RG9. Computational Biochemistry

ACS Catalysis, 2022, 12, 698-708.

Martí, S.; Arafet, K.; Lodola, A.; Mulholland, A.J.; Świderek, K.; Moliner, V.

Impact of Warhead Modulations on the Covalent Inhibition of SARS-CoV-2 Mpro Explored by QM/MM Simulations.

Int. J. Mol. Sci., 2022, 23, 300.

Silva, J.R.A.; Urban, J.; Araújo, E.; Lameira, J.; Moliner, V.; Alves, C.N.

Exploring the Catalytic Mechanism of the RNA Cap Modification by nsp16-nsp10 Complex of SARS-CoV-2 through a QM/MM Approach.

Chemical Science, 2022, 13, 4779.

Galmés, M.À.; Nödling, A.R.; He, K.; Luk, L.Y.P.; Świderek, K.; Moliner, V.

Computational design of an amidase by combining the best electrostatic features of two promiscuous hydrolases.

ACS Catalysis, 2022, 12, 14667–14678.

Akintola, O.; Farren-Dai, M.; Ren, W.; Bhosale, S.; Britton, R.; Świderek, K.; Moliner, V.; Bennet, A.J.

Glycoside Hydrolase Catalysis: Do Substrates and Mechanism-Based Covalent Inhibitors React via Matching Transition States?.

mathematics, 2022, 10, 4632.

Pérez, G.Alfonso; Castillo, R.

Identification of systemic sclerosis through machine learning algorithms and gene expression.

Int. J. Mol. Sci., 2022, 23, 7049.

Pla-López, A.; Castillo, R.; Cejudo-Marín, R.; García-Pedrero, O.; Bakir-Laso, M.; Falomir, E.; Carda, M.

Synthesis and Biological Evaluation of Small Molecule as Potential Anticancer Multitarget Agents.

Top Catalysis, 2021, 1-12.

Serrano-Aparicio, N.; Świderek, K.; Tuñón, I.; Moliner, V.; Bertran, J.

Theoretical Studies of the Self Cleavage Pistol Ribozyme Mechanism.

ACS Catalysis, 2021, 11, 10383-10393.

Farren-Dai, M.; Sannikova, N.; Świderek, K.; Moliner, V.; Bennet, A.J.

Fundamental Insight into Glycoside Hydrolase-Catalyzed Hydrolysis of the Universal Koshland Substrates–Glycopyranosyl Fluorides.

Chemical Science, 2021, 12, 13686-13703.

Chan, H.T.H.; Moesser, M.A.; Walters, R.K.; Malla, T.R.; Twidale, R.M.; John, T.; Deeks, H.M.; Johnston-Wood, T.; Mikhailov, V.; Sessions, R.B.; Dawsonl, W.; Saleh, E.; Lukacik, P.; Strain-Damerell, C.; Owen, C.D.; Nakajima, T.; Świderek, K.; Lodola, A.; Moliner, V.; Glowacki, D.R.; Spencer, J.; Walsh, M.A.A.; Schofield, .J.; Genovese, L.; Shoemark, D.K.; Mulholland, A.J.; Duarte, F.; Morris, G.M.

Discovery of SARS-CoV-2 Mpro Peptide Inhibitors from Modelling Substrate and Ligand Binding.

Journal of Chemical Informatics and Modeling, 2021, 61, 4582–4593.

Movilla, S.; Martí, S.; Roca, M.; Moliner, V.

Unrevealing the Proteolytic Activity of RgpB Gingipain from Computational Simulations.

ACS Catalysis, 2021, 11, 11806–11819.

Serrano-Aparicio, N.; Moliner, V.; Świderek, K.

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

Org. Biomol. Chem., 2021, 19, 10424-10431.

Nödling, A.R.; Santi, N.; Castillo, R.; Lipka-Lloyd, M.; Jin, Y.; Morrill, L.C.; Świderek, K.; Moliner, V.; Luk, L.Y.P.

The role of streptavidin and its variants in catalysis by biotinylated secondary amines..

Journal of Chemical Informatics and Modeling, 2021, 61, 3604–3614.

Galmés, M.À.; Świderek, K.; Moliner, V.

Computational Studies Suggest Promiscuous Candida antarctica Lipase B as an Environmentally Friendly Alternative for the Production of Epoxides.

ACS Catalysis, 2021, 11, 8635–8644.

Galmés, M.À.; Nödling, A.R.; Luk, L.; Świderek, K.; Moliner, V.

Combined Theoretical and Experimental Study to Unravel the Differences in Promiscuous Amidase Activity of Two Nonhomologous Enzymes.

Journal of Chemical Informatics and Modeling, 2021, 61, 3041–3051.

Boneta, S.; Arafet, K.; Moliner, V.

QM/MM Study of the Enzymatic Biodegradation Mechanism of Polyethylene Terephthalate.

Article page: https://pubs.acs.org/doi/10.1021/acs.jcim.1c00394

PROTEINS: Structure, Function and Bioinformatics, 2021, 1-13.

da Costa, C.Henrique S.; Santos, A.M. dos; Alves, C.audioNahum; Martí, S.; Moliner, V.; Santana, K.; Lameira, J.

Assessment of the PETase conformational changes induced by poly(ethylene terephthalate) binding.

Article page: https://onlinelibrary.wiley.com/doi/pdf/10.1002/prot.26155

ACS Catalysis, 2021, 11, 8211–8225.

Glanowski, M.; Wójcik, P.; Procner, M.; Borowski, T.; Lupa, D.; Mielczarek, P.; Oszajca, M.; Moliner, V.; Świderek, K.; Bojarski, A.J.; Szaleniec, M.

Enzymatic Δ1-Dehydrogenation of 3-Ketosteroids—Reconciliation of Kinetic Isotope Effects with the Reaction Mechanism.

Article page: https://pubs.acs.org/doi/10.1021/acscatal.1c01479?fig=abs1&ref=pdf

Journal of Computational Chemistry, 2021, 42, 447–457.

Martí, S.

QMCube (QM3): An all-purpose suite for multiscale QM/MM calculations.

Article page: https://onlinelibrary.wiley.com/doi/full/10.1002/jcc.26465

Chemical Communications, 2021, 57, 5306–5309.

De Raffele, D.; Martí, S.; Moliner, V.

A QM/MM study on the origin of retro-aldolase activity of a catalytic antibody.

Article page: https://pubs.rsc.org/en/content/articlepdf/2021/cc/d1cc01081f

Chemistry - A European Journal, 2021, 27, 1-10.

Arafet, K.; González, F.V.; Moliner, V.

Elucidating the dual mode of action of dipeptidyl enoates in the inhibition of rhodesain cysteine proteases.

Article page: https://chemistry-europe.onlinelibrary.wiley.com/doi/epdf/10.1002/chem.202100892