Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

A Currin, N Swainston, PJ Day, DB Kell - Chemical Society Reviews, 2015 - pubs.rsc.org
The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …

Enzymatic transition states and drug design

VL Schramm - Chemical reviews, 2018 - ACS Publications
Transition state theory teaches that chemically stable mimics of enzymatic transition states
will bind tightly to their cognate enzymes. Kinetic isotope effects combined with …

Quantum chemical approaches in structure-based virtual screening and lead optimization

CN Cavasotto, NS Adler, MG Aucar - Frontiers in chemistry, 2018 - frontiersin.org
Today computational chemistry is a consolidated tool in drug lead discovery endeavors. Due
to methodological developments and to the enormous advance in computer hardware …

Recent advances in biocatalytic promiscuity: hydrolase‐catalyzed reactions for nonconventional transformations

M López‐Iglesias, V Gotor‐Fernández - The Chemical Record, 2015 - Wiley Online Library
Enzymes have emerged in recent decades as ideal catalysts for synthetic transformations
under mild reaction conditions. Their capacity to accelerate a myriad of biotransformations …

Promoting vibrations and the function of enzymes. Emerging theoretical and experimental convergence

VL Schramm, SD Schwartz - Biochemistry, 2018 - ACS Publications
A complete understanding of enzyme catalysis requires knowledge of both transition state
features and the detailed motions of atoms that cause reactant molecules to form and …

Electrostatic Preorganization in Three Distinct Heterogeneous Proteasome β-Subunits

S Ferrer, V Moliner, K Świderek - ACS catalysis, 2024 - ACS Publications
The origin of the enzyme's powerful role in accelerating chemical reactions is one of the
most critical and still widely discussed questions. It is already accepted that enzymes impose …

Binding free energy calculation using quantum mechanics aimed for drug lead optimization

CN Cavasotto - Quantum mechanics in drug discovery, 2020 - Springer
The routine use of in silico tools is already established in drug lead design. Besides the use
of molecular docking methods to screen large chemical libraries and thus prioritize …

Dynamic and electrostatic effects on the reaction catalyzed by HIV-1 protease

A Krzeminska, V Moliner… - Journal of the American …, 2016 - ACS Publications
HIV-1 Protease (HIV-1 PR) is one of the three enzymes essential for the replication process
of HIV-1 virus, which explains why it has been the main target for design of drugs against …

Transition states and transition state analogue interactions with enzymes

VL Schramm - Accounts of Chemical Research, 2015 - ACS Publications
Conspectus Enzymatic transition states have lifetimes of a few femtoseconds (fs).
Computational analysis of enzyme motions leading to transition state formation suggests …

Advances in sustainable catalysis: A computational perspective

MG Quesne, F Silveri, NH De Leeuw… - Frontiers in …, 2019 - frontiersin.org
The enormous challenge of moving our societies to a more sustainable future offers several
exciting opportunities for computational chemists. The first principles approach to “catalysis …