Active learning-assisted directed evolution

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: Jan. 16, 2025

Abstract Directed evolution (DE) is a powerful tool to optimize protein fitness for specific application. However, DE can be inefficient when mutations exhibit non-additive, or epistatic, behavior. Here, we present Active Learning-assisted Evolution (ALDE), an iterative machine learning-assisted workflow that leverages uncertainty quantification explore the search space of proteins more efficiently than current methods. We apply ALDE engineering landscape challenging DE: optimization five epistatic residues in active site enzyme. In three rounds wet-lab experimentation, improve yield desired product non-native cyclopropanation reaction from 12% 93%. also perform computational simulations on existing sequence-fitness datasets support our argument effective DE. Overall, practical and broadly applicable strategy unlock improved outcomes.

Language: Английский

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Directed Evolution and Unusual Protonation Mechanism of Pyridoxal Radical C–C Coupling Enzymes for the Enantiodivergent Photobiocatalytic Synthesis of Noncanonical Amino Acids

Journal of the American Chemical Society, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 23, 2025

Visible light-driven pyridoxal radical biocatalysis has emerged as a new strategy for the stereoselective synthesis of valuable noncanonical amino acids in protecting-group-free fashion. In our previously developed dehydroxylative C–C coupling using engineered PLP-dependent tryptophan synthases, an enzyme-controlled unusual α-stereochemistry reversal and pH-controlled enantiopreference were observed. Herein, through high-throughput photobiocatalysis, we evolved set stereochemically complementary PLP enzymes, allowing both l- d-amino with enhanced enantiocontrol across broad pH window. These newly acid synthases permitted use range organoboron substrates, including boronates, trifluoroborates, boronic acids, excellent efficiency. Mechanistic studies unveiled unexpected racemase activity earlier enzyme variants. This promiscuous was abolished shedding light on origin enantiocontrol. Further mechanistic investigations suggest switch proton donor to account stereoinvertive formation highlighting stereoinversion mechanism that is rare conventional two-electron enzymology.

Language: Английский

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Diastereo- and Enantioselective Chemoenzymatic Synthesis of Chiral Tricyclic Intermediate of Anti-HIV Drug Lenacapavir

ACS Catalysis, Journal Year: 2025, Volume and Issue: 15(3), P. 2045 - 2052

Published: Jan. 21, 2025

Despite its great potential, the development and implementation of scalable new-to-nature biocatalytic transformations in chemoenzymatic synthesis clinically significant pharmaceuticals still present a considerable challenge. We developed very recently anti-HIV drug lenacapavir's 5/5/3 fused tricyclic fragment featuring an unusual chiral cyclopropane moiety. Key to this is biocatalyst-controlled, fully diastereo- enantiodivergent cyclopropanation highly functionalized vinylpyrazole substrate, granting access all four possible stereoisomers lenacapavir cyclopropane. High-throughput experimentation led discovery heme-dependent globins, including nitrous oxide dioxygenase (NOD) protoglobin (Pgb), as promising biocatalysts. Directed evolution furnished enantioselective (up 99:1 d.r. e.r.). Further downstream chemical cyclization afforded desired tricycle with stereochemical purity.

Language: Английский

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Rational Engineering of Self-Sufficient P450s to Boost Catalytic Efficiency of Carbene-Mediated C–S Bond Formation

ACS Catalysis, Journal Year: 2025, Volume and Issue: unknown, P. 5993 - 6004

Published: March 27, 2025

Language: Английский

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LARGE SCALE ENERGY DECOMPOSITION FOR THE ANALYSIS OF PROTEIN STABILITY

Cell Stress and Chaperones, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

To carry out their functions in cells, proteins are required to fold into well-defined three-dimensional conformations. The stability of the folded state dictates several aspects protein life, such as evolution, interactions, and selection structures that ultimately linked activity. Sequence mutations may change profile consequently impact structure function. Here we use a simple, molecular dynamics-based energy decomposition approach map response each aminoacid sequences set five test with different lengths, folds, topologies. this end make residue-pair nonbonded matrix. We show parameters obtained from analysis, namely main eigenvalue reporting on most stabilizing contributions spectral gap matrix (ENergy Gap (ENG)), reproduce experimentally determined trends. At same time, our identifies couplings play key roles defining 3D properties certain fold. discuss relevance these results for design mutants experimental applications possibility complement other computational analyses conformational stability. Keywords.

Language: Английский

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Fabrication of imine-based COFs with different linker lengths for HRP and GOx immobilization and colorimetric detection of glucose and H2O2

Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy, Journal Year: 2025, Volume and Issue: 333, P. 125892 - 125892

Published: Feb. 12, 2025

Language: Английский

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Enzymatic Oxidation of Hydroxytyrosol in Deep Eutectic Solvents for Chitosan Functionalization and Preparation of Bioactive Nanogels

Catalysts, Journal Year: 2025, Volume and Issue: 15(2), P. 180 - 180

Published: Feb. 14, 2025

Biocatalytic processes for the formation of bioactive compounds and biopolymer preparations that can be applied in pharmaceuticals cosmetics are gaining increasing interest due to their safety sustainability, relying on environmentally friendly approaches biocompatible compounds. In this work, we investigate implementation various Deep Eutectic Solvents (DES) laccase-catalyzed oxidation hydroxytyrosol (HT), aiming produce its oligomer derivatives such as HT dimer trimer. The composition reaction mixture which oligomers’ yield was highest 70% v/v Bet:PG (1:4 molar ratio). oligomers formed were subsequently used non-enzymatic grafting chitosan (CS) development chitosan-based nanogels (NG). Grafted prepared by ionic gelation using sodium tripolyphosphate (TPP) a cross-linking agent. functionalized characterized Fourier-Transform Infrared (FTIR) Nuclear Magnetic Resonance (NMR) spectroscopy, while Scanning Electron Microscopy (SEM) employed nanogel characterization. Compared unmodified nanogels, grafted exhibited almost ten-fold higher antioxidant activity approximately 20% greater antibacterial activity.

Language: Английский

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Recent applications of stimulus-responsive smart hydrogels for osteoarthritis therapy

Frontiers in Bioengineering and Biotechnology, Journal Year: 2025, Volume and Issue: 13

Published: Feb. 17, 2025

Osteoarthritis is one of the most common degenerative joint diseases, which seriously affects life middle-aged and elderly people. Traditional treatments such as surgical treatment systemic medication, often do not achieve expected or optimal results, leads to severe trauma a variety side effects. Therefore, there an urgent need develop novel therapeutic options overcome these problems. Hydrogels are widely used in biomedical tissue repairing platform for loading drugs, proteins stem cells. In recent years, smart-responsive hydrogels have achieved excellent results drug delivery systems osteoarthritis. This review focuses on advances endogenous stimuli (including enzymes, pH, reactive oxygen species temperature, etc.) responsive exogenous light, shear, ultrasound magnetism, osteoarthritis treatment. Finally, current limitations application future prospects smart summarized.

Language: Английский

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Calculating the Energy Profile of an Enzymatic Reaction on a Quantum Computer

Journal of Chemical Theory and Computation, Journal Year: 2025, Volume and Issue: unknown

Published: March 31, 2025

Quantum computing (QC) provides a promising avenue for enabling quantum chemistry calculations, which are classically impossible due to computational complexity that increases exponentially with system size. As fully fault-tolerant algorithms and hardware, an exponential speedup is predicted, currently out of reach, recent research efforts have been dedicated developing scaling Noisy Intermediate-Scale (NISQ) devices showcase the practical usefulness such machines. To demonstrate NISQ in field chemistry, we apply our recently developed FAST-VQE algorithm state-of-the-art gate reduction strategy based on propositional satisfiability together standard optimization tools simulation rate-determining proton transfer step CO2 hydration catalyzed by carbonic anhydrase resulting first application device enzymatic reaction. this end, combined classical force simulations mechanical methods computers hybrid calculation approach. The presented technique significantly enhances accuracy capabilities QC-based molecular modeling finally pushes it into compelling realistic applications. framework general can be applied beyond case enzymology.

Language: Английский

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Enzymatic synthesis and sensory evaluation of N-cinnamoyl-L-phenylalanine as a novel flavor enhancer: Impact on taste perception and mechanistic insights

Food Chemistry, Journal Year: 2025, Volume and Issue: 485, P. 144542 - 144542

Published: April 26, 2025

Language: Английский

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