Past, present, and future perspectives on computer-aided drug design methodologies

D Bassani, S Moro - Molecules, 2023 - mdpi.com
The application of computational approaches in drug discovery has been consolidated in
the last decades. These families of techniques are usually grouped under the common …

Role of protein phosphorylation in cell signaling, disease, and the intervention therapy

K Pang, W Wang, JX Qin, ZD Shi, L Hao, YY Ma… - MedComm, 2022 - Wiley Online Library
Protein phosphorylation is an important post‐transcriptional modification involving an
extremely wide range of intracellular signaling transduction pathways, making it an …

1, 2, 4-Amino-triazine derivatives as pyruvate dehydrogenase kinase inhibitors: Synthesis and pharmacological evaluation

C Pecoraro, M De Franco, D Carbone… - European Journal of …, 2023 - Elsevier
Among the different hallmarks of cancer, deregulation of cellular metabolism turned out to be
an essential mechanism in promoting cancer resistance and progression. The pyruvate …

Structural manipulations of marine natural products inspire a new library of 3-amino-1, 2, 4-triazine PDK inhibitors endowed with antitumor activity in pancreatic ductal …

D Carbone, M De Franco, C Pecoraro, D Bassani… - Marine Drugs, 2023 - mdpi.com
Pancreatic ductal adenocarcinoma (PDAC) is one of the main aggressive types of cancer,
characterized by late prognosis and drug resistance. Among the main factors sustaining …

Implementing a scoring function based on interaction fingerprint for Autogrow4: Protein Kinase CK1δ as a case study

M Pavan, S Menin, D Bassani, M Sturlese… - Frontiers in Molecular …, 2022 - frontiersin.org
In the last 20 years, fragment-based drug discovery (FBDD) has become a popular and
consolidated approach within the drug discovery pipeline, due to its ability to bring several …

Re-Exploring the Ability of Common Docking Programs to Correctly Reproduce the Binding Modes of Non-Covalent Inhibitors of SARS-CoV-2 Protease Mpro

D Bassani, M Pavan, G Bolcato, M Sturlese, S Moro - Pharmaceuticals, 2022 - mdpi.com
In the latest few decades, molecular docking has imposed itself as one of the most used
approaches for computational drug discovery. Several docking benchmarks have been …

Federated learning in computational toxicology: an industrial perspective on the Effiris Hackathon

D Bassani, A Brigo… - Chemical Research in …, 2023 - ACS Publications
In silico approaches have acquired a towering role in pharmaceutical research and
development, allowing laboratories all around the world to design, create, and optimize …

Investigating RNA–protein recognition mechanisms through supervised molecular dynamics (SuMD) simulations

M Pavan, D Bassani, M Sturlese… - NAR Genomics and …, 2022 - academic.oup.com
Ribonucleic acid (RNA) plays a key regulatory role within the cell, cooperating with proteins
to control the genome expression and several biological processes. Due to its characteristic …

Qualitative estimation of protein–ligand complex stability through thermal titration molecular dynamics simulations

M Pavan, S Menin, D Bassani… - Journal of Chemical …, 2022 - ACS Publications
The prediction of ligand efficacy has long been linked to thermodynamic properties such as
the equilibrium dissociation constant, which considers both the association and the …

Molecular modeling unveils the effective interaction of B-RAF inhibitors with rare B-RAF insertion variants

MC Scaini, L Piccin, D Bassani, A Scapinello… - International Journal of …, 2023 - mdpi.com
The Food and Drug Administration (FDA) has approved MAPK inhibitors as a treatment for
melanoma patients carrying a mutation in codon V600 of the BRAF gene exclusively …