Proteins contain small pockets that form due to imperfections in residue packing or the rotational and conformational movement of amino acids. In this work, we used the fluorescent probe 1-aminoanthracene (AMA) to detect a small ligand pocket in the hydrophobic core of human proliferating cell nuclear antigen (PCNA), which is a critical protein for DNA replication and repair. Fluorescence measurements of AMA reported that the core of PCNA had a dielectric constant (ε) of 4, which was very apolar and similar to cyclohexane (ε = 2). Protein mutagenesis, photoaffinity labeling, and molecular dynamics simulations localized the binding site for AMA next to PCNA residues L90 and L101, which also interacted with general anesthetics (sevoflurane and propofol). The ligand binding site was cryptic, i.e., it formed transiently and was only detectable in certain structural states of PCNA. Ligand binding to the cryptic site on PCNA structurally stabilized the trimeric protein and reduced its ability to disassemble and reassemble its subunits. Thus, the cryptic site in PCNA’s core serves to destabilize the assembled protein and promotes structural and oligomeric flexibility. Finally, the hydrophobic site is widely conserved among homologous β clamp proteins with a similar fold as PCNA. This work highlights how small fluorescent probes can reveal ligand sites within proteins, defines the chemical features of protein hydrophobic cores, and introduces a novel approach to modulate the oligomeric stability of PCNA.

General anesthetics are widely used to induce reversible unconsciousness, yet their molecular mechanisms remain incompletely understood. Despite their low binding affinities and broad protein-binding promiscuity, general anesthetics still interact with neuronal proteins in a structurally selective manner. Experimentally, chemically modified probes have been used to map their protein targets. However, the biases introduced by the structural modifications of these remain unknown, raising the key question of how reliable such experiments are in capturing true anesthetic-protein interactions. In this study, we present an interactome-scale computational approach to characterize anesthetic-protein interactions using high-throughput molecular docking. We screened two families of anesthetic ligands-propofol and etomidate, as well as chemically modified analogs of each-against a set of 2,388 experimentally determined mouse neuronal protein structures. By comparing parent and modified ligands, we reveal how functional group-specific biases, introduced by chemical modifications, altering ligands engage protein environments across the interactome. Docking poses and energies identify recurrent binding-site features and quantify how small modifications reshape interaction profiles. Using 3D spatial distribution functions, we summarize local amino acid environments surrounding each ligand, providing intuitive visualizations of interaction hotspots. This analysis exposes conserved and variable elements of anesthetic recognition and clarifies how probe modifications shape observed patterns. Our results offer a statistical and structural description of anesthetic binding across an interactome, providing mechanistic insight into affinity-based protein profiling mapping biases and guiding improved probe and drug design.

This study describes a unique method for administering volatile anesthetics, such as isoflurane and sevoflurane, to larval zebrafish during behavioral experiments. While zebrafish offer numerous advantages as a vertebrate model organism -- including complex behaviors, genetic tractability, transparent embryos, and rapid development -- their use in studying volatile anesthetics has been limited. The administration of volatile anesthetics often requires complex or cumbersome apparatuses that may not be broadly accessible, creating barriers to the pharmacologic study of volatile anesthetics in aqueous model organisms. This method presents a straightforward technique using adhesive silicone sheets to create a gas-tight seal on glass 96-well plates. Validation was performed through the assessment of spontaneous movement, which showed no significant differences between sealed and open wells over a 90-min period. Additionally, anesthetic concentration remained stable over time, as measured by HPLC. Representative results include the experimental determination of median effective concentration (EC50) values for sevoflurane. This study provides a simple and accessible approach for pharmacologic experiments using volatile anesthetics, which can be easily adapted to study other volatile agents and experimental endpoints.

General anesthetics like propofol are widely used, but their molecular mechanisms remain poorly understood, limiting the rational design of novel anesthetics or antagonists to enhance safety. We evaluated nine propofol derivatives for their ability to immobilize, or modulate propofol-induced immobilization, in larval zebrafish, using spontaneous and elicited movement as distinct endpoints. We hypothesized that compounds unable to act as hydrogen-bond donors would antagonize immobilization─evidenced by rightward EC50 shifts─while hydrogen-bond-capable derivatives would retain immobilizing effects. Results confirmed that nondonor analogues antagonized propofol's effects, whereas donor molecules had sedative activity, and a hydrocarbon control did not shift the EC50 curve. Quantum-mechanical calculations of hydrogen-bond acidity were correlated to behavioral outcomes, supporting their predictive potential. Notably, a tertiary amine analogue (PEARL 6, N,N-dimethyl-2,6-diisopropylaniline) antagonized most strongly (25.6-fold increase in propofol's EC50 for spontaneous movement and a 1.86-fold increase for elicited movement) without causing excitation when administered alone. These findings identify structural features that distinguish sedative from antagonistic activity and provide characterization of a key feature of propofol derivatives.

Proliferating cell nuclear antigen (PCNA) is a conserved eukaryotic DNA sliding clamp that is essential to DNA metabolism. PCNA interacts with hundreds of DNA replication and repair proteins, and inhibition of clamp function compromises genomic integrity and cell survival. Here, we discovered a novel cryptic binding site on PCNA that interacts with general anesthetics and their fluorescent analog, 1-aminoanthracene, which has environment-dependent properties. The fluorescence of 1-aminoanthracene blue-shifted 80 nm and increased 200-fold upon PCNA binding. 1-aminoanthracene was competed off PCNA by propofol and sevoflurane, indicating the site binds more than one class of general anesthetic. LC-MS/MS identified two residues on PCNA (L90, L101) that interacted with a photoactive propofol analog. Molecular dynamics simulations (>1 μs) confirmed that a cryptic site of suitable volume for the ligands (213 Å3) was formed adjacent to L90, L101 and neighboring residues, confirming the mass spectrometry results. Additionally, mutagenesis of L90 or L101 to polar residues red-shifted the fluorescence of 1-aminoanthracene relative to its emission when bound to wild-type PCNA. Characterization of the cryptic site properties, and experiments to determine the functional relevance of ligand binding, are ongoing.

Despite their frequent use across many clinical settings, general anesthetics are medications with lethal side effects and no reversal agents. A fluorinated analogue of propofol has previously been shown to antagonize propofol anesthesia in tadpoles and zebrafish, but little further investigation of this class of molecules as anesthetic antagonists has been conducted. A 13-member library of alkyl-fluorobenzene derivatives was tested in an established behavioral model of anesthesia in zebrafish at 5 days post fertilization. These compounds were examined for their ability to antagonize propofol and two volatile anesthetics, as well as their interaction with the anesthetic-binding model protein apoferritin. Two compounds provided significant antagonism of propofol, and when combined, were synergistic, suggesting more than one antagonist sensitive target site. These compounds did not antagonize the volatile anesthetics, indicating some selectivity amongst general anesthetics. For the compounds with the most antagonistic potency, similarities in structure and binding to apoferritin may be suggestive of competitive antagonism; however, this was not supported by a Schild analysis. This is consistent with multiple targets contributing to general anesthesia, but whether these are physiologic antagonists or are antagonists at only some subset of the many anesthetic potential targets remains unclear, and will require additional investigation.

The mechanisms of general anesthetics have been debated in the literature for many years and continue to be of great interest. As anesthetic molecules are notoriously difficult to study due to their low binding affinities and multitude of binding partners, it is advantageous to have additional tools to study these interactions. Fropofol is a hydroxyl to fluorine-substituted propofol analogue that is able to antagonize the actions of propofol. Understanding fropofol's ability to antagonize propofol would facilitate further characterization of the binding interactions of propofol that may contribute to its anesthetic actions. However, the study of fropofol's molecular interactions has many of the same difficulties as its parent compound. Here, we present the synthesis and characterization of ortho-azi-fropofol (AziFo) as a suitable photoaffinity label (PAL) of fropofol that can be used to covalently label proteins of interest to characterize fropofol's binding interactions and their contribution to general anesthetic antagonism. [Graphics]

Agonists at the α2 adrenergic receptor produce sedation, increase focus, provide analgesia, and induce centrally mediated hypotension and bradycardia, yet neither their dynamic interactions with adrenergic receptors nor their modulation of neuronal circuit activity is completely understood. Photoaffinity ligands of α2 adrenergic agonists have the potential both to capture discrete moments of ligand-receptor interactions and to prolong naturalistic drug effects in discrete regions of tissue in vivo. We present here the synthesis and characterization of a novel α2 adrenergic agonist photolabel based on the imidazole medetomidine called azi-medetomidine. Azi-medetomidine shares protein association characteristics with its parent compound in experimental model systems and by molecular dynamics simulation of interactions with the α2A adrenergic receptor. Azi-medetomidine acts as an agonist at α2A adrenergic receptors, and produces hypnosis in Xenopus laevis tadpoles. Azi-medetomidine competes with the α2 agonist clonidine at α2A adrenergic receptors, which is potentiated by photolabeling, and azi-medetomidine labels moieties on the α2A adrenergic receptor as determined by mass spectrometry in a manner consistent with a simulated model. This novel α2 adrenergic agonist photolabel can serve as a powerful tool for in vitro and in vivo investigations of adrenergic signaling.

Many intracellular protein-protein interactions are mediated by the phosphorylation of serine, and phosphoserine-containing peptides can inhibit these interactions. However, hydrolysis of the phosphate by phosphatases, and the poor cell permeability associated with phosphorylated peptides has limited their utility in cellular and in vivo contexts. Compounding the problem, strategies to replace phosphoserine in peptide inhibitors with easily accessible mimetics (such as Glu or Asp) routinely fail. Here, we present an in vitro selection strategy for replacement of phosphoserine. Using mRNA display, we created a 10 trillion member structurally diverse unnatural peptide library. From this library, we found a peptide that specifically binds to the C-terminal domain (BRCT)2 of breast cancer associated protein 1 (BRCA1) with an affinity comparable to phosphorylated peptides. A crystal structure of the peptide bound reveals that the pSer-x-x-Phe motif normally found in BRCA1 (BRCT)2 binding partners is replaced by a Glu-x-x-4-fluoroPhe and that the peptide picks up additional contacts on the protein surface not observed in cognate phosphopeptide binding. Expression of the peptide in human cells led to defects in DNA repair by homologous recombination, a process BRCA1 is known to coordinate. Overall, this work validates a new in vitro selection approach for the development of inhibitors of protein-protein interactions mediated by serine phosphorylation.

Abstract A growing body of literature suggests Breast Cancer-Associated Protein 1 (BRCA1) is important not only as a cause, but also as a target in the quest for cancer treatment. BRCA1 deficient cells treated with radiation as well as PARP inhibitors and other chemotherapeutics demonstrate a greater sensitivity than cells with wild type BRCA1. Inhibitors of BRCA1 would take advantage of this synthetic lethality and represent a significant advance in cancer treatment as well as an understanding of the biology of DNA repair. Despite significant study of BRCA1 protein and function, it is a large protein (208 KDa) that is still largely uncharacterized, but its N- and C-terminal domains have been described by significant structural data. The BRCT (BRCA1 C-Terminal) Domain is a phosphoprotein binding domain that is commonly mutated or lost in cancers and has a binding cleft seemingly very suitable for drug design. Small molecule screens have been conducted against this domain, but the resulting hits with moderate affinity have not been shown to induce BRCA1 deficient phenotypes. Phosphopeptides have also been studied as potential BRCA1 inhibitors, yet despite some having affinities in the mid-nanomolar range the presence of a phosphate is not without its pharmacologic challenges. We generated an mRNA display library with 1.3 x 10ˆ13 cyclized peptides covalently attached to the mRNA that encoded them. Eight rounds of selection exposing the library to a GST-BRCT fusion resulted in non-phosphorylated peptides that bind to a BRCT domain of BRCA1. The sequences resulting from the selection have common homologies and initial characterization has shown that these peptides may be the first viable non-phosphoserine containing inhibitors of BRCA1. Citation Format: E. Railey White, Zhong Ma, David E. Hacker, Jason M. Beckta, Melissa B. Huie, David C. Williams, Kristoffer Valerie, Matthew C. Hartman. Selection of non-phophorylated peptide inhibitors of BRCA1. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 4539. doi:10.1158/1538-7445.AM2013-4539

Despite intense studies, questions still remain regarding the molecular mechanisms leading to the development of hereditary breast and ovarian cancers. Research focused on elucidating the role of the breast cancer susceptibility gene 1 (BRCA1) in the DNA damage response may be of the most critical importance to understanding these processes. The BRCA1 protein has an N-terminal RING domain possessing E3 ubiquitinligase activity and a C-terminal BRCT domain involved in binding specific phosphoproteins. These domains are involved directly or indirectly in DNA double-strand break (DSB) repair. As the two terminal domains of BRCA1 represent two separate entities, understanding how these domains communicate and are functionally altered in regards to DSB repair is critical for understanding the development of BRCA1-related breast and ovarian cancers and for developing novel therapeutics. Herein, we review recent findings of how altered functions of these domains might lead to cancer through a mechanism of increased aberrant homologous recombination and possible implications for the development of BRCA1 inhibitors.

Here, we describe a strategy for synthesis of peptides with multiple unnatural amino acids (UAAs) using in vitro translation. Our method involves removing a natural amino acid and replacing it with an UAA variant in a reconstituted translation system. Whereas other systems require engineered components or chemical synthesis to charge UAAs onto tRNAs prior to translation, our strategy utilizes the wild-type machinery and charging occurs concomitant with translation. The design of the system allows for easy quantification of the UAA’s incorporation efficiency and fidelity.

This study examined whether acquisition of neonatal reflexes in newborn rhesus macaques was influenced by receipt of a single neonatal dose of hepatitis B vaccine containing the preservative thimerosal (Th). Hepatitis B vaccine containing a weight-adjusted Th dose was administered to male macaques within 24 h of birth (n = 13). Unexposed animals received saline placebo (n = 4) or no injection (n = 3). Infants were tested daily for acquisition of nine survival, motor, and sensorimotor reflexes. In exposed animals there was a significant delay in the acquisition of root, snout, and suck reflexes, compared with unexposed animals. No neonatal responses were significantly delayed in unexposed animals. Gestational age (GA) and birth weight (BW) were not significantly correlated. Cox regression models were used to evaluate main effects and interactions of exposure with BW and GA as independent predictors and time-invariant covariates. Significant main effects remained for exposure on root and suck when controlling for GA and BW, such that exposed animals were relatively delayed in time-to-criterion. Interaction models indicated there were various interactions between exposure, GA, and BW and that inclusion of the relevant interaction terms significantly improved model fit. This, in turn, indicated that lower BW and/or lower GA exacerbated the adverse effects following vaccine exposure. This primate model provides a possible means of assessing adverse neurodevelopmental outcomes from neonatal Th-containing hepatitis B vaccine exposure, particularly in infants of lower GA or BW. The mechanisms underlying these effects and the requirements for Th requires further study.