Learning from Protein Engineering by Deconvolution of Multi‐Mutational Variants

Angewandte Chemie International Edition, Год журнала: 2024, Номер 63(36)

Опубликована: Июнь 17, 2024

Abstract This review analyzes a development in biochemistry, enzymology and biotechnology that originally came as surprise. Following the establishment of directed evolution stereoselective enzymes organic chemistry, concept partial or complete deconvolution selective multi‐mutational variants was introduced. Early experiments led to finding mutations can interact cooperatively antagonistically with one another, not just additively. During past decade, this phenomenon shown be general. In some studies, molecular dynamics (MD) quantum mechanics/molecular mechanics (QM/MM) computations were performed order shed light on origin non‐additivity at all stages an evolutionary upward climb. Data used construct unique multi‐dimensional rugged fitness pathway landscapes, which provide mechanistic insights different from traditional landscapes. Along related line, biochemists have long tested result introducing two point enzyme for reasons, followed by comparison respective double mutant so‐called cycles, showed only additive effects, but more recently also uncovered cooperative antagonistic non‐additive effects. We conclude suggestions future work, call unified overall picture epistasis.

Язык: Английский

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Tertiary Alcohol: Reaping the Benefits but Minimizing the Drawbacks of Hydroxy Groups in Drug Discovery

Journal of Medicinal Chemistry, Год журнала: 2025, Номер unknown

Опубликована: Апрель 15, 2025

Among the smaller substituents in medicinal chemist's toolbox, hydroxy (OH) group can bestow one of largest impacts drug-like properties a molecule. A previous study showed that an H-to-OH structural modification effectively decreases lipophilicity, increases solubility, and hERG inhibition. Despite these benefits, OH is not always recommended drug molecules because it presents metabolic "soft spot" for oxidation glucuronidation primary secondary alcohols. Furthermore, challenges permeability. In contrast, tertiary alcohols (3° ROH) often display improved profile at 3° ROH possible, geminal alkyl groups could sterically shield from permeability challenges. Through series matched molecular pairs, this Perspective highlights as motif reap benefits but minimize drawbacks discovery.

Язык: Английский

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Machine learning guided rational design of a non-heme iron-based lysine dioxygenase improves its total turnover number

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Июнь 5, 2024

Highly selective C-H functionalization remains an ongoing challenge in organic synthetic methodologies. Biocatalysts are robust tools for achieving these difficult chemical transformations. Biocatalyst engineering has often required directed evolution or structure-based rational design campaigns to improve their activities. In recent years, machine learning been integrated into workflows the discovery of beneficial enzyme variants. this work, we combine a machine-learning algorithm with classical molecular dynamics simulations down select mutations non-heme iron-dependent lysine dioxygenase, LDO. This approach consistently resulted functional LDO mutants and circumvents need extensive study mutational activity before-hand. Our rationally designed single purified up 2-fold higher yields than WT displayed total turnover numbers (TTN). Combining five such pentamutant variant, LPNYI LDO, leads 40% improvement TTN (218±3) as compared (TTN = 160±2). Overall, work offers low-barrier those seeking synergize algorithms pre-existing protein strategies.

Язык: Английский

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Lernen aus Protein‐Engineering durch Dekonvolution von Multi‐Mutationalen Enzymvarianten**

Angewandte Chemie, Год журнала: 2024, Номер 136(36)

Опубликована: Июнь 17, 2024

Abstract Diese Übersicht analysiert eine Entwicklung in der Biochemie, Enzymologie und Biotechnologie, die ursprünglich als Überraschung betrachtet wurde. Nach Etablierung gerichteten Evolution stereoselektiver Enzyme organischen Chemie wurde das Konzept partiellen oder vollständigen Dekonvolution selektiver multi‐mutationaler Varianten eingeführt. Frühe Dekonvolutionsexperimente von stereoselektiven Enzymvarianten führten zu Erkenntnis, dass Mutationen kooperativ antagonistisch miteinander interagieren können, nicht nur additiv. Im letzten Jahrzehnt dieses Phänomen allgemeingültig nachgewiesen. In einigen Studien wurden molekulardynamische (MD) quantenmechanische/ molekülmechanische (QM/MM) Berechnungen durchgeführt, um Licht auf den Ursprung Nicht‐Additivität allen Phasen eines evolutionären Aufstiegs werfen. Daten können verwendet werden, einzigartige mehrdimensionale, zerklüftete („rugged“) Fitness‐Pfad‐Landschaften experimentell konstruieren. Sie bieten mechanistische Einblicke, sich traditionellen Fitnesslandschaften erheblich unterscheiden. einem verwandten Bereich haben Biochemiker lange Ergebnis Einführung zwei Punktmutationen Enzym aus mechanistischen Gründen getestet, gefolgt Vergleich mit entsprechenden Doppelmutante sogenannten Doppelmutanten‐Zyklen, additive Effekte zeigten. jüngerer Zeit auch hier kooperative antagonistische nicht‐additive aufgedeckt. Wir schließen Vorschlägen für zukünftige Arbeiten fordern ein einheitliches Gesamtbild Epistasis.

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Manfred T. Reetz – A Pioneer in Chemical Synthesis

Molecular Catalysis, Год журнала: 2024, Номер 565, С. 114374 - 114374

Опубликована: Июль 8, 2024

Язык: Английский

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