Is target-based drug discovery efficient? Discovery and “off-target” mechanisms of all drugs

A Sadri - Journal of medicinal chemistry, 2023 - ACS Publications
Target-based drug discovery is the dominant paradigm of drug discovery; however, a
comprehensive evaluation of its real-world efficiency is lacking. Here, a manual systematic …

A comprehensive survey of prospective structure-based virtual screening for early drug discovery in the past fifteen years

H Zhu, Y Zhang, W Li, N Huang - International Journal of Molecular …, 2022 - mdpi.com
Structure-based virtual screening (SBVS), also known as molecular docking, has been
increasingly applied to discover small-molecule ligands based on the protein structures in …

Modeling the expansion of virtual screening libraries

J Lyu, JJ Irwin, BK Shoichet - Nature chemical biology, 2023 - nature.com
Recently,'tangible'virtual libraries have made billions of molecules readily available.
Prioritizing these molecules for synthesis and testing demands computational approaches …

Design and structural validation of peptide–drug conjugate ligands of the kappa-opioid receptor

E Muratspahić, K Deibler, J Han, N Tomašević… - Nature …, 2023 - nature.com
Despite the increasing number of GPCR structures and recent advances in peptide design,
the development of efficient technologies allowing rational design of high-affinity peptide …

AlphaFold accelerated discovery of psychotropic agonists targeting the trace amine–associated receptor 1

A Díaz-Holguín, M Saarinen, DD Vo, A Sturchio… - Science …, 2024 - science.org
Artificial intelligence is revolutionizing protein structure prediction, providing unprecedented
opportunities for drug design. To assess the potential impact on ligand discovery, we …

Docking for EP4R antagonists active against inflammatory pain

S Gahbauer, C DeLeon, JM Braz, V Craik… - Nature …, 2023 - nature.com
The lipid prostaglandin E2 (PGE2) mediates inflammatory pain by activating G protein-
coupled receptors, including the prostaglandin E2 receptor 4 (EP4R). Nonsteroidal anti …

The art and science of molecular docking

JM Paggi, A Pandit, RO Dror - Annual Review of Biochemistry, 2024 - annualreviews.org
Molecular docking has become an essential part of a structural biologist's and medicinal
chemist's toolkits. Given a chemical compound and the three-dimensional structure of a …

Large library docking identifies positive allosteric modulators of the calcium-sensing receptor

F Liu, CG Wu, CL Tu, I Glenn, J Meyerowitz, AL Kaplan… - Science, 2024 - science.org
Positive allosteric modulator (PAM) drugs enhance the activation of the calcium-sensing
receptor (CaSR) and suppress parathyroid hormone (PTH) secretion. Unfortunately, these …

Kee** pace with the explosive growth of chemical libraries with structure‐based virtual screening

J Kuan, M Radaeva, A Avenido… - Wiley …, 2023 - Wiley Online Library
Recent efforts to synthetically expand drug‐like chemical libraries have led to the
emergence of unprecedently large virtual databases. This surge of make‐on‐demand …

Advances in the discovery of new chemotypes through ultra-large library docking

F Potlitz, A Link, L Schulig - Expert opinion on drug discovery, 2023 - Taylor & Francis
Introduction The size and complexity of virtual screening libraries in drug discovery have
skyrocketed in recent years, reaching up to multiple billions of accessible compounds …