scholarly journals Bacterial Cytological Profiling Identifies Rhodanine-containing PAINS Analogs as Specific Inhibitors of E. coli Thymidylate Kinase in Vivo

2021 ◽  
Author(s):  
Elizabeth T. Montaño ◽  
Jason F. Nideffer ◽  
Joseph Sugie ◽  
Eray Enustun ◽  
Adam B. Shapiro ◽  
...  
Keyword(s):  
Dna Replication ◽  
Specific Activity ◽  
Structural Similarity ◽  
Mechanisms Of Action ◽  
Thymidylate Kinase ◽  
E Coli ◽  
Bacterial Cytological Profiling ◽  
Cytological Profiling

In this study, we sought to determine if an in vivo assay for studying antibiotic mechanisms of action could provide insight into the activity of compounds that may inhibit multiple targets. Thus, we conducted an activity screen of 31 structural analogs of rhodanine-containing pan-assay interference compounds (PAINS). We identified nine active molecules against E. coli and classified them according to their in vivo mechanisms of action. The mechanisms of action of PAINS are generally difficult to identify due to their promiscuity. However, we leveraged bacterial cytological profiling, a fluorescence microscopy technique, to study these complex mechanisms. Ultimately, we found that although some of our molecules promiscuously inhibit multiple cellular pathways, a few molecules specifically inhibit DNA replication despite structural similarity to related PAINS. A genetic analysis of resistant mutants revealed thymidylate kinase (essential for DNA synthesis) as an intracellular target of some of these rhodanine-containing antibiotics. This finding was supported by in vitro activity assays as well as experiments utilizing a thymidylate kinase overexpression system. The analog that demonstrated the lowest IC 50 in vitro and MIC in vivo displayed the greatest specificity for inhibition of the DNA replication pathway, despite containing a rhodamine moiety. While it’s thought that PAINS cannot be developed as antibiotics, this work showcases novel inhibitors of E. coli thymidylate kinase. But perhaps more importantly, this work highlights the utility of bacterial cytological profiling for studying the in vivo specificity of antibiotics and demonstrates that BCP can identify multiple pathways that are inhibited by an individual molecule. Importance: We demonstrate that bacterial cytological profiling is a powerful tool for directing antibiotic discovery efforts because it can be used to determine the specificity of an antibiotic's in vivo mechanism of action. By assaying analogs of PAINS, molecules that are notoriously intractable and non-specific, we (surprisingly) identify molecules with specific activity against E. coli thymidylate kinase. This suggests that structural modifications to PAINS can confer stronger inhibition by targeting a specific cellular pathway. While in vitro inhibition assays are susceptible to false positive results (especially from PAINS), bacterial cytological profiling provides the resolution to identify molecules with specific in vivo activity.

scholarly journals Bacterial Cytological Profiling Identifies Rhodanine-containing PAINS Analogs as Specific Inhibitors of E. coli Thymidylate Kinase in Vivo

2021 ◽  
Author(s):  
Elizabeth T. Montaño ◽  
Jason F. Nideffer ◽  
Joseph Sugie ◽  
Eray Enustun ◽  
Adam B. Shapiro ◽  
...  
Keyword(s):  
Dna Replication ◽  
Specific Activity ◽  
Structural Similarity ◽  
Mechanisms Of Action ◽  
Thymidylate Kinase ◽  
E Coli ◽  
Bacterial Cytological Profiling ◽  
Cytological Profiling

AbstractIn this study, we conducted an activity screen of 31 structural analogs of rhodanine-containing pan-assay interference compounds (PAINS). We identified nine active molecules inhibiting the growth of E. coli and classified them according to their in vivo mechanisms of action. The mechanisms of action of PAINS are generally difficult to identify due to their promiscuity. However, we leveraged bacterial cytological profiling, a fluorescence microscopy technique, to study these complex mechanisms. Ultimately, we found that although some of our molecules promiscuously inhibit multiple cellular pathways, a few molecules specifically inhibit DNA replication despite their structural similarity to related PAINS. A genetic analysis of resistant mutants revealed that thymidylate kinase (an enzyme essential for DNA synthesis) is an intracellular target of some of these rhodanine-containing antibiotics. This finding was supported by assays of in vitro activity as well as experiments utilizing a thymidylate kinase overexpression system. The analog that demonstrated the lowest IC50in vitro and MIC in vivo displayed the greatest specificity for the inhibition of DNA replication in E. coli, despite containing a rhodamine moiety. While it’s generally thought that PAINS cannot be developed as antibiotics, this work highlights the utility of bacterial cytological profiling for studying the in vivo specificity of antibiotics, and it showcases novel inhibitors of E. coli thymidylate kinase.ImportanceWe demonstrate that bacterial cytological profiling is a powerful tool for directing antibiotic discovery efforts because it can be used to determine the specificity of an antibiotic’s in vivo mechanism of action. By assaying analogs of PAINS, molecules that are notoriously intractable and non-specific, we (surprisingly) identify molecules with specific activity against E. coli thymidylate kinase. This suggests that structural modifications to PAINS can confer stronger inhibition by targeting a specific cellular pathway. While in vitro inhibition assays are susceptible to false positive results (especially from PAINS), bacterial cytological profiling provides the resolution to identify molecules with specific in vivo activity.

scholarly journals Near-continuously synthesized leading strands inEscherichia coliare broken by ribonucleotide excision

2019 ◽  
Vol 116 (4) ◽  
pp. 1251-1260 ◽  
Author(s):  
Glen E. Cronan ◽  
Elena A. Kouzminova ◽  
Andrei Kuzminov
Keyword(s):  
Dna Replication ◽  
Excision Repair ◽  
Chromosomal Dna ◽  
E Coli ◽  
Okazaki Fragments ◽  
Leading Strand ◽  
Replication Intermediates ◽  
Lagging Strand

In vitro, purified replisomes drive model replication forks to synthesize continuous leading strands, even without ligase, supporting the semidiscontinuous model of DNA replication. However, nascent replication intermediates isolated from ligase-deficientEscherichia colicomprise only short (on average 1.2-kb) Okazaki fragments. It was long suspected that cells replicate their chromosomal DNA by the semidiscontinuous mode observed in vitro but that, in vivo, the nascent leading strand was artifactually fragmented postsynthesis by excision repair. Here, using high-resolution separation of pulse-labeled replication intermediates coupled with strand-specific hybridization, we show that excision-proficientE. coligenerates leading-strand intermediates >10-fold longer than lagging-strand Okazaki fragments. Inactivation of DNA-repair activities, including ribonucleotide excision, further increased nascent leading-strand size to ∼80 kb, while lagging-strand Okazaki fragments remained unaffected. We conclude that in vivo, repriming occurs ∼70× less frequently on the leading versus lagging strands, and that DNA replication inE. coliis effectively semidiscontinuous.

scholarly journals THE ACTION OF SULFONAMIDES ON THE RESPIRATION OF BACTERIA AND YEAST

1942 ◽  
Vol 25 (6) ◽  
pp. 805-817 ◽  
Author(s):  
M. G. Sevag ◽  
M. Shelburne ◽  
Stuart Mudd
Keyword(s):  
Structural Similarity ◽  
Inhibitory Effect ◽  
Brewer’S Yeast ◽  
Respiratory Enzymes ◽  
Staph Aureus ◽  
E Coli ◽  
Brewer's Yeast ◽  
Inhibiting Effect

The inhibiting effects of sulfonamide drugs and their derivatives on the anaerobic decarboxylation of pyruvic acid by Staphylococcus aureus, Escherichia coli, baker's and brewer's yeast, and a carboxylase preparation from brewer's yeast have been investigated. These drugs are: sulfanilamide, sulfapyridine, sulfadiazine, sulfamethyldiazine, sulfathiazole, sulfamethylthiazole, sulfanilamido-5-ethyl-4-thiazolone, 2-aminopyrimidine, 2-aminothiazole, and 2-aminopyridine. The sulfathiazole ring appears to exercise decidedly greater specific inhibiting effect on the carboxylases of Staph. aureus and E. coli. The inhibiting effect on yeast carboxylase is non-differentiable among all the substances tried, except sulfamethyldiazine which is completely ineffective on the carboxylases of the organisms studied. The specific inhibitory effect of sulfathiazole on the carboxylases of Staph. aureus and E. coli in comparison to sulfanilamide, sulfapyridine, and sulfadiazine is in harmony with in vivo and in vitro experimental results of other investigators. The results of the present investigation appear to support the hypothesis (1) that sulfonamides exert their bacteriostatic action through chemical affinity for the carrier proteins of certain respiratory enzymes of the bacterial cell, and that this affinity may in part be related to structural similarity between components of the drugs and the corresponding respiratory coenzymes.

The mutant β E202K sliding clamp protein impairs DNA polymerase III replication activity

2021 ◽  
Author(s):  
Caleb Homiski ◽  
Michelle K. Scotland ◽  
Vignesh M. P. Babu ◽  
Sundari Chodavarapu ◽  
Robert W. Maul ◽  
...  
Keyword(s):  
Dna Replication ◽  
Dna Polymerase ◽  
Genetic Selection ◽  
Cellular Level ◽  
Dna Polymerase Iii ◽  
E Coli ◽  
Polymerase Iii ◽  
Pol Iii

Expression of the E. coli dnaN -encoded β clamp at ≥10-fold higher than chromosomally-expressed levels impedes growth by interfering with DNA replication. We hypothesized that the excess β clamp sequesters the replicative DNA polymerase III (Pol III) to inhibit replication. As a test of this hypothesis, we measured the ability of eight mutant clamps obtained by their inability to impede growth to stimulate Pol III replication in vitro . Compared with the wild type clamp, seven of the mutants were defective, consistent with their elevated cellular levels failing to sequester Pol III. However, the β E202K mutant, which bears a glutamic acid-to-lysine substitution at residue 202 displayed an increased affinity for Pol IIIα and Pol III core (Pol IIIαεθ), suggesting that it could still effectively sequester Pol III. Of interest, β E202K supported in vitro DNA replication by Pol II and Pol IV, but was defective with Pol III. Genetic experiments indicated that the dnaN E202K strain remained proficient in DNA damage-induced mutagenesis, but was modestly induced for SOS and displayed sensitivity to ultraviolet light and methyl methanesulfonate. These results correlate an impaired ability of the mutant β E202K clamp to support Pol III replication in vivo with its in vitro defect in DNA replication. Taken together, our results: (i) support the model that sequestration of Pol III contributes to growth inhibition, (ii) argue for existence of an additional mechanism that contributes to lethality and (iii) suggest that physical and functional interactions of the β clamp with Pol III are more extensive than currently appreciated. IMPORTANCE The β clamp plays critically important roles in managing the actions of multiple proteins at the replication fork. However, we lack a molecular understanding of both how the clamp interacts with these different partners, and the mechanisms by which it manages their respective actions. We previously exploited the finding that an elevated cellular level of the β clamp impedes E. coli growth by interfering with DNA replication. Using a genetic selection method, we obtained novel mutant β clamps that fail to inhibit growth. Their analysis revealed that β E202K is unique among them. Our work offers new insights into how the β clamp interacts with and manages the actions of E. coli DNA polymerases II, III and IV.

GENETIC ANALYSIS OF DNA REPLICATION IN BACTERIA: dna B MUTATIONS THAT SUPPRESS dnaC MUTATIONS AND dnaQ MUTATIONS THAT SUPPRESS dnaE MUTATIONS IN SALMONELLA TYPHIMURIUM

Genetics ◽  
1984 ◽  
Vol 108 (1) ◽  
pp. 25-38 ◽  
Author(s):  
Russell Maurer ◽  
Barbara C Osmond ◽  
David Botstein
Keyword(s):  
Dna Replication ◽  
Salmonella Typhimurium ◽  
Target Genes ◽  
E Coli ◽  
Suppressor Mutations ◽  
Extragenic Suppressors ◽  
Derivatives Of ◽  
Functional Homologues

ABSTRACT We have isolated and characterized extragenic suppressors of mutations in two different target genes that affect DNA replication in Salmonella typhimurium. Both the target and the suppressor genes are functional homologues of known replication genes of E. coli that were identified in intergeneric complementation tests. Our results point to interactions in vivo involving the dnaB and dnaC proteins in one case and the dnaQ and dnaE proteins in the other case. The suppressor mutations, which were isolated as derivatives of λ-Salmonella in vitro recombinants, were detected by an adaptation of the red plaque complementation assay. This method was applicable even when the locus of suppressor mutations was not chosen in advance.

scholarly journals A systems-guided approach to discover the intracellular target of a novel evolution-drug lead

2021 ◽  
Author(s):  
Sourav Chowdhury ◽  
Daniel Craig Zielinski ◽  
Christopher Dalldorf ◽  
Joao V Rodrigues ◽  
Bernhard Palsson ◽  
...  
Keyword(s):  
Structural Similarity ◽  
Difficult Problem ◽  
E Coli ◽  
Metabolic Network Analysis ◽  
Drug Lead ◽  
Intracellular Target ◽  
Bacterial Growth Inhibition ◽  
Intracellular Targets

Understanding intracellular antibiotic targeting and the associated mechanisms leading to bacterial growth inhibition has been a difficult problem. Here, we discovered the additional intracellular targets of the novelevolution-drug lead CD15-3 designed to delay the emergence of antibiotic resistance by inhibiting bacterial DHFR and its Trimethoprim resistant variants. Overexpression of DHFR only partially rescued inhibition of E. coli growth by CD15.3 suggesting that CD15.3 also inhibits a non-DHFR target in the cell. We utilized untargeted global metabolomics and the metabolic network analysis along with structural similarity search of the putative targets to identify the additional target of CD15-3. We validated in vivo and in vitro that besides DHFR CD15-3 inhibits HPPK (folK), an essential protein upstream of DHFR in bacterial folate metabolism. This bivalent cellular targeting makes CD15-3 a promising lead to develop a monotherapy analogue of combination drugs.

scholarly journals Defining Stage-Specific Activity of Potent New Inhibitors of Cryptosporidium parvum Growth In Vitro

mBio ◽  
2020 ◽  
Vol 11 (2) ◽  
Author(s):  
Lisa J. Funkhouser-Jones ◽  
Soumya Ravindran ◽  
L. David Sibley
Keyword(s):  
Life Cycle ◽  
Cryptosporidium Parvum ◽  
Specific Activity ◽  
Trna Synthetase ◽  
Mechanisms Of Action ◽  
Cryptosporidium Hominis ◽  
Content Type

ABSTRACT Cryptosporidium parvum and Cryptosporidium hominis have emerged as major enteric pathogens of infants in the developing world, in addition to their known importance in immunocompromised adults. Although there has been recent progress in identifying new small molecules that inhibit Cryptosporidium sp. growth in vitro or in animal models, we lack information about their mechanism of action, potency across the life cycle, and cidal versus static activities. Here, we explored four potent classes of compounds that include inhibitors that likely target phosphatidylinositol 4 kinase (PI4K), phenylalanine-tRNA synthetase (PheRS), and several potent inhibitors with unknown mechanisms of action. We utilized monoclonal antibodies and gene expression probes for staging life cycle development to define the timing of when inhibitors were active during the life cycle of Cryptosporidium parvum grown in vitro. These different classes of inhibitors targeted different stages of the life cycle, including compounds that blocked replication (PheRS inhibitors), prevented the segmentation of daughter cells and thus blocked egress (PI4K inhibitors), or affected sexual-stage development (a piperazine compound of unknown mechanism). Long-term cultivation of C. parvum in epithelial cell monolayers derived from intestinal stem cells was used to distinguish between cidal and static activities based on the ability of parasites to recover from treatment. Collectively, these approaches should aid in identifying mechanisms of action and for designing in vivo efficacy studies based on time-dependent concentrations needed to achieve cidal activity. IMPORTANCE Currently, nitazoxanide is the only FDA-approved treatment for cryptosporidiosis; unfortunately, it is ineffective in immunocompromised patients, has varied efficacy in immunocompetent individuals, and is not approved in infants under 1 year of age. Identifying new inhibitors for the treatment of cryptosporidiosis requires standardized and quantifiable in vitro assays for assessing potency, selectivity, timing of activity, and reversibility. Here, we provide new protocols for defining which stages of the life cycle are susceptible to four highly active compound classes that likely inhibit different targets in the parasite. We also utilize a newly developed long-term culture system to define assays for monitoring reversibility as a means of defining cidal activity as a function of concentration and time of treatment. These assays should provide valuable in vitro parameters to establish conditions for efficacious in vivo treatment.

Elevated levels of the E. coli nrdAB -encoded ribonucleotide reductase counteract the toxicity caused by an increased abundance of the β clamp

2021 ◽  
Author(s):  
Vignesh M. P. Babu ◽  
Caleb Homiski ◽  
Michelle K. Scotland ◽  
Sundari Chodavarapu ◽  
Jon M. Kaguni ◽  
...  
Keyword(s):  
Dna Replication ◽  
Ribonucleotide Reductase ◽  
Growth Defect ◽  
Wild Type ◽  
E Coli ◽  
Elevated Expression ◽  
Catalytic Role ◽  
Pol Iii

Expression of the E. coli dnaN -encoded β clamp at ≥10 fold higher than chromosomally expressed levels impedes growth by interfering with DNA replication. The β E202K clamp (glutamic acid-to-lysine substitution at residue 202) binds to DNA polymerase III (Pol III) with higher affinity compared with the wild type clamp, suggesting that its failure to impede growth is independent of its ability to sequester Pol III away from the replication fork. Our results demonstrate that the dnaN E202K strain underinitiates DNA replication due to insufficient levels of DnaA-ATP and expresses several DnaA-regulated genes at altered levels, including nrdAB that encode the class 1a ribonucleotide reductase (RNR). Elevated expression of nrdAB was dependent on hda function. As the β clamp-Hda complex regulates the activity of DnaA by stimulating its intrinsic ATPase activity, this finding suggests that the dnaN E202K allele supports an elevated level of Hda activity in vivo compared with the wild type strain. In contrast, using an in vitro assay reconstituted with purified components the β E202K and wild type clamp proteins supported comparable levels of Hda activity. Nevertheless, co-overexpression of the nrdAB -encoded RNR relieved the growth defect caused by elevated levels of the β clamp. These results support a model in which increased cellular levels of DNA precursors relieve the ability of elevated β clamp levels to impede growth, and suggest that either multiple effects stemming from the dnaN E202K mutation contribute to elevated nrdAB levels, or Hda plays a non-catalytic role in regulating DnaA-ATP by sequestering it to reduce its availability. IMPORTANCE DnaA bound to ATP acts in initiation of DNA replication and regulates the expression of several genes whose products act in DNA metabolism. The state of the ATP bound to DnaA is regulated in part by the β clamp-Hda complex. The dnaN E202K allele was identified by virtue of its inability to impede growth when expressed at ≥10 fold higher than chromosomally expressed levels. While the dnaN E202K strain exhibits several phenotypes consistent with heightened Hda activity, the wild type and β E202K clamp proteins support equivalent levels of Hda activity in vitro . Taken together, these results suggest that β E202K -Hda plays a non-catalytic role in regulating DnaA-ATP. This as well as alternative models are discussed.

Soluble Thrombomodulin Purified from Human Urine Exhibits a Potent Anticoagulant Effect In Vitro and In Vivo

1995 ◽  
Vol 73 (05) ◽  
pp. 805-811 ◽  
Author(s):  
Yasuo Takahashi ◽  
Yoshitaka Hosaka ◽  
Hiromi Niina ◽  
Katsuaki Nagasawa ◽  
Masaaki Naotsuka ◽  
...  
Keyword(s):  
Human Urine ◽  
Specific Activity ◽  
Anticoagulant Activity ◽  
Rabbit Lung ◽  
Soluble Thrombomodulin ◽  
Molecular Weights ◽  
Dose Dependent Fashion ◽  
Dose Dependent

SummaryWe examined the anticoagulant activity of two major molecules of soluble thrombomodulin purified from human urine. The apparent molecular weights of these urinary thrombomodulins (UTMs) were 72,000 and 79,000, respectively. Both UTMs showed more potent cofactor activity for protein C activation [specific activity >5,000 thrombomodulin units (TMU)/mg] than human placental thrombomodulin (2,180 TMU/mg) and rabbit lung thrombomodulin (1,980 TMU/mg). The UTMs prolonged thrombin-induced fibrinogen clotting time (>1 TMU/ml), APTT (>5 TMU/ml), TT (>5 TMU/ml) and PT (>40 TMU/ml) in a dose-dependent fashion. These effects appeared in the concentration range of soluble thrombomodulins present in human plasma and urine. In the rat DIC model induced by thromboplastin, administration of UTMs by infusion (300-3,000 TMU/kg) restored the hematological abnormalities derived from DIC in a dose-dependent fashion. These results demonstrate that UTMs exhibit potent anticoagulant and antithrombotic activities, and could play a physiologically important role in microcirculation.

Effects of Heparin Oligosaccharides with High Affinity for Antithrombin III in Experimental Venous Thrombosis

1982 ◽  
Vol 47 (03) ◽  
pp. 244-248 ◽  
Author(s):  
D P Thomas ◽  
Rosemary E Merton ◽  
T W Barrowcliffe ◽  
L Thunberg ◽  
U Lindahl
Keyword(s):  
Antithrombin Iii ◽  
Specific Activity ◽  
High Specific Activity ◽  
Factor Xa ◽  
Blood Levels ◽  
Thrombin Time ◽  
High Affinity ◽  
Very High

SummaryThe in vitro and in vivo characteristics of two oligosaccharide heparin fragments have been compared to those of unfractionated mucosal heparin. A decasaccharide fragment had essentially no activity by APTT or calcium thrombin time assays in vitro, but possessed very high specific activity by anti-Factor Xa assays. When injected into rabbits at doses of up to 80 ¼g/kg, this fragment was relatively ineffective in impairing stasis thrombosis despite producing high blood levels by anti-Xa assays. A 16-18 monosaccharide fragment had even higher specific activity (almost 2000 iu/mg) by chromogenic substrate anti-Xa assay, with minimal activity by APTT. When injected in vivo, this fragment gave low blood levels by APTT, very high anti-Xa levels, and was more effective in preventing thrombosis than the decasaccharide fragment. However, in comparison with unfractionated heparin, the 16-18 monosaccharide fragment was only partially effective in preventing thrombosis, despite producing much higher blood levels by anti-Xa assays.It is concluded that the high-affinity binding of a heparin fragment to antithrombin III does not by itself impair venous thrombogenesis, and that the anti-Factor Xa activity of heparin is only a partial expression of its therapeutic potential.

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