Small-molecule inhibitors of the cell cycle

Joint masking and self-supervised strategies for inferring small molecule-miRNA associations

Inferring small molecule-miRNA associations (MMAs) is crucial for revealing the intricacies of biological processes and disease mechanisms. Deep learning, renowned for its exceptional speed and accuracy, is extensively used for predicting MMAs. However, given their heavy reliance on data, inaccuracies during data collection can make these methods susceptible to noise interference. To address this challenge, we introduce the joint masking and self-supervised (JMSS)-MMA model. This model synergizes graph autoencoders with a probability distribution-based masking strategy, effectively countering the impact of noisy data and enabling precise predictions of unknown MMAs. Operating in a self-supervised manner, it deeply encodes the relationship data of small molecules and miRNA through the graph autoencoder, delving into its latent information. Our masking strategy has successfully reduced data noise, enhancing prediction accuracy. To our knowledge, this is the pioneering integration of a masking strategy with graph autoencoders for MMA prediction. Furthermore, the JMSS-MMA model incorporates a node-degree-based decoder, deepening the understanding of the network's structure. Experiments on two mainstream datasets confirm the model's efficiency and precision, and ablation studies further attest to its robustness. We firmly believe that this model will revolutionize drug development, personalized medicine, and biomedical research.

Insights into the selectivity of a brain-penetrant CDK4/6 vs CDK1/2 inhibitor for glioblastoma used in multiple replica molecular dynamics simulations

Cyclin dependent kinases (CDKs) play an important role in cell cycle regulation and their dysfunction is associated with many cancers. That is why CDKs have been attractive targets for the treatment of cancer. Glioblastoma is a cancer caused by the aberrant expression of CDK4/6, so exploring the mechanism of the selection of CDK4/6 toward inhibitors relative to the other family members CDK1/2 is essential. In this work, multiple replica molecular dynamics (MRMD) simulations, principal component analysis (PCA), free energy landscapes (FELs), molecular mechanics Poisson-Boltzmann/Generalized Born surface area (MM-PB/GBSA) and other methods were integrated to decipher the selectively binding mechanism of the inhibitor N1J to CDK4/6 and CDK1/2. Molecular electrostatic potential (MESP) analysis provides an explanation for the N1J selectivity. Residue-based free energy decomposition reveals that most of the hot residues are located at the same location of CDKs proteins, but the different types of residues in different proteins cause changes in binding energy, which is considered as a potential developmental direction to improve the selectivity of inhibitors to CDK4/6. These results provide insights into the source of inhibitor and CDK4/6 selectivity for the future development of more selective inhibitors.Communicated by Ramaswamy H. Sarma.

Gene module analysis of juvenile myelomonocytic leukemia and screening of anticancer drugs

Juvenile myelomonocytic leukemia (JMML) is a rare but severe primary hemopoietic system tumor of childhood, most frequent in children 4 years and younger. There are currently no specific anticancer therapies targeting JMML, and the underlying gene expression changes have not been revealed. To define molecular targets and possible biomarkers for early diagnosis, optimal treatment, and prognosis, we conducted microarray data analysis using the Gene Expression Omnibus, and constructed protein‑protein interaction networks of all differentially expressed genes. Modular bioinformatics analysis revealed four core functional modules for JMML. We analyzed the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway functions associated with these modules. Using the CMap database, nine potential anticancer drugs were identified that modulate expression levels of many JMML‑associated genes. In addition, we identified possible miRNAs and transcription factors regulating these differentially expressed genes. This study defines a new research strategy for developing JMML‑targeted chemotherapies.

Green tea polyphenols induce cell death in breast cancer MCF-7 cells through induction of cell cycle arrest and mitochondrial-mediated apoptosis

In order to study the molecular mechanisms of green tea polyphenols (GTPs) in treatment or prevention of breast cancer, the cytotoxic effects of GTPs on five human cell lines (MCF-7, A549, Hela, PC3, and HepG2 cells) were determined and the antitumor mechanisms of GTPs in MCF-7 cells were analyzed. The results showed that GTPs exhibited a broad spectrum of inhibition against the detected cancer cell lines, particularly the MCF-7 cells. Studies on the mechanisms revealed that the main modes of cell death induced by GTPs were cell cycle arrest and mitochondrial-mediated apoptosis. Flow cytometric analysis showed that GTPs mediated cell cycle arrest at both G1/M and G2/M transitions. GTP dose dependently led to apoptosis of MCF-7 cells via the mitochondrial pathways, as evidenced by induction of chromatin condensation, reduction of mitochondrial membrane potential (ΔΨ_m), improvement in the generation of reactive oxygen species (ROS), induction of DNA fragmentation, and activations of caspase-3 and caspase-9 in the present paper.

The Use of Withaferin A to Study Intermediate Filaments

Withaferin A (WFA), initially identified as a compound that inhibits experimental angiogenesis, has been shown to bind to soluble vimentin (sVim) and other type III intermediate filament (IF) proteins. We review WFA's dose-related activities (Section 1), examining nanomolar concentrations effects on sVim in cell proliferation and submicromolar effects on lamellipodia and focal adhesion formation. WFA effects on polymeric IFs are especially interesting to the study of cell migration and invasion that depend on IF mechanical contractile properties. WFA interferes with NF-κB signaling, though this anti-inflammatory mechanism may occur via perturbation of sVim-protein complexes, and possibly also via targeting IκB kinase β directly. However, micromolar concentrations that induce vimentin cleavage to promote apoptosis may increasingly show off-target effects via targeting other IFs (neurofilaments and keratin) and non-IFs (tubulin, heat-shock proteins, proteasome). Thus, in Section 2, we describe our studies combining cell cultures with animal models of injury to validate relevant type III IF-targeting mechanisms of WFA. In Section 3, we illuminate from investigating myofibroblast differentiation how sVim phosphorylation may govern cell type-selective sensitivity to WFA, offering impetus for exploring vimentin phosphorylation isoforms as targets and biomarkers of fibrosis. These different WFA targets and activities are listed in a summary table.

Synthesis and molecular modeling of six novel monastrol analogues: evaluation of cytotoxicity and kinesin inhibitory activity against HeLa cell line

Background and the purpose of the study

A common approach in cancer chemotherapy is development of drugs that interrupt the mitosis phase of cell division. Dimethylenastron is a known kinesin inhibitor. In this study, six novel dimethylenastron analogues (4a-f), in which 3-hydroxyphenyl substituent has been replaced with substituted benzylimidazolyl, were synthesized through Biginelli reaction.

Methods

Six novel Biginelli compounds (4a-f) were synthesized through one step Biginelli reaction of imidazole aldehydes (3a-c), dimedone and urea or thioura. In vitro cytotoxicities of prepared compounds were investigated using MTT assay. Furthermore the ELIPA kit was implemented to study inhibitory effects of synthesized compounds on ATPase activity of kinesin by measuring of organic phosphate.

Results

Our results indicated that analogue 4c is the most toxic and analogues 4f, 4b and dimethylenasteron were less cytotoxic in compare with other analogues. On the other hand, analogue 4a, 4b, 4c and 4e showed stronger Kinesin inhibition as compared with analogue 4f and dimethylenasteron. None of synthesized compounds were as potent kinesin inhibitor as Taxol. Docking analysis revealed that hydrogen bond formation and hydrophobic interactions were the key factors affecting inhibitory effects of these compounds.

Conclusion

Newly synthesized compounds were found to have moderate to good cytotoxicity against HeLa cancer cell. Our results may be helpful in further design of dihydropyrimidine as potential anticancer agents.

Targeted Degradation of Proteins by PROTACs

In recent years, small interference RNAs (siRNAs) have greatly enhanced our understanding of protein functions by allowing knockdown of targeted proteins at the mRNA level. Similarly, in an effort to achieve degradation of targeted proteins at the post-translational level, chimeric small molecules called "PROTACs" (PROteolysis TArgeting Chimeric molecules) have been developed. The PROTAC approach utilizes chimeric small molecules which recruit targeted proteins to the ubiquitin-proteasome pathway, a major intracellular protein degradation system. Unlike conventional small molecules that bind to protein and inhibit its function, the PROTAC approach induces destruction of target protein via the ubiquitin-proteasome system. This article presents a typical strategy for PROTAC design and preparation and biological characterization. Curr. Protoc. Chem Biol. 2:71-87. © 2010 by John Wiley & Sons, Inc.

Exploring the selectivity of a ligand complex with CDK2/CDK1: a molecular dynamics simulation approach

Cyclin-dependent kinases (CDKs) are core components of the cell cycle machinery that govern the transition between phases during cell cycle progression. Abnormalities in CDKs activity and regulation are common features of cancer, making CDK family members attractive targets for the development of anticancer drugs. Their inhibitors have entered in clinical trials to treat cancer. Very recently, Heathcote et al. (J. Med. Chem. 2010, 53:8508-8522) have found a ligand BS194 that has a high affinity with CDK2 (IC(50) = 3 nM) but shows low affinity with CDK1 (IC(50) = 30 nM). To understand the selectivity, we used homology modeling, molecular docking, molecular dynamics, and free-energy calculation to analyze the interactions. A rational three-dimensional model of the CDK1/BS194 complex is built. We found that Leu83 is a key residue that recognizes BS194 more effectively with CDK2 with good binding free energies rather than CDK1. Energetic analysis reveals that van der Waals interaction and non-polar contributions to solvent are favorable in the formation of complexes and amine group of the ligand, which plays a crucial role for binding selectivity between CDK2 and CDK1.

Violaceols function as actin inhibitors inducing cell shape elongation in fibroblast cells

Violaceol-I and -II were isolated from a fractionated library of marine-derived fungal metabolites. These compounds increased the calcium ion concentration inside the cell and caused F-actin aggregation in rat fibroblast 3Y1 cells within 3 h resulting in cell shape elongation. Calcium chelator BAPTA-AM (1,2-bis(2-aminophenoxy)ethane-N,N,N',N'-tetraacetic acid tetrakis (acetoxymethyl ester) inhibited violaceol-I and -II induced F-actin aggregation in 3Y1 cells, and hence violaceol-I and -II act in a calcium dependent manner. Violaceol-I and -II inhibited G-actin polymerization in vitro in a dose-dependent manner and strongly associated with G-actin, at dissociation equilibrium constants of 1.44 × 10(-8) M and 2.52 × 10(-9) M respectively. Here we report the identification of a novel function of violaceol-I and -II as actin inhibitors. Violaceol-I and -II induced cell shape elongation through F-actin aggregation in 3Y1 fibroblasts. These compounds may give researchers new insights into the role of actin in tumorigenesis and lead to the development of additional anti-tumor drugs.

Revisiting the role of the immunoproteasome in the activation of the canonical NF-κB pathway

The discovery of NF-κB signaling pathways has greatly enhanced our understanding of inflammatory and immune responses. In the canonical NF-κB pathway, the proteasomal degradation of IκBα, an inhibitory protein of NF-κB, is widely accepted to be a key regulatory step. However, contradictory findings have been reported as to whether the immunoproteasome plays an obligatory role in the degradation of IκBα and activation of the canonical NF-κB pathway. Such results were obtained mainly using traditional gene deletion strategies. Here, we have revisited the involvement of the immunoproteasome in the canonical NF-κB pathway using small molecule inhibitors of the immunoproteasome, namely UK-101 and LKS01 targeting β1i and β5i, respectively. H23 and Panc-1 cancer cells were pretreated with UK-101, LKS01 or epoxomicin (a prototypic inhibitor targeting both the constitutive proteasome and immunoproteasome). We then examined whether these pretreatments lead to any defect in activating the canonical NF-κB pathway following TNFα exposure by monitoring the phosphorylation and degradation of IκBα, nuclear translocation of NF-κB proteins and DNA binding and transcriptional activity of NF-κB. Our results consistently indicated that there is no defect in activating the canonical NF-κB pathway following selective inhibition of the immunoproteasome catalytic subunits β1i, β5i or both using UK-101 and LKS01, in contrast to epoxomicin. In summary, our current results using chemical genetic approaches strongly support that the catalytic activity of the immunoproteasome subunits β1i and β5i is not required for canonical NF-κB activation in lung and pancreatic adenocarcinoma cell line models.

Facile synthesis of 4-substituted 3,4-dihydrocoumarins via an organocatalytic double decarboxylation process

3,4-Dihydrocoumarins, considered to be valuable building blocks, have attracted considerable attention due to their various biological activities. Herein, we have documented an efficient and convenient double decarboxylation process for the synthesis of 4-substituted 3,4-dihydrocoumarin in moderate to excellent yields under mild reaction conditions (up to 98%).

Synthesis and structure-activity relationships of dehydroaltenusin derivatives as selective DNA polymerase alpha inhibitors

Herein, we describe the synthesis and structure-activity relationships of dehydroaltenusin derivatives as inhibitors of a mammalian DNA polymerase alpha. We have newly synthesized nine dehydroaltenusin derivatives modified at the side chains or benzoquinone moiety. We also achieved the first synthesis of desmethylaltenusin and desmethyldehydroaltenusin, metabolites of Alternaria sp. or Talaromyces flavus, respectively. Among all synthesized derivatives, demethoxydehydroaltenusin was the most selective inhibitor of DNA polymerase alpha. The o-hydroxy-p-benzoquinone (2-hydroxycyclohexa-2,5-dienone) moiety is essential for the inhibition of DNA polymerases. Substitution at the 5-position of dehydroaltenusin is important for the inhibitory potency. Because dehydroaltenusin is conjugated with N-acetylcysteine methyl ester at the o-hydroxy-p-benzoquinone moiety, one or more cysteine residues of DNA polymerase alpha may act as a target for this compound.

Explaining the inhibition of cyclin-dependent kinase 5 by peptides derived from p25 with molecular dynamics simulations and MM-PBSA

A cyclin-dependent kinase (CDK) 5 inhibitory peptide (CIP) from p25 was recently reported to inhibit CDK5/p25 activity in vitro but had no effect on endogenous cdc2 kinase activity. This may lead to a specific CDK5 inhibition strategy in the treatment of neurodegeneration. However, the mechanism of the inhibition remains unclear. In this work, molecular dynamics simulations and energy decomposition calculation models were set up to investigate the deregulation mechanisms of CIP on CDK5 activity. The results show that truncation of the N, and C terminals of p25 introduces important conformational changes into a hydrophobic pocket that is crucial for accommodating Ile153 on the activation loop of CDK5. In addition, such truncations lead to distortion and displacement of the activation loop and consequently affect binding of the substrate peptide. New inhibition sites for selectively inhibiting the activity of CDK5 are also suggested.

Synthesis of natural product inspired compound collections

Natural products, their derivatives, and their analogues are among the most important sources for new drug candidates and tools for chemical biology and medicinal chemistry research. Therefore, there is a need for the development of efficient synthesis methods which give access to natural product derived and inspired compound collections. To meet this challenge, the requirements of multistep stereoselective syntheses, and the logic and methodology of natural product total synthesis need to be translated and adapted to the methods and formats for the synthesis of compound collections. Recent developments in the synthesis of natural product inspired compound collections having carbocyclic and heterocyclic scaffolds highlight the fact that this goal can be successfully attained. The progress made has paved the way for the integration of natural product inspired compound collections into medicinal chemistry and chemical biology research.

Combining Synthetic and Analytical Strategies for Preparative HPLC Enantioseparation of Monastrol Racemic Mixture

Large-scale resolution of racemic monastrol has been carried out by normal-phase mode HPLC on an amylose-based chiral stationary phase. Because monastrol solubility, in media of proper compositions for normal-mode HPLC separations (in terms of retention factors and selectivity), was significantly low and impractical for preparative scopes, racemic monastrol was transformed into the corresponding O-tert-butyldimethylsilyl derivative. The tert-butyldimethylsilyl group was chosen as a suitable derivatizing agent because it induced approximatively a six-times higher solubility and allowed for an almost quantitative recovery of pure monastrol from the derivatization-deprotection sequence. The competitive isotherms of the O-tert-butyldimethylsilyl compounds, measured through frontal analysis, were fitted to competitive Langmuir and four-parameter bi-Langmuir models. The equilibrium dispersive model of chromatography was used for modeling the nonlinear separation of the racemate and to optimize the experimental conditions for collection of highly concentrated fractions of pure (R,S)-O-tert-butyldimethylsilyl compounds, from which significant amounts of the corresponding enantiomers of monastrol (about 100 mg of each enantiomer with 30 runs on an analytical-scale column) were obtained by quantitative back-derivatization.

Significance of water molecules in the inhibition of cylin-dependent kinase 2 and 5 complexes

Interest in CDK2 and CDK5 has stemmed mainly from their association with cancer and neuronal migration or differentiation related diseases and the need to design selective inhibitors for these kinases. In the present paper, eight Molecular Dynamics (MD) simulations are carried out to examine the importance of structure and dynamics of water in the active site of both CDK2 and CDK5 complexes with roscovitine and indirubin analogues. Together with previous results, the current work shows a highly conserved water-involved hydrogen bonding (HB) network in both CDK2- and CDK5-indirubin combinations to complete information from the X-ray crystallography. The simulations suggest the importance of such a network for combining the inhibitor to the host protein as well as the significance of using an activated CDK as a template when designing new inhibitors. Different binding patterns of roscovitine in CDK2 and CDK5 are detected during the simulations because of the different binding conformations of the group on the C2 side chain, which might offer a clue toward finding highly selective inhibitors with regards to CDK2 and CDK5.

New thiopyrazolo[3,4-d]pyrimidine derivatives as anti-mycobacterial agents

The multiple parallel synthesis of a series of N,S-bis-alkylated thiopyrazolo[3,4-d]pyrimidines, based on sequential S- then N-alkylation, is reported. These compounds showed significant anti-mycobacterial activity (MICs down to 2mug/ml) and their potential as significant drug-like leads is substantiated through cytotoxicity evaluation and in silico profiling.

Design, synthesis, and antiproliferative and CDK2-cyclin a inhibitory activity of novel flavopiridol analogues

The design and synthesis of a small library of 8-amidoflavone, 8-sulfonamidoflavone, 8-amido-7-hydroxyflavone, and heterocyclic analogues of flavopiridol is reported. The potential activity of these compounds as kinase inhibitors was evaluated by cytotoxicity studies in MCF-7 and ID-8 cancer cell lines and inhibition of CDK2-Cyclin A enzyme activity in vitro. The antiproliferative and CDK2-Cyclin A inhibitory activity of these analogues was significantly lower than the activity of flavopiridol. Molecular docking simulations were carried out and these studies suggested a different binding orientation inside the CDK2 binding pocket for these analogues compared to flavopiridol.

Molecular dynamics simulations on the inhibition of cyclin-dependent kinases 2 and 5 in the presence of activators

Interests in CDK2 and CDK5 have stemmed mainly from their association with cancer and neuronal migration or differentiation related diseases and the need to design selective inhibitors for these kinases. Molecular dynamics (MD) simulations have not only become a viable approach to drug design because of advances in computer technology but are increasingly an integral part of drug discovery processes. It is common in MD simulations of inhibitor/CDK complexes to exclude the activator of the CDKs in the structural models to keep computational time tractable. In this paper, we present simulation results of CDK2 and CDK5 with roscovitine using models with and without their activators (cyclinA and p25). While p25 was found to induce slight changes in CDK5, the calculations support that cyclinA leads to significant conformational changes near the active site of CDK2. This suggests that detailed and structure-based inhibitor design targeted at these CDKs should employ activator-included models of the kinases. Comparisons between P/CDK2/cyclinA/roscovitine and CDK5/p25/roscovitine complexes reveal differences in the conformations of the glutamine around the active sites, which may be exploited to find highly selective inhibitors with respect to CDK2 and CDK5.

Study of the inhibition of cyclin-dependent kinases with roscovitine and indirubin-3'-oxime from molecular dynamics simulations

Molecular dynamics simulations were performed to elucidate the interactions of CDK2 and CDK5 complexes with three inhibitors: R-roscovitine, S-roscovitine, and indirubin-3'-oxime. The preference of the two complexes for R-roscovitine over the S enantiomer, as reported by the experiment, was also found by the simulations. More importantly, the simulations showed that the cause of the stronger affinity for the R enantiomer is the presence of an important hydrogen bond between R-roscovitine and the kinases not found with S-roscovitine. The simulations also showed two amino acid mutations in the active site of CDK5/R-roscovitine that favor binding-enhanced electrostatic contributions, making the inhibitor more effective for CDK5 than for CDK2. This suggests that the effectiveness of roscovitine-like inhibitors can be improved by enhancing their electrostatic interaction with the kinases. Finally, molecular mechanics-Possion-Boltzmann/surface area calculations of the CDK5/indirubin-3'-oxime system in both water-excluded and water-included environments gave significantly different electrostatic contributions to the binding. The simulations detected the displacement of a water molecule in the active site of the water-included CDK/indirubin-3'-oxime system. This resulted in a more conserved binding pattern than the water-excluded structure. Hence, in the design of new indirubin-like inhibitors, it is important to include the water molecule in the analysis.

SAR studies of 2-methoxyestradiol and development of its analogs as probes of anti-tumor mechanisms

The major estrogen metabolite 2-methoxyestradiol (2ME) has been shown to target tumor cells without severe side effects and is currently being evaluated in clinical trials for several types of cancer. Despite its promise for use in clinical setting, the mechanism(s) by which 2ME exerts its anti-tumor activity is not clearly defined at this time. Employing organic chemistry tools, we synthesized 2ME analogs with which 2ME affinity column was prepared, enabling us to detect a protein that selectively interacts with 2ME. This 2ME analog will be useful as a probe to identify the biological target(s) of 2ME and study their functions in tumor cells.

Exploring New Chemical Space by Stereocontrolled Diversity-Oriented Synthesis

Natural products that act as highly specific, small-molecule protein-binding agents and as modulators of protein-protein interactions are highly complex and exhibit functional groups with three-dimensional and stereochemical diversity. The complex three-dimensional display of chiral functional groups appears to be crucial for exhibiting specificity in protein binding and in differentiating between closely related proteins. The development of methods that allow a high-throughput access to three-dimensional, skelatally complex, polycyclic compounds having few asymmetric diversity sites is essential and a highly challenging task. In the postgenomic chemical biology age, in which there is a great desire to understand protein-protein interactions and to dissect protein networking-based signaling pathways by small molecules, the need for developing "stereocontrolled, diversity-oriented synthesis" methods to generate natural product-like libraries is of utmost importance.

Degradation of target protein in living cells by small-molecule proteolysis inducer

Ubiquitin-dependent proteolysis of cellular proteins is one of the major pathways to regulate protein function posttranslationally. Here we demonstrate a potentially general method of degrading any targeted proteins by the ubiquitin-dependent proteolysis in living cells, using small-molecule proteolysis inducer (SMPI).

Targeting cell division: small-molecule inhibitors of FtsZ GTPase perturb cytokinetic ring assembly and induce bacterial lethality

FtsZ, the ancestral homolog of eukaryotic tubulins, is a GTPase that assembles into a cytokinetic ring structure essential for cell division in prokaryotic cells. Similar to tubulin, purified FtsZ polymerizes into dynamic protofilaments in the presence of GTP; polymer assembly is accompanied by GTP hydrolysis. We used a high-throughput protein-based chemical screen to identify small molecules that target assembly-dependent GTPase activity of FtsZ. Here, we report the identification of five structurally diverse compounds, named Zantrins, which inhibit FtsZ GTPase either by destabilizing the FtsZ protofilaments or by inducing filament hyperstability through increased lateral association. These two classes of FtsZ inhibitors are reminiscent of the antitubulin drugs colchicine and Taxol, respectively. We also show that Zantrins perturb FtsZ ring assembly in Escherichia coli cells and cause lethality to a variety of bacteria in broth cultures, indicating that FtsZ antagonists may serve as chemical leads for the development of new broad-spectrum antibacterial agents. Our results illustrate the utility of small-molecule chemical probes to study FtsZ polymerization dynamics and the feasibility of FtsZ as a novel therapeutic target.

A Solution- and Solid-Phase Approach to Tetrahydroquinoline-Derived Polycyclics Having a 10-Membered Ring

With the goal of library generation using a polycyclic derivative 5 having an enamide functional group, a simple and practical, enantioselective synthesis of tetrahydroquinoline derivative 2 was achieved. The phenolic hydroxyl group in compound 2 was utilized as an anchoring site for solid-phase synthesis. The ring closing metathesis approach yielded the desired polycyclic product 5 on solid phase in five steps (overall 40% yield). Compound 5 is a novel scaffold for the library generation of natural product-like polycyclics having a functionalized medium ring for obtaining a new class of small molecules to be utilized as chemical probes.

Solution- and Solid-Phase Synthesis of Natural Product-Like Tetrahydroquinoline-Based Polycyclics Having a Medium Size Ring

A solid-phase synthesis of tetrahydroquinoline-derived polycyclic 4, having a medium size ring with an enamide functionality, was achieved from tetrahydroquinoline derivative 3 in five steps with overall 40-45% yield. An enantiopure, tetrahydroquinoline-derived beta-amino ester, 1, was converted into compound 2 that has a free phenolic hydroxyl group as an anchoring site for solid-phase synthesis. The solid-phase worked well for this sequence, in which the synthesis of the unsaturated eight-membered enamide lactam was obtained by a ring-closing metathesis approach. Compound 4 is a novel, natural product-like polycyclic derivative that could further be utilized in library generation for developing small molecule chemical probes.

A novel small-molecule inhibitor of the chromosome segregation process in yeast

The centromeres of budding yeasts contain specific and essential DNA sequences, in contrast to the regional heterochromatic centromeres found in higher organisms. Small molecules that perturb centromere function in budding yeast could be valuable candidates for identifying yeast-specific growth inhibitors. A combination of two in vivo assays, one based on transcription blockade of a reporter gene by the centromeric DNA-protein complex, the other on a test for mitotic minichromosome stability, was used to identify small molecules that affect the process of chromosome segregation. One compound, here named incentrom A, leads to a minichromosome loss phenotype, and is cytotoxic to the budding yeast Saccharomyces cerevisiae. Furthermore, whereas cells carrying a conditional mutation in a gene for an essential kinetochore protein, skp1-4, are hypersensitive to incentrom A, cells that overexpress the SKP1 gene are resistant to the compound. Incentrom A also results in mitotic loss of a centromere-bearing plasmid, and inhibits the growth of the pathogenic yeast Candida glabrata. Incentrom A will therefore be a useful tool for studying the molecular basis of yeast chromosome segregation and could form the basis for the development of novel antifungal drugs.

Total synthesis of (+)-belactosin A

A concise first total synthesis of the antitumour antibiotic belactosin A is reported, involving coupling of beta-lactone carboxylic acid 3 with N-Ala-aminocyclopropyl alanine 11.

Brief total synthesis of the cell cycle inhibitor tryprostatin B and related preparation of its alanine analogue

Tryprostatin B was synthesized in 32% overall yield from the readily available dipeptide anhydride cyclo-(l-Trp-l-Pro). Its tandem C-3 prenylation/cyclization gave the corresponding pentacyclic pyrroloindole systems bearing a prenyl group at the indole C-3 position. These compounds were then submitted to acid-catalyzed opening of the newly formed ring, with concomitant migration of the prenyl group to the indole C-2 position. The alanine analogue of tryprostatin B was also prepared using a similar sequence. The successful implementation of this strategy strengthens the case for a biosynthetic route for the tryprostatins along similar lines.

Chemical genetics: tailoring tools for cell biology

Chemical genetics is a research approach that uses small molecules as probes to study protein functions in cells or whole organisms. Here, I review the parallels between classical genetic and chemical-genetic approaches and discuss the merits of small molecules to dissect dynamic cellular processes. I then consider the pros and cons of different screening approaches and specify strategies aimed at identifying and validating cellular target proteins. Finally, I highlight the impact of chemical genetics on our current understanding of cell biology and its potential for the future.

Nordihydroguaiaretic acid, of a new family of microtubule-stabilizing agents, shows effects differentiated from paclitaxel

Nordihydroguaiaretic acid (NDGA) protected microtubules in NRK cells from depolymerization caused by structurally and functionally diverse drugs such as nocodazole, colchicine, vinblastine, and ilimaquinone. Hitherto reported drugs, although structurally unrelated to paclitaxel, stabilize microtubules in a way similar to that of paclitaxel and compete for paclitaxel binding to tubulin. However, NDGA had activity toward microtubules different from the effects of paclitaxel. In NRK cells, paclitaxel caused microtubule bundle formation in the presence and absence of microtubule-depolymerizing drugs. However, microtubule bundle did not form, and microtubules radiated from the microtubule-organizing center, in cells treated with NDGA. Acceleration of tubulin polymerization in vitro by paclitaxel was strong but that by NDGA was weak. Microtubules polymerized in vitro in the presence of paclitaxel, but not those polymerized in the presence of NDGA, resisted the effects of cold. NDGA seemed to bind to tubulin, but did not compete for [3H]paclitaxel binding to tubulin. These observations indicate that NDGA belongs to a novel family of microtubule-stabilizing drugs.

Dynamics and binding modes of free cdk2 and its two complexes with inhibitors studied by computer simulations

This article presents a molecular dynamics (MD) study of the cdk2 enzyme and its two complexes with the inhibitors isopentenyladenine and roscovitine using the Cornell et al. force field from the AMBER software package. The results show that inserting an inhibitor into the enzyme active site does not considerably change enzyme structure but it seemingly changes the distribution of internal motions. The inhibitor causes differences in the domain motions in free cdk2 and in its complexes. It was found out that repulsion of roscovitine N9 substituent causes conformational change on Lys 33 side chain. Isopentenyladenine forms with Lys 33 side chain terminal amino group a hydrogen bond. It implies that the cavity, where N9 substituent of roscovitine is buried, can adopt larger substituent due to Lys 33 side chain flexibility. The composition of electrostatic and van der Waals interactions between the inhibitor and the enzyme were also calculated along both cdk2/inhibitor MD trajectories together with MM-PB/GBSA analysis. These results show that isopentenyladenine-like inhibitors could be more effective after modifications leading to an increase in their van der Waals contact with the enzyme. We suggest that a way leading to better inhibitors occupying isopentenyladenine binding mode could be: to keep N9 and N7 purine positions free, to keep 3,3-dimethylallylamino group at C6 position, and to add, e.g., benzylamino group at C2 position. The results support the idea that the isopentenyladenine binding mode can be used for cdk2 inhibitors design and that all possibilities to improve this binding mode were not uncovered yet.

Ras-MAP kinase signaling pathways and control of cell proliferation: relevance to cancer therapy

The mitogen-activated protein (MAP) kinase pathways represent several families of signal transduction cascades that mediate information provided by extracellular stimuli. MAP kinase pathways regulate a wide range of physiological responses, including cell proliferation, apoptosis, cell differentiation, and tissue development. Constitutive activation of MAP kinase proteins in experimental models has been shown to cause cell transformation and is implicated in tumorigenesis. Of clinical importance, MAP kinase pathways are regulated by Ras G-proteins, which are found to be mutated and constitutively active in approximately 30% of all human cancers. Thus, a major goal in the treatment of cancer is the development of specific compounds that target Ras and critical downstream signaling proteins responsible for uncontrolled cell growth. A variety of biochemical, molecular, and structural approaches have been used to develop drug compounds that target signaling proteins important for MAP kinase pathway activation. These compounds have been useful tools for identifying the mechanisms of MAP kinase pathway signaling and hold promise for clinical use. This review will present an overview of the major proteins involved in Ras and MAP kinase signaling pathways and their function in regulating cell cycle events and proliferation. In addition, some of the relevant compounds that have been developed to inhibit the activities of these proteins and MAP kinase signaling are discussed.

Progress toward the development of agents to modulate the cell cycle

With taxanes continuing to prove useful in the clinical treatment of cancer, the next generation of antimitotic agents has entered clinical trials. Other mechanisms awaiting proof-of-concept for the treatment of antiproliferative diseases include inhibition of cyclin-dependent kinases (Cdks). Flavopiridol and UCN-01 are continuing in clinical trials, and newer more selective Cdk inhibitors are now entering clinical evaluation.

Characterization of a novel mammalian phosphatase having sequence similarity to Schizosaccharomyces pombe PHO2 and Saccharomyces cerevisiae PHO13

p34, a specific p-nitrophenyl phosphatase (pNPPase) was identified and purified from the murine cell line EL4 in a screen for the intracellular molecular targets of the antiinflammatory natural product parthenolide. A BLAST search analysis revealed that it has a high degree of sequence similarity to two yeast alkaline phosphatases. We have cloned, sequenced, and expressed p34 as a GST-tagged fusion protein in Escherichia coli and an EE-epitope-tagged fusion protein in mammalian cells. Using p-nitrophenyl phosphate (pNPP) as a substrate, p34 is optimally active at pH 7.6 with a K(m) of 1.36 mM and K(cat) of 0.052 min(-1). Addition of 1 mM Mg(2+) to the reaction mixture increases its activity by 14-fold. Other divalent metal ions such as Co(2+) and Mn(2+) also stimulated the activity of the enzyme, while Zn(2+), Fe(2+), and Cu(2+) had no effect. Furthermore, both NaCl and KCl enhanced the activity of the enzyme, having maximal effect at 50 and 75 mM, respectively. The enzyme is inhibited by sodium orthovanadate but not by sodium fluoride or okadaic acid. Mutational analysis data suggest that p34 belongs to the group of phosphatases characterized by the sequence motif DXDX(T/V).

Toward high-throughput synthesis of complex natural product-like compounds in the genomics and proteomics age

In the age of high-throughput biology, novel genes and proteins are emerging quickly. The need for developing organic synthesis-derived methods that allow rapid access to polyfunctional, complex natural product-like compounds is growing constantly, largely because these small-molecule-based compounds serve as smart, powerful tools both in understanding the roles and functions of emerging biological targets and in validating their biological responses. Developing asymmetric synthesis-derived organic reactions on solid phase allows the synthesis of complex natural product-like compounds in a high-throughput manner. Solid phase organic synthesis is now commonly utilized in the library synthesis of rather simple compounds (i.e., compounds with no multiple stereogenic centers). With few exceptions, the synthesis of complex natural product-like derivatives is still in its infancy. Some recent efforts made in this area indicate opportunities yet to be explored.

To cycle or not to cycle: a critical decision in cancer

Tumour cells undergo uncontrolled proliferation, yet tumours most often originate from adult tissues, in which most cells are quiescent. So, the proliferative advantage of tumour cells arises from their ability to bypass quiescence. This can be due to increased mitogenic signalling and/or alterations that lower the threshold required for cell-cycle commitment. Understanding the molecular mechanisms that underlie this commitment should provide important insights into how normal cells become tumorigenic and how new anticancer strategies can be devised.

Natural-product-like chiral derivatives by solid-phase synthesis

In this genomics and proteomics age, highly functionalized natural products or natural-product-like compounds are likely to play important roles in understanding the functions of emerging biological targets because they serve as small-molecule chemical probes in modulating a target's specific actions (i.e. activation or deactivation). Development of stereoselective reaction-derived methods on solid phase provides a means of obtaining functionalized chiral core structures that may be used for high-throughout syntheses.