Navigating the landscape of enzyme design: from molecular simulations to machine learning

J Zhou, M Huang - Chemical Society Reviews, 2024 - pubs.rsc.org
Global environmental issues and sustainable development call for new technologies for fine
chemical synthesis and waste valorization. Biocatalysis has attracted great attention as the …

Molecular basis for DarT ADP-ribosylation of a DNA base

M Schuller, RE Butler, A Ariza, C Tromans-Coia… - Nature, 2021 - nature.com
ADP-ribosyltransferases use NAD+ to catalyse substrate ADP-ribosylation, and thereby
regulate cellular pathways or contribute to toxin-mediated pathogenicity of bacteria …

New trends in the biocatalytic production of nucleosidic active pharmaceutical ingredients using 2′-deoxyribosyltransferases

J Del Arco, J Acosta, J Fernández-Lucas - Biotechnology Advances, 2021 - Elsevier
Nowadays, pharmaceutical industry demands competitive and eco-friendly processes for
active pharmaceutical ingredients (APIs) manufacturing. In this context, enzyme and whole …

Snapshots of the reaction coordinate of a thermophilic 2′-deoxyribonucleoside/ribonucleoside transferase

P Tang, CJ Harding, AL Dickson, RG da Silva… - ACS …, 2024 - ACS Publications
Nucleosides are ubiquitous to life and are required for the synthesis of DNA, RNA, and other
molecules crucial for cell survival. Despite the notoriously difficult organic synthesis of …

Immobilized enzyme reactors based on nucleoside phosphorylases and 2′-deoxyribosyltransferase for the in-flow synthesis of pharmaceutically relevant nucleoside …

F Rinaldi, J Fernández-Lucas, D de La Fuente… - Bioresource …, 2020 - Elsevier
In this work, a mono-and a bi-enzymatic analytical immobilized enzyme reactors (IMERs)
were developed as prototypes for biosynthetic purposes and their performances in the in …

[HTML][HTML] Novel Directed Enzyme Prodrug Therapy for Cancer Treatment Based on 2′-Deoxyribosyltransferase-Conjugated Magnetic Nanoparticles

E Pérez, J Acosta, V Pisabarro, M Cordani… - Biomolecules, 2024 - mdpi.com
Directed enzyme prodrug therapy (DEPT) strategies show promise in mitigating
chemotherapy side effects during cancer treatment. Among these, the use of immobilized …

Rational design of a thermostable 2′-deoxyribosyltransferase for nelarabine production by prediction of disulfide bond engineering sites

G Cruz, J Acosta, JM Mancheño, J Del Arco… - International journal of …, 2022 - mdpi.com
One of the major drawbacks of the industrial implementation of enzymatic processes is the
low operational stability of the enzymes under tough industrial conditions. In this respect, the …

Computational evidence of glycosyl cations

P Merino, I Delso, S Pereira, S Orta… - Organic & …, 2021 - pubs.rsc.org
Glycosyl cations are key intermediates in the glycosylation reactions taking place through a
SN1-type mechanism. To obtain a reliable description of the glycosylation reaction …

Prediction of enzyme catalysis by computing reaction energy barriers via steered QM/MM molecular dynamics simulations and machine learning

D Platero-Rochart, T Krivobokova… - Journal of Chemical …, 2023 - ACS Publications
The prediction of enzyme activity is one of the main challenges in catalysis. With computer-
aided methods, it is possible to simulate the reaction mechanism at the atomic level …

Biocatalytic Synthesis of Ribonucleoside Analogues Using Nucleoside Transglycosylase-2

GA Burley, A Taladriz-Sender, A Salihovic… - Chemical …, 2025 - pubs.rsc.org
2ʹ-Ribonucleosides are essential building blocks used extensively in antiviral and
oligonucleotide therapeutics. A major challenge in the further development of nucleoside …