Real‐Time Analysis of Folding upon Binding of a Disordered Protein by Using Dissolution DNP NMR Spectroscopy

The kinase inhibitory domain of the cell cycle regulatory protein p27^Kip1 (p27) was nuclear spin hyperpolarized using dissolution dynamic nuclear polarization (D‐DNP). While intrinsically disordered in isolation, p27 adopts secondary structural motifs, including an α‐helical structure, upon binding to cyclin‐dependent kinase 2 (Cdk2)/cyclin A. The sensitivity gains obtained with hyperpolarization enable the real‐time observation of ¹³C NMR signals during p27 folding upon binding to Cdk2/cyclin A on a time scale of several seconds. Time‐dependent intensity changes are dependent on the extent of folding and binding, as manifested in differential spin relaxation. The analysis of signal decay rates suggests the existence of a partially folded p27 intermediate during the timescale of the D‐DNP NMR experiment.     

Real-Time Analysis of Folding upon Binding of a Disordered Protein by Using Dissolution DNP NMR Spectroscopy

The kinase inhibitory domain of the cell cycle regulatory protein p27^Kip1 (p27) was nuclear spin hyperpolarized using dissolution dynamic nuclear polarization (D-DNP). While intrinsically disordered in isolation, p27 adopts secondary structural motifs, including an α-helical structure, upon binding to cyclin-dependent kinase 2 (Cdk2)/cyclin A. The sensitivity gains obtained with hyperpolarization enable the real-time observation of ¹³C NMR signals during p27 folding upon binding to Cdk2/cyclin A on a time scale of several seconds. Time-dependent intensity changes are dependent on the extent of folding and binding, as manifested in differential spin relaxation. The analysis of signal decay rates suggests the existence of a partially folded p27 intermediate during the timescale of the D-DNP NMR experiment.     

Biochemical characterizations reveal different properties between CDK4/cyclin D1 and CDK2/cyclin A

CDK2 and CDK4 known promoter of cell cycling catalyze phosphorylation of RB protein. Enzyme specificity between two CDKs that work at a different cell cycle phase is not clearly understood. In order to define kinase properties of CDK2 and CDK4 in complex with cycline A or cycline D1 in relation to their respective role in cell cycling regulation, we examined enzymatic properties of both CDK4/cycline D1 and CDK2/cycline A in vitro. Association constant, Km for ATP in CDK4/cyclin D1 was found as 418 microM, a value unusually high whereas CDK2/cyclin A was 23 microM, a value close to most of other regulatory protein kinases. Turnover value for both CDK4/cyclin D1 and CDK2/cyclin A were estimated as 3.4 and 3.9 min(-1) respectively. Kinetic efficiency estimation indicates far over one order magnitude less efficiency for CDK4/cyclin D1 than the value of CDK2/cycline A (9.3 pM(-1) min(-1) and 170 pM(-1) min(-1) respectively). In addition, inhibition of cellular CDK4 caused increase of cellular levels of ATP, even though inhibition of CDK2 did not change it noticeably. These data suggest cellular CDK4/cyclin D1 activity is tightly associated with cellular ATP concentration. Also, analysis of phosphorylated serine/threonine sites on RB catalyzed by CDK4/cyclin D1 and CDK2/cyclin A showed significant differences in their preference of phosphorylation sites in RB C-terminal domain. Since RB is known to regulate various cellular proteins by binding and this binding is controlled by its phosphorylation, these data shown here clearly indicate significant difference in their biochemical properties between CDK4/cyclin D1 and CDK2/cyclin A affecting regulation of cellular RB function.     

The Dynamic Multisite Interactions between Two Intrinsically Disordered Proteins

Protein interactions involving intrinsically disordered proteins (IDPs) comprise a variety of binding modes, from the well‐characterized folding upon binding to dynamic fuzzy complexes. To date, most studies concern the binding of an IDP to a structured protein, while the interaction between two IDPs is poorly understood. In this study, NMR, smFRET, and molecular dynamics (MD) simulation are combined to characterize the interaction between two IDPs, the C‐terminal domain (CTD) of protein 4.1G and the nuclear mitotic apparatus (NuMA) protein. It is revealed that CTD and NuMA form a fuzzy complex with remaining structural disorder. Multiple binding sites on both proteins were identified by molecular dynamics and mutagenesis studies. This study provides an atomic scenario in which two IDPs bearing multiple binding sites interact with each other in dynamic equilibrium. The combined approach employed here could be widely applicable for investigating IDPs and their dynamic interactions.     

Synthesis and ligand binding properties of triptycene-linked porphyrin arrays

Multiporphyrin arrays are a complex class of molecules with numerous potential applications in energy transfer, photomedicine, and light harvesting. We have developed a facile/versatile route to a class of triptycene-linked porphyrin arrays via both Suzuki and Sonogashira cross-coupling methods, which makes use of the rigid three-pronged orientation of triptycene to construct trimeric porphyrin arrays linked either in the meso or β-position with various linker groups. In order to understand the properties of these potential antenna systems and probe their potential applications, the coordination behavior of zinc(II) derivatives with mono- and bidentate N-donor ligands was investigated. Depending on ligand concentration, both one- and two-point binding was observed with a bidentate ligand. Also/in addition, different cavity sizes, obtained by the use of different linker groups, resulted in differences in the binding properties of each trimeric system.     

Changes in expression of cell cycle regulators after G1 progression upon repetitive thioacetamide treatment in rat liver

Repetitive low dose thioacetamide (TA) treatment of hepatocytes was found to induce cells in G2 arrest. In the present study, an attempt was made to investigate alterations in expression of cell cycle regulators after G1 progression in the same repetitive low dose TA treated hepatocytes system and to define the determinators involved in G2 arrest. TA was daily administered intraperitoneally, with a dose of 50 mg/kg for 7 days. Expression levels of cyclin E and CDK2 were similar, increased at day 1 and reached a peak at day 2. And they recycled from day 3 reaching a second peak at day 5. Expression level of cyclin A was similar to p27(Kip1) and p57(Kip2) but not to CDK2 and increased to a peak level at day 2. Expression levels of cyclin B1 and cdc2 were similar although the cyclin B1 level was generally low, decreased from day 1 to basal levels at day 3 and persisted at a low level till day 7. The expression level of cyclin G1 was similar to p53 that peaked at day 3 and again at day 6 elevated over basal level. BrdU-labeled hepatocytic nuclei increased from 12 h, reached a peak at day 2, then decreased, and were not detectable from day 6. The number of PCNA-labeled nuclei increased immediately, peaked at day 2, and maintained till day 7. These results suggest that G2 arrest induced by repeated TA treatment might be p53-dependent, via activation of cyclin G1, rather than inhibition of cyclin B1- cdc2 complex, and inhibitors holding S phase progression might be p27(Kip1) and p57(Kip2).     

Current literature highlights - August 2002.

Cdk4 Inhibitors: Cyclins and cyclin-dependent kinases (Cdks) play important roles in regulation of the cell cycle. In particular, D-type cyclins, which are activated by rearrangement or amplification in several tumours, associate Cdk4/6. Cyclin D-Cdk4/6 complexes phosphorylate the retinoblastoma protein (pRB) and regulate the cell cycle during G₁/S transition. Loss of function or deletion of p16^ink4a (endogenous Cdk4/6 specific inhibitor protein) frequently occurs in clinical cancer cells. As a next generation of Cdk inhibitors, selective inhibitors of only one target Cdk are expected to cause cell cycle arrest specifically. Suppression of tumour growth by G₁ arrest is thought to reduce the stress for normal cells more than in other phases, because normal cells are usually resting in the G₀-G₁ phase. Thus, the design of Cdk4 selective inhibitors that cause cell cycle arrest in the G₁ phase has been attempted [2] (Structure-based generation of a new class of potent Cdk4 inhibitors: New de novo design strategy and library design, Honma, T. et. al., J. Med. Chem., 44, (2001), 4615-4627). To obtain highly selective and potent Cdk4 inhibitors a structure-based design was performed which consisted of lead generation of a new class of Cdk4 inhibitors based on a Cdk4 homology model, and enhancement of Cdk4 selectivity of lead compounds over Cdk1/2 and other kinases based on the binding modes and structural differences between Cdk4 and other kinases. This methodology was applied to search the Available Chemicals Directory and 382 commercial compounds were selected for screening in cyclin D-Cdk4 assays at concentrations up to 1mM. From this set, 18 compounds were found which possessed an IC₅₀ value of under 500 mM. From these hits, a class of diarylureas were identified with the potential for parallel synthesis follow up to validate the potential of the scaffold and to obtain preliminary SAR. 410 Urea compounds were then designed and synthesised as singles in solution, the design based on the diarylurea hits, and they were screened in a Cdk4 inhibition assay. One of the most potent compounds isolated was (i) which possessed an IC₅₀ value of 34 nM. This work has utilised a structure-based lead generation approach consisting of homology modelling of the target protein, construction of a library of compounds, followed by modification of hits obtained based on predicted binding mode. This strategy has provided potent compounds from a new class of diarylurea Cdk4 inhibitors and may lay the foundation for further work to improve potency in this series.     

Direct Monitoring of Initiation Factor Dynamics through Formation of 30S and 70S Translation–Initiation Complexes on a Quartz Crystal Microbalance

Translation initiation is a dynamic and complicated process requiring the building a 70S initiation complex (70S‐IC) composed of a ribosome, mRNA, and an initiator tRNA. During the formation of the 70S‐IC, initiation factors (IFs: IF1, IF2, and IF3) interact with a ribosome to form a 30S initiation complex (30S‐IC) and a 70S‐IC. Although some spectroscopic analyses have been performed, the mechanism of binding and dissociation of IFs remains unclear. Here, we employed a 27 MHz quartz crystal microbalance (QCM) to evaluate the process of bacterial IC formation in translation initiation by following frequency changes (mass changes). IFs (IF1, IF2, and IF3), N‐terminally fused to biotin carboxyl carrier protein (bio‐BCCP), were immobilized on a Neutravidin‐covered QCM plate. By using bio‐BCCP‐IF2 immobilized to the QCM, three steps of the formation of ribosomal initiation complex could be sequentially observed as simple mass changes in real time: binding of a 30S complex to the immobilized IF2, a recruitment of 50S to the 30S‐IC, and formation of the 70S‐IC. The kinetic parameters implied that the release of IF2 from the 70S‐IC could be the rate‐limiting step in translation initiation. The IF3‐immobilized QCM revealed that the affinity of IF3 for the 30S complex decreased upon the addition of mRNA and fMet‐tRNA^fMet but did not lead to complete dissociation from the 30S‐IC. These results suggest that IF3 binds and stays bound to ICs, and its interaction mode is altered during the formation of 30S‐IC and 70S‐IC and is finally induced to dissociate from ICs by 50S binding. This methodology demonstrated here is applicable to investigate the role of IFs in translation initiation driven by other pathways.     

Self-assembly of cis and trans forms of the copper(II) complex with 1-aminocyclopropane-1-carboxylate into discrete trimers in the solid state

A copper(II) complex with 1-aminocyclopropane-1-carboxylic acid assembles by apical Cu...O bonds and hydrogen-bonding interactions into discrete trimeric units that exhibit both cis and trans binding modes.     

Total Synthesis and Biological Evaluation of Grassypeptolide A

Herein, we describe in full our investigations into the synthesis of grassypeptolide A ( 1 ) in 17 linear steps with an overall yield of 11.3 %. In particular, this work features the late‐stage introduction of sensitive bis(thiazoline) heterocycles and 31‐membered macrocyclization conducted at the sterically congested secondary amide site in superb conversion (72 % yield). Biological evaluation indicated that grassypeptolide A significantly inhibited cancer cell proliferation in a dose‐dependent manner. It induced cancer cell apoptosis, which was associated with increased cleavage of poly(ADP‐ribose) polymerase (PARP) and decreased expression of bcl‐2 and bcl‐xL. Furthermore, grassypeptolide A also caused cell cycle redistribution by increasing cells in the G1 phase and decreasing cells in the S and G2 phases. In addition, cell cycle arrest was correlated with downregulation of cyclin D and upregulation of p27 and p21.     

Scaffold Repurposing of In-House Small Molecule Candidates Leads to Discovery of First-in-Class CDK-1/HER-2 Dual Inhibitors: In Vitro and In Silico Screening

Recently, multitargeted drugs are considered a potential approach in treating cancer. In this study, twelve in-house indole-based derivatives were preliminary evaluated for their inhibitory activities over VEGFR-2, CDK-1/cyclin B and HER-2. Compound 15l showed the most inhibitory activities among the tested derivatives over CDK-1/cyclin B and HER-2. Compound 15l was tested for its selectivity in a small kinase panel. It showed dual selectivity for CDK-1/cyclin B and HER-2. Moreover, in vitro cytotoxicity assay was assessed for the selected series against nine NCI cell lines. Compound 15l showed the most potent inhibitory activities among the tested compounds. A deep in silico molecular docking study was conducted for compound 15l to identify the possible binding modes into CDK-1/cyclin B and HER-2. The docking results revealed that compound 15l displayed interesting binding modes with the key amino acids in the binding sites of both kinases. In vitro and in silico studies demonstrate the indole-based derivative 15l as a selective dual CDK-1 and HER-2 inhibitor. This emphasizes a new challenge in drug development strategies and signals a significant milestone for further structural and molecular optimization of these indole-based derivatives in order to achieve a drug-like property.     

Current literature highlights - June 2002

Selective Cdk4 Inhibitors: Cyclins and cyclin-dependent kinases (Cdks) play important roles in regulation of the cell cycle. In particular, D-type cyclins, which have been shown to be amplified or over-expressed in several tumour cells, associate with Cdk4/6 to activate their phosphorylation activity. Cyclin D-Cdk4/6 complexes phosphorylate the retinoblastoma protein (pRB) and regulate the cell cycle during G₁/S transition. Loss of function or deletion of p16^ink4a (endogenous Cdk4/6 specific inhibitor protein) frequently occurs in clinical cancer cells. Thus, selective Cdk4/6 inhibitors should be useful as a new class of cytostatic antitumour agents. In order to overcome the problem of selectivity for Cdk4/6 over the hundreds of homologous kinases in the superfamily, specific amino acid residues were identified around the ATP binding pocket of Cdk4 by comparing the amino acid sequences of 390 representative kinases. Subsequently, a chemical library was designed using this information about the locations of these amino acid residues (A novel approach for the development of selective Cdk4 inhibitors: Library design based on locations of Cdk4 specific amino acid residues, Honma, T. et. al., J. Med. Chem., 44, (2001), 4628-4640).     

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.     

Design, synthesis, biological activity and structural analysis of cyclic peptide inhibitors targeting the substrate recruitment site of cyclin-dependent kinase complexes

Inhibition of cyclin A- and cyclin E-associated cyclin-dependent kinase-2 (CDK2) activities is an effective way of selective induction of apoptotic cell death via the E2F pathway in tumour cells. The cyclin groove recognition motif (CRM) in the natural CDK-inhibitory (CDKI) tumour suppressor protein p27KIP1 was used as the basis for the design and synthesis of a series of cyclic peptides whose biological activity and structural characterisation by NMR and X-ray crystallography is reported. Whereas linear p27KIP1 sequence peptides were comparatively ineffective, introduction of side chain-to-tail constraints was found to be productive. An optimal macrocyclic ring size for the conformational constraint was determined, mimicking the intramolecular H-bonding system of p27. Molecular dynamics calculations of various macrocycles suggested a close correlation between ring flexibility and biological activity. Truncated inhibitor peptide analogues also confirmed the hypothesis that introduction of a cyclic conformational constraint is favourable in terms of affinity and potency. The structural basis for the potency increase in cyclic versus linear peptides was demonstrated through the determination and interpretation of X-ray crystal structures of complexes between CDK2/cylin A (CDK2A) and a constrained pentapeptide.     

BrO-H2O 及 HOBr-H2O复合物偶合方式的理论研究

在6-311++G(d,p)水平上采用四种方法讨论了两种BrO-H₂O和三种HOBr-H₂O复合物的构型性质。在两种BrO-H₂O复合物中，结合能为11.37–13.92 J/mol的复合物2 （电子态为²A′）最稳定，该复合物是通过BrO中的Br原子和水中的O原子结合的。三种HOBr-H₂O复合物中，复合物3和4的结合能约为16.30–21.32 J/mol，三种复合物的稳定顺序为：复合物3 ≈ 复合物4 > 复合物5。