A Covalent Binding Mode of a Pyrazole-Based CD38 Inhibitor

Brain concentrations of nicotinamide adenine dinucleotide (NAD⁺), an important cellular co-factor, tend to decrease with age and in neurodegeneration. As the NADase cluster of differentiation 38 (CD38) significantly contributes to NAD⁺ consumption, we reasoned that CD38 inhibition may be of therapeutic value for CNS disorders. The new pyrazole compound was designed based on a known CD38 inhibitor and showed good inhibitory potency. Several attempts to co-crystallise this pyrazole with CD38 and cyclic adenosine diphosphate ribose (cADPR) culminated in a high-resolution X-ray structure, in which the pyrazolyl group in the new compound formed a covalent bond with one of the ribosyl units of cADPR. This reaction proceeded under retention of configuration and resulted in a neutral ribosyl-pyrazole conjugate that is embedded within the active site of the enzyme. An analysis of this structural complex gave rise to design principles that enabled the preparation of more potent CD38 inhibitors with drug-like properties.     

A Designed Conformational Shift To Control Protein Binding Specificity

In a conformational selection scenario, manipulating the populations of binding‐competent states should be expected to affect protein binding. We demonstrate how in silico designed point mutations within the core of ubiquitin, remote from the binding interface, change the binding specificity by shifting the conformational equilibrium of the ground‐state ensemble between open and closed substates that have a similar population in the wild‐type protein. Binding affinities determined by NMR titration experiments agree with the predictions, thereby showing that, indeed, a shift in the conformational equilibrium enables us to alter ubiquitin’s binding specificity and hence its function. Thus, we present a novel route towards designing specific binding by a conformational shift through exploiting the fact that conformational selection depends on the concentration of binding‐competent substates.     

Unique Curing Properties through Living Polymerization in Crosslinking Materials: Polyurethane Photopolymers from Vinyl Ether Building Blocks

Photopolymers with unique curing capabilities were produced by combining living cationic polymerization with network formation and restricted polymer motion. A vinyl ether diol was synthesized as a functional building block and reacted with isophorone diisocyanate to form a highly functionalized vinyl ether polyurethane as a model system with high crosslinking ability. When using a cationic photoinitiator, fast polymerization is observed upon short UV irradiation. Curing proceeds in the absence of light and under ambient conditions without oxygen inhibition. Cationic active sites become trapped dormant species upon network‐induced vitrification and surprisingly remain living for several days. The polymerization can be reactivated by additional UV irradiation and/or raised temperature. The curing behavior was studied in detail by using UV and FT‐NIR coupled rheology and photo‐DSC to simultaneously study spectroscopic and mechanical information, as well as thermal effects.     

Inhibitor Ionization as a Determinant of Binding to 3-Dehydroquinate Synthase

Phosphinomethyl and carboxymethyl monoacids along with succinyl, malonyl ether, malonyl, and hydroxymalonyl diacids were substituted for phosphorylmethyl, phosphonoethyl, and phosphonomethyl groups in carbocyclic inhibitors of DHQ synthase. All but one of the carbocyclic inhibitors were synthesized via intermediacy of a 2,3-butane bisacetal-protected 3-dehydroquinic acid. Carbaphosphinate (K(i) = 20 x 10(-)(6) M) was a modest competitive inhibitor of DHQ synthase, while carbaacetate was a linear mixed-type inhibitor (K(i) = 3 x 10(-)(6) M, K(i)' = 20 x 10(-)(6) M). Carbasuccinate (K(i) = 5 x 10(-)(6) M), carbamalonate ether (K(i) = 7 x 10(-)(6) M), carbamalonate (K(i) = 0.7 x 10(-)(6) M), and carbahydroxymalonate (K(i) = 0.3 x 10(-)(6) M) were all competitive inhibitors. Carbaacetate was the only inhibitor that was not oxidized by DHQ synthase. On the basis of these data, carbocyclic inhibitors with malonyl and hydroxymalonyl groups are apparently bound by DHQ synthase as tightly as carbocyclic inhibitors possessing phosphorylmethyl and phosphonoethyl moieties.     

分子动力学研究2-乙酸苯并噻吩在HIV-1蛋白酶与抑制剂结合中的作用

为了研究别构小分子2-乙酸苯并噻吩(2FX)在HIV-1蛋白酶与抑制剂结合中的作用, 利用分子动力学方法分别对未结合和结合2FX的HIV-1蛋白酶抑制剂体系进行了100 ns的模拟, 模拟计算中对每种体系均采用两种新的分子力场ff99SBildn和ff12SB. 研究了2FX对体系构象的影响和两体系在不同力场下的动力学行为, 分析了两体系的均方根偏差和残基的B因子, 比较了计算结构和晶体结构, 最后采用MM-PB/GBSA两种方法计算了两体系的结合自由能. 研究表明, 两种力场计算的结果虽有差异, 但都说明2FX的结合导致蛋白酶构象的变化, 使得体系更加稳定, 尤其是flap的柔性减弱, 使得蛋白酶和抑制剂的结合更牢固; 另外, 还发现ff12SB力场动力学过程更稳定. 研究结果有助于为设计新的别构抑制剂提供理论依据.     

An Electrophoretic Mobility Shift Assay Identifies a Mechanistically Unique Inhibitor of Protein Sumoylation

1. Download : Download high-res image (111KB)
2. Download : Download full-size image

Highlights? Capillary electrophoresis assay using a mobility shift as a readout to study sumoylation ? Assay identified a 2-D08 (2′,3′,4′-trihydroxyflavone) as a potent sumoylation inhibitor ? 2-D08 acts by inhibiting the transfer of SUMO-1 from the E2 thioester to the SUMO substrate ? 2-D08 inhibits sumoylation of topo-I in two different breast cancer cell lines     

A Fluorescent Kinase Inhibitor that Exhibits Diagnostic Changes in Emission upon Binding

The development of a fluorescent LCK inhibitor that exhibits favourable solvatochromic properties upon binding the kinase is described. Fluorescent properties were realised through the inclusion of a prodan‐derived fluorophore into the pharmacophore of an ATP‐competitive kinase inhibitor. Fluorescence titration experiments demonstrate the solvatochromic properties of the inhibitor, in which dramatic increase in emission intensity and hypsochromic shift in emission maxima are clearly observed upon binding LCK. Microscopy experiments in cellular contexts together with flow cytometry show that the fluorescence intensity of the inhibitor correlates with the LCK concentration. Furthermore, multiphoton microscopy experiments demonstrate both the rapid cellular uptake of the inhibitor and that the two‐photon cross section of the inhibitor is amenable for excitation at 700 nm.     

The Binding Mode of a Tau Peptide with Tubulin

The microtubule‐associated protein Tau promotes the polymerization of tubulin and modulates the function of microtubules. As a consequence of the dynamic nature of the Tau–tubulin interaction, the structural basis of this complex has remained largely elusive. By using NMR methods optimized for ligand–receptor interactions in combination with site‐directed mutagenesis we demonstrate that the flanking domain downstream of the four microtubule‐binding repeats of Tau binds competitively to a site on the α‐tubulin surface. The binding process is complex, involves partial coupling of different interacting regions, and is modulated by phosphorylation at Y394 and S396. This study strengthens the hypothesis of an intimate relationship between Tau phosphorylation and tubulin binding and highlights the power of the INPHARMA NMR method to characterize the interaction of peptides derived from intrinsically disordered proteins with their molecular partners.     

Infrared Spectroscopy Elucidates the Inhibitor Binding Sites in a Metal-Dependent Formate Dehydrogenase

Biological carbon dioxide (CO₂) reduction is an important step by which organisms form valuable energy-richer molecules required for further metabolic processes. The Mo-dependent formate dehydrogenase (FDH) from Rhodobacter capsulatus catalyzes reversible formate oxidation to CO₂ at a bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor. To elucidate potential substrate binding sites relevant for the mechanism, we studied herein the interaction with the inhibitory molecules azide and cyanate, which are isoelectronic to CO₂ and charged as formate. We employed infrared (IR) spectroscopy in combination with density functional theory (DFT) and inhibition kinetics. One distinct inhibitory molecule was found to bind to either a non-competitive or a competitive binding site in the secondary coordination sphere of the active site. Site-directed mutagenesis of key amino acid residues in the vicinity of the bis-MGD cofactor revealed changes in both non-competitive and competitive binding, whereby the inhibitor is in case of the latter interaction presumably bound between the cofactor and the adjacent Arg587.     

Substrate Binding by a Parallel Metal Sheet Sandwich Complex: A Unique Role of an Additional Metal Atom

A unique metal addition to the edge of a triangular palladium sandwich cluster is reported. While the edge coordination sites of a parallel sandwich complex are narrow because of two sterically encumbering π‐ligands, association of an additional metal atom to a metal sheet gives a wider coordination site. It was proved that the additional metal atom plays a crucial role in binding of cyclopentadienyl by a Pd₃ sheet sandwich complex.     

Organic Ligand Binding by a Hydrophobic Cavity in a Designed Tetrameric Coiled‐Coil Protein

The design and characterization of a hydrophobic cavity in de novo designed proteins provides a wide range of information about the functions of de novo proteins. We designed a de novo tetrameric coiled‐coil protein with a hydrophobic pocketlike cavity. Tetrameric coiled coils with hydrophobic cavities have previously been reported. By replacing one Leu residue at the a position with Ala, hydrophobic cavities that did not flatten out due to loose peptide chains were reliably created. To perform a detailed examination of the ligand‐binding characteristics of the cavities, we originally designed two other coiled‐coil proteins: AM2, with eight Ala substitutions at the adjacent a and d positions at the center of a bundled structure, and AM2W, with one Trp and seven Ala substitutions at the same positions. To increase the association of the helical peptides, each helical peptide was connected with flexible linkers, which resulted in a single peptide chain. These proteins exhibited CD spectra corresponding to superhelical structures, despite weakened hydrophobic packing. AM2W exhibited binding affinity for size‐complementary organic compounds. The dissociation constants, K_d, of AM2W were 220 nM for adamantane, 81 μM for 1‐adamantanol, and 294 μM for 1‐adamantaneacetic acid, as measured by fluorescence titration analyses. Although it was contrary to expectations, AM2 did not exhibit any binding affinity, probably due to structural defects around the designed hydrophobic cavity. Interestingly, AM2W exhibited incremental structure stability through ligand binding. Plugging of structural defects with organic ligands would be expected to facilitate protein folding.     

The Unique Antithrombin III Binding Domain of Heparin: A Lead to New Synthetic Antithrombotics

Heparin, a sulfated glycosaminoglycan, is well known for its anticoagulant effect mediated by the serine protease inhibitor antithrombin III (AT III). Heparin has been used clinically for more than half a century for the prophylaxis and treatment of venous thrombosis and thromboembolism. Up until the 1980s it was assumed that the biological activity of heparin was mainly caused by its polyanionic character. However, this paradigm was contradicted when it was discovered that part of the heparin polysaccharides contains a well-defined pentasaccharide domain that specifically binds and activates AT III. The specificity of the interaction between the characteristic pentasaccharide and AT III has become more obvious after the synthesis and biological testing of various heparin analogues. This article reviews the synthesis of the heparin pentasaccharide, some closely related counterparts, and some highly modified analogues. With the aid of molecular modeling and through “tailored” molecular modifications of the pentasaccharide, much knowledge has been gained concerning structure-activity relationships. On this basis not only have more potent and simplified derivatives been developed, but also the recognition between heparin and AT III can now be understood in greater detail at the molecular level.     

Spectroscopic and Theoretical Insights on Non-covalent Binding of PyC60 with a Designed Diporphyrin in Solution

The present paper reports the spectroscopic and theoretical investigations on non-covalent interaction of a functionalized fullerene, namely, C₆₀ pyrrolidine tris-acid ethyl ester (PyC₆₀) with a designed diporphyrin (1) in solvents having varying polarity: toluene and benzonitrile. UV–Vis studies reveal that PyC₆₀ undergoes an appreciable amount of ground state electronic interaction with 1 as the intensity of the Soret absorption band of 1 suffers a considerable decrease in the presence of PyC₆₀ in both solvents. Steady state fluorescence studies elicit efficient quenching of the fluorescence of 1 in the presence of PyC₆₀. The binding constant (K) values of the PyC₆₀/1 complex follow the trend: PyC₆₀/1 (in toluene, K = 2,825 dm³·mol^?1) < PyC₆₀/1 (in benzonitrile, K = 3,540 dm³·mol^?1). Time resolved emission studies establish a relatively long-lived charge separated state for the PyC₆₀/1 complex in benzonitrile. The magnitude of the quantum yield of the charge separated state for the PyC₆₀/1 complex indicates that, while energy transfer is feasible in toluene, there is strong propensity of electron transfer in benzonitrile.     

Dual Binding Mode of Metallacarborane Produces a Robust Shield on Proteins

An inorganic sandwich molecule, Na[Co(C₂B₉H₁₁)₂], able to produce vesicles through self-assembly and known to produce strong dihydrogen-bond interactions with amine groups is capable of interacting with proteins. This dual non-bonding ability of Na[Co(C₂B₉H₁₁)₂] is what makes this molecule unique: it can be firmly anchored to a protein surface and is capable of extending over it. To prove this, the widely available bovine serum albumin (BSA), which has many pendant amino groups in its structure, has been taken as the model protein. It has been found that around 100 molecules of Na[Co(C₂B₉H₁₁)₂] preserve the native structure of BSA, while endorsing it with a significantly increased stability with respect to chemical- and thermal-induced denaturation due to efficient encapsulation. The advantages of this encapsulation technique are two-fold; the first is its simplicity as it relies on the anchoring capacity of Na[Co(C₂B₉H₁₁)₂] to the surface of the protein through the amine-containing residues and the second is its self-assembling capacity allowing it to spread across the surface. The dense shield of protection offered by Na[Co(C₂B₉H₁₁)₂] has been demonstrated by the inhibition of BSA pseudo-esterase activity, which indicates that the inorganic corset around BSA protects its reactive surface residues, thereby preventing their acetylation.