In silico and in vitro evaluation of dermaseptin for antibacterial activity in resistant strains of S. aureus
The current crisis of antibiotic-resistant bacteria such as Methicillin-resistant Staphylococcus aureus (MRSA) causes the need for a faster and more efficient methodology for drug discovery. Deep learning approaches show promising results for Virtual Screening (VS). Herein we perform an in silico an...
- Autores:
-
Hernández Celis, Andrés Adolfo
- Tipo de recurso:
- Trabajo de grado de pregrado
- Fecha de publicación:
- 2022
- Institución:
- Universidad de los Andes
- Repositorio:
- Séneca: repositorio Uniandes
- Idioma:
- eng
- OAI Identifier:
- oai:repositorio.uniandes.edu.co:1992/58726
- Acceso en línea:
- http://hdl.handle.net/1992/58726
- Palabra clave:
- MRSA
Antimicrobial peptide
Dermaseptin
Antibacterial assay
Virtual screening
Drug discovery
Microbiología
- Rights
- openAccess
- License
- Attribution-NonCommercial-NoDerivatives 4.0 Internacional
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In silico and in vitro evaluation of dermaseptin for antibacterial activity in resistant strains of S. aureus |
| title |
In silico and in vitro evaluation of dermaseptin for antibacterial activity in resistant strains of S. aureus |
| spellingShingle |
In silico and in vitro evaluation of dermaseptin for antibacterial activity in resistant strains of S. aureus MRSA Antimicrobial peptide Dermaseptin Antibacterial assay Virtual screening Drug discovery Microbiología |
| title_short |
In silico and in vitro evaluation of dermaseptin for antibacterial activity in resistant strains of S. aureus |
| title_full |
In silico and in vitro evaluation of dermaseptin for antibacterial activity in resistant strains of S. aureus |
| title_fullStr |
In silico and in vitro evaluation of dermaseptin for antibacterial activity in resistant strains of S. aureus |
| title_full_unstemmed |
In silico and in vitro evaluation of dermaseptin for antibacterial activity in resistant strains of S. aureus |
| title_sort |
In silico and in vitro evaluation of dermaseptin for antibacterial activity in resistant strains of S. aureus |
| dc.creator.fl_str_mv |
Hernández Celis, Andrés Adolfo |
| dc.contributor.advisor.none.fl_str_mv |
Muñoz Camargo, Carolina Cruz Jiménez, Juan Carlos |
| dc.contributor.author.none.fl_str_mv |
Hernández Celis, Andrés Adolfo |
| dc.contributor.researchgroup.es_CO.fl_str_mv |
Grupo de Investigación en Nanomateriales, Ingeniería Celular y Bioimpresión Center for Research and Formation in Artificial Intelligence |
| dc.subject.keyword.none.fl_str_mv |
MRSA Antimicrobial peptide Dermaseptin Antibacterial assay Virtual screening Drug discovery |
| topic |
MRSA Antimicrobial peptide Dermaseptin Antibacterial assay Virtual screening Drug discovery Microbiología |
| dc.subject.themes.es_CO.fl_str_mv |
Microbiología |
| description |
The current crisis of antibiotic-resistant bacteria such as Methicillin-resistant Staphylococcus aureus (MRSA) causes the need for a faster and more efficient methodology for drug discovery. Deep learning approaches show promising results for Virtual Screening (VS). Herein we perform an in silico and in vitro evaluation of a new peptide from the dermaseptin family for anti-MRSA activity. We perform VS using two neural networks: AMP-Net, which predicts antimicrobial properties and PLA-Net, which predicts interactions with human cell receptors. Moreover, we perform an antibacterial microdilution assay with two multi-resistant and one reference strain. The in silico screening showed that the peptide has a strong antibacterial and anti-tumorigenic effect. Also, the antibacterial assay shows a minimum inhibitory concentration of > 12.5 uM in MRSA strains, which presents the same efficiency as cefalexin and a higher efficiency than common antibiotics such as ampicillin and vancomycin. We conclude that this research shows the potential of VS to speed up the drug discovery and repurposing process. Finally, we state that further research should aim to assess the multi-functionality of this peptide as a potential anti-carcinogenic agent. |
| publishDate |
2022 |
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2022-07-11T20:24:23Z |
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2022-07-11T20:24:23Z |
| dc.date.issued.none.fl_str_mv |
2022 |
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Trabajo de grado - Pregrado |
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info:eu-repo/semantics/bachelorThesis |
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info:eu-repo/semantics/acceptedVersion |
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http://purl.org/coar/resource_type/c_7a1f |
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http://purl.org/redcol/resource_type/TP |
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http://hdl.handle.net/1992/58726 |
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instname:Universidad de los Andes |
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eng |
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eng |
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Prakash SK. Nosocomial Infection: An Overview. Maulana Azad Medical College, New Delhi 2001;6:1-13. Eriksen H, Iversen BG, Aavitsland P. Prevalence of nosocomial infections in hospitals in Norway, 2002 and 2003. Journal of Hospital Infection 2005;60(1):40-45. Brusaferro S, Arnoldo L, Cattani G, Fabbro E, Cookson B, Gallagher R, et al. Harmonizing and supporting infection control training in Europe. Journal of Hospital Infection 2015;89(4):351-356. Obiero CW, Seale AC, Berkley JA. Empiric treatment of neonatal sepsis in developing countries. The Pediatric infectious disease journal 2015;34(6):659. Gatermann S, Funfstuck R, Handrick W, Leitritz L, Naber K, Podbielski A, et al. MIQ 02: Urinary Tract Infections: Quality standards for microbiological infections. Munchen: Urban & Fischer 2005;p. 8-21. Gastmeier P, Kampf G,Wischnewski Na, Hauer T, Schulgen G, SchumacherM, et al. Prevalence of nosocomial infections in representative German hospitals. Journal of Hospital infection 1998;38(1):37-49. Khan HA, Ahmad A, Mehboob R. Nosocomial infections and their control strategies. Asian pacific journal of tropical biomedicine 2015;5(7):509-514. Mahmoud AB, Zahran WA, Hindawi GR, Labib AZ, Galal R. Prevalence ofmultidrug-resistant Pseudomonas aeruginosa in patients with nosocomial infections at a university hospital in Egypt, with special reference to typingmethods. J Virol Microbiol 2013;13:165-59. Lu Q, Eggimann P, Luyt CE,WolffM, TammM, François B, et al. Pseudomonas aeruginosa serotypes in nosocomial pneumonia: prevalence and clinical outcomes. Critical care 2014;18(1):1-9. Mitov I, Strateva T,Markova B. Prevalence of virulence genes among bulgarian nosocomial and cystic fibrosis isolates of Pseudomonas aeruginosa. Brazilian Journal of Microbiology 2010;41(3):588-595. Tacconelli E, TumbarelloM, Bertagnolio S, Citton R, Spanu T, Fadda G, et al. Multidrug-resistant Pseudomonas aeruginosa bloodstream infections: analysis of trends in prevalence and epidemiology. Emerging infectious diseases 2002;8(2):220. Ullah F,Malik S, Ahmed J. Antibiotic susceptibility pattern and ESBL prevalence in nosocomial Escherichia coli fromurinary tract infections in Pakistan. African Journal of Biotechnology 2009;8(16). Lizioli A, Privitera G, Alliata E, Banfi EA, Boselli L, PanceriM, et al. Prevalence of nosocomial infections in Italy: result from the Lombardy survey in 2000. Journal of Hospital Infection 2003;54(2):141-148. MbimEN,MbotoCI,AgboBE. Areviewofnosocomial infections in Sub-Saharan Africa. British Microbiology Research Journal 2016;15(1):1-11. Urase T, OkazakiM, Tsutsui H. Prevalence of ESBL-producing Escherichia coli and carbapenem-resistant Enterobacteriaceae in treated wastewater: a comparison with nosocomial infection surveillance. Journal ofWater and Health 2020;18(6):899-910. Yazdansetad S, Alkhudhairy MK, Najafpour R, Farajtabrizi E, Al-Mosawi RM, Saki M, et al. Preliminary survey of extended-spectrum -lactamases (ESBLs) in nosocomial uropathogen Klebsiella pneumoniae in north-central Iran. Heliyon 2019;5(9):e02349 Alcántar-Curiel MD, Ledezma-Escalante CA, Jarillo-Quijada MD, Gayosso-Vázquez C,Morfín-Otero R, Rodríguez-Noriega E, et al. Association of antibiotic resistance, cell adherence, and biofilm production with the endemicity of nosocomial Klebsiella pneumoniae. BioMed research international 2018; 2018. Ghashghaee A, BehzadifarM, Azari S, Farhadi Z, Bragazzi NL, Behzadifar M, et al. Prevalence of nosocomial infections in Iran: A systematic review andmeta-analysis. Medical journal of the Islamic Republic of Iran 2018;32:48. Liu C, Du P, Xiao N, Ji F, Russo TA, Guo J. Hypervirulent Klebsiella pneumoniae is emerging as an increasingly prevalent K. pneumoniae pathotype responsible for nosocomial and healthcare-associated infections in Beijing, China. Virulence 2020;11(1):1215-1224. Hsueh PR, Teng LJ, Chen WH, Pan HJ, Chen ML, Chang SC, et al. Increasing prevalence of methicillin-resistant Staphylococcus aureus causing nosocomial infections at a university hospital in Taiwan from 1986 to 2001. Antimicrobial agents and chemotherapy 2004;48(4):1361-1364. Shrestha B, Singh W, Raj VS, Pokhrel BM, Mohapatra TM. High prevalence of Panton-Valentine leukocidin (PVL) genes in nosocomial-acquired Staphylococcus aureus isolated from tertiary care hospitals in Nepal. BioMed Research International 2014;2014. Espadinha D, Faria NA, MiragaiaM, Lito LM,Melo-Cristino J, de Lencastre H, et al. Extensive dissemination ofmethicillinresistant Staphylococcus aureus (MRSA) between the hospital and the community in a country with a high prevalence of nosocomial MRSA. PloS one 2013;8(4):e59960 Aires-de Sousa M, Conceicao Td, De Lencastre H. Unusually high prevalence of nosocomial Panton-Valentine leukocidinpositive Staphylococcus aureus isolates in Cape Verde Islands. Journal of Clinical Microbiology 2006;44(10):3790-3793. Shrestha B, Pokhrel BM, Mohapatra TM. Phenotypic characterization of nosocomial isolates of Staphylococcus aureus with reference to MRSA. The Journal of Infection in Developing Countries 2009;3(07):554-560 Vandenesch F, Lina G, Henry T. Staphylococcus aureus hemolysins, bi-component leukocidins, and cytolytic peptides: a redundant arsenal ofmembrane-damaging virulence factors Frontiers in cellular and infection microbiology 2012;2:12. Liu CM, Price LB, Hungate BA, Abraham AG, Larsen LA, Christensen K, et al. Staphylococcus aureus and the ecology of the nasal microbiome. Science advances 2015;1(5):e1400216. Nomura R, Nakaminami H, Takasao K,Muramatsu S, Kato Y, Wajima T, et al. A class A ¿-lactamase produced by borderline oxacillin-resistant Staphylococcus aureus hydrolyses oxacillin. Journal of Global Antimicrobial Resistance 2020;22:244-247. Kavanagh KT, Calderon LE, Saman DM. a response to Screening and isolation to controlmethicillin-resistant Staphylococcus aureus: sense, nonsense, and evidence. Antimicrobial Resistance and Infection Control 2015;4(1):1-5. DulonM, Haamann F, Peters C, Schablon A, Nienhaus A. MRSA prevalence in European healthcare settings: a review. BMC infectious diseases 2011;11(1):1¿13. Wu Q, Sabokroo N, Wang Y, Hashemian M, Karamollahi S, Kouhsari E. Systematic review and meta-analysis of the epidemiology of vancomycin-resistance Staphylococcus aureus isolates. Antimicrobial Resistance & Infection Control 2021;10(1):1-13. Mahmoud ERA, Ahmed HAH, Abo-senna ASM, Riad OKM, Abo MMAAR, et al. Isolation and characterization of six gammairradiated bacteriophages specific for MRSA and VRSA isolated fromskin infections. Journal of Radiation Research and Applied Sciences 2021;14(1):34-43. Rodriguez JM,Woodworth BA, Fackler J, Brownstein MJ, et al. Case Report: successful use of phage therapy in refractory MRSA chronic rhinosinusitis. International Journal of Infectious Diseases 2022;. Du H, Chi H, Yao H, Lu Z, Bie X, Zhang C, et al. The antibacterial activity of plantaricin GZ1¿27 against MRSA and its bio-preservative effect on chilled pork in combination with chitosan. International Journal of Food Microbiology 2022;365:109539. Garcia MA, Theodoro RS, Sardi JC, Santos MB, Ayusso GM, Pavan FR, et al. Design, synthesis and antibacterial activity of chalcones against MSSA and MRSA planktonic cells and biofilms. Bioorganic Chemistry 2021;116:105279. Chanawanno K, Thuptimdang P, Chantrapromma S, Fun HK. New Tunable Pyridinium Benzenesulfonate Amphiphiles as Anti-MRSA QuaternaryAmmonium Compounds (QACs). Journal ofMolecular Structure 2022;p. 132389. ZhuM,Wang ZJ,He YJ, Qin Y, Zhou Y, QiZH, et al. Bioguided isolation, identification and bioactivity evaluation of anti-MRSA constituents fromMorus alba Linn. Journal of Ethnopharmacology 2021;281:114542. Park CB, Kim MS, Kim SC. A novel antimicrobial peptide frombufo bufo gargarizans. Biochemical and biophysical research communications 1996;218(1):408-413. Wang B, Wei PW, Yao Y, Song CR, Wang X, Yang YX, et al. Functional and expression characteristics identification of Phormicins, novel AMPs from Musca domestica with anti-MRSA biofilm activity, in response to different stimuli. International Journal of BiologicalMacromolecules 2022;209:299-314. Yuan Y, Zai Y, Xi X, Ma C, Wang L, Zhou M, et al. A novel membrane-disruptive antimicrobial peptide from frog skin secretion against cystic fibrosis isolates and evaluation of anti- MRSAeffect using Galleriamellonellamodel. Biochimica et Biophysica Acta (BBA)-General Subjects 019;1863(5):849-856. Muñoz Camargo C, et al. Búsqueda de péptidos antimicrobianos nuevos en secreciones de piel de ranas. PhD thesis, Uniandes; 2017. García SRC. Actividad biológica de nuevos péptidos de piel de ranas con potencial antimicrobiano en macrófagos y microorganismos resistentes. PhD thesis, Uniandes; 2016. BahiM, BatoucheM. Deep learning for ligand-based virtual screening in drug discovery. In: 2018 3rd International Conference on Pattern Analysis and Intelligent Systems (PAIS) IEEE; 2018. p. 1-5. Puentes PR, Rueda-Gensini L, Valderrama N, Hernández I, González C,Daza L, et al.Modeling Protein-Ligand Interactions with Graph Convolutional Networks for Interpretable Pharmaceutical Discovery 2022;. Li G, Xiong C, Thabet A, Ghanem B. Deepergcn: All you need to train deeper gcns. arXiv preprint arXiv:200607739 2020. Mysinger MM, Carchia M, Irwin JJ, Shoichet BK. Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. Journal ofmedicinal chemistry 2012;55(14):6582-6594 Ruíz-Puentes P,Henao C, Cifuentes J,Muñoz-Camargo C, Cruz J, Arbelaez P. Rational discovery of antimicrobial peptides by means of artificial intelligence. unpublished 2022. Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, andmultithreading. Journal of computational chemistry 2010;31(2):455-461. Muñoz L, Jaramillo V, Gantiva-Diaz M, Cifuentes J, Muñoz- Camargo C, Cruz J, et al. Formulation of an Antibacterial Topical Treatment Based onMagnetite-Buforin-II Nanobioconjugates. unpublished 2022. Barrero-Guevara LA, Bolaños N, ParraM, González JM, Groot H, Muñoz-Camargo C. New peptides with immunomodulatory activity in macrophages and antibacterial activity against multiresistant Staphylococcus aureus. bioRxiv 2019; p. 838201. Navon-Venezia S, Feder R, Gaidukov L, Carmeli Y, Mor A. Antibacterial properties of dermaseptin S4 derivatives with in vivo activity. Antimicrobial agents and chemotherapy 2002;46(3):689-694. Gong Z, Pei X, Ren S, Chen X, Wang L, Ma C, et al. Identification and rational design of a novel antibacterial peptide dermaseptin-AC fromthe skin secretion of the red-eyed tree frog Agalychnis callidryas. Antibiotics 2020;9(5):243. Rotem S, Radzishevsky I,Mor A. Physicochemical properties that enhance discriminative antibacterial activity of short dermaseptin derivatives. Antimicrobial agents and chemotherapy 2006;50(8):2666-2672. Valderrama N, Ruíz P, Hernández A, Arbelaez P, Cruz J,Muñoz- Camargo C. Evaluation of Dermaseptin in two approaches: AIbased Virtual Screening and Antimicrobial assay in S. aureus Resistant Strains 2022. Dong F, GuoW, Zhang L,Wu S, Teraishi F, Davis JJ, et al. Downregulation of XIAP and induction of apoptosis by the synthetic cyclin-dependent kinase inhibitor GW8510 in non-small cell lung cancer cells. Cancer biology & therapy 2006;5(2):165-170. Bartels EJH, Dekker D, Amiche M. ermaseptins,multifunctional antimicrobial peptides: A review of their pharmacology, effectivity,mechanismof action, and possible future directions. Frontiers in pharmacology 2019;p. 1421. Nomura R, Nakaminami H, Takasao K,Muramatsu S, Kato Y, Wajima T, et al. A class A ¿-lactamase produced by borderline oxacillin-resistant Staphylococcus aureus hydrolyses oxacillin. Journal of Global Antimicrobial Resistance 2020;22:244-247. Zhang M, Zhang L, Hei R, Li X, Cai H, Wu X, et al. CDK inhibitors in cancer therapy, an overview of recent development. American journal of cancer research 2021;11(5):1913. Evans M, Sauer S, Nath S, Robinson T, Morse M, Devi G. Xlinked inhibitor of apoptosis proteinmediates tumor cell resistance to antibody-dependent cellular cytotoxicity. Cell death & disease 2016;7(1):e2073 e2073. |
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Attribution-NonCommercial-NoDerivatives 4.0 Internacionalhttp://creativecommons.org/licenses/by-nc-nd/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2Muñoz Camargo, Carolina071edf99-bd66-41dd-a318-d3bf41c08590600Cruz Jiménez, Juan Carlosccd9a6dc-893a-4968-b2e3-ba11de54ffeb600Hernández Celis, Andrés Adolfo2143d25b-174a-427b-a206-3fa7ee9ff026600Grupo de Investigación en Nanomateriales, Ingeniería Celular y BioimpresiónCenter for Research and Formation in Artificial Intelligence2022-07-11T20:24:23Z2022-07-11T20:24:23Z2022http://hdl.handle.net/1992/58726instname:Universidad de los Andesreponame:Repositorio Institucional Sénecarepourl:https://repositorio.uniandes.edu.co/The current crisis of antibiotic-resistant bacteria such as Methicillin-resistant Staphylococcus aureus (MRSA) causes the need for a faster and more efficient methodology for drug discovery. Deep learning approaches show promising results for Virtual Screening (VS). Herein we perform an in silico and in vitro evaluation of a new peptide from the dermaseptin family for anti-MRSA activity. We perform VS using two neural networks: AMP-Net, which predicts antimicrobial properties and PLA-Net, which predicts interactions with human cell receptors. Moreover, we perform an antibacterial microdilution assay with two multi-resistant and one reference strain. The in silico screening showed that the peptide has a strong antibacterial and anti-tumorigenic effect. Also, the antibacterial assay shows a minimum inhibitory concentration of > 12.5 uM in MRSA strains, which presents the same efficiency as cefalexin and a higher efficiency than common antibiotics such as ampicillin and vancomycin. We conclude that this research shows the potential of VS to speed up the drug discovery and repurposing process. Finally, we state that further research should aim to assess the multi-functionality of this peptide as a potential anti-carcinogenic agent.MicrobiólogoPregradoDrug discovery6 páginasapplication/pdfengUniversidad de los AndesMicrobiologíaFacultad de CienciasDepartamento de Ciencias BiológicasIn silico and in vitro evaluation of dermaseptin for antibacterial activity in resistant strains of S. aureusTrabajo de grado - Pregradoinfo:eu-repo/semantics/bachelorThesisinfo:eu-repo/semantics/acceptedVersionhttp://purl.org/coar/resource_type/c_7a1fTexthttp://purl.org/redcol/resource_type/TPMRSAAntimicrobial peptideDermaseptinAntibacterial assayVirtual screeningDrug discoveryMicrobiologíaPrakash SK. Nosocomial Infection: An Overview. Maulana Azad Medical College, New Delhi 2001;6:1-13.Eriksen H, Iversen BG, Aavitsland P. Prevalence of nosocomial infections in hospitals in Norway, 2002 and 2003. Journal of Hospital Infection 2005;60(1):40-45.Brusaferro S, Arnoldo L, Cattani G, Fabbro E, Cookson B, Gallagher R, et al. Harmonizing and supporting infection control training in Europe. Journal of Hospital Infection 2015;89(4):351-356.Obiero CW, Seale AC, Berkley JA. Empiric treatment of neonatal sepsis in developing countries. The Pediatric infectious disease journal 2015;34(6):659.Gatermann S, Funfstuck R, Handrick W, Leitritz L, Naber K, Podbielski A, et al. MIQ 02: Urinary Tract Infections: Quality standards for microbiological infections. Munchen: Urban & Fischer 2005;p. 8-21.Gastmeier P, Kampf G,Wischnewski Na, Hauer T, Schulgen G, SchumacherM, et al. Prevalence of nosocomial infections in representative German hospitals. Journal of Hospital infection 1998;38(1):37-49.Khan HA, Ahmad A, Mehboob R. Nosocomial infections and their control strategies. Asian pacific journal of tropical biomedicine 2015;5(7):509-514.Mahmoud AB, Zahran WA, Hindawi GR, Labib AZ, Galal R. Prevalence ofmultidrug-resistant Pseudomonas aeruginosa in patients with nosocomial infections at a university hospital in Egypt, with special reference to typingmethods. J Virol Microbiol 2013;13:165-59.Lu Q, Eggimann P, Luyt CE,WolffM, TammM, François B, et al. Pseudomonas aeruginosa serotypes in nosocomial pneumonia: prevalence and clinical outcomes. Critical care 2014;18(1):1-9.Mitov I, Strateva T,Markova B. Prevalence of virulence genes among bulgarian nosocomial and cystic fibrosis isolates of Pseudomonas aeruginosa. Brazilian Journal of Microbiology 2010;41(3):588-595.Tacconelli E, TumbarelloM, Bertagnolio S, Citton R, Spanu T, Fadda G, et al. Multidrug-resistant Pseudomonas aeruginosa bloodstream infections: analysis of trends in prevalence and epidemiology. Emerging infectious diseases 2002;8(2):220.Ullah F,Malik S, Ahmed J. Antibiotic susceptibility pattern and ESBL prevalence in nosocomial Escherichia coli fromurinary tract infections in Pakistan. African Journal of Biotechnology 2009;8(16).Lizioli A, Privitera G, Alliata E, Banfi EA, Boselli L, PanceriM, et al. Prevalence of nosocomial infections in Italy: result from the Lombardy survey in 2000. Journal of Hospital Infection 2003;54(2):141-148.MbimEN,MbotoCI,AgboBE. Areviewofnosocomial infections in Sub-Saharan Africa. British Microbiology Research Journal 2016;15(1):1-11.Urase T, OkazakiM, Tsutsui H. Prevalence of ESBL-producing Escherichia coli and carbapenem-resistant Enterobacteriaceae in treated wastewater: a comparison with nosocomial infection surveillance. Journal ofWater and Health 2020;18(6):899-910.Yazdansetad S, Alkhudhairy MK, Najafpour R, Farajtabrizi E, Al-Mosawi RM, Saki M, et al. Preliminary survey of extended-spectrum -lactamases (ESBLs) in nosocomial uropathogen Klebsiella pneumoniae in north-central Iran. Heliyon 2019;5(9):e02349Alcántar-Curiel MD, Ledezma-Escalante CA, Jarillo-Quijada MD, Gayosso-Vázquez C,Morfín-Otero R, Rodríguez-Noriega E, et al. Association of antibiotic resistance, cell adherence, and biofilm production with the endemicity of nosocomial Klebsiella pneumoniae. BioMed research international 2018; 2018.Ghashghaee A, BehzadifarM, Azari S, Farhadi Z, Bragazzi NL, Behzadifar M, et al. Prevalence of nosocomial infections in Iran: A systematic review andmeta-analysis. Medical journal of the Islamic Republic of Iran 2018;32:48.Liu C, Du P, Xiao N, Ji F, Russo TA, Guo J. Hypervirulent Klebsiella pneumoniae is emerging as an increasingly prevalent K. pneumoniae pathotype responsible for nosocomial and healthcare-associated infections in Beijing, China. Virulence 2020;11(1):1215-1224.Hsueh PR, Teng LJ, Chen WH, Pan HJ, Chen ML, Chang SC, et al. Increasing prevalence of methicillin-resistant Staphylococcus aureus causing nosocomial infections at a university hospital in Taiwan from 1986 to 2001. Antimicrobial agents and chemotherapy 2004;48(4):1361-1364.Shrestha B, Singh W, Raj VS, Pokhrel BM, Mohapatra TM. High prevalence of Panton-Valentine leukocidin (PVL) genes in nosocomial-acquired Staphylococcus aureus isolated from tertiary care hospitals in Nepal. BioMed Research International 2014;2014.Espadinha D, Faria NA, MiragaiaM, Lito LM,Melo-Cristino J, de Lencastre H, et al. Extensive dissemination ofmethicillinresistant Staphylococcus aureus (MRSA) between the hospital and the community in a country with a high prevalence of nosocomial MRSA. PloS one 2013;8(4):e59960Aires-de Sousa M, Conceicao Td, De Lencastre H. Unusually high prevalence of nosocomial Panton-Valentine leukocidinpositive Staphylococcus aureus isolates in Cape Verde Islands. Journal of Clinical Microbiology 2006;44(10):3790-3793.Shrestha B, Pokhrel BM, Mohapatra TM. Phenotypic characterization of nosocomial isolates of Staphylococcus aureus with reference to MRSA. The Journal of Infection in Developing Countries 2009;3(07):554-560Vandenesch F, Lina G, Henry T. Staphylococcus aureus hemolysins, bi-component leukocidins, and cytolytic peptides: a redundant arsenal ofmembrane-damaging virulence factors Frontiers in cellular and infection microbiology 2012;2:12.Liu CM, Price LB, Hungate BA, Abraham AG, Larsen LA, Christensen K, et al. Staphylococcus aureus and the ecology of the nasal microbiome. Science advances 2015;1(5):e1400216.Nomura R, Nakaminami H, Takasao K,Muramatsu S, Kato Y, Wajima T, et al. A class A ¿-lactamase produced by borderline oxacillin-resistant Staphylococcus aureus hydrolyses oxacillin. Journal of Global Antimicrobial Resistance 2020;22:244-247.Kavanagh KT, Calderon LE, Saman DM. a response to Screening and isolation to controlmethicillin-resistant Staphylococcus aureus: sense, nonsense, and evidence. Antimicrobial Resistance and Infection Control 2015;4(1):1-5.DulonM, Haamann F, Peters C, Schablon A, Nienhaus A. MRSA prevalence in European healthcare settings: a review. BMC infectious diseases 2011;11(1):1¿13.Wu Q, Sabokroo N, Wang Y, Hashemian M, Karamollahi S, Kouhsari E. Systematic review and meta-analysis of the epidemiology of vancomycin-resistance Staphylococcus aureus isolates. Antimicrobial Resistance & Infection Control 2021;10(1):1-13.Mahmoud ERA, Ahmed HAH, Abo-senna ASM, Riad OKM, Abo MMAAR, et al. Isolation and characterization of six gammairradiated bacteriophages specific for MRSA and VRSA isolated fromskin infections. Journal of Radiation Research and Applied Sciences 2021;14(1):34-43.Rodriguez JM,Woodworth BA, Fackler J, Brownstein MJ, et al. Case Report: successful use of phage therapy in refractory MRSA chronic rhinosinusitis. International Journal of Infectious Diseases 2022;.Du H, Chi H, Yao H, Lu Z, Bie X, Zhang C, et al. The antibacterial activity of plantaricin GZ1¿27 against MRSA and its bio-preservative effect on chilled pork in combination with chitosan. International Journal of Food Microbiology 2022;365:109539.Garcia MA, Theodoro RS, Sardi JC, Santos MB, Ayusso GM, Pavan FR, et al. Design, synthesis and antibacterial activity of chalcones against MSSA and MRSA planktonic cells and biofilms. Bioorganic Chemistry 2021;116:105279.Chanawanno K, Thuptimdang P, Chantrapromma S, Fun HK. New Tunable Pyridinium Benzenesulfonate Amphiphiles as Anti-MRSA QuaternaryAmmonium Compounds (QACs). Journal ofMolecular Structure 2022;p. 132389.ZhuM,Wang ZJ,He YJ, Qin Y, Zhou Y, QiZH, et al. Bioguided isolation, identification and bioactivity evaluation of anti-MRSA constituents fromMorus alba Linn. Journal of Ethnopharmacology 2021;281:114542.Park CB, Kim MS, Kim SC. A novel antimicrobial peptide frombufo bufo gargarizans. Biochemical and biophysical research communications 1996;218(1):408-413.Wang B, Wei PW, Yao Y, Song CR, Wang X, Yang YX, et al. Functional and expression characteristics identification of Phormicins, novel AMPs from Musca domestica with anti-MRSA biofilm activity, in response to different stimuli. International Journal of BiologicalMacromolecules 2022;209:299-314.Yuan Y, Zai Y, Xi X, Ma C, Wang L, Zhou M, et al. A novel membrane-disruptive antimicrobial peptide from frog skin secretion against cystic fibrosis isolates and evaluation of anti- MRSAeffect using Galleriamellonellamodel. Biochimica et Biophysica Acta (BBA)-General Subjects 019;1863(5):849-856.Muñoz Camargo C, et al. Búsqueda de péptidos antimicrobianos nuevos en secreciones de piel de ranas. PhD thesis, Uniandes; 2017.García SRC. Actividad biológica de nuevos péptidos de piel de ranas con potencial antimicrobiano en macrófagos y microorganismos resistentes. PhD thesis, Uniandes; 2016.BahiM, BatoucheM. Deep learning for ligand-based virtual screening in drug discovery. In: 2018 3rd International Conference on Pattern Analysis and Intelligent Systems (PAIS) IEEE; 2018. p. 1-5.Puentes PR, Rueda-Gensini L, Valderrama N, Hernández I, González C,Daza L, et al.Modeling Protein-Ligand Interactions with Graph Convolutional Networks for Interpretable Pharmaceutical Discovery 2022;.Li G, Xiong C, Thabet A, Ghanem B. Deepergcn: All you need to train deeper gcns. arXiv preprint arXiv:200607739 2020.Mysinger MM, Carchia M, Irwin JJ, Shoichet BK. Directory of useful decoys, enhanced (DUD-E): better ligands and decoys for better benchmarking. Journal ofmedicinal chemistry 2012;55(14):6582-6594Ruíz-Puentes P,Henao C, Cifuentes J,Muñoz-Camargo C, Cruz J, Arbelaez P. Rational discovery of antimicrobial peptides by means of artificial intelligence. unpublished 2022.Trott O, Olson AJ. AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization, andmultithreading. Journal of computational chemistry 2010;31(2):455-461.Muñoz L, Jaramillo V, Gantiva-Diaz M, Cifuentes J, Muñoz- Camargo C, Cruz J, et al. Formulation of an Antibacterial Topical Treatment Based onMagnetite-Buforin-II Nanobioconjugates. unpublished 2022.Barrero-Guevara LA, Bolaños N, ParraM, González JM, Groot H, Muñoz-Camargo C. New peptides with immunomodulatory activity in macrophages and antibacterial activity against multiresistant Staphylococcus aureus. bioRxiv 2019; p. 838201.Navon-Venezia S, Feder R, Gaidukov L, Carmeli Y, Mor A. Antibacterial properties of dermaseptin S4 derivatives with in vivo activity. Antimicrobial agents and chemotherapy 2002;46(3):689-694.Gong Z, Pei X, Ren S, Chen X, Wang L, Ma C, et al. Identification and rational design of a novel antibacterial peptide dermaseptin-AC fromthe skin secretion of the red-eyed tree frog Agalychnis callidryas. Antibiotics 2020;9(5):243.Rotem S, Radzishevsky I,Mor A. Physicochemical properties that enhance discriminative antibacterial activity of short dermaseptin derivatives. Antimicrobial agents and chemotherapy 2006;50(8):2666-2672.Valderrama N, Ruíz P, Hernández A, Arbelaez P, Cruz J,Muñoz- Camargo C. Evaluation of Dermaseptin in two approaches: AIbased Virtual Screening and Antimicrobial assay in S. aureus Resistant Strains 2022.Dong F, GuoW, Zhang L,Wu S, Teraishi F, Davis JJ, et al. Downregulation of XIAP and induction of apoptosis by the synthetic cyclin-dependent kinase inhibitor GW8510 in non-small cell lung cancer cells. Cancer biology & therapy 2006;5(2):165-170.Bartels EJH, Dekker D, Amiche M. ermaseptins,multifunctional antimicrobial peptides: A review of their pharmacology, effectivity,mechanismof action, and possible future directions. Frontiers in pharmacology 2019;p. 1421.Nomura R, Nakaminami H, Takasao K,Muramatsu S, Kato Y, Wajima T, et al. A class A ¿-lactamase produced by borderline oxacillin-resistant Staphylococcus aureus hydrolyses oxacillin. Journal of Global Antimicrobial Resistance 2020;22:244-247.Zhang M, Zhang L, Hei R, Li X, Cai H, Wu X, et al. CDK inhibitors in cancer therapy, an overview of recent development. American journal of cancer research 2021;11(5):1913.Evans M, Sauer S, Nath S, Robinson T, Morse M, Devi G. Xlinked inhibitor of apoptosis proteinmediates tumor cell resistance to antibody-dependent cellular cytotoxicity. 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