scholarly journals Development of antibacterial compounds that constrain evolutionary pathways to resistance

eLife ◽  
2021 ◽  
Vol 10 ◽  
Author(s):  
Yanmin Zhang ◽  
Sourav Chowdhury ◽  
João V Rodrigues ◽  
Eugene I Shakhnovich
Keyword(s):  
Dihydrofolate Reductase ◽  
Experimental Approach ◽  
Whole Genome ◽  
Bacterial Protein ◽  
Antibacterial Compounds ◽  
E Coli ◽  
Resistant Strains ◽  
Evolutionary Pathways ◽  
Resistant Mutants

Antibiotic resistance is a worldwide challenge. A potential approach to block resistance is to simultaneously inhibit WT and known escape variants of the target bacterial protein. Here we applied an integrated computational and experimental approach to discover compounds that inhibit both WT and trimethoprim (TMP) resistant mutants of E. coli dihydrofolate reductase (DHFR). We identified a novel compound (CD15-3) that inhibits WT DHFR and its TMP resistant variants L28R, P21L and A26T with IC50 50-75 µM against WT and TMP-resistant strains. Resistance to CD15-3 was dramatically delayed compared to TMP in in vitro evolution. Whole genome sequencing of CD15-3 resistant strains showed no mutations in the target folA locus. Rather, gene duplication of several efflux pumps gave rise to weak (about twofold increase in IC50) resistance against CD15-3. Altogether, our results demonstrate the promise of strategy to develop evolution drugs - compounds which constrain evolutionary escape routes in pathogens.

scholarly journals Development of evolution drugs - antibacterial compounds that block pathways to resistance

2020 ◽  
Author(s):  
Yanmin Zhang ◽  
Sourav Chowdhury ◽  
João V. Rodrigues ◽  
Eugene Shakhnovich
Keyword(s):  
Antibiotic Resistance ◽  
Dihydrofolate Reductase ◽  
Experimental Approach ◽  
Whole Genome ◽  
Bacterial Protein ◽  
Antibacterial Compounds ◽  
E Coli ◽  
Resistant Strains ◽  
Resistant Mutants

AbstractAntibiotic resistance is a worldwide challenge. A potential approach to block resistance is to simultaneously inhibit WT and known escape variants of the target bacterial protein. Here we applied an integrated computational and experimental approach to discover compounds that inhibit both WT and trimethoprim (TMP) resistant mutants of E. coli dihydrofolate reductase (DHFR). We identified a novel compound (CD15-3) that inhibits WT DHFR and its TMP resistant variants L28R, P21L and A26T with IC50 50-75 μM against WT and TMP-resistant strains. Resistance to CD15-3 was dramatically delayed compared to TMP in in vitro evolution. Whole genome sequencing of CD15-3 resistant strains showed no mutations in the target folA locus. Rather, gene duplication of several efflux pumps gave rise to weak (about twofold increase in IC50) resistance against CD15-3. Altogether, our results demonstrate the promise of strategy to develop evolution drugs - compounds which block evolutionary escape routes in pathogens.

scholarly journals Switching an active site helix in dihydrofolate reductase reveals limits to sub-domain modularity

2021 ◽  
Author(s):  
Victor Y. Zhao ◽  
João V. Rodrigues ◽  
Elena R. Lozovsky ◽  
Daniel L. Hartl ◽  
Eugene I. Shakhnovich
Keyword(s):  
Catalytic Activity ◽  
Dihydrofolate Reductase ◽  
Strongly Correlated ◽  
Thermal Stabilities ◽  
E Coli ◽  
In Vitro Measurements ◽  
Flux Model ◽  
Α Helix ◽  
Dynamics Simulations

To what degree are individual structural elements within proteins modular such that similar structures from unrelated proteins can be interchanged? We study sub-domain modularity by creating 20 chimeras of an enzyme, E. coli dihydrofolate reductase (DHFR), in which a catalytically important, 10-residue α-helical sequence is replaced by α-helical sequences from a diverse set of proteins. The chimeras stably fold but have a range of diminished thermal stabilities and catalytic activities. Evolutionary coupling analysis indicates that the residues of this α-helix are under selection pressure to maintain catalytic activity in DHFR. We performed molecular dynamics simulations using replica exchange with solute-tempering. Chimeras with low catalytic activity exhibit non-helical conformations that block the binding site and disrupt the positioning of the catalytically essential residue D27. Simulation observables and in vitro measurements of thermal stability and substrate binding affinity are strongly correlated. Several E. coli strains with chromosomally integrated chimeric DHFRs can grow, with growth rates that follow predictions from a kinetic flux model that depends on the intracellular abundance and catalytic activity of DHFR. Our findings show that although α-helices are not universally substitutable, the molecular and fitness effects of modular segments can be predicted by the biophysical compatibility of the replacement segment.

scholarly journals Mutations Conferring Aminoglycoside and Spectinomycin Resistance in Borrelia burgdorferi

2006 ◽  
Vol 50 (2) ◽  
pp. 445-452 ◽  
Author(s):  
Daniel Criswell ◽  
Virginia L. Tobiason ◽  
J. Stephen Lodmell ◽  
D. Scott Samuels
Keyword(s):  
16S Rrna ◽  
Borrelia Burgdorferi ◽  
Type Strain ◽  
Wild Type Strain ◽  
Small Subunit ◽  
Wild Type ◽  
Spectinomycin Resistance ◽  
E Coli ◽  
Resistant Mutants

ABSTRACT We have isolated and characterized in vitro mutants of the Lyme disease agent Borrelia burgdorferi that are resistant to spectinomycin, kanamycin, gentamicin, or streptomycin, antibiotics that target the small subunit of the ribosome. 16S rRNA mutations A1185G and C1186U, homologous to Escherichia coli nucleotides A1191 and C1192, conferred >2,200-fold and 1,300-fold resistance to spectinomycin, respectively. A 16S rRNA A1402G mutation, homologous to E. coli A1408, conferred >90-fold resistance to kanamycin and >240-fold resistance to gentamicin. Two mutations were identified in the gene for ribosomal protein S12, at a site homologous to E. coli residue Lys-87, in mutants selected in streptomycin. Substitutions at codon 88, K88R and K88E, conferred 7-fold resistance and 10-fold resistance, respectively, to streptomycin on B. burgdorferi. The 16S rRNA A1185G and C1186U mutations, associated with spectinomycin resistance, appeared in a population of B. burgdorferi parental strain B31 at a high frequency of 6 × 10−6. These spectinomycin-resistant mutants successfully competed with the wild-type strain during 100 generations of coculture in vitro. The aminoglycoside-resistant mutants appeared at a frequency of 3 × 10−9 to 1 ×10−7 in a population and were unable to compete with wild-type strain B31 after 100 generations. This is the first description of mutations in the B. burgdorferi ribosome that confer resistance to antibiotics. These results have implications for the evolution of antibiotic resistance, because the 16S rRNA mutations conferring spectinomycin resistance have no significant fitness cost in vitro, and for the development of new selectable markers.

scholarly journals Antibacterial activities of epiroprim, a new dihydrofolate reductase inhibitor, alone and in combination with dapsone.

1996 ◽  
Vol 40 (6) ◽  
pp. 1376-1381 ◽  
Author(s):  
H H Locher ◽  
H Schlunegger ◽  
P G Hartman ◽  
P Angehrn ◽  
R L Then
Keyword(s):  
Dihydrofolate Reductase ◽  
Biological Fluids ◽  
Pneumocystis Carinii ◽  
Antibacterial Activities ◽  
Gram Negative Bacteria ◽  
Highly Active ◽  
Excellent Activity ◽  
Resistant Strains ◽  
Better Than

Epiroprim (EPM; Ro 11-8958) is a new selective inhibitor of microbial dihydrofolate reductase. EPM displayed excellent activity against staphylococci, enterococci, pneumococci, and streptococci which was considerably better than that of trimethoprim (TMP). EPM was also active against TMP-resistant strains, although the MICs were still relatively high. Its combination with dapsone (DDS) was synergistic and showed as in vitro activity superior to that of the TMP combination with sulfamethoxazole (SMZ). The EPM-DDS (ratio, 1:19) combination inhibited more than 90% of all important gram-positive pathogens at a concentration of 2 + 38 micrograms/ml. Only a few highly TMP-resistant staphylococci and enterococci were not inhibited. EPM was also more active than TMP against Moraxella catarrhalis, Neisseria meningitidis, and Bacteroides spp., but it was less active than TMP against all other gram-negative bacteria tested. Atypical mycobacteria were poorly susceptible to EPM, but the combination with DDS was synergistic and active at concentrations most probably achievable in biological fluids (MICs from 0.25 +/- 4.75 to 4 + 76 micrograms/ml). EPM and the EPM-DDS combination were also highly active against experimental staphylococcal infections in a mouse septicemia model. The combination EPM-DDS has previously been shown to exhibit activity in Pneumocystis carinii and Toxoplasma models and, as shown in the present study, also shows good activity against a broad range of bacteria including many strains resistant to TMP and TMP-SMZ.

scholarly journals In Vitro Activity of a Novel Siderophore-Cephalosporin, GT-1 and Serine-Type β-Lactamase Inhibitor, GT-055, against Escherichia coli, Klebsiella pneumoniae and Acinetobacter spp. Panel Strains

Antibiotics ◽  
2020 ◽  
Vol 9 (5) ◽  
pp. 267 ◽  
Author(s):  
Le Phuong Nguyen ◽  
Naina Adren Pinto ◽  
Thao Nguyen Vu ◽  
Hyunsook Lee ◽  
Young Lag Cho ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Klebsiella Pneumoniae ◽  
Vitro Activity ◽  
Intrinsic Activity ◽  
In Vitro Activity ◽  
E Coli ◽  
Acinetobacter Spp ◽  
Resistant Strains ◽  
Lactamase Inhibitor

This study investigates GT-1 (also known as LCB10-0200), a novel-siderophore cephalosporin, inhibited multidrug-resistant (MDR) Gram-negative pathogen, via a Trojan horse strategy exploiting iron-uptake systems. We investigated GT-1 activity and the role of siderophore uptake systems, and the combination of GT-1 and a non-β-lactam β-lactamase inhibitor (BLI) of diazabicyclooctane, GT-055, (also referred to as LCB18-055) against molecularly characterised resistant Escherichia coli, Klebsiella pneumoniae and Acinetobacter spp. isolates. GT-1 and GT-1/GT-055 were tested in vitro against comparators among three different characterised panel strain sets. Bacterial resistome and siderophore uptake systems were characterised to elucidate the genetic basis for GT-1 minimum inhibitory concentrations (MICs). GT-1 exhibited in vitro activity (≤2 μg/mL MICs) against many MDR isolates, including extended-spectrum β-lactamase (ESBL)- and carbapenemase-producing E. coli and K. pneumoniae and oxacillinase (OXA)-producing Acinetobacter spp. GT-1 also inhibited strains with mutated siderophore transporters and porins. Although BLI GT-055 exhibited intrinsic activity (MIC 2–8 μg/mL) against most E. coli and K. pneumoniae isolates, GT-055 enhanced the activity of GT-1 against many GT-1–resistant strains. Compared with CAZ-AVI, GT-1/GT-055 exhibited lower MICs against E. coli and K. pneumoniae isolates. GT-1 demonstrated potent in vitro activity against clinical panel strains of E. coli, K. pneumoniae and Acinetobacter spp. GT-055 enhanced the in vitro activity of GT-1 against many GT-1–resistant strains.

scholarly journals In Vitro and In Vivo Antibacterial Activities of SM-216601, a New Broad-Spectrum Parenteral Carbapenem

2005 ◽  
Vol 49 (10) ◽  
pp. 4185-4196 ◽  
Author(s):  
Yutaka Ueda ◽  
Katsunori Kanazawa ◽  
Ken Eguchi ◽  
Koji Takemoto ◽  
Yoshiro Eriguchi ◽  
...  
Keyword(s):  
Bacterial Infections ◽  
Antibacterial Activities ◽  
Multiresistant Pathogens ◽  
E Coli ◽  
Wide Range ◽  
Agar Dilution ◽  
Resistant Strains ◽  
Mrsa Strains

ABSTRACT SM-216601 is a novel parenteral 1β-methylcarbapenem. In agar dilution susceptibility testing, the MIC of SM-216601 for 90% of the methicillin-resistant Staphylococcus aureus (MRSA) strains tested (MIC90) was 2 μg/ml, which was comparable to those of vancomycin and linezolid. SM-216601 was also very potent against Enterococcus faecium, including vancomycin-resistant strains (MIC90 = 8 μg/ml). SM-216601 exhibited potent activity against penicillin-resistant Streptococcus pneumoniae, ampicillin-resistant Haemophilus influenzae, Moraxella catarrhalis, Escherichia coli, Klebsiella pneumoniae, and Proteus mirabilis, with MIC90s of less than 0.5 μg/ml, and intermediate activity against Citrobacter freundii, Enterobacter cloacae, Serratia marcescens, and Pseudomonas aeruginosa. The therapeutic efficacy of SM-216601 against experimentally induced infections in mice caused by S. aureus, E. faecium, E. coli, and P. aeruginosa reflected its in vitro activity and plasma level. Thus, SM-216601 is a promising candidate for nosocomial bacterial infections caused by a wide range of gram-positive and gram-negative bacteria, including multiresistant pathogens.

Efficient expression of E. coli dihydrofolate reductase gene by an in vitro translation system using phosphorothioate mRNA

1994 ◽  
Vol 34 (1) ◽  
pp. 61-69 ◽  
Author(s):  
Hideki Tohda ◽  
Nobutoshi Chikazumi ◽  
Takuya Ueda ◽  
Kazuya Nishikawa ◽  
Kimitsuna Watanabe
Keyword(s):  
Dihydrofolate Reductase ◽  
In Vitro Translation ◽  
Translation System ◽  
E Coli ◽  
Reductase Gene ◽  
Efficient Expression

scholarly journals In Vitro Activity of CEM-101 against Streptococcus pneumoniae and Streptococcus pyogenes with Defined Macrolide Resistance Mechanisms

2009 ◽  
Vol 54 (1) ◽  
pp. 230-238 ◽  
Author(s):  
Pamela McGhee ◽  
Catherine Clark ◽  
Klaudia M. Kosowska-Shick ◽  
Kensuke Nagai ◽  
Bonifacio Dewasse ◽  
...  
Keyword(s):  
Streptococcus Pyogenes ◽  
Bacterial Species ◽  
Resistance Mechanisms ◽  
Macrolide Resistance ◽  
23S Rrna ◽  
Resistant Strains ◽  
Resistant Mutants ◽  
The One ◽  
Selection Of

ABSTRACT CEM-101 had MIC ranges of 0.002 to 0.016 μg/ml against macrolide-susceptible pneumococci and 0.004 to 1 μg/ml against macrolide-resistant phenotypes. Only 3 strains with erm(B), with or without mef(A), had CEM-101 MICs of 1 μg/ml, and 218/221 strains had CEM-101 MICs of ≤0.5 μg/ml. CEM-101 MICs were as much as 4-fold lower than telithromycin MICs against all strains. For Streptococcus pyogenes, CEM-101 MICs ranged from 0.008 to 0.03 μg/ml against macrolide-susceptible strains and from 0.015 to 1 μg/ml against macrolide-resistant strains. Against erm(B) strains, erythromycin, azithromycin, and clarithromycin MICs were 32 to >64 μg/ml, while 17/19 strains had telithromycin MICs of 4 to 16 μg/ml; CEM-101 MICs were 0.015 to 1 μg/ml. By comparison, erm(A) and mef(A) strains had CEM-101 MICs of 0.015 to 0.5 μg/ml, clindamycin and telithromycin MICs of ≤1 μg/ml, and erythromycin, azithromycin, and clarithromycin MICs of 0.5 to >64 μg/ml. Pneumococcal multistep resistance studies showed that although CEM-101 yielded clones with higher MICs for all eight strains tested, seven of eight strains had clones with CEM-101 MICs that rose from 0.004 to 0.03 μg/ml (parental strains) to 0.06 to 0.5 μg/ml (resistant clones); for only one erm(B) mef(A) strain with a parental MIC of 1 μg/ml was there a resistant clone with a MIC of 32 μg/ml, with no detectable mutations in the L4, L22, or 23S rRNA sequence. Among two of five S. pyogenes strains tested, CEM-101 MICs rose from 0.03 to 0.25 μg/ml, and only for the one strain with erm(B) did CEM-101 MICs rise from 1 to 8 μg/ml, with no changes occurring in any macrolide resistance determinant. CEM-101 had low MICs as well as low potential for the selection of resistant mutants, independent of bacterial species or resistance phenotypes in pneumococci and S. pyogenes.

scholarly journals Effects of oxygen on aerosol survival of radiation sensitive and resistant strains ofEscherichia coliB

1971 ◽  
Vol 69 (4) ◽  
pp. 661-672 ◽  
Author(s):  
C. S. Cox ◽  
M. C. Bondurant ◽  
M. T. Hatch
Keyword(s):  
Escherichia Coli ◽  
Relative Humidity ◽  
Metabolic Activity ◽  
Radiation Sensitivity ◽  
The Other ◽  
E Coli ◽  
Radiation Induced ◽  
Resistant Strains ◽  
Resistant Mutants ◽  
Survival In Air

SUMMARYThe aerosol survivals in air and nitrogen of radiation sensitive and resistant mutants ofEscherichia coliB have been determined with logarithmic and resting phase bacteria. No consistent correlation was found between radiation sensitivity and aerosol sensitivity in the strains tested. Hence, the phenotypes Fil Her Exr, which determine sensitivity to radiation, do not influence aerosol survival, i.e. these known mechanisms which repair radiation-induced damage do not operate in aerosol stressedE. coli. In all cases the survival in air was less than that in nitrogen particularly so forE. coliBs-1. The effect is explained in terms of a toxic action of oxygen. Comparison of survival of log and resting phase bacteria show that log phase cells are less aerosol stable than are resting phase cells. The ability to synthesize DNA in bacteria collected from the aerosol was less than in control unstressed bacteria, and this effect was independent of the presence of oxygen. Reduced ability to synthesize DNA could have been caused by reduced metabolic activity. It is shown that two different death mechanisms occur simultaneously in aerosols at low relative humidity. One mechanism is oxygen dependent and the other oxygen independent. The former was not through a decrease in metabolic activity, whereas the latter could be.

scholarly journals Trimethoprim-resistant mutants ofE. coliK12: preliminary genetic mapping

1975 ◽  
Vol 25 (3) ◽  
pp. 207-214 ◽  
Author(s):  
A. S. Breeze ◽  
P. Sims ◽  
K. A. Stacey
Keyword(s):  
Genetic Mapping ◽  
Structural Gene ◽  
Dihydrofolate Reductase ◽  
Bacteriophage P1 ◽  
E Coli ◽  
Resistant Mutants ◽  
High Level ◽  
Increased Activity ◽  
Level Resistance ◽  
Target Enzyme

SUMMARYTrimethoprim-resistant mutants ofE. coliK12 have been isolated by-serial subculture in progressively higher concentrations of trimethoprim. High-level resistance depends on the accumulation of several mutational changes. Transduction with bacteriophage P1 has shown that all the mutations involved in resistance are associated with a locus, to be calledtmr, betweenpyr AandpdxAand closely linked topdxA. Resistance is accompanied by, and presumably due to, an increased activity of the target enzyme, dihydrofolate reductase. Thetmrlocus may include the structural gene for dihydrofolate reductase but the only mutations that have so far been observed are concerned with regulation.

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