Polypeptide conjugate binders that discriminate between two isoforms of human carbonic anhydrase in human blood

Two binder candidates 4‐C37L34‐B and 3‐C15L8‐B from a 16‐membered set of 42‐residue polypeptide conjugates designed to bind human carbonic anhydrase II (HCAII), were shown to bind HCAII with high affinity in a fluorescence‐based screening assay. Two carbonic anhydrase isoforms with 60 % homology exist in human blood with HCAI being present in five‐ to sevenfold excess over HCAII. The ability of the binders to discriminate between HCAI and HCAII was evaluated with regard to what selectivity could be achieved by the conjugation of polypeptides from a 16‐membered set to a small organic molecule that binds both isoforms with similar affinities. The polypeptide conjugate 4‐C37L34‐B bound HCAII with a K_D of 17 nM and HCAI with a K_D of 470 nM , that is, with a 30‐fold difference in affinity. The corresponding dissociation constants for the complexes formed from 3‐C15L8‐B and the two carbonic anhydrases were 60 and 390 nM , respectively. This demonstration of selectivity between two very similar proteins is striking in view of the fact that the molecular weight of each one of the conjugate molecules is little more than 5000, the fold is unordered, and the polypeptide sequences were designed de novo and have no prior relationship to carbonic anhydrases. The results suggest that synthetic polypeptide conjugates can be prepared from organic molecules that are considered to be weak binders with low selectivity, yielding conjugates with properties that make them attractive alternatives to biologically generated binders in biotechnology and biomedicine.     

Slowly on,Slowly off: Bisubstrate‐Analogue Conjugates of 5‐Iodotubercidin and Histone H3 Peptide Targeting Protein Kinase Haspin

The atypical protein kinase haspin is a key player in mitosis by catalysing the phosphorylation of Thr3 in histone H3, and thus ensuring the normal function of the chromosomal passenger complex. Here, we report the development of bisubstrate‐analogue inhibitors targeting haspin. The compounds were constructed by linking 5‐iodotubercidin to the N terminus of histone H3 peptide. The new conjugates show high affinity (sub‐nanomolar K_D) towards haspin as well as slow kinetics of association and dissociation (residence time of several hours). This reflects a unique binding mode and translated into improved selectivity. The latter was confirmed in a biochemical binding/displacement assay with a panel of ten protein kinases, in a thermal shift assay with off‐targets of 5‐iodotubercidin (adenosine kinase and the Cdc2‐like kinase family) and in assay with spiked HeLa cell lysate.     

A DFT Study on the Structures and Energies of Isomers of 4‐Amino‐1,3‐dinitro‐1,2,4‐triazol‐5‐one‐2‐oxide: New High Energy Density Compounds

Isomers of 4‐amino‐1,3‐dinitrotriazol‐5‐one‐2‐oxide (ADNTONO) are of interest in the contest of insensitive explosives and were found to have true local energy minima at the DFT‐B3LYP/aug‐cc‐pVDZ level. The optimized structures, vibrational frequencies and thermodynamic values for triazol‐5‐one N‐oxides were obtained in their ground state. Kamlet‐Jacob equations were used to evaluate the performance properties. The detonation properties of ADNTONO (D=10.15 to 10.46 km s⁻¹, P=50.86 to 54.25 GPa) are higher compared with those of 1,1‐diamino‐2,2‐dinitroethylene (D=8.87 km s⁻¹, P=32.75 GPa), 5‐nitro‐1,2,4‐triazol‐3‐one (D=8.56 km s⁻¹, P=31.12 GPa), 1,2,4,5‐tetrazine‐3,6‐diamine‐1,4‐dioxide (D=8.78 km s⁻¹, P=31.0 GPa), 1‐amino‐3,4,5‐trinitropyrazole (D=9.31 km s⁻¹, P=40.13 GPa), 4,4′‐dinitro‐3,3′‐bifurazan (D=8.80 km s⁻¹, P=35.60 GPa) and 3,4‐bis(3‐nitrofurazan‐4‐yl)furoxan (D=9.25 km s⁻¹, P=39.54 GPa). The  NH₂ group(s) appears to be particularly promising area for investigation since it may lead to two desirable consequences of higher stability (insensitivity), higher density, and thus detonation velocity and pressure.     

Lasioglossins: Three Novel Antimicrobial Peptides from the Venom of the Eusocial Bee Lasioglossum laticeps (Hymenoptera: Halictidae)

Three novel structurally related pentadecapeptides, named lasioglossins, were isolated from the venom of the eusocial bee Lasioglossum laticeps. Their primary sequences were established as H‐Val‐Asn‐Trp‐Lys‐Lys‐Val‐Leu‐Gly‐Lys‐Ile‐Ile‐Lys‐Val‐Ala‐Lys‐NH₂ (LL‐I), H‐Val‐Asn‐Trp‐Lys‐Lys‐Ile‐Leu‐Gly‐Lys‐Ile‐Ile‐Lys‐Val‐Ala‐Lys‐NH₂ (LL‐II) and H‐Val‐Asn‐Trp‐Lys‐Lys‐Ile‐Leu‐Gly‐Lys‐Ile‐Ile‐Lys‐Val‐Val‐Lys‐NH₂ (LL‐III). These lasioglossins exhibited potent antimicrobial activity against both Gram‐positive and Gram‐negative bacteria, low haemolytic and mast cell degranulation activity, and a potency to kill various cancer cells in vitro. The lasioglossin CD spectra were measured in the presence of trifluoroethanol and sodium dodecyl sulfate solution and indicated a high degree of α‐helical conformation. NMR spectroscopy, which was carried out in trifluoroethanol/water confirmed a curved α‐helical conformation with a concave hydrophobic and convex hydrophilic side. To understand the role of this bend on biological activity, we studied lasioglossin analogues in which the Gly in the centre of the molecule was replaced by other amino acid residues (Ala, Lys, Pro). The importance of the N‐terminal part of the molecule to the antimicrobial activity was revealed through truncation of five residues from both the N and C termini of the LL‐III peptide. C‐terminal deamidation of LL‐III resulted in a drop in antimicrobial activity, but esterification of the C terminus had no effect. Molecular modelling of LL‐III and the observed NOE contacts indicated the possible formation of a bifurcated H‐bond between hydrogen from the Lys15 CONH peptide bond and one H of the C‐terminal CONH₂ to the Ile11 oxygen atom. Such interactions cannot form with C‐terminal esterification.     

Structure‐Based Virtual Screening for Dopamine D2 Receptor Ligands as Potential Antipsychotics

Structure‐based virtual screening using a D₂ receptor homology model was performed to identify dopamine D₂ receptor ligands as potential antipsychotics. From screening a library of 6.5 million compounds, 21 were selected and were subjected to experimental validation. From these 21 compounds tested, ten D₂ ligands were identified (47.6 % success rate, among them D₂ receptor antagonists, as expected) that have additional affinity for other receptors tested, in particular 5‐HT_2A receptors. The affinity (K_i values) of the compounds ranged from 58 nm to about 24 μm . Similarity and fragment analysis indicated a significant degree of structural novelty among the identified compounds. We found one D₂ receptor antagonist that did not have a protonatable nitrogen atom, which is a key structural element of the classical D₂ pharmacophore model necessary for interaction with the conserved Asp(3.32) residue. This compound exhibited greater than 20‐fold binding selectivity for the D₂ receptor over the D₃ receptor. We provide additional evidence that the amide hydrogen atom of this compound forms a hydrogen bond with Asp(3.32), as determined by tests of its derivatives that cannot maintain this interaction.     

2‐Amino[1,2,4]triazolo[1,5‐c]quinazolines and Derived Novel Heterocycles: Syntheses and Structure–Activity Relationships of Potent Adenosine Receptor Antagonists

2‐Amino[1,2,4]triazolo[1,5‐c]quinazolines were identified as potent adenosine receptor (AR) antagonists. Synthetic strategies were devised to gain access to a broad range of derivatives including novel polyheterocyclic compounds. Potent and selective A₃AR antagonists were discovered, including 3,5‐diphenyl[1,2,4]triazolo[4,3‐c]quinazoline ( 17 , K_i human A₃AR 1.16 nm ) and 5′‐phenyl‐1,2‐dihydro‐3′H‐spiro[indole‐3,2′‐[1,2,4]triazolo[1,5‐c]quinazolin]‐2‐one ( 20 , K_i human A₃AR 6.94 nm ). In addition, multitarget antagonists were obtained, such as the dual A₁/A₃ antagonist 2,5‐diphenyl[1,2,4]triazolo[1,5‐c]quinazoline ( 13 b , K_i human A₁AR 51.6 nm , human A₃AR 11.1 nm ), and the balanced pan‐AR antagonists 5‐(2‐thienyl)[1,2,4]triazolo[1,5‐c]quinazolin‐2‐amine ( 11 c , K_i human A₁AR 131 nm , A_2AAR 32.7 nm , A_2BAR 150 nm , A₃AR 47.5 nm ) and 9‐bromo‐5‐phenyl[1,2,4]triazolo[1,5‐c]quinazolin‐2‐amine ( 11 q , K_i human A₁AR 67.7 nm , A_2AAR 13.6 nm , A_2BAR 75.0 nm , A₃AR 703 nm ). In many cases, significantly different affinities for human and rat receptors were observed, which emphasizes the need for caution in extrapolating conclusions between different species.     

High‐Pressure Behavior of Mullite: An X‐Ray Diffraction Investigation

Using synchrotron X‐ray diffraction and diamond anvil cells we performed in situ high‐pressure studies of mullite‐type phases of general formula Al_4+2xSi_2?2xO_10?x and differing in the amount of oxygen vacancies: 2:1‐mullite (x = 0.4), 3:2‐mullite (x = 0.25), and sillimanite (x = 0). The structural stability of 2:1‐mullite, 3:2‐mullite, and sillimanite was investigated up to 40.8, 27.3, and 44.6 GPa, respectively, in quasi‐hydrostatic conditions, at ambient temperature. This is the first report of a static high‐pressure investigation of Al₂O₃–SiO₂ mullites. It was found that oxygen vacancies play a significant role in the compression mechanisms of the mullites by decreasing the mechanical stability of the phases with the number of vacancies. Elevated pressure leads to an irreversible amorphization above ~20 GPa for 2:1‐mullite and above 22 GPa for 3:2‐mullite. In sillimanite, only a partial amorphization is observed above 30 GPa. Based on Rietveld structural refinements of high‐pressure X‐ray diffraction patterns, the pressure‐driven evolution of unit cell parameters is presented. The experimental bulk moduli obtained are as follows: K₀ = 162(7) GPa with K₀′ = 2.2(6) for 2:1‐mullite, K₀ = 173(7) GPa with K₀′ = 2.3(2) for 3:2‐mullite, K₀ = 167(7) GPa with K₀′ = 2.1(4) for sillimanite.     

Lipocalin‐Type Prostaglandin D Synthase Is a Novel Phytocannabinoid‐Binding Protein

Lipocalin‐type prostaglandin D synthase (L‐PGDS; EC:5.3.99.2) is an enzyme with dual functional roles as a prostaglandin D₂‐synthesizing enzyme and as an extracellular transporter for diverse lipophilic compounds in the cerebrospinal fluid (CSF). Transport of hydrophobic endocannabinoids is mediated by serum albumin in the blood and intracellularly by the fatty acid binding proteins, but no analogous transport mechanism has yet been described in CSF. L‐PGDS has been reported to promiscuously bind a wide variety of lipophilic ligands and is among the most abundant proteins found in the CSF. Here, we examine the binding of several classes of endogenous and synthetic ligands to L‐PGDS. Endocannabinoids exhibited low affinity toward L‐PGDS, while cannabinoid metabolites and synthetic cannabinoids displayed higher affinities for L‐PGDS. These results indicate that L‐PGDS is unlikely to function as a carrier for endocannabinoids in the CSF, but it may bind and transport a subset of cannabinoids.     

Synthesis of Modified 4H‐1,2,4‐Benzothiadiazine‐1,1‐dioxides and Determination of their Affinity and Selectivity for Different Types of KATP Channels

4H‐1,2,4‐Benzothiadiazine‐1,1‐dioxides with various substituents in positions 3, 5, and 7 were synthesized and tested as K_ATP channel agonists in artificial cell systems (CHO cells transfected with SUR1/Kir6.2, and HEK 293 transfected with SUR2B/Kir6.1) as model systems for insulin‐secreting pancreatic β‐cells and for smooth muscle cells, respectively. The effects of agonists were tested in intact cells using DiBAC4(3) [bis‐(1,3‐dibarbituric acid)trimethine oxanol] as a membrane potential dye, and the results compared with their binding affinity for the SUR2B‐type K_ATP channels using the radioligand [³H]P1075. Compounds with cycloalkyl and (cycloalkyl)methyl side chains in position 3 had higher affinities towards the SUR2B/Kir6.1 receptor compared with the parent compound diazoxide ( 1 a ). Compounds with bulky, nonpolar residues in position 3 exhibited remarkable selectivity for SUR2B‐type K_ATP channels. The compound substituted with a bulky (1‐adamantyl)methyl residue exhibited micromolar affinity and activity on SUR2B‐type K_ATP channels without being able to activate the SUR1‐type K_ATP channels.     

Chiral Aryloxyalkylamines: Selective 5‐HT1B/1D Activation and Analgesic Activity

A series of chiral 2,3‐dichlorophenoxy and 1‐naphthyloxy alkylamines were synthesized, and their binding affinities towards 5‐HT_1D and h5‐HT_1B receptors were evaluated. In the naphthyloxy series, the (R)‐prolinol derivative was the most selective 5‐HT_1D ligand, while (S)‐N‐methyl‐2‐(1‐naphthyloxy)propan‐1‐amine showed the highest selectivity for h5‐HT_1B. Both compounds performed as 5‐HT_1D agonists in the isolated guinea pig assay and showed higher analgesic activity than both sumatriptan and the achiral analogue 20 b in the mouse hot‐plate test. Neither ligand displayed any affinity for nicotinic ACh receptors present in mouse brain membranes, thus indicating that their analgesic activity does not arise through interaction with these receptors.     

Antibody Epitope of Human α‐Galactosidase A Revealed by Affinity Mass Spectrometry: A Basis for Reversing Immunoreactivity in Enzyme Replacement Therapy of Fabry Disease

α‐Galactosidase (αGal) is a lysosomal enzyme that hydrolyses the terminal α‐galactosyl moiety from glycosphingolipids. Mutations in the encoding genes for αGal lead to defective or misfolded enzyme, which results in substrate accumulation and subsequent organ dysfunction. The metabolic disease caused by a deficiency of human α‐galactosidase A is known as Fabry disease or Fabry–Anderson disease, and it belongs to a larger group known as lysosomal storage diseases. An effective treatment for Fabry disease has been developed by enzyme replacement therapy (ERT), which involves infusions of purified recombinant enzyme in order to increase enzyme levels and decrease the amounts of accumulated substrate. However, immunoreactivity and IgG antibody formation are major, therapy‐limiting, and eventually life‐threatening complications of ERT. The present study focused on the epitope determination of human α‐galactosidase A against its antibody formed. Here we report the identification of the epitope of human αGal(309–332) recognized by a human monoclonal anti‐αGal antibody, using a combination of proteolytic excision of the immobilized immune complex and surface plasmon resonance biosensing mass spectrometry. The epitope peptide, αGal(309–332), was synthesized by solid‐phase peptide synthesis. Determination of its affinity by surface plasmon resonance analysis revealed a high binding affinity for the antibody (K_D=39×10^?9 m ), which is nearly identical to that of the full‐length enzyme (K_D=16×10^?9 m ). The proteolytic excision affinity mass spectrometry method is shown here to be an efficient tool for epitope identification of an immunogenic lysosomal enzyme. Because the full‐length αGal and the antibody epitope showed similar binding affinities, this provides a basis for reversing immunogenicity upon ERT by: 1) treatment of patients with the epitope peptide to neutralize antibodies, or 2) removal of antibodies by apheresis, and thus significantly improving the response to ERT.     

Synthesis of magnetic nanocomposite microparticles for binding of chlorinated organics in contaminated water sources

In this work, the development of novel magnetic nanocomposite microparticles (MNMs) via free radical polymerization for their application in the remediation of contaminated water is presented. Acrylated plant-based polyphenols, curcumin multiacrylate (CMA) and quercetin multiacrylate (QMA), were incorporated as functional monomers to create high affinity binding sites for the capture of polychlorinated biphenyls (PCBs), as a model pollutant. The MNMs were characterized by Fourier transform infrared spectroscopy, thermogravimetric analysis, scanning electron microscopy, dynamic light scattering, and UV–visible spectroscopy. The affinity of these novel materials for PCB 126 was evaluated and fitted to the nonlinear Langmuir model to determine binding affinities (K_D). The results suggest the presence of the polyphenolic moieties enhances the binding affinity for PCB 126, with K_D values comparable to that of antibodies. This demonstrates that these nanocomposite materials have promising potential as environmental remediation adsorbents for harmful contaminants.     

A DNA‐Encoded Library of Chemical Compounds Based on Common Scaffolding Structures Reveals the Impact of Ligand Geometry on Protein Recognition

A DNA‐encoded chemical library (DECL) with 1.2 million compounds was synthesized by combinatorial reaction of seven central scaffolds with two sets of 343×492 building blocks. Library screening by affinity capture revealed that for some target proteins, the chemical nature of building blocks dominated the selection results, whereas for other proteins, the central scaffold also crucially contributed to ligand affinity. Molecules based on a 3,5‐bis(aminomethyl)benzoic acid core structure were found to bind human serum albumin with a K_d value of 6 nm , while compounds with the same substituents on an equidistant but flexible l ‐lysine scaffold showed 140‐fold lower affinity. A 18 nm tankyrase‐1 binder featured l ‐lysine as linking moiety, while molecules based on d ‐Lysine or (2S,4S)‐amino‐l ‐proline showed no detectable binding to the target. This work suggests that central scaffolds which predispose the orientation of chemical building blocks toward the protein target may enhance the screening productivity of encoded libraries.     

Bis‐(1,2,3,4‐tetrahydroisoquinolinium): A Chiral Scaffold for Developing High‐Affinity Ligands for SK Channels

N‐Methyl‐bis‐(1,2,3,4‐tetrahydroisoquinolinium) analogues derived from AG525 (1,1′‐(propane‐1,3‐diyl)‐bis‐(6,7‐dimethoxy‐2‐methyl‐1,2,3,4‐tetrahydroisoquinoline)) stereoisomers and tetrandrine, a rigid bis‐(1,2,3,4‐tetrahydroisoquinoline) analogue with an S,S configuration, were synthesized and tested for their affinity for small‐conductance calcium‐activated potassium channel (SK/K_Ca2) subtypes using radioligand binding assays. A significant increase in affinity was observed for the quaternized analogues over the parent 1,2,3,4‐tetrahydroisoquinoline compounds. Interestingly, the impact of stereochemistry was not the same in the two groups of compounds. For quaternized analogues, affinities of S,S and R,R isomers for SK2 and SK3 channels were similar and in both cases higher than that of the meso derivative. Among the bis‐tetrahydroisoquinoline compounds, the S,S isomers exhibited high affinity, while the R,R and meso isomers had similarly lower affinities. Furthermore, the SK2/SK3 selectivity ratio was slightly increased for quaternized analogues. Bis‐(1,2,3,4‐tetrahydroisoquinolinium) represents a new scaffold for the development of high‐affinity ligands for SK channel subtypes.     

Copper is a Cofactor of the Formylglycine‐Generating Enzyme

Formylglycine‐generating enzyme (FGE) is an O₂‐utilizing oxidase that converts specific cysteine residues of client proteins to formylglycine. We show that Cu^I is an integral cofactor of this enzyme and binds with high affinity (K_D=of 10^?17 m ) to a pair of active‐site cysteines. These findings establish FGE as a novel type of copper enzyme.     

Probing Ligand Structure–Activity Relationships in Pregnane X Receptor (PXR): Efavirenz and 8‐Hydroxyefavirenz Exhibit Divergence in Activation

Efavirenz (EFV), an antiretroviral that interacts clinically with co‐administered drugs via activation of the pregnane X receptor (PXR), is extensively metabolized by the cytochromes P450. We tested whether its primary metabolite, 8‐hydroxyEFV (8‐OHEFV) can activate PXR and potentially contribute to PXR‐mediated drug–drug interactions attributed to EFV. Luciferase reporter assays revealed that despite only differing from EFV by an oxygen atom, 8‐OHEFV does not activate PXR. Corroborating this, treatment with EFV for 72 h elevated the mRNA abundance of the PXR target gene, Cyp3a11, by approximately 28‐fold in primary hepatocytes isolated from PXR‐humanized mice, whereas treatment with 8‐OHEFV did not result in a change in Cyp3A11 mRNA levels. FRET‐based competitive binding assays and isothermal calorimetry demonstrated that even with the lack of ability to activate PXR, 8‐OHEFV displays an affinity for PXR (IC₅₀ 12.1 μm ; K_D 7.9 μm ) nearly identical to that of EFV (IC₅₀ 18.7 μm ; K_D 12.5 μm ). The use of 16 EFV analogues suggest that other discreet changes to the EFV structure beyond the 8‐position are well tolerated. Molecular docking simulations implicate an 8‐OHEFV binding mode that may underlie its divergence in PXR activation from EFV.     

Binding properties of peptidic affinity ligands for plasmid DNA capture and detection

Peptides constructed from α‐helical subunits of the Lac repressor protein (LacI) were designed then tailored to achieve particular binding kinetics and dissociation constants for plasmid DNA purification and detection. Surface plasmon resonance was employed for quantification and characterization of the binding of double stranded Escherichia coli plasmid DNA (pUC19) via the lac operon (lacO) to “biomimics” of the DNA binding domain of LacI. Equilibrium dissociation constants (K_D), association (k_a), and dissociation rates (k_d) for the interaction between a suite of peptide sequences and pUC19 were determined. K_D values measured for the binding of pUC19 to the 47mer, 27mer, 16mer, and 14mer peptides were 8.8 ± 1.3 × 10^?10 M, 7.2 ± 0.6 × 10^?10 M, 4.5 ± 0.5 × 10^?8 M, and 6.2 ± 0.9 × 10^?6 M, respectively. These findings show that affinity peptides, composed of subunits from a naturally occurring operon–repressor interaction, can be designed to achieve binding characteristics suitable for affinity chromatography and biosensor devices. © 2008 American Institute of Chemical Engineers AIChE J, 2009     

Development of 3‐Phenyl‐N‐(2‐(3‐phenylureido)ethyl)‐thiophene‐2‐sulfonamide Compounds as Inhibitors of Antiapoptotic Bcl‐2 Family Proteins

Antiapoptotic Bcl‐2 family proteins, such as Bcl‐x_L, Bcl‐2, and Mcl‐1, are often overexpressed in tumor cells, which contributes to tumor cell resistance to chemotherapies and radiotherapies. Inhibitors of these proteins thus have potential applications in cancer treatment. We discovered, through structure‐based virtual screening, a lead compound with micromolar binding affinity to Mcl‐1 (inhibition constant (K_i)=3 μM ). It contains a phenyltetrazole and a hydrazinecarbothioamide moiety, and it represents a structural scaffold not observed among known Bcl‐2 inhibitors. This work presents the structural optimization of this lead compound. By following the scaffold‐hopping strategy, we have designed and synthesized a total of 82 compounds in three sets. All of the compounds were evaluated in a fluorescence‐polarization binding assay to measure their binding affinities to Bcl‐x_L, Bcl‐2, and Mcl‐1. Some of the compounds with a 3‐phenylthiophene‐2‐sulfonamide core moiety showed sub‐micromolar binding affinities to Mcl‐1 (K_i=0.3–0.4 μM ) or Bcl‐2 (K_i≈1 μM ). They also showed obvious cytotoxicity on tumor cells (IC₅₀<10 μM ). Two‐dimensional heteronuclear single quantum coherence NMR spectra of three selected compounds, that is, YCW‐E5, YCW‐E10, and YCW‐E11, indicated that they bind to the BH3‐binding groove on Bcl‐x_L in a similar mode to ABT‐737. Several apoptotic assays conducted on HL‐60 cells demonstrated that these compounds are able to induce cell apoptosis through the mitochondrial pathway. We propose that the compounds with the 3‐phenylthiophene‐2‐sulfonamide core moiety are worth further optimization as effective apoptosis inducers with an interesting selectivity towards Mcl‐1 and Bcl‐2.