Advancements in biocatalysis: From computational to metabolic engineering

Through several waves of technological research and un-matched innovation strategies, bio-catalysis has been widely used at the industrial level. Because of the value of enzymes, methods for producing value-added compounds and industrially-relevant fine chemicals through biological methods have been developed. A broad spectrum of numerous biochemical pathways is catalyzed by enzymes, including enzymes that have not been identified. However, low catalytic efficacy, low stability, inhibition by non-cognate substrates, and intolerance to the harsh reaction conditions required for some chemical processes are considered as major limitations in applied bio-catalysis. Thus, the development of green catalysts with multi-catalytic features along with higher efficacy and induced stability are important for bio-catalysis. Implementation of computational science with metabolic engineering, synthetic biology, and machine learning routes offers novel alternatives for engineering novel catalysts. Here, we describe the role of synthetic biology and metabolic engineering in catalysis. Machine learning algorithms for catalysis and the choice of an algorithm for predicting protein-ligand interactions are discussed. The importance of molecular docking in predicting binding and catalytic functions is reviewed. Finally, we describe future challenges and perspectives.     

New analogs of temporin-LK1 as inhibitors of multidrug-resistant (MDR) bacterial pathogens

The peptide temporin-LK1 (1) was obtained from the skin secretion of frog Limnonectes kuhlii (Ranidae). It is a unique antimicrobial peptide with 17 residues, including four L-phenylalanines and single glycine. Mass spectrometry and Edmand degradation were used for the determination of sequence of amino acids in temporin-LK 1 (1), and confirmed by cDNA cloning. We report here the synthesis and structural studies of temporin-LK1 (1) and its analogs 2–4. Peptides 2–4 were prepared by substitution of achiral glycine residue of temporin-LK1 (1) with D-alanine, L-phenylglycine, and L-naphthylalanine, respectively. Peptides 1–4 were evaluated against multidrug-resistant (MDR) strains of Staphylococcus aureus and Pseudomonas aeruginosa. Analog 2 was found active against all MDR strains of S. aureus and P. aeruginosa at a much lower dose than the clinically used antibiotics.     

Synthesis of silica nanoparticles doped with [Ru(bpy)3]2+ and decorated with silver nanoclusters for the ratiometric photoluminescent determination and intracellular imaging of Cu(II) ions

Microchimica Acta - A sensitive and selective luminescent nanoprobe (referred to as DEPN) is designed for the determination of Cu(II) ions. DEPN shows two emission peaks, one at 602 nm and...     

Spectral and electro-chemical characterization of transition metal complexes of a modified [N<Subscript>6</Subscript>] macrocycle. A mimic to cyclic hexapeptide

The 16-membered modified [N₆] macrocylic ligand (L), a mimic to cyclic, hexapeptide is reacted with MCl₂ and MCl₃ resulting in complexes with stoichiometrices [MLCl₂] (M = Cr, Mn, Co, Ni, Cu), [MLCl₃] (M = Pt, Pd) and [MLCl₂]Cl (M = Fe, Ru). Its reactions with the precursors [M(Ph₃P)₂Cl₂] (M = Co, Ni, Pt, Pd) follow a ligand displacement path affording the final products which do not contain coordinated Ph₃P. Complexes have been characterized from results of elemental analyses, conductometric, magnetic susceptibility, i.r. and u.v.–vis (ligand field) spectral studies. Magnetic susceptibility and ligand field spectral data are consistent with a hexacoordinate geometry for Cr²⁺, Mn²⁺, Fe³⁺, Co²⁺, Ni²⁺ and Cu²⁺ and four coordinate square-planar geometry for Pt²⁺ and Pd²⁺. Molecular orbital computations using CSChem ultra MOPAC software for an optimized minimum energy plot of the structure shows that the ligand binds metal ions as a tetradentate (N,N,N,N) chelating agent. Cyclic voltammetric studies indicate formation of stable reversible or quasi-reversible redox couples in solutions, which corroborates a kinetic stability of these complexes in their variable oxidation states.     

Spectral and electrochemical characterization of bimetallic complexes of a novel 32-membered unsymmetrical [N<Subscript>12</Subscript>] macrocycle

Reactions of a 32-membered [N₁₂] macrocyclic ligand, L.2HClO₄ with metal salts MCl₃ (M=Cr or Fe) and MCl₂ (M=Co, Ni or Cu) have produced complexes of stoichiometries M₂LCl₄(ClO₄)₂ and M₂LCl₂(ClO₄)₂, respectively. However, reactions with [M(Ph₃P)₂Cl₂] (M=Co or Ni) and [(η⁵-C₅H₅)Ni(Ph₃P)I] follow a ligand substitution path resulting in products with stoichiometries M₂LCl₂(ClO₄)₂ and [(η⁵-C₅H₅)₂Ni₂L(ClO₄)₂], respectively. The mode of bonding and geometry of the complexes have been derived on the basis of i.r., ligand field spectral and magnetic susceptibility measurements. EPR of Cu^II complex shows anisotropy with , G < 4.0 and orbital reduction factor . Thermodynamic first ionic association constants (K₁) and the corresponding free energy change (ΔG) of complexes in DMSO have been determined and discussed. Cyclic voltammetric studies indicate the presence of a quasi-reversible redox couples Cr^III/II, Co^II/I, Ni^II/I, Ni^II/III and Cu^II/I in solutions suggesting flexible nature of the macrocyclic cavity.     

Synthesis of diaryl ethers based on one-pot [3+3] cyclizations of 1,3-bis(silyl enol ethers)

Functionalized and sterically encumbered diaryl ethers were prepared by [3+3] cyclization of 1,3-bis(silyl enol ethers) with 2-aryloxy-3-(silyloxy)alk-2-en-1-ones.     

Cooperative B–H bond activation: dual site borane activation by redox active κ2-N,S-chelated complexes

Cooperative dual site activation of boranes by redox-active 1,3-N,S-chelated ruthenium species, mer-[PR₃{κ²-N,S-(L)}₂Ru{κ¹-S-(L)}], (mer-2a: R = Cy, mer-2b: R = Ph; L = NC₇H₄S₂), generated from the aerial oxidation of borate complexes, [PR₃{κ²-N,S-(L)}Ru{κ³-H,S,S′-BH₂(L)₂}] (trans–mer-1a: R = Cy, trans–mer-1b: R = Ph; L = NC₇H₄S₂), has been investigated. Utilizing the rich electronic behaviour of these 1,3-N,S-chelated ruthenium species, we have established that a combination of redox-active ligands and metal–ligand cooperativity has a big influence on the multisite borane activation. For example, treatment of mer-2a–b with BH₃·THF led to the isolation of fac-[PR₃Ru{κ³-H,S,S′-(NH₂BSBH₂N)(S₂C₇H₄)₂}] (fac-3a: R = Cy and fac-3b: R = Ph) that captured boranes at both sites of the κ²-N,S-chelated ruthenacycles. The core structure of fac-3a and fac-3b consists of two five-membered ruthenacycles [RuBNCS] which are fused by one butterfly moiety [RuB₂S]. Analogous fac-3c, [PPh₃Ru{κ³-H,S,S′-(NH₂BSBH₂N)(SC₅H₄)₂}], can also be synthesized from the reaction of BH₃·THF with [PPh₃{κ²-N,S-(SNC₅H₄)}{κ³-H,S,S′-BH₂(SNH₄C₅)₂}Ru], cis–fac-1c. In stark contrast, when mer-2b was treated with BH₂Mes (Mes = 2,4,6-trimethyl phenyl) it led to the formation of trans- and cis-bis(dihydroborate) complexes [{κ³-S,H,H-(NH₂BMes)Ru(S₂C₇H₄)}₂], (trans-4 and cis-4). Both the complexes have two five-membered [Ru–(H)₂–B–NCS] ruthenacycles with κ²-H–H coordination modes. Density functional theory (DFT) calculations suggest that the activation of boranes across the dual Ru–N site is more facile than the Ru–S one.

Redox-active ruthenium complexes supported by hemilabile κ²-N,S-chelated ruthenacycles undergo unusual dual site B–H bond activation through metal–ligand cooperation with free and bulky boranes.     

Evolution of phase,texture, microstructure and magnetic properties of Fe–Cr–Co–Mo–Ti permanent magnets

Magnetic phase evolution, crystallographic texture, microstructure and magnetic properties of Fe–28Cr–15Co–3.5Mo–1.8Ti alloy have been investigated by X-ray diffractometry, scanning transmission electron microscopy and magnetometry techniques as a function of processing conditions. Heat treatment conditions for obtaining optimum textural, microstructural and magnetic properties have been established by the experimentations. The Goss {110}〈001〉 and cube type {001}〈010〉 textures have been developed in an optimal treated Fe–28Cr–15Co–3.5Mo–1.8Ti magnets. The coercive force in Fe–28Cr–15Co–3.5Mo–1.8Ti magnets depends critically on the shape anisotropy of rod-like Fe Co Ti-rich α₁ particles and remanence on the alignment and elongation of α₁ particles parallel to applied magnetic field 〈100〉 directions. The optimum magnetic properties obtained in Fe–28Cr–15Co–3.5Mo–1.8Ti alloy are intrinsic coercive force, _iH_c, of 78.8 kA/m (990 Oe), remanence, B_r of 1.12 T (11.2 kG) and energy product, (BH)_max of 52.5 kJ/m³ (6.5 MGOe). The development of Fe–28Cr–15Co–3.5Mo–1.8Ti magnets as well as characterization of texture, microstructural and magnetic properties in the current study would be helpful in designing the new Fe–Cr–Co–Mo based magnets suitable for scientific and technological applications.     

Highly sensitive determination of atropine using cobalt oxide nanostructures: Influence of functional groups on the signal sensitivity

This study describes sensitive determination of atropine using glassy carbon electrodes (GCE) modified with Co₃O₄ nanostructures. The as-synthesised nanostructures were grown using cysteine (CYS), glutathione (GSH) and histidine (HYS) as effective templates under hydrothermal action. The obtained morphologies revealed interesting structural features, including both cavity-based and flower-shaped structures. The as-synthesised morphologies were noted to actively participate in electro-catalysis of atropine (AT) drug where GSH-assisted structures exhibited the best signal response in terms of current density and over-potential value. The study also discusses the influence of functional groups on the signal sensitivity of atropine electro-oxidation. The functionalisation was carried with the amino acids originally used as effective templates for the growth of Co₃O₄ nanostructures. The highest increment was obtained when GSH was used as the surface functionalising agent. The GSH-functionalised Co₃O₄-modified electrode was utilised for the electro-chemical sensing of AT in a concentration range of 0.01–0.46 μM. The developed sensor exhibited excellent working linearity (R² = 0.999) and signal sensitivity up to 0.001 μM of AT. The noted high sensitivity of the sensor is associated with the synergy of superb surface architectures and favourable interaction facilitating the electron transfer kinetics for the electro-catalytic oxidation of AT. Significantly, the developed sensor demonstrated excellent working capability when used for AT detection in human urine samples with strong anti-interference potential against common co-existing species, such as glucose, fructose, cysteine, uric acid, dopamine and ascorbic acid.