MECHANISMS OF IMINE-BASED INHIBITORS OF DAHP SYNTHASE, AN ANTIMICROBIAL TARGET.
Bibliographic record
Abstract
Bacterial 3-deoxy-D-arabinoheptulosonate 7-phosphate synthase (DAHPS) is an antimicrobial target. A transition state (TS) mimic inhibitor of DAHPS, DAHP oxime, was developed in our lab, with Ki = 1.5 μM. Despite being a potent inhibitor, some of DAHP oxime’s properties could hinder its efficacy in blocking bacterial growth. One problem was that DAHP oxime bound competitively with respect to the metal cofactor, Mn2+. Identifying the origin of this competition was crucial for in vivo success of DAHPS inhibitors, as the abundance of metal ions in living cells could hinder DAHP oxime’s effectiveness. Mutant enzymes and fragment-based inhibitors demonstrated that the competition originated in interactions involving the O4 hydroxyl of DAHP oxime and residues Asp326, and Cys61. This suggested improved inhibitor designs to avoid metal competition. Another drawback was the highly negatively charged nature of DAHP oxime and other DAHPS inhibitors. The charge hindered cell membrane penetration, and therefore its effectiveness in cells. Truncating DAHP oxime to a fragment reduced its hydrophilicity and charge, while the introduction of fluorine in the oxime’s α-position increased potency. DAHPS-specific bacterial growth inhibition was obtained with this fragment. DAHPS inhibition by high DAHP oxime concentrations resulted in a 15% residual activity. This residual activity would be sufficient for bacterial survival, so two derivatives, DAHP hydrazone and DAHP O-(2-fluoroethyl) oxime that showed complete inhibition were characterized. DAHP hydrazone was successfully co-crystallized with DAHPS. Its 100-fold higher potency relative to DAHP oxime was attributed to an extra water bound in the active site. The inhibitor bound in all four of the enzyme’s subunits. However, the observed subunit asymmetry showed that the subunits communicate with each other and that there is a significant energetic penalty to enforcing full subunit symmetry.
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How this classification was reachedexpand
Full frame distilled prediction
Teacher imitationNot calibrated prevalence, not ground truth. Human validation pending. Learned from the 10,348 direct Codex labels and 10,348 direct Gemma labels. Candidate is the union of thresholded teacher heads; consensus is their intersection. These outputs are machine_predicted_unvalidated and are not human labels or direct frontier model labels.
Codex and Gemma teacher scores by category
| Category | Codex | Gemma |
|---|---|---|
| Metaresearch | 0.000 | 0.000 |
| Meta-epidemiology (narrow) | 0.000 | 0.000 |
| Meta-epidemiology (broad) | 0.000 | 0.000 |
| Bibliometrics | 0.000 | 0.000 |
| Science and technology studies | 0.000 | 0.000 |
| Scholarly communication | 0.000 | 0.000 |
| Open science | 0.000 | 0.000 |
| Research integrity | 0.000 | 0.000 |
| Insufficient payload (model declined to judge) | 0.005 | 0.000 |
Machine scores (provisional)
The two teacher heads of the student model, read on this work. A score orders the frame for review; it never asserts a category, and the validation status ships verbatim with every row.
Baseline scores from an immature model (maturity gate not passed, 7 training rounds). Scores rank; they never assert a category.
score_only:v0-immature-baseline · verbatim from the scoring run: score_only means the number may rank works, and no category label ships from itClassification
machine, unvalidatedMachine predicted; a candidate call from one teacher head, not a consensus.
How this classification was reached, model by model and score by score, is at the end of the page under "How this classification was reached".