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Bharti S. Harnessing the potential of bimetallic nanoparticles: Exploring a novel approach to address antimicrobial resistance. World J Microbiol Biotechnol 2024; 40:89. [PMID: 38337082 DOI: 10.1007/s11274-024-03923-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Accepted: 02/05/2024] [Indexed: 02/12/2024]
Abstract
The growing global importance of antimicrobial resistance (AMR) in public health has prompted the creation of innovative approaches to combating the issue. In this study, the promising potential of bimetallic nanoparticles (BMNPs) was investigated as a novel weapon against AMR. This research begins by elaborating on the gravity of the AMR problem, outlining its scope in terms of the effects on healthcare systems, and stressing the urgent need for novel solutions. Because of their unusual features and wide range of potential uses, bimetallic nanoparticles (BMNPs), which are tiny particles consisting of two different metal elements, have attracted a lot of interest in numerous fields. This review article provides a comprehensive analysis of the composition, structural characteristics, and several synthesis processes employed in the production of BMNPs. Additionally, it delves into the unique properties and synergistic effects that set BMNPs apart from other materials. This review also focuses on the various antimicrobial activities shown by bimetallic nanoparticles, such as the rupturing of microbial cell membranes, the production of reactive oxygen species (ROS), and the regulation of biofilm formation. An extensive review of in vitro studies confirms the remarkable antibacterial activity of BMNPs against a variety of pathogens and sheds light on the dose-response relationship. The efficacy and safety of BMNPs in practical applications are assessed in this study. It also delves into the synergistic effects of BMNPs with traditional antimicrobial drugs and their ability to overcome multidrug resistance, providing mechanistic insight into these phenomena. Wound healing, infection prevention, and antimicrobial coatings on medical equipment are only some of the clinical applications of BMNPs that are examined, along with the difficulties and possible rewards of clinical translation. This review covers nanoparticle-based antibacterial regulation and emerging uses. The essay concludes with prospects for hybrid systems, site-specific targeting, and nanoparticle-mediated gene and drug delivery. In summary, bimetallic nanoparticles have surfaced as a potential solution, offering the public a more promising and healthier future.
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Affiliation(s)
- Sharda Bharti
- Department of Biotechnology, National Institute of Technology (NIT) Raipur, Raipur, Chhattisgarh, 492010, India.
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2
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Di Napoli M, Castagliuolo G, Pio S, Di Nardo I, Russo T, Antonini D, Notomista E, Varcamonti M, Zanfardino A. Study of the Antimicrobial Activity of the Human Peptide SQQ30 against Pathogenic Bacteria. Antibiotics (Basel) 2024; 13:145. [PMID: 38391531 PMCID: PMC10886087 DOI: 10.3390/antibiotics13020145] [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: 12/22/2023] [Revised: 01/19/2024] [Accepted: 01/30/2024] [Indexed: 02/24/2024] Open
Abstract
Given the continuous increase in antibiotic resistance, research has been driven towards the isolation of new antimicrobial molecules. Short, charged, and very hydrophobic antimicrobial peptides have a direct action against biological membranes, which are less prone to developing resistance. Using a bioinformatic tool, we chose the SQQ30 peptide, isolated from the human SOGA1 protein. The antimicrobial activity of this peptide against various Gram-negative and Gram-positive bacterial strains and against a fungal strain was studied. A mechanism of action directed against biological membranes was outlined. When administered in combination with the antibiotic ciprofloxacin and with the TRS21 (buforin II), another antimicrobial peptide, SQQ30 can be used with a lower MIC, showing additivity and synergism, respectively. Particularly interesting is the ability of SQQ30 to bind LPS in Gram-negative strains, preventing the eukaryotic cell from releasing inflammatory mediators. Our study indicates SQQ30 as a novel and promising antimicrobial agent.
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Affiliation(s)
- Michela Di Napoli
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Giusy Castagliuolo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Sara Pio
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Ilaria Di Nardo
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Teresa Russo
- IPCB-Institute for Polymers, Composites and Biomaterials, National Research Council of Italy, 80125 Naples, Italy
| | - Dario Antonini
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Eugenio Notomista
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Mario Varcamonti
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
| | - Anna Zanfardino
- Department of Biology, University of Naples Federico II, 80126 Naples, Italy
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Costa L, Sousa E, Fernandes C. Cyclic Peptides in Pipeline: What Future for These Great Molecules? Pharmaceuticals (Basel) 2023; 16:996. [PMID: 37513908 PMCID: PMC10386233 DOI: 10.3390/ph16070996] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 07/06/2023] [Accepted: 07/08/2023] [Indexed: 07/30/2023] Open
Abstract
Cyclic peptides are molecules that are already used as drugs in therapies approved for various pharmacological activities, for example, as antibiotics, antifungals, anticancer, and immunosuppressants. Interest in these molecules has been growing due to the improved pharmacokinetic and pharmacodynamic properties of the cyclic structure over linear peptides and by the evolution of chemical synthesis, computational, and in vitro methods. To date, 53 cyclic peptides have been approved by different regulatory authorities, and many others are in clinical trials for a wide diversity of conditions. In this review, the potential of cyclic peptides is presented, and general aspects of their synthesis and development are discussed. Furthermore, an overview of already approved cyclic peptides is also given, and the cyclic peptides in clinical trials are summarized.
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Affiliation(s)
- Lia Costa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
| | - Emília Sousa
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
| | - Carla Fernandes
- Laboratório de Química Orgânica e Farmacêutica, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal;
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Edifício do Terminal de Cruzeiros do Porto de Leixões, Av. General Norton de Matos s/n, 4050-208 Matosinhos, Portugal
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4
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Chen Q, Yang C, Xie Y, Wang Y, Li X, Wang K, Huang J, Yan W. GM-Pep: A High Efficiency Strategy to De Novo Design Functional Peptide Sequences. J Chem Inf Model 2022; 62:2617-2629. [PMID: 35533298 DOI: 10.1021/acs.jcim.2c00089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Although peptides are regarded as ideal therapeutic agents, only a small proportion of the marketed drugs are peptides. In the past decade, pharmacists have paid great attention to the development of peptide therapeutics. Except a few approved chemically/rationally designed peptides, most attempts failed due to unsatisfactory efficacy or safety. Luckily, computation methods, such as artificial intelligence, have been utilized to accelerate the discovery of therapeutic peptides by predicting the activity, toxicity, and absorption, distribution, metabolism, and excretion of polypeptides. Usually, a specific biological activity of a peptide could be accurately determined by an interest-oriented binary classification constructed of a positive set and another un-experimentally validated negative set regardless of other characteristics, which suggests that it could be challenging to realize the comprehensive evaluation of the research object in the early stage of drug research and development. Herein, we proposed an integrated method (GM-Pep) that contained a conditional variational autoencoder model (CVAE) and a positive sample training multiclassifier (Deep-Multiclassifier) to effectively generate a single bioactive peptide sequence without toxicity and referential side effects. The results showed that our Deep-Multiclassifier model gave a sequence accuracy of up to 96.41% [toxicity (94.48%), antifungal (96.58%), antihypertensive (97.18%), and antibacterial (96.91%), respectively]. The properties of Deep-Multiclassifier and CVAE were validated through 12 first synthesized antibacterial peptides or compared to random peptides. The source code and data sets are available at https://github.com/TimothyChen225/GM-Pep.
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Affiliation(s)
- Qushuo Chen
- The Institute of Pharmacology, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Changyan Yang
- The Institute of Pharmacology, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Yihao Xie
- The Institute of Pharmacology, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Yuqiang Wang
- School of Stomatology, Lanzhou University,Lanzhou, Gansu 730000, China
| | - Xiaoxu Li
- School of Computer and Communication, Lanzhou University of Technology, Lanzhou, Gansu 730050, China
| | - Kairong Wang
- The Institute of Pharmacology, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
| | - Jinqi Huang
- Department of Hematology, Affiliated Hospital of Guangdong Medical University, Zhanjiang, Guangdong 524000, China
| | - Wenjin Yan
- The Institute of Pharmacology, Key Laboratory of Preclinical Study for New Drugs of Gansu Province, School of Basic Medical Sciences, Lanzhou University, Lanzhou, Gansu 730000, China
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5
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Dos Santos-Silva CA, Zupin L, Oliveira-Lima M, Vilela LMB, Bezerra-Neto JP, Ferreira-Neto JR, Ferreira JDC, de Oliveira-Silva RL, Pires CDJ, Aburjaile FF, de Oliveira MF, Kido EA, Crovella S, Benko-Iseppon AM. Plant Antimicrobial Peptides: State of the Art, In Silico Prediction and Perspectives in the Omics Era. Bioinform Biol Insights 2020; 14:1177932220952739. [PMID: 32952397 PMCID: PMC7476358 DOI: 10.1177/1177932220952739] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 07/30/2020] [Indexed: 12/14/2022] Open
Abstract
Even before the perception or interaction with pathogens, plants rely on constitutively guardian molecules, often specific to tissue or stage, with further expression after contact with the pathogen. These guardians include small molecules as antimicrobial peptides (AMPs), generally cysteine-rich, functioning to prevent pathogen establishment. Some of these AMPs are shared among eukaryotes (eg, defensins and cyclotides), others are plant specific (eg, snakins), while some are specific to certain plant families (such as heveins). When compared with other organisms, plants tend to present a higher amount of AMP isoforms due to gene duplications or polyploidy, an occurrence possibly also associated with the sessile habit of plants, which prevents them from evading biotic and environmental stresses. Therefore, plants arise as a rich resource for new AMPs. As these molecules are difficult to retrieve from databases using simple sequence alignments, a description of their characteristics and in silico (bioinformatics) approaches used to retrieve them is provided, considering resources and databases available. The possibilities and applications based on tools versus database approaches are considerable and have been so far underestimated.
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Affiliation(s)
| | - Luisa Zupin
- Genetic Immunology laboratory, Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, Trieste, Italy
| | - Marx Oliveira-Lima
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
| | | | | | | | - José Diogo Cavalcanti Ferreira
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil.,Departamento de Genética, Instituto Federal de Pernambuco, Pesqueira, Brazil
| | | | | | | | | | - Ederson Akio Kido
- Departamento de Genética, Universidade Federal de Pernambuco, Recife, Brazil
| | - Sergio Crovella
- Genetic Immunology laboratory, Institute for Maternal and Child Health-IRCCS, Burlo Garofolo, Trieste, Italy.,Department of Medicine, Surgery and Health Sciences, University of Trieste, Trieste, Italy
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6
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Qutb AM, Wei F, Dong W. Prediction and Characterization of Cationic Arginine-Rich Plant Antimicrobial Peptide SM-985 From Teosinte ( Zea mays ssp. mexicana). Front Microbiol 2020; 11:1353. [PMID: 32636825 PMCID: PMC7318549 DOI: 10.3389/fmicb.2020.01353] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 05/26/2020] [Indexed: 12/17/2022] Open
Abstract
Antimicrobial peptides (AMPs) are effective against different plant pathogens and newly considered as part of plant defense systems. From prokaryotes to eukaryotes, AMPs can exist in all forms of life. SM-985 is a cationic AMP (CAMP) isolated from the cDNA library of Mexican teosinte (Zea mays ssp. mexicana). A computational prediction server running with different algorithms was used to screen the teosinte cDNA library for AMPs, and the SM-985 peptide was predicted as an AMP with high probability prediction values. SM-985 is an arginine-rich peptide and composed of 21 amino acids (MW: 2671.06 Da). The physicochemical properties of SM-985 are very promising as an AMP, including the net charge (+8), hydrophobicity ratio of 23%, Boman index of 5.19 kcal/mol, and isoelectric point of 12.95. The SM-985 peptide has amphipathic α-helix conformations. The antimicrobial activity of SM-985 was confirmed against six bacterial plant pathogens, and the MIC of SM-985 against Gram-positive indicators was 8 μM, while the MIC of SM-985 against Gram-negative indicators was 4 μM. The SM-985 interacting with the bacterial membrane and this interaction were examined by treatment of the bacterial indicators with FITC-SM-985 peptide, which showed a high binding affinity of SM-985 to the bacterial membrane (whether Gram-positive or Gram-negative). Scanning electron microscopy (SEM) and transmission electron microscopy (TEM) images of the treated bacteria with SM-985 demonstrated cell membrane damage and cell lysis. In vivo antimicrobial activity was examined, and SM-985 prevented leaf spot disease infection caused by Pst DC3000 on Solanum lycopersicum. Moreover, SM-985 showed sensitivity to calcium chloride salt, which is a common feature of CAMPs.
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Affiliation(s)
- Abdelrahman M. Qutb
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
- Department of Agricultural Botany, Faculty of Agriculture, Al-Azhar University, Cairo, Egypt
| | - Feng Wei
- State Key Laboratory of Agricultural Microbiology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Wubei Dong
- Department of Plant Pathology, College of Plant Science and Technology and the Key Lab of Crop Disease Monitoring and Safety Control in Hubei Province, Huazhong Agricultural University, Wuhan, China
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7
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Flores-Holguín N, Frau J, Glossman-Mitnik D. Computational Peptidology Assisted by Conceptual Density Functional Theory for the Study of Five New Antifungal Tripeptides. ACS OMEGA 2019; 4:12555-12560. [PMID: 31460375 PMCID: PMC6682088 DOI: 10.1021/acsomega.9b01463] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
A well-behaved model chemistry previously validated for the study of the chemical reactivity of peptides was considered for the calculation of the molecular properties and structures of a group of five new antifungal tripeptides, namely (2R)-2-[(2S)-2-[(2S)-2-amino-3-phenylpropanamido]propanamido]-5-[(diaminomethylidene)amino]pentanoic acid, (2S)-2-[(2S)-2-[(2S)-2-amino-3-phenyl propanamido]propanamido]-3-(4-hydroxyphenyl)propanoic acid, (2S)-2-[(2S)-2-[(2S)-2-amino-3-phenylpropanamido]-3-methylbutanamido]-3-(4-hydroxyphenyl)propanoic acid, (2R)-2-[(2S)-2-[(2S)-2-amino-3-phenylpropanamido]-3-(1H-indol-3-yl)propanamido]-3-sulfanylpropanoic acid, and (2S)-2-[(2S)-2-[(2S)-2-amino-3-phenylpropanamido]-3-(1H-indol-3-yl)propanamido]-3-(4-hydroxyphenyl)propanoic acid, according to their amino acid sequences. A methodology based on conceptual density functional theory was chosen for the determination of the reactivity descriptors. The molecular active sites were associated with the active regions of the molecules that were associated with the nucleophilic, electrophilic, and radical Fukui functions. Additionally, the pK a values for the different peptides are predicted with great accuracy, which constitutes a useful knowledge for the process of drug design. Finally, the bioactivity scores for the new antifungal peptides are predicted through a homology methodology relating them with the calculated reactivity descriptors.
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Affiliation(s)
- Norma Flores-Holguín
- Laboratorio
Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico
| | - Juan Frau
- Departament
de Química, Universitat de les Illes
Balears, Palma
de Mallorca 07122, Spain
| | - Daniel Glossman-Mitnik
- Laboratorio
Virtual NANOCOSMOS, Departamento de Medio Ambiente y Energía, Centro de Investigación en Materiales Avanzados, Chihuahua 31136, Mexico
- Departament
de Química, Universitat de les Illes
Balears, Palma
de Mallorca 07122, Spain
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8
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Xu P, Huang M. Small Peptides as Modulators of Serine Proteases. Curr Med Chem 2018; 27:3686-3705. [PMID: 30332941 DOI: 10.2174/0929867325666181016163630] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 09/26/2018] [Accepted: 10/09/2018] [Indexed: 02/08/2023]
Abstract
Serine proteases play critical roles in many physiological and pathological processes, and are proven diagnostic and therapeutic targets in a number of clinical indications. Suppression of the aberrant proteolytic activities of these proteases has been clinically used for the treatments of relevant diseases. Polypeptides with 10-20 residues are of great interests as medicinal modulators of serine proteases, because these peptides demonstrate the characteristics of both small molecule drugs and macromolecular drugs. In this review, we summarized the recent development of peptide-based inhibitors against serine proteases with potent inhibitory and high specificity comparable to monoclonal antibodies. In addition, we also discussed the strategies of enhancing plasma half-life and bioavailability of peptides in vivo, which is the main hurdle that limits the clinical translation of peptide-based drugs. This review advocates new avenue for the development of effective serine protease inhibitors and highlights the prospect of the medicinal use of these inhibitors.
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Affiliation(s)
- Peng Xu
- College of Biological Science and Engineering, Fuzhou University, Fuzhou, Fujian 350116, China
| | - Mingdong Huang
- College of Chemistry, Fuzhou University, Fuzhou, Fujian 350116, China
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Yao X, Zhao W, Yang R, Wang J, Zhao F, Wang S. Preparation and applications of guard cell protoplasts from the leaf epidermis of Solanum lycopersicum. PLANT METHODS 2018; 14:26. [PMID: 29593827 PMCID: PMC5866509 DOI: 10.1186/s13007-018-0294-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 03/16/2018] [Indexed: 05/12/2023]
Abstract
BACKGROUND Guard cell protoplasts (GCPs) isolated from various plants have proven to be especially useful for studies of signal transduction pathways and plant development. But it is not easy to isolate highly purified preparations of large numbers of GCPs from plants. In this research, our focus is on a method to isolate large numbers of guard cells from tomato leaves. The protocols described yield millions of highly purified, viable GCPs, which are also suitable for studies on guard cell physiology. RESULTS We developed an efficient method for isolating GCPs from epidermal fragments of tomato leaves. The protocol requires a two-step digestion to isolate high-quality tomato GCPs. In this procedure, cellulysin (in method L) was replaced by cellulose "Onozuka" RS (in method S) in the first digestion step, which indicated that cellulase RS was more effective than cellulysin. Method S dramatically shortened the time required for obtaining high yields and high-quality GCPs. Moreover, according to the GCP yields, hydroponic plants were more effective than substrate-cultured plants. CONCLUSIONS In this paper, protocols for large-scale preparation of GCPs and mesophyll cell protoplasts were described, followed by some success examples of their use in biochemical and molecular approaches such as reverse-transcription polymerase chain reaction, real-time polymerase chain reaction and sodium dodecyl sulfate-polyacrylamide gel electrophoresis. The method was proved to be a more efficient GCP-isolating method, capable of providing high yields with better quality in less time.
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Affiliation(s)
- Xuehui Yao
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206 People’s Republic of China
| | - Wenchao Zhao
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206 People’s Republic of China
| | - Rui Yang
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206 People’s Republic of China
| | - Jianli Wang
- Beijing Key Laboratory of New Technology in Agricultural Application, National Demonstration Center for Experimental Plant Production Education, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206 People’s Republic of China
| | - Fukuan Zhao
- Biological Science and Technology College, Beijing University of Agriculture, No. 7 BeiNong Road, Changping District, Beijing, 102206 People’s Republic of China
| | - Shaohui Wang
- College of Plant Science and Technology, Beijing University of Agriculture, No. 7 Beinong Road, Changping District, Beijing, 102206 People’s Republic of China
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Abstract
AIM Toxicity arising from hemolytic activity of peptides hinders its further progress as drug candidates. MATERIALS & METHODS This study describes a sequence-based predictor based on a random forest classifier using amino acid composition, dipeptide composition and physicochemical descriptors (named HemoPred). RESULTS This approach could outperform previously reported method and typical classification methods (e.g., support vector machine and decision tree) verified by fivefold cross-validation and external validation with accuracy and Matthews correlation coefficient in excess of 95% and 0.91, respectively. Results revealed the importance of hydrophobic and Cys residues on α-helix and β-sheet, respectively, on the hemolytic activity. CONCLUSION A sequence-based predictor which is publicly available as the web service of HemoPred, is proposed to predict and analyze the hemolytic activity of peptides.
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11
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Allen SE, Dokholyan NV, Bowers AA. Dynamic Docking of Conformationally Constrained Macrocycles: Methods and Applications. ACS Chem Biol 2016; 11:10-24. [PMID: 26575401 DOI: 10.1021/acschembio.5b00663] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Many natural products consist of large and flexible macrocycles that engage their targets via multiple contact points. This combination of contained flexibility and large contact area often allows natural products to bind at target surfaces rather than deep pockets, making them attractive scaffolds for inhibiting protein-protein interactions and other challenging therapeutic targets. The increasing ability to manipulate such compounds either biosynthetically or via semisynthetic modification means that these compounds can now be considered as starting points for medchem campaigns rather than solely as ends. Modern medchem benefits substantially from rational improvements made on the basis of molecular docking. As such, docking methods have been enhanced in recent years to deal with the complicated binding modalities and flexible scaffolds of macrocyclic natural products and natural product-like structures. Here, we comprehensively review methods for treating and docking these large macrocyclic scaffolds and discuss some of the resulting advances in medicinal chemistry.
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Affiliation(s)
- Scott E. Allen
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Nikolay V. Dokholyan
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Albert A. Bowers
- Division of Chemical Biology and Medicinal Chemistry, Eshelman School of Pharmacy, and ‡Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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12
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Di Luca M, Maccari G, Maisetta G, Batoni G. BaAMPs: the database of biofilm-active antimicrobial peptides. BIOFOULING 2015; 31:193-9. [PMID: 25760404 DOI: 10.1080/08927014.2015.1021340] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Antimicrobial peptides (AMPs) are increasingly being considered as novel agents against biofilms. The development of AMP-based anti-biofilm strategies strongly relies on the design of sequences optimized to target specific features of sessile bacterial/fungal communities. Although several AMP databases have been created and successfully exploited for AMP design, all of these use data collected on peptides tested against planktonic microorganisms. Here, an open-access, manually curated database of AMPs specifically assayed against microbial biofilms (BaAMPs) is presented for the first time. In collecting relevant data from the literature an effort was made to define a minimal standard set of essential information including, for each AMP, the microbial species and biofilm conditions against which it was tested, and the specific assay and peptide concentration used. The availability of these data in an organized framework will benefit anti-biofilm research and support the design of novel molecules active against biofilm. BaAMPs is accessible at http://www.baamps.it.
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Affiliation(s)
- Mariagrazia Di Luca
- a NEST, Istituto Nanoscienze-CNR and Scuola Normale Superiore , Pisa , Italy
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