Biology subjects

Dickson, C. J.

Publications and source records attributed to Dickson, C. J..

5 recordsLinked to original sources

bioRxiv2025

An analysis of free energy methods to quantify and displace the KRasG12D Thr58 water

The KRasG12D mutant is an attractive target in oncology and can now be drugged via the switch-II allosteric pocket. Non-covalent ligands typically bind in the presence of a conserved structural water, which interacts with Thr58 and Gly10. In this work, we use a dataset of published non-covalent KRasG12D inhibitors to evaluate free energy methods for the interaction with or displacement of this conserved water molecule. We find that the Thr58 water and a second proximal water site are predicted to be unstable relative to bulk water and that relative binding free energy methods capture suitably well the binding affinities of ligands that disturb or replace these waters. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=62 SRC="FIGDIR/small/648534v1_ufig1.gif" ALT="Figure 1"> View larger version (17K): org.highwire.dtl.DTLVardef@172f751org.highwire.dtl.DTLVardef@cb2314org.highwire.dtl.DTLVardef@6c1e75org.highwire.dtl.DTLVardef@43d21d_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2024

A cereblon (CRBN) molecular glue degrader of NIMA-related kinase 7 (NEK7) reveals a context-dependent role in NLRP3 inflammasome activation

The NLRP3 (NACHT-, leucine-rich repeat [LRR]- and pyrin domain [PYD]- containing protein 3) inflammasome is a cytoplasmic signaling complex that promotes inflammation in response to signals from infection and cellular damage. Increased activation of the NLRP3 inflammasome is linked to numerous diseases including gout, osteoarthritis, cardiovascular disease, neuroinflammatory diseases and cancer, which has prompted the search for therapeutics that can inhibit the NLRP3 pathway. Recent work suggested that NIMA-related kinase 7 (NEK7) may be required for proper assembly and activation of the NLRP3 inflammasome independent of its kinase activity, and that hence reduction of NEK7 protein levels may block NLRP3 activation. Since NEK7 contains a glycine beta hairpin loop structural degron found in many targets of cereblon (CRBN) molecular glue degraders, we used this strategy to degrade NEK7 and inhibit the NLRP3 inflammasome. We identified NK7-902, a CRBN glue degrader of NEK7. NK7-902 potently and selectively degraded NEK7 in human primary monocytes, peripheral blood mononuclear cells (PBMCs) and whole blood. Unexpectedly, full NEK7 degradation led to only partial blockade of NLRP3-dependent interleukin-1{beta} (IL-1{beta}) release in these cells under different stimulation conditions, with the extent of IL-1{beta} inhibition varying greatly across donors. Unlike most CRBN glue degraders, NK7-902 degraded NEK7 in mouse cells and efficiently inhibited NLRP3-dependent IL-1{beta} release in a mouse cryopyrin-associated syndrome (CAPS) model. By contrast, oral administration of NK7-902 in non-human primates led to profound and long lasting NEK7 degradation but only transiently blocked IL-1{beta} production in blood. Collectively, our data suggest that NEK7 is involved but may not be strictly required for NLRP3 activation in primates and humans. HighlightsO_LIIdentification of NK7-902, a CRBN molecular glue degrader of NEK7 C_LIO_LINK7-902 fully degrades NEK7 in human primary monocytes and whole blood but only partially inhibits NLRP3-dependent IL-1{beta} production C_LIO_LIUnlike most CRBN glue degraders, NK7-902 shows activity in murine systems C_LIO_LIIn vivo oral administration of NK7-902 in non-human primates leads to profound and long-lasting NEK7 degradation but only transiently blocks NLRP3 inflammasome activation C_LI

immunology↗

bioRxiv2024

Scorpion α-toxin LqhαIT specifically interacts with a glycan at the pore domain of voltage-gated sodium channels

Voltage-gated sodium (Nav) channels sense membrane potential and drive cellular electrical activity. Numerous protein toxins have been identified that modulate Nav gating, and structures of Nav channels in complex with these toxins helped elucidate the molecular mechanisms of voltage-dependent channel gating. The deathstalker scorpion -toxin LqhIT exerts a strong action potential prolonging effect on Nav channels. Biochemical studies show that LqhIT features a functionally essential epitope at its C-terminus that is not shared with related scorpion -toxins. To elucidate the mechanism of action of LqhIT, we determined a 3.9 [A] cryo-electron microscopy (cryo-EM) structure of LqhIT in complex with the Nav channel from Periplaneta americana (NavPas). We found that LqhIT binds to voltage sensor domain 4 and traps it in a "S4 down" conformation to stabilize the open state. To promote binding, the functionally essential C-terminal epitope of LqhIT forms an extensive interface with the glycan scaffold linked to Asn330 of NavPas that augments a small protein-protein interface between NavPas and LqhIT. A combination of molecular dynamics simulations, structural comparisons, and prior mutagenesis experiments demonstrate the functional importance of this toxin-glycan interaction. These findings help establish a structural basis for the specificity achieved by scorpion -toxins and provide crucial insights for the development and optimization of new Nav channel modulators.

biophysics↗

bioRxiv2021

Combined free energy calculation and machine learning methods for understanding ligand unbinding kinetics

The determination of drug residence times, which define the time an inhibitor is in complex with its target, is a fundamental part of the drug discovery process. Synthesis and experimental measurements of kinetic rate constants are, however, expensive, and time-consuming. In this work, we aimed to obtain drug residence times computationally. Furthermore, we propose a novel algorithm to identify molecular design objectives based on ligand unbinding kinetics. We designed an enhanced sampling technique to accurately predict the free energy profiles of the ligand unbinding process, focusing on the free energy barrier for unbinding. Our method first identifies unbinding paths determining a corresponding set of internal coordinates (IC) that form contacts between the protein and the ligand, it then iteratively updates these interactions during a series of biased molecular-dynamics (MD) simulations to reveal the ICs that are important for the whole of the unbinding process. Subsequently, we performed finite temperature string simulations to obtain the free energy barrier for unbinding using the set of ICs as a complex reaction coordinate. Importantly, we also aimed to enable further design of drugs focusing on improved residence times. To this end, we developed a supervised machine learning (ML) approach with inputs from unbiased "downhill" trajectories initiated near the transition state (TS) ensemble of the string unbinding path. We demonstrate that our ML method can identify key ligand-protein interactions driving the system through the TS. Some of the most important drugs for cancer treatment are kinase inhibitors. One of these kinase targets is Cyclin Dependent Kinase 2 (CDK2), an appealing target for anticancer drug development. Here, we tested our method using two different CDK2 inhibitors for potential further development of these compounds. We compared the free energy barriers obtained from our calculations with those observed in available experimental data. We highlighted important interactions at the distal ends of the ligands that can be targeted for improved residence times. Our method provides a new tool to determine unbinding rates, and to identify key structural features of the inhibitors that can be used as starting points for novel design strategies in drug discovery.

biophysics↗

bioRxiv2020

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

The main protease (Mpro) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an attractive target for antiviral therapeutics. Recently, many high-resolution apo and inhibitor-bound structures of Mpro, a cysteine protease, have been determined, facilitating structure-based drug design. Mpro plays a central role in the viral life cycle by catalyzing the cleavage of SARS-CoV-2 polyproteins. In addition to the catalytic dyad His41-Cys145, Mpro contains multiple histidines including His163, His164, and His172. The protonation states of these histidines and the catalytic nu-cleophile Cys145 have been debated in previous studies of SARS-CoV Mpro, but have yet to be investigated for SARS-CoV-2. In this work we have used molecular dynamics simulations to determine the structural stability of SARS-CoV-2 Mpro as a function of the protonation assignments for these residues. We simulated both the apo and inhibitor-bound enzyme and found that the conformational stability of the binding site, bound inhibitors, and the hydrogen bond networks of Mpro are highly sensitive to these assignments. Additionally, the two inhibitors studied, the peptidomimetic N3 and an -ketoamide, display distinct His41/His164 protonation-state-dependent stabilities. While the apo and the N3-bound systems favored N{delta} (HD) and N{epsilon} (HE) protonation of His41 and His164, respectively, the -ketoamide was not stably bound in this state. Our results illustrate the importance of using appropriate histidine protonation states to accurately model the structure and dynamics of SARS-CoV-2 Mpro in both the apo and inhibitor-bound states, a necessary prerequisite for drug-design efforts.

biophysics↗