Structural and mechanistic insights into oxidative biaryl coupling to form the arylomycin core by an engineered CYP450.

Arylomycin, a potent antibiotic targeting bacterial signal peptidase, is difficult to synthesize experimentally due to its poor to moderate yields and the formation of a mixture of compounds. A recent experimental bioengineering work shows that the core of arylomycin can be efficiently synthesized by engineering the cytochrome P450 enzyme from sp.; however, the mechanism of the same was not elucidated.

Mechanism of a novel metal-free carbonic anhydrase.

The recently discovered metal-free carbonic anhydrase (CA) enzyme may significantly impact the global carbon dioxide (CO) cycle, as it can irreversibly perform the CO hydration reaction. In this study, we investigated several key aspects of metal-free CA, including the identification of the catalytic site, the determination of the CO binding site, and the mechanism of catalysis. This is achieved through classical molecular dynamics (MD) simulations, quantum chemical density functional theory (DFT), and hybrid quantum mechanics/molecular mechanics (QM/MM) calculations.

Understanding the Functional Dynamics of the TokK Enzyme in Carbapenem Biosynthesis via MD Simulations and QM/MM Calculations.

Due to the recent surge in antibiotic resistance, developing novel antibiotics is the demand of the time, and thus, a precise understanding of the catalytic mechanisms of enzymes involved in antibiotic biosynthesis becomes crucial. Here, we present a comprehensive investigation into the catalytic mechanism of TokK, a freshly characterized B-dependent RSMT enzyme that plays an important role in carbapenem biosynthesis. Using MD simulations, we show how the plasticity of the active site facilitates substrate recognition while the quantum mechanics/molecular mechanics calculations provide a detailed mechanistic understanding of the methyl transfer process, elucidating stereochemical preferences.

Computational investigation of novel synthetic analogs of C-1'β substituted remdesivir against RNA-dependent RNA-polymerase of SARS-CoV-2.

Remdesivir, a C-nucleotide prodrug binds to the viral RNA-dependent-RNA polymerase () and inhibits the viral replication by terminating RNA transcription prematurely. It is reported in literature that interaction between the C-1'β-CN moiety of Remdesivir () and the Ser861 residue in enzyme, causes a delayed chain termination during the RNA replication process and is one of the important aspect of its mechanism of action. In the pursuance of increasing the biological activity of and enhancing the SAR studies, against RNA viruses, we have designed its fourteen C1'β substituted analogs, - bearing 4/5-membered heterocyclic rings.

Phytocompounds as versatile drug-leads targeting mProtease in the SARS-CoV-2 virus: insights from a molecular dynamics study.

SARS-CoV-2 is one of the deadly outbreaks in the present era and still showing its presence around the globe. Researchers have produced various vaccines that offer protection against infection, but we have not yet found a cure for COVID-19. Currently, efforts are focused on identifying effective therapeutic approaches to treat this infectious disease.

The mechanistic insights into different aspects of promiscuity in metalloenzymes.

Enzymes are nature's ultimate machinery to catalyze complex reactions. Though enzymes are evolved to catalyze specific reactions, they also show significant promiscuity in reactions and substrate selection. Metalloenzymes contain a metal ion or metal cofactor in their active site, which is crucial in their catalytic activity.

On the engineering of reductase-based-monooxygenase activity in CYP450 peroxygenases.

Recent bioengineering of CYP450 shows that peroxide-based CYP450 can be converted to a reductase-based self-sufficient enzyme, which is capable of showing efficient hydroxylation and decarboxylation activity for a wide range of substrates. The so-generated enzyme creates several mechanistic puzzles: (A) as CYP450 peroxygenases lack the conventional acid-alcohol pair, what is the source of two protons that are required to create the ultimate oxidant Cpd I? (B) Why is it only CYP450 that shows the reductase-based activity but no other CYP members? The present study provides a mechanistic solution to these puzzles using comprehensive MD simulations and hybrid QM/MM calculations. We show that the fusion of the reductase domain to the heme-binding domain triggers significant conformational rearrangement, which is gated by the propionate side chain, which constitutes a new water aqueduct the carboxylate end of the substrate that ultimately participates in Cpd I formation.

Rational design of a cyclohexanone dehydrogenase for enhanced α,β-desaturation and substrate specificity.

The selective α,β-desaturation of cyclic carbonyl compounds, which are found in the core of many steroid and bioactive molecules, using green chemistry is highly desirable. To achieve this task, we have for the first time described and solved the structure of a member of the cyclohexanone dehydrogenase class of enzymes. The breadth of substrate specificity was investigated by assaying the cyclohexanone dehydrogenase, from , against several cyclic ketones, lactones and lactams.

Amyloidogenic Propensity of Metabolites in the Uric Acid Pathway and Urea Cycle Critically Impacts the Etiology of Metabolic Disorders.

Novel insights into the etiology of metabolic disorders have recently been uncovered through the study of metabolite amyloids. In particular, inborn errors of metabolism (IEMs), including gout, Lesch-Nyhan syndrome (LNS), xanthinuria, citrullinemia, and hyperornithinemia-hyperammonemia-homocitrullinuria (HHH) syndrome, are attributed to the dysfunction of the urea cycle and uric acid pathway. In this study, we endeavored to understand and mechanistically characterize the aggregative property exhibited by the principal metabolites of the urea cycle and uric acid pathway, specifically hypoxanthine, xanthine, citrulline, and ornithine.

Designed Local Electric Fields-Promising Tools for Enzyme Engineering.

Designing efficient catalysts is one of the ultimate goals of chemists. In this Perspective, we discuss how local electric fields (LEFs) can be exploited to improve the catalytic performance of supramolecular catalysts, such as enzymes. More specifically, this Perspective starts by laying out the fundamentals of how local electric fields affect chemical reactivity and review the computational tools available to study electric fields in various settings.

Computationally guided bioengineering of the active site, substrate access pathway, and water channels of thermostable cytochrome P450, CYP175A1, for catalyzing the alkane hydroxylation reaction.

Understanding structure-function relationships in proteins is pivotal in their development as industrial biocatalysts. In this regard, rational engineering of protein active site access pathways and various tunnels and channels plays a central role in designing competent enzymes with high stability and enhanced efficiency. Here, we report the rational evolution of a thermostable cytochrome P450, CYP175A1, to catalyze the C-H activation reaction of longer-chain alkanes.

Tyr 118-Mediated Electron Transfer is Key to the Chlorite Decomposition in Heme-Dependent Chlorite Dismutase.

Chlorite dismutase (Cld) is a crucial enzyme that catalyzes the decomposition of chlorite ions into chloride ions (Cl) and molecular oxygen (O). Despite playing an important role in the detoxification of toxic chlorite ions, the mechanism of cleavage of the Cl-O bond by Cld remains highly debatable. The present study highlights the mechanism of such Cl-O bond cleavage in Cld using sophisticated computational tools such as hybrid quantum mechanical/molecular mechanical calculations and long-time scale molecular dynamics simulations.

A porphyrin-based molecular cage guided by designed local-electric field is highly selective and efficient.

The present work outlines a general methodology for designing efficient catalytic machineries that can easily be tweaked to meet the demands of the target reactions. This work utilizes a principle of the designed local electric field (LEF) as the driver for an efficient catalyst. It is demonstrated that by tweaking the LEF, we can catalyze the desired hydroxylation products with enantioselectivity that can be changed at will.

Electro-Freezing of Supercooled Water Is Induced by Hydrated Al and Mg Ions: Experimental and Theoretical Studies.

This work reports that the octahedral hydrated Al and Mg ions operate within electrolytic cells as kosmotropic (long-range order-making) "ice makers" of supercooled water (SCW). 10 M solutions of hydrated Al and Mg ions each trigger, near the cathode (-20 ± 5 V), electro-freezing of SCW at -4 °C. The hydrated Al ions do so with 100% efficiency, whereas the Mg ions induce icing with 40% efficiency.

Design and Synthesis of Co-initiators via Base-Catalysed Sequential Conjugate Addition: Application in Photoinduced Radical Polymerisation Reaction.

Applications of photochemistry are becoming very popular in modern-day life due to its operational simplicity, environmentally friendly and economically sustainable nature in comparison to thermochemistry. In particular photoinduced radical polymerisation (PRP) reactions are finding more biological applications and especially in the areas of dental restoration processes, tissue engineering and artificial bone generation. A type-II photoinitiator and co-initiator-promoted PRP turned out to be a cost-effective protocol, and herein we report the design and synthesis of a new efficient co-initiator for a PRP reaction via a barrierless sequential conjugate addition reaction.

A single site mutation can induce functional promiscuity in homoserine kinase.

L-Homoserine kinase is crucial in the biosynthesis of L-threonine, L-isoleucine, and L-methionine, where it catalyzes ATP-dependent phosphorylation of L-homoserine (Hse) to yield L-homoserine phosphate as its native activity. However, a single site mutation of H138 → L shows the emergence of ATPase activity as a secondary function. However, a previous mechanistic study proposes direct involvement of ATP and the substrate without any catalytic base; therefore, how the mutation of H138 → L causes the secondary function remains an enigma.

Substrate Conformation Regulates Aromatic C-H Vs C-F Bond Activation in Heme-Dependent Tyrosine Hydroxylase.

A recently discovered heme-dependent enzyme tyrosine hydroxylase (TyrH) offers a green approach for functionalizing the high-strength C-H and C-F bonds in aromatic compounds. However, there is ambiguity regarding the nature of the oxidant (compound 0 or compound I) involved in activating these bonds. Herein, using comprehensive molecular dynamics (MD) simulations and hybrid quantum mechanical/molecular mechanical calculations, we reveal that it is compound I (Cpd I) that acts as the primary oxidant involved in the functionalization of both C-F and C-H bonds.

Decarboxylation and Protonation Enigma in the H85Q Mutant of Cytochrome P450.

Cytochrome P450 (CYP450), a member of CYP450 peroxygenases, catalyzes unusual decarboxylation activity. Unlike other members of the peroxygenases family, CYP450 possesses a histidine at the 85th position, which was supposed to be the root cause of the decarboxylation activity in CYP450. This work addresses the His85 → Gln mutant paradox, where mutation of His → Gln still shows efficient decarboxylation activity in CYP450.

Unraveling topoisomerase IA gate dynamics in presence of PPEF and its preclinical evaluation against multidrug-resistant pathogens.

Type IA topoisomerases maintain DNA topology by cleaving ssDNA and relaxing negative supercoils. The inhibition of its activity in bacteria prevents the relaxation of negative supercoils, which in turn impedes DNA metabolic processes leading to cell death. Using this hypothesis, two bisbenzimidazoles, PPEF and BPVF are synthesized, selectively inhibiting bacterial TopoIA and TopoIII.

How Can Static and Oscillating Electric Fields Serve in Decomposing Alzheimer's and Other Senile Plaques?

Alzheimer's disease is one of the most common neurodegenerative conditions, which are ascribed to extracellular accumulation of β-amyloid peptides into plaques. This phenomenon seems to typify other related neurodegenerative diseases. The present study uses classical molecular-dynamics simulations to decipher the aggregation-disintegration behavior of β-amyloid peptide plaques in the presence of static and oscillating oriented external electric fields (OEEFs).

Development of indolealkylamine derivatives as potential multi-target agents for COVID-19 treatment.

COVID-19 is a complex disease with short-term and long-term respiratory, inflammatory and neurological symptoms that are triggered by the infection with SARS-CoV-2. As many drugs targeting single targets showed only limited effectiveness against COVID-19, here, we aimed to explore a multi-target strategy. We synthesized a focused compound library based on C2-substituted indolealkylamines (tryptamines and 5-hydroxytryptamines) with activity for three potential COVID-19-related proteins, namely melatonin receptors, calmodulin and human angiotensin converting enzyme 2 (hACE2).

Local Electric Fields: From Enzyme Catalysis to Synthetic Catalyst Design.

This Mini-Review Article outlines recent advances in the study of local electric field (LEF) governed enzyme catalysis and the application of the LEF principle in synthetic catalyst design. We start by discussing the electrostatics principles that drive enzyme catalysis, and its experimental verifications through vibrational Stark spectroscopy. Subsequently, we describe aspects of LEFs other than catalysis, i.

Unraveling key interactions and the mechanism of demethylation during hAGT-mediated DNA repair simulations.

Alkylating agents pose the biggest threat to the genomic integrity of cells by damaging DNA bases through regular alkylation. Such damages are repaired by several automated types of machinery inside the cell. O6-alkylguanine-DNA alkyltransferase (AGT) is an enzyme that performs the direct repair of an alkylated guanine base by transferring the alkyl group to a cysteine residue.

Computations reveal a crucial role of an aromatic dyad in the catalytic function of plant cytochrome P450 mint superfamily.

Enzymes are highly specific for their native functions, however with advances in bioengineering tools such as directed evolution, several enzymes are being repurposed for the secondary function of contemporary significance(Khersonsky and Tawfik, 2010 [1]. Due to the functional versatility, the Cytochrome P450 (CYP450) superfamily has become the ideal scaffold for such bioengineering. In the current study, using MD (molecular dynamics) simulations and hybrid QM/MM (Quantum mechanics/molecular mechanics) calculations, we have studied the mechanism of spontaneous emergence of a secondary function due to a single site mutation in two plant CYP450 enzymes from the mint family.