Structural Characterization of Human Histone H4.1 by Tandem Nonlinear and Linear Ion Mobility Spectrometry Complemented with Molecular Dynamics Simulations

Extracellular histone H4 is an attractive drug target owing to its roles in organ failure in sepsis and other diseases. To identify inhibitors using in silico methods, information on histone H4 structural dynamics and three-dimensional (3D) structural coordinates is required. Here, DNA-free histone H4 type 1 (H4.1) was characterized by utilizing tandem nonlinear and linear ion mobility spectrometry (FAIMS-TIMS) coupled to mass spectrometry (MS) complemented with molecular dynamics (MD) simulations. The gas-phase structures of H4.1 are dependent on the starting solution conditions, evidenced by differences in charge state distributions, mobility distributions, and collision-induced unfolding (CIU) pathways. The experimental results show that H4.1 adopts diverse conformational types from compact (C) to partially folded (P) and subsequently elongated (E) structures. Molecular dynamics simulations provided candidate structures for the histone H4.1 monomer in solution and for the gas-phase structures observed using FAIMS-IMS-TOF MS as a function of the charge state and mobility distribution. A combination of the FAIMS-TIMS experimental results with theoretical dipole calculations reveals the important role of charge distribution in the dipole alignment of H4.1 elongated structures at high electric fields. A comparison of the secondary and primary structures of DNA-free H2A.1 and H4.1 is made based on the experimental IMS-MS and MD findings.

Structural Heterogeneity of Human Histone H2A.1

Histones are highly basic chromatin proteins that tightly package and order eukaryotic DNA into nucleosomes. While the atomic structure of the nucleosomes has been determined, the three-dimensional structure of DNA-free histones remains unresolved. Here, we combine tandem nonlinear and linear ion mobility spectrometry (FAIMS-TIMS) coupled to mass spectrometry in parallel with molecular modeling to study the conformational space of a DNA-free histone H2A type 1 (H2A.1). Experimental results showed the dependence of the gas-phase structures on the starting solution conditions, characterized by charge state distributions, mobility distributions, and collision-induced-unfolding pathways. The measured H2A.1 gas-phase structures showed a high diversity of structural features ranging from compact (C) to partially folded (P) and then highly elongated (E) conformations. Molecular dynamics simulations provided candidate structures for the solution H2A.1 native conformation with folded N- and C-terminal tails, as well as gas-phase candidate structures associated with the mobility trends. Complementary collision cross section and dipole calculations showed that the charge distribution in the case of elongated gas-phase structures, where basic and acidic residues are mostly exposed (e.g., z > 15+), is sufficient to induce differences in the dipole alignment at high electric fields, in good agreement with the trends observed during the FAIMS-TIMS experiments.

The effect of red wine in modifying the salivary pellicle and modulating dental erosion kinetics

This study investigated the potential of red wine in modulating dental erosion kinetics in the presence or absence of salivary pellicle. Polished human enamel specimens were used in two conditions; presence or absence of acquired enamel pellicle; and subdivided according to exposure: red wine, orange juice, apple juice, or citric acid. The specimens were incubated in clarified whole human saliva (presence of acquired enamel pellicle) or in a humid chamber (absence of acquired enamel pellicle) for 2 h at 37°C, then in the test substances for 1 min, at 25°C, under shaking. This was repeated four times. Surface hardness was measured initially and after each cycle and surface reflection intensity was measured initially and after all cycles. In the presence of acquired enamel pellicle, red wine caused the least surface hardness loss, followed by orange juice, apple juice, and citric acid. Statistically significantly less surface reflection intensity loss was observed for red wine and orange juice than for apple juice and citric acid. In the absence of acquired enamel pellicle, red wine and orange juice caused less surface hardness loss than apple juice and citric acid. Orange juice showed the least surface reflection intensity loss, followed by red wine, citric acid, and apple juice. The polyphenol composition of these drinks can notably modulate the erosion kinetics.

Conformational Plasticity in Human Heme-Based Dioxygenases

Human indoleamine 2,3-dioxygenase 1 (hIDO1) and human tryptophan dioxygenase (hTDO) are two important heme proteins that degrade the essential amino acid, l-tryptophan (Trp), along the kynurenine pathway. The two enzymes share a similar active site structure and an analogous catalytic mechanism, but they exhibit a variety of distinct functional properties. Here we used carbon monoxide (CO) as a structural probe to interrogate how the functionalities of the two enzymes are encoded in their structures. With X-ray crystallography, we detected an unexpected photochemical intermediate trapped in a crystal of the hIDO1-CO-Trp complex, where CO is photolyzed from the heme iron by X-rays at cryogenic temperatures (100 K). The CO photolysis triggers a large-scale migration of the substrate Trp, as well as the photolyzed CO, from the active site to a temporary binding site, Sa*. It is accompanied by a large conformational change to an active site loop, JK-Loop^C, despite the severely restricted protein motion under the frozen conditions, which highlights the remarkable conformational plasticity of the hIDO1 protein. Comparative studies of a crystal of the hTDO-CO-Trp complex show that CO and Trp remain bound in the active site under comparable X-ray illumination, indicating a much more rigid protein architecture. The data offer important new insights into the structure and function relationships of the heme-based dioxygenases and provide new guidelines for structure-based design of inhibitors targeting them.

Structural Basis of Inhibitor Selectivity in Human Indoleamine 2,3-Dioxygenase 1 and Tryptophan Dioxygenase

Indoleamine 2,3-dioxygenase 1 (hIDO1) and tryptophan dioxygenase (hTDO) are two of the only three heme-based dioxygenases in humans. They have recently been identified as key cancer immunotherapeutic drug targets. While structures of hIDO1 in complex with inhibitors have been documented, so far there are no structures of hTDO-inhibitor complexes available. Here we use PF-06840003 (IPD), a hIDO1-selective inhibitor in clinical trials, as a structural probe to elucidate inhibitor-selectivity in hIDO1 versus hTDO. Spectroscopic studies show that IPD exhibits 400-fold higher inhibition activity toward hIDO1 with respect to hTDO. Crystallographic structures reveal that the binding pocket of IPD in the active site in hIDO1 is much more flexible as compared to that in hTDO, which offers a molecular explanation for the superior inhibition activity of IPD in hIDO1 with respect to hTDO. In addition to the IPD bound in the active site, a second IPD molecule was identified in an inhibitory site on the proximal side of the heme in hIDO1 and in an exosite that is ∼40 Å away from the active site in hTDO. Taken together the data provide new insights into structure-based design of mono and dual inhibitors targeting hIDO1 and/or hTDO.

Diaryl hydroxylamines as pan or dual inhibitors of indoleamine 2,3-dioxygenase-1, indoleamine 2,3-dioxygenase-2 and tryptophan dioxygenase

Tryptophan (Trp) catabolizing enzymes play an important and complex role in the development of cancer. Significant evidence implicates them in a range of inflammatory and immunosuppressive activities. Whereas inhibitors of indoleamine 2,3-dioxygenase-1 (IDO1) have been reported and analyzed in the clinic, fewer inhibitors have been described for tryptophan dioxygenase (TDO) and indoleamine 2,3-dioxygenase-2 (IDO2) which also have been implicated more recently in cancer, inflammation and immune control. Consequently the development of dual or pan inhibitors of these Trp catabolizing enzymes may represent a therapeutically important area of research. This is the first report to describe the development of dual and pan inhibitors of IDO1, TDO and IDO2.

Mapping the Binding Trajectory of a Suicide Inhibitor in Human Indoleamine 2,3-Dioxygenase 1

Human indoleamine 2,3-dioxygenase 1 (hIDO1) is an important heme-containing enzyme that is a key drug target for cancer immunotherapy. Several hIDO1 inhibitors have entered clinical trials, among which BMS-986205 (BMS) stands out as the only suicide inhibitor. Despite its "best-in-class" activity, the action mechanism of BMS remains elusive. Here, we report three crystal structures of hIDO1-BMS complexes that define the complete binding trajectory of the inhibitor. BMS first binds in a solvent exposed surface cleft near the active site in an extended conformation. The initial binding partially unfolds the active site, which triggers heme release, thereby exposing a new binding pocket. The inhibitor then undergoes a large scale movement to this new binding pocket, where it binds by adopting a high energy kinked conformation. Finally, the inhibitor relaxes to a bent conformation, via an additional large scale rearrangement, culminating in the energy minimum state. The structural data offer a molecular explanation for the remarkable efficacy and suicide inhibition activity of the inhibitor. They also suggest a novel strategy that can be applied for drug development targeting hIDO1 and related enzymes.

Structural insights into substrate and inhibitor binding sites in human indoleamine 2,3-dioxygenase 1

Human indoleamine 2,3-dioxygenase 1 (hIDO1) is an attractive cancer immunotherapeutic target owing to its role in promoting tumoral immune escape. However, drug development has been hindered by limited structural information. Here, we report the crystal structures of hIDO1 in complex with its substrate, Trp, an inhibitor, epacadostat, and/or an effector, indole ethanol (IDE). The data reveal structural features of the active site (Sa) critical for substrate activation; in addition, they disclose a new inhibitor-binding mode and a distinct small molecule binding site (Si). Structure-guided mutation of a critical residue, F270, to glycine perturbs the Si site, allowing structural determination of an inhibitory complex, where both the Sa and Si sites are occupied by Trp. The Si site offers a novel target site for allosteric inhibitors and a molecular explanation for the previously baffling substrate-inhibition behavior of the enzyme. Taken together, the data open exciting new avenues for structure-based drug design.

Human indoleamine 2,3-dioxygenase 1 (hIDO1) is an immunotherapeutic target for cancer therapy. Here, the authors present the substrate-, inhibitor- and effector-bound hIDO1 crystal structures, which give insights into the mechanism and reveal a second small molecule binding site, which is of interest for drug design.

RETRACTED: Surface modification for stability of nano-sized silica colloids

The surfaces of commercial 30-nm colloidal silica particles were modified by reacting with functional silanes. The high specific surface area and reactivity of the particles due to the small size make the process susceptible to irreversible aggregation not found previously with larger particles. This study compares surface charge results from different reaction conditions and characterization methods. Measurements of the zeta potential as a function of pH and gelation kinetics shed light on the mechanism of instability in nano-sized silica suspensions. Experimental results showed that very stable particles can be suspended in a nonaqueous solvent after refluxing of the silica particles, while maintaining the original particles physical properties of size and electrochemical behavior. Extremely stable particles are obtained by aminosilane surface modification. Factors affecting susceptibility of small particles to irreversible aggregation caused by a nonaqueous solvent or a high concentration of a trialkoxysilane, including the large amount of reactive silanol groups on the surface gel layer of the particles, are discussed.

Surface Charge Modification of Nano-Sized Silica Colloid

The surface of commercial 30-nm colloidal silica particles were modified by reaction with functional silanes. The high specific surface area and reactivity of the particles, due to their small size, makes the process susceptible to irreversible aggregation not found previously with larger particles. The present study compares surface charge results from amino silanes with one or three alkoxy groups. Measurements of the zeta potential as a function of pH, and gelation kinetics shed light on the mechanism of surface charge changes from the modification. Instability in suspensions before and after the surface modification is also studied using a new data analysis technique from simple light-scattering equipment. Experimental results show very stable particles are obtained by amino silane surface modification. Factors affecting susceptibility of small particles to irreversible aggregation caused by a non-aqueous solvent or high concentration of a trialkoxy silane, including the large number of reactive silanol groups in the surface gel layer of the particles, are discussed.

Glasses in hard spheres with short-range attraction

We report a detailed experimental study of the structure and dynamics of glassy states in hard spheres with short-range attraction. The system is a suspension of nearly hard-sphere colloidal particles and nonadsorbing linear polymer which induces a depletion attraction between the particles. Observation of crystallization reveals a reentrant glass transition. Static light scattering shows a continuous change in the static structure factors upon increasing attraction. Dynamic light scattering results, which cover 11 orders of magnitude in time, are consistent with the existence of two distinct kinds of glasses, those dominated by interparticle repulsion and caging, and those dominated by attraction. Samples close to the "A3 point" predicted by mode coupling theory for such systems show very slow, logarithmic dynamics.

Multiple glassy states in a simple model system

Experiments, theory, and simulation were used to study glass formation in a simple model system composed of hard spheres with short-range attraction ("sticky hard spheres"). The experiments, using well-characterized colloids, revealed a reentrant glass transition line. Mode-coupling theory calculations and molecular dynamics simulations suggest that the reentrance is due to the existence of two qualitatively different glassy states: one dominated by repulsion (with structural arrest due to caging) and the other by attraction (with structural arrest due to bonding). This picture is consistent with a study of the particle dynamics in the colloid using dynamic light scattering.

Current Chemistry: Synthetic Opal as Two-Dimensional and Three-Dimensional Nanotemplates

Manuscript received: 3 October 2001. Final version: 7 January 2002.