Recombinant silicateins as model biocatalysts in organosiloxane chemistry

On the biocatalytic synthesis of silicone polymers

Polysiloxanes, with poly(dimethyl)siloxane (PDMS) being the most common example, are widely used in various industrial and consumer applications due to the physicochemical properties imparted by their Si-O-Si backbone structure. The conventional synthesis of PDMS involves the hydrolysis of dichlorodimethylsilane, which raises environmental concerns due to the usage of chlorinated compounds. Herein, a biocatalytic approach for PDMS synthesis is demonstrated using silicatein-α (Silα), an enzyme from marine sponges that is known to catalyse the hydrolysis and condensation of Si-O bonds. Using dialkoxysilane precursors, it was found that Silα catalyses the formation of PDMS in non-aqueous media, yielding polymers with higher molecular weights (approximately 1000-2000 Da). However, on prolonged exposure, the gradual degradation of the polymers was also observed. Overall these observations indicate that Silα catalyses the formation polysiloxanes, demonstrating the potential of biocatalysis for more sustainable polysiloxane production.

The Physiological Inorganic Polymers Biosilica and Polyphosphate as Key Drivers for Biomedical Materials in Regenerative Nanomedicine

There is a need for novel nanomaterials with properties not yet exploited in regenerative nanomedicine. Based on lessons learned from the oldest metazoan phylum, sponges, it has been recognized that two previously ignored or insufficiently recognized principles play an essential role in tissue regeneration, including biomineral formation/repair and wound healing. Firstly, the dependence on enzymes as a driving force and secondly, the availability of metabolic energy. The discovery of enzymatic synthesis and regenerative activity of amorphous biosilica that builds the mineral skeleton of siliceous sponges formed the basis for the development of successful strategies for the treatment of osteochondral impairments in humans. In addition, the elucidation of the functional significance of a second regeneratively active inorganic material, namely inorganic polyphosphate (polyP) and its amorphous nanoparticles, present from sponges to humans, has pushed forward the development of innovative materials for both soft (skin, cartilage) and hard tissue (bone) repair. This energy-rich molecule exhibits a property not shown by any other biopolymer: the delivery of metabolic energy, even extracellularly, necessary for the ATP-dependent tissue regeneration. This review summarizes the latest developments in nanobiomaterials based on these two evolutionarily old, regeneratively active materials, amorphous silica and amorphous polyP, highlighting their specific, partly unique properties and mode of action, and discussing their possible applications in human therapy. The results of initial proof-of-concept studies on patients demonstrating complete healing of chronic wounds are outlined.

Lipase-Mediated Conversion of Protecting Group Silyl Ethers: An Unspecific Side Reaction

Silyl ether protecting groups are important tools in organic synthesis, ensuring selective reactions of hydroxyl functional groups. Enantiospecific formation or cleavage could simultaneously enable the resolution of racemic mixtures and thus significantly increase the efficiency of complex synthetic pathways. Based on reports that lipases, which today are already particularly important tools in chemical synthesis, can catalyze the enantiospecific turnover of trimethylsilanol (TMS)-protected alcohols, the goal of this study was to determine the conditions under which such a catalysis occurs. Through detailed experimental and mechanistic investigation, we demonstrated that although lipases mediate the turnover of TMS-protected alcohols, this occurs independently of the known catalytic triad, as this is unable to stabilize a tetrahedral intermediate. The reaction is essentially non-specific and therefore most likely completely independent of the active site. This rules out lipases as catalysts for the resolution of racemic mixtures of alcohols through protection or deprotection with silyl groups.

Inorganic Polymeric Materials for Injured Tissue Repair: Biocatalytic Formation and Exploitation

Two biocatalytically produced inorganic biomaterials show great potential for use in regenerative medicine but also other medical applications: bio-silica and bio-polyphosphate (bio-polyP or polyP). Biosilica is synthesized by a group of enzymes called silicateins, which mediate the formation of amorphous hydrated silica from monomeric precursors. The polymeric silicic acid formed by these enzymes, which have been cloned from various siliceous sponge species, then undergoes a maturation process to form a solid biosilica material. The second biomaterial, polyP, has the extraordinary property that it not only has morphogenetic activity similar to biosilica, i.e., can induce cell differentiation through specific gene expression, but also provides metabolic energy through enzymatic cleavage of its high-energy phosphoanhydride bonds. This reaction is catalyzed by alkaline phosphatase, a ubiquitous enzyme that, in combination with adenylate kinase, forms adenosine triphosphate (ATP) from polyP. This article attempts to highlight the biomedical importance of the inorganic polymeric materials biosilica and polyP as well as the enzymes silicatein and alkaline phosphatase, which are involved in their metabolism or mediate their biological activity.

Solubilization and aggregation control of silica-polymerizing enzyme fused with a removable soluble protein

Silicatein, a silica-polymerizing enzyme, is an attractive and promising biocatalyst in many applications such as the synthesis of bio-functionalized inorganic materials under mild conditions. However, its unfavorable aggregation in aqueous media due to its intermolecular hydrophobic interactions causes difficulties in handling and applications. This study aimed to enhance the solubility of silicatein via fusion with a small soluble protein, ProS2. ProS2-Sil showed high solubility and stability in aqueous media for more than 24 h. The aggregation property of ProS2-silicatein fusion protein (ProS2-Sil) was investigated with and without cleavage of ProS2 tag by site-specific protease. When ProS2 tag was removed, silicatein became aggregated, which was analyzed by transmission electron microscope and fluorescence microscope. ProS2-Sil and mature silicatein showed similar activities in silica polymerization. The present approach allows the utilization of silicatein in the fabrication of novel and functional inorganic biohybrid materials.

Biocatalytic Silylation: The Condensation of Phenols and Alcohols with Triethylsilanol

Silicatein-α (Silα), a hydrolytic enzyme derived from siliceous marine sponges, is one of the few enzymes in nature capable of catalysing the metathesis of silicon–oxygen bonds. It is therefore of interest as a possible biocatalyst for the synthesis of organosiloxanes. To further investigate the substrate scope of this enzyme, a series of condensation reactions with a variety of phenols and aliphatic alcohols were carried out. In general, it was observed that Silα demonstrated a preference for phenols, though the conversions were relatively modest in most cases. In the two pairs of chiral alcohols that were investigated, it was found that the enzyme displayed a preference for the silylation of the S-enantiomers. Additionally, the enzyme’s tolerance to a range of solvents was tested. Silα had the highest level of substrate conversion in the nonpolar solvents n-octane and toluene, although the inclusion of up to 20% of 1,4-dioxane was tolerated. These results suggest that Silα is a potential candidate for directed evolution toward future application as a robust and selective biocatalyst for organosiloxane chemistry.

Biocatalytic Transformations of Silicon-the Other Group 14 Element

Significant inroads have been made using biocatalysts to perform new-to-nature reactions with high selectivity and efficiency. Meanwhile, advances in organosilicon chemistry have led to rich sets of reactions holding great synthetic value. Merging biocatalysis and silicon chemistry could yield new methods for the preparation of valuable organosilicon molecules as well as the degradation and valorization of undesired ones. Despite silicon's importance in the biosphere for its role in plant and diatom construction, it is not known to be incorporated into any primary or secondary metabolites. Enzymes have been found that act on silicon-containing molecules, but only a few are known to act directly on silicon centers. Protein engineering and evolution has and could continue to enable enzymes to catalyze useful organosilicon transformations, complementing and expanding upon current synthetic methods. The role of silicon in biology and the enzymes that act on silicon-containing molecules are reviewed to set the stage for a discussion of where biocatalysis and organosilicon chemistry may intersect.

Improved Production and Biophysical Analysis of Recombinant Silicatein-α

Silicatein-α is a hydrolase found in siliceous sea sponges with a unique ability to condense and hydrolyse silicon–oxygen bonds. The enzyme is thus of interest from the perspective of its unusual enzymology, and for potential applications in the sustainable synthesis of siloxane-containing compounds. However, research into this enzyme has previously been hindered by the tendency of silicatein-α towards aggregation and insolubility. Herein, we report the development of an improved method for the production of a trigger factor-silicatein fusion protein by switching the previous hexahistidine tag for a Strep-II tag, resulting in 244-fold improvement in protein yield compared to previous methods. Light scattering and thermal denaturation analyses show that under the best storage conditions, although oligomerisation is never entirely abolished, these nanoscale aggregates of the Strep-tagged protein exhibit improved colloidal stability and solubility. Enzymatic assays show that the Strep-tagged protein retains catalytic competency, but exhibits lower activity compared to the His₆-tagged protein. These results suggest that the hexahistidine tag is capable of non-specific catalysis through their imidazole side chains, highlighting the importance of careful consideration when selecting a purification tag. Overall, the Strep-tagged fusion protein reported here can be produced to a higher yield, exhibits greater stability, and allows the native catalytic properties of this protein to be assessed.

Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life

The diversity of life relies on a handful of chemical elements (carbon, oxygen, hydrogen, nitrogen, sulfur and phosphorus) as part of essential building blocks; some other atoms are needed to a lesser extent, but most of the remaining elements are excluded from biology. This circumstance limits the scope of biochemical reactions in extant metabolism - yet it offers a phenomenal playground for synthetic biology. Xenobiology aims to bring novel bricks to life that could be exploited for (xeno)metabolite synthesis. In particular, the assembly of novel pathways engineered to handle nonbiological elements (neometabolism) will broaden chemical space beyond the reach of natural evolution. In this review, xeno-elements that could be blended into nature's biosynthetic portfolio are discussed together with their physicochemical properties and tools and strategies to incorporate them into biochemistry. We argue that current bioproduction methods can be revolutionized by bridging xenobiology and neometabolism for the synthesis of new-to-nature molecules, such as organohalides.

Genetical Surface Display of Silicatein on Yarrowia lipolytica Confers Living and Renewable Biosilica-Yeast Hybrid Materials

In this work, a biological engineering-based biosilica-yeast hybrid material was developed. It was obtained by the aggregation of Yarrowia lipolytica through biosilicification catalyzed using genetically displayed silicatein on its cell surface. With orthosilicate or seawater as the substrate, the silicatein-displayed yeast could aggregate into flocs with a flocculation efficiency of nearly 100%. The resulting floc was found to be a sheetlike biosilica-yeast hybrid material formed by the biosilica-mediated immobilization of yeast cells via cross-linking and embedding, turning the original hydrophilicity of yeast cells into hydrophobicity. In addition, this material was characterized to be porous with an average pore diameter of approximately 10 μm and porosity of over 70%. Because of these properties, this hybrid material could achieve enhanced removal efficiencies for chromium ions and n-hexadecane, which were both above 99%, as compared to the free cells of Y. lipolytica in aqueous environments. Importantly, this hybrid material could be recultivated to generate new batches of yeast cells that maintain parallel properties to the first generation so that the same hybrid material could be reproduced with unchanged highly efficient removal of chromium and n-hexadecane to those of the first generation, demonstrating that this biosilica-yeast hybrid material was living and renewable. This work presented a novel way of harnessing silicatein and Y. lipolytica to achieve biological synthesis of a living inorganic-organic hybrid material that has potential to be applied in water treatment.

A biradical oxo-molybdenum complex containing semiquinone and o-aminophenol benzoxazole-based ligands

We report a new mononuclear molybdenum(iv) complex, MoOL^BISL^SQ, in which L^SQ (2,4-di-tert-butyl o-semibenzoquinone ligand) has been prepared from the reaction of the o-iminosemibenzoquinone form of a tridentate non-innocent benzoxazole ligand, L^BIS, and MoO₂(acac)₂. The complex was characterized by X-ray crystallography, elemental analysis, IR and UV-vis spectroscopy and magnetic susceptibility measurements. The crystal structure of MoOL^BISL^SQ revealed a distorted octahedral geometry around the metal centre, surrounded by one O and two N atoms of L^BIS and two O atoms of L^SQ. The effective magnetic moment (μ_eff) of MoOL^BISL^SQ decreased from 2.36 to 0.2 μ_B in the temperature range of 290 to 2 K, indicating a singlet ground state caused by antiferromagnetic coupling between the metal and ligand centred unpaired electrons. Also, the latter led to the EPR silence of the complex. Cyclic voltammetry (CV) studies indicate both ligand and metal-centered redox processes. MoOL^BISL^SQ was applied as a catalyst for the oxidative cleavage of cyclohexene to adipic acid and selective oxidation of sulfides to sulfones with aqueous hydrogen peroxide.

Biradical molybdenum(iv) complex, MoOL^BISL^SQ, has been prepared from the reaction of the o-iminosemibenzoquinone form of a tridentate non-innocent benzoxazole ligand, L^BIS, and MoO₂(acac)₂ and used as catalyst in oxidation reaction..

Chemoselective Transformations of Aromatic Methoxymethyl Ethers Using Trialkylsilyl Triflate and 2,2'-Bipyridyl

Aromatic methoxymethyl (MOM) ethers behave differently from aliphatic MOM ethers upon treatment with trialkylsilyl triflate (R₃SiOTf) and 2,2'-bipyridyl. The aromatic MOM ethers are first converted to silyl ethers and subsequently deprotected by hydrolysis to give the mother alcohols when the R₃SiOTf used is trimethylsilyl triflate (TMSOTf). Conversely, direct conversion of aromatic MOM ethers to aromatic triethylsilyl (TES) ethers is possible when the R₃SiOTf used is triethylsilyl triflate (TESOTf).

Efficient silica synthesis from tetra(glycerol)orthosilicate with cathepsin- and silicatein-like proteins

Silicateins play a key role in biosynthesis of spicules in marine sponges; they are also capable to catalyze formation of amorphous silica in vitro. Silicateins are highly homologous to cathepsins L – a family of cysteine proteases. Molecular mechanisms of silicatein activity remain controversial. Here site-directed mutagenesis was used to clarify significance of selected residues in silica polymerization. A number of mutations were introduced into two sponge proteins – silicatein A1 and cathepsin L from Latrunculia oparinae, as well as into human cathepsin L. First direction was alanine scanning of the proposed catalytic residues. Also, reciprocal mutations were introduced at selected positions that differ between cathepsins L and silicateins. Surprisingly, all the wild type and mutant proteins were capable to catalyze amorphous silica formation with a water-soluble silica precursor tetra(glycerol)orthosilicate. Some mutants possessed several-fold enhanced silica-forming activity and can potentially be useful for nanomaterial synthesis applications. Our findings contradict to the previously suggested mechanisms of silicatein action via a catalytic triad analogous to that in cathepsins L. Instead, a surface-templated biosilification by silicateins and related proteins can be proposed.

Quantum Mechanics/Molecular Mechanics Studies on the Relative Reactivities of Compound I and II in Cytochrome P450 Enzymes

The cytochromes P450 are drug metabolizing enzymes in the body that typically react with substrates through a monoxygenation reaction. During the catalytic cycle two reduction and protonation steps generate a high-valent iron (IV)-oxo heme cation radical species called Compound I. However, with sufficient reduction equivalents present, the catalytic cycle should be able to continue to the reduced species of Compound I, called Compound II, rather than a reaction of Compound I with substrate. In particular, since electron transfer is usually on faster timescales than atom transfer, we considered this process feasible and decided to investigate the reaction computationally. In this work we present a computational study using density functional theory methods on active site model complexes alongside quantum mechanics/molecular mechanics calculations on full enzyme structures of cytochrome P450 enzymes. Specifically, we focus on the relative reactivity of Compound I and II with a model substrate for O⁻H bond activation. We show that generally the barrier heights for hydrogen atom abstraction are higher in energy for Compound II than Compound I for O⁻H bond activation. Nevertheless, for the activation of such bonds, Compound II should still be an active oxidant under enzymatic conditions. As such, our computational modelling predicts that under high-reduction environments the cytochromes P450 can react with substrates via Compound II but the rates will be much slower.

A water-soluble precursor for efficient silica polymerization by silicateins

Silicateins, the spicule-forming proteins from marine demosponges capable to polymerize silica, are popular objects of biomineralization studies due to their ability to form particles varied in shape and composition under physiological conditions. Despite the occurrence of the many approaches to nanomaterial synthesis using silicateins, biochemical properties of this protein family are poorly characterized. The main reason for this is that tetraethyl orthosilicate (TEOS), the commonly used silica acid precursor, is almost insoluble in water and thus is poorly available for the protein. To solve this problem, we synthesized new water-soluble silica precursor, tetra(glycerol)orthosilicate (TGS), and characterized biochemical properties of the silicatein A1 from marine sponge Latrunculia oparinae. Compared to TEOS, TGS ensured much greater activity of silicatein and was less toxic for the mammalian cell culture. We evaluated optimum conditions for the enzyme - pH range, temperature and TGS concentration. We concluded that TGS is a useful silica acid precursor that can be used for silica particles synthesis and in vivo applications.