Differences In Binding Affinity Research Articles

In silico design and molecular basis for the selectivity of Olinone toward the first over the second bromodomain of BRD4.

Bromodomains (BrDs), a conserved structural module in chromatin-associated proteins, are well known for recognizing ε-N-acetyl lysine residues on histones. One of the most relevant BrDs is BRD4, a tandem BrD containing protein (BrD1 and BrD2) that plays a critical role in numerous diseases including cancer. Growing evidence shows that the two BrDs of BRD4 have different biological functions; hence selective ligands that can be used to study their functions are of great interest. Here, as a follow-up of our previous work, we first provide a detailed characterization study of the in silico rational design of Olinone as part of a series of five tetrahydropyrido indole-based compounds as BRD4 BrD1 inhibitors. Additionally, we investigated the molecular basis for Olinone's selective recognition by BrD1 over BrD2. Molecular dynamics simulations, free energy calculations, and conformational analyses of the apo-BRD4-BrD1|2 and BRD4-BrD1|2/Olinone complexes showed that Olinone's selectivity is facilitated by five key residues: Leu92 in BrD1|385 in BrD2 of ZA loop, Asn140|433, Asp144|His437 and Asp145|Glu438 of BC loop, and Ile146|Val49 of helix C. Furthermore, the difference in hydrogen bonds number and in mobility of the ZA and BC loops of the acetyl-lysine binding site between BRD4 BrD1/Olinone and BrD2/Olinone complexes also contribute to the difference in Olinone's binding affinity and selectivity toward BrD1 over BrD2. Altogether, our computer-aided molecular design techniques can effectively guide the development of small-molecule BRD4 BrD1 inhibitors, explain their selectivity origin, and further open doors to the design of new therapeutically improved derivatives.

Structural analysis of fungal pathogenicity-related casein kinase \u03b1 subunit, Cka1, in the human fungal pathogen Cryptococcus neoformans

CK2α is a constitutively active and highly conserved serine/threonine protein kinase that is involved in the regulation of key cellular metabolic pathways and associated with a variety of tumours and cancers. The most well-known CK2α inhibitor is the human clinical trial candidate CX-4945, which has recently shown to exhibit not only anti-cancer, but also anti-fungal properties. This prompted us to work on the CK2α orthologue, Cka1, from the pathogenic fungus Cryptococcus neoformans, which causes life-threatening systemic cryptococcosis and meningoencephalitis mainly in immunocompromised individuals. At present, treatment of cryptococcosis remains a challenge due to limited anti-cryptococcal therapeutic strategies. Hence, expanding therapeutic options for the treatment of the disease is highly clinically relevant. Herein, we report the structures of Cka1-AMPPNP-Mg2+ (2.40 Å) and Cka1-CX-4945 (2.09 Å). Structural comparisons of Cka1-AMPPNP-Mg2+ with other orthologues revealed the dynamic architecture of the N-lobe across species. This may explain for the difference in binding affinities and deviations in protein-inhibitor interactions between Cka1-CX-4945 and human CK2α-CX-4945. Supporting it, in vitro kinase assay demonstrated that CX-4945 inhibited human CK2α much more efficiently than Cka1. Our results provide structural insights into the design of more selective inhibitors against Cka1.

1259P - The role of tumour neoantigens in the differential response to immunotherapy (IO) in EGFR and BRAF mutated lung cancers: Quantity or quality?

BackgroundLung cancer patients with activating EGFR mutations tend to respond poorly to IO, but this is not true for all activating mutation driven lung cancers. Recent data show that patients with BRAF mutations tend to respond better to IO. Our study estimated the tumor neoantigen burden in these tumors, and the likelihood of their presentation to cytotoxic T cells by estimating their binding affinity to major histocompatibility complex (MHC). MethodsWhole exome data for 68 patients with EGFR mutant lung adenocarcinoma and 33 with BRAF mutations were extracted from the Cancer Genome Atlas. MAFTOOLs was used to determine the tumor mutational load. Nonamers were estimated by simulating possible nonamer neoantigens from MAF files. The neoantigen (MT) and wildtype (WT) binding affinities to MHC-I were calculated using the NetMHC 4.0 server. The differential binding affinity of the neoantigens in comparison to wildtype was calculated as mean differential agretopicity index (DAI) = WT - MT. Patient survival was estimated by the Kaplan-Meier method. ResultsPatients with mutated BRAF had higher median mutational burden (445, range 165-776) than those with EGFR mutations (90.5, range 60.5-219.5, p=0.001). The median number of simulated neoantigens was higher in the BRAF (9536.5, range 3839.5-14626.0) vs the EGFR group (1895.5, range 1148.5-4766.5, p<0.001). Mean DAI for BRAF and EGFR patients were 1046 and 1033, respectively, p=0.86. In the BRAF mutant group, patients with DAI < 1,000 had significantly better 5-year survival (80% vs 40%, p=0.022) compared to patients with DAI > 1,000. No such survival benefit was identified in the EGFR mutant group (56% vs 58%, p=0.81). ConclusionsBRAF mutant lung cancers are characterized by higher neoantigen burden, but their neoantigen differential binding affinity to MHC-I complex was not different from EGFR mutant lung cancers. Our analysis suggests that the improved response to IO in the BRAF mutant population is due to increased quantity in neoantigen burden and not a qualitative difference in MHC-I binding. Further, DAI had a prognostic impact in the BRAF population suggesting that it may be a measure of tumor neoantigen immunogenicity. Legal entity responsible for the studyThe authors. FundingHas not received any funding. DisclosureJ. Subramanian: Advisory / Consultancy, Speaker Bureau / Expert testimony: AstraZeneca; Advisory / Consultancy: Pfizer; Advisory / Consultancy, Speaker Bureau / Expert testimony: Boehringer Ingelheim; Advisory / Consultancy, Research grant / Funding (institution): Paradigm; Speaker Bureau / Expert testimony: Lilly; Research grant / Funding (institution): Biocept. All other authors have declared no conflicts of interest.

Regional Variation of Bitter Taste and Aftertaste in Humans.

Despite widespread and persistent myths of a tongue map, all 5 prototypical taste qualities are sensed over the entire tongue. However, modern psychophysical data also suggest there may be more nuanced differences in suprathreshold intensity across oral loci, especially for bitterness. Here, we test whether bitter stimuli matched for whole-mouth intensity differ in perceived intensity across regions of the oral cavity in 2 experiments. Experiment 1 consisted of a whole-mouth sip and spit approach and Experiment 2 consisted of a spatial taste test using cotton swabs. In Experiment 1, participants (n = 63) rated overall intensity of 3 bitter solutions at 5 different loci (front, middle, back of tongue; roof of mouth; and lip). Temporal effects were explored using in-mouth and aftertaste ratings. In Experiment 2, participants (n = 48) rated the intensity of quinine and Tetralone solutions after solutions were painted on fungiform, circumvallate, and foliate papillae with a swab. After the spatial taste test, participants completed a questionnaire on self-reported beer intake. Analysis of variance results of both experiments show a significant locus by stimulus interaction, suggesting different bitterants were perceived differently across the various loci. This result was apparently driven by low-intensity ratings for Tetralone on the anterior tongue. Aftertaste ratings in Experiment 1 also revealed significant temporal effects: ratings on the anterior tongue decreased for all bitterants and ratings for quinine decreased at all loci. Reasons for these effects are not known but may suggest differential expression of bitter taste receptors or differences in bitter agonist-receptor binding affinity across tongue regions.

A Potent Neutralizing Site III-Specific Human Antibody Neutralizes Human Metapneumovirus In Vivo.

Human metapneumovirus (hMPV) is a leading cause of viral lower respiratory tract infection in children. The sole target of neutralizing antibodies targeting hMPV is the fusion (F) protein, a class I viral fusion protein mediating virus-cell membrane fusion. There have been several monoclonal antibodies (mAbs) isolated that neutralize hMPV; however, determining the antigenic sites on the hMPV F protein mediating such neutralizing antibody generation would assist efforts for effective vaccine design. In this report, the isolation and characterization of four new human mAbs, termed MPV196, MPV201, MPV314, and MPV364, are described. Among the four mAbs, MPV364 was found to be the most potent neutralizing mAb in vitro Binding studies with monomeric and trimeric hMPV F revealed that MPV364 had the weakest binding affinity for monomeric hMPV F compared to the other three mAbs, yet binding experiments with trimeric hMPV F showed limited differences in binding affinity, suggesting that MPV364 targets an antigenic site incorporating two protomers. Epitope binning studies showed that MPV364 targets antigenic site III on the hMPV F protein and competes for binding with previously discovered mAbs MPE8 and 25P13, both of which cross-react with the respiratory syncytial virus (RSV) F protein. However, MPV364 does not cross-react with the RSV F protein, and the competition profile suggests that it binds to the hMPV F protein in a binding pose slightly shifted from mAbs MPE8 and 25P13. MPV364 was further assessed in vivo and was shown to substantially reduce viral replication in the lungs of BALB/c mice. Overall, these data reveal a new binding region near antigenic site III of the hMPV F protein that elicits potent neutralizing hMPV F-specific mAbs and provide a new panel of neutralizing mAbs that are candidates for therapeutic development.IMPORTANCE Recent progress in understanding the human immune response to respiratory syncytial virus has paved the way for new vaccine antigens and therapeutics to prevent and treat disease. Progress toward understanding the immune response to human metapneumovirus (hMPV) has lagged behind, although hMPV is a leading cause of lower respiratory tract infection in children. In this report, we advanced the field by isolating a panel of human mAbs to the hMPV F protein. One potent neutralizing mAb, MPV364, targets antigenic site III on the hMPV F protein and incorporates two protomers into its epitope yet is unique from previously discovered site III mAbs, as it does not cross-react with the RSV F protein. We further examined MPV364 in vivo and found that it limits viral replication in BALB/c mice. Altogether, these data provide new mAb candidates for therapeutic development and provide insights into hMPV vaccine development.

MhuD from Mycobacterium tuberculosis: Probing a Dual Role in Heme Storage and Degradation.

The Mycobacterium tuberculosis (Mtb) heme oxygenase MhuD liberates free iron by degrading heme to the linear tetrapyrrole mycobilin. The MhuD dimer binds up to two hemes within the active site of each monomer. Binding the first solvent-exposed heme allows heme degradation and releases free iron. Binding a second heme renders MhuD inactive, allowing heme storage. Native-mass spectrometry revealed little difference in binding affinity between solvent-exposed and solvent-protected hemes. Hence, diheme-MhuD is formed even when a large proportion of the MhuD population is in the apo form. Apomyoglobin heme transfer assays showed MhuD-diheme dissociation is far slower than monoheme dissociation at ∼0.12 min-1 and ∼0.25 s-1, respectively, indicating that MhuD has a strong affinity for diheme. MhuD has not evolved to preferentially occupy the monoheme form and, through formation of a diheme complex, it functions as part of a larger network to tightly regulate both heme and iron levels in Mtb.

Colorimetric Sensor Array Based on Wulff-Type Boronate Functionalized AgNPs at Various pH for Bacteria Identification

The efficient identification of bacteria is of considerable significance in clinical diagnosis. Herein, a novel colorimetric sensor array was developed for the detection and identification of bacteria based on the specific affinity and electrostatic interaction between Wulff-type 4-mercaptophenylboronic acid (MPBA)-mercaptoethylamine (MA) cofunctionalized AgNPs (MPBA-MA@AgNPs) and bacteria at various pH. In the neutral and alkaline conditions, AgNPs tended to be dispersed due to the specific affinity between cis-diol residues contained in carbohydrate-rich compositions on the bacterial cell surface and MPBA. Bacterial cells have different carbohydrate compositions on their surface. The differential binding affinity of MPBA on the surface of AgNPs to cis-diol residues of various carbohydrates resulted in a different color change of AgNPs, which could be tuned by pH. On the contrary, AgNPs tended to be aggregated due to the electrostatic interaction between positively charged MA and negatively charged bacteria under acidic conditions. Therefore, using various pH buffer solutions as the sensing elements and MPBA-MA@AgNPs as the indicator, bacteria could be differentiated from each other by their own color response patterns. Moreover, the complex bacteria mixtures could be well discriminated. The method is simple, efficient, and visual and has a potential application in pathogen diagnosis.

Time-resolved FRET and NMR analyses reveal selective binding of peptides containing the LC3-interacting region to ATG8 family proteins

Selective autophagy sequesters cytoplasmic cargo for lysosomal degradation via the binding of autophagy receptors to Atg8 (autophagy-related 8) family proteins on the autophagic membrane. The sole yeast Atg8 gene has six mAtg8 (mammalian Atg8) homologs, including the MAP1LC3 (microtubule-associated protein-1 light chain 3) family and the GABA receptor-associated proteins. Selective autophagy receptors interact with two conserved hydrophobic pockets (termed the W-site and L-site) of mATG8 proteins through a linear motif called the LC3-interacting region (LIR) with the general composition (W/F/Y)XX(I/L/V). To address a lack in our knowledge regarding LIR peptide specificity toward each mATG8 homolog, here we used competitive time-resolved FRET to sensitively and quantitatively characterize the interactions between LIRs and mAtg8. We report that 14 representative LIR-containing peptides display differential binding affinities toward the mAtg8 proteins and identified the LIR domain peptide of TP53INP1 as exhibiting high affinity for all six mATG8 proteins. Using peptide truncation studies, we found that both N- and C-terminal acidic residues, as well as the C-terminal Cys residue of the TP53INP1 LIR peptide, are required for its high-affinity binding to LC3A and LC3B, whereas binding to the GABARAP subfamily proteins was facilitated by residues either N-terminal or C-terminal to the core motif. Finally, we used NMR chemical shift perturbation analysis to gain molecular insights into these findings. Collectively, our results may aid in the development of molecules that selectively disrupt specific mATG8-LIR interactions to dissect the biological roles of the six mATG8 homologs for potential therapeutic applications.

Species differences in ligand interaction and activation of estrogen receptors in fish and human

Estrogen receptor (ER) sequences vary between species and this suggests that there are differences in the ligand-specificity, leading to species-specific effects. This would indicate that it is not possible to generalize effects across species. In this study, we investigated the differences in activation potencies and binding affinities of ER´s alpha (α) and beta (β) in human, zebrafish and sea bream to elucidate species differences in response to estradiol, estrone, estriol and methyltestosterone. In vitro analysis showed that estradiol had the highest activity for all the ER´s except for human ERβ and seabream ERβ2. Alignment of the ligand binding domain and ligand binding pocket (LBP) residues of the three species showed that different residues were involved in the LBPs which led to differences in pocket volume, affected binding affinity and orientation of the ligands. By combining in silico and in vitro results, it was possible to identify the ligand specificities of ER´s. The results demonstrated that the human ER´s show lower resolution in ligand-dependent activation, suggesting higher promiscuity, than the zebrafish and seabream ER´s. These results show species-specificity of ER´s and suggest that species-specific differences must be taken into consideration when studying different exposure scenarios.

Zein Particle-Stabilized Water-In-Water Emulsion as a Vehicle for Hydrophilic Bioactive Compound Loading of Riboflavin.

Vitamins and flavonoids are two kinds of essential trace bioactives which are prone to photodegradation during food processing and storage. In this study, a particle-stabilized water-in-water (W/W) emulsion system composed of soy protein isolate (SPI) and guar gum (GG) was applied in loading riboflavin. Based on the significant binding affinity differences of SPI (Ka = 1.11 × 105 L mol-1) and GG (Ka = 9.00 × 103 L mol-1) to riboflavin, this hydrophilic and light-sensitive bioactive compound was loaded in SPI-rich droplets. Confocal images indicated that a stable microstructure of SPI-rich droplets suspended in GG-rich continuous phase was successfully constructed by manipulating the proportion of the two polymeric components and using zein-based particles (ZPs) as stabilizers. These negatively charged particles modified by pectin with a hydrodynamic diameter of 533 ± 5.7 nm were able to adsorb at the SPI/GG interface and subsequently stabilized the SPI-in-GG emulsion. Fluorescence spectra of riboflavin suggested that the formation of such W/W emulsion could effectively delay the photodegradation of riboflavin during an 8 h ultraviolet irradiation, and its color was maintained to a maximum extent. Therefore, this structured W/W emulsion could be a desired architecture for delivering light-sensitive cargo.

Differential binding affinity of tau repeat region R2 with neuronal-specific \u03b2-tubulin isotypes

Tau is a microtubule-associated protein whose C-terminal domain consisting of four repeat regions R1, R2, R3 and R4 binds to microtubules to stabilize them. In several neurodegenerative diseases, tau detaches from microtubules to form insoluble aggregates leading to tauopathy. Microtubules are made up of αβ tubulin subunits. Seven α-tubulin and nine β-tubulin isotypes have been reported to be present in humans till date. These tubulin isotypes show residue composition variations mainly at C-terminal region and bind to motor proteins and anti-mitotic drugs differently. These tubulin isotypes show tissue specific expression as their relative proportion varies significantly in different type of cells. It is also known that tau binds differently to different cell lines and can either promote or demote microtubule polymerization. However, the relative binding affinity of tau to the different β-tubulin isotypes present in different cell lines is completely unknown. Here, we study relative binding affinity of Tau repeat region R2 to neuronal specific tubulin isotypes βI, βIIb, and βIII using molecular modelling approach. The order of binding energy of tau with tubulin is βIII > βIIb > βI. Our strategy can be potentially adapted to understand differential binding affinity of tau towards β-tubulin isotypes present in other cell lines.

A Novel Determinant of PSMD9 PDZ Binding Guides the Evolution of the First Generation of Super Binding Peptides.

The PDZ domain is one of the most widespread protein interaction domains found in nature. Due to their integral role in numerous biological functions, their ability to act as scaffolds for signal amplification, and the occurrence of mutations linked to human diseases, PDZ domains are attractive therapeutic targets. On the basis of the differential binding affinities of selected C-terminal peptides of the human proteome for one such PDZ domain (PSMD9) and by exploring structure-activity relationships, we design and convert a low-affinity tetrapeptide (∼439 μM) to a tight binding sequence (∼5 μM). The peptide inhibits PSMD9-hnRNPA1 interactions that are critical in basal and stimulus-induced NF-κB signaling and a potential therapeutic target in cancers, including chemotherapy or radiation-induced therapy resistance. Extensive application of computer modeling, including ligand mapping and all-atom molecular dynamics simulations, helps us to rationalize the structural basis for the huge differences in binding affinity and inform us about the residue-wise contributions to the binding energy. Our findings are in accord with the classical preference of the (PSMD9) PDZ domain for C-terminal sequences that contain hydrophobic residues at the P0 (C-terminal) position. In addition, for the first time, we identify a hitherto unknown occupancy for cysteine at the P-2 position that drives high-affinity interaction in a PDZ domain.

Homology Modeling and Molecular Docking Studies of Glutamate Dehydrogenase (GDH) from Cyanobacterium Synechocystis sp. PCC 6803

Glutamate dehydrogenase (GDH), which is present in most bacteria and eukaryotes’ mitochondria, plays an important role in amino acid metabolism. In general, GDH converts 2-oxoglutarate to l-glutamate using NAD(P)H as a cofactor, and vice versa. Acquiring more structural information about the GDH of Synechocystis sp. PCC 6803 could be helpful in many studies related to amino acid metabolism in cyanobacteria. In this study, homology modeling studies were conducted to achieve an acceptable structure of the GDH using recognized templates. To this end, a computational approach was used to demonstrate the coenzyme specificity of GDH for NADPH and NADH. The present study involved homology modeling of GDH and docking analyses of NADPH, NADH, 2-oxoglutarate, and l-glutamate into the predictive model of GDH. The results of this study suggest that GDH has similar coenzyme specificity for NADH and NADPH, while NADH has a better binding affinity than NADPH. Furthermore, the binding sites of 2-oxoglutarate and l-glutamate are similar to each other with differences in binding affinity.

Differences in the Binding Affinity of an HIV-1 V2 Apex-Specific Antibody for the SIVsmm/mac Envelope Glycoprotein Uncouple Antibody-Dependent Cellular Cytotoxicity from Neutralization.

As a consequence of their independent evolutionary origins in apes and Old World monkeys, human immunodeficiency virus type 1 (HIV-1) and simian immunodeficiency viruses of the SIVsmm/mac lineage express phylogenetically and antigenically distinct envelope glycoproteins. Thus, HIV-1 Env-specific antibodies do not typically cross-react with the Env proteins of SIVsmm/mac isolates. Here we show that PGT145, a broadly neutralizing antibody to a quaternary epitope at the V2 apex of HIV-1 Env, directs the lysis of SIVsmm/mac-infected cells by antibody-dependent cellular cytotoxicity (ADCC) but does not neutralize SIVsmm/mac infectivity. Amino acid substitutions in the V2 loop of SIVmac239 corresponding to the epitope for PGT145 in HIV-1 Env modulate sensitivity to this antibody. Whereas a substitution in a conserved N-linked glycosylation site (N171Q) eliminates sensitivity to ADCC, a lysine-to-serine substitution in this region (K180S) increases ADCC and renders the virus susceptible to neutralization. These differences in function correlate with an increase in the affinity of PGT145 binding to Env on the surface of virus-infected cells and to soluble Env trimers. To our knowledge, this represents the first instance of an HIV-1 Env-specific antibody that cross-reacts with SIVsmm/mac Env and illustrates how differences in antibody binding affinity for Env can differentiate sensitivity to ADCC from neutralization.IMPORTANCE Here we show that PGT145, a potent broadly neutralizing antibody to HIV-1, directs the lysis of SIV-infected cells by antibody-dependent cellular cytotoxicity but does not neutralize SIV infectivity. This represents the first instance of cross-reactivity of an HIV-1 Env-specific antibody with SIVsmm/mac Env and reveals that antibody binding affinity can differentiate sensitivity to ADCC from neutralization.

Role of Host–Guest Charge Transfer in Cyclodextrin Complexation: A Computational Study

Charge transfer (CT) was proposed to play a role in the cyclodextrin (CD) complexation with guest molecules. To elucidate the importance of CT interactions, here we used computational methods of quantum mechanics, docking, and molecular dynamics (MD) to investigate α-CD complexes with aromatic guest molecules of nitrobenzene, carboxybenzene, benzoate, 4-nitrophenol, and 4-nitrophenolate. Considering host–guest CT in the docking has more of a chance to search reasonable guest orientations relative to α-CD matching the experiment, compared to that without CT. The CT interaction enlarges the difference in binding affinities of varied guests, as evidenced from potential of mean force (PMF) MD calculations. Energy decomposition of the total enthalpy and entropy shows the CT influence on the binding reactions in detail and indicates that there are considerable compensating effects of individual contributions from the binding partners and surrounding water. Charge transfer reduces the total dipole of α-CD by 9% ...

Abstract 2014: A novel small molecule inhibitor to suppress Notch1 activation in CRC

Abstract Introduction: Earlier we reported that aberrant overexpression of Notch1 in colon cancer patients is responsible for aggressiveness and progression of the disease. Current, therapeutic interventions of notch1 inhibitors that binds catalytic unit of γ-secretase and disrupts the cleavage activity cause gastrointestinal toxicity in clinical trial. Therefore, our study aims to develop a small molecule inhibitor, which inhibits Notch1 signaling but binds outside of γ-secretase’s catalytic unit thereby substantially reducing associated toxicity attributes. Through structure-activity relationship (SAR) studies based on naturally occurring Withaferin A (WA) structure, we have recently identified a WA-difuroate analog ASR458 as one such small molecule. Methods: To analyze the effect of ASR490 on HCT116 and HCT116/Notch1 cells, we performed phenotypic, western blot and in vivo analysis. Results: Notch1 overexpressing CRC cells (HCT/Notch1) showed aggressive cell growth (42%) as compared to HCT116 cells, however, ASR490 treatment inhibited cell growth in both HCT116 (IC50: 600 nM) as well as HCT/Notch1 cells (IC50: 850 nM). ASR458 significantly inhibited Notch1 expression and its downstream events in both the transfected cell lines. As a result, we observed shutdown of pro-survival machinery and induction of pro-apoptotic events (Bax, caspases and PARP) resulting in apoptotic cell death in ASR456 treated HCT116 and Notch1/HCT116 cells. Since Notch1 is responsible for epithelial mesenchyme transition (EMT); we analyzed EMT drivers and readout invasion/migration assays. ASR458 treatment reversed the mesenchymal characteristics by restoring the function of E-cadherin, which resulted in the suppression of invasion and migration in readout assays of HCT116 transfectants. Our ongoing Xenotransplanted mice experiments may suggest whether ASR458 inhibits the growth of HCT116 and HCT116/Notch1 tumors. Conclusion: Restrained gastrointestinal toxicity of Notch1 targeting therapeutics is achievable with novel small molecules displaying a differential binding affinity to γ-secretase. ASR458 inhibits cell growth in Notch1 overexpressing cells and abrogates Notch1 induced EMT. Ongoing molecular docking and in vivo studies may confirm ASR458 binding sites in γ-secretase and validate our in vitro findings respectively. Citation Format: Chendil Damodaran, Ashish Tyagi, Balaji Chandrasekaran, Venkatesh Kolluru, Ibrahim Jojua, Srinivasa Ramisetti, Arun K. Sharma, Murali K. Ankem. A novel small molecule inhibitor to suppress Notch1 activation in CRC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 2014.

Chromatin accessibility plays a key role in selective targeting of Hox proteins

BackgroundHox transcription factors specify segmental diversity along the anterior-posterior body axis in metazoans. While the different Hox family members show clear functional specificity in vivo, they all show similar binding specificity in vitro and a satisfactory understanding of in vivo Hox target selectivity is still lacking.ResultsUsing transient transfection in Kc167 cells, we systematically analyze the binding of all eight Drosophila Hox proteins. We find that Hox proteins show considerable binding selectivity in vivo even in the absence of canonical Hox cofactors Extradenticle and Homothorax. Hox binding selectivity is strongly associated with chromatin accessibility, being highest in less accessible chromatin. Individual Hox proteins exhibit different propensities to bind less accessible chromatin, and high binding selectivity is associated with high-affinity binding regions, leading to a model where Hox proteins derive binding selectivity through affinity-based competition with nucleosomes. Extradenticle/Homothorax cofactors generally facilitate Hox binding, promoting binding to regions in less accessible chromatin but with little effect on the overall selectivity of Hox targeting. These cofactors collaborate with Hox proteins in opening chromatin, in contrast to the pioneer factor, Glial cells missing, which facilitates Hox binding by independently generating accessible chromatin regions.ConclusionsThese studies indicate that chromatin accessibility plays a key role in Hox selectivity. We propose that relative chromatin accessibility provides a basis for subtle differences in binding specificity and affinity to generate significantly different sets of in vivo genomic targets for different Hox proteins.

Precise Generation of Selective Surface-Confined Glycoprotein Recognition Sites.

Since glycoproteins have become increasingly recognized as key players in a wide variety of disease processes, there is an increasing need for advanced affinity materials for highly selective glycoprotein binding. Herein, for the first time, a surface-initiated controlled radical polymerization is integrated with supramolecular templating and molecular imprinting to yield highly reproducible synthetic recognition sites on surfaces with dissociation constants (KD) in the low micromolar range for target glycoproteins and minimal binding to nontarget glycoproteins. Importantly, it is shown that the synthetic strategy has a remarkable ability to distinguish the glycosylated and nonglycosylated forms of the same glycoprotein, with a >5-fold difference in binding affinity. The precise control over the polymer film thickness and positioning of multiple carbohydrate receptors plays a crucial role in achieving an enhanced affinity and selectivity. The generated functional materials of unprecedented glycoprotein recognition performance open up a wealth of opportunities in the biotechnological and biomedical fields.

Structures and chitin-binding properties of two N-terminal lysin motifs (LysMs) found in a chitinase from Volvox carteri.

Two N-terminal lysin motifs (LysMs) found in a chitinase from the green alga Volvox carteri (VcLysM1 and VcLysM2) were produced, and their structures and chitin-binding properties were characterized. The binding affinities of VcLysM1 toward chitin oligomers determined by isothermal titration calorimetry (ITC) were higher than those of VcLysM2 by 0.8-1.1 kcal/mol of ΔG°. Based on the NMR solution structures of the two LysMs, the differences in binding affinities were found to result from amino acid substitutions at the binding site. The NMR spectrum of a two-domain protein (VcLysM1+2), in which VcLysM1 and VcLysM2 are linked in tandem through a flexible linker, suggested that the individual domains of VcLysM1+2 independently fold and do not interact with each other. ITC analysis of chitin-oligomer binding revealed two different binding sites in VcLysM1+2, showing no cooperativity. The binding affinities of the VcLysM1 domain in VcLysM1+2 were lower than those of VcLysM1 alone, probably due to the flexible linker destabilizing the interaction between the chito-oligosaccahrides and VcLysM1 domain. Overall, two LysMs attached to the chitinase from the primitive plant species, V. carteri, were found to resemble bacterial LysMs reported thus far.

Species‐specific differences in heparin‐induced modulation of IL‐12 family cytokines

IL‐12 family cytokines play a central role in the immune system by connecting the activities of innate and adaptive immunity. IL‐12 family members, IL‐12 and IL‐23, share a common p40 subunit that contains a prominent heparin binding domain. We have previously exploited this heparin binding segment for heparin affinity‐based purification of recombinant IL‐12. We also demonstrated that exogenous heparin can enhance IL‐12‐mediated interferon‐gamma (IFN‐g) production. However, the interaction between heparin and IL‐12/IL‐23 at the molecular level and the mechanisms by which heparin modulates the biological functions of these cytokines have not been explored. In addition, little is known about the species dependence of IL‐12 and IL‐23 in the context of sulfated glycosaminoglycans. Using isothermal titration calorimetry (ITC), we found that heparin can bind at micromolar concentrations to both human IL‐12 (hIL‐12) (Kd=9.8±0.2 mM) and murine IL‐12 (mIL‐12) (Kd=45.2±1.1 mM). ITC studies also showed that only heparin molecules longer that 8 saccharide units are able to bind to IL‐12. We confirmed the interaction of heparan sulfate (HS)‐derived compounds and hIL‐12/mIL‐12 via a novel, high throughput glycan microarray. Results from the microarray demonstrated that only HS‐derived molecules with 3 sulfate groups per disaccharide can bind to hIL‐12 and mIL‐12. In bioactivity studies, heparin was found to enhance hIL‐12 and human IL‐23 (hIL‐23) in human cells. On the other hand, though heparin did not increase the activity of mIL‐2 in 2D6 murine lymphocytes or C57BL/6 splenocytes, heparin enhanced the activity of mouse IL‐23 (mIL‐23) in C57BL/6 splenocytes. In cross‐species studies, heparin enhanced mIL‐12 activity in human NK‐9MI cells (1.55‐fold) whereas hIL‐12 was inactive in murine 2D6 cells and remained inactive in the presence of heparin. Interestingly, heparin was found to enhance mIL‐23 in human HEK Blue™ IL‐23 cells and hIL‐23 bioactivities in C57BL/6 splenocytes. Based on these and other data, we developed a working model in which heparin serves as a co‐receptor by stabilizing the hIL‐12/hIL‐12 receptor complex. We hypothesize that the mIL‐12/mIL‐12 receptor complex is sufficiently stable so that it does not benefit from heparin involvement. On the other hand, the interactions of hIL‐12/hIL‐12R, hIL‐23/hIL‐23R, and mIL‐23/mIL‐23R may be less stable so as to benefit from the addition of heparin. Ongoing ITC studies will evaluate the thermodynamics of the hIL‐12/hIL‐12R, mIL‐12/mIL‐12R, hIL‐23/hIL‐23R, and mIL‐23/mIL‐23R complexes in the presence and absence of heparin. Differences in binding affinity may help explain the species‐specific nature of heparin‐enhanced activity of the IL‐12 family cytokines.Support or Funding InformationThis work was supported by funding from the National Institutes of Health, National Cancer Institute (R01CA172631), the Arkansas Biosciences Institute.This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.