Structural Basis for the Improved RNA Clamping of Amidino-Rocaglates to eIF4A1 DOI Creative Commons

James F. Conley,

Lauren E. Brown, James McNeely

et al.

ACS Omega, Journal Year: 2025, Volume and Issue: 10(6), P. 5795 - 5808

Published: Feb. 10, 2025

Eukaryotic initiation factor 4A-1 (eIF4A1) is an ATP-dependent RNA helicase that unwinds 5'-UTR mRNA secondary structures to facilitate cap-dependent translation initiation. Rocaglates, a class of natural products typified by rocaglamide A (RocA), possess antineoplastic and anti-infectious activity mediated their interaction with eIF4A1. Rocaglates inhibit "clamping" eIF4A1 onto polypurine RNA, which impedes ribosome scanning. novel rocaglate derivatives, amidino-rocaglates (ADRs) feature amidine ring fused the core, particularly effective at promoting eIF4A1-RNA-clamping compared other congeners. Herein, we present X-ray crystal structure ADR in complex eIF4A1, nonhydrolyzable ATP ground-state mimic adenylyl-imidodiphosphate (AMPPNP), poly r(AG)5 refined 1.69 Å resolution. The binding pose interactions do not differ substantially from those RocA, prompting investigation basis for enhanced target engagement. Computational modeling suggests rigidified scaffold inherently preorganized eIF4A1-RNA binding-competent conformation, thereby avoiding entropic penalties associated RocA binding. This study illustrates how conformational rigidification can be leveraged improve potency development rocaglates as potential anticancer agents.

Language: Английский

A Guide to In Silico Drug Design DOI Creative Commons
Yiqun Chang, Bryson A. Hawkins, Jonathan J. Du

et al.

Pharmaceutics, Journal Year: 2022, Volume and Issue: 15(1), P. 49 - 49

Published: Dec. 23, 2022

The drug discovery process is a rocky path that full of challenges, with the result very few candidates progress from hit compound to commercially available product, often due factors, such as poor binding affinity, off-target effects, or physicochemical properties, solubility stability. This further complicated by high research and development costs time requirements. It thus important optimise every step in order maximise chances success. As recent advancements computer power technology, computer-aided design (CADD) has become an integral part modern guide accelerate process. In this review, we present overview CADD methods applications, silico structure prediction, refinement, modelling target validation, are commonly used area.

Language: Английский

Citations

127
Recent advances, application and prospect in g-C3N4-based S-scheme heterojunction photocatalysts DOI
Pengyu Hao,

Zhouze Chen,

Yujie Yan

et al.

Separation and Purification Technology, Journal Year: 2023, Volume and Issue: 330, P. 125302 - 125302

Published: Oct. 12, 2023

Language: Английский

Citations

89
Electric effects reinforce charge carrier behaviour for photocatalysis DOI

Aoqiang Shu,

Chencheng Qin,

Miao Li

et al.

Energy & Environmental Science, Journal Year: 2024, Volume and Issue: 17(14), P. 4907 - 4928

Published: Jan. 1, 2024

Recent studies on enhancing charge carrier behavior through electric effects for efficient photocatalysis are summarized, evaluating the in-depth function of these effects. This provides unique perspectives to optimize photocatalytic processes.

Language: Английский

Citations

27
Quantum chemical investigation of choline chloride-based deep eutectic solvents DOI

Zubera Naseem,

Rao Aqil Shehzad,

Sobia Jabeen

et al.

Chemical Physics, Journal Year: 2023, Volume and Issue: 571, P. 111936 - 111936

Published: April 10, 2023

Language: Английский

Citations

31
A comparative analysis of the influence of hydrofluoroethers as diluents on solvation structure and electrochemical performance in non-flammable electrolytes DOI Creative Commons
Wessel van Ekeren, Marcelo Albuquerque, Gustav Ek

et al.

Journal of Materials Chemistry A, Journal Year: 2023, Volume and Issue: 11(8), P. 4111 - 4125

Published: Jan. 1, 2023

TTE (1,1,2,2-tetrafluoroethyl 2,2,3,3-tetrafluoropropyl ether) shows better performance than BTFE (bis(2,2,2-trifluoroethyl)ether as diluent in a localized highly concentrated electrolyte based on lithium bis(fluorosulfonyl)imide triethylposphate.

Language: Английский

Citations

28
Extension of the D3 and D4 London Dispersion Corrections to the full Actinides Series DOI Creative Commons
Lukas Wittmann, Igor Gordiy, Marvin Friede

et al.

Physical Chemistry Chemical Physics, Journal Year: 2024, Volume and Issue: 26(32), P. 21379 - 21394

Published: Jan. 1, 2024

Efficient dispersion corrections are an indispensable component of modern density functional theory, semi-empirical quantum mechanical, and even force field methods. In this work, we extend the well established D3 D4 London to full actinides series, francium, radium. To keep consistency with existing versions, original parameterization strategy model was only slightly modified. This includes improved reference Hirshfeld atomic partial charges at ωB97M-V/ma-def-TZVP level fit required electronegativity equilibration charge (EEQ) model. context, developed a new actinide data set called AcQM, which covers most common molecular compound space. Furthermore, efficient calculation dynamic polarizabilities that needed construct

Language: Английский

Citations

13
In Defense of (Certain) Pople-Type Basis Sets DOI Creative Commons
Montgomery Gray, Paige E. Bowling, John M. Herbert

et al.

Published: Jan. 22, 2024

A recent study suggests that Gaussian basis sets in the 6-311G family are inappropriate for thermochemical calculations based on density functional theory, emphasizing need polarization functions but omitting tests of Pople containing a full complement thereof. Here, we point out certain category yield error statistics with respect to benchmark comparable def2-TZVP, at about half cost. More elaborate can rival accuracy def2-QZVPD 5-10% We also clarify role integral thresholds achieving robust convergence presence diffuse functions.

Language: Английский

Citations

9
Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder DOI Creative Commons
Justin Villard, Martin P. Bircher, Ursula Röthlisberger

et al.

Chemical Science, Journal Year: 2024, Volume and Issue: 15(12), P. 4434 - 4451

Published: Jan. 1, 2024

This study incorporates Minnesota density functionals into the current knowledge of describing structural and dynamical properties liquid water through ab initio molecular dynamics, with M06-2X(-D3) showing most promise.

Language: Английский

Citations

9
Functional monomer design for synthetically accessible polymers DOI Creative Commons
Seonghwan Kim, Charles M. Schroeder, Nicholas E. Jackson

et al.

Chemical Science, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 1, 2025

Active learning combined with quantum chemistry reveals the nature of functional monomer design across a diverse chemical space 12M synthetically accessible polymers.

Language: Английский

Citations

1
Do Optimally Tuned Range-Separated Hybrid Functionals Require a Reparametrization of the Dispersion Correction? It Depends DOI
Marvin Friede, Sebastian Ehlert, Stefan Grimme

et al.

Journal of Chemical Theory and Computation, Journal Year: 2023, Volume and Issue: 19(22), P. 8097 - 8107

Published: Nov. 13, 2023

For ground- and excited-state studies of large molecules, it is the state art to combine (time-dependent) DFT with dispersion-corrected range-separated hybrid functionals (RSHs), which ensures an asymptotically correct description exchange effects London dispersion. Specifically for studying excited states, common practice tune range-separation parameter ω (optimal tuning), can further improve accuracy. However, since optimal tuning essentially changes functional, unclear if how much parameters used dispersion correction depend on chosen value. To answer this question, we explore interdependency by refitting DFT-D4 model six established RSHs over a wide range values (0.05-0.45 a0-1) using set noncovalently bound molecular complexes. The results reveal some surprising differences among investigated functionals: While PBE-based ωB97M-D4 generally exhibit weak robust performance values, B88-based RSHs, specifically LC-BLYP, are strongly affected. these, even minor reduction from default value manifests in strong systematic overbinding poor typical optimally tuned values. Finally, discuss strategies mitigate these issues reflect context employed D4 optimization algorithm fit set, outlining future improvements.

Language: Английский

Citations

19