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Wan F, Torres MDT, Peng J, de la Fuente-Nunez C. Deep-learning-enabled antibiotic discovery through molecular de-extinction. Nat Biomed Eng 2024:10.1038/s41551-024-01201-x. [PMID: 38862735 DOI: 10.1038/s41551-024-01201-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/25/2024] [Indexed: 06/13/2024]
Abstract
Molecular de-extinction aims at resurrecting molecules to solve antibiotic resistance and other present-day biological and biomedical problems. Here we show that deep learning can be used to mine the proteomes of all available extinct organisms for the discovery of antibiotic peptides. We trained ensembles of deep-learning models consisting of a peptide-sequence encoder coupled with neural networks for the prediction of antimicrobial activity and used it to mine 10,311,899 peptides. The models predicted 37,176 sequences with broad-spectrum antimicrobial activity, 11,035 of which were not found in extant organisms. We synthesized 69 peptides and experimentally confirmed their activity against bacterial pathogens. Most peptides killed bacteria by depolarizing their cytoplasmic membrane, contrary to known antimicrobial peptides, which tend to target the outer membrane. Notably, lead compounds (including mammuthusin-2 from the woolly mammoth, elephasin-2 from the straight-tusked elephant, hydrodamin-1 from the ancient sea cow, mylodonin-2 from the giant sloth and megalocerin-1 from the extinct giant elk) showed anti-infective activity in mice with skin abscess or thigh infections. Molecular de-extinction aided by deep learning may accelerate the discovery of therapeutic molecules.
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Affiliation(s)
- Fangping Wan
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Marcelo D T Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA
| | - Jacqueline Peng
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, PA, USA.
- Department of Chemistry, School of Arts and Sciences, University of Pennsylvania, Philadelphia, PA, USA.
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, PA, USA.
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA.
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2
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Maqsood Q, Sumrin A, Ali Q, Hussain N, Malook SU, Ali D. In-silico analysis of ribosome inactivating protein (RIP) of the Cucurbitaceae family. AMB Express 2024; 14:61. [PMID: 38801471 PMCID: PMC11130107 DOI: 10.1186/s13568-024-01718-z] [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: 11/09/2023] [Accepted: 05/08/2024] [Indexed: 05/29/2024] Open
Abstract
Ribosome-inactivating proteins (RIPs) are highly active N-glycosidases that depurinate both bacterial and eukaryotic rRNAs, halting protein synthesis during translation. Found in a diverse spectrum of plant species and tissues, RIPs possess antifungal, antibacterial, antiviral, and insecticidal properties linked to plant defense. In this study, we investigated the physiochemical properties of RIP peptides from the Cucurbitaceae family through bioinformatics approaches. Molecular weight, isoelectric point, aliphatic index, extinction coefficient, and secondary structures were analyzed, revealing their hydrophobic nature. The novelty of this work lies in the comprehensive examination of RIPs from the Cucurbitaceae family and their potential therapeutic applications. The study also elucidated the binding interactions of Cucurbitaceae RIPs with key biological targets, including Interleukin-6 (IL-6). Strong hydrogen bond interactions between RIPs and these targets suggest potential for innovative insilico drug design and therapeutic applications, particularly in cancer treatment. Comprehensive analysis of bond lengths using Ligpolt + software provides insights for optimizing molecular interactions, offering a valuable tool for drug design and structural biology studies.
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Affiliation(s)
- Quratulain Maqsood
- Department of Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Aleena Sumrin
- Department of Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Qurban Ali
- Department of Plant Breeding and Genetics, University of the Punjab, Lahore, Pakistan.
| | - Nazim Hussain
- Department of Centre for Applied Molecular Biology, University of the Punjab, Lahore, Pakistan.
| | - Saif Ul Malook
- Department of Entomology and Nematology, University of Florida, Gainesville, USA
| | - Daoud Ali
- Department of Zoology, College of Science, King Saud University, PO Box 2455, Riyadh, 11451, Saudi Arabia
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3
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Ismail S, Masi M, Gaglione R, Arciello A, Cimmino A. Antimicrobial and antibiofilm activity of specialized metabolites isolated from Centaurea hyalolepis. PeerJ 2024; 12:e16973. [PMID: 38560449 PMCID: PMC10979744 DOI: 10.7717/peerj.16973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 01/29/2024] [Indexed: 04/04/2024] Open
Abstract
The discovery of plant-derived compounds that are able to combat antibiotic-resistant pathogens is an urgent demand. Over years, Centaurea hyalolepis attracted considerable attention because of its beneficial medical properties. Phytochemical analyses revealed that Centaurea plant species contain several metabolites, such as sesquiterpene lactones (STLs), essential oils, flavonoids, alkaloids, and lignans.The organic extract of C. hyalolepis plant, collected in Palestine, showed significant antimicrobial properties towards a panel of Gram-negative and Gram-positive bacterial strains when the Minimal Inhibitory Concentration (MIC) values were evaluated by broth microdilution assays. A bio-guided fractionation of the active extract via multiple steps of column and thin layer chromatography allowed us to obtain three main compounds. The isolated metabolites were identified as the STLs cnicin, 11β,13-dihydrosalonitenolide and salonitenolide by spectroscopic and spectrometric analyses. Cnicin conferred the strongest antimicrobial activity among the identified compounds. Moreover, the evaluation of its antibiofilm activity by biomass assays through crystal violet staining revealed almost 30% inhibition of biofilm formation in the case of A. baumannii ATCC 17878 strain. Furthermore, the quantification of carbohydrates and proteins present in the extracellular polymeric substance (EPS) revealed the ability of cnicin to significantly perturb biofilm structure. Based on these promising results, further investigations might open interesting perspectives to its applicability in biomedical field to counteract multidrug resistant infections.
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Affiliation(s)
- Shurooq Ismail
- University of Naples Federico II, Naples, Italy
- An-Najah National University, Nablus, Palestine
| | - Marco Masi
- University of Naples Federico II, Naples, Italy
| | - Rosa Gaglione
- University of Naples Federico II, Naples, Italy
- Istituto Nazionale di Biostrutture e Biosistemi, Rome, Italy
| | - Angela Arciello
- University of Naples Federico II, Naples, Italy
- Istituto Nazionale di Biostrutture e Biosistemi, Rome, Italy
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4
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Satchanska G, Davidova S, Gergova A. Diversity and Mechanisms of Action of Plant, Animal, and Human Antimicrobial Peptides. Antibiotics (Basel) 2024; 13:202. [PMID: 38534637 DOI: 10.3390/antibiotics13030202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 01/05/2024] [Accepted: 01/17/2024] [Indexed: 03/28/2024] Open
Abstract
Antimicrobial peptides (AMPs) are usually made up of fewer than 100 amino acid residues. They are found in many living organisms and are an important factor in those organisms' innate immune systems. AMPs can be extracted from various living sources, including bacteria, plants, animals, and even humans. They are usually cationic peptides with an amphiphilic structure, which allows them to easily bind and interact with the cellular membranes of viruses, bacteria, fungi, and other pathogens. They can act against both Gram-negative and Gram-positive pathogens and have various modes of action against them. Some attack the pathogens' membranes, while others target their intracellular organelles, as well as their nucleic acids, proteins, and metabolic pathways. A crucial area of AMP use is related to their ability to help with emerging antibiotic resistance: some AMPs are active against resistant strains and are susceptible to peptide engineering. This review considers AMPs from three key sources-plants, animals, and humans-as well as their modes of action and some AMP sequences.
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Affiliation(s)
- Galina Satchanska
- BioLaboratory-MF-NBU, Department of Natural Sciences, New Bulgarian University, 1618 Sofia, Bulgaria
| | - Slavena Davidova
- BioLaboratory-MF-NBU, Department of Natural Sciences, New Bulgarian University, 1618 Sofia, Bulgaria
| | - Alexandra Gergova
- BioLaboratory-MF-NBU, Department of Natural Sciences, New Bulgarian University, 1618 Sofia, Bulgaria
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5
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Torres MDT, Brooks E, Cesaro A, Sberro H, Nicolaou C, Bhatt AS, de la Fuente-Nunez C. Human gut metagenomic mining reveals an untapped source of peptide antibiotics. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.31.555711. [PMID: 37693399 PMCID: PMC10491270 DOI: 10.1101/2023.08.31.555711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally mined 444,054 families of putative small proteins from 1,773 human gut metagenomes, identifying 323 peptide antibiotics encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro, with 59% displaying activity against either pathogens or commensals. Since these peptides were unique compared to previously reported antimicrobial peptides, we termed them smORF-encoded peptides (SEPs). SEPs killed bacteria by targeting their membrane, synergized with each other, and modulated gut commensals, indicating that they may play a role in reconfiguring microbiome communities in addition to counteracting pathogens. The lead candidates were anti-infective in both murine skin abscess and deep thigh infection models. Notably, prevotellin-2 from Prevotella copri presented activity comparable to the commonly used antibiotic polymyxin B. We report the discovery of hundreds of peptide sequences in the human gut.
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Affiliation(s)
- Marcelo D. T. Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
| | - Erin Brooks
- Department of Medicine (Hematology; Blood and Marrow Transplantation), Stanford University, Stanford, CA, United States of America
| | - Angela Cesaro
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
| | - Hila Sberro
- Department of Medicine (Hematology; Blood and Marrow Transplantation), Stanford University, Stanford, CA, United States of America
| | - Cosmos Nicolaou
- Department of Medicine (Hematology; Blood and Marrow Transplantation), Stanford University, Stanford, CA, United States of America
| | - Ami S. Bhatt
- Department of Medicine (Hematology; Blood and Marrow Transplantation), Stanford University, Stanford, CA, United States of America
- Department of Genetics, Stanford University, Stanford, CA, United States of America
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
- Departments of Bioengineering and Chemical and Biomolecular Engineering, School of Engineering and Applied Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
- Penn Institute for Computational Science, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States of America
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6
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Ephedra foeminea as a Novel Source of Antimicrobial and Anti-Biofilm Compounds to Fight Multidrug Resistance Phenotype. Int J Mol Sci 2023; 24:ijms24043284. [PMID: 36834695 PMCID: PMC9965181 DOI: 10.3390/ijms24043284] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/28/2023] [Accepted: 02/02/2023] [Indexed: 02/10/2023] Open
Abstract
Plants are considered a wealthy resource of novel natural drugs effective in the treatment of multidrug-resistant infections. Here, a bioguided purification of Ephedra foeminea extracts was performed to identify bioactive compounds. The determination of antimicrobial properties was achieved by broth microdilution assays to evaluate minimal inhibitory concentration (MIC) values and by crystal violet staining and confocal laser scanning microscopy analyses (CLSM) to investigate the antibiofilm capacity of the isolated compounds. Assays were performed on a panel of three gram-positive and three gram-negative bacterial strains. Six compounds were isolated from E. foeminea extracts for the first time. They were identified by nuclear magnetic resonance (NMR) spectroscopy and mass spectrometry (MS) analyses as the well-known monoterpenoid phenols carvacrol and thymol and as four acylated kaempferol glycosides. Among them, the compound kaempferol-3-O-α-L-(2″,4″-di-E-p-coumaroyl)-rhamnopyranoside was found to be endowed with strong antibacterial properties and significant antibiofilm activity against S. aureus bacterial strains. Moreover, molecular docking studies on this compound suggested that the antibacterial activity of the tested ligand against S. aureus strains might be correlated to the inhibition of Sortase A and/or of tyrosyl tRNA synthase. Collectively, the results achieved open interesting perspectives to kaempferol-3-O-α-L-(2″,4″-di-E-p-coumaroyl)-rhamnopyranoside applicability in different fields, such as biomedical applications and biotechnological purposes such as food preservation and active packaging.
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7
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Huang M, Wei X, Wu T, Li M, Zhou L, Chai L, Ruan C, Li H. Inhibition of TNBS-induced intestinal inflammation in crucian carp (Carassius carassius) by oral administration of bioactive Bioactive food derived peptides. FISH & SHELLFISH IMMUNOLOGY 2022; 131:999-1005. [PMID: 36195269 DOI: 10.1016/j.fsi.2022.09.044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 09/14/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Intestinal enteritis is a main issue in crucian carp production which results in massive economic loss. Traditional antibiotics used for disease prevention of crucian carp (Carassius carassius) have been banned, thus an alternative approach needs to be identified. In this study, the bioactive peptide was evaluated as a diet supplement for preventing intestinal inflammation in crucian carp. Intestinal inflammation was induced by intrarectal administration of a 2,4,6-trinitrobenzene sulfonic acid (TNBS) solution. The fish samples were fed with different diets for 14 days. The disease activity index (DAI), which included, fish swimming, food intake, anal inflammation, body surface, and ascites was determined daily. Intestine segments were stained with haematoxylin and eosin (H.E.) for histopathological analysis. The expression of cytokines, including interleukin-1β (IL-1β), interleukin-8 (IL-8), tumor necrosis factor α (TNF-α), and myeloperoxidase (MPO) in crucian carp were determined. In TNBS-induced groups, the DAI scores were dramatically increased compared to the control group. The histopathological analysis showed that the damage of the fish intestine after the injection of TNBS. The relative expression levels of pro-inflammation cytokines (TNF-α, IL-1β, IL-8, MPO) were significantly increased compared to the control group on day 1. In the TNBS-induced group feed with a diet supplemented with bioactive peptide, the symptoms of intestinal inflammation were relieved on day 3 and the mRNA expression levels of pro-inflammation cytokines (TNF-α, IL-1β, IL-8, MPO) were reduced compared to day 1. On day 7, the fish samples enrofloxacin group and bioactive peptide group were recovered from TNBS-induced intestinal inflammation. This study showed that the fish diet supplemented with bioactive peptide could help to prevent and recover from intestinal inflammation. Thus, the bioactive peptide can be used as a replacement for antibiotics to prevent disease in aquaculture production.
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Affiliation(s)
- Meijuan Huang
- Institute of Hematology, Fijian Union Hospital, attached to Fujian Medical University, Fujian, China
| | - Xinyao Wei
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Tiecheng Wu
- Fujian University of Traditional Chinese Medicine, Fujian, China
| | - Mengyan Li
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Lei Zhou
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Libing Chai
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Chengxu Ruan
- College of Biological Science and Engineering, Fuzhou University, Fujian, China
| | - Hao Li
- College of Biological Science and Engineering, Fuzhou University, Fujian, China.
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8
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Sydor BG, Ramos-Milaré ÁCFH, Pereira MB, Brustolin AÁ, Montaholi DC, Lera-Nonose DSSL, Negri M, de Lima Scodro RB, Teixeira JJV, Lonardoni MVC. Plants of the Phytolaccaceae family with antimicrobial activity: A systematic review. Phytother Res 2022; 36:3505-3528. [PMID: 35858779 DOI: 10.1002/ptr.7557] [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: 04/27/2021] [Revised: 01/24/2022] [Accepted: 06/22/2022] [Indexed: 12/09/2022]
Abstract
Phytolaccaceae is a plant family of the order Caryophyllales, which includes species used in traditional medicine to treat diseases. The purpose of this study was to investigate Phytolaccaceae family plants with potential antimicrobial action, through a systematic review. The study was conducted following the criteria of PRISMA protocol. The search was performed in the electronic databases PubMed, Web of Science, Scopus, and LILACS, in March 2021. The search strategy used free descriptors and terms, limiting articles to the English language, regardless of publication year. The risk of bias and the quality of publications were based on the CONSORT checklist, modified for in vitro studies and SYRCLE's RoB tool for in vivo study. Five independent judges performed quality assessments of publications and risk of bias analysis. Ninety-five publications were retrieved from the databases and, after screening and eligibility criteria, 22 articles remained, from 1998 to 2019. In the selected studies, the plants were obtained from eight countries. In vivo and in vitro studies of extracts from the Phytolaccaceae family plants, evaluating antibacterial (8 publications), antifungal (8), anti-Trypanosoma (2), anti-Leishmania (2), antiviral (1), and antiamoebic (1) activities, are included. The plant species identified belong to genera Petiveria, Phytolacca, Gallesia, Trichostigma, and Seguieria. The risk of bias in the 22 publications both in vitro and in vitro was suboptimal. The evidence obtained showed that the Phytolaccaceae family, a source of plants with antimicrobial action, can serve as a basis for the creation of new herbal medicines, expanding the possibility of treatment for infectious diseases and stimulating their preservation and biodiversity. However, more high-quality studies are needed to establish the clinical efficacy of the plant.
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Affiliation(s)
- Bruna Gomes Sydor
- Postgraduate Program in Health Sciences, State University of Maringá, Maringá, Brazil
| | | | | | - Aline Ávila Brustolin
- Postgraduate Program in Health Sciences, State University of Maringá, Maringá, Brazil
| | | | | | - Melyssa Negri
- Postgraduate Program in Health Sciences, State University of Maringá, Maringá, Brazil
| | | | | | - Maria Valdrinez Campana Lonardoni
- Postgraduate Program in Health Sciences, State University of Maringá, Maringá, Brazil.,Postgraduate Program in Biosciences and Physiopathology, State University of Maringá, Maringá, Brazil
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9
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Gaglione R, Pane K, De Luca M, Franzese M, Arciello A, Trama F, Brancorsini S, Salvatore M, Illiano E, Costantini E. Novel Antimicrobial Strategies to Prevent Biofilm Infections in Catheters after Radical Cystectomy: A Pilot Study. Life (Basel) 2022; 12:life12060802. [PMID: 35743833 PMCID: PMC9225455 DOI: 10.3390/life12060802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/23/2022] [Accepted: 05/25/2022] [Indexed: 12/03/2022] Open
Abstract
Catheter-associated infections in bladder cancer patients, following radical cystectomy or ureterocutaneostomy, are very frequent, and the development of antibiotic resistance poses great challenges for treating biofilm-based infections. Here, we characterized bacterial communities from catheters of patients who had undergone radical cystectomy for muscle-invasive bladder cancer. We evaluated the efficacy of conventional antibiotics, alone or combined with the human ApoB-derived antimicrobial peptide r(P)ApoBLAla, to treat ureteral catheter-colonizing bacterial communities on clinically isolated bacteria. Microbial communities adhering to indwelling catheters were collected during the patients’ regular catheter change schedules (28 days) and extracted within 48 h. Living bacteria were characterized using selective media and biochemical assays. Biofilm growth and novel antimicrobial strategies were analyzed using confocal laser scanning microscopy. Statistical analyses confirmed the relevance of the biofilm reduction induced by conventional antibiotics (fosfomycin, ceftriaxone, ciprofloxacin, gentamicin, and tetracycline) and a well-characterized human antimicrobial peptide r(P)ApoBLAla (1:20 ratio, respectively). Catheters showed polymicrobial communities, with Enterobactericiae and Proteus isolates predominating. In all samples, we recorded a meaningful reduction in biofilms, in both biomass and thickness, upon treatment with the antimicrobial peptide r(P)ApoBLAla in combination with low concentrations of conventional antibiotics. The results suggest that combinations of conventional antibiotics and human antimicrobial peptides might synergistically counteract biofilm growth on ureteral catheters, suggesting novel avenues for preventing catheter-associated infections in patients who have undergone radical cystectomy and ureterocutaneostomy.
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Affiliation(s)
- Rosa Gaglione
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (R.G.); (M.D.L.); (A.A.)
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), 00136 Rome, Italy
| | - Katia Pane
- IRCCS Synlab SDN, Via E. Gianturco 113, 80143 Naples, Italy; (M.F.); (M.S.)
- Correspondence:
| | - Maria De Luca
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (R.G.); (M.D.L.); (A.A.)
| | - Monica Franzese
- IRCCS Synlab SDN, Via E. Gianturco 113, 80143 Naples, Italy; (M.F.); (M.S.)
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (R.G.); (M.D.L.); (A.A.)
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), 00136 Rome, Italy
| | - Francesco Trama
- Andrological and Urogynecological Clinic, Santa Maria Terni Hospital, University of Perugia, 05100 Terni, Italy; (F.T.); (E.I.); (E.C.)
| | - Stefano Brancorsini
- Department of Experimental Medicine, University of Perugia, 06132 Perugia, Italy;
| | - Marco Salvatore
- IRCCS Synlab SDN, Via E. Gianturco 113, 80143 Naples, Italy; (M.F.); (M.S.)
| | - Ester Illiano
- Andrological and Urogynecological Clinic, Santa Maria Terni Hospital, University of Perugia, 05100 Terni, Italy; (F.T.); (E.I.); (E.C.)
| | - Elisabetta Costantini
- Andrological and Urogynecological Clinic, Santa Maria Terni Hospital, University of Perugia, 05100 Terni, Italy; (F.T.); (E.I.); (E.C.)
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10
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Amiss AS, Henriques ST, Lawrence N. Antimicrobial peptides provide wider coverage for targeting drug‐resistant bacterial pathogens. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Anna S. Amiss
- Institute for Molecular Bioscience The University of Queensland Brisbane Queensland Australia
| | - Sónia Troeira Henriques
- Institute for Molecular Bioscience The University of Queensland Brisbane Queensland Australia
- School of Biomedical Sciences Queensland University of Technology, Translational Research Institute Brisbane Queensland Australia
| | - Nicole Lawrence
- Institute for Molecular Bioscience The University of Queensland Brisbane Queensland Australia
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11
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Gaglione R, Smaldone G, Cesaro A, Rumolo M, De Luca M, Di Girolamo R, Petraccone L, Del Vecchio P, Oliva R, Notomista E, Pedone E, Arciello A. Impact of a Single Point Mutation on the Antimicrobial and Fibrillogenic Properties of Cryptides from Human Apolipoprotein B. Pharmaceuticals (Basel) 2021; 14:ph14070631. [PMID: 34209895 PMCID: PMC8308739 DOI: 10.3390/ph14070631] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2021] [Revised: 06/23/2021] [Accepted: 06/25/2021] [Indexed: 12/21/2022] Open
Abstract
Host defense peptides (HDPs) are gaining increasing interest, since they are endowed with multiple activities, are often effective on multidrug resistant bacteria and do not generally lead to the development of resistance phenotypes. Cryptic HDPs have been recently identified in human apolipoprotein B and found to be endowed with a broad-spectrum antimicrobial activity, with anti-biofilm, wound healing and immunomodulatory properties, and with the ability to synergistically act in combination with conventional antibiotics, while being not toxic for eukaryotic cells. Here, a multidisciplinary approach was used, including time killing curves, differential scanning calorimetry, circular dichroism, ThT binding assays, and transmission electron microscopy analyses. The effects of a single point mutation (Pro → Ala in position 7) on the biological properties of ApoB-derived peptide r(P)ApoBLPro have been evaluated. Although the two versions of the peptide share similar antimicrobial and anti-biofilm properties, only r(P)ApoBLAla peptide was found to exert bactericidal effects. Interestingly, antimicrobial activity of both peptide versions appears to be dependent from their interaction with specific components of bacterial surfaces, such as LPS or LTA, which induce peptides to form β-sheet-rich amyloid-like structures. Altogether, obtained data indicate a correlation between ApoB-derived peptides self-assembling state and their antibacterial activity.
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Affiliation(s)
- Rosa Gaglione
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (R.G.); (A.C.); (M.R.); (M.D.L.); (R.D.G.); (L.P.); (P.D.V.)
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), 00136 Rome, Italy
| | | | - Angela Cesaro
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (R.G.); (A.C.); (M.R.); (M.D.L.); (R.D.G.); (L.P.); (P.D.V.)
| | - Mariano Rumolo
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (R.G.); (A.C.); (M.R.); (M.D.L.); (R.D.G.); (L.P.); (P.D.V.)
| | - Maria De Luca
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (R.G.); (A.C.); (M.R.); (M.D.L.); (R.D.G.); (L.P.); (P.D.V.)
| | - Rocco Di Girolamo
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (R.G.); (A.C.); (M.R.); (M.D.L.); (R.D.G.); (L.P.); (P.D.V.)
| | - Luigi Petraccone
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (R.G.); (A.C.); (M.R.); (M.D.L.); (R.D.G.); (L.P.); (P.D.V.)
| | - Pompea Del Vecchio
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (R.G.); (A.C.); (M.R.); (M.D.L.); (R.D.G.); (L.P.); (P.D.V.)
| | - Rosario Oliva
- Physical Chemistry I—Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, TU Dortmund University, 44227 Dortmund, Germany;
| | - Eugenio Notomista
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy;
| | - Emilia Pedone
- Istituto di Biostrutture e Bioimmagini, CNR, 80134 Naples, Italy;
- Research Centre on Bioactive Peptides (CIRPeB), University of Naples Federico II, Via Mezzocannone 16, 80134 Naples, Italy
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, 80126 Naples, Italy; (R.G.); (A.C.); (M.R.); (M.D.L.); (R.D.G.); (L.P.); (P.D.V.)
- Istituto Nazionale di Biostrutture e Biosistemi (INBB), 00136 Rome, Italy
- Correspondence: ; Tel.: +39-081-679147
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12
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Ciociola T, Pertinhez TA, De Simone T, Magliani W, Ferrari E, Belletti S, D’Adda T, Conti S, Giovati L. In Vitro and In Vivo Anti- Candida Activity and Structural Analysis of Killer Peptide (KP)-Derivatives. J Fungi (Basel) 2021; 7:129. [PMID: 33578728 PMCID: PMC7916522 DOI: 10.3390/jof7020129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 02/05/2021] [Accepted: 02/06/2021] [Indexed: 12/11/2022] Open
Abstract
The previously described decapeptide AKVTMTCSAS (killer peptide, KP), derived from the variable region of a recombinant yeast killer toxin-like anti-idiotypic antibody, proved to exert a variety of antimicrobial, antiviral, and immunomodulatory activities. It also showed a peculiar self-assembly ability, likely responsible for the therapeutic effect in animal models of systemic and mucosal candidiasis. The present study analyzed the biological and structural properties of peptides derived from KP by substitution or deletion of the first residue, leaving unchanged the remaining amino acids. The investigated peptides proved to exert differential in vitro and/or in vivo anti-Candida activity without showing toxic effects on mammalian cells. The change of the first residue in KP amino acidic sequence affected the conformation of the resulting peptides in solution, as assessed by circular dichroism spectroscopy. KP-derivatives, except one, were able to induce apoptosis in yeast cells, like KP itself. ROS production and changes in mitochondrial transmembrane potential were also observed. Confocal and transmission electron microscopy studies allowed to establish that selected peptides could penetrate within C. albicans cells and cause gross morphological alterations. Overall, the physical and chemical properties of the first residue were found to be important for peptide conformation, candidacidal activity and possible mechanism of action. Small antimicrobial peptides could be exploited for the development of a new generation of antifungal drugs, given their relative low cost and ease of production as well as the possibility of devising novel delivery systems.
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Affiliation(s)
- Tecla Ciociola
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (T.C.); (T.A.P.); (T.D.S.); (W.M.); (E.F.); (S.B.); (T.D.); (L.G.)
| | - Thelma A. Pertinhez
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (T.C.); (T.A.P.); (T.D.S.); (W.M.); (E.F.); (S.B.); (T.D.); (L.G.)
- Transfusion Medicine Unit, Azienda USL-IRCCS di Reggio Emilia, 42122 Reggio Emilia, Italy
| | - Tiziano De Simone
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (T.C.); (T.A.P.); (T.D.S.); (W.M.); (E.F.); (S.B.); (T.D.); (L.G.)
| | - Walter Magliani
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (T.C.); (T.A.P.); (T.D.S.); (W.M.); (E.F.); (S.B.); (T.D.); (L.G.)
| | - Elena Ferrari
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (T.C.); (T.A.P.); (T.D.S.); (W.M.); (E.F.); (S.B.); (T.D.); (L.G.)
| | - Silvana Belletti
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (T.C.); (T.A.P.); (T.D.S.); (W.M.); (E.F.); (S.B.); (T.D.); (L.G.)
| | - Tiziana D’Adda
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (T.C.); (T.A.P.); (T.D.S.); (W.M.); (E.F.); (S.B.); (T.D.); (L.G.)
| | - Stefania Conti
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (T.C.); (T.A.P.); (T.D.S.); (W.M.); (E.F.); (S.B.); (T.D.); (L.G.)
| | - Laura Giovati
- Department of Medicine and Surgery, University of Parma, 43126 Parma, Italy; (T.C.); (T.A.P.); (T.D.S.); (W.M.); (E.F.); (S.B.); (T.D.); (L.G.)
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13
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Murtas G, Sacchi S, Tedeschi G, Maffioli E, Notomista E, Cafaro V, Abbondi M, Mothet JP, Pollegioni L. Antimicrobial D-amino acid oxidase-derived peptides specify gut microbiota. Cell Mol Life Sci 2021; 78:3607-3620. [PMID: 33484270 PMCID: PMC8038955 DOI: 10.1007/s00018-020-03755-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 12/16/2020] [Accepted: 12/30/2020] [Indexed: 12/15/2022]
Abstract
The flavoenzyme d-amino acid oxidase (DAAO) is deputed to the degradation of d-enantiomers of amino acids. DAAO plays various relevant physiological roles in different organisms and tissues. Thus, it has been recently suggested that the goblet cells of the mucosal epithelia secrete into the lumen of intestine, a processed and active form of DAAO that uses the intestinal d-amino acids to generate hydrogen peroxide (H2O2), an immune messenger that helps fighting gut pathogens, and by doing so controls the homeostasis of gut microbiota. Here, we show that the DAAO form lacking the 1–16 amino acid residues (the putative secretion signal) is unstable and inactive, and that DAAO is present in the epithelial layer and the mucosa of mouse gut, where it is largely proteolyzed. In silico predicted DAAO-derived antimicrobial peptides show activity against various Gram-positive and Gram-negative bacteria but not on Lactobacilli species, which represent the commensal microbiota. Peptidomic analysis reveals the presence of such peptides in the mucosal fraction. Collectively, we identify a novel mechanism for gut microbiota selection implying DAAO-derived antimicrobial peptides which are generated by intestinal proteases and that are secreted in the gut lumen. In conclusion, we herein report an additional, ancillary role for mammalian DAAO, unrelated to its enzymatic activity.
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Affiliation(s)
- Giulia Murtas
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy
| | - Silvia Sacchi
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy.,DAAIR, D-Amino Acid International Research Center, Gerenzano, Italy
| | - Gabriella Tedeschi
- Department of Veterinary Medicine, University of Milan, Milan, Italy.,Cimaina, University of Milan, Milan, Italy
| | - Elisa Maffioli
- Department of Veterinary Medicine, University of Milan, Milan, Italy.,Cimaina, University of Milan, Milan, Italy
| | - Eugenio Notomista
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Valeria Cafaro
- Department of Biology, University of Naples Federico II, Naples, Italy
| | - Monica Abbondi
- DAAIR, D-Amino Acid International Research Center, Gerenzano, Italy.,Fondazione Istituto Insubrico Ricerca Per La Vita (FIIRV), Gerenzano, Italy
| | - Jean-Pierre Mothet
- LuMIn, Université Paris-Saclay, CNRS, ENS Paris-Saclay, CentraleSupélec, 91190, Gif-sur-Yvette, France
| | - Loredano Pollegioni
- Department of Biotechnology and Life Sciences, University of Insubria, Via J. H. Dunant 3, 21100, Varese, Italy.
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14
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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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15
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Liu D, Chen L, Chen C, An X, Zhang Y, Wang Y, Li Q. Full-length transcriptome analysis of Phytolacca americana and its congener P. icosandra and gene expression normalization in three Phytolaccaceae species. BMC PLANT BIOLOGY 2020; 20:396. [PMID: 32854620 PMCID: PMC7450566 DOI: 10.1186/s12870-020-02608-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
BACKGROUND Phytolaccaceae species in China are not only ornamental plants but also perennial herbs that are closely related to human health. However, both large-scale full-length cDNA sequencing and reference gene validation of Phytolaccaceae members are still lacking. Therefore, single-molecule real-time sequencing technology was employed to generate full-length transcriptome in invasive Phytolacca americana and non-invasive exotic P. icosandra. Based on the transcriptome data, RT-qPCR was employed to evaluate the gene expression stability in the two plant species and another indigenous congener P. acinosa. RESULTS Total of 19.96 Gb and 19.75 Gb clean reads of P. americana and P. icosandra were generated, including 200,857 and 208,865 full length non-chimeric (FLNC) reads, respectively. Transcript clustering analysis of FLNC reads identified 89,082 and 98,448 consensus isoforms, including 86,989 and 96,764 high-quality ones. After removing redundant reads, 46,369 and 50,220 transcripts were obtained. Based on structure analysis, total 1675 and 1908 alternative splicing variants, 25,641 and 31,800 simple sequence repeats (SSR) as well as 34,971 and 36,841 complete coding sequences were detected separately. Furthermore, 3574 and 3833 lncRNA were predicted and 41,676 and 45,050 transcripts were annotated respectively. Subsequently, seven reference genes in the two plant species and a native species P. acinosa were selected and evaluated by RT-qPCR for gene expression analysis. When tested in different tissues (leaves, stems, roots and flowers), 18S rRNA showed the highest stability in P. americana, whether infested by Spodoptera litura or not. EF2 had the most stable expression in P. icosandra, while EF1-α was the most appropriate one when attacked by S. litura. EF1-α showed the highest stability in P.acinosa, whereas GAPDH was recommended when infested by S. litura. Moreover, EF1-α was the most stable one among the three plant species whenever germinating seeds or flowers only were considered. CONCLUSION Full-length transcriptome of P. americana and P. icosandra were produced individually. Based on the transcriptome data, the expression stability of seven candidate reference genes under different experimental conditions was evaluated. These results would facilitate further exploration of functional and comparative genomic studies in Phytolaccaceae and provide insights into invasion success of P. americana.
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Affiliation(s)
- Danfeng Liu
- Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, Yunnan University, Kunming, 650504, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650504, China
| | - Li Chen
- Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, Yunnan University, Kunming, 650504, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650504, China
| | - Chao Chen
- Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, Yunnan University, Kunming, 650504, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650504, China
| | - Xingkui An
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100191, China
| | - Yongjun Zhang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, 100191, China
| | - Yi Wang
- Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, Yunnan University, Kunming, 650504, China.
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650504, China.
| | - Qingjun Li
- Yunnan Key Laboratory of Plant Reproductive Adaption and Evolutionary Ecology, Yunnan University, Kunming, 650504, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650504, China
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16
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Antiviral Activity of PD-L1 and PD-L4, Type 1 Ribosome Inactivating Proteins from Leaves of Phytolacca dioica L. in the Pathosystem Phaseolus vulgaris-Tobacco Necrosis Virus (TNV). Toxins (Basel) 2020; 12:toxins12080524. [PMID: 32824023 PMCID: PMC7472211 DOI: 10.3390/toxins12080524] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 08/07/2020] [Accepted: 08/13/2020] [Indexed: 02/06/2023] Open
Abstract
Using the pathosystem Phaseolus vulgaris-tobacco necrosis virus (TNV), we demonstrated that PD-L1 and PD-L4, type-1 ribosome inactivating proteins (RIPs) from leaves of Phytolacca dioica L., possess a strong antiviral activity. This activity was exerted both when the RIPs and the virus were inoculated together in the same leaf and when they were inoculated or applied separately in the adaxial and abaxial leaf surfaces. This suggests that virus inhibition would mainly occur inside plant cells at the onset of infection. Histochemical studies showed that both PD-L1 and PD-L4 were not able to induce oxidative burst and cell death in treated leaves, which were instead elicited by inoculation of the virus alone. Furthermore, when RIPs and TNV were inoculated together, no sign of H2O2 deposits and cell death were detectable, indicating that the virus could have been inactivated in a very early stage of infection, before the elicitation of a hypersensitivity reaction. In conclusion, the strong antiviral activity is likely exerted inside host cells as soon the virus disassembles to start translation of the viral genome. This activity is likely directed towards both viral and ribosomal RNA, explaining the almost complete abolition of infection when virus and RIP enter together into the cells.
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17
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Paenibacillus alvei MP1 as a Producer of the Proteinaceous Compound with Activity against Important Human Pathogens, Including Staphylococcus aureus and Listeria monocytogenes. Pathogens 2020; 9:pathogens9050319. [PMID: 32344843 PMCID: PMC7281493 DOI: 10.3390/pathogens9050319] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 04/20/2020] [Accepted: 04/23/2020] [Indexed: 01/15/2023] Open
Abstract
An emerging need for new classes of antibiotics is, on the one hand, evident as antimicrobial resistance continues to rise. On the other hand, the awareness of the pros and cons of chemically synthesized compounds’ extensive use leads to a search for new metabolites in already known reservoirs. Previous research showed that Paenibacillus strain (P. alvei MP1) recovered from a buckwheat honey sample presented a wide spectrum of antimicrobial activity against both Gram-positive and Gram-negative pathogens. Recent investigation has confirmed that P. alvei MP1 (deposited at DDBJ/ENA/GenBank under the accession WSQB00000000) produces a proteinaceous, heat-stable compound(s) with the maximum antimicrobial production obtained after 18 h of P. alvei MP1 growth in LB medium at 37 °C with continuous shaking at 200 RPM. The highest activity was found in the 40% ammonium sulfate precipitate, with high activity also remaining in the 50% and 60% ammonium sulfate precipitates. Moderate to high antimicrobial activity that is insensitive to proteases or heat treatment, was confirmed against pathogenic bacteria that included L. monocytogenes FSL – X1-0001 (strain 10403S), S. aureus L1 – 0030 and E. coli O157: H7. Further studies, including de novo sequencing of peptides by mass spectrometry, are in progress.
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18
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Wong JH, Bao H, Ng TB, Chan HHL, Ng CCW, Man GCW, Wang H, Guan S, Zhao S, Fang EF, Rolka K, Liu Q, Li C, Sha O, Xia L. New ribosome-inactivating proteins and other proteins with protein synthesis-inhibiting activities. Appl Microbiol Biotechnol 2020; 104:4211-4226. [PMID: 32193575 DOI: 10.1007/s00253-020-10457-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2019] [Revised: 02/05/2020] [Accepted: 02/10/2020] [Indexed: 12/21/2022]
Abstract
Ribosome-inactivating proteins (RIPs) consist of three varieties. Type 1 RIPs are single-chained and approximately 30-kDa in molecular weight. Type 2 RIPs are double-chained and composed of a type 1 RIP chain and a lectin chain. Type III RIPs, such as maize b-32 barley and JIP60 which are produced as single-domain proenzymes, possess an N-terminal domain corresponding to the A domain of RIPs and fused to a C-terminal domain. In addition to the aforementioned three types of RIPs originating from flowering plants, there are recently discovered proteins and peptides with ribosome-inactivating and protein synthesis inhibitory activities but which are endowed with characteristics such as molecular weights distinctive from those of the regular RIPs. These new/unusual RIPs discussed in the present review encompass metazoan RIPs from Anopheles and Culex mosquitos, antimicrobial peptides derived from RIP of the pokeweed Phytolacca dioica, maize RIP (a type III RIP derived from a precursor form), RIPs from the garden pea and the kelp. In addition, RIPs with a molecular weight smaller than those of regular type 1 RIPs are produced by plants in the Cucurbitaceae family including the bitter gourd, bottle gourd, sponge gourd, ridge gourd, wax gourd, hairy gourd, pumpkin, and Chinese cucumber. A small type II RIP from camphor tree (Cinnamomum camphora) seeds and a snake gourd type II RIP with its catalytic chain cleaved into two have been reported. RIPs produced from mushrooms including the golden needle mushroom, king tuber mushroom, straw mushroom, and puffball mushroom are also discussed in addition to a type II RIP from the mushroom Polyporus umbellatus. Bacterial (Spiroplasma) RIPs associated with the fruitfly, Shiga toxin, and Streptomyces coelicolor RIP are also dealt with. The aforementioned proteins display a diversity of molecular weights, amino acid sequences, and mechanisms of action. Some of them are endowed with exploitable antipathogenic activities.
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Affiliation(s)
- Jack Ho Wong
- Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Shenzhen University, Shenzhen, China.
- State Key Laboratory of Respiratory Disease for Allergy, School of Medicine, Shenzhen University, Shenzhen, Guangdong, China.
| | - Hui Bao
- State Key Laboratory of Respiratory Disease for Allergy, School of Medicine, Shenzhen University, Shenzhen, Guangdong, China
| | - Tzi Bun Ng
- School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong, China.
| | | | | | - Gene Chi Wai Man
- Department of Orthopedics and Traumatology, The Chinese University of Hong Kong, Hong Kong, China
| | - Hexiang Wang
- Department of Microbiology, China Agricultural University, Beijing, China
| | - Suzhen Guan
- Department of Social Medicine, College of Public Health, Xinjiang Medical University, Urumqi, China
| | - Shuang Zhao
- Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, and Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Key Laboratory of Vegetable Postharvest Processing, Ministry of Agriculture, Beijing, China
| | - Evandro Fei Fang
- Department of Clinical Molecular Biology, University of Oslo and Akershus University Hospital, Lørenskog, Norway
- The Norwegian Centre on Healthy Ageing (NO-Age), Oslo, Norway
| | - Krzysztof Rolka
- Department of Molecular Biochemistry, Faculty of Chemistry, University of Gdańsk, Wita Stwosza 63, Gdańsk, Poland
| | - Qin Liu
- Institute of Plant Nutrition, Agricultural Resources and Environmental Science, Henan Academy of Agricultural Sciences, Zhengzhou, China
| | - Chunman Li
- Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Shenzhen University, Shenzhen, China
| | - Ou Sha
- Department of Anatomy, Histology and Embryology, School of Basic Medical Sciences, Shenzhen University, Shenzhen, China
| | - Lixin Xia
- State Key Laboratory of Respiratory Disease for Allergy, School of Medicine, Shenzhen University, Shenzhen, Guangdong, China.
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Cryptides Identified in Human Apolipoprotein B as New Weapons to Fight Antibiotic Resistance in Cystic Fibrosis Disease. Int J Mol Sci 2020; 21:ijms21062049. [PMID: 32192076 PMCID: PMC7139702 DOI: 10.3390/ijms21062049] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2020] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 01/24/2023] Open
Abstract
Chronic respiratory infections are the main cause of morbidity and mortality in cystic fibrosis (CF) patients, and are characterized by the development of multidrug resistance (MDR) phenotype and biofilm formation, generally recalcitrant to treatment with conventional antibiotics. Hence, novel effective strategies are urgently needed. Antimicrobial peptides represent new promising therapeutic agents. Here, we analyze for the first time the efficacy of three versions of a cryptide identified in human apolipoprotein B (ApoB, residues 887-922) towards bacterial strains clinically isolated from CF patients. Antimicrobial and anti-biofilm properties of ApoB-derived cryptides have been analyzed by broth microdilution assays, crystal violet assays, confocal laser scanning microscopy and scanning electron microscopy. Cell proliferation assays have been performed to test cryptide effects on human host cells. ApoB-derived cryptides have been found to be endowed with significant antimicrobial and anti-biofilm properties towards Pseudomonas and Burkholderia strains clinically isolated from CF patients. Peptides have been also found to be able to act in combination with the antibiotic ciprofloxacin, and they are harmless when tested on human bronchial epithelial mesothelial cells. These findings open interesting perspectives to cryptide applicability in the treatment of chronic lung infections associated with CF disease.
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Munusamy S, Conde R, Bertrand B, Munoz-Garay C. Biophysical approaches for exploring lipopeptide-lipid interactions. Biochimie 2020; 170:173-202. [PMID: 31978418 PMCID: PMC7116911 DOI: 10.1016/j.biochi.2020.01.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 01/19/2020] [Indexed: 02/07/2023]
Abstract
In recent years, lipopeptides (LPs) have attracted a lot of attention in the pharmaceutical industry due to their broad-spectrum of antimicrobial activity against a variety of pathogens and their unique mode of action. This class of compounds has enormous potential for application as an alternative to conventional antibiotics and for pest control. Understanding how LPs work from a structural and biophysical standpoint through investigating their interaction with cell membranes is crucial for the rational design of these biomolecules. Various analytical techniques have been developed for studying intramolecular interactions with high resolution. However, these tools have been barely exploited in lipopeptide-lipid interactions studies. These biophysical approaches would give precise insight on these interactions. Here, we reviewed these state-of-the-art analytical techniques. Knowledge at this level is indispensable for understanding LPs activity and particularly their potential specificity, which is relevant information for safe application. Additionally, the principle of each analytical technique is presented and the information acquired is discussed. The key challenges, such as the selection of the membrane model are also been briefly reviewed. A brief overview of topics to understand the generalities of lipopeptide (LP) science. Main analytical techniques used to reveal the interaction and the distorting effect of LP on artificial membranes. Guidelines for selecting of the most adequate membrane models for the given analytical technique.
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Affiliation(s)
- Sathishkumar Munusamy
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Renaud Conde
- Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Brandt Bertrand
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico
| | - Carlos Munoz-Garay
- Instituto de Ciencias Físicas, Universidad Nacional Autónoma de México, Av. Universidad 2001, Col. Chamilpa, 62210, Cuernavaca, Mexico.
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21
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Der Torossian Torres M, de la Fuente-Nunez C. Reprogramming biological peptides to combat infectious diseases. Chem Commun (Camb) 2019; 55:15020-15032. [PMID: 31782426 DOI: 10.1039/c9cc07898c] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
With the rapid spread of resistance among parasites and bacterial pathogens, antibiotic-resistant infections have drawn much attention worldwide. Consequently, there is an urgent need to develop new strategies to treat neglected diseases and drug-resistant infections. Here, we outline several new strategies that have been developed to counter pathogenic microorganisms by designing and constructing antimicrobial peptides (AMPs). In addition to traditional discovery and design mechanisms guided by chemical biology, synthetic biology and computationally-based approaches offer useful tools for the discovery and generation of bioactive peptides. We believe that the convergence of such fields, coupled with systematic experimentation in animal models, will help translate biological peptides into the clinic. The future of anti-infective therapeutics is headed towards specifically designed molecules whose form is driven by computer-based frameworks. These molecules are selective, stable, and active at therapeutic doses.
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Affiliation(s)
- Marcelo Der Torossian Torres
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
| | - Cesar de la Fuente-Nunez
- Machine Biology Group, Departments of Psychiatry and Microbiology, Institute for Biomedical Informatics, Institute for Translational Medicine and Therapeutics, Perelman School of Medicine, and Department of Bioengineering, University of Pennsylvania, Philadelphia, Pennsylvania, USA.
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22
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Vincenzi M, Mercurio FA, Leone M. About TFE: Old and New Findings. Curr Protein Pept Sci 2019; 20:425-451. [PMID: 30767740 DOI: 10.2174/1389203720666190214152439] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 01/28/2023]
Abstract
The fluorinated alcohol 2,2,2-Trifluoroethanol (TFE) has been implemented for many decades now in conformational studies of proteins and peptides. In peptides, which are often disordered in aqueous solutions, TFE acts as secondary structure stabilizer and primarily induces an α -helical conformation. The exact mechanism through which TFE plays its stabilizing roles is still debated and direct and indirect routes, relying either on straight interaction between TFE and molecules or indirect pathways based on perturbation of solvation sphere, have been proposed. Another still unanswered question is the capacity of TFE to favor in peptides a bioactive or a native-like conformation rather than simply stimulate the raise of secondary structure elements that reflect only the inherent propensity of a specific amino-acid sequence. In protein studies, TFE destroys unique protein tertiary structure and often leads to the formation of non-native secondary structure elements, but, interestingly, gives some hints about early folding intermediates. In this review, we will summarize proposed mechanisms of TFE actions. We will also describe several examples, in which TFE has been successfully used to reveal structural properties of different molecular systems, including antimicrobial and aggregation-prone peptides, as well as globular folded and intrinsically disordered proteins.
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Affiliation(s)
- Marian Vincenzi
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy
| | - Flavia A Mercurio
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
| | - Marilisa Leone
- Institute of Biostructures and Bioimaging, National Research Council (CNR), Via Mezzocannone 16, 80134 Naples, Italy.,Cirpeb, InterUniversity Research Centre on Bioactive Peptides, University of Naples "Federico II", Via Mezzocannone 16, 80134 Naples, Italy
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23
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Torres MD, Sothiselvam S, Lu TK, de la Fuente-Nunez C. Peptide Design Principles for Antimicrobial Applications. J Mol Biol 2019; 431:3547-3567. [DOI: 10.1016/j.jmb.2018.12.015] [Citation(s) in RCA: 184] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Revised: 12/19/2018] [Accepted: 12/22/2018] [Indexed: 02/08/2023]
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24
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Gaglione R, Cesaro A, Dell'Olmo E, Della Ventura B, Casillo A, Di Girolamo R, Velotta R, Notomista E, Veldhuizen EJA, Corsaro MM, De Rosa C, Arciello A. Effects of human antimicrobial cryptides identified in apolipoprotein B depend on specific features of bacterial strains. Sci Rep 2019; 9:6728. [PMID: 31040323 PMCID: PMC6491590 DOI: 10.1038/s41598-019-43063-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Accepted: 04/12/2019] [Indexed: 12/03/2022] Open
Abstract
Cationic Host Defense Peptides (HDPs) are endowed with a broad variety of activities, including direct antimicrobial properties and modulatory roles in the innate immune response. Even if it has been widely demonstrated that bacterial membrane represents the main target of peptide antimicrobial activity, the molecular mechanisms underlying membrane perturbation by HDPs have not been fully clarified yet. Recently, two cryptic HDPs have been identified in human apolipoprotein B and found to be endowed with a broad-spectrum antimicrobial activity, and with anti-biofilm, wound healing and immunomodulatory properties. Moreover, ApoB derived HDPs are able to synergistically act in combination with conventional antibiotics, while being not toxic for eukaryotic cells. Here, by using a multidisciplinary approach, including time killing curves, Zeta potential measurements, membrane permeabilization assays, electron microscopy analyses, and isothermal titration calorimetry studies, the antimicrobial effects of ApoB cryptides have been analysed on bacterial strains either susceptible or resistant to peptide toxicity. Intriguingly, it emerged that even if electrostatic interactions between negatively charged bacterial membranes and positively charged HDPs play a key role in mediating peptide toxicity, they are strongly influenced by the composition of negatively charged bacterial surfaces and by defined extracellular microenvironments.
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Affiliation(s)
- Rosa Gaglione
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Angela Cesaro
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Eliana Dell'Olmo
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | | | - Angela Casillo
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Rocco Di Girolamo
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Raffaele Velotta
- Department of Physics, University of Naples Federico II, 80126, Naples, Italy
| | - Eugenio Notomista
- Department of Biology, University of Naples Federico II, 80126, Naples, Italy
| | - Edwin J A Veldhuizen
- Department of Infectious Diseases and Immunology, Division Molecular Host Defence, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Maria Michela Corsaro
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Claudio De Rosa
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy
| | - Angela Arciello
- Department of Chemical Sciences, University of Naples Federico II, 80126, Naples, Italy. .,Istituto Nazionale di Biostrutture e Biosistemi (INBB), Rome, Italy.
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25
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Pane K, Cafaro V, Avitabile A, Torres MDT, Vollaro A, De Gregorio E, Catania MR, Di Maro A, Bosso A, Gallo G, Zanfardino A, Varcamonti M, Pizzo E, Di Donato A, Lu TK, de la Fuente-Nunez C, Notomista E. Identification of Novel Cryptic Multifunctional Antimicrobial Peptides from the Human Stomach Enabled by a Computational-Experimental Platform. ACS Synth Biol 2018; 7:2105-2115. [PMID: 30124040 DOI: 10.1021/acssynbio.8b00084] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Novel approaches are needed to combat antibiotic resistance. Here, we describe a computational-experimental framework for the discovery of novel cryptic antimicrobial peptides (AMPs). The computational platform, based on previously validated antimicrobial scoring functions, indicated the activation peptide of pepsin A, the main human stomach protease, and its N- and C-terminal halves as antimicrobial peptides. The three peptides from pepsinogen A3 isoform were prepared in a recombinant form using a fusion carrier specifically developed to express toxic peptides in Escherichia coli. Recombinant pepsinogen A3-derived peptides proved to be wide-spectrum antimicrobial agents with MIC values in the range 1.56-50 μM (1.56-12.5 μM for the whole activation peptide). Moreover, the activation peptide was bactericidal at pH 3.5 for relevant foodborne pathogens, suggesting that this new class of previously unexplored AMPs may contribute to microbial surveillance within the human stomach. The peptides showed no toxicity toward human cells and exhibited anti-infective activity in vivo, reducing by up to 4 orders of magnitude the bacterial load in a mouse skin infection model. These peptides thus represent a promising new class of antibiotics. We envision that computationally guided data mining approaches such as the one described here will lead to the discovery of antibiotics from previously unexplored sources.
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Affiliation(s)
- Katia Pane
- IRCCS SDN, Via E. Gianturco, 113, 80143 Naples, Italy
| | - Valeria Cafaro
- Department of Biology, University of Naples Federico II, Naples 80126, Italy
| | - Angela Avitabile
- Department of Biology, University of Naples Federico II, Naples 80126, Italy
| | - Marcelo Der Torossian Torres
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
- The Center for Microbiome Informatics and Therapeutics, Cambridge, Massachusetts 02139, United States
| | - Adriana Vollaro
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples 80131, Italy
| | - Eliana De Gregorio
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples 80131, Italy
| | - Maria Rosaria Catania
- Department of Molecular Medicine and Medical Biotechnologies, University of Naples Federico II, Naples 80131, Italy
| | - Antimo Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Naples, Vanvitelli, Caserta 81100, Italy
| | - Andrea Bosso
- Department of Biology, University of Naples Federico II, Naples 80126, Italy
| | - Giovanni Gallo
- Department of Biology, University of Naples Federico II, Naples 80126, Italy
| | - Anna Zanfardino
- Department of Biology, University of Naples Federico II, Naples 80126, Italy
| | - Mario Varcamonti
- Department of Biology, University of Naples Federico II, Naples 80126, Italy
| | - Elio Pizzo
- Department of Biology, University of Naples Federico II, Naples 80126, Italy
| | - Alberto Di Donato
- Department of Biology, University of Naples Federico II, Naples 80126, Italy
| | - Timothy K. Lu
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
- The Center for Microbiome Informatics and Therapeutics, Cambridge, Massachusetts 02139, United States
| | - Cesar de la Fuente-Nunez
- Synthetic Biology Group, MIT Synthetic Biology Center, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Biological Engineering, and Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02139, United States
- The Center for Microbiome Informatics and Therapeutics, Cambridge, Massachusetts 02139, United States
| | - Eugenio Notomista
- Department of Biology, University of Naples Federico II, Naples 80126, Italy
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