Molecular dynamics simulations in drug discovery and pharmaceutical development

OMH Salo-Ahen, I Alanko, R Bhadane, AMJJ Bonvin… - Processes, 2020 - mdpi.com
Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …

Bioinformatics approaches to discovering food-derived bioactive peptides: Reviews and perspectives

Z Du, J Comer, Y Li - TrAC Trends in Analytical Chemistry, 2023 - Elsevier
Food-derived bioactive peptides (FBPs) are gaining interest due to their great potential in
agricultural byproduct valorization and high-activity peptide screening. The introduction of …

SwissDock 2024: major enhancements for small-molecule docking with Attracting Cavities and AutoDock Vina

M Bugnon, UF Röhrig, M Goullieux… - Nucleic acids …, 2024 - academic.oup.com
Drug discovery aims to identify potential therapeutic compounds capable of modulating the
activity of specific biological targets. Molecular docking can efficiently support this process …

Structure of SARS-CoV-2 membrane protein essential for virus assembly

Z Zhang, N Nomura, Y Muramoto, T Ekimoto… - Nature …, 2022 - nature.com
The coronavirus membrane protein (M) is the most abundant viral structural protein and
plays a central role in virus assembly and morphogenesis. However, the process of M …

Nirmatrelvir-resistant SARS-CoV-2 variants with high fitness in an infectious cell culture system

Y Zhou, KA Gammeltoft, LA Ryberg, LV Pham… - Science …, 2022 - science.org
The oral protease inhibitor nirmatrelvir is of key importance for prevention of severe
coronavirus disease 2019 (COVID-19). To facilitate resistance monitoring, we studied …

SwissParam 2023: a modern web-based tool for efficient small molecule parametrization

M Bugnon, M Goullieux, UF Röhrig… - Journal of chemical …, 2023 - ACS Publications
Most steps of drug discovery are now routinely supported and accelerated by computer-
aided drug design tools. Among them, structure-based approaches use the three …

N501Y mutation of spike protein in SARS-CoV-2 strengthens its binding to receptor ACE2

F Tian, B Tong, L Sun, S Shi, B Zheng, Z Wang, X Dong… - elife, 2021 - elifesciences.org
SARS-CoV-2 has been spreading around the world for the past year. Recently, several
variants such as B. 1.1. 7 (alpha), B. 1.351 (beta), and P. 1 (gamma), which share a key …

Tailoring coordination environments of single-atom electrocatalysts for hydrogen evolution by topological heteroatom transfer

S Qian, F Xu, Y Fan, N Cheng, H Xue, Y Yuan… - Nature …, 2024 - nature.com
The rational design of carbon-supported transition-metal single-atom catalysts requires the
precise arrangement of heteroatoms within the single-atom catalysts. However, achieving …

Magnetic sensitivity of cryptochrome 4 from a migratory songbird

J Xu, LE Jarocha, T Zollitsch, M Konowalczyk… - Nature, 2021 - nature.com
Night-migratory songbirds are remarkably proficient navigators. Flying alone and often over
great distances, they use various directional cues including, crucially, a light-dependent …

Characterization and engineering of a two-enzyme system for plastics depolymerization

BC Knott, E Erickson, MD Allen, JE Gado… - Proceedings of the …, 2020 - pnas.org
Plastics pollution represents a global environmental crisis. In response, microbes are
evolving the capacity to utilize synthetic polymers as carbon and energy sources. Recently …