-2024-
L. Williams, I.M. Taily, L Hatton, A.A. Berezin, Y.L. Wu, V. Moliner, K. Świderek, Y. Tsai, L.Y.P Luk "Secondary Amine Catalysis in Enzyme Design: Broadening Protein Template Diversity through Genetic Code Expansion" Angew. Chemie Int. Ed. e202403098 (2024) DOI:10.1002/ange.202403098
K. Świderek, S. Marti, K. Arafet, V. Moliner "Computational study of the Mechanism of a polyurethane esterase A (PueA) from Pseudomonas chlororaphis" Faraday Discussions Accepted Manuscript (2024) DOI: 10.1039/D4FD00022F
J.J. Ruiz-Pernía, K. Świderek, J. Bertran, V. Moliner, I. Tuñón "Electrostatics as a Guiding Principle in Understanding and Designing Enzymes" J. Chem. Theory Comput. 20, 1783 (2024) DOI:10.1021/acs.jctc.3c01395
E. Gabirondo, K. Świderek, E. Marin, A. Maiz-Iginitz, A. Larranaga, V. Moliner, A. Etxeberria, H. Sardon "A Single Amino Acid Able to Promote High-Temperature Ring-Opening Polymerization by Dual Activation" Adv. Sci., 2308956 (2024) DOI: 10.1002/advs.202308956
F. J. Medrano, S. de la Hoz-Rodríguez, S. Martí, K. Arafet, T. Schirmeister, S. J. Hammerschmidt, C. Müller, Á. González-Martínez, E. Santillana, J. Ziebuhr, A. Romero, C. Zimmer, A. Weldert, R. Zimmermann, A. Lodola, K. Świderek, V. Moliner, F. V. González "Peptidyl nitroalkene inhibitors of main protease rationalized by computational and crystallographic investigations as antivirals against SARS-CoV-2." Commun Chem 7, 15 (2024). https://doi.org/10.1038/s42004-024-01104-7
-2023-
A. Fernández-de-la-Pradilla, S. Royo, T. Schirmeister, F. Barthels, K. Świderek, F. V. González, V. Moliner "Impact of the Warhead of Dipeptidyl Keto Michael Acceptors on the Inhibition Mechanism of Cysteine Protease Cathepsin L" ACS Catal. 13, 13354-13368 (2023) doi:10.1021/acscatal.3c02748
S.A. Abdel-Rahman, K. Świderek, M.T. Gabr "First-in-class small molecule inhibitors of ICOS/ICOSL interaction as a novel class of immunomodulators" RSC Med. Chem. 14, 1767-1777 (2023) doi:10.1039/D3MD00150D
K. Świderek, S. Velasco-Lozano, M. À. Galmés, I. Olazabal, H. Sardon, F. López-Gallego, V. Moliner "Mechanistic studies of a lipase unveil effect of pH on hydrolysis products of small PET modules" Nat. Commun. 14:3556. (2023) doi: 10.1038/s41467-023-39201-1
K Arafet, S Royo, T Schirmeister, F Barthels, FV González, V Moliner "Impact of the Recognition Part of Dipeptidyl Nitroalkene Compounds on the Inhibition Mechanism of Cysteine Proteases Cruzain and Cathepsin L" ACS Catal. 13, 6289-6300 (2023)
S. Movilla, M. Roca, V. Moliner, A. Magistrato "Molecular Basis of RNA-Driven ATP Hydrolysis in DExH-Box Helicases" J. Am. Chem. Soc. 145, 12, 6691–6701 (2023)
K Arafet, L Scalvini, F Galvani, S Martí, V Moliner, M Mor, A Lodola "Mechanistic Modeling of Lys745 Sulfonylation in EGFR C797S Reveals Chemical Determinants for Inhibitor Activity and Discriminates Reversible from Irreversible Agents" J. Chem. Inf. Mod. 63, 1301-1312 (2023)
S. Movilla, S. Martí, M. Roca, and V. Moliner Computational Study of the Inhibition of RgpB Gingipain, a Promising Target for the Treatment of Alzheimer’s Disease. J. Chem. Inf. Model. (2023) https://doi.org/10.1021/acs.jcim.2c01198
P. Gomez de Santos, A. González-Benjumea, A. Fernandez-Garcia, C. Aranda, Y. Wu, A. But, P. Molina-Espeja, D. Mate Maté, D. Gonzalez-Perez, W. Zhang, J. Kiebist, K. Scheibner, M. Hofrichter, K. Świderek, V. Moliner, J. Sanz-Aparicio, F. Hollmann, A. Gutiérrez, M. Alcalde "Engineering a Highly Regioselective Fungal Peroxygenase for the Synthesis of Hydroxy Fatty Acids" Angew. Chemie Int. Ed. 62, e202217372 (2023) doi: 10.1002/anie.202217372
-2022-
O. Akintola, M. Farren-Dai, W. Ren, S. Bhosale, R. Britton, K. Świderek, V. Moliner, and A. J. Bennet "Glycoside Hydrolase Catalysis: Do Substrates and Mechanism-Based Covalent Inhibitors React via Matching Transition States?" ACS Catal. 12, 14667–14678 (2022). doi: 10.1021/acscatal.2c04027
N. Serrano-Aparicio, S. Ferrer, K. Świderek "Covalent Inhibition of the Human 20S Proteasome with Homobelactosin C Inquired by QM/MM Studies"
Pharmaceuticals 15, 531, (2022). doi:10.3390/ph15050531
M. À. Galmés, A. R. Nodling, K. He, L. Y. P. Luk, K. Świderek, V. Moliner "Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases" Chem. Sci. 13, 4779-4787 (2022) doi:10.1039/d2sc00778a
S. Martí, K. Arafet, A. Lodola, A. J. Mulholland, K. Świderek, V. Moliner "Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 Mpro Explored by QM/MM Simulations" ACS Catal. 12, 1, 698–708 (2022) doi:10.1021/acscatal.1c04661
J.R.A. Silva, J. Urban, E. Araújo, J. Lameira, V. Moliner, C.N. Alves "Exploring the Catalytic Mechanism of the RNA Cap Modification by nsp16-nsp10 Complex of SARS-CoV-2 through a QM/MM Approach" Int. J. Mol. Sci. 23, 300 (2022) doi:10.3390/ijms23010300
-2021-
A. R. Nödling, N. Santi, R. Castillo, M. Lipka-Lloyd, Y. Jin, L. C. Morrill, K. Świderek, V. Moliner, L. Y. P. Luk "The role of streptavidin and its variants in catalysis by biotinylated secondary amines" Org. Biomol. Chem. 19, 10424-10431, (2021). doi:10.1039/D1OB01947CN. Serrano-Aparicio, V.Moliner, K. Świderek "On the Origin of the Different Reversible Characters of Salinosporamide A and Homosalinosporamide A in the Covalent Inhibition of the Human 20S Proteasome" ACS Catal. 11, 11806–11819, (2021) doi:10.1021/acscatal.1c02614
H.T.H. Chan, M.A. Moesser, R.K. Walters, T.R. Malla, R.M. Twidale, T. John, H.M. Deeks, T. Johnston-Wood, V. Mikhailov, R.B. Sessions, W. Dawson, E. Saleh, P. Lukacik, C. Strain-Damerell, C.D. Owen, T. Nakajima, K. Świderek, A. Lodola, V. Moliner, D.R. Glowacki, J. Spencer, M.A.A. Walsh, C.J. Schofield, L. Genovese, D.K. Shoemark, A.J. Mulholland, F. Duarte, G.M. Morris "Discovery of SARS-CoV-2 Mpro Peptide Inhibitors from Modelling Substrate and Ligand Binding" Chem. Sci. 12, 13686-13703 (2021) Accepted Manuscript doi:10.1039/D1SC03628A
N. Serrano-Aparicio, K. Świderek, I. Tuñón, V.Moliner, J. Bertran "Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism" Top Catal 1-12 (2021) doi:10.1007/s11244-021-01494-1
S. Movilla, S. Marti, M. Roca, Vicent Moliner "Unrevealing the Proteolytic Activity of RgpB Gingipain from Computational Simulations" J. Chem. Inf. Model. (2021) doi.org/10.1021/acs.jcim.1c00666
M. Farren-Dai, N. Sannikova, K. Świderek, V. Moliner, A.J. Bennet "Fundamental Insight into Glycoside Hydrolase-Catalyzed Hydrolysis of the Universal Koshland Substrates–Glycopyranosyl Fluorides" ACS Catal. 11, 10383-10393 (2021) doi:10.1021/acscatal.1c01918
M. A. Galmés, K. Świderek, V. Moliner "Computational Studies Suggest Promiscuous Candida antarctica Lipase B as an Environmentally Friendly Alternative for the Production of Epoxides" J. Chem. Inf. Model. 61, 3604–3614 (2021) doi:10.1021/acs.jcim.1c00425
M. A. Galmés, A. R. Nödling, L. Luk, K. Świderek, V. Moliner "Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes" ACS Catal. 11, 8635–8644 (2021) doi:10.1021/acscatal.1c02150
M. Glanowski, P. Wójcik, M. Procner, T. Borowski, D. Lupa, P. Mielczarek, M. Oszajca, K. Świderek, V. Moliner, A. J. Bojarski, M. Szaleniec "Enzymatic Δ1-Dehydrogenation of 3-Ketosteroids—Reconciliation of Kinetic Isotope Effects with the Reaction Mechanism" ACS Catal. 11, 8211–8225 (2021) doi: 10.1021/acscatal.1c01479
S. Boneta, K. Arafet, V. Moliner “QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate” J. Chem. Inf. Model. (2021) doi: 10.1021/acs.jcim.1c00394
D. De Raffele, S. Martí, V. Moliner "A QM/MM study on the origin of retro-aldolase activity of a catalytic antibody" Chem. Commun. Advance Article (2021) doi: 10.1039/d1cc01081f
K. Arafet, K.; F.V. González, V. Moliner "Elucidating the dual mode of action of dipeptidyl enoates in the inhibition of rhodesain cysteine proteases." Chem.Eur. J. (2021) doi: 10.1002/chem.202100892
S.A. Kholodar, J. S.Finer-Moore, K. Świderek, K. Arafet, V. Moliner, R. M. Stroud, A. Kohen, "Caught in Action: X-ray Structure of Thymidylate Synthase with Noncovalent Intermediate Analog." Biochemistry, 60 (16), 1243-1247 (2021) doi: 10.1021/acs.biochem.1c00063
N. Serrano-Aparicio, V.Moliner, K. Świderek "Nature of Irreversible Inhibition of Human 20S Proteasome by Salinosporamide A. The Critical Role of Lys–Asp Dyad Revealed from Electrostatic Effects Analysis" ACS Catal. 11, 3575–3589, (2021) doi:10.1021/acscatal.0c05313 Cover of Volume 11, Issue 6
N. Santi, L. C. Morrill, K. Świderek, V. Moliner, L.Y.P. Luk "Transfer Hydrogenations catalyzed by Streptavidin-hosted Secondary Amine Organocatalyst" Chem. Commun. 57, 1919-1922 (2021) doi:10.1039/D0CC08142F
K. Arafet, N. Serrano-Aparicio A. Lodola A. Mulholland, F. V. González, K. Świderek*, V. Moliner* "Mechanism of Inhibition of SARS-CoV-2 Mpro by N3 Peptidyl Michael Acceptor Explained by QM/MM Simulations and Design of New Derivatives with Tunable Chemical Reactivity." Chem. Sci. 12, 1433-1444 (2021) ChemRxiv Preprint Doi: 10.26434/chemrxiv.12941819.v1
