Use of an altered sugar-nucleotide to unmask the transition state for alpha(2-->6) sialyltransferase

Recent advances in the development of sialyltransferase inhibitors to control cancer metastasis: A comprehensive review

Metastasis accounts for the majority of cancer-associated mortalities, representing a huge health and economic burden. One of the mechanisms that enables metastasis is hypersialylation, characterized by an overabundance of sialylated glycans on the tumor surface, which leads to repulsion and detachment of cells from the original tumor. Once the tumor cells are mobilized, sialylated glycans hijack the natural killer T-cells through self-molecular mimicry and activatea downstream cascade of molecular events that result in inhibition of cytotoxicity and inflammatory responses against cancer cells, ultimately leading to immune evasion. Sialylation is mediated by a family of enzymes known as sialyltransferases (STs), which catalyse the transfer of sialic acid residue from the donor, CMP-sialic acid, onto the terminal end of an acceptor such as N-acetylgalactosamine on the cell-surface. Upregulation of STs increases tumor hypersialylation by up to 60% which is considered a distinctive hallmark of several types of cancers such as pancreatic, breast, and ovarian cancer. Therefore, inhibiting STs has emerged as a potential strategy to prevent metastasis. In this comprehensive review, we discuss the recent advances in designing novel sialyltransferase inhibitors using ligand-based drug design and high-throughput screening of natural and synthetic entities, emphasizing the most successful approaches. We analyse the limitations and challenges of designing selective, potent, and cell-permeable ST inhibitors that hindered further development of ST inhibitors into clinical trials. We conclude by analysing emerging opportunities, including advanced delivery methods which further increase the potential of these inhibitors to enrich the clinics with novel therapeutics to combat metastasis.

Sialyltransferase Inhibitors for the Treatment of Cancer Metastasis: Current Challenges and Future Perspectives

Potent, cell-permeable, and subtype-selective sialyltransferase inhibitors represent an attractive family of substances that can potentially be used for the clinical treatment of cancer metastasis. These substances operate by specifically inhibiting sialyltransferase-mediated hypersialylation of cell surface glycoproteins or glycolipids, which then blocks the sialic acid recognition pathway and leads to deterioration of cell motility and invasion. A vast amount of evidence for the in vitro and in vivo effects of sialyltransferase inhibition or knockdown on tumor progression and tumor cell metastasis or colonization has been accumulated over the past decades. In this regard, this review comprehensively discusses the results of studies that have led to the recent discovery and development of sialyltransferase inhibitors, their potential biomedical applications in the treatment of cancer metastasis, and their current limitations and future opportunities.

Transition State-Based Sialyltransferase Inhibitors: Mimicking Oxocarbenium Ion by Simple Amide

In the new transition-state based sialyltransferase inhibitors, an amide group was placed at the corresponding C-2 position of CMP-sialic acid to mimic the geometry and charge distribution in the transition state, and simple aromatic or aliphatic rings were used instead of the sialic acid moiety. All synthetic compounds exhibited excellent α(2-6)-sialyltransferase inhibition, resulting in up to a 2600-fold higher affinity for the enzyme than CMP-Neu5Ac, suggesting that amide is a key element for simulating transition-state features.

Quantum Mechanics/Molecular Mechanics Study of the Sialyltransferase Reaction Mechanism

The sialyltransferase is an enzyme that transfers the sialic acid moiety from cytidine 5'-monophospho-N-acetyl-neuraminic acid (CMP-NeuAc) to the terminal position of glycans. To elucidate the catalytic mechanism of sialyltransferase, we explored the potential energy surface along the sialic acid transfer reaction coordinates by the hybrid quantum mechanics/molecular mechanics method on the basis of the crystal structure of sialyltransferase CstII. Our calculation demonstrated that CstII employed an S_N1-like reaction mechanism via the formation of a short-lived oxocarbenium ion intermediate. The computational barrier height was 19.5 kcal/mol, which reasonably corresponded with the experimental reaction rate. We also found that two tyrosine residues (Tyr156 and Tyr162) played a vital role in stabilizing the intermediate and the transition states by quantum mechanical interaction with CMP.

Highly Substituted Cyclopentane-CMP Conjugates as Potent Sialyltransferase Inhibitors

Sialylconjugates on cell surfaces are involved in many biological events such as cellular recognition, signal transduction, and immune response. It has been reported that aberrant sialylation at the nonreducing end of glycoconjugates and overexpression of sialyltransferases (STs) in cells are correlated with the malignance, invasion, and metastasis of tumors. Therefore, inhibitors of STs would provide valuable leads for the discovery of antitumor drugs. On the basis of the transition state of the enzyme-catalyzed sialylation reaction, we proposed that the cyclopentane skeleton in its two puckered conformations might mimic the planar structure of the donor (CMP-Neu5Ac) in the transition state. A series of cyclopentane-containing compounds were designed and synthesized by coupling different cyclopentane α-hydroxyphosphonates with cytidine phosphoramidite. Their inhibitory activities against recombinant human ST6Gal-I were assayed, and a potent inhibitor 48l with a Ki of 0.028 ± 0.006 μM was identified. The results show that the cyclopentanoid-type compounds could become a new type of sialyltransferase inhibitors as biological probes or drug leads.

Chemoenzymatic synthesis of ring 18O-labeled sialic acid

Methyl 4,6-O-benzylidene-α-D-glucopyranoside was converted into methyl 2-azido-2-deoxy-4,6-O-benzylidene-α-D-altropyranoside via a synthetic route that incorporated two inversions of configuration. Activation of the C-3 hydroxyl group as a triflate ester followed by an SN2 reaction with O-18 labeled benzoate gave, after standard functional group manipulations, 2-acetamido-2-deoxy-D-(3-18O)mannose. Coupling of the labeled N-acetyl-mannosamine with pyruvate was catalyzed by sialic acid aldolase to give ring-oxygen-labeled sialic acid in an overall yield of 11.4% over 10 steps.Key words: N-acetylneuraminic acid, sialic acid oxygen-18, chemoenzymatic.

A kinetic and thermodynamic study of the glycosidic bond cleavage in deoxyuridine

Density functional theory was used to study the thermodynamics and kinetics for the glycosidic bond cleavage in deoxyuridine. Two reaction pathways were characterized for the unimolecular decomposition in vacuo. However, these processes are associated with large reaction barriers and highly endothermic reaction energies, which is in agreement with experiments that suggest a (water) nucleophile is required for the nonenzymatic glycosidic bond cleavage. Two (S(N)1 and S(N)2) reaction pathways were characterized for direct hydrolysis of the glycosidic bond by a single water molecule; however, both pathways also involve very large barriers. Activation of the water nucleophile via partial proton abstraction steadily decreases the barrier and leads to a more exothermic reaction energy as the proton affinity of the molecule interacting with water increases. Indeed, our data suggests that the barrier heights and reaction energies range from that for hydrolysis by water to that for hydrolysis by the hydroxyl anion, which represents the extreme of (full) water activation (deprotonation). Hydrogen bonds between small molecules (hydrogen fluoride, water, or ammonia) and the nucleobase were found to further decrease the barrier and overall reaction energy but not to the extent that the same hydrogen-bonding interactions increase the acidity of the nucleobase. Our results suggest that the nature of the nucleophile plays a more important role in reducing the barrier to glycosidic bond cleavage than the nature of the small molecule bound, and models with more than one hydrogen fluoride molecule interacting with the nucleobase provide further support for this conclusion. Our results lead to a greater fundamental understanding of the effects of the nucleophile, activation of the nucleophile, and interactions with the nucleobase for this important biological reaction.

Potential sialyltransferase inhibitors based on neuraminyl substitution by hetaryl rings

Replacement of the neuraminyl residue by a wide range of aryl rings in transition-state analogs of CMP-Neu5Ac led to readily accessible and potent inhibitors of alpha-(2-->6)- and alpha-(2-->3)-sialyltransferases. The synthesis of a series of potential sialyltransferase inhibitors in which the neuraminyl residue is replaced by hetaryl methylphosphonate residues (thiazole, benzothiazole, benzoxazole, benzothiophene and thiophene) is described in this paper.

Synthesis of Bisubstrate and Donor Analogues of Sialyltransferase and Their Inhibitory Activities

[reaction: see text] Sialyltransferases (STs) are involved in the biosynthesis of glycoconjugates with important biological activities. Most STs utilize cytidine-5'-monophospho-N-acetylneuraminic acid (CMP-Neu5Ac) as a common donor substrate. A bisubstrate analogue containing the donor substrate (CMP-Neu5Ac mimic) and the acceptor substrate (galactose) was synthesized. Four donor analogues having the partial structure of the bisubstrate analogue were also synthesized to support study of the structure-activity relationship. Each analogue contains an ethylene group in place of the exocyclic anomeric oxygen of CMP-Neu5Ac. The bisubstrate analogue exhibited only weak inhibitory activity to rat recombinant alpha-2,3- and alpha-2,6-ST (IC(50) = 1.3, 2.4 mM). Conversion of the C-1 carboxylate of the Neu5Ac moiety to carboxyamide, hydroxymethyl, or methylene phosphate each resulted in a reduction in inhibitory activity. Among the synthesized analogues, cytidin-5'-yl sialylethylphosphonate (4) was the most potent inhibitor against rat recombinant alpha-2,3- and alpha-2,6-ST (IC(50) = 0.047, 0.34 mM).

Asymmetric synthesis and affinity of potent sialyltransferase inhibitors based on transition-state analogues

Inhibitors that are structurally related to the transition-state model of the proposed SN1-type mechanism of sialyl transfer, exhibit particularly high binding affinities to alpha(2-6)sialyltransferases. Furthermore, replacing the neuraminyl residue with a simple aryl or hetaryl ring and substituting the carboxylate group for a phosphonate moiety, improves both binding affinity and synthetic accessibility. Herein we report on the synthesis and inhibition of a wide range of novel, potent transition-state analogue based alpha(2-6)sialyltransferase inhibitors comprising a planar anomeric carbon, an increased distance between the anomeric carbon and the CMP leaving group, and at least two negative charges. We also present a short, efficient asymmetric synthesis of the most promising benzyl inhibitors, providing rapid access to large quantities of highly potent, stereochemically-pure (>96% de) inhibitors for further biological investigation (e.g.(R)-3b, Ki = 70 nM).

Dependence of Transition State Structure on Substrate: The Intrinsic C-13 Kinetic Isotope Effect Is Different for Physiological and Slow Substrates of the Ornithine Decarboxylase Reaction Because of Different Hydrogen Bonding Structures

Ornithine decarboxylase is the first and the rate-controlling enzyme in polyamine biosynthesis; it decarboxylates l-ornithine to form the diamine putrescine. We present calculations performed using a combined quantum mechanical and molecular mechanical (QM/MM) method with the AM1 semiempirical Hamiltonian for the wild-type ornithine decarboxylase reaction with ornithine (the physiological substrate) and lysine (a "slow" substrate) and for mutant E274A with ornithine substrate. The dynamical method is variational transition state theory with quantized vibrations. We employ a single reaction coordinate equal to the carbon-carbon distance of the dissociating bond, and we find a large difference between the intrinsic kinetic isotope effect for the physiological substrate, which equals 1.04, and that for the slow substrate, which equals 1.06. This shows that, contrary to a commonly accepted assumption, kinetic isotope effects on slow substrates are not always good models of intrinsic kinetic isotope effects on physiological substrates. Furthermore, analysis of free-energy-based samples of transition state structures shows that the differences in kinetic isotope effects may be traced to different numbers of hydrogen bonds at the different transition states of the different reactions.

Stereoselective synthesis of phosphoramidate alpha(2-6)sialyltransferase transition-state analogue inhibitors

The asymmetric synthesis of novel, potent phosphoramidate alpha(2-6)sialyltransferase transition-state analogue inhibitors such as (R)-9 (K(i)=68 microM) is described, via condensation of cytidine phosphitamide 6 with key chiral, non-racemic alpha-aminophosphonates, prepared in >98% ee by Mitsunobu azidation followed by Staudinger reduction of the corresponding chiral, non-racemic alpha-hydroxyphosphonates.

Recent development in the design of sialyltransferase inhibitors

Sialylation at the non-reducing end of glycoconjugates is an important biological process in cellular recognitions, tumor metastases, and immune responses, which are mediated by a family of enzymes known as sialyltransferases. Inhibition of sialyltransferases may prove useful in elucidating the biological functions of sialylation and may have therapeutic applications. This review summarizes the recent development in this field with particular focus on the strategies used for the design of carbohydrate mimetics and the structure-activity relationships of substrate-based sialyltransferase inhibitors.

Transition state variation in enzymatic reactions

Experimental analysis of enzymatic transition states by kinetic isotope effect methods has established geometric variation in related transition state structures. Differences are apparent in development of the reaction coordinate, in solvolytic transition states relative to those in enzymatic catalytic sites, in the stereochemistry of related substrates at the transition state, and in reactions catalyzed by related enzymes.