Synthesis of Naphthyridine Dimers with Conformational Restriction and Binding to DNA and RNA

One of the important determinants in the efficiency of a molecular interaction is the necessity for conformational changes in host and/or guest molecules upon binding. In small‐molecule interactions with nucleic acids, conformational changes on both molecules are often involved, especially in intercalating binding. Mismatch binding ligands (MBLs) we described here consist of two heterocycles that predominantly exist in one conformation, so it is of interest to determine if such molecules can bind to any DNA and RNA structures. One molecule, 1 ‐NHR, which predominantly exists as the unstacked conformation in aqueous solvent, has been successfully synthesized and characterized. Compound 1 ‐NHR did not efficiently bind to GX/Y DNA and RNA sequences, but the binding pattern is different from that of authentic MBL naphthyridine carbamate dimer. In vitro selection of RNA that specifically binds to 1 ‐NHR was performed from pre‐miR‐29a loop library RNA, and one RNA, to which 1 ‐NHR bound with high affinity, has been successfully identified. Although it was anticipated that 1 ‐NHR, with a predominantly unstacked conformation, would show entropy‐driven binding, isothermal titration calorimetry analysis suggested that the binding of 1 ‐NHR to RNA was enthalpy driven with an apparent K _d of about 100 nm .     

Tri- and tetraurea piperazine cyclophanes: synthesis and complexation studies of preorganized and folded receptor molecules

A series of symmetrical tri‐ and tetrameric N‐ethyl‐ and N‐phenylurea‐functionalized cyclophanes have been prepared in nearly quantitative yields (86–99 %) from the corresponding tri‐ and tetraamino‐functionalized piperazine cyclophanes and ethyl or phenyl isocyanates. Their conformational and complexation properties have been studied by single‐crystal X‐ray diffraction, variable‐temperature NMR spectroscopy, and ESI‐MS analysis. The rigid 27‐membered trimeric cyclophane skeleton assisted by a seam of intramolecular hydrogen bonds results in a preorganized ditopic recognition site with an all‐syn conformation of the urea moieties that, complemented by a lipophilic cavity of the cyclophane, binds molecular and ionic guests as well as ion pairs. The all‐syn conformation persists in acidic conditions and the triprotonated triurea cyclophane binds an unprecedented anion pair, H₂PO₄^????HPO₄^2?, in the solid state. The tetra‐N‐ethylurea cyclophane is less rigid and demonstrates an induced‐fit recognition of diisopropyl ether in the solid state. The guest was encapsulated within the lipophilic interior of a quasicapsule, formed by intramolecular hydrogen‐bond‐driven folding of the 36‐membered cyclophane skeleton. In the gas phase, the essential role of the urea moieties in the binding was demonstrated by the formation of monomeric 1:1 complexes with K⁺, TMA⁺, and TMP⁺ as well as the ion‐pair complexes [KI+K]⁺, [TMABr+TMA]⁺ and [TMPBr+TMP]⁺. In the positive‐mode ESI‐MS analysis, ion‐pair binding was found to be more pronounced with the larger tetraurea cyclophanes. In the negative mode, owing to the large size of the binding site, a general binding preference towards larger anions, such as the iodide, over smaller anions, such as the fluoride, was observed.     

An Unusual Intramolecular Halogen Bond Guides Conformational Selection

PIK‐75 is a phosphoinositide‐3‐kinase (PI3K) α‐isoform‐selective inhibitor with high potency. Although published structure–activity relationship data show the importance of the NO₂ and the Br substituents in PIK‐75, none of the published studies could correctly determine the underlying reason for their importance. In this publication, we report the first X‐ray crystal structure of PIK‐75 in complex with the kinase GSK‐3β. The structure shows an unusual U‐shaped conformation of PIK‐75 within the active site of GSK‐3β that is likely stabilized by an atypical intramolecular Br???NO₂ halogen bond. NMR and MD simulations show that this conformation presumably also exists in solution and leads to a binding‐competent preorganization of the PIK‐75 molecule, thus explaining its high potency. We therefore suggest that the site‐specific incorporation of halogen bonds could be generally used to design conformationally restricted bioactive substances with increased potencies.     

Acid-sensitive auxiliary assisted atypical diubiquitin synthesis exploiting thiol-ene coupling

Atypical ubiquitin (Ub) chains are generally involved in intracellular physiological processes, while the molecular mechanisms underlying their regulation remain unclear. In this work, we report an acid-sensitive auxiliary group based bifunctional handle that can prepare Lys27-, Lys29- and Lys33-diUb analogs by thiol-ene coupling (TEC) in combination with native chemical ligation (NCL). A prominent advantage of this method is the rapid and effective removal of acid-sensitive auxiliary groups after the formation of the isopeptide bond mimic. Collectively, this work illustrates the utility of the new strategy in the simple and efficient production of homogeneous atypical diUb analogs for biochemical and biophysical studies.     

Dynamic Equilibrium of the Aurora A Kinase Activation Loop Revealed by Single‐Molecule Spectroscopy

The conformation of the activation loop (T‐loop) of protein kinases underlies enzymatic activity and influences the binding of small‐molecule inhibitors. By using single‐molecule fluorescence spectroscopy, we have determined that phosphorylated Aurora A kinase is in dynamic equilibrium between a DFG‐in‐like active T‐loop conformation and a DFG‐out‐like inactive conformation, and have measured the rate constants of interconversion. Addition of the Aurora A activating protein TPX2 shifts the equilibrium towards an active T‐loop conformation whereas addition of the inhibitors MLN8054 and CD532 favors an inactive T‐loop. We show that Aurora A binds TPX2 and MLN8054 simultaneously and provide a new model for kinase conformational behavior. Our approach will enable conformation‐specific effects to be integrated into inhibitor discovery across the kinome, and we outline some immediate consequences for structure‐based drug discovery.     

Lanosterol Biosynthesis: The Critical Role of the Methyl‐29 Group of 2,3‐Oxidosqualene for the Correct Folding of this Substrate and for the Construction of the Five‐Membered D Ring

Lanosterol synthase catalyzes the polycyclization reaction of (3S)‐2,3‐oxidosqualene ( 1 ) into tetracyclic lanosterol 2 by folding 1 in a chair‐boat‐chair‐chair conformation. 27‐Nor‐ and 29‐noroxidosqaulenes ( 7 and 8 , respectively) were incubated with this enzyme to investigate the role of the methyl groups on 1 for the polycyclization cascade. Compound 7 afforded two enzymatic products, namely, 30‐norlanosterol ( 12 ) and 26‐normalabaricatriene ( 13 ; 12 / 13 9:1), which were produced through the normal chair‐boat‐chair‐chair conformation and an atypical chair‐chair‐boat conformation, respectively. Compound 8 gave two products 14 and 15 ( 14 / 15 4:5), which were generated by the normal and the unusual polycyclization pathways through a chair‐chair‐boat‐chair conformation, respectively. It is remarkable that the twist‐boat structure for the B‐ring formation was changed to an energetically favored chair structure for the generation of 15 . Surprisingly, 14 and 15 consisted of a novel 6,6,6,6‐fused tetracyclic ring system, thus differing from the 6,6,6,5‐fused lanosterol skeleton. Together with previous results, we conclude that the methyl‐29 group is critical to the correct folding of 1 , with lesser contributions from the other branched methyl groups, such as methyl‐26, ‐27, and ‐28. Furthermore, we demonstrate that the methyl‐29 group has a crucial role in the formation of the five‐membered D ring of the lanosterol scaffold.     

Dynamics simulation on the flexibility and backbone motions of HP1 chromodomain bound to free and lysine 9‐methylated histone H3 tails

Histone methylation has emerged as a central epigenetic modification with both activating and repressive roles in eukaryotic chromatin. Drosophila HP1 (heterochromatin‐associated protein 1) is one of the chromodomain proteins that contain the essential aromatic residues as the recognition pocket for lysine methylated histone H3 tail. The aromatic cage indicates that the complex of chromodomain protein binding lysine methylated histone H3 tail can be seen as a typical host–guest system between protein and protein. About 10‐ns molecular dynamics simulations have been carried out in this study to examine how the presence of mono‐, trimethylated lysine 9 histone H3 tail (Me1K9, Me3K9 H3) influences the motions of HP1 protein receptor. The study shows that the conformation of HP1 protein free of H3 tail easily changes, whereas that of HP1 protein bound to methylated H3 tail does not. But the conformation of inserted Me1K9 H3 changes obviously as the Me1K recognition makes hydrogen‐bonded interactions associated with the aromatic cage even more unstable than those in free HP1 protein. The conformational change of Me1K9 H3 is correlated with the motions of HP1 protein. As the recognition factor going from Me1K to Me3K produces a more favorable interaction for aromatic ring, hydrogen‐bonded interactions associated with aromatic cage in Me3K9 H3‐HP1 complex were observed to be much more stable than those in Me1K9 H3‐HP1 complex and free HP1. Because of correlation, the flexibility of Me3K9 H3 decreases. The simulations indicate that both the MeK and the surrounding histone tail sequence are necessary features of recognition which significantly affect the flexibility and backbone motions of HP1 chromodomain. These findings confirm a regulatory mechanism of protein–protein interactions through a trimethylated post‐translational modification. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Selective Inhibitors of FKBP51 Employ Conformational Selection of Dynamic Invisible States

The recently discovered SAFit class of inhibitors against the Hsp90 co‐chaperone FKBP51 show greater than 10 000‐fold selectivity over its closely related paralogue FKBP52. However, the mechanism underlying this selectivity remained unknown. By combining NMR spectroscopy, biophysical and computational methods with mutational analysis, we show that the SAFit molecules bind to a transient pocket in FKBP51. This represents a weakly populated conformation resembling the inhibitor‐bound state of FKBP51, suggesting conformational selection rather than induced fit as the major binding mechanism. The inhibitor‐bound conformation of FKBP51 is stabilized by an allosteric network of residues located away from the inhibitor‐binding site. These residues stabilize the Phe67 side chain in a dynamic outward conformation and are distinct in FKBP52, thus rationalizing the basis for the selectivity of SAFit inhibitors. Our results represent a paradigm for the selective inhibition of transient binding pockets.     

Thermodynamics of Hydrophobic Interactions: Entropic Recognition of a Hydrophobic Moiety by Poly(Ethylene Oxide)–Zinc Porphyrin Conjugates

The recognition of 4‐alkylpyridines by water‐soluble poly(ethylene oxide)–zinc porphyrin conjugates was studied with a focus on the thermodynamic parameters of binding. Microcalorimetric studies indicated that binding of the alkyl group of the guest in water is driven by the entropic term (δΔH⁰=ΔH⁰(4‐pentylpyridine)? ΔH⁰(4‐methylpyridine)=+1.7 kJ mol^?1, δTΔS⁰=TΔS⁰(4‐pentylpyridine)? TΔS⁰(4‐methylpyridine)=+11.8 kJ mol^?1 at 298 K), thus showing the significance of water reorganization during host–guest interaction. The enthalpy–entropy compensation temperature of binding of 4‐alkylpyridines was as low as 38 K; only below this temperature could the enthalpic term be a driving force. The binding affinity was modulated by the addition of cations and by varying the degree of polymerization of poly(ethylene oxide), which suggests that guest binding is coupled with polymer conformation.     

Conformational Switching of Resorcin[4]arene Cavitands by Protonation,Preliminary Communication

The synthesis of the quinoxaline‐bridged resorcin[4]arene cavitand 1 was accomplished from 2‐[3,5‐di(tert‐butyl)phenyl]acetaldehyde via formation of the intermediate octol 2 . Such cavitands are known to occur in an open `kite' conformation at low temperature (<213 K) but to adopt a `vase' conformation at elevated temperatures (>318 K). We discovered that protonation of cavitand 1 at room temperature by common acids, such as CF₃COOH, also causes reversible switching from `vase' to `kite', and that this conformational change can be conveniently monitored by both ¹H‐NMR and UV/VIS spectroscopy.     

Deactivation of Mcl‐1 by Dual‐Function Small‐Molecule Inhibitors Targeting the Bcl‐2 Homology 3 Domain and Facilitating Mcl‐1 Ubiquitination

By means of limited proteolysis assay, three‐dimensional NMR, X‐ray crystallography and alanine mutations, a dynamic region at the Q221R222N223 motif in the Bcl‐2 homology 3 (BH3) domain of Mcl‐1 has been identified as a conformational switch which controls Mcl‐1 ubiquitination. Noxa^BH3 binding biases the QRN motif toward a helical conformation, thus leading to an enhanced in vitro ubiquitination of Mcl‐1. In contrast, Bim^BH3 binding biases the QRN motif toward a nonhelical conformation, thus leading to the inhibition of ubiquitination. A dual function Mcl‐1 inhibitor, which locates at the BH3 domain of Mcl‐1 and forms hydrogen bond with His224 to drive a helical QRN conformation, so that it not only interferes with the pro‐apoptotic partners, but also facilitates Mcl‐1 ubiquitination in living cells, is described. As a result, this inhibitor manifests a more effective apoptosis induction in Mcl‐1‐dependent cancer cells than other inhibitors exhibiting a similar binding affinity with it.     

Conformational analysis of a secondary hydroxamic acid in aqueous solution by NOE spectroscopy

Hydroxamic acids are metal‐binding compounds used by micro‐organisms and possess applications in medicine and industry. Hydroxamic acids favor two conformations, E and Z; metal binding is limited to the Z conformation. The Z conformation may be identifiable by NOE spectroscopy, but analysis is complicated by the potential for long‐range coupling as well as for relayed NOEs due to conformational switching. In this report, we re‐examine the reported conformational preference of N‐methyl acetohydroxamic acid (NMHA) in D₂O using NOE spectroscopy. We find that the favored conformation of NMHA in aqueous solution is the E conformation, contrary to an earlier report. NOE build‐up curves are proposed as a valuable tool to probe conformational behavior in similar systems. Copyright © 2013 John Wiley & Sons, Ltd.     

Active‐Metal Template Synthesis of a Halogen‐Bonding Rotaxane for Anion Recognition

The synthesis of an all‐halogen‐bonding rotaxane for anion recognition is achieved by using active‐metal templation. A flexible bis‐iodotriazole‐containing macrocycle is exploited for the metal‐directed rotaxane synthesis. Endotopic binding of a Cu^I template facilitates an active‐metal CuAAC iodotriazole axle formation reaction that captures the interlocked rotaxane product. Following copper‐template removal, exotopic coordination of a more sterically demanding rhenium(I) complex induces an inversion in the conformation of the macrocycle component, directing the iodotriazole halogen‐bond donors into the rotaxane’s interlocked binding cavity to facilitate anion recognition.     

Direct observations of conformational distributions of intrinsically disordered p53 peptides using UV Raman and explicit solvent simulations

We report the first experimental measurements of Ramachandran Ψ-angle distributions for intrinsically disordered peptides: the N-terminal peptide fragment of tumor suppressor p53 and its P27S mutant form. To provide atomically detailed views of the conformational distributions, we performed classical, explicit-solvent molecular dynamics simulations on the microsecond time scale. Upon binding its partner protein, MDM2, wild-type p53 peptide adopts an α-helical conformation. Mutation of Pro27 to serine results in the highest affinity yet observed for MDM2-binding of the p53 peptide. Both UV resonance Raman spectroscopy (UVRR) and simulations reveal that the P27S mutation decreases the extent of PPII helical content and increases the probability for conformations that are similar to the α-helical MDM2-bound conformation. In addition, UVRR measurements were performed on peptides that were isotopically labeled at the Leu26 residue preceding the Pro27 in order to determine the conformational distributions of Leu26 in the wild-type and mutant peptides. The UVRR and simulation results are in quantitative agreement in terms of the change in the population of non-PPII conformations involving Leu26 upon mutation of Pro27 to serine. Finally, our simulations reveal that the MDM2-bound conformation of the peptide is significantly populated in both the wild-type and mutant isolated peptide ensembles in their unbound states, suggesting that MDM2 binding of the p53 peptides may involve conformational selection.     

Atomistic detailed free‐energy landscape of intrinsically disordered protein studied by multi‐scale divide‐and‐conquer molecular dynamics simulation

Calcineurin (CaN) is a eukaryotic serine/threonine protein phosphatase activated by both Ca²⁺ and calmodulin (CaM), including intrinsically disordered region (IDR). The region undergoes folding into an α‐helix form in the presence Ca²⁺‐loaded CaM. To sample the ordered structure of the IDR by conventional all atom model (AAM) molecular dynamics (MD) simulation, the IDR and Ca²⁺‐loaded CaM must be simultaneously treated. However, it is time‐consuming task because the coupled folding and binding should include repeated binding and dissociation. Then, in this study, we propose novel multi‐scale divide‐and‐conquer MD (MSDC‐MD), which combines AAM‐MD and coarse‐grained model MD (CGM‐MD). To speed up the conformation sampling, MSDC‐MD simulation first treats the IDR by CGM to sample conformations from wide conformation space; then, multiple AAM‐MD in a limited area is initiated using the resultant CGM conformation, which is reconstructed by homology modeling method. To investigate performance, we sampled the ordered conformation of the IDR using MSDC‐MD; the root‐mean‐square distance (RMSD) with respect to the experimental structure was 2.23 Å.     

Optical Modulation of Azobenzene‐Modified Peptide for Gold Surface Binding

The ability to precisely and remotely modulate reversible binding interactions between biomolecules and abiotic surfaces is appealing for many applications. To achieve this level of control, an azobenzene‐based optical switch is added to nanoparticle‐binding peptides in order to switch peptide conformation and attenuate binding affinity to gold surfaces via binding and dissociation of peptides.     

分子动力学模拟极端嗜热核糖结合蛋白的热力学稳定性

采用分子动力学模拟方法研究极端嗜热性核糖结合蛋白(tteRBP)的嗜热机理.在常温(300 K)和最佳活性温度(375 K)时,分别对tteRBP分子进行动力学模拟,结果表明,整体分子均保持结构稳定,但分子内部的协调运动不同.在375 K时蛋白整体柔性显著提高,使分子能够局部调整构象以适应极端高温.蛋白结构变化的分析也确认了高温时构象局部微调对蛋白极端高温稳定性的关键作用.     

Functionalization of Quinazolin‐4‐ones Part 3: Synthesis,Structures Elucidation,DNA‐PK,PI3K,and Cytotoxicity of Novel 8‐Aryl‐2‐morpholino‐quinazolin‐4‐ones

A series of novel 8‐aryl‐2‐morpholino quinazolines ( 11a – n , 12a – d , 14a – f , and 15 ) were synthesized from the precursor 2‐thioxo quinazolin‐4‐ones 8 . The 8‐aryl‐2‐morpholino quinazolines compounds were assayed for DNA‐PK and PI3K. All compounds showed low DNA‐PK % inhibition activity at 10 μM compound concertation, and the most active was 8‐(dibenzo[b,d]thiophen‐4‐yl) 12d with 38% inhibition. Similar pattern of PI3K α, β, γ, and δ isoforms inhibition activity at 10 μM were observed. The most active isoform was PI3K δ of 41% inhibition for 8‐(dibenzo[b,d]furan‐4‐yl) compound 11 . Most compounds were less active than expected in spite of the strong structural resemblance to known inhibitors ( NU7441 , 3 , 4 , and 6 ). Loss of activity could be attributed to the tautomerization to the aromatic enol (4‐OH), which could specify that the important functional group for the activity is the 4‐carbonyl (C=O) group. Alternatively, the aromatization of the pyrimidine heterocyclic ring could alter the conformation, and thus binding site, of the 2‐morpholine ring, which could reduce the compound‐receptor hydrogen bonding to the morpholine 4‐oxygen. Selected compounds displayed appreciable cytotoxicity with 6‐chloro‐8‐(dibenzo[b,d]thiophen‐4‐yl)‐2‐morpholinoquinazolin‐4(1H)‐one 11j exhibiting the greatest activity with an IC₅₀ of 9.95 μM. Therefore, the mechanism of the cytotoxicity of compound 11j were not through DNA‐PK or PI3K inhibition activity.     

Influence of the size of the counter-ion on the conformational stability of the alkali metal complexes of 2,2'-dithienyl ketyl

The ratio between the trans—trans and cis—trans isomers has been measured in the 2,2'-dithienyl ketyl and in its Li, Na, K and Cs complexes. The stability of the trans—trans conformation was found to increase with increasing size of the alkali counter-ion. This trend has been interpreted in terms of steric interaction between the cation and the atoms adjacent to the binding site.     

Folding pathways of human telomeric type-1 and type-2 G-quadruplex structures

We have investigated new folding pathways of human telomeric type-1 and type-2 G-quadruplex conformations via intermediate hairpin and triplex structures. The stabilization energies calculated by ab initio methods evidenced the formation of a hairpin structure with Hoogsteen GG base pairs. Further calculations revealed that the G-triplet is more stable than the hairpin conformation and equally stable when compared to the G-tetrad. This indicated the possibility of a triplex intermediate. The overall folding is facilitated by K(+) association in each step, as it decreases the electrostatic repulsion. The K(+) binding site was identified by molecular dynamics simulations. We then focused on the syn/anti arrangement and found that the anti conformation of deoxyguanosine is more stable than the syn conformation, which indicated that folding would increase the number of anti conformations. The K(+) binding to a hairpin near the second lateral TTA loop was found to be preferable, considering entropic effects. Stacking of G-tetrads with the same conformation (anti/anti or syn/syn) is more stable than mixed stacking (anti/syn and vice versa). These results suggest the formation of type-1 and type-2 G-quadruplex structures with the possibility of hairpin and triplex intermediates.