Unique Binding Site Research Articles

A Selective Adenylyl Cyclase 1 Inhibitor Relieves Pain Without Causing Tolerance.

Among the ten different adenylyl cyclase isoforms, studies with knockout animals indicate that inhibition of AC1 can relieve pain and reduce behaviors linked to opioid dependence. We previously identified ST034307 as a selective inhibitor of AC1. The development of an AC1-selective inhibitor now provides the opportunity to further study the therapeutic potential of inhibiting this protein in pre-clinical animal models of pain and related adverse reactions. In the present study we have shown that ST034307 relives pain in mouse models of formalin-induced inflammatory pain, acid-induced visceral pain, and acid-depressed nesting. In addition, ST034307 did not cause analgesic tolerance after chronic dosing. We were unable to detect ST034307 in mouse brain following subcutaneous injections but showed a significant reduction in cAMP concentration in dorsal root ganglia of the animals. Considering the unprecedented selectivity of ST034307, we also report the predicted molecular interaction between ST034307 and AC1. Our results indicate that AC1 inhibitors represent a promising new class of analgesic agents that treat pain and do not result in tolerance or cause disruption of normal behavior in mice. In addition, we outline a unique binding site for ST034307 at the interface of the enzyme’s catalytic domain.

Synthesis and Visualization of Entangled 3D Covalent Organic Frameworks with High-Valency Stereoscopic Molecular Nodes for Gas Separation.

The structural diversity of three-dimensional (3D) covalent organic frameworks (COFs) are limited as there are only a few choices of building units with multiple symmetrically distributed connection sites. To date, 4 and 6-connected stereoscopic nodes with Td , D3h , D3d and C3 symmetries have been mostly reported, delivering limited 3D topologies. We propose an efficient approach to expand the 3D COF repertoire by introducing a high-valency quadrangular prism (D4h ) stereoscopic node with a connectivity of eight, based on which two isoreticular 3D imine-linked COFs can be created. Low-dose electron microscopy allows the direct visualization of their 2-fold interpenetrated bcu networks. These 3D COFs are endowed with unique pore architectures and strong molecular binding sites, and exhibit excellent performance in separating C2 H2 /CO2 and C2 H2 /CH4 gas pairs. The introduction of high-valency stereoscopic nodes would lead to an outburst of new topologies for 3D COFs.

Synthesis and Visualization of Entangled 3D Covalent Organic Frameworks with High‐Valency Stereoscopic Molecular Nodes for Gas Separation

AbstractThe structural diversity of three‐dimensional (3D) covalent organic frameworks (COFs) are limited as there are only a few choices of building units with multiple symmetrically distributed connection sites. To date, 4 and 6‐connected stereoscopic nodes with Td, D3h, D3d and C3 symmetries have been mostly reported, delivering limited 3D topologies. We propose an efficient approach to expand the 3D COF repertoire by introducing a high‐valency quadrangular prism (D4h) stereoscopic node with a connectivity of eight, based on which two isoreticular 3D imine‐linked COFs can be created. Low‐dose electron microscopy allows the direct visualization of their 2‐fold interpenetrated bcu networks. These 3D COFs are endowed with unique pore architectures and strong molecular binding sites, and exhibit excellent performance in separating C2H2/CO2 and C2H2/CH4 gas pairs. The introduction of high‐valency stereoscopic nodes would lead to an outburst of new topologies for 3D COFs.

Functional characterization and substrate promiscuity analysis of UDP-glucose dehydrogenases from licorice (Glycyrrhiza uralensis)

Uridine diphosphate glucose dehydrogenase (UGDH) has a crucial role in the synthesis of UDP-glucuronic acid (UDPGA), which is the important sugar donor in the glucuronosylation of bioactive triterpene saponins in the traditional Chinese medicine Glycyrrhiza uralensis Fisch. UGDHs usually exist as isoforms in plants, but knowledge of their unique binding sites and patterns remains largely incomplete. Here, we mined five UGDH isoforms in G. uralensis transcriptome that catalyze the oxidation of UDP-glucose (UDPG) to UDPGA and had different catalytic efficiencies. Molecular modeling and molecular dynamics simulation revealed the potential catalytic residues for the catalytic efficiencies of the isoforms. Moreover, the UGDH isoforms exhibited substrate promiscuity by catalyzing two structurally diverse UDPG derivatives, which was further demonstrated by docking studies. This work gives new insights into the UGDH isoforms involved in the biosynthesis of glucuronides in G. uralensis, and extends the understanding of the versatility of UGDHs.

Cistrome and transcriptome analysis identifies unique androgen receptor (AR) and AR-V7 splice variant chromatin binding and transcriptional activities

The constitutively active androgen receptor (AR) splice variant, AR-V7, plays an important role in resistance to androgen deprivation therapy in castration resistant prostate cancer (CRPC). Studies seeking to determine whether AR-V7 is a partial mimic of the AR, or also has unique activities, and whether the AR-V7 cistrome contains unique binding sites have yielded conflicting results. One limitation in many studies has been the low level of AR variant compared to AR. Here, LNCaP and VCaP cell lines in which AR-V7 expression can be induced to match the level of AR, were used to compare the activities of AR and AR-V7. The two AR isoforms shared many targets, but overall had distinct transcriptomes. Optimal induction of novel targets sometimes required more receptor isoform than classical targets such as PSA. The isoforms displayed remarkably different cistromes with numerous differential binding sites. Some of the unique AR-V7 sites were located proximal to the transcription start sites (TSS). A de novo binding motif similar to a half ARE was identified in many AR-V7 preferential sites and, in contrast to conventional half ARE sites that bind AR-V7, FOXA1 was not enriched at these sites. This supports the concept that the AR isoforms have unique actions with the potential to serve as biomarkers or novel therapeutic targets.

Allosteric regulation by membranes and hydrophobic subsites in phospholipase A2 enzymes determine their substrate specificity

Lipids play critical roles in several major chronic diseases of our times, including those that involve inflammatory sequelae such as metabolic syndrome including obesity, insulin sensitivity, and cardiovascular diseases. However, defining the substrate specificity of enzymes of lipid metabolism is a challenging task. For example, phospholipase A2 (PLA2) enzymes constitute a superfamily of degradative, biosynthetic, and signaling enzymes that all act stereospecifically to hydrolyze and release the fatty acids of membrane phospholipids. This review focuses on how membranes interact allosterically with enzymes to regulate cell signaling and metabolic pathways leading to inflammation and other diseases. Our group has developed “substrate lipidomics” to quantify the substrate phospholipid specificity of each PLA2 and coupled this with molecular dynamics simulations to reveal that enzyme specificity is linked to specific hydrophobic binding subsites for membrane phospholipid substrates. We have also defined unexpected headgroup and acyl chain specificity for each of the major human PLA2 enzymes, which explains the observed specificity at a structural level. Finally, we discovered that a unique hydrophobic binding site—and not each enzyme’s catalytic residues or polar headgroup binding site—predominantly determines enzyme specificity. We also discuss how PLA2s release specific fatty acids after allosteric enzyme association with membranes and extraction of the phospholipid substrate, which can be blocked by stereospecific inhibitors. After decades of work, we can now correlate PLA2 specificity and inhibition potency with molecular structure and physiological function.

Stoichiometric analysis reveals a unique phosphatidylserine binding site in coagulation factor X

BackgroundCellular trauma or activation exposes phosphatidylserine (PS) and the substantially more abundant phospholipid, phosphatidylethanolamine (PE), on the outer layer of the plasma membrane, thereby allowing binding of many blood clotting proteins. We previously proposed the Anything But Choline (ABC) hypothesis to explain how PS and PE synergize to support binding of clotting proteins with gamma‐carboxyglutamate (Gla)‐rich domains, which posited that each Gla domain binds to a limited number of PS molecules and multiple PE molecules. However, the minimal number of PS molecules required to stably bind a Gla‐domain–containing blood clotting protein in the presence of excess PE was unknown. ObjectiveTo test the ABC hypothesis for factor X by determining the threshold binding requirement of PS molecules under conditions of PS–PE synergy. MethodsWe used surface plasmon resonance to investigate the stoichiometry of factor X binding to nanoscale membrane bilayers (Nanodiscs) of varying phospholipid composition. Results and ConclusionsWe quantified 1.05 ± 0.2 PS molecules per bound factor X molecule in Nanodiscs containing a mixture of 10% PS, 60% PE, and 30% phosphatidylcholine. Hence, there appears to be one truly PS‐specific binding site per Gla domain, while the remaining membrane binding interactions can be satisfied by PE.

Robust and Radiation-Resistant Hofmann-Type Metal-Organic Frameworks for Record Xenon/Krypton Separation.

The discovery of high-performance adsorbents for highly efficient separation of xenon from krypton is an important but challenging task in the chemical industry due to their similar size and inert spherical nature. Herein, we report two robust and radiation-resistant Hofmann-type MOFs, Co(pyz)[Ni(CN)4] and Co(pyz)[Pd(CN)4] (termed as ZJU-74a-Ni and ZJU-74a-Pd), featuring oppositely adjacent open metal sites and perfect pore sizes (4.1 and 3.8 Å) comparable to the kinetic diameter of xenon (4.047 Å), affording the benchmark binding affinity for polarizable Xe gas. These materials thus exhibit both record-high Xe uptake capacities (89.3 and 98.4 cm3 cm-3 at 296 K and 0.2 bar) and Xe/Kr selectivities (74.1 and 103.4) at ambient conditions, all of which are the highest among all the state-of-the-art materials reported so far. The locations of Xe molecules within ZJU-74a-Ni have been visualized by single-crystal X-ray diffraction studies, in which two oppositely adjacent metal centers combined with the right aperture size can construct a unique sandwich-like binding site to offer unprecedented and ultrastrong Ni2+-Xe-Ni2+ interactions with xenon, thus leading to the record Xe capture capacity and selectivity. The excellent separation capacity of ZJU-74a-Pd was verified by breakthrough experiments for Xe/Kr gas mixtures, providing both unprecedentedly high xenon uptake capacity (4.63 mmol cm-3) and krypton productivity (214 cm3 g-1).

Structures of the Plasmodium falciparum heat-shock protein 70-x ATPase domain in complex with chemical fragments identify conserved and unique binding sites.

Plasmodium falciparum invades erythrocytes and extensively modifies them in a manner that increases the virulence of this malaria parasite. A single heat-shock 70 kDa-type chaperone, PfHsp70-x, is among the parasite proteins exported to the host cell. PfHsp70-x assists in the formation of a key protein complex that underpins parasite virulence and supports parasite growth during febrile episodes. Previous work resolved the crystallographic structures of the PfHsp70-x ATPase and substrate-binding domains, and showed them to be highly similar to those of their human counterparts. Here, 233 chemical fragments were screened for binding to the PfHsp70-x ATPase domain, resulting in three crystallographic structures of this domain in complex with ligands. Two binding sites were identified, with most ligands binding proximal to the ATPase nucleotide-binding pocket. Although amino acids participating in direct ligand interactions are conserved between the parasite and human erythrocytic chaperones, one nonconserved residue is also present near the ligand. This work suggests that PfHsp70-x features binding sites that may be exploitable by small-molecule ligands towards the specific inhibition of the parasite chaperone.

Hydrogen bonding networks and cooperativity effects in the aqueous solvation of trimethylene oxide and sulfide rings by microwave spectroscopy and computational chemistry.

The intermolecular interactions responsible for the microsolvation of the highly flexible trimethylene oxide (TMO) and trimethylene sulfide (TMS) rings with one and two water (w) molecules were investigated using rotational spectroscopy (8-22GHz) and quantum chemical calculations. The observed patterns of transitions are consistent with the most stable geometries of the TMO-w, TMO-(w)2, and TMS-w complexes at the B2PLYP-D3(BJ)/aug-cc-pVTZ level and were confirmed using spectra of the 18O isotopologue. Due to its effectively planar backbone, TMO offers one unique binding site for solvation, while water can bind to the puckered TMS ring in either an axial or equatorial site of the heteroatom. In all clusters, the first water molecule binds in the σv symmetry plane of the ring monomer and serves as a hydrogen bond donor to the heteroatom. The second water molecule is predicted to form a cooperative hydrogen bonding network between the three moieties. Secondary C-H⋯O interactions are a key stabilizing influence in trimers and also drive the preferred binding site in the TMS clusters with the axial binding site preferred in TMS-w and the equatorial form calculated to be more stable in the dihydrate. Using an energy partition scheme from the symmetry-adapted perturbation theory for the O, S, and Se containing mono- and dihydrates, the intermolecular interactions are revealed to be mainly electrostatic, but the dispersive character of the contacts is enhanced with the increasing size of the ring's heteroatom due to the key role of longer-range secondary interactions.

Abstract 2450: A systemic approach to decipher the interactome of RET receptor isoforms

Abstract The REarranged during Transfection (RET) receptor tyrosine kinase is pivotal for normal tissue development, but is also an oncogene driver involved in several human cancers. Alternative splicing at the 3' end of the RET gene leads to expression of two conserved protein isoforms, RET9 and RET51, that differ in their subcellular localization and protein trafficking, as well as their functional roles in tumorigenesis and metastatic processes. Importantly, RET9 and RET51 have unique C-terminal phospho-tyrosine binding sites, suggesting that they may also differ in their interactomes. We used a combination of cell-based screening and in silico approaches to identify novel potential interaction partners of RET isoforms. We performed a Mammalian Membrane Two-Hybrid (MaMTH) screen using a library of SH2 domain-containing adaptor and signaling proteins, to identify interactions with each RET isoform. We complemented these studies by using sequence homology detection models (HMM, PSSM), based on SH2 domain sequences known to interact with RET, to rank the SH2 library members and predict novel interactions. Independently, we compared published consensus binding sequences for each SH2 domain library member with predicted RET phosphotyrosine motifs to identify potential interactors. Predicted interactions were validated in co-immunoprecipitation assays. We confirmed previously known interactions of RET with SH2 domain proteins including SHC1, GRB2 and GRB10, and identified additional novel RET-binding proteins, a subset of which showed differential interactions that were mediated through RET isoform-specific docking sites. Our results suggest that combinations of distinct interaction partners may contribute to RET isoform-specific functions. Together, our research has developed a systematic approach to map and characterize RET isoform interactions. Our data suggest that no single method identified all confirmed RET interactions, and that a combination of multiple approaches improves characterization of growth factor receptor interactomes. Citation Format: Samira Kheitan, Annika E. Pedersen, Brandy D. Hyndman, Luka Drecun, Punit Saraon, Igor Stagliar, Lois M. Mulligan. A systemic approach to decipher the interactome of RET receptor isoforms [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2450.

Abstract 292: A dual CTLA4 and PD1 microbially derived inhibitor shows efficacy in anti-PD1 mAb unresponsive tumor models through a unique allosteric mechanism of action

Abstract Background Maintenance of a symbiotic relationship with microbes has led to the evolution of a complex host immune recognition system. How microbes achieve homeostasis with their hosts is an unexploited source of novel chemistry and targets for cancer immunotherapy. Peptides are a proven and powerful medium through which microbes communicate amongst themselves and with the host immune system [Hilchie et al. Nat Chem Biol. 2013 and Hancock Nat Rev Microbiol 2012]. Accordingly, we have developed a platform to mine bioactive peptides from microbial databases/libraries. As proof of concept of our screening technology we targeted PD1 to (A) determine if the PD1 “rheostat” is a target of the microbial immune manipulation, and (B) characterize the activity of the peptide(s) towards developing a novel checkpoint inhibitor therapeutic modality. Methods A microbiome database was queried against previously identified PD1 binding peptides [Kotraiah V Front. Immunol. 2020] and identified peptides were computationally modeled to determine binding site. Reporter assays and ex vivo models were used to measure binding and quantify receptor antagonism. Syngeneic tumor models responsive and unresponsive to anti-PD1 monoclonal antibodies were used to test the efficacy of the peptides. Further, an infectious disease therapeutic model was used to measure and characterize the T-cell response of the peptides in vivo. Results A 22-amino acid peptide, BtLD01, from Bacillus thuringiensis was computationally shown to target a novel allosteric binding site on PD1 which is shared by the related CD28 family receptor, CTLA4. Indeed, BtLD01 antagonizes PD1 and CTLA4 simultaneously as measured in a cell-based reporter assay. Using ex vivo assays we show that BtLD reverses exhaustion-like phenotype in human PBMC recall and that they can stimulate T-Cell proliferation in the presence of PD-L1 blockade. Intriguingly, BtLD checkpoint inhibition is not dependent on PD-L1 blockade but by potentially recruiting or stabilizing the PD1:PD-L1 complex. In vivo studies with sygeneic, mouse tumor models displayed activity in both anti-PD1 mAb responsive and unresponsive tumors. Further, in a lethal malaria model of T-cell activation, we saw that BtLD01 not only protects mice and forms a memory recall response, but also suppresses Tregs. Conclusions Novel Microbially-Derived BtLD peptides target PD1/CTLA4 receptors. The unique allosteric binding site allows peptides to function non-competitively with PD-L1. This novel combined checkpoint inhibition mechanism of activating Tcells and suppressing Tregs along with the rapid and transient modulating nature of peptide may provide a safe and potent means to treat tumors refractory to anti-PD1 mAb therapy alone in clinic. Citation Format: Gabriel M. Gutierrez, Timothy W. Phares, Vinayaka Kotraiah, Peter Buontempo, James Pannucci, Llew Keltner. A dual CTLA4 and PD1 microbially derived inhibitor shows efficacy in anti-PD1 mAb unresponsive tumor models through a unique allosteric mechanism of action [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 292.

The Genome-Wide Binding Profile for Human RE1 Silencing Transcription Factor Unveils a Unique Genetic Circuitry in Hippocampus.

Early studies in mouse neurodevelopment led to the discovery of the RE1 Silencing Transcription Factor (REST) and its role as a master repressor of neuronal gene expression. Recently, REST was reported to also repress neuronal genes in the human adult brain. These genes were found to be involved in pro-apoptotic pathways; and their repression, associated with increased REST levels during aging, were found to be neuroprotective and conserved across species. However, direct genome-wide REST binding profiles for REST in adult brain have not been identified for any species. Here, we apply this approach to mouse and human hippocampus. We find an expansion of REST binding sites in the human hippocampus that are lacking in both mouse hippocampus and other human non-neuronal cell types. The unique human REST binding sites are associated with genes involved in innate immunity processes and inflammation signaling which, on the basis of histology and recent public transcriptomic analyses, suggest that these new target genes are repressed in glia. We propose that the increases in REST expression in mid-adulthood presage the beginning of brain aging, and that human REST function has evolved to protect the longevity and function of both neurons and glia in human brain.SIGNIFICANCE STATEMENT The RE1 Silencing Transcription Factor (REST) repressor has served historically as a model for gene regulation during mouse neurogenesis. Recent studies of REST have also suggested a conserved role for REST repressor function across lower species during aging. However, direct genome-wide studies for REST have been lacking for human brain. Here, we perform the first genome-wide analysis of REST binding in both human and mouse hippocampus. The majority of REST-occupied genes in human hippocampus are distinct from those in mouse. Further, the REST-associated genes unique to human hippocampus represent a new set related to innate immunity and inflammation, where their gene dysregulation has been implicated in aging-related neuropathology, such as Alzheimer's disease.

Structural basis for CSPG4 as a receptor for TcdB and a therapeutic target in Clostridioides difficile infection

C. difficile is a major cause of antibiotic-associated gastrointestinal infections. Two C. difficile exotoxins (TcdA and TcdB) are major virulence factors associated with these infections, and chondroitin sulfate proteoglycan 4 (CSPG4) is a potential receptor for TcdB, but its pathophysiological relevance and the molecular details that govern recognition remain unknown. Here, we determine the cryo-EM structure of a TcdB–CSPG4 complex, revealing a unique binding site spatially composed of multiple discontinuous regions across TcdB. Mutations that selectively disrupt CSPG4 binding reduce TcdB toxicity in mice, while CSPG4-knockout mice show reduced damage to colonic tissues during C. difficile infections. We further show that bezlotoxumab, the only FDA approved anti-TcdB antibody, blocks CSPG4 binding via an allosteric mechanism, but it displays low neutralizing potency on many TcdB variants from epidemic hypervirulent strains due to sequence variations in its epitopes. In contrast, a CSPG4-mimicking decoy neutralizes major TcdB variants, suggesting a strategy to develop broad-spectrum therapeutics against TcdB.

Dual-Selective Catalysis in Dephosphorylation Tuned by Hf6-Containing Metal-Organic Frameworks Mimicking Phosphatase.

Selective dephosphorylation is full of great challenges in the field of biomimetic catalysis. To mimic the active sites of protein phosphatase, Hf-OH-Hf motif-containing metal–organic frameworks (MOFs) were obtained and structurally characterized, which are assembled from [Hf48Ni6] cubic nanocages and exhibit good stability in various solvents and acid/base solutions. Catalytic investigations suggest as-synthesized Hf–Ni and Hf–Ni–NH2 display accurate type-selectivity (selectively catalyzed P–O rather than S–O or C–O bonds) and position-selectivity (selectively catalyzed phosphomonoesters over phosphodiesters) for the hydrolysis of phosphoesters. Reaction kinetic studies further revealed the high activity of the catalytic sites in these catalysts, and the unique catalytic selectivity and high activity are comparable to phosphatase. Additionally, these MOF catalysts possess good recursivity and hypotoxicity. Control experiments (including Hf- and Zr-based isomorphous MOFs) and theoretical calculations indicate that both triplet nickel and Hf6 clusters play significant roles in the unique binding site and favorable binding energy. To our knowledge, this is the first example of selective dephosphorylation through MOF catalysts as mimic enzymes, which paves a potential way for the development of specific therapeutic MOFs.

Phospholipase A 2 : A Paradigm for Allosteric Regulation by Membranes and Cell Signaling

Our laboratory discovered and demonstrated that membranes interact allosterically with enzymes to regulate cell signaling and metabolic pathways leading to inflammation1. We have recently employed substrate lipidomics coupled with molecular dynamics to reveal enzyme specificity linked to highly specific hydrophobic binding sites for the sn-2 fatty acyl chains in membrane phospholipid substrates2. We discovered unexpected headgroup and acyl chain specificity for each of the major human phospholipase A2 (PLA2) enzymes that explains the observed specificity at a new atomic level. A unique hydrophobic binding site — and not each enzyme's catalytic residues or polar headgroup binding site — dominates each enzyme's specificity. Each PLA2 shows unique specificity for its required fatty acid ranging from pro-inflammatory omega-6 arachidonic acid or anti-inflammatory fish oil omega-3 EPA and DHA; others favor membrane remodeling linolenic acid, or antibacterial saturated fatty acids, or oxidized fatty acids in LDL. Each PLA2 releases a specific fatty acid after the enzyme associates allosterically with membranes and extracts a single phospholipid substrate into its catalytic site. Stereospecific inhibitors3 have been designed for the specific sites. After decades of advances in lipid research, we can now correlate PLA2 specificity and inhibition potency with molecular structure and physiological function using a novel lipidomics platform that provides a paradigm for protein-membrane lipid interactions in general. From the cell signaling and inflammation perspective, the omics revolution began with genomics, proteomics and metabolomics, but lipidomics now dominates as the largest number of cellular metabolites are lipids, many playing critical roles in cell signaling, and over 40,000 distinct molecular species have been identified by the LIPID MAPS Consortium (www.lipidmaps.org). We have also employed lipidomics analysis to characterize the in vivo role of specific PLA2 enzymes in initiating the inflammatory response and cellular lipid signaling of Toll-like (TLR4) and purinergic (P2X7) receptors in stimulated macrophages as models of bacterial infection and inflammation4. We can now explain in vivo cellular specificity by in vitro enzyme specificity, inhibition and pro-inflammatory and pro-resolution lipid mediator formation pathways and inhibition5. 1Dennis EA (2016) REFLECTIONS: Liberating chiral lipid mediators, inflammatory enzymes and LIPID MAPS from biological grease, J Biol Chem, 291, 24431–48. 2Mouchlis VC, Chen Y, McCammon JA, Dennis EA (2018) Membrane allostery and unique hydrophobic sites promote enzyme substrate specificity, J Am Chem Soc, 140, 3285-91. 3Mouchlis VD, Armando AM, Dennis EA (2019) Substrate specific inhibition constants for phospholipase A2 acting on unique phospholipid substrates in mixed micelles and membranes using lipidomics. J Med Chem, 62, 1999-2007. 4Dennis EA, Norris PA (2015) Eicosanoid storm in infection and inflammation. Nature Immunology Reviews, 15, 511-523. 5Navratil AR, Shchepinov MS, Dennis EA (2018) Lipidomics reveals dramatic physiological kinetic isotope effects during the enzymatic oxygenation of polyunsaturated fatty acids ex vivo. J Am Chem Soc, 140, 235-43.

AGO HITS-CLIP reveals distinct miRNA regulation of white and brown adipose tissue identity.

MicroRNAs (miRNAs) are short, noncoding RNAs that associate with Argonaute (AGO) to influence mRNA stability and translation, thereby regulating cellular determination and phenotype. While several individual miRNAs have been shown to control adipocyte function, including energy storage in white fat and energy dissipation in brown fat, a comprehensive analysis of miRNA activity in these tissues has not been performed. We used high-throughput sequencing of RNA isolated by cross-linking immunoprecipitation (HITS-CLIP) to comprehensively characterize the network of high-confidence, in vivo mRNA:miRNA interactions across white and brown fat, revealing >20,000 unique AGO binding sites. When coupled with miRNA and mRNA sequencing, we found an inverse correlation between depot-enriched miRNAs and their targets. To illustrate the functionality of our HITS-CLIP data set in identifying specific miRNA:mRNA interactions, we show that miR-29 is a novel regulator of leptin, an adipocyte-derived hormone that coordinates food intake and energy homeostasis. Two independent miR-29 binding sites in the leptin 3' UTR were validated using luciferase assays, and miR-29 gain and loss of function modulated leptin mRNA and protein secretion in primary adipocytes. This work represents the only experimentally generated miRNA targetome in adipose tissue and identifies multiple regulatory pathways that may specify the unique identities of white and brown fat.

Covalent Occlusion of the RORγt Ligand Binding Pocket Allows Unambiguous Targeting of an Allosteric Site.

The nuclear receptor RORγt is a key positive regulator in the differentiation and proliferation of T helper 17 (Th17) cells and the production of proinflammatory cytokines like IL-17a. Dysregulation of this pathway can result in the development of various autoimmune diseases, and inhibition of RORγt with small molecules thus holds great potential as a therapeutic strategy. RORγt has a unique allosteric ligand binding site in the ligand binding domain, which is distinct from the canonical, orthosteric binding site. Allosteric modulation of RORγt shows high potential, but the targeted discovery of novel allosteric ligands is highly challenging via currently available methods. Here, we introduce covalent, orthosteric chemical probes for RORγt that occlude the binding of canonical, orthosteric ligands but still allow allosteric ligand binding. Ultimately, these probes could be used to underpin screening approaches for the unambiguous and rapid identification of novel allosteric RORγt ligands.

The role of Popeye domain-containing protein 1 (POPDC1) in the progression of the malignant phenotype.

The Popeye domain-containing protein 1 (POPDC1), a tight junction-associated transmembrane protein with a unique binding site for cAMP, has been shown to act as a tumour suppressor in cancer cells. Through interaction with many downstream effectors and signalling pathways, POPDC1 promotes cell adhesion and inhibits uncontrolled cell proliferation, epithelial-to-mesenchymal transition and metastasis. However, POPDC1 expression is down-regulated in many types of cancer, thereby reducing its tumour-suppressive actions. This review discusses the role of POPDC1 in the progression of the malignant phenotype and highlights the broad range of benefits POPDC1 stabilisation may achieve therapeutically. Cancer stem cells (CSCs) are a key hallmark of malignancies and commonly promote treatment resistance. This article provides a comprehensive overview of CSC signalling mechanisms, many of which have been shown to be regulated by POPDC1 in other cell types, thus suggesting an additional therapeutic benefit for POPDC1-stabilising anti-cancer drugs. LINKED ARTICLES: This article is part of a themed issue on New avenues in cancer prevention and treatment (BJP 75th Anniversary). To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v179.12/issuetoc.

Yeast Hsp110 Has a Unique Substrate Binding Site Essential for Chaperone Activity

110 kD Heat Shock proteins (Hsp110s) have unique chaperone activities in eukaryotic cytosol which assist in protein folding, transport and degradation, and preventing protein aggregation. They are chaperones by themselves and co-chaperones for Hsp70s, which is another essential class of molecular chaperones. Hsp110s show high activity in preventing protein aggregation through directly binding to polypeptide substrate and function to ensure the efficient folding activity of the Hsp70 chaperone machinery.