Hydroxyl groups in synthetic and natural-product-derived therapeutics: a perspective on a common functional group

J Cramer, CP Sager, B Ernst - Journal of medicinal chemistry, 2019 - ACS Publications
By forming extended hydrogen-bond networks, the contribution of hydroxyl groups to affinity
can reach several orders of magnitude. However, because of the high directionality of their …

Protein crystallography for aspiring crystallographers or how to avoid pitfalls and traps in macromolecular structure determination

A Wlodawer, W Minor, Z Dauter… - The FEBS journal, 2013 - Wiley Online Library
The number of macromolecular structures deposited in the Protein Data Bank now
approaches 100 000, with the vast majority of them determined by crystallographic methods …

Joint X-ray and neutron refinement with phenix. refine

PV Afonine, M Mustyakimov… - … Section D: Biological …, 2010 - journals.iucr.org
Approximately 85% of the structures deposited in the Protein Data Bank have been solved
using X-ray crystallography, making it the leading method for three-dimensional structure …

Structure-based design of β-site APP cleaving enzyme 1 (BACE1) inhibitors for the treatment of Alzheimer's disease

J Yuan, S Venkatraman, Y Zheng… - Journal of medicinal …, 2013 - ACS Publications
The amyloid hypothesis asserts that excess production or reduced clearance of the amyloid-
β (Aβ) peptides in the brain initiates a sequence of events that ultimately lead to Alzheimer's …

A small nonrule of 3 compatible fragment library provides high hit rate of endothiapepsin crystal structures with various fragment chemotypes

H Köster, T Craan, S Brass, C Herhaus… - Journal of medicinal …, 2011 - ACS Publications
Druglike molecules are defined by Lipinski's rule of 5, to characterize fragment thresholds,
they have been reduced from 5 to 3 (Astex's rule of 3). They are applied to assemble …

Low barrier hydrogen bonds in protein structure and function

MT Kemp, EM Lewandowski, Y Chen - Biochimica et Biophysica Acta (BBA) …, 2021 - Elsevier
Low-barrier hydrogen bonds (LBHBs) are a special type of short hydrogen bond (HB) that is
characterized by the equal sharing of a hydrogen atom. The existence and catalytic role of …

Mechanisms of proteolytic enzymes and their inhibition in QM/MM studies

B Elsässer, P Goettig - International Journal of Molecular Sciences, 2021 - mdpi.com
Experimental evidence for enzymatic mechanisms is often scarce, and in many cases
inadvertently biased by the employed methods. Thus, apparently contradictory model …

Fragment Linking and Optimization of Inhibitors of the Aspartic Protease Endothiapepsin: Fragment‐Based Drug Design Facilitated by Dynamic Combinatorial …

M Mondal, N Radeva, H Fanlo‐Virgós… - Angewandte Chemie …, 2016 - Wiley Online Library
Fragment‐based drug design (FBDD) affords active compounds for biological targets. While
there are numerous reports on FBDD by fragment growing/optimization, fragment linking has …

Neutron crystallography: opportunities, challenges, and limitations

MP Blakeley, P Langan, N Niimura… - Current opinion in …, 2008 - Elsevier
Neutron crystallography has had an important, but relatively small role in structural biology
over the years. In this review of recently determined neutron structures, a theme emerges of …

Elucidating the protonation state of the γ-secretase catalytic dyad

DC Guzmán-Ocampo, R Aguayo-Ortiz… - ACS Chemical …, 2022 - ACS Publications
γ-Secretase (GS) is an intramembrane aspartyl protease that participates in the sequential
cleavage of C99 to generate different isoforms of the amyloid-β (Aβ) peptides that are …