Molecular dynamics simulations and novel drug discovery

X Liu, D Shi, S Zhou, H Liu, H Liu… - Expert opinion on drug …, 2018 - Taylor & Francis
Introduction: Molecular dynamics (MD) simulations can provide not only plentiful dynamical
structural information on biomacromolecules but also a wealth of energetic information …

Amyloid β protein and Alzheimer's disease: When computer simulations complement experimental studies

J Nasica-Labouze, PH Nguyen, F Sterpone… - Chemical …, 2015 - ACS Publications
Alzheimer's disease (AD) challenges our society with an annual estimated cost of $1.08
trillion in the United States alone by 2050. 1 AD is a progressive irreversible neurological …

Simulation studies of amyloidogenic polypeptides and their aggregates

IM Ilie, A Caflisch - Chemical reviews, 2019 - ACS Publications
Amyloids, fibrillar assembly of (poly) peptide chains, are associated with neurodegenerative
illnesses such as Alzheimer's and Parkinson's diseases, for which there are no cures. The …

Condensates in RNA repeat sequences are heterogeneously organized and exhibit reptation dynamics

HT Nguyen, N Hori, D Thirumalai - Nature chemistry, 2022 - nature.com
Although it is known that RNA undergoes liquid–liquid phase separation, the interplay
between the molecular driving forces and the emergent features of the condensates, such as …

Role of water in protein aggregation and amyloid polymorphism

D Thirumalai, G Reddy, JE Straub - Accounts of chemical …, 2012 - ACS Publications
A variety of neurodegenerative diseases are associated with amyloid plaques, which begin
as soluble protein oligomers but develop into amyloid fibrils. Our incomplete understanding …

Different force fields give rise to different amyloid aggregation pathways in molecular dynamics simulations

S Samantray, F Yin, B Kav… - Journal of chemical …, 2020 - ACS Publications
The progress toward understanding the molecular basis of Alzheimers's disease is strongly
connected to elucidating the early aggregation events of the amyloid-β (Aβ) peptide …

Polymorphism in Alzheimer Aβ amyloid organization reflects conformational selection in a rugged energy landscape

Y Miller, B Ma, R Nussinov - Chemical reviews, 2010 - ACS Publications
Amyloids can have normal biological functions. 1r3 However, amyloidogenic proteins can
also form unwanted oligomeric or polymeric aggregates when disturbed from their native …

Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of Aβ16–22 Dimer

VH Man, X He, P Derreumaux, B Ji… - Journal of chemical …, 2019 - ACS Publications
We investigated the effects of 17 widely used atomistic molecular mechanics force fields
(MMFFs) on the structures and kinetics of amyloid peptide assembly. To this end, we …

Toward a molecular theory of early and late events in monomer to amyloid fibril formation

JE Straub, D Thirumalai - Annual review of physical chemistry, 2011 - annualreviews.org
Quantitative understanding of the kinetics of fibril formation and the molecular mechanism of
transition from monomers to fibrils is needed to obtain insights into the growth of amyloid …

High-resolution probing of early events in amyloid-β aggregation related to Alzheimer's disease

BR Sahoo, SJ Cox, A Ramamoorthy - Chemical Communications, 2020 - pubs.rsc.org
In Alzheimer's disease (AD), soluble oligomers of amyloid-β (Aβ) are emerging as a crucial
entity in driving disease progression as compared to insoluble amyloid deposits. The lacuna …