have severe side effects. Therefore, antimicrobial peptides (AMPs) seem to be good candidates for new therapeutic strategies. On the one hand AMPs can be used as a single drug or in combination with conventional antibiotics to directly kill mycobacteria, or on the other hand to act as immunstimulatory agents. This review summarizes the findings on the role of endogenous human AMPs being involved in TB, the antimycobacterial activity of various AMPs, and the molecular modes of action. Most active AMPs interact with the mycobacterial cell envelope and in particular with the mycomembrane and the plasma membrane. The mycomembrane is a very rigid membrane probably leading to a lower activity of the AMPs against mycobacteria as compared to other Gram-negative or Gram-positive bacteria. For some AMPs also other targets have been identified. Because of the complex environment of intracellular mycobacteria being trapped in the phagosome, within the macrophage, within the granuloma, within the lung, the external administration of AMPs in the latent phase of TB is a challenge. However, in the acute phase the AMPs can attack mycobacteria in a direct way. This article is part of a Special Issue entitled: Antimicrobial peptides edited by Karl Lohner and Kai Hilpert.
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Affiliation(s)
- Thomas Gutsmann
- Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Priority Area Infections, Division of Biophysics, Parkallee 10, 23845 Borstel, Germany.
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Elmose C, Sverrild A, van der Sluis S, Kyvik KO, Backer V, Thomsen SF. Genetic factors explain half of all variance in serum eosinophil cationic protein. Clin Exp Allergy 2015; 44:1525-30. [PMID: 25354326 DOI: 10.1111/cea.12445] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Revised: 09/15/2014] [Accepted: 09/22/2014] [Indexed: 11/30/2022]
Abstract
BACKGROUND Eosinophil cationic protein (ECP) is one of four basic proteins of the secretory granules of eosinophils. It has a variety of functions associated with inflammatory responses. Little is known about the causes for variation in serum ECP levels. AIM To identify factors associated with variation in serum ECP and to determine the relative proportion of the variation in ECP due to genetic and non-genetic factors, in an adult twin sample. METHODS A sample of 575 twins, selected through a proband with self-reported asthma, had serum ECP, lung function, airway responsiveness to methacholine, exhaled nitric oxide, and skin test reactivity, measured. Linear regression analysis and variance component models were used to study factors associated with variation in ECP and the relative genetic influence on ECP levels. RESULTS Sex (regression coefficient = -0.107, P < 0.001), body mass index (BMI) (0.007, P = 0.028), and airway responsiveness to methacholine (0.074, P = 0.001) were significantly associated with ECP. Adjusted for these factors, ECP correlated 0.53 (P < 0.001) and 0.27 (P = 0.001) in monozygotic and dizygotic twins, respectively (P-value for difference = 0.05). According to the most parsimonious variance component model, genetic factors accounted for 57% (CI: 42-72%, P < 0.001) of the variance in ECP levels, whereas the remainder (43%) was ascribable to non-shared environmental factors. The genetic correlation between ECP and airway responsiveness to methacholine was statistically non-significant (r = -0.11, P = 0.50). CONCLUSION Around half of all variance in serum ECP is explained by genetic factors. Serum ECP is influenced by sex, BMI, and airway responsiveness. Serum ECP and airway responsiveness seem not to share genetic variance.
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Affiliation(s)
- C Elmose
- Department of Dermato-allergology, Gentofte Hospital, Hellerup, Denmark
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Parks MM, Lawrence CE, Raphael BJ. Detecting non-allelic homologous recombination from high-throughput sequencing data. Genome Biol 2015; 16:72. [PMID: 25886137 PMCID: PMC4425883 DOI: 10.1186/s13059-015-0633-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2015] [Accepted: 03/16/2015] [Indexed: 12/27/2022] Open
Abstract
Non-allelic homologous recombination (NAHR) is a common mechanism for generating genome rearrangements and is implicated in numerous genetic disorders, but its detection in high-throughput sequencing data poses a serious challenge. We present a probabilistic model of NAHR and demonstrate its ability to find NAHR in low-coverage sequencing data from 44 individuals. We identify NAHR-mediated deletions or duplications in 109 of 324 potential NAHR loci in at least one of the individuals. These calls segregate by ancestry, are more common in closely spaced repeats, often result in duplicated genes or pseudogenes, and affect highly studied genes such as GBA and CYP2E1.
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Affiliation(s)
- Matthew M Parks
- Division of Applied Mathematics, Brown University, Providence, USA.
| | - Charles E Lawrence
- Division of Applied Mathematics, Brown University, Providence, USA. .,Center for Computational Molecular Biology, Brown University, Providence, USA.
| | - Benjamin J Raphael
- Center for Computational Molecular Biology, Brown University, Providence, USA. .,Department of Computer Science, Brown University, Providence, USA.
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