Cheminformatics-driven Discovery of Hit Compounds Against Paracoccidioides spp.

References

• Shikanai-Yasuda MA , MendesRP , ColomboALet al. Brazilian guidelines for the clinical management of paracoccidioidomycosis. Rev. Soc. Bras. Med. Trop.50(5), 715–740 (2017).
   PubMed Web of Science ®Google Scholar
• Shikanai-Yasuda MA . Paracoccidioidomycosis treatment. Rev. Inst. Med. Trop. S. Paulo.57(Suppl. 19), 31–37 (2015).
   PubMedGoogle Scholar
• Capasso C , SupuranCT. Sulfa and trimethoprim-like drugs – antimetabolites acting as carbonic anhydrase, dihydropteroate synthase and dihydrofolate reductase inhibitors. J. Enzyme Inhib. Med. Chem.29(3), 379–387 (2014).
   PubMed Web of Science ®Google Scholar
• Calderone R , SunN , Gay-AndrieuFet al. Antifungal drug discovery: the process and outcomes. Future Microbiol.9(6), 791–805 (2014).
   PubMed Web of Science ®Google Scholar
• Macalino SJY , GosuV , HongS , ChoiS. Role of computer-aided drug design in modern drug discovery. Arch. Pharm. Res.38(9), 1686–1701 (2015).
   PubMed Web of Science ®Google Scholar
• Silva LC , NevesBJ , GomesMNet al. Computer-aided identification of novel anti-paracoccidioidomycosis compounds. Future Microbiol.13(13), 1523–1535 (2018).
   PubMed Web of Science ®Google Scholar
• de Carvalho Tavares L , JohannS , Mariade Almeida Alves Tet al. Quinolinyl and quinolinyl N-oxide chalcones: Synthesis, antifungal and cytotoxic activities. Eur. J. Med. Chem.46(9), 4448–4456 (2011).
   PubMed Web of Science ®Google Scholar
• Fourches D , MuratovE , TropshaA. Trust, but verify II: a practical guide to chemogenomics data curation. J. Chem. Inf. Model.56(7), 1243–1252 (2016).
   PubMed Web of Science ®Google Scholar
• Riniker S , LandrumGA. Similarity maps – a visualization strategy for molecular fingerprints and machine-learning methods. J. Cheminform.5(1), 43 (2013).
   PubMedGoogle Scholar
• Wang X , ShenY , WangSet al. PharmMapper 2017 update: a web server for potential drug target identification with a comprehensive target pharmacophore database. Nucleic Acids Res.45(W1), W356–W360 (2017).
   PubMed Web of Science ®Google Scholar
• The UniProt Consortium , BatemanA , MartinM-Jet al.UniProt: the universal protein knowledgebase in 2021. Nucleic Acids Res.49(D1), D480–D489 (2021).
   PubMed Web of Science ®Google Scholar
• Schwede T . SWISS-MODEL: an automated protein homology-modeling server. Nucleic Acids Res.31(13), 3381–3385 (2003).
   PubMed Web of Science ®Google Scholar
• Anandakrishnan R , AguilarB , OnufrievAV. H++ 3.0: automating pK prediction and the preparation of biomolecular structures for atomistic molecular modeling and simulations. Nucleic Acids Res.40(W1), W537–W541 (2012).
   PubMed Web of Science ®Google Scholar
• OpenEye Scientific Software . OMEGA v.4.2.0.1. www.eyesopen.com
   Google Scholar
• OpenEye Scientific Software . QUACPAC v.2.2.0.1. www.eyeopen.com
   Google Scholar
• OpenEye Scientific Software . OEDocking (2017). www.eyesopen.com
   Google Scholar
• McGann M . FRED pose prediction and virtual screening accuracy. J. Chem. Inf. Model.51(3), 578–596 (2011).
   PubMed Web of Science ®Google Scholar
• von Mering C . STRING: known and predicted protein–protein associations, integrated and transferred across organisms. Nucleic Acids Res.33(Database issue), D433–D437 (2004).
   Google Scholar
• Lipinski CA , LombardoF , DominyBW , FeeneyPJ. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Deliv. Rev.23(1), 3–25 (1997).
   Web of Science ®Google Scholar
• Katsuno K , BurrowsJN , DuncanKet al. Hit and lead criteria in drug discovery for infectious diseases of the developing world. Nat. Rev. Drug Discov.14(11), 751–758 (2015).
   PubMed Web of Science ®Google Scholar
• da Silva LS , BarbosaUR , SilvaLDC , SoaresCM , PereiraM , da SilvaRA. Identification of a new antifungal compound against isocitrate lyase of Paracoccidioides brasiliensis.Future Microbiol.14(18), 1589–1606 (2019).
   PubMed Web of Science ®Google Scholar
• Costa FG , daSilva Neto BR , GonçalvesRLet al. Alkaloids as inhibitors of malate synthase from Paracoccidioides spp.: receptor–ligand interaction-based virtual screening and molecular docking studies, antifungal activity, and the adhesion process. Antimicrob. Agents Chemother.59(9), 5581–5594 (2015).
   PubMed Web of Science ®Google Scholar
• Lima RM , Freitase Silva KS , SilvaLDCet al. A structure-based approach for the discovery of inhibitors against methylcitrate synthase of Paracoccidioides lutzii. J. Biomol. Struct. Dyn.40(19), 9361–9373 (2022).
   PubMed Web of Science ®Google Scholar
• Espinel-Ingroff A . Germinated and nongerminated conidial suspensions for testing of susceptibilities of Aspergillus spp. to amphotericin B, itraconazole, posaconazole, ravuconazole, and voriconazole. Antimicrob. Agents Chemother.45(2), 605–607 (2001).
   PubMed Web of Science ®Google Scholar
• Mazu TK , BrickerBA , Flores-RozasH , AblordeppeySY. The mechanistic targets of antifungal agents: an overview. MRMC16(7), 555–578 (2016).
   Google Scholar
• do Carmo Silva L , de OliveiraAA , de SouzaDRet al. Overview of antifungal drugs against paracoccidioidomycosis: how do we start, where are we, and where are we going? J. Fungi (Basel) 6(4), 300 (2020).
   PubMedGoogle Scholar
• Skwarczynska M , OttmannC. Protein–protein interactions as drug targets. Future Medicin. Chem.7(16), 2195–2219 (2015).
   PubMed Web of Science ®Google Scholar
• Szklarczyk D , GableAL , NastouKCet al. The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets. Nucleic Acids Res.49(D1), D605–D612 (2021).
   PubMed Web of Science ®Google Scholar
• Cheng H , SugiuraR , WuWet al. Role of the Rab GTP-binding protein Ypt3 in the fission yeast exocytic pathway and its connection to calcineurin function. MBoC13(8), 2963–2976 (2002).
   Google Scholar
• Campos CBL , DiBenedette JPT , MoraisFV , OvalleR , NobregaMP. Evidence for the role of calcineurin in morphogenesis and calcium homeostasis during mycelium-to-yeast dimorphism of Paracoccidioides brasiliensis. Eukaryot. Cell.7(10), 1856–1864 (2008).
   PubMedGoogle Scholar
• Sorais F , BarretoL , LealJA , BernabéM , San-BlasG , Niño-VegaGA. Cell wall glucan synthases and GTPases in Paracoccidioides brasiliensis. Med. Mycol.48(1), 35–47 (2010).
   PubMed Web of Science ®Google Scholar
• Madaule P , AxelR , MyersAM. Characterization of two members of the rho gene family from the yeast Saccharomyces cerevisiae. Proc. Natl Acad. Sci. USA84(3), 779–783 (1987).
   PubMed Web of Science ®Google Scholar
• Peres da Silva R , LongoLGV , da CunhaJPCet al. Comparison of the RNA content of extracellular vesicles derived from Paracoccidioides brasiliensis and Paracoccidioides lutzii. Cells8(7), 765 (2019).
   PubMed Web of Science ®Google Scholar
• Vallejo MC , NakayasuES , MatsuoALet al. Vesicle and vesicle-free extracellular proteome of Paracoccidioides brasiliensis: comparative analysis with other pathogenic fungi. J. Proteome Res.11(3), 1676–1685 (2012).
   PubMed Web of Science ®Google Scholar
• Miller KE , KangPJ , ParkH-O. Regulation of Cdc42 for polarized growth in budding yeast. Microb. Cell7(7), 175–189 (2020).
   PubMed Web of Science ®Google Scholar
• Menino JF , OsórioNS , SturmeMHJet al. Morphological heterogeneity of Paracoccidioides brasiliensis: relevance of the Rho-like GTPase PbCDC42. Med. Mycol.50(7), 768–774 (2012).
   PubMed Web of Science ®Google Scholar
• Kosova AA , KhodyrevaSN , LavrikOI. Role of glyceraldehyde-3-phosphate dehydrogenase (GAPDH) in DNA repair. Biochem. Moscow82(6), 643–654 (2017).
   PubMed Web of Science ®Google Scholar
• Longo LVG , da CunhaJPC , SobreiraTJP , PucciaR. Proteome of cell wall-extracts from pathogenic Paracoccidioides brasiliensis: comparison among morphological phases, isolates, and reported fungal extracellular vesicle proteins. EuPA Open Proteomics3, 216–228 (2014).
   Google Scholar
• de Sousa Lima P , CasalettiL , BailãoAM , de VasconcelosAT , daRocha Fernandes G , SoaresCM. Transcriptional and proteomic responses to carbon starvation in paracoccidioides. PLOS Negl. Trop. Dis.8(5), e2855 (2014).
   PubMed Web of Science ®Google Scholar
• de Arruda Grossklaus D , BailãoAM , Vieira RezendeTCet al. Response to oxidative stress in Paracoccidioides yeast cells as determined by proteomic analysis. Microbes Infect.15(5), 347–364 (2013).
   PubMed Web of Science ®Google Scholar
• Dantas AS , AndradeRV , de CarvalhoMJ , FelipeMSS , CamposÉG. Oxidative stress response in Paracoccidioides brasiliensis: assessing catalase and cytochrome c peroxidase. Mycol. Res.112(6), 747–756 (2008).
   PubMedGoogle Scholar
• Dunn MF , Ramírez-TrujilloJA , Hernández-LucasI. Major roles of isocitrate lyase and malate synthase in bacterial and fungal pathogenesis. Microbiology155(10), 3166–3175 (2009).
   PubMedGoogle Scholar
• Lourenço dos Santos S , PetropoulosI , FriguetB. The oxidized protein repair enzymes methionine sulfoxide reductases and their roles in protecting against oxidative stress, in ageing and in regulating protein function. Antioxidants7(12), 191 (2018).
   Web of Science ®Google Scholar
• Abadio AKR , KioshimaES , LerouxV , MartinsNF , MaigretB , FelipeMSS. Identification of new antifungal compounds targeting thioredoxin reductase of Paracoccidioides genus. PLOS ONE10(11), e0142926 (2015).
   PubMed Web of Science ®Google Scholar
• Jastrzębowska K , GabrielI. Inhibitors of amino acids biosynthesis as antifungal agents. Amino Acids47(2), 227–249 (2015).
   PubMed Web of Science ®Google Scholar
• Ramachandran S , KotaP , DingF , DokholyanNV. Automated minimization of steric clashes in protein structures. Proteins79(1), 261–270 (2011).
   PubMed Web of Science ®Google Scholar
• Chen VB , WedellJR , WengerRK , UlrichEL , MarkleyJL. MolProbity for the masses – of data. J. Biomol. NMR63(1), 77–83 (2015).
   PubMed Web of Science ®Google Scholar
• Williams CJ , HeaddJJ , MoriartyNWet al. MolProbity: more and better reference data for improved all-atom structure validation. Prot. Sci.27(1), 293–315 (2018).
   PubMed Web of Science ®Google Scholar
• Huang Q , XieJ , SeetharamanJ. Crystal structure of Schizosaccharomyces pombe Rho1 reveals its evolutionary relationship with other Rho GTPases. Biology11(11), 1627 (2022).
   PubMedGoogle Scholar
• Sun D , GaoW , HuH , ZhouS. Why 90% of clinical drug development fails and how to improve it?Acta Pharm. Sin. B.12(7), 3049–3062 (2022).
   PubMed Web of Science ®Google Scholar
• Pedroso VSP , deCarvalho Vilela M , PedrosoERP , TeixeiraAL. Paracoccidioidomicose com comprometimento do sistema nervoso central: revisão de literatura. Rev. Bras. Neurol.44(3), 33–40 (2008).
   Google Scholar
• Santos-Gandelman J , Machado-SilvaA. Drug development for cryptococcosis treatment: what can patents tell us?Mem. Inst. Oswaldo Cruz.114, e180391 (2019).
   PubMed Web of Science ®Google Scholar
• Wei T , ZhengN , ZhengHet al. Proteomic perspective of azole resistance in Aspergillus fumigatus biofilm extracellular matrix in response to itraconazole. Med. Mycol. doi: 10.1093/mmy/myac084 (2022).
   Web of Science ®Google Scholar
• Hahn RC , MoratoConceição YT , SantosNL , FerreiraJF , HamdanJS. Disseminated paracoccidioidomycosis: correlation between clinical and in vitro resistance to ketoconazole and trimethoprim sulphamethoxazole. Mycoses46(8), 342–347 (2003).
   PubMed Web of Science ®Google Scholar
• Silva LC , dosSantos Filho RF , de OliveiraAAet al. 3-phenacylideneoxindoles as a new class of antifungal compounds against Paracoccidioides spp. Future Microbiol.18(2), 93–105 (2023).
   PubMed Web of Science ®Google Scholar
• Wang J , YunD , YaoJet al. Design, synthesis and QSAR study of novel isatin analogues inspired Michael acceptor as potential anticancer compounds. Eur. J. Med. Chem.144, 493–503 (2018).
   PubMed Web of Science ®Google Scholar
• Woodard CL , LiZ , KathcartAKet al. Oxindole-based compounds are selective inhibitors of Plasmodium falciparum cyclin dependent protein kinases. J. Med. Chem.46(18), 3877–3882 (2003).
   PubMed Web of Science ®Google Scholar
• Gupta AK , KalpanaS , MalikJK. Synthesis and in vitro antioxidant activity of new 3-substituted-2-oxindole derivatives. Indian J. Pharm. Sci.74(5), 481–486 (2012).
   PubMed Web of Science ®Google Scholar
• Koca M , ServiS , KirilmisCet al. Synthesis and antimicrobial activity of some novel derivatives of benzofuran: part 1. Synthesis and antimicrobial activity of (benzofuran-2-yl)(3-phenyl-3-methylcyclobutyl) ketoxime derivatives. Eur. J. Med. Chem.40(12), 1351–1358 (2005).
   PubMed Web of Science ®Google Scholar
• Kirilmis C , AhmedzadeM , ServiS , KocaM , KizirgilA , KazazC. Synthesis and antimicrobial activity of some novel derivatives of benzofuran: Part 2. The synthesis and antimicrobial activity of some novel 1-(1-benzofuran-2-yl)-2-mesitylethanone derivatives. Eur. J. Med. Chem.43(2), 300–308 (2008).
   PubMed Web of Science ®Google Scholar
• Chand K , Rajeshwari , HiremathadA , SinghM , SantosMA , KeriRS. A review on antioxidant potential of bioactive heterocycle benzofuran: natural and synthetic derivatives. Pharmacol. Reports69(2), 281–295 (2017).
   PubMed Web of Science ®Google Scholar
• Hannemann K , PuchtaV , SimonE , ZieglerH , ZieglerG , SpitellerG. The common occurrence of furan fatty acids in plants. Lipids24(4), 296–298 (1989).
   PubMed Web of Science ®Google Scholar
• Boselli E , GrobK , LerckerG. Determination of furan fatty acids in extra virgin olive oil. J. Agric. Food Chem.48(7), 2868–2873 (2000).
   PubMed Web of Science ®Google Scholar
• Kim DK , KwakJH. A furan derivative from Cornus officinalis.Arch. Pharm. Res.21(6), 787 (1998).
   PubMed Web of Science ®Google Scholar
• Spiteller G . Furan fatty acids: occurrence, synthesis, and reactions. Are furan fatty acids responsible for the cardioprotective effects of a fish diet?Lipids40(8), 755–771 (2005).
   PubMed Web of Science ®Google Scholar
• Mousavi R , AlizadehM , Saleh-GhadimiS. Consumption of 5-hydroxymethylfurfural-rich dried fruits is associated with reduction in urinary excretion of 8-hydroxy-2′-deoxyguanosine: a randomized clinical trial. Eur. Food Res. Technol.242(5), 677–684 (2016).
   Web of Science ®Google Scholar