Substrate Ligand Research Articles

Molecular characterization and computational analysis of a highly specific L-glutaminase from a marine bacterium Bacillus australimaris NIOT30

An alkaline active L-glutaminase (BALG) producing bacterium was screened and identified from seamount sediment samples of the Arabian Sea. The isolate was confirmed to be Bacillus australimaris NIOT30 based on morphological characteristics and 16 S rRNA gene sequencing. The glutaminase gene, balg was PCR amplified, cloned and expressed in E. coli BL21 (DE3) host. The molecular weight of purified BALG was estimated to be 36 kDa and the enzyme showed a specific activity of 507 ± 27 Umg−1 against L-glutamine under optimal assay conditions of pH 7.0 and temperature at 37 °C for 15 min. The enzyme showed maximum activity at pH 7 and retained 95% activity at pH 10. BALG retained a relative activity of about 82% and 45% at 45 °C and 60 °C respectively. The kinetic parameters of BALG, Km and Kcat/Km were determined to be of 210 ± 11 mM and 4.4 × 102 M s−1 respectively. Homology modeling and substrate ligand interaction studies revealed the stability of the enzyme-substrate complex. The present study highlights the characterization of a highly active L-glutaminase from B. australimaris NIOT30. Further, mutational analyses of ligand binding residues would show insights into the affinity of L-Glutaminase.

Mechanistic Diversity and Functional Roles Define the Substrate Specificity and Ligand Binding of Bacterial PGP Phosphatases

Phosphatidylglycerol (PG) is a critical membrane phospholipid in microorganisms, synthesized via the dephosphorylation of phosphatidylglycerol-phosphate (PGP) by three membrane-bound phosphatases: PgpA, PgpB, and PgpC. While any one of these enzymes can produce PG at wild-type levels, the reason for the presence of all three in bacteria remains unclear. To address this question, we characterized these phosphatases in vitro to uncover their mechanistic differences. Our assays demonstrated that all three enzymes catalyze the hydrolysis of PGP but exhibit distinct substrate selectivity. PgpB displays a broad substrate range, dephosphorylating various lipid phosphates, while PgpA and PgpC show a higher specificity for lysophosphatidic acid and PGP. Notably, PgpA also effectively dephosphorylates soluble metabolites, such as glycerol-3-phosphate and glyceraldehyde-3-phosphate, suggesting its unique substrate-binding mechanism that relies on precise recognition of the glycerol head group rather than the fatty acid. Inhibitor screening with synthetic substrate analogs revealed that PgpB is inhibited by lipid-like compounds XY-14 and XY-55, whereas PgpA and PgpC are unaffected. Structural analysis and mutational studies identified two charged residues at the catalytic site entry for inhibitor binding in PgpB and support the notion that the PgpB maintains a large substrate binding site to accommodate multiple ligand binding conformations. These findings underscore the distinct substrate recognition mechanisms and possible functional roles of PgpA, PgpB, and PgpC in bacterial lipid metabolism and offer insights for developing novel inhibitors targeting bacterial membrane phospholipid biosynthesis.

Protein engineering of an alkaline protease from Bacillus licheniformis (BLAP) for efficient and specific chiral resolution of the racemic ethyl tetrahydrofuroate

Enzymatic resolution of ethyl tetrahydrofuroate to produce (S)-2-ethyl tetrahydrofuroate and (R)-2-tetrahydrofuroic acid is a green biomanufacturing strategy. However, enzymatic activity and selectivity are still limiting factors of their industrial applications and development. In previous study, we incidentally found that a Bacillus licheniformis alkaline protease (BLAP), not a lipase, could specifically resolve ethyl tetrahydrofuroate to produce (S)-2-ethyl tetrahydrofuroate and (R)-2-tetrahydrofuroic acid. In this study, the point-saturation-mutation libraries based on the seven amino acid sites (L105, I113, P114, L115, V309, Y310, and M326) were constructed and screened using the molecular docking technology. It was found that activity of the mutant BLAPY310E reached 182.78 U/mL with high stereoselectivity, 3.14 times higher than that of the wild-type BLAP. Further simulated mutation analysis showed that the Y310E mutation increased the distance from the substrate ligand to the binding pocket from 2.3 Å to 4.5 Å, reducing steric hindrance to the active center. Under the optimal conditions and after 3.5 h of reaction catalyzed by BLAPY310E, 200 mM ethyl tetrahydrofuroate was converted to (S)-2-ethyl tetrahydrofuroate and (R)-2-tetrahydrofuroic acid with the ee values of 99.9 % and 68.63 %, respectively. The enantiomeric ratio of BLAPY310E was 105.5, which was 30.23 times higher than that of BLAP. This study advances the comprehension of protease activity and selectivity mechanisms in resolving ester substances and lays a robust foundation for the industrial production of the optically pure (S)-2-ethyl tetrahydrofuroate and (R)-2-tetrahydrofuroic acid via biological enzymatic methods.

Computational Design of Ligands for the Ir-Catalyzed C5-Borylation of Indoles through Tuning Dispersion Interactions.

The indole moiety is ubiquitous in natural products and pharmaceuticals. C-H borylation of the benzenoid moiety of indoles is a challenging task, especially at the C5 position. We have combined computational and experimental studies to introduce multiple noncovalent interactions, especially dispersion, between the substrate and catalytic ligand to realize C5-borylation of indoles with high reactivity and selectivity. The successful computational predictions of new ligands should be suitable for ligand design in other transition-metal catalyzed reactions.

Superposition of Substrate Deformation Fields Induced by Molecular Clutches Explains Cell Spatial Sensing of Ligands.

Cells can sense the physical properties of the extracellular matrices (ECMs), such as stiffness and ligand density, through cell adhesions to actively regulate their behaviors. Recent studies have shown that varying ligand spacing of ECMs can influence adhesion size, cell spreading, and even stem cell differentiation, indicating that cells have the spatial sensing ability of ECM ligands. However, the mechanism of the cells' spatial sensing remains unclear. In this study, we have developed a lattice-spring motor-clutch model by integrating cell membrane deformation, the talin unfolding mechanism, and the lattice spring for substrate ligand distribution to explore how the spatial distribution of integrin ligands and substrate stiffness influence cell spreading and adhesion dynamics. By applying the Gillespie algorithm, we found that large ligand spacing reduces the superposition effect of the substrate's displacement fields generated by pulling force from motor-clutch units, increasing the effective stiffness probed by the force-sensitive receptors; this finding explains a series of previous experiments. Furthermore, using the mean-field theory, we obtain the effective stiffness sensed by bound clutches analytically; our analysis shows that the bound clutch number and ligand spacing are the two key factors that affect the superposition effects of deformation fields and, hence, the effective stiffness. Overall, our study reveals the mechanism of cells' spatial sensing, i.e., ligand spacing changes the effective stiffness sensed by cells due to the superposition effect of deformation fields, which provides a physical clue for designing and developing biological materials that effectively control cell behavior and function.

Synthesis of Tetrasubstituted Alkenes by Rhodium-Catalyzed Regioselective Cyano Transfer.

We describe herein a novel, general, and robust approach to structurally diversified alkenyl nitriles through a Rh-catalyzed cyano transfer reaction between alkynyl-malononitrile derivatives and aryl/alkenyl boronic acids. This reaction exhibits high chemo- and regioselectivity and a broad substrate scope. The tetrasubstituted alkenyl dinitriles (34 examples, average 58% yield) are obtained through substrate tuning and ligand control.

Mechanistic Insights into Rare-Earth-Catalyzed Alternating Copolymerization through C-H Polyaddition of Functionalized Organic Compounds to Unconjugated Dienes.

Density functional theory (DFT) calculations have been conducted to elucidate the detailed mechanisms of yttrium-catalyzed C-H polyaddition of 1,4-dimethoxybenzene (DMB) to 1,4-divinylbenzene (DVB). It was computationally determined that DMB not only serves as a substrate but also performs a crucial role as a ligand, stabilizing the catalytically active species and promoting alkene insertion. Side pathways involving Cβ-H activation and C═C continuous insertion were excluded due to steric and electronic factors, respectively, explaining why the reaction occurred efficiently and selectively to give perfectly alternating DMB-DVB polymers. Interestingly, the theoretical prediction of the reactivity of N,N-dimethyl-1,4-phenylenediamine and 2,2'-biethyl-4,4'-bipyridine reveals significant differences in the coordination effects of these substrates, leading to distinct mechanisms, primarily influenced by their steric effects. These findings shed new light on the previously overlooked role of substrate ligand effects in rare-earth-catalyzed step-growth copolymerization reactions.

Regulating Spin-Valence States of Vanadium-Based Single-Atom Oxygen Reduction Catalysts through Substrate and Axial Ligand Engineering

Regulating Spin-Valence States of Vanadium-Based Single-Atom Oxygen Reduction Catalysts through Substrate and Axial Ligand Engineering

Theoretical Insights into the Regiodivergence in Ni-Catalyzed [2+2+2] Cycloaddition of Unsymmetric Diynes and CO2

To achieve the peak of carbon dioxide emission and carbon neutrality, utilizing it as a renewable carbon unit in organic synthesis presents an effective chemical solution for sustainable development. In this study, we report a theoretical investigation into the reaction mechanism and the regiodivergence of the Ni-catalyzed [2+2+2] cycloaddition of unsymmetric diynes and CO2 by using DFT calculations. The reaction mechanisms can be classified into two types: one is related to the oxidative coupling of the C≡C moiety with CO2, and the other is related to the oxidative coupling of the two C≡C moieties of diyne. In each type, two possible paths were proposed depending upon the positions of the substituents (H and silyl). Our calculation results indicate that the oxidative coupling of the C≡C moiety and CO2 favors the positions of H-substituent, while the oxidative coupling of the two C≡C moieties is beneficial for inserting CO2 at the positions of silyl-substituent. The regiodivergence is controlled by substrate chain-length and ligand in the different reaction mechanisms.

A regenerative dual-functional platform combining dendritic silica and anthraquinone amide: advancing seawater lithium detection and recovery with biosensing capabilities

A novel material with a dendritic silica substrate and anthraquinone amide ligand enables simultaneous lithium detection and adsorption in water, offering green-emissive sensing, high adsorption capacity, fast kinetics, and biosensing.

Catalyst Deactivation of a Monoligated CyJohnPhos-bound Nickel(0) Complex.

Cross-coupling catalysts are prone to unproductive side reactivity that can limit their practical use in synthetic chemistry. A detailed understanding of these pathways and the conditions that enable them is important for reaction optimization and rational catalyst design. In this work, we report the off-cycle reactivity of a monoligated, CyJohnPhos-bound Ni0 complex following product-forming reductive elimination. In the absence of substrate, free phosphine ligand, or π-accepting additives, dimerization of (CyJohnPhos)Ni0 occurs, followed by C-P bond activation of the ligand to form a phosphido-bridged Ni0/NiII dimer; both the Ni0/Ni0 and Ni0/NiII dimers were structurally characterized. Monomeric (CyJohnPhos)Ni0 must be intercepted by substrate or free ligand to prevent irreversible dimerization and catalyst deactivation.

Physical biology of cell-substrate interactions under cyclic stretch.

Mechanosensitive focal adhesion (FA) complexes mediate dynamic interactions between cells and substrates and regulate cellular function. Integrins in FA complexes link substrate ligands to stress fibers (SFs) and aid load transfer and traction generation. We developed a one-dimensional, multi-scale, stochastic finite element model of a fibroblast on a substrate that includes calcium signaling, SF remodeling, and FA dynamics. We linked stochastic dynamics, describing the formation and clustering of integrins to substrate ligands via motor-clutches, to a continuum level SF contractility model at various locations along the cell length. We quantified changes in cellular responses with substrate stiffness, ligand density, and cyclic stretch. Results show that tractions and integrin recruitments varied along the cell length; tractions were maximum at lamellar regions and reduced to zero at the cell center. Optimal substrate stiffness, based on maximum tractions exerted by the cell, shifted toward stiffer substrates at high ligand densities. Mean tractions varied biphasically with substrate stiffness and peaked at the optimal substrate stiffness. Cytosolic calcium increased monotonically with substrate stiffness and accumulated near lamellipodial regions. Cyclic stretch increased the cytosolic calcium, integrin concentrations, and tractions at lamellipodial and intermediate regions on compliant substrates. The optimal substrate stiffness under stretch shifted toward compliant substrates for a given ligand density. Stretch also caused cell deadhesions beyond a critical substrate stiffness. FA's destabilized on stiff substrates under cyclic stretch. An increase in substrate stiffness and cyclic stretch resulted in higher fibroblast contractility. These results show that chemomechanical coupling is essential in mechanosensing responses underlying cell-substrate interactions.

Directional Cell Migration Guided by a Strain Gradient.

Strain gradients widely exist in development and physiological activities. The directional movement of cells is essential for proper cell localization, and directional cell migration in responses to gradients of chemicals, rigidity, density, and topography of extracellular matrices have been well-established. However; it is unclear whether strain gradients imposed on cells are sufficient to drive directional cell migration. In this work, a programmable uniaxial cell stretch device is developed that creates controllable strain gradients without changing substrate stiffness or ligand distributions. It is demonstrated that over 60% of the single rat embryonic fibroblasts migrate toward the lower strain side in static and the 0.1Hz cyclic stretch conditions at ≈4% per mm strain gradients. It is confirmed that such responses are distinct from durotaxis or haptotaxis. Focal adhesion analysis confirms higher rates of contact area and protrusion formation on the lower strain side of the cell. A 2D extended motor-clutch model is developed to demonstrate that the strain-introduced traction force determines integrin fibronectin pairs' catch-release dynamics, which drives such directional migration. Together, these results establish strain gradient as a novel cue to regulate directional cell migration and may provide new insights in development and tissue repairs.

Investigation of bifunctionality of FePc-functionalized graphene for enhanced ORR/OER activity

Iron phthalocyanine monolayer supported on a graphene substrate (GFePc) is a promising Pt-free oxygen reduction reaction catalyst. The electronic properties of GFePc can be tuned via the ligand exchange of FePc, substate doping, and defect incorporation into the graphene substrate. Boron and nitrogen were chosen as substrate dopants due to their comparability to carbon in size. Two of the most common graphene defects, single and double (585) vacancies, were chosen to represent defects that can naturally occur on the graphene substrate. Tetra-substituted phthalocyanines (carboxy-, nitro-, and amino-) and hexadeca-substituted phthalocyanines (chloro‑, fluoro-, and amino-) were tested due to their availability in the current market. Utilizing ab initio spin polarized density functional theory (DFT) calculations, the dominating pathways of both the oxygen reduction (ORR) and oxygen evolution reactions (OER) have been simulated along with defining their rate-limiting step to quantify the ORR/OER overpotentials (indicator of catalyst reactivity/performance). The DFT results show that ∼1 at.% Boron doping in conjunction with a mono-vacancy graphene substrate offers the best ORR performance but a worse OER performance when compared to the pristine GFePc. Generally, an increase in ORR activity exhibited a decrease in OER activity. A qualitative volcano correlation between electronic descriptors and ORR overpotential for modified GFePc systems was observed. The present study allows for expanded understanding and definition of substituted iron phthalocyanine functionalized graphene and the effects of both substrate modification and ligand exchange on GFePc's performance as a potential bifunctional single-metal-atom based electro-catalyst.

Enantioselective Rhodium‐Catalyzed Pauson–Khand Reactions of 1,6‐Chloroenynes with 1,1‐Disubstituted Olefins

AbstractAn enantioselective rhodium(I)‐catalyzed Pauson–Khand reaction (PKR) using 1,6‐chloroenynes that contain challenging 1,1‐disubstituted olefins is described. In contrast to the previous studies with these types of substrates, which are only suitable for a single type of tether and alkyne substituent, the new approach results in a more expansive substrate scope, including carbon and heteroatom tethers with polar and non‐polar substituents on the alkene. DFT calculations provide critical insight into the role of the halide, which pre‐polarizes the alkyne to lower the barrier for metallacycle formation and provides the proper steric profile to promote a favorable enantiodetermining interaction between substrate and chiral diphosphine ligand. Hence, the chloroalkyne enables the efficient and enantioselective PKR with 1,6‐enynes that contain challenging 1,1‐disubstituted olefins, thereby representing a new paradigm for enantioselective reactions involving 1,6‐enynes.

Enantioselective Rhodium-Catalyzed Pauson-Khand Reactions of 1,6-Chloroenynes with 1,1-Disubstituted Olefins.

An enantioselective rhodium(I)-catalyzed Pauson-Khand reaction (PKR) using 1,6-chloroenynes that contain challenging 1,1-disubstituted olefins is described. In contrast to the previous studies with these types of substrates, which is only suitable for a single type of tether and alkyne substituent, the new approach results in a more expansive substrate scope, including carbon and heteroatom tethers with polar and non-polar substituents on the alkene. DFT calculations provide critical insight into the role of the halide, which pre-polarizes the alkyne to lower the barrier for the metallacycle formation and provides the proper steric profile to promote a favorable enantiodetermining interaction between substrate and chiral diphosphine ligand. Hence, the chloroalkyne enables the efficient and enantioselective PKR with 1,6-enynes that contain challenging 1,1-disubstituted olefins, which represents a new paradigm for enantioselective reactions involving 1,6-enynes.

MIL-101-NH2(Fe)-Coated Nylon Microfibers for Immobilized Photocatalysts in RhB and Cr(VI) Removal.

MIL-101-NH2(Fe) is one of the effective photocatalytic metal-organic frameworks (MOFs) working under visible light. However, its powder-type form inhibits reusability in practical applications. In this study, we immobilized MIL-101-NH2(Fe) on a polymeric microfiber mesh to improve reusability while minimizing the loss of catalytic performance. To overcome the lack of surface functionality of the nylon fibers, an atomic layer deposition Al2O3 layer and NH2-BDC linker were introduced to facilitate uniform coating of the MOF on the fiber surface. The reactions of the metal precursor to the nylon substrate and NH2-BDC ligand of the MOF allow chemical bonding from the core to the shell of the entire hybrid catalytic materials. The resulting fiber-immobilized MOFs (Nylon@Al2O3@MOF) demonstrated high photocatalytic performance in the removal of RhB and Cr(VI) as representatives of organic dyes and heavy metals, respectively, while retaining over 85% of its efficiency after five cycles.

Iodide-Assisted Pd Catalysis as an Attractive Alternative to Rh Catalysis for the Industrially Relevant Isoselective Hydroformylation of Simple Aliphatic Alkenes

AbstractThe hydroformylation of simple aliphatic alkenes, such as propylene, is one of the largest homogenous catalyzed processes in the chemical industry, producing over 10 million metric tons of different aldehydes each year. Typically, such processes are catalyzed by Co or Rh catalysts, yielding mostly linear aldehydes, such as n-butanal. However, the increasing demand for branched aldehydes, such as isobutanal, triggered further investigation to develop efficient isoselective protocols, which remain scarce. In this Synpacts article, we discuss our recent work on iodide-assisted Pd catalysis as an attractive alternative strategy for the development of isoselective methods. This article is presented considering the state of the art for Rh-catalyzed processes. Additionally, we discuss the limitations and challenges that need to be addressed in order to successfully transfer the technology to industry.1 Introduction2 State of the Art for the Isoselective Rh-Catalyzed Hydroformylation of Unbiased Aliphatic Alkenes2.1 Decomposition-Driven Isoselectivity2.2 Substrate-Dependent Isoselectivity2.3 Equiselective Catalysis2.4 Isoselective Rh Catalysts Bearing Small-Bite-Angle Ligands2.5 Isoselective Rh Catalyst Bearing a Tridentate Ligand2.6 Isoselective Catalysis Driven by Rh Encapsulation2.7 Isoselective Catalysis Driven by Specific Noncovalent Substrate–Ligand Interactions3 Pd-Catalyzed Isoselective Hydroformylation of Unbiased Aliphatic Alkenes3.1 Selectivity Patterns in Pd-Catalyzed Hydroformylation of Alkenes3.2 Unusual Iodide-Assisted Binuclear Pd(I)–Pd(I) Mechanism3.3 Development of Pd-Catalyzed Isoselective Hydroformylation of Unbiased Aliphatic Alkenes4 Conclusions and Outlook

Extraordinary Acceleration of an Electrophilic Reaction Driven by the Polar Surface of 2D Aluminosilicate Nanosheets.

To increase chemical reaction rates, general solutions include increasing the concentration/temperature and introducing catalysts. In this study, the rate constant of an electrophilic metal coordination reaction is accelerated 23-fold on the surface of layered aluminosilicate (LAS), where the reaction substrate (ligand molecule) induces dielectric polarization owing to the polar and anionic surface. According to the Arrhenius plot, the frequency factor (A) is increased by almost three orders of magnitude on the surface. This leads to the conclusion that the collision efficiency between the ligands and metal ions is enhanced on the surface due to the dielectric polarization. This is surprising because one side of the ligand is obscured by the surface, so the collision efficiency is expected to be decreased. This unique method to accelerate the chemical reaction is expected to expand the range of utilization of LASs, which are chemically inert, abundant, and environmentally friendly. The concept is also applicable to other metal oxides which have polar surfaces, which will be useful for various chemical reactions in the future.

Enantioselective Hydrosilylation of β,β‐Disubstituted Enamides to Construct α‐Aminosilanes with Vicinal Stereocenters

AbstractDespite the advances in the area of catalytic alkene hydrosilylation, the enantioselective hydrosilylation of alkenes bearing a heteroatom substituent is scarce. Here we report a rhodium‐catalyzed hydrosilylation of β,β‐disubstituted enamides to directly afford valuable α‐aminosilanes in a highly regio‐, diastereo‐, and enantioselective manner. Stereodivergent synthesis could be achieved by regulating substrate geometry and ligand configuration to generate all the possible stereoisomers in high enantio‐purity.