Mechanism-guided Discovery of Fluoroacetate Dehalogenase (FAcD) Variants for Enzymatic PFAS Defluorination
- 1Section of Plant Glycobiology, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C-1871, Denmark.
Abstract
Per- and polyfluoroalkyl substances (PFAS) are persistent anthropogenic "forever chemicals" whose strong C-F bonds (~460-533 kJ mol-1) resist defluorination, and the recast EU Drinking Water Directive sets parametric values of 0.10 ug L-1 for the sum of 20 specified PFAS and 0.50 ug L-1 for total PFAS. Here, we present DeFluorX, a mechanism-first pipeline that uses Boltz-2 to co-fold 2,150 bacterial fluoroacetate dehalogenase (FAcD) variants with 26 PFAS and fluoroacetate, generating uniformly high model confidence (rho = +0.08) but poorly tracked catalytic competence. Thus, the complexes were ranked and tiered by SN2-defluorination geometry based on the known mechanism of control of FAcDs RPA1163 with fluoroacetate: Odelta...C-alpha distance and Odelta-C-alpha-F angle; relay; carboxylate clamp; F-stabiliser; F-cradle; and penalties for scissile bond strength, backside occlusion, beta-fluorination and bond multiplicity. The tiering identified eight complexes (med angle 173.2 degrees, distance 2.91 A) with a high probability of degradation, including Alphaproteobacterial enzymes, with mono-, di- and trifluoroacetate attacking at 172-178 degrees versus 163 degrees for the control. We performed WaterMap, restrained 1 us Desmond MD, MM-GBSA and scans of the three WaterMap-aware best MD frames per complex using B3LYP/6-31G** QM/MM. All 12 frames exhibited product-end C-F cleavage with barriers ranging from 1.1 to 11.8 kcal mol-1, and the departing fluoride carried -0.43 to -0.63 e. The Laboratory validation is ongoing.
Related
- Integrative Single-Cell Transcriptomics and Explainable AI for Disease Mechanism and Biomarker Discovery in Triple-Negative Breast Cancer
- Enzymatic glycosylation of rooibos plant extract to improve stability of active compounds
- Thymol as a potential botanical insecticide against Tuta absoluta: life history parameters, toxicity and enzymatic responses
- Enzymatic attachment of antigens to probe immune modulation by skin commensals
- Early signaling events as vital regulators of enzymatic browning in fresh-cut fruits and vegetables: a mini-review
BibTeX
@misc{ahmad2026mechanismguided,
title = {{Mechanism-guided Discovery of Fluoroacetate Dehalogenase (FAcD) Variants for Enzymatic PFAS Defluorination}},
author = {S. Ahmad and A. Forouzandeh and B. Togni and J. B. Randloev and M. Ogden and T. K. Nielsen},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.11.758284},
url = {https://www.biorxiv.org/content/10.64898/2026.10.11.758284v1},
note = {CC BY-NC},
}
RIS
TY - UNPB
TI - Mechanism-guided Discovery of Fluoroacetate Dehalogenase (FAcD) Variants for Enzymatic PFAS Defluorination
AU - S. Ahmad
AU - A. Forouzandeh
AU - B. Togni
AU - J. B. Randloev
AU - M. Ogden
AU - T. K. Nielsen
PY - 2026
DA - 2026/10/11
PB - bioRxiv
DO - 10.64898/2026.10.11.758284
UR - https://www.biorxiv.org/content/10.64898/2026.10.11.758284v1
AB - Per- and polyfluoroalkyl substances (PFAS) are persistent anthropogenic "forever chemicals" whose strong C-F bonds (~460-533 kJ mol-1) resist defluorination, and the recast EU Drinking Water Directive sets parametric values of 0.10 ug L-1 for the sum of 20 specified PFAS and 0.50 ug L-1 for total PFAS. Here, we present DeFluorX, a mechanism-first pipeline that uses Boltz-2 to co-fold 2,150 bacterial fluoroacetate dehalogenase (FAcD) variants with 26 PFAS and fluoroacetate, generating uniformly high model confidence (rho = +0.08) but poorly tracked catalytic competence. Thus, the complexes were ranked and tiered by SN2-defluorination geometry based on the known mechanism of control of FAcDs RPA1163 with fluoroacetate: Odelta...C-alpha distance and Odelta-C-alpha-F angle; relay; carboxylate clamp; F-stabiliser; F-cradle; and penalties for scissile bond strength, backside occlusion, beta-fluorination and bond multiplicity. The tiering identified eight complexes (med angle 173.2 degrees, distance 2.91 A) with a high probability of degradation, including Alphaproteobacterial enzymes, with mono-, di- and trifluoroacetate attacking at 172-178 degrees versus 163 degrees for the control. We performed WaterMap, restrained 1 us Desmond MD, MM-GBSA and scans of the three WaterMap-aware best MD frames per complex using B3LYP/6-31G** QM/MM. All 12 frames exhibited product-end C-F cleavage with barriers ranging from 1.1 to 11.8 kcal mol-1, and the departing fluoride carried -0.43 to -0.63 e. The Laboratory validation is ongoing.
ER -