In the fight against disease and illness, nature has provided mankind some of our best therapeutics in the form of secondary metabolites. The plant, fungi and animal phyla inhabiting the Earth produce diverse and unique chemistry that can be used in our fight against disease. In the growing threat of drug resistance and pathogen evolution, the field of natural products chemistry strives to explore new biological and chemical diversity sources, and develop innovative methodology to identify and isolate new chemistry faster than ever. The dissertation herein presented is one such effort to find new, bioactive chemistry from the marine environments. New biodiversity sources, from the tropical Floridian mangrove forests to the cold waters of the Antarctic oceans, were evaluated for the new, unique chemistry they produce. A large-scale screening of epigenetically modulated mangrove fungi was undertaken, producing a large, biologically and chemically diverse extract library. New methodology was developed in order to evaluate these extracts, leading to rapid identification and isolation of known and new bioactive metabolites. From the Southern Oceans, a collection of sponges was studied, and a new, highly unique peptide was isolated and characterized. These efforts were undertaken in the continued effort to isolate new, unique lead compounds.

Natural products have, historically, played an important role in drug discovery. Nevertheless, drug resistance, pathogen evolution, and global climate change threaten human health and nearly all current anti-infective treatments on the market today. It is undeniable that new drug discovery efforts are needed with increasing urgency. Bolstered by a rich history of discovering treatments in the world around us, natural products chemists continue to look to the environment with increasing understanding and emerging technologies that allow efficient, effective isolation of new chemical entities. This thesis will describe one such endeavor. Focusing on fungal natural products, herein is described the isolation and structure elucidation of new, bio-active natural products. Further, the development and implementation of a large fungal screening program will be discussed, the results of which stand to advance microbial drug discovery in the Baker lab for years to come.

Bactérias multirresistentes (MRs) pertencentes ao grupo ESKAPE (i.e., Enterococcus faecium resistente à vancomicina, VRE; Staphylococcus aureus resistente à meticilina, MRSA; Klebsiella spp., e Escherichia coli produtoras de β-lactamases de amplo espectro; Acinetobacter baumannii, Pseudomonas aeruginosa e Enterobacter spp. resistentes aos carbapenêmicos) são importantes patógenos de infecções relacionadas à assistência à saúde (IRAS), onde a sua endemicidade e prevalência tem sido decorrente da seleção de linhagens clonais. Embora, o fenótipo MR decorra da expressão de mecanismos mediados por genes intrínsecos e/ou adquiridos, o crescimento bacteriano na forma de biofilme contribui para um importante fenômeno fisiológico de resistência, o qual é inespecífico quanto ao substrato antimicrobiano. O presente estudo teve como objetivo avaliar a eficácia de agentes físicos e químicos contra biofilmes produzidos por clones de bactérias MRs de importância clínica e epidemiológica no Brasil. Cerdas de poliamida foram utilizadas como modelo de superfície de adesão para o crescimento de biofilmes, os quais foram monitorados por microscopia eletrônica de varredura (MEV). In vivo, o modelo de biofilme foi avaliado pela inserção das cerdas na proleg de larvas de Galleria mellonella, enquanto que, diferentes tratamentos foram aplicados para inibir a formação do biofilme. Adicionalmente, mediante ao ensaio de bioluminescência, o modelo de biofilme produzido pela cepa de P. aeruginosa PAO1/lecA::lux foi avaliado na presença de soluções hipertônicas de cloreto de sódio (NaCl). In vitro, soluções hipertônicas de cloreto de sódio (> 6%) utilizadas de maneira profilática, apresentaram efeito bacteriostático (CIM90= 1,7 M) contra biofilmes produzidos por todos os isolados analisados. Além disso, através do uso profilático de soluções hipertônicas de NaCl, foi possível visualizar a inibição da motilidade dos isolados. Por outro lado, os compostos quaternários de amônio (CQAs) cloreto de benzalcônio (CBA) e cloreto de cetilpiridínio (CCP) apresentaram efeito bactericida (CBM90= 256 µg/mL) contra biofilmes previamente formados em 24h. A atividade de ambos os CQAs foi potencializada na presença de soluções salinas hipertônicas, como avaliado pela metodologia de checkerboard, tendo um efeito sinérgico contra E. coli (ST10, ST101) MCR-1 (∑FIC= 0,5); parcialmente sinérgico contra A. baumannii OXA-23 (ST79), E. cloacae CTX-M-8 (ST131), E. faecium VRE (ST478) e K. pneumoniae KPC-2 (ST340) (∑FIC= 0,75); e indiferente contra cepas de P. aeruginosa SPM-1 (ST277) e S. aureus MRSA (ST5). Adicionalmente, a CIM de carbapenêmicos, fluoroquinolonas e aminoglicosídeos contra biofilmes de bactérias Gram-negativas MRs foi potencializada na presença de solução salina hipertônica resultando em uma queda da CIM >=2. Finalmente, in vivo, para todas as espécies MRs estudadas, biofilmes formados em 08, 12 e 24h resultaram em 100% de morte das larvas de G. mellonella em até 96 horas pós-infecção. O mesmo comportamento foi observado para a cepa PAO1/lecA::lux, sendo possível detectar sinais intensos de bioluminescência nas larvas infectadas com os biofilmes. Entretanto, para os biofilmes previamente tratados com solução salina hipertônica, observou-se a diminuição dos sinais de bioluminescência em até 60%. Já para biofilmes formados em 24, 12 e 08h, o tratamento prévio em solução salina hipertônica e posteriormente com antibióticos resultou em um aumento de até 40, 70 e 80% da sobrevida de G. mellonella, respectivamente. / ESKAPE pathogens (ie, vancomycin-resistant (VRE) Enterococcus faecium; methicillin-resistant (MRSA) Staphylococcus aureus; extended spectrum β-lactamase-producing Klebsiella spp., and Escherichia coli; Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. Resistant to carbapenems), represents an important group of multidrug-resistant (MDR) bacteria related to healthcare-associated infections (HAIs), whereas endemicity have been associated with selection and predominance of clones. Although the MR phenotype derives from the expression of mechanisms mediated by intrinsic and/or acquired genes, bacterial growth in the biofilm form contributes to an important physiological phenomenon of resistance, which is non-specific to the antimicrobial substrate. The present study aimed to evaluate the efficacy of physical and chemical agents against biofilms produced by clones of MDR bacteria of clinical and epidemiological importance, in Brazil. Polyamide bristles were used as adhesion surface model for the growth of biofilms, which were monitored by scanning electron microscopy (SEM). In vivo, the biofilm model was evaluated by the insertion of the bristles into the proleg of larvae of Galleria mellonella, while different treatments and physicochemical conditions were applied to inhibit biofilm formation. Additionally, the biofilm model produced by the P. aeruginosa PAO1/lecA::lux strain was evaluated in the presence of hypertonic solutions of sodium chloride (NaCl). In vitro, hypertonic solutions of sodium chloride presented a bacteriostatic effect (MIC90 = 1.7 M) against biofilm formation of all the isolates analyzed. Moreover, through the prophylactic use of hypertonic solutions of NaCl, it was possible to observe the inhibition of the motility of the isolates. On the other hand, the ammonium quaternary compounds (QACs) benzalkonium chloride (BAC) and cetylpyridinium chloride (CPC) had a bactericidal effect (CBM90 = 256 µg / mL) against previously formed biofilms in 24h. The activity of both QACs was potentiated in the presence of hypertonic saline solutions, as evaluated by the checkerboard methodology, having a synergistic effect against E. coli (ST10, ST101) MCR-1 (∑FIC = 0.5); (ST340) (∑FIC = 0.75), E. faecium VRE (ST478) and K. pneumoniae KPC-2 (ST340), E. cloacae CTX-M-8 (ST131); and indifferent effect against strains of P. aeruginosa SPM-1 (ST277) and S. aureus MRSA (ST5). Furthermore, the MIC of carbapenems, fluoroquinolones and aminoglycosides against biofilms of MDR Gram-negative bacteria was potentiated in the presence of hypertonic saline solution resulting in a decrease in MIC >=2-fold. Finally, for all MDR species studied, biofilms formed at 08, 12 and 24h resulted in 100% death of G. mellonella larvae within 96h post-infection. In fact, the same behavior was observed for the strain PAO1/lecA::lux, and it is possible to detect intense bioluminescence signals in the larvae infected with biofilms. However, for biofilms previously treated with hypertonic saline solution, bioluminescence signs decreased by up to 60%. As for biofilms formed at 24, 12 and 8h, pretreatment in hypertonic saline solution and later with antibiotics resulted in an increase of up to 40, 70 and 80% of the survival of G. mellonella, respectively.

Bactérias multirresistentes (MRs) pertencentes ao grupo ESKAPE (i.e., Enterococcus faecium resistente à vancomicina, VRE; Staphylococcus aureus resistente à meticilina, MRSA; Klebsiella spp., e Escherichia coli produtoras de β-lactamases de amplo espectro; Acinetobacter baumannii, Pseudomonas aeruginosa e Enterobacter spp. resistentes aos carbapenêmicos) são importantes patógenos de infecções relacionadas à assistência à saúde (IRAS), onde a sua endemicidade e prevalência tem sido decorrente da seleção de linhagens clonais. Embora, o fenótipo MR decorra da expressão de mecanismos mediados por genes intrínsecos e/ou adquiridos, o crescimento bacteriano na forma de biofilme contribui para um importante fenômeno fisiológico de resistência, o qual é inespecífico quanto ao substrato antimicrobiano. O presente estudo teve como objetivo avaliar a eficácia de agentes físicos e químicos contra biofilmes produzidos por clones de bactérias MRs de importância clínica e epidemiológica no Brasil. Cerdas de poliamida foram utilizadas como modelo de superfície de adesão para o crescimento de biofilmes, os quais foram monitorados por microscopia eletrônica de varredura (MEV). In vivo, o modelo de biofilme foi avaliado pela inserção das cerdas na proleg de larvas de Galleria mellonella, enquanto que, diferentes tratamentos foram aplicados para inibir a formação do biofilme. Adicionalmente, mediante ao ensaio de bioluminescência, o modelo de biofilme produzido pela cepa de P. aeruginosa PAO1/lecA::lux foi avaliado na presença de soluções hipertônicas de cloreto de sódio (NaCl). In vitro, soluções hipertônicas de cloreto de sódio (> 6%) utilizadas de maneira profilática, apresentaram efeito bacteriostático (CIM90= 1,7 M) contra biofilmes produzidos por todos os isolados analisados. Além disso, através do uso profilático de soluções hipertônicas de NaCl, foi possível visualizar a inibição da motilidade dos isolados. Por outro lado, os compostos quaternários de amônio (CQAs) cloreto de benzalcônio (CBA) e cloreto de cetilpiridínio (CCP) apresentaram efeito bactericida (CBM90= 256 µg/mL) contra biofilmes previamente formados em 24h. A atividade de ambos os CQAs foi potencializada na presença de soluções salinas hipertônicas, como avaliado pela metodologia de checkerboard, tendo um efeito sinérgico contra E. coli (ST10, ST101) MCR-1 (∑FIC= 0,5); parcialmente sinérgico contra A. baumannii OXA-23 (ST79), E. cloacae CTX-M-8 (ST131), E. faecium VRE (ST478) e K. pneumoniae KPC-2 (ST340) (∑FIC= 0,75); e indiferente contra cepas de P. aeruginosa SPM-1 (ST277) e S. aureus MRSA (ST5). Adicionalmente, a CIM de carbapenêmicos, fluoroquinolonas e aminoglicosídeos contra biofilmes de bactérias Gram-negativas MRs foi potencializada na presença de solução salina hipertônica resultando em uma queda da CIM >=2. Finalmente, in vivo, para todas as espécies MRs estudadas, biofilmes formados em 08, 12 e 24h resultaram em 100% de morte das larvas de G. mellonella em até 96 horas pós-infecção. O mesmo comportamento foi observado para a cepa PAO1/lecA::lux, sendo possível detectar sinais intensos de bioluminescência nas larvas infectadas com os biofilmes. Entretanto, para os biofilmes previamente tratados com solução salina hipertônica, observou-se a diminuição dos sinais de bioluminescência em até 60%. Já para biofilmes formados em 24, 12 e 08h, o tratamento prévio em solução salina hipertônica e posteriormente com antibióticos resultou em um aumento de até 40, 70 e 80% da sobrevida de G. mellonella, respectivamente. / ESKAPE pathogens (ie, vancomycin-resistant (VRE) Enterococcus faecium; methicillin-resistant (MRSA) Staphylococcus aureus; extended spectrum β-lactamase-producing Klebsiella spp., and Escherichia coli; Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. Resistant to carbapenems), represents an important group of multidrug-resistant (MDR) bacteria related to healthcare-associated infections (HAIs), whereas endemicity have been associated with selection and predominance of clones. Although the MR phenotype derives from the expression of mechanisms mediated by intrinsic and/or acquired genes, bacterial growth in the biofilm form contributes to an important physiological phenomenon of resistance, which is non-specific to the antimicrobial substrate. The present study aimed to evaluate the efficacy of physical and chemical agents against biofilms produced by clones of MDR bacteria of clinical and epidemiological importance, in Brazil. Polyamide bristles were used as adhesion surface model for the growth of biofilms, which were monitored by scanning electron microscopy (SEM). In vivo, the biofilm model was evaluated by the insertion of the bristles into the proleg of larvae of Galleria mellonella, while different treatments and physicochemical conditions were applied to inhibit biofilm formation. Additionally, the biofilm model produced by the P. aeruginosa PAO1/lecA::lux strain was evaluated in the presence of hypertonic solutions of sodium chloride (NaCl). In vitro, hypertonic solutions of sodium chloride presented a bacteriostatic effect (MIC90 = 1.7 M) against biofilm formation of all the isolates analyzed. Moreover, through the prophylactic use of hypertonic solutions of NaCl, it was possible to observe the inhibition of the motility of the isolates. On the other hand, the ammonium quaternary compounds (QACs) benzalkonium chloride (BAC) and cetylpyridinium chloride (CPC) had a bactericidal effect (CBM90 = 256 µg / mL) against previously formed biofilms in 24h. The activity of both QACs was potentiated in the presence of hypertonic saline solutions, as evaluated by the checkerboard methodology, having a synergistic effect against E. coli (ST10, ST101) MCR-1 (∑FIC = 0.5); (ST340) (∑FIC = 0.75), E. faecium VRE (ST478) and K. pneumoniae KPC-2 (ST340), E. cloacae CTX-M-8 (ST131); and indifferent effect against strains of P. aeruginosa SPM-1 (ST277) and S. aureus MRSA (ST5). Furthermore, the MIC of carbapenems, fluoroquinolones and aminoglycosides against biofilms of MDR Gram-negative bacteria was potentiated in the presence of hypertonic saline solution resulting in a decrease in MIC >=2-fold. Finally, for all MDR species studied, biofilms formed at 08, 12 and 24h resulted in 100% death of G. mellonella larvae within 96h post-infection. In fact, the same behavior was observed for the strain PAO1/lecA::lux, and it is possible to detect intense bioluminescence signals in the larvae infected with biofilms. However, for biofilms previously treated with hypertonic saline solution, bioluminescence signs decreased by up to 60%. As for biofilms formed at 24, 12 and 8h, pretreatment in hypertonic saline solution and later with antibiotics resulted in an increase of up to 40, 70 and 80% of the survival of G. mellonella, respectively.

We recently reported results from a high-throughput screening effort that identified 235 inhibitors of the Escherichia coli GroEL/ES chaperonin system [Bioorg. Med. Chem. Lett. 2014, 24, 786]. As the GroEL/ES chaperonin system is essential for growth under all conditions, we reasoned that targeting GroEL/ES with small molecule inhibitors could be a viable antibacterial strategy. Extending from our initial screen, we report here the antibacterial activities of 22 GroEL/ES inhibitors against a panel of Gram-positive and Gram-negative bacteria, including E. coli, Bacillus subtilis, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae. GroEL/ES inhibitors were more effective at blocking the proliferation of Gram-positive bacteria, in particular S. aureus, where lead compounds exhibited antibiotic effects from the low-lM to mid-nM range. While several compounds inhibited the human HSP60/10 refolding cycle, some were able to selectively target the bacterial GroEL/ES system. Despite inhibiting HSP60/10, many compounds exhibited low to no cytotoxicity against human liver and kidney cell lines. Two lead candidates emerged from the panel, compounds 8 and 18, that exhibit >50-fold selectivity for inhibiting S. aureus growth compared to liver or kidney cell cytotoxicity. Compounds 8 and 18 inhibited drug-sensitive and methicillin-resistant S. aureus strains with potencies comparable to vancomycin, daptomycin, and streptomycin, and are promising candidates to explore for validating the GroEL/ES chaperonin system as a viable antibiotic target.

ESKAPE pathogens are notorious in causing nosocomial infections and escaping current antibiotic treatments. There has been a dramatic increase in nosocomial infections accompanied with a decrease in the number of antibiotics developed, leading to significant increase in morbidity and mortality among patients. In an attempt to combat this problem, derivatives of ciprofloxacin, rifabutin and beta-lactam antibiotics were synthesized and tested against the ESKAPE pathogens. From minimum inhibitory concentration assays, 4 ciprofloxacin analogs and 8 beta-lactam analogs were found to be effective against multiple bacterial species. Additionally, 12 rifabutin analogs and 23 beta-lactam analogs were potent against single bacterial species, primarily toward methicillin-resistant Staphylococcus aureus (MRSA) at a concentration of ≤ 25 µg mL-1. Based on the effectiveness against methicillin-resistant Staphylococcus aureus (MRSA), three rifabutin analogs were selected for further testing. Two rifabutin analogs (DU644 and DU645) were found to possess between a one to twofold mean increase of inhibitory activities, while the other rifabutin analogs (DU650) demonstrated up to a twofold decrease of inhibitory activity when compared to the parent drug. These compounds were then examined for their bactericidal and antibiofilm activities against MRSA. From these assays, we found that DU644 and DU645 were 4 times more bactericidal and antibiofilm against MRSA when compared to the parent drug. In addition, rpoB mutation validation results confirmed that modification of these rifabutin derivatives at the C3 and C4 positions, and bearing an imidazolyl ring carrying substituted spiropiperidyl ring, did not change their mechanism of action towards the beta-subunit of RNA polymerase. Cytotoxicity testing performed using human hepatocellular carcinoma epithelial cells (hepG2) showed that at concentrations ranged from 1.25 µg mL-1 to 25 µg mL-1, DU644 and DU645 showed very low toxicity. Collectively, structural drugs modifications of these obsolete drugs are able to restore their antibacterial activities against MRSA, which is notable as the most infectious nosocomial pathogen. Therefore, further development and application of rifabutin analogs might be beneficial for medical use to combat MRSA infections.

The rapid progression of Klebsiella pneumoniae towards antibiotic resistance is a significant concern, primarily due to its protective extracellular polysaccharide (EPS) capsule that shields the bacteria from host immunity. Our previous research demonstrated that antimicrobial peptides could disrupt the EPS capsule of K. pneumoniae. Further analysis identified Bac7 (1-35), a proline-rich antimicrobial peptide (PrAMP), as having the greatest ability to aggregate with the K. pneumoniae EPS capsule, exhibiting potent antimicrobial activity. However, the relationship between key features facilitating EPS and membrane interactions, as well as antimicrobial efficacy, remains poorly understood. Here, we used natural PrAMPs from diverse organisms to investigate their interactions with the cell envelope of K. pneumoniae. Apidaecin Cd3+, Tur1A, and PR-39 peptides demonstrated activity against all tested strains, with a minimum inhibitory concentration ≤ 1 µg/mL. These peptides shared a proline content exceeding 36% and a charge greater than +5. Active PrAMPs induced membrane depolarization in K. pneumoniae, with the extent of depolarization directly correlating with peptide charge, suggesting membrane depolarization as a potential mechanism for PrAMP entry into the cell. Checkerboard assays of active PrAMPs with PepC, an inactive peptide, suggested the membrane actions of PrAMPs have potential to rescue a therapeutic unable to access the bacterial membrane. Consistent with our findings with bac7(1-35) truncated analogs, both active and inactive PrAMPs aggregated with K. pneumoniae EPS, suggesting that the antimicrobial activities and polysaccharide aggregation potential of this class of peptides can be studied independently. Furthermore, the treatment of biofilms with active peptides revealed unique structure-based biofilm changes, with Tur1A causing more structural collapse than PR-39. Our findings highlight a potential membrane mediated peptide uptake into the cell which is dependent on the charge of the peptide. Differential biofilm interactions between similar peptides and EPS aggregation of inactive peptides warrant these attributes of PrAMPs to be further studied independently.