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For: Porto WF, Irazazabal L, Alves ESF, Ribeiro SM, Matos CO, Pires ÁS, Fensterseifer ICM, Miranda VJ, Haney EF, Humblot V, Torres MDT, Hancock REW, Liao LM, Ladram A, Lu TK, de la Fuente-Nunez C, Franco OL. In silico optimization of a guava antimicrobial peptide enables combinatorial exploration for peptide design. Nat Commun 2018;9:1490. [PMID: 29662055 DOI: 10.1038/s41467-018-03746-3] [Citation(s) in RCA: 196] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Accepted: 03/02/2018] [Indexed: 12/29/2022]  Open
Number Cited by Other Article(s)
1
Zhang Q, Wang B, Jessica, Ghalandari B, Chen Y, Xu Z, Zhou Q, Ding X. PISAD: De novo peptide design for target protein with iterative stochastic searching algorithm and docking assessment. Biosens Bioelectron 2025;278:117338. [PMID: 40054153 DOI: 10.1016/j.bios.2025.117338] [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: 11/10/2024] [Revised: 02/15/2025] [Accepted: 03/03/2025] [Indexed: 03/30/2025]
2
Shang Y, Huang Y, Meng Q, Yu Z, Wen Z, Yu F. Fingolimod as a potent anti-Staphylococcus aureus: pH-dependent cell envelope damage and eradication of biofilms/persisters. BMC Microbiol 2025;25:299. [PMID: 40380090 PMCID: PMC12083125 DOI: 10.1186/s12866-025-03973-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2024] [Accepted: 04/16/2025] [Indexed: 05/19/2025]  Open
3
Wan F, Torres MDT, Guan C, de la Fuente-Nunez C. Tutorial: guidelines for the use of machine learning methods to mine genomes and proteomes for antibiotic discovery. Nat Protoc 2025:10.1038/s41596-025-01144-w. [PMID: 40369233 DOI: 10.1038/s41596-025-01144-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 01/08/2025] [Indexed: 05/16/2025]
4
Bermúdez-Puga S, Mendes B, Ramos-Galarza JP, Oliveira de Souza de Azevedo P, Converti A, Molinari F, Moore SJ, Almeida JR, Pinheiro de Souza Oliveira R. Revolutionizing agroindustry: Towards the industrial application of antimicrobial peptides against pathogens and pests. Biotechnol Adv 2025;82:108605. [PMID: 40368115 DOI: 10.1016/j.biotechadv.2025.108605] [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: 12/14/2024] [Revised: 04/09/2025] [Accepted: 05/10/2025] [Indexed: 05/16/2025]
5
Hu M, Li Y, Cha S, Zhao L, Liu C, Sui M, Xue C, Dong N. Development of targeted antimicrobial peptides for Escherichia coli: Combining phage display and rational design for food safety application. Food Chem 2025;470:142685. [PMID: 39756081 DOI: 10.1016/j.foodchem.2024.142685] [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: 09/20/2024] [Revised: 12/18/2024] [Accepted: 12/25/2024] [Indexed: 01/07/2025]
6
Ageitos L, Boaro A, Cesaro A, Torres MDT, Broset E, de la Fuente-Nunez C. Frog-derived synthetic peptides display anti-infective activity against Gram-negative pathogens. Trends Biotechnol 2025:S0167-7799(25)00044-7. [PMID: 40140310 DOI: 10.1016/j.tibtech.2025.02.007] [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: 04/29/2024] [Revised: 02/03/2025] [Accepted: 02/05/2025] [Indexed: 03/28/2025]
7
Chen X, Song M, Tian L, Shan X, Mao C, Chen M, Zhao J, Sami A, Yin H, Ali U, Shi J, Li H, Zhang Y, Zhang J, Wang S, Shi CL, Chen Y, Du XD, Zhu K, Wu L. A plant peptide with dual activity against multidrug-resistant bacterial and fungal pathogens. SCIENCE ADVANCES 2025;11:eadt8239. [PMID: 40106560 PMCID: PMC11922054 DOI: 10.1126/sciadv.adt8239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2024] [Accepted: 02/11/2025] [Indexed: 03/22/2025]
8
Chen R, You Y, Liu Y, Sun X, Ma T, Lao X, Zheng H. Deep-Learning-Based Approaches for Rational Design of Stapled Peptides With High Antimicrobial Activity and Stability. Microb Biotechnol 2025;18:e70121. [PMID: 40042163 PMCID: PMC11881016 DOI: 10.1111/1751-7915.70121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2024] [Revised: 02/09/2025] [Accepted: 02/15/2025] [Indexed: 05/12/2025]  Open
9
Osiro KO, Gil-Ley A, Fernandes FC, de Oliveira KBS, de la Fuente-Nunez C, Franco OL. Paving the way for new antimicrobial peptides through molecular de-extinction. MICROBIAL CELL (GRAZ, AUSTRIA) 2025;12:1-8. [PMID: 40012704 PMCID: PMC11853161 DOI: 10.15698/mic2025.02.841] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2024] [Revised: 01/02/2025] [Accepted: 01/07/2025] [Indexed: 02/28/2025]
10
Kumar G. Natural peptides and their synthetic congeners acting against Acinetobacter baumannii through the membrane and cell wall: latest progress. RSC Med Chem 2025;16:561-604. [PMID: 39664362 PMCID: PMC11629675 DOI: 10.1039/d4md00745j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Accepted: 11/18/2024] [Indexed: 12/13/2024]  Open
11
Cândido ES, Gasparetto LS, Luchi LV, Pimentel JP, Cardoso MH, Macedo ML, de la Fuente-Nunez C, Franco OL. Small and Versatile Cyclotides as Anti-infective Agents. ACS Infect Dis 2025;11:386-397. [PMID: 39842000 PMCID: PMC11833872 DOI: 10.1021/acsinfecdis.4c00957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2024] [Revised: 12/31/2024] [Accepted: 01/08/2025] [Indexed: 01/24/2025]
12
Zhang H, Wang Y, Zhu Y, Huang P, Gao Q, Li X, Chen Z, Liu Y, Jiang J, Gao Y, Huang J, Qin Z. Machine learning and genetic algorithm-guided directed evolution for the development of antimicrobial peptides. J Adv Res 2025;68:415-428. [PMID: 38431124 PMCID: PMC11785909 DOI: 10.1016/j.jare.2024.02.016] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/05/2024]  Open
13
Bilal H, Khan MN, Khan S, Shafiq M, Fang W, Khan RU, Rahman MU, Li X, Lv QL, Xu B. The role of artificial intelligence and machine learning in predicting and combating antimicrobial resistance. Comput Struct Biotechnol J 2025;27:423-439. [PMID: 39906157 PMCID: PMC11791014 DOI: 10.1016/j.csbj.2025.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2024] [Revised: 01/06/2025] [Accepted: 01/13/2025] [Indexed: 02/06/2025]  Open
14
Guan C, Fernandes FC, Franco OL, de la Fuente-Nunez C. Leveraging large language models for peptide antibiotic design. CELL REPORTS. PHYSICAL SCIENCE 2025;6:102359. [PMID: 39949833 PMCID: PMC11823563 DOI: 10.1016/j.xcrp.2024.102359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/16/2025]
15
Cesaro A, Hoffman SC, Das P, de la Fuente-Nunez C. Challenges and applications of artificial intelligence in infectious diseases and antimicrobial resistance. NPJ ANTIMICROBIALS AND RESISTANCE 2025;3:2. [PMID: 39843587 PMCID: PMC11721440 DOI: 10.1038/s44259-024-00068-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 11/26/2024] [Indexed: 01/24/2025]
16
Hasan Pour B. Superficial Fungal Infections and Artificial Intelligence: A Review on Current Advances and Opportunities: REVISION. Mycoses 2025;68:e70007. [PMID: 39775855 DOI: 10.1111/myc.70007] [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: 08/18/2024] [Revised: 10/27/2024] [Accepted: 11/03/2024] [Indexed: 01/11/2025]
17
Brizuela CA, Liu G, Stokes JM, de la Fuente‐Nunez C. AI Methods for Antimicrobial Peptides: Progress and Challenges. Microb Biotechnol 2025;18:e70072. [PMID: 39754551 PMCID: PMC11702388 DOI: 10.1111/1751-7915.70072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Revised: 11/18/2024] [Accepted: 12/16/2024] [Indexed: 01/06/2025]  Open
18
Torres MDT, Cesaro A, de la Fuente-Nunez C. Peptides from non-immune proteins target infections through antimicrobial and immunomodulatory properties. Trends Biotechnol 2025;43:184-205. [PMID: 39472252 DOI: 10.1016/j.tibtech.2024.09.008] [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: 05/21/2024] [Revised: 09/02/2024] [Accepted: 09/09/2024] [Indexed: 11/06/2024]
19
Ho CS, Wong CTH, Aung TT, Lakshminarayanan R, Mehta JS, Rauz S, McNally A, Kintses B, Peacock SJ, de la Fuente-Nunez C, Hancock REW, Ting DSJ. Antimicrobial resistance: a concise update. THE LANCET. MICROBE 2025;6:100947. [PMID: 39305919 DOI: 10.1016/j.lanmic.2024.07.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 07/07/2024] [Accepted: 07/08/2024] [Indexed: 01/04/2025]
20
Guan C, Torres MDT, Li S, de la Fuente-Nunez C. Venomics AI: a computational exploration of global venoms for antibiotic discovery. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.12.17.628923. [PMID: 39764027 PMCID: PMC11702808 DOI: 10.1101/2024.12.17.628923] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/19/2025]
21
Rios TB, Rezende SB, Maximiano MR, Cardoso MH, Malmsten M, de la Fuente-Nunez C, Franco OL. Computational Approaches for Antimicrobial Peptide Delivery. Bioconjug Chem 2024;35:1873-1882. [PMID: 39541149 DOI: 10.1021/acs.bioconjchem.4c00406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2024]
22
Liu X, Luo J, Wang X, Zhang Y, Chen J. Directed evolution of antimicrobial peptides using multi-objective zeroth-order optimization. Brief Bioinform 2024;26:bbae715. [PMID: 39800873 PMCID: PMC11725395 DOI: 10.1093/bib/bbae715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2024] [Revised: 12/08/2024] [Accepted: 12/27/2024] [Indexed: 01/16/2025]  Open
23
Oh JW, Shin MK, Park HR, Kim S, Lee B, Yoo JS, Chi WJ, Sung JS. PA-Win2: In Silico-Based Discovery of a Novel Peptide with Dual Antibacterial and Anti-Biofilm Activity. Antibiotics (Basel) 2024;13:1113. [PMID: 39766503 PMCID: PMC11672609 DOI: 10.3390/antibiotics13121113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2024] [Revised: 11/15/2024] [Accepted: 11/20/2024] [Indexed: 01/11/2025]  Open
24
Li Y, Cui X, Yang X, Liu G, Zhang J. Artificial intelligence in predicting pathogenic microorganisms' antimicrobial resistance: challenges, progress, and prospects. Front Cell Infect Microbiol 2024;14:1482186. [PMID: 39554812 PMCID: PMC11564165 DOI: 10.3389/fcimb.2024.1482186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2024] [Accepted: 10/07/2024] [Indexed: 11/19/2024]  Open
25
Singh A, Tanwar M, Singh TP, Sharma S, Sharma P. An escape from ESKAPE pathogens: A comprehensive review on current and emerging therapeutics against antibiotic resistance. Int J Biol Macromol 2024;279:135253. [PMID: 39244118 DOI: 10.1016/j.ijbiomac.2024.135253] [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: 05/22/2024] [Revised: 08/29/2024] [Accepted: 08/30/2024] [Indexed: 09/09/2024]
26
Prusty JS, Kumar A, Kumar A. Anti-fungal peptides: an emerging category with enthralling therapeutic prospects in the treatment of candidiasis. Crit Rev Microbiol 2024:1-37. [PMID: 39440616 DOI: 10.1080/1040841x.2024.2418125] [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: 02/04/2024] [Revised: 10/10/2024] [Accepted: 10/13/2024] [Indexed: 10/25/2024]
27
Mantena S, Pillai PP, Petros BA, Welch NL, Myhrvold C, Sabeti PC, Metsky HC. Model-directed generation of artificial CRISPR-Cas13a guide RNA sequences improves nucleic acid detection. Nat Biotechnol 2024:10.1038/s41587-024-02422-w. [PMID: 39394482 DOI: 10.1038/s41587-024-02422-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 09/04/2024] [Indexed: 10/13/2024]
28
Gagat P, Ostrówka M, Duda-Madej A, Mackiewicz P. Enhancing Antimicrobial Peptide Activity through Modifications of Charge, Hydrophobicity, and Structure. Int J Mol Sci 2024;25:10821. [PMID: 39409150 PMCID: PMC11476776 DOI: 10.3390/ijms251910821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Revised: 10/04/2024] [Accepted: 10/07/2024] [Indexed: 10/20/2024]  Open
29
Bhaumik KN, Spohn R, Dunai A, Daruka L, Olajos G, Zákány F, Hetényi A, Pál C, Martinek TA. Chemically diverse antimicrobial peptides induce hyperpolarization of the E. coli membrane. Commun Biol 2024;7:1264. [PMID: 39367191 PMCID: PMC11452689 DOI: 10.1038/s42003-024-06946-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 09/24/2024] [Indexed: 10/06/2024]  Open
30
Wang Y, Luo L, Zhang T, Hu JR, Wang H, Bao F, Li C, Sun Y, Li J. Strategically Engineered Ru(II) Complexes with Enhanced ROS Activity Enabling Potent Sonodynamic Effect against Multidrug-Resistant Biofilms. ACS APPLIED MATERIALS & INTERFACES 2024;16:52068-52079. [PMID: 39297327 DOI: 10.1021/acsami.4c11650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2024]
31
Li S, Liu J, Zhang T, Lu J, Li M, Zhang M, Chen H. Chemical modification, structure elucidation and antifungal mechanism studies of a peptide extracted from garlic (Allium sativum L.). JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024;104:8037-8049. [PMID: 38855916 DOI: 10.1002/jsfa.13633] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 04/02/2024] [Accepted: 05/12/2024] [Indexed: 06/11/2024]
32
Torres MDT, Brooks EF, Cesaro A, Sberro H, Gill MO, Nicolaou C, Bhatt AS, de la Fuente-Nunez C. Mining human microbiomes reveals an untapped source of peptide antibiotics. Cell 2024;187:5453-5467.e15. [PMID: 39163860 DOI: 10.1016/j.cell.2024.07.027] [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: 08/08/2023] [Revised: 05/09/2024] [Accepted: 07/17/2024] [Indexed: 08/22/2024]
33
Panjla A, Joshi S, Singh G, Bamford SE, Mechler A, Verma S. Applying Machine Learning for Antibiotic Development and Prediction of Microbial Resistance. Chem Asian J 2024;19:e202400102. [PMID: 38948939 DOI: 10.1002/asia.202400102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 06/30/2024] [Accepted: 07/01/2024] [Indexed: 07/02/2024]
34
Li T, Ren X, Luo X, Wang Z, Li Z, Luo X, Shen J, Li Y, Yuan D, Nussinov R, Zeng X, Shi J, Cheng F. A Foundation Model Identifies Broad-Spectrum Antimicrobial Peptides against Drug-Resistant Bacterial Infection. Nat Commun 2024;15:7538. [PMID: 39214978 PMCID: PMC11364768 DOI: 10.1038/s41467-024-51933-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Accepted: 08/20/2024] [Indexed: 09/04/2024]  Open
35
Deb R, Torres MDT, Boudný M, Koběrská M, Cappiello F, Popper M, Dvořáková Bendová K, Drabinová M, Hanáčková A, Jeannot K, Petřík M, Mangoni ML, Balíková Novotná G, Mráz M, de la Fuente-Nunez C, Vácha R. Computational Design of Pore-Forming Peptides with Potent Antimicrobial and Anticancer Activities. J Med Chem 2024;67:14040-14061. [PMID: 39116273 PMCID: PMC11345766 DOI: 10.1021/acs.jmedchem.4c00912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 07/05/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024]
36
Hong S, Gao H, Chen H, Wang C. Engineered fungus containing a caterpillar gene kills insects rapidly by disrupting their ecto- and endo-microbiomes. Commun Biol 2024;7:955. [PMID: 39112633 PMCID: PMC11306560 DOI: 10.1038/s42003-024-06670-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2024] [Accepted: 08/01/2024] [Indexed: 08/10/2024]  Open
37
de la Lastra JMP, Wardell SJT, Pal T, de la Fuente-Nunez C, Pletzer D. From Data to Decisions: Leveraging Artificial Intelligence and Machine Learning in Combating Antimicrobial Resistance - a Comprehensive Review. J Med Syst 2024;48:71. [PMID: 39088151 PMCID: PMC11294375 DOI: 10.1007/s10916-024-02089-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 07/12/2024] [Indexed: 08/02/2024]
38
Gupta YD, Bhandary S. Artificial Intelligence for Understanding Mechanisms of Antimicrobial Resistance and Antimicrobial Discovery. ARTIFICIAL INTELLIGENCE AND MACHINE LEARNING IN DRUG DESIGN AND DEVELOPMENT 2024:117-156. [DOI: 10.1002/9781394234196.ch5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2025]
39
Santos-Júnior CD, Torres MDT, Duan Y, Rodríguez Del Río Á, Schmidt TSB, Chong H, Fullam A, Kuhn M, Zhu C, Houseman A, Somborski J, Vines A, Zhao XM, Bork P, Huerta-Cepas J, de la Fuente-Nunez C, Coelho LP. Discovery of antimicrobial peptides in the global microbiome with machine learning. Cell 2024;187:3761-3778.e16. [PMID: 38843834 PMCID: PMC11666328 DOI: 10.1016/j.cell.2024.05.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 04/11/2024] [Accepted: 05/06/2024] [Indexed: 06/25/2024]
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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;8:854-871. [PMID: 38862735 PMCID: PMC11310081 DOI: 10.1038/s41551-024-01201-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 03/25/2024] [Indexed: 06/13/2024]
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Bashi M, Madanchi H, Yousefi B. Investigation of cytotoxic effect and action mechanism of a synthetic peptide derivative of rabbit cathelicidin against MDA-MB-231 breast cancer cell line. Sci Rep 2024;14:13497. [PMID: 38866982 PMCID: PMC11169400 DOI: 10.1038/s41598-024-64400-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2024] [Accepted: 06/07/2024] [Indexed: 06/14/2024]  Open
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Yin K, Xu W, Ren S, Xu Q, Zhang S, Zhang R, Jiang M, Zhang Y, Xu D, Li R. Machine Learning Accelerates De Novo Design of Antimicrobial Peptides. Interdiscip Sci 2024;16:392-403. [PMID: 38416364 DOI: 10.1007/s12539-024-00612-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/17/2024] [Accepted: 01/23/2024] [Indexed: 02/29/2024]
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Coelho LP, Santos-Júnior CD, de la Fuente-Nunez C. Challenges in computational discovery of bioactive peptides in 'omics data. Proteomics 2024;24:e2300105. [PMID: 38458994 PMCID: PMC11537280 DOI: 10.1002/pmic.202300105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 02/06/2024] [Accepted: 02/06/2024] [Indexed: 03/10/2024]
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Darwish RM, Salama AH. Developing antibacterial peptides as a promising therapy for combating antibiotic-resistant Pseudomonas aeruginosa infections. Vet World 2024;17:1259-1264. [PMID: 39077460 PMCID: PMC11283607 DOI: 10.14202/vetworld.2024.1259-1264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Accepted: 05/17/2024] [Indexed: 07/31/2024]  Open
45
Wan F, Wong F, Collins JJ, de la Fuente-Nunez C. Machine learning for antimicrobial peptide identification and design. NATURE REVIEWS BIOENGINEERING 2024;2:392-407. [PMID: 39850516 PMCID: PMC11756916 DOI: 10.1038/s44222-024-00152-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2025]
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Lin L, Li C, Zhang T, Xia C, Bai Q, Jin L, Shen Y. An in silico scheme for optimizing the enzymatic acquisition of natural biologically active peptides based on machine learning and virtual digestion. Anal Chim Acta 2024;1298:342419. [PMID: 38462343 DOI: 10.1016/j.aca.2024.342419] [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: 08/20/2023] [Revised: 12/23/2023] [Accepted: 02/26/2024] [Indexed: 03/12/2024]
47
Scalzitti N, Miralavy I, Korenchan DE, Farrar CT, Gilad AA, Banzhaf W. Computational peptide discovery with a genetic programming approach. J Comput Aided Mol Des 2024;38:17. [PMID: 38570405 PMCID: PMC11416381 DOI: 10.1007/s10822-024-00558-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
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Methorst J, van Hilten N, Hoti A, Stroh KS, Risselada HJ. When Data Are Lacking: Physics-Based Inverse Design of Biopolymers Interacting with Complex, Fluid Phases. J Chem Theory Comput 2024;20:1763-1776. [PMID: 38413010 PMCID: PMC10938504 DOI: 10.1021/acs.jctc.3c00874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/29/2024]
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Nazarian-Firouzabadi F, Torres MDT, de la Fuente-Nunez C. Recombinant production of antimicrobial peptides in plants. Biotechnol Adv 2024;71:108296. [PMID: 38042311 PMCID: PMC11537283 DOI: 10.1016/j.biotechadv.2023.108296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 11/10/2023] [Accepted: 11/26/2023] [Indexed: 12/04/2023]
50
de la Fuente-Nunez C. AI in infectious diseases: The role of datasets. Drug Resist Updat 2024;73:101067. [PMID: 38387282 PMCID: PMC11537278 DOI: 10.1016/j.drup.2024.101067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/24/2024]
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