Enzymatic Regeneration of 3'-Phosphoadenosine-5'-Phosphosulfate Using Aryl Sulfotransferase for the Preparative Enzymatic Synthesis of Sulfated Carbohydrates

Unraveling the intricacies of glycosaminoglycan biosynthesis: Decoding the molecular symphony in understanding complex polysaccharide assembly

Glycosaminoglycans (GAGs) are extensively utilized in clinical, cosmetic, and healthcare field, as well as in the treatment of thrombosis, osteoarthritis, rheumatism, and cancer. The biological production of GAGs is a strategy that has garnered significant attention due to its numerous advantages over traditional preparation methods. In this review, we embark on a journey to decode the intricate molecular symphony that orchestrates the biosynthesis of glycosaminoglycans. By unraveling the complex interplay of related enzymes and thorough excavation of the intricate metabolic cascades involved, GAGs chain aggregation and transportation, which efficiently and controllably modulate GAGs sulfation patterns involved in biosynthetic pathway, we endeavor to offer a thorough comprehension of how these remarkable GAGs are intricately assembled and pushes the boundaries of our understanding in GAGs biosynthesis.

Enhancing the expression of chondroitin 4-O-sulfotransferase for one-pot enzymatic synthesis of chondroitin sulfate A

Chondroitin sulfate (CS) stands as a pivotal compound in dietary supplements for osteoarthritis treatment, propelling significant interest in the biotechnological pursuit of environmentally friendly and safe CS production. Enzymatic synthesis of CS for instance CSA has been considered as one of the most promising methods. However, the bottleneck consistently encountered is the active expression of chondroitin 4-O-sulfotransferase (C4ST) during CSA biosynthesis. This study meticulously delved into optimizing C4ST expression through systematic enhancements in transcription, translation, and secretion mechanisms via modifications in the 5' untranslated region, the N-terminal encoding sequence, and the Komagataella phaffii chassis. Ultimately, the active C4ST expression escalated to 2713.1 U/L, representing a striking 43.7-fold increase. By applying the culture broth supernatant of C4ST and integrating the 3'-phosphoadenosine-5'-phosphosulfate (PAPS) biosynthesis module, we constructed a one-pot enzymatic system for CSA biosynthesis, achieving a remarkable sulfonation degree of up to 97.0 %. The substantial enhancement in C4ST expression and the development of an engineered one-pot enzymatic synthesis system promises to expedite large-scale CSA biosynthesis with customizable sulfonation degrees.

Advances and challenges in biotechnological production of chondroitin sulfate and its oligosaccharides

Chondroitin sulfate (CS) is a member of glycosaminoglycans (GAGs) and has critical physiological functions. CS is widely applied in medical and clinical fields. Currently, the supply of CS relies on traditional animal tissue extraction methods. From the perspective of medical applications, the biggest drawback of animal-derived CS is its uncontrollable molecular weight and sulfonated patterns, which are key factors affecting CS activities. The advances of cell-free enzyme catalyzed systems and de novo biosynthesis strategies have paved the way to rationally regulate CS sulfonated pattern and molecular weight. In this review, we first present a general overview of biosynthesized CS and its oligosaccharides. Then, the advances in chondroitin biosynthesis, 3'-phosphoadenosine-5'-phosphosulfate (PAPS) synthesis and regeneration, and CS biosynthesis catalyzed by sulfotransferases are discussed. Moreover, the progress of mining and expression of chondroitin depolymerizing enzymes for preparation of CS oligosaccharides is also summarized. Finally, we analyze and discuss the challenges faced in synthesizing CS and its oligosaccharides using microbial and enzymatic methods. In summary, the biotechnological production of CS and its oligosaccharides is a promising method in addressing the drawbacks associated with animal-derived CS and enabling the production of CS oligosaccharides with defined structures.

Engineering sulfonate group donor regeneration systems to boost biosynthesis of sulfated compounds

Sulfonation as one of the most important modification reactions in nature is essential for many biological macromolecules to function. Development of green sulfonate group donor regeneration systems to efficiently sulfonate compounds of interest is always attractive. Here, we design and engineer two different sulfonate group donor regeneration systems to boost the biosynthesis of sulfated compounds. First, we assemble three modules to construct a 3'-phosphoadenosine-5'-phosphosulfate (PAPS) regeneration system and demonstrate its applicability for living cells. After discovering adenosine 5'-phosphosulfate (APS) as another active sulfonate group donor, we engineer a more simplified APS regeneration system that couples specific sulfotransferase. Next, we develop a rapid indicating system for characterizing the activity of APS-mediated sulfotransferase to rapidly screen sulfotransferase variants with increased activity towards APS. Eventually, the active sulfonate group equivalent values of the APS regeneration systems towards trehalose and p-coumaric acid reach 3.26 and 4.03, respectively. The present PAPS and APS regeneration systems are environmentally friendly and applicable for scaling up the biomanufacturing of sulfated products.

From Steroid and Drug Metabolism to Glycobiology, Using Sulfotransferase Structures to Understand and Tailor Function

Sulfotransferases are ubiquitous enzymes that transfer a sulfo group from the universal cofactor donor 3'-phosphoadenosine 5'-phosphosulfate to a broad range of acceptor substrates. In humans, the cytosolic sulfotransferases are involved in the sulfation of endogenous compounds such as steroids, neurotransmitters, hormones, and bile acids as well as xenobiotics including drugs, toxins, and environmental chemicals. The Golgi associated membrane-bound sulfotransferases are involved in post-translational modification of macromolecules from glycosaminoglycans to proteins. The sulfation of small molecules can have profound biologic effects on the functionality of the acceptor, including activation, deactivation, or enhanced metabolism and elimination. Sulfation of macromolecules has been shown to regulate a number of physiologic and pathophysiological pathways by enhancing binding affinity to regulatory proteins or binding partners. Over the last 25 years, crystal structures of these enzymes have provided a wealth of information on the mechanisms of this process and the specificity of these enzymes. This review will focus on the general commonalities of the sulfotransferases, from enzyme structure to catalytic mechanism as well as providing examples into how structural information is being used to either design drugs that inhibit sulfotransferases or to modify the enzymes to improve drug synthesis. SIGNIFICANCE STATEMENT: This manuscript honors Dr. Masahiko Negishi's contribution to the understanding of sulfotransferase mechanism, specificity, and roles in biology by analyzing the crystal structures that have been solved over the last 25 years.

Round, round we go - strategies for enzymatic cofactor regeneration

Covering: up to the beginning of 2020Enzymes depending on cofactors are essential in many biosynthetic pathways of natural products. They are often involved in key steps: catalytic conversions that are difficult to achieve purely with synthetic organic chemistry. Hence, cofactor-dependent enzymes have great potential for biocatalysis, on the condition that a corresponding cofactor regeneration system is available. For some cofactors, these regeneration systems require multiple steps; such complex enzyme cascades/multi-enzyme systems are (still) challenging for in vitro biocatalysis. Further, artificial cofactor analogues have been synthesised that are more stable, show an altered reaction range, or act as inhibitors. The development of bio-orthogonal systems that can be used for the production of modified natural products in vivo is an ongoing challenge. In light of the recent progress in this field, this review aims to provide an overview of general strategies involving enzyme cofactors, cofactor analogues, and regeneration systems; highlighting the current possibilities for application of enzymes using some of the most common cofactors.

Secretory expression of the rat aryl sulfotransferases IV with improved catalytic efficiency by molecular engineering

The rat aryl sulfotransferases IV (AST IV) has been used to catalyze 3'-phosphoadenosine-5'-phosphate (PAP) into the sulfuryl group donor 3'-phosphoadenosine-5'-phosphosulfate (PAPS) in biotechnological production of glycosaminoglycans. The performance of native AST IV is not satisfying due to the lower catalytic activity with substrate PAP. In the present study, we achieved secretory expression of the AST IV and improved its catalytic efficiency by molecular engineering. Fusion with signal peptides Cex, YebF and PelB allow for secretory expression of AST IV and the secreted AST IV yield reached 4.21 ± 0.23 U/mL, 8.67 ± 0.34 U/mL and 21.35 ± 0.87 U/mL, respectively. Modification of PelB further increased the secretory expression by more than fourfold, to 89.67 ± 1.34 U/mL. On this basis, molecular evolution of the predicted PAP-binding pocket gate loop was performed and a positive mutant L89S/E90L with higher activity was identified. Considering the importance of the sites Leu⁸⁹ and Glu⁹⁰, we performed site-saturation mutagenesis and found the mutant L89M/E90Q with much higher PAP affinity (K _m= 0.46 ± 0.02 mM) and catalytic efficiency (k _cat/K _m = 1816.32 ± 12.72/s/M). The secretory expression of the AST IV variant L89M/E90Q with higher catalytic efficiency should facilitate the studies on biosynthesis of sulfated polysaccharides.

Human Enzymes for Organic Synthesis

Human enzymes have been widely studied in various disciplines. The number of reactions taking place in the human body is vast, and so is the number of potential catalysts for synthesis. Herein, we focus on the application of human enzymes that catalyze chemical reactions in course of the metabolism of drugs and xenobiotics. Some of these reactions have been explored on the preparative scale. The major field of application of human enzymes is currently drug development, where they are applied for the synthesis of drug metabolites.

Chemoenzymatic synthesis of 3'-phosphoadenosine-5'-phosphosulfate coupling with an ATP regeneration system

3'-Phosphoadenosine-5'-phosphosulfate (PAPS) is the obligate cosubstrate and source of the sulfonate group in the chemoenzymatic synthesis of heparin, a commonly used anticoagulant drug. Previously, using ATP as the substrate, we had developed a one-pot synthesis to prepare PAPS with 47% ATP conversion efficiency. During the reaction, 47% of ATP was converted into the by-product, ADP. Here, to increase the conversion ratio of ATP to PAPS, an ATP regeneration system was developed to couple with PAPS synthesis. In the ATP regeneration system, the chemical compound, monopotassium phosphoenolpyruvate (PEP^-K⁺), was synthesized and used as the phospho-donor. By using 3-bromopyruvic acid as the starting material, the total yield of PEP^-K⁺ synthesis was over 50% at low cost. Then, the enzyme PykA from Escherichia coli was overexpressed, purified, and used to convert the by-product ADP into ATP. When coupled the ATP regeneration system with PAPS synthesis, the higher ratio of PEP^-K⁺ to ADP was associated with higher ATP conversion efficiency. By using the ATP regeneration system, the conversion ratio of ATP to PAPS was increased to 98% as determined by PAMN-HPLC analysis, and 5 g of PAPS was produced in 1 L of the reaction mixture. Furthermore, the chemoenzymatic synthesized PAPS was purified and freeze-dried without observed decomposition. However, the powdery PAPS was more unstable than the PAPS sodium salt in aqueous solution at ambient temperature. This developed chemoenzymatic approach of PAPS production will contribute to the synthesis of heparin, in which PAPS is necessary as the individual sulfo-donor.

Hydrolysis of by-product adenosine diphosphate from 3'-phosphoadenosine-5'-phosphosulfate preparation using Nudix hydrolase NudJ

3'-Phosphoadenosine-5'-phosphosulfate (PAPS) is the obligate cosubstrate and source of the sulfonate group in the chemoenzymatic synthesis of heparin, a clinically used anticoagulant drug. Previously, we have developed a method to synthesize PAPS with Escherichia coli crude extracts, which include three overexpressed enzymes and a fourth unidentified protein. The unknown protein degrades adenosine diphosphate (ADP), the by-product of PAPS synthesis reaction. To further understand and control the process of in vitro enzymatic PAPS synthesis, we decide to identify the fourth protein and develop a defined method to synthesize PAPS using purified enzymes. Here, we show that the purified Nudix hydrolase NudJ degrades ADP at high efficiency and serves as the fourth enzyme in PAPS synthesis. Under the defined condition of PAPS synthesis, all of the 10-mM ADP is hydrolyzed to form adenosine monophosphate (AMP) in a 15-min reaction. ADP is a better substrate for NudJ than adenosine triphosphate (ATP). Most importantly, the purified NudJ does not cleave the product PAPS. The removal of ADP makes the PAPS peak more separable from other components in the chromatographic purification process. This developed enzymatic approach of PAPS production will contribute to the chemoenzymatic synthesis of heparin.

A tandem chemoenzymatic methylation by S-adenosyl-L-methionine

Keep 'em methylated: The in situ preparation of the cofactor AdoMet was achieved by allowing the biosynthetic enzyme SalL to operate in the reverse direction by presentation of 5'-chloro-5'-deoxyadenosine at low salt concentrations. This reaction was readily coupled with DNA and small molecule methyltransferases to afford a regioselective method for chemo-enzymatic methylation and isotope incorporation.

Toward automated oligosaccharide synthesis

Carbohydrates have been shown to play important roles in biological processes. The pace of development in carbohydrate research is, however, relatively slow due to the problems associated with the complexity of carbohydrate structures and the lack of general synthetic methods and tools available for the study of this class of biomolecules. Recent advances in synthesis have demonstrated that many of these problems can be circumvented. In this Review, we describe the methods developed to tackle the problems of carbohydrate-mediated biological processes, with particular focus on the issue related to the development of the automated synthesis of oligosaccharides. Further applications of carbohydrate microarrays and vaccines to human diseases are also highlighted.

Overview of the synthesis of nucleoside phosphates and polyphosphates

This overview summarizes methodology used for the synthesis of nucleoside mono-, di-, and triphosphates. Selected techniques such as the Mitsunobu reaction, displacement reactions involving nucleoside 5'-tosylates, "anion-exchange" techniques, and phosphoramidite and phosphoramidate methodologies are highlighted. The chemistry of phosphorylation is detailed with respect to advantages and limitations under various conditions. Applicability of the methods toward the synthesis of analogs such as imidophosphates, phosphorothioates, and radiolabeled nucleotides is also addressed.

Protein Glycosylation: New Challenges and Opportunities

Protein glycosylation is the most complex post-translational modification process. More than 50% of proteins in humans are glycosylated, while bacteria such as E. coli does not have this modification machinery. Many small-molecule natural products also require glycosylation in order to express their function. Development of effective synthetic tools for use in understanding the effect of glycosylation on the structure and function of biomolecules will lead to the development of new strategies to tackle major problems associated with carbohydrate-mediated biological recognitions.

Enzymes in the synthesis of bioactive compounds: the prodigious decades

The growing demand for enantiomerically pure pharmaceuticals has impelled research on enzymes as catalysts for asymmetric synthetic transformations. However, the use of enzymes for this purpose was rather limited until the discovery that enzymes can work in organic solvents. Since the advent of the PCR the number of available enzymes has been growing rapidly and the tailor-made biocatalysts are becoming a reality. Thus, it has been possible the use of enzymes for the synthesis of new innovative medicines such as carbohydrates and their incorporation to modern methods for drug development, such as combinatorial chemistry. Finally, the genomic research is allowing the manipulation of whole genomes opening the door to the combinatorial biosynthesis of compounds. In this review, our intention is to highlight the main landmarks that have led to transfer the chemical efficiency shown by the enzymes in the cell to the synthesis of bioactive molecules in the lab during the last 20 years.

Regeneration of cofactors for use in biocatalysis

Cofactor-dependent enzymes catalyze many synthetically useful reactions. The high cost of cofactors, however, necessitates in situ cofactor regeneration for preparative applications. After two decades of research, several cofactors can now be effectively regenerated using enzyme or whole-cell based methods. Significant advances have been made in this area in the past three years and include the development of novel or improved methods for regenerating ATP, sugar nucleotides and 3-phosphoadenosine-5'-phosphosulphate. These approaches have found novel applications in biocatalysis.

Synthesis of 6'-sulfodisaccharides by beta-N-acetylhexosaminidase-catalyzed transglycosylation

Presulfated N-acetylglucosaminyl donor (pNP beta-D-6-SO3-GlcNAc) was applied for the synthesis of sulfosugars using the beta-N-acetylhexosaminidase-catalyzed transglycosylation, to afford the critically stereocontrolled sulfodisaccharides carrying the 6-sulfo GlcNAc residue at the non-reducing sides in one step.

Enzymes for chemical synthesis

New catalytic synthetic methods in organic chemistry that satisfy increasingly stringent environmental constraints are in great demand by the pharmaceutical and chemical industries. In addition, novel catalytic procedures are necessary to produce the emerging classes of organic compounds that are becoming the targets of molecular and biomedical research. Enzyme-catalysed chemical transformations are now widely recognized as practical alternatives to traditional (non-biological) organic synthesis, and as convenient solutions to certain intractable synthetic problems.

Complex carbohydrate synthesis tools for glycobiologists: enzyme-based approach and programmable one-pot strategies

The ultimate goal in complex carbohydrate synthesis is to develop synthetic tools which are simple and easily accessible to glycobiologists. This review will describe methods which have the potential to reach this goal, with particular focus on enzymatic and computer-based one-pot approaches for the preparation of complex carbohydrates and glycoconjugates.

Regeneration of PAPS for the enzymatic synthesis of sulfated oligosaccharides

This paper describes the study of 3'-phosphoadenosine-5'-phosphosulfate (PAPS) regeneration from 3'-phosphoadenosine-5'-phosphate (PAP) for use in practical syntheses of carbohydrate sulfates which are catalyzed by sulfotransferases. Among the regeneration systems, the one with recombinant aryl sulfotransferase proved to be the most practical. This regeneration system was coupled with a sulfotransferase-catalyzed reaction, using a recombinant Nod factor sulfotransferase, for the synthesis of various oligosaccharide sulfates that were further glycosylated using glycosyltransferases.

Emerging themes in medicinal glycoscience

The recognition of complex carbohydrates and glycoconjugates as mediators of important biological processes has stimulated investigation into their therapeutic potential. New approaches for the simplification of glycoconjugate synthesis are overcoming the limitations of existing methods and providing a diverse array of these biomolecules. As the accessibility of glycoconjugates increases, carbohydrate-based constructs are becoming available for analysis as medicinal agents in a wide range of therapies.

Lanthanide chalcogenolate complexes: synthesis and crystal structures of the isoleptic series [Sm(TpMe,Me)2ER] (E = O, S, Se, Te; TpMe,Me = tris-3,5-dimethylpyrazolylborate)

A series of lanthanide complexes containing a chalcogenolate ligand supported by two TpMe,Me (tris-3,5-dimethylpyrazolylborate) groups has been prepared and crystallized and provides direct comparisons of bonding to hard and soft ligands at lanthanide centers. Reaction of [Sm(TpMe,Me)2Cl] with NaOR (R = Ph, Ph-Bu(t)) gives [Sm(TpMe,Me)2OR] (1a and 1b, respectively) in good yields. Reductive cleavage of dichalcogenides by samarium(II) was used to prepare the heavier congeners. Complexes of the type [Sm(TpMe,Me)2ER] for E = S, R = Ph (2a), E = S, R = Ph-4-Me (2b), E = S, R = CH2Ph (2c), E = Se, R = Ph (3a), E = Se, R = Ph-4-Bu(t) (3b), E = Se, R = CH2Ph (3c), and E = Te, R = Ph (4) have been prepared together with the corresponding complexes with TpMe,Me,4-Et as ancillary. The X-ray crystal structures of 1b, 2b, 3a, 3b, and 4 have been determined. The crystal of 1b (C40H57B2N12OSm.C7H8) was monoclinic, P2(1)/c, a = 10.6845(6) A, b = 18.5573(11) A, c = 24.4075(14) A, beta = 91.616(2) degrees, Z = 4. The crystal of 2b (C37H51B2N12SSm) was monoclinic, P2(1)/n, a = 15.0154(9) A, b = 13.1853(8) A, c = 21.1254(13) A, beta = 108.628(2) degrees, Z = 4. The crystal of 3a (C36H49B2N12SeSm.C7H8) was triclinic, P1, a = 10.7819(6) A, b = 19.3011(10) A, c = 23.0235(12) A, alpha = 79.443(2) degrees, beta = 77.428(2) degrees, gamma = 89.827(2) degrees, Z = 4. The crystal of 3b (C40H57B2N12SeSm) was triclinic, P1, a = 10.1801(6) A, b = 10.2622(6) A, c = 23.4367(14) A, alpha = 88.313(2) degrees, beta = 86.268(2) degrees, gamma = 62.503(2) degrees, Z = 2. The crystal of 4 (C36H49B2N12TeSm.C7H8) was monoclinic, P2(1)/c, a = 18.7440(10) A, b = 10.3892(6) A, c = 23.8351(13) A, beta = 94.854(2) degrees, Z = 4. The compounds form an isoleptic series of seven-coordinate complexes with terminal chalcogenolate ligands. Examination of 1b and other crystallographically characterized lanthanide alkoxides suggests that there is little correlation between bond angle and bond length. The structures of 3a and 3b, however, contain molecules in which one of the pyrazolylborate ligands undergoes a major distortion arising from twisting around a B-N bond so as to give an effectively eight-coordinate complex with pi-stacking of the phenyl group with one pyrazolyl ring. These distortions shed light on the fluxionality of these systems.