Biology subjects

Ledwitch, K.

Publications and source records attributed to Ledwitch, K..

5 recordsLinked to original sources

bioRxiv2026

Profiling the CFTR Variant Selectivity and Off-Target Interactions of VX-121

More than 1,200 variants of the cystic fibrosis transmembrane conductance regulator gene (CFTR) are associated with cystic fibrosis (CF), an autosomal recessive pulmonary disease affecting over 100,000 people. Most people with CF bear a common CFTR variant (F508del) that can be treated with therapeutics containing "correctors" that suppress the misfolding of the CFTR chloride channel. However, the pharmacological responsiveness of other rare CF variants can vary tremendously. The approval of VX-121, a VX-445 analog that serves as a key component of AlyftrekTM, potentially provides a new therapeutic option for those with rare CF variants. Nevertheless, it remains unclear whether VX-121 offers superior rescue across the entire spectrum of rare CF variants. In this work, we use deep mutational scanning (DMS) to survey the impact of VX-121 on the plasma membrane expression of 232 rare CF variants. Our results show that VX-121 generally enhances CF variant expression more than VX-445 and is most potent towards variants with mutations in the first membrane spanning domain (MSD1). However, we identify one variant (Y1032C) with diminished proteostatic and functional selectivity for VX-121 relative to VX-445. Computational docking suggests that the native Y1032 side chain forms favorable interactions with VX-121 that are disrupted by this mutation in a manner that alters its coordination. Finally, using photo-crosslinking, we show that VX-121 avoids a key off-target interaction of VX-445. Together, our findings provide new insights into the similarities and differences between current approved CF therapeutics.

pharmacology and toxicology↗

bioRxiv2025

High Throughput Screening Identifies a Small Molecule Trafficking Corrector for Long-QT Syndrome Associated KCNQ1 Variants

Congenital long QT syndrome (LQTS) promotes risk for life-threatening cardiac arrhythmia and sudden death in children and young adults. Pathogenic variants in the voltage-gated potassium channel KCNQ1 are the most frequently discovered genetic cause. Most LQTS-associated KCNQ1 variants cause loss-of-function secondary to impaired trafficking of the channel to the plasma membrane. There are currently no therapeutic approaches that address this underlying molecular defect. Using a high throughput screening paradigm, we identified VU0494372, a small molecule that increases total and cell surface expression, and trafficking efficiency of wildtype (WT) KCNQ1 as well as three LQTS-associated variants. Additionally, 16-hour treatment of cells with VU0494372 increased current density for WT KCNQ1 and the LQTS-associated variant V207M. VU0494372 had no impact on KCNQ1 transcription, degradation, or thermal stability. We identified a potential direct interaction site with KCNQ1 at or near the binding site of the KCNQ1 potentiator ML277. Together, these findings demonstrate that small molecules can increase the expression levels and cell surface trafficking of KCNQ1 and introduce a potential new pharmacological approach for treating LQTS.

biochemistry↗

bioRxiv2022

Rosetta 's Predictive Ability for Low-Affinity Ligand Binding in Fragment-Based Drug Discovery

Fragment-based drug discovery begins with the identification of small molecules with a molecular weight of usually less than 250 Da that weakly bind to the protein of interest. This technique is challenging for computational docking methods as binding is determined by only a few specific interactions. Inaccuracies in the energy function or slight deviations in the docking pose can lead to the prediction of incorrect binding or difficulties in ranking fragments in in silico screening. Here we test RosettaLigand by docking a series of fragments to a cysteine-depleted variant of the TIM-barrel protein, HisF. We compare the computational results with experimental NMR spectroscopy screens. NMR spectroscopy gives details on binding affinities of individual ligands, which allows assessment of the ligand-ranking ability by RosettaLigand, and also provides feedback on the location of the binding pocket, which serves as a reliable test of RosettaLigands ability to identify plausible binding poses. From a library screen of 3456 fragments, we identified a set of 31 ligands with intrinsic affinities to HisF with dissociation constants as low as 400 {micro}M. The same library of fragments was blindly screened in silico. RosettaLigand was able to rank binders before non-binders with an area under the curve (AUC) of the receiver operating characteristics (ROC) of 0.74. The docking poses observed for binders agreed with the binding pocket identified by NMR chemical shift perturbations for all fragments. Taken together, these results provide a baseline performance of RosettaLigand in a fragment-based drug discovery setting.

biochemistry↗

bioRxiv2022

First crystal structure of a non-canonical amino acid linked to a paramagnetic lanthanide tag facilitates protein structure determination using NMR-derived restraints

Site-directed spin labeling of proteins via non-canonical amino acids (ncAAs) is a non-traditional method for the measurement of pseudocontact shifts (PCSs) by nuclear magnetic resonance (NMR) spectroscopy. PCSs provide long-range distance and orientational information between a paramagnetic center and protein nuclei that can be used as restraints for computational structural modeling techniques. Here, we present the first experimental structure of an ncAA chemically linked to a lanthanide tag conjugated to the protein, T4-Lysozyme (T4L). T4L was crystallized with a cyclen-based C3 tag coordinated to the paramagnetic ion terbium (Tb3+). The paramagnetic C3-lanthanide tag generated PCSs measured at four different ncAA sites. We show that the addition of these restraints improves structure prediction protocols for T4L using the RosettaNMR framework. Generated models provide insight into T4L conformational flexibility sampled in solution. This integrative modeling protocol is readily transferable to larger proteins. Methods to predict protein structures are advancing into an exciting arena such that reliable experimental data will play important roles for evaluating the biophysical relevance of predicted structural models. Our contribution here caters to the growing interest in using ncAAs for a range of biophysical studies, and these methods can be readily transferred to larger protein systems of interest.

biophysics↗

bioRxiv2021

Psychomotor impairments and therapeutic implications revealed by a mutation linked with Infantile Parkinsonism-Dystonia

Parkinson disease (PD) is a progressive, neurodegenerative disorder affecting over 6.1 million people worldwide. Although the cause of PD remains unclear, studies of highly-penetrant mutations identified in early-onset familial parkinsonism have contributed to our understanding of the molecular mechanisms underlying disease pathology. Dopamine (DA) transporter (DAT) deficiency syndrome (DTDS) is a distinct type of infantile parkinsonism-dystonia that shares key clinical features with PD, including motor deficits (progressive bradykinesia, tremor, hypomimia) and altered DA neurotransmission. Here, we define structural, functional, and behavioral consequences of a Cys substitution at R445 in human DAT (hDAT R445C), identified in a patient with DTDS. We found that this R445 substitution disrupts a phylogenetically conserved intracellular (IC) network of interactions that compromise the hDAT IC gate. This is demonstrated by both Rosetta molecular modeling and fine-grained simulations using hDAT R445C, as well as EPR analysis and X-ray crystallography of the bacterial homolog leucine transporter. Notably, the disruption of this IC network of interactions supported a channel-like intermediate of hDAT and compromised hDAT function. We demonstrate that Drosophila melanogaster expressing hDAT R445C show impaired hDAT activity, which is associated with DA dysfunction in isolated brains and with abnormal behaviors monitored at high-speed time resolution. We show that hDAT R445C Drosophila exhibit motor deficits, lack of motor coordination (i.e. flight coordination) and phenotypic heterogeneity in these behaviors that is typically associated with DTDS and PD. These behaviors are linked with altered dopaminergic signaling stemming from loss of DA neurons and decreased DA availability. We rescued flight coordination through enhanced DAT surface expression via the lysosomal inhibitor chloroquine. Together, these studies shed light on how a DTDS-linked DAT mutation underlies DA dysfunction and, more broadly, the clinical phenotypes shared by DTDS and PD.

neuroscience↗