Structure‐Based and in silico Design of Hsp90 Inhibitors

The molecular chaperone Hsp90 is responsible for activation and stabilization of several oncoproteins in cancer cells, and has emerged as an important target in cancer treatment because of this pivotal role. In recent years, interests have arisen around structure‐based design of small molecules aimed at inhibiting the chaperone activity of Hsp90. In this review, we illustrate the recent advances in structure‐based and in silico strategies aimed at discovering and optimizing Hsp90 inhibitors.     

Structure‐Based and Fragment‐Based GPCR Drug Discovery

G protein‐coupled receptors (GPCRs) are an important family of membrane proteins; historically, drug discovery in this target class has been fruitful, with many of the world’s top‐selling drugs being GPCR modulators. Until recently, the modern techniques of structure‐ and fragment‐based drug discovery had not been fully applied to GPCRs, primarily because of the instability of these proteins when isolated from their cell membrane environments. Recent advances in receptor stabilisation have facilitated major advances in GPCR structural biology over the past six years, with 21 new receptor targets successfully crystallised with one or more ligands. The dramatic increase in GPCR structural information has yielded an increased use of structure‐based methods for hit identification and progression, which are reviewed herein. Additionally, a number of fragment‐based drug discovery techniques have been validated for use with GPCRs in recent years; these approaches and their use in hit identification are reviewed.     

Truncation and Optimisation of Peptide Inhibitors of Cyclin‐Dependent Kinase 2‐Cyclin A Through Structure‐Guided Design

Peptides that inhibit cyclin‐dependent kinase 2 by blocking the macromolecular substrate recruitment site of cyclin A were simplified, for example, by replacement of dipeptide units with β‐amino acids. The smallest inhibitor retaining activity was a tripeptide, whose binding mode was confirmed by X‐ray crystallography. This result suggests that nonpeptidic cyclin groove inhibitors may be feasible therapeutic agents.

     

Perspectives on Inhibiting β‐Amyloid Aggregation through Structure‐Based Drug Design

Targeting β‐amyloid (Aβ) remains the most desired strategy in Alzheimer’s disease (AD) drug discovery research. Many peptides that specifically target Aβ aggregates are known, encompassing efforts from both industrial and academic research settings. However, in clinical terms, not much success has been gained with peptide research; in turn, small drug‐like molecules are already globally recognized as showing promise as an alternate approach. Aβ aggregation inhibitors are the most important part of the multifunctional drug design regimen for treating AD. Unfortunately, rational drug design approaches with small molecules are still in the initial stages. Herein we highlight, update, and elaborate on the structural anatomy of Aβ and known Aβ aggregation inhibitors in hopes of helping to optimize their use in structure‐based drug design approaches toward inhibitors with greater specificity. Furthermore, we present the first review of efforts to target a previously uncharacterized region of acetylcholinesterase: the N‐terminal 7–20 sub‐region, which was experimentally elucidated to participate in Aβ aggregation and deposition.     

Structure‐Based Design of a Monosaccharide Ligand Targeting Galectin‐8

Galectin‐8 is a β‐galactoside‐recognising protein that has a role in the regulation of bone remodelling and is an emerging new target for tackling diseases with associated bone loss. We have designed and synthesised methyl 3‐O‐[1‐carboxyethyl]‐β‐d ‐galactopyranoside (compound 6 ) as a ligand to target the N‐terminal domain of galectin‐8 (galectin‐8N). Our design involved molecular dynamics (MD) simulations that predicted 6 to mimic the interactions made by the galactose ring as well as the carboxylic acid group of 3′‐O‐sialylated lactose (3′‐SiaLac), with galectin‐8N. Isothermal titration calorimetry (ITC) determined that the binding affinity of galectin‐8N for 6 was 32.8 μm , whereas no significant affinity was detected for the C‐terminal domain of galectin‐8 (galectin‐8C). The crystal structure of the galectin‐8N– 6 complex validated the predicted binding conformation and revealed the exact protein–ligand interactions that involve evolutionarily conserved amino acids of galectin and also those unique to galectin‐8N for recognition. Overall, we have initiated and demonstrated a rational ligand design campaign to develop a monosaccharide‐based scaffold as a binder of galectin‐8.     

Prospective Virtual Screening in a Sparse Data Scenario: Design of Small‐Molecule TLR2 Antagonists

Toll‐like receptors (TLRs) are critical signaling molecules with roles in various severe clinical conditions such as sepsis and rheumatoid arthritis, and have therefore been advocated as promising drug targets for the treatment of these diseases. The aim of this study was to discover small‐molecule antagonists of TLR2 by computer‐aided drug design. This goal poses several challenges due to the lack of available data on TLR2 modulators. To overcome these hurdles we developed a combined structure‐ and ligand‐based virtual screening approach. First, we calculated molecular interaction fields of the TLR2 binding site to derive a structure‐based 3D pharmacophore, which was then used for virtual screening. We then performed a two‐step shape‐ and feature‐based similarity search using known TLR2 ligands as query structures. A selection of virtual screening hits was biologically tested in a cell‐based assay for TLR2 signaling inhibition, leading to the identification of several compounds with antagonistic activity (IC₅₀ values) in the low‐micromolar range.     

Structure‐Based Design,Synthesis, and Evaluation of 2′‐(2‐Hydroxyethyl)‐2′‐deoxyadenosine and the 5′‐Diphosphate Derivative as Ribonucleotide Reductase Inhibitors

Analysis of the recently solved X‐ray crystal structures of Saccharomyces cerevisiae ribonucleotide reductase I (ScRnr1) in complex with effectors and substrates led to the discovery of a conserved water molecule located at the active site that interacted with the 2′‐hydroxy group of the nucleoside ribose. In this study 2′‐(2‐hydroxyethyl)‐2′‐deoxyadenosine 1 and the 5′‐diphosphate derivative 2 were designed and synthesized to see if the conserved water molecule could be displaced by a hydroxymethylene group, to generate novel RNR inhibitors as potential antitumor agents. Herein we report the synthesis of analogues 1 and 2 , and the co‐crystal structure of adenosine diphosphate analogue 2 bound to ScRnr1, which shows the conserved water molecule is displaced as hypothesized.     

Pharmacophore‐Based Design of Novel Oxadiazoles as Selective Sphingosine‐1‐phosphate (S1P) Receptor Agonists with in vivo Efficacy

Sphingosine‐1‐phosphate (S1P) receptor agonists have shown promise as therapeutic agents for multiple sclerosis (MS) due to their regulatory roles within the immune, central nervous system, and cardiovascular system. Here, the design and optimization of novel [1,2,4]oxadiazole derivatives as selective S1P receptor agonists are described. The structure–activity relationship exploration was carried out on the three dominant segments of the series: modification of the polar head group (P), replacement of the oxadiazole linker (L) with different five‐membered heterocycles, and the use of diverse 2,2′‐disubstituted biphenyl moieties as the hydrophobic tail (H). All three segments have a significant impact on potency, S1P receptor subtype selectivity, physicochemical properties, and in vitro absorption, distribution, metabolism, excretion and toxicity (ADMET) profile of the compounds. From these optimization studies, a selective S1P₁ agonist, N‐methyl‐N‐(4‐{5‐[2‐methyl‐2′‐(trifluoromethyl)biphenyl‐4‐yl]‐1,2,4‐oxadiazol‐3‐yl}benzyl)glycine ( 45 ), and a dual S1P_1,5 agonist, N‐methyl‐N‐(3‐{5‐[2′‐methyl‐2‐(trifluoromethyl)biphenyl‐4‐yl]‐1,2,4‐oxadiazol‐3‐yl}benzyl)glycine ( 49 ), emerged as frontrunners. These compounds distribute predominantly in lymph nodes and brain over plasma and induce long lasting decreases in lymphocyte count after oral administration. When evaluated head‐to‐head in an experimental autoimmune encephalomyelitis mouse model, together with the marketed drug fingolimod, a pan‐S1P receptor agonist, S1P_1,5 agonist 49 demonstrated comparable efficacy while S1P₁‐selective agonist 45 was less potent. Compound 49 is not a prodrug, and its improved property profile should translate into a safer treatment of relapsing forms of MS.     

Structure‐Based Design of Potent Small‐Molecule Binders to the S‐Component of the ECF Transporter for Thiamine

Energy‐coupling factor (ECF) transporters are membrane‐protein complexes that mediate vitamin uptake in prokaryotes. They bind the substrate through the action of a specific integral membrane subunit (S‐component) and power transport by hydrolysis of ATP in the three‐subunit ECF module. Here, we have studied the binding of thiamine derivatives to ThiT, a thiamine‐specific S‐component. We designed and synthesized derivatives of thiamine that bind to ThiT with high affinity; this allowed us to evaluate the contribution of the functional groups to the binding affinity. We determined six crystal structures of ThiT in complex with our derivatives. The structure of the substrate‐binding site in ThiT remains almost unchanged despite substantial differences in affinity. This work indicates that the structural organization of the binding site is robust and suggests that substrate release, which is required for transport, requires additional changes in conformation in ThiT that might be imposed by the ECF module.     

Development of Tetrachlorophthalimides as Liver X Receptor β (LXRβ)‐Selective Agonists

Liver X receptor (LXR) agonists are candidates for the treatment of atherosclerosis via induction of ABCA1 (ATP‐binding cassette A1) gene expression, which contributes to reverse cholesterol transport (RCT) and to cholesterol efflux from the liver and intestine. However, LXR agonists also induce genes involved in lipogenesis, such as SREBP‐1c (sterol regulatory binding element protein 1c) and FAS (fatty acid synthase), thereby causing an undesirable increase in plasma and hepatic triglyceride (TG) levels. Recent studies indicate that LXRα contributes to lipogenesis in liver, and selective LXRβ activation improves RCT in mice. Therefore, LXRβ‐selective agonists are promising candidates to improve atherosclerosis without increasing plasma or hepatic TG levels. However, the ligand‐binding domains in the two LXR isoforms α/β share high sequence identity, and few LXR ligands show subtype selectivity. In this study we identified a tetrachlorophthalimide analogue as an LXRβ‐selective agonist. Structural development led to (E)‐4,5,6,7‐tetrachloro‐2‐(2‐styrylphenyl)isoindoline‐1,3‐dione ( 24 a ), which shows potent and selective LXRβ agonistic activity in reporter gene assays. In binding assays, compound 24 a bound to LXRβ preferentially over LXRα. It also induced the expression of ABCA1 mRNA but not SREBP‐1c mRNA in cells. Compound 24 a appears to be a promising lead compound for therapeutic agents to treat atherosclerosis without the side effects induced by LXRα/β dual agonists.     

Structure‐Based Design of a Eukaryote‐Selective Antiprotozoal Fluorinated Aminoglycoside

Aminoglycosides (AG) are antibiotics that lower the accuracy of protein synthesis by targeting a highly conserved RNA helix of the ribosomal A‐site. The discovery of AGs that selectively target the eukaryotic ribosome, but lack activity in prokaryotes, are promising as antiprotozoals for the treatment of neglected tropical diseases, and as therapies to read‐through point‐mutation genetic diseases. However, a single nucleobase change A1408G in the eukaryotic A‐site leads to negligible affinity for most AGs. Herein we report the synthesis of 6′‐fluorosisomicin, the first 6′‐fluorinated aminoglycoside, which specifically interacts with the protozoal cytoplasmic rRNA A‐site, but not the bacterial A‐site, as evidenced by X‐ray co‐crystal structures. The respective dispositions of 6′‐fluorosisomicin within the bacterial and protozoal A‐sites reveal that the fluorine atom acts only as a hydrogen‐bond acceptor to favorably interact with G1408 of the protozoal A‐site. Unlike aminoglycosides containing a 6′‐ammonium group, 6′‐fluorosisomicin cannot participate in the hydrogen‐bonding pattern that characterizes stable pseudo‐base‐pairs with A1408 of the bacterial A‐sites. Based on these structural observations it may be possible to shift the biological activity of aminoglycosides to act preferentially as antiprotozoal agents. These findings expand the repertoire of small molecules targeting the eukaryotic ribosome and demonstrate the usefulness of fluorine as a design element.     

Structure‐Based Design of Small‐Molecule Ligands of Phosphofructokinase‐2 Activating or Inhibiting Glycolysis

Glycolysis lies at the basis of metabolism and cell energy supply. The disregulation of glycolysis is involved in such pathological processes as cancer proliferation, neurodegenerative diseases, and amplification of ischemic damage. Phosphofructokinase‐2 (PFK‐2), a bifunctional enzyme and regulator of glycolytic flux, has recently emerged as a promising anticancer target. Herein, the computer‐aided design of a new class of aminofurazan‐triazole regulators of PFK‐2 is described along with the results of their in vitro evaluation. The aminofurazan‐triazoles differ from other recently described inhibitors of PFK‐2 and demonstrate the ability to modulate glycolytic flux in rat muscle lysate, producing a twofold decrease by inhibitors and fourfold increase by activators. The most potent compounds in the series were shown to inhibit the kinase activity of the hypoxia‐inducible form of PFK‐2, PFKFB3, as well as proliferation of HeLa, lung adenocarcinoma, colon adenocarcinoma, and breast cancer cells at concentrations in the low micromolar range.     

Novel method of preparation of a charged mosaic membrane by using dipole‐like microspheres. II. Preparation of dumbbell/egg‐like microspheres

The dumbbell‐like/egglike microspheres of poly(4‐vinylpyridine/n‐butyl acrylate)/polystyrene [P(4VP/nBA)/PS] were prepared by soap‐free seed emulsion polymerization. The effects of various polymerization parameters, such as the amount of ethyl acetate (EA) in the continuous phase, swelling time, degree of crosslinking of seed polymer, polymerization temperature, and compatibility of seed polymer and the secondary polymer, and so forth, on the formation of dumbbell‐like/egglike morphology were investigated by scanning electron microscopy (SEM) and transmission electron microscopy (TEM). It was found that secondary particles could be eliminated either by drastically increasing the number of seed particles or by stripping EA from the seed latex by dialysis and evaporation under a vacuum. Swelling the seed particle with the secondary monomer was essential for the preparation of egglike microspheres. For the localization of PS domains on one side of the egglike particle, the most effective factors were to elevate the polymerization temperature up to 90°C and simultaneously to lower the compatibility of the polymer on the seed particle surface with the phase of PS, while using the uncrosslinked seed latex. Crosslinking the seed latex was not suitable for localizing the PS domains in the seed particle, especially when the degree of crosslinking exceeded 0.5 wt % of EGDMA. © 2001 John Wiley & Sons, Inc. J Appl Polym Sci 80: 2002–2017, 2001     

Synthesis and characterization of ethoxy‐terminated ladder‐like polymethylsilsesquioxane oligomer

A fully ethoxy‐terminated ladder‐like polymethylsilsesquioxane oligomer (EtO‐Me‐T) has been synthesized and characterized for the first time using an effective transient catalyst (tetramethylammonium hydroxide, TMAH) via the dehydration alcoholysis reaction of hydroxy‐terminated ladder‐like polymethylsilsesquioxane (HO‐Me‐T) prepared by a modified stepwise coupling polymerization approach. Compared with the common acidic or basic catalysts, use of the transient catalyst TMAH can not only make the HO‐Me‐T molecules fully ethoxy‐terminated but also enables the catalyst to be readily and thoroughly removed after completion of the alcoholysis reaction. It is noteworthy that the common acidic or basic catalysts widely used in the dehydration alcoholysis reaction are clearly unsuitable for the preparation of EtO‐Me‐T oligomer because the latter would be hydrolyzed unavoidably back to the parent HO‐Me‐T during the washing process. In addition, preliminary exploration indicates that, when compared with the tetraethyl orthosilicate (Si(OEt)₄) generally used as a crosslinking agent for the room‐temperature vulcanization of silicone rubber (RTV‐SR), the oligomer EtO‐Me‐T is a promising replacement which can greatly improve the mechanical properties of RTV‐SR Copyright © 2003 Society of Chemical Industry     

EPA and DHA Exposure Alters the Inflammatory Response but not the Surface Expression of Toll‐like Receptor 4 in Macrophages

Dietary intake of eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA) and their respective enrichment in cell membranes have been negatively associated with atherosclerotic lesion development. This effect may be mediated, in part, by dampened inflammatory response of macrophages triggered by toll‐like receptor 4 (TLR4) activation. This study investigated the influence of membrane fatty acid profile on TLR4‐mediated inflammation in RAW 264.7 macrophages. Cells pretreated with myristic acid (MA), EPA, DHA or vehicle control for 24 h were stimulated with ultra‐pure LPS, a specific TLR4 agonist, for 6 or 24 h, corresponding to early and late stages of TNFα and IL‐6 protein induction. Treatment significantly increased cell membrane MA, EPA, and DHA by 4.5‐, 20.6‐, and 8.9‐fold, respectively. MA significantly increased IL‐6 secretion 6 h post‐exposure to the fatty acid, but did not change TNFα secretion in response to any other treatment condition. EPA and DHA significantly reduced TNFα secretion by 36 and 41 %, respectively, in cells stimulated for 24 h but not 6 h. In contrast, EPA and DHA significantly reduced IL‐6 secretion at both 6 h (67 and 72 %, respectively) and 24 h (69 and 72 %, respectively). MA or DHA treatment had no significant effect compared to vehicle on factors influencing cellular LPS recognition, including LPS‐cell association, and cell surface expression of TLR4, TLR4‐MD2 complex, and CD14. These data suggest that membrane fatty acid profiles influence the TLR4‐mediated inflammatory response in macrophages, via mechanisms that occur downstream of TLR4 receptor activation.     

Preparation and property of raspberry‐like AS/SiO2 nanocomposite particles

Surfactant‐free poly(acrylonitrile‐co‐styrene)/silica (AS/SiO₂) nanocomposite particles was synthesized in the presence of cheap, commercially amorphous aqueous silica sol at ambient temperature. Thermogravimetric analysis (TGA) indicated silica contents ranging from 5 wt % to 29 wt %, depending on reaction conditions. Particle size distributions and morphologies were studied using dynamic light scattering (DLS) and transmission electron microscopy (TEM), which clearly showed that most of the colloidal nanocomposites comprised approximately spherical particle with raspberry‐like morphology and relatively narrow size distributions. The optical clarity of solution‐cast nanocomposite films was assessed using UV–vis spectrometer, with high transmission being obtained over the whole visible spectrum. Differential scanning calorimetry (DSC) studies showed that the glass transition temperature of AS/SiO₂ nanocomposites can be higher than the corresponding pure AS, resulting from the hydrophilicity of the nanometer silica. The robustness and simplicity of this method may make large‐scale manufacture of this nanocomposite possible. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 415–421, 2007     

Structure‐Based Design of New KSP‐Eg5 Inhibitors Assisted by a Targeted Multicomponent Reaction

An integrated multidisciplinary approach that combined structure‐based drug design, multicomponent reaction synthetic approaches and functional characterization in enzymatic and cell assays led to the discovery of new kinesin spindle protein (KSP) inhibitors with antiproliferative activity. A focused library of new benzimidazoles obtained by a Ugi+Boc removal/cyclization reaction sequence generated low‐micromolar‐range KSP inhibitors as promising anticancer prototypes. The design and functional studies of the new chemotypes were assessed by computational modeling and molecular biology techniques. The most active compounds— 20 (IC₅₀=1.49 μM , EC₅₀=3.63 μM ) and 22 (IC₅₀=1.37 μM , EC₅₀=6.90 μM )—were synthesized with high efficiency by taking advantage of the multicomponent reactions.