Benefits of hybrid QM/MM over traditional classical mechanics in pharmaceutical systems

RK Kar - Drug Discovery Today, 2023 - Elsevier
Highlights•This review highlights the role of the hybrid quantum mechanics/molecular
mechanics (QM/MM) technique in the drug design process.•It discusses the methodological …

Electrostatics as a Guiding Principle in Understanding and Designing Enzymes

JJ Ruiz-Pernía, K Swiderek, J Bertran… - Journal of Chemical …, 2024 - ACS Publications
Enzyme design faces challenges related to the implementation of the basic principles that
govern the catalytic activity in natural enzymes. In this work, we revisit basic electrostatic …

First-in-class small molecule inhibitors of ICOS/ICOSL interaction as a novel class of immunomodulators

SA Abdel-Rahman, K Świderek, MT Gabr - RSC Medicinal Chemistry, 2023 - pubs.rsc.org
The interaction of the inducible co-stimulator (ICOS) with its ligand (ICOSL) plays key roles
in T-cell differentiation and activation of T-cell to B-cell functions. The ICOS/ICOSL pathway …

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 …

Elucidation of the α-Ketoamide Inhibition Mechanism: Revealing the Critical Role of the Electrostatic Reorganization Effect of Asp17 in the Active Site of the 20S …

J Zhou, X Sang, J Wang, Y Xu, J An, ZT Chu… - ACS …, 2023 - ACS Publications
The 20S proteasome is an attractive drug target for the development of anticancer agents
because it plays an important role in cellular protein degradation. It has a threonine residue …

Combined theoretical and experimental study to unravel the differences in promiscuous amidase activity of two nonhomologous enzymes

MA Galmes, AR Nodling, L Luk, K Swiderek… - ACS catalysis, 2021 - ACS Publications
Convergent evolution has resulted in nonhomologous enzymes that contain similar active
sites that catalyze the same primary and secondary reactions. Comparing how these …

A Single Amino Acid Able to Promote High‐Temperature Ring‐Opening Polymerization by Dual Activation

E Gabirondo, K Świderek, E Marin… - Advanced …, 2024 - Wiley Online Library
Amino acids are indispensable compounds in the body, performing several biological
processes that enable proper functioning. In this work, it is demonstrated that a single amino …

On the Origin of the Different Reversible Characters of Salinosporamide A and Homosalinosporamide A in the Covalent Inhibition of the Human 20S Proteasome

N Serrano-Aparicio, V Moliner, K Swiderek - ACS Catalysis, 2021 - ACS Publications
Covalent inhibition of the 20S proteasome is one of the strategies used in the fight against
cancer, Chagas' disease, malaria, tuberculosis, or neurodegenerative disorders. In this …

[HTML][HTML] Mechanistic and thermodynamic characterization of oxathiazolones as potent and selective covalent immunoproteasome inhibitors

LM Mihalovits, GG Ferenczy, GM Keserű - Computational and Structural …, 2021 - Elsevier
The ubiquitin–proteasome system is responsible for the degradation of proteins and plays a
critical role in key cellular processes. While the constitutive proteasome (cPS) is expressed …

Investigation of the compatibility between warheads and peptidomimetic sequences of protease inhibitors—a comprehensive reactivity and selectivity study

P Müller, M Meta, JL Meidner, M Schwickert… - International Journal of …, 2023 - mdpi.com
Covalent peptidomimetic protease inhibitors have gained a lot of attention in drug
development in recent years. They are designed to covalently bind the catalytically active …