Emerging computational methods for the rational discovery of allosteric drugs

JR Wagner, CT Lee, JD Durrant, RD Malmstrom… - Chemical …, 2016 - ACS Publications
Allosteric drug development holds promise for delivering medicines that are more selective
and less toxic than those that target orthosteric sites. To date, the discovery of allosteric …

Role of conformational dynamics in the evolution of novel enzyme function

MA Maria-Solano, E Serrano-Hervás… - Chemical …, 2018 - pubs.rsc.org
The free energy landscape concept that describes enzymes as an ensemble of differently
populated conformational sub-states in dynamic equilibrium is key for evaluating enzyme …

Cell-free chemoenzymatic starch synthesis from carbon dioxide

T Cai, H Sun, J Qiao, L Zhu, F Zhang, J Zhang, Z Tang… - Science, 2021 - science.org
Starches, a storage form of carbohydrates, are a major source of calories in the human diet
and a primary feedstock for bioindustry. We report a chemical-biochemical hybrid pathway …

POVME 3.0: software for mapping binding pocket flexibility

JR Wagner, J Sørensen, N Hensley… - Journal of chemical …, 2017 - ACS Publications
We present a substantial update to the open-source POVME binding pocket analysis
software. New capabilities of POVME 3.0 include a flexible chemical coloring scheme for …

FAD-dependent enzyme-catalysed intermolecular [4+ 2] cycloaddition in natural product biosynthesis

L Gao, C Su, X Du, R Wang, S Chen, Y Zhou, C Liu… - Nature Chemistry, 2020 - nature.com
Abstract The Diels–Alder reaction is one of the most powerful and widely used methods in
synthetic chemistry for the stereospecific construction of carbon–carbon bonds. Despite the …

How μ-opioid receptor recognizes fentanyl

QN Vo, P Mahinthichaichan, J Shen, CR Ellis - Nature communications, 2021 - nature.com
Roughly half of the drug overdose-related deaths in the United States are related to
synthetic opioids represented by fentanyl which is a potent agonist of mu-opioid receptor …

Mesoscale all-atom influenza virus simulations suggest new substrate binding mechanism

JD Durrant, SE Kochanek, L Casalino… - ACS central …, 2020 - ACS Publications
Influenza virus circulates in human, avian, and swine hosts, causing seasonal epidemic and
occasional pandemic outbreaks. Influenza neuraminidase, a viral surface glycoprotein, has …

ProteinVR: Web-based molecular visualization in virtual reality

KC Cassidy, J Šefčík, Y Raghav, A Chang… - PLoS computational …, 2020 - journals.plos.org
Protein structure determines biological function. Accurately conceptualizing 3D
protein/ligand structures is thus vital to scientific research and education. Virtual reality (VR) …

Molecular basis for high-affinity agonist binding in GPCRs

T Warne, PC Edwards, AS Doré, AGW Leslie, CG Tate - Science, 2019 - science.org
G protein–coupled receptors (GPCRs) in the G protein–coupled active state have higher
affinity for agonists as compared with when they are in the inactive state, but the molecular …

[HTML][HTML] PARP1: Structural insights and pharmacological targets for inhibition

JO Spiegel, B Van Houten, JD Durrant - DNA repair, 2021 - Elsevier
Abstract Poly (ADP-ribose) polymerase 1 (PARP1, also known as ADPRT1) is a
multifunctional human ADP-ribosyltransferase. It plays a role in multiple DNA repair …