Targeting bacterial growth in biofilm conditions: rational design of novel inhibitors to mitigate clinical and food contamination using QSAR

References

• Mah TF, O’Toole GA. Mechanisms of biofilm resistance to antimicrobial agents. Trends Microbiol. 2001;9(1):1–19.
   Web of Science ®Google Scholar
• Ferri M, Ranucci E, Romagnoli P, Giaccone V. Antimicrobial resistance: a global emerging threat to public health systems. Crit Rev Food Sci Nutr. 2017;57(13):2857–2876.
   PubMed Web of Science ®Google Scholar
• Podschun R, Ullmann U. Klebsiella spp. as nosocomial pathogens: epidemiology, taxonomy, typing methods, and pathogenicity factors. Clin Microbiol Rev. 1998;11(4):589–603.
   PubMed Web of Science ®Google Scholar
• Diekema DJ, Hsueh PR, Mendes RE, Pfaller MA, RolstonKV, Sader HS, Jones RN. The microbiology of bloodstream infection: 20-year trends from the SENTRY antimicrobial surveillance pro. Antimicrob Agents Chemother. 2019;63(7):e00355-19.
   PubMed Web of Science ®Google Scholar
• Wyres KL, Hold KG. Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. Curr Opin Microbiol. 2018;45:131–139.
   PubMed Web of Science ®Google Scholar
• Souza-Guerra ME, Destro G, Vieira B, Lima AS, Caldas-Ferraz LF, Hakansson AP, Darrieux M, Rojas-Converso T. Klebsiella pneumoniae biofilms and their role in disease pathogenesis. Front Cell Infect Microbiol. 2022;12:877995.
   PubMedGoogle Scholar
• Otto M. Staphylococcal biofilms. Curr Top Microbiol Immunol. 2016;322:207–228.
   Google Scholar
• Chipolombwe J, Török ME, Mbelle N, Nyasulu P. Methicillin-resistant Staphylococcus aureus multiple sites surveillance: a systemic review of the literature. Infect Drug Resist. 2016;9:35–42.
   PubMed Web of Science ®Google Scholar
• Vadyvaloo V, Otto M. Molecular genetics of Staphylococcus epidermidis biofilms on indwelling medical devices. Int J Artif Organs. 2005;28(11):1069–1078.
   PubMed Web of Science ®Google Scholar
• Bottone EJ. Bacillus cereus, a volatile human pathogen. Clin Microbiol Rev. 2010;23(2):382–398.
   PubMed Web of Science ®Google Scholar
• Antequera-Gómez ML, Díaz-Martínez L, Guadix JA, Sánchez-Tévar AM, Sopeña-Torres S, Hierrezuelo J, Doan HK, Leveau JHJ, De Vicente A, Romero D. Sporulation is dispensable for the vegetable-associated life cycle of the human pathogen Bacillus cereus. Microb Biotechnol. 2021;14(4):1550–1565.
   PubMed Web of Science ®Google Scholar
• Mirzaei R, Mohammadzadeh R, Alikhani MY, Moghadam MS, Karampoor S, Kazemi S, Barfipoursalar A, Yousefimashouf R. The Biofilm-associated bacterial infections unrelated to indwelling devices. Iubmb Life . 2020;72(7):1271–1285.
   PubMed Web of Science ®Google Scholar
• Romero D, Aguilar C, Losick R, Kolter R. Amyloid fibers provide structural integrity to Bacillus subtilis biofilms. Proc Natl Acad Sci USA. 2010;107(5):2230–2234.
   PubMed Web of Science ®Google Scholar
• Romero D, Vlamakis H, Losick R, Kolter R. Funtional analysis of the accesory protein TapA in Bacillus subtilis amyloid fiber assembly. J Bacteriol. 2014;196(8):1505–1513.
   PubMedGoogle Scholar
• Romero D, Kolter R. Functional amyloids in bacteria. Res Rev. 2014;17:65–73.
   Google Scholar
• Gram L, Ravn L, Rasch M, Bruhn JB, Christensen AB, Givskov M. Food spoilage-interactions between food spoilage bacteria. Int J Food Microbiol. 2002;78(1–2):79–97.
   PubMed Web of Science ®Google Scholar
• Vamathevan J, Clark D, Czodrowski P, Dunham I, Ferran E, Lee G, Li B, Madabhushi A, Shah P, Spitzer M, et al. Applications of machine learning in drug discovery and development. Nat Rev Drug Discov. 2019;18(6):463–477.
   PubMed Web of Science ®Google Scholar
• Macalino SJ, Gosu V, Hong S, Choi S. Role of computer-aided drug design in modern drug discovery. Arch Pharm Res. 2015;38(9):1686–1701.
   PubMed Web of Science ®Google Scholar
• Lin X, Li X, Lin X. A review on applications of computational methods in drug screening and design. Molecules. 2020;25(6):1375.
   PubMed Web of Science ®Google Scholar
• Shaker B, Ahmad S, Lee J, Jung C, Na D. In silico methods and tools for drug discovery. Comput Biol Med. 2021;137:104851.
   PubMed Web of Science ®Google Scholar
• Bruno A, Costantino G, Sartori L, Radi M. The in silico drug discovery toolbox: applications in lead discovery and optimization. Curr Med Chem. 2019;26(21):3838–3873.
   PubMed Web of Science ®Google Scholar
• Zagotto G, Bortoli M. Drug design: where we are and future prospects. Molecules. 2021;26(22):7061.
   PubMed Web of Science ®Google Scholar
• Dean PM, Lloyd DG, Todorov NP. De novo drug design: integration of structure-based and ligand-based methods. Curr Opin Drug Discov Devel. 2004;7(3):347–353.
   PubMed Web of Science ®Google Scholar
• Bueso-Bordils JI, Alemán-López PA, Suay-García B, Martín-Algarra R, Duart MJ, Falcó A, Antón-Fos GM. Molecular topology for the discovery of new broad-spectrum antibacterial drugs. Biomolecules. 2020;10(9):1343.
   PubMed Web of Science ®Google Scholar
• Bueso-Bordils JI, Alemán-López PA, Martín-Algarra R, Duart MJ, Falcó A, Antón-Fos GM. Molecular topology for the search of new anti-MRSA compounds. Int J Mol Sci. 2021;22(11):5823.
   PubMed Web of Science ®Google Scholar
• Zanni R, Galvez-Llompart M, Machuca J, Garcia-Domenech R, Recacha E, Pascual A, Rodriguez-Martinez JM, Galvez J. Molecular topology: a new strategy for antimicrobial resistance control. Eur J Med Chem. 2017;137:233–246.
   PubMed Web of Science ®Google Scholar
• Zanni R, Martínez-Cruz J, Gálvez-Llompart M, Fernández-Ortuño D, Romero D, García-Domènech R, Pérez-García A, Gálvez J. Rational design of chitin deacetylase inhibitors for sustainable agricultural use based on molecular topology. J Agric Food Chem. 2022;70(41):13118–13131.
   PubMedGoogle Scholar
• Zanni R, Galvez-Llompart M, Garcia-Domenech R, Galvez J. What place does molecular topology have in today’s drug discovery? Expert Opin Drug Discov. 2020;15(10):1133–1144.
   PubMed Web of Science ®Google Scholar
• Blay V, García-Domenech R, Gálvez J. Problem solving with Molecular Topology: a walkthrough. ChemTexts. 2017;3(2):1–5.
   PubMedGoogle Scholar
• Kim S, Chen J, Cheng T, Gindulyte A, He J, He S, Li Q, Shoemaker BA, Thiessen PA, Yu B, et al. PubChem in 2021: new data content and improved web interfaces. Nucleic Acids Res. 2021;49:1388–D1395.
   PubMed Web of Science ®Google Scholar
• (a) Mills N. ChemDraw Ultra 10.0. CambridgeSoft, 100 Cambridge Park Drive, Cambridge, MA 02140. www.cambridgesoft.com. J Am Chem Soc. 2006;128:13649–13650.(b) Cousins K. ChemDraw Ultra 9.0. CambridgeSoft, 100 Cambridge Park Drive, Cambridge, MA 02140. www.cambridgesoft.com. J Am Chem Soc. 2005;127:4115–4116.
   Google Scholar
• Mauri A. alvaDesc: a tool to calculate and analyze molecular descriptors and fingerprints. In: Roy K, editor. Ecotoxicological QSARs. New York (NY): Humana; 2020. Chapter, Methods in pharmacology and toxicology; p. 801–820.
   Google Scholar
• Solberg HE. Discriminant analysis. CRC Crit Rev Clin Lab Sci. 1978;9(3):209–242.
   PubMed Web of Science ®Google Scholar
• StatSoft I. 2001 STATISTICA (data analysis software system), version 6. Vol. 150. Tulsa (OK): StatSoft, 734 Inc.; p. 91–94.
   Google Scholar
• Gálvez J, García-Domenech R, de Gregorio Alapont C, de Julián-Ortiz JV, Popa L. Pharmacological distribution diagrams: a tool for de novo drug design. J Mol Graph. 1996;14(5):272–276.
   PubMedGoogle Scholar
• Flemming HC, Wuertz S. Bacteria and archaea on Earth and their abundance in biofilms. Nat Rev Microbiol. 2019;17(4):247–260.
   PubMed Web of Science ®Google Scholar
• Qvortrup K, Hultqvist LD, Nilsson M, Jakobsen TH, Jansen CU, Uhd J, Andersen JB, Nielsen TE, Givskov M, Tolker-Nielsen T. Small molecule anti-biofilm agents developed on the basis of mechanistic understanding of biofilm formation. Front Chem. 2019;7:742.
   PubMed Web of Science ®Google Scholar
• Geesi MH. Synthesis, antibacterial evaluation, Crystal Structure and Hirshfeld surface analysis of a new 2-Benzylsulfanyl-3-(4-fluoro-phenyl)-6-methyl-3H-quinazolin-4-one. J Mol Struct. 2020;1208:127894.
   Web of Science ®Google Scholar
• Khazi IM, Koti RS, Chadha MV, Mahajanshetti CS, Gadad AK. Synthesis and evaluation of the antibacterial and antitubercular activity of some N1-aral-N4-(3-chloro-4-fluorophenyl) thiosemicarbazones and their copper(I) complexes. Arzneimittelforschung. 2005;55(2):107–113.
   PubMed Web of Science ®Google Scholar
• Romero D, Sanabria-Valentín E, Vlamakis H, Kolter R. Biofilm inhibitors that target amyloid proteins. Chem Biol. 2020;20(1):102–110.
   Google Scholar
• Majik MS, Gawas UB, Mandrekar VK. Next generation quorum sensing inhibitors: accounts on structure activity relationship studies and biological activities. Bioorg Med Chem. 2020;28(21):115728.
   PubMed Web of Science ®Google Scholar
• Petri GL, Spanò V, Spatola R, Holl R, Raimondi MV, Barraja P, Montalbano A. Bioactive pyrrole-based compounds with target selectivity. Eur J Med Chem. 2020;208:112783.
   PubMed Web of Science ®Google Scholar
• Sardessai Y, Bhosle S. Tolerance of bacteria to organic solvents. Res Microbiol. 2002;153(5):263–268.
   PubMed Web of Science ®Google Scholar
• Shinde S, Lee LH, Chu T. Inhibition of biofilm formation by the synergistic action of EGCG-S and antibiotics. Antibiotics. 2021;10(2):102.
   Google Scholar
• Stenvang M, Dueholm MS, Vad BS, Seviour T, Zeng G, Geifman-Shochat S, Søndergaard MT, Christiansen G, Meyer RL, Kjelleberg S, et al. Epigallocatechin gallate remodels overexpressed functional amyloids in Pseudomonas aeruginosa and increases biofilm susceptibility to antibiotic treatment. J Biol Chem. 2016;291(51):26540–26553.
   PubMed Web of Science ®Google Scholar
• Spengler G, Kincses A, Mosolygó T, Marć MA, Nové M, Gajdács M, Sanmartín C, McNeil HE, Blair JMA, Domínguez-Álvarez E. Antiviral, antimicrobial and antibiofilm activity of selenoesters and selenoanhydrides. Molecules. 2019;24(23):4264–4280.
   PubMed Web of Science ®Google Scholar
• Xiong G, Wu Z, Yi J, Fu L, Yang Z, Hsieh C, Yin M, Zeng X, Wu C, Lu A, et al. ADMETlab 2.0: an integrated online platform for accurate and comprehensive predictions of ADMET properties. Nucleic Acids Res. 2021;49(W1):W5–W14.
   PubMed Web of Science ®Google Scholar