Literature DB >> 30949587

Multiscale Methods in Drug Design Bridge Chemical and Biological Complexity in the Search for Cures.

Rommie E Amaro1, Adrian J Mulholland2.   

Abstract

Drug action is inherently multiscale: it connects molecular interactions to emergent properties at cellular and larger scales. Simulation techniques at each of these different scales are already central to drug design and development, but methods capable of connecting across these scales will extend understanding of complex mechanisms and the ability to predict biological effects. Improved algorithms, ever-more-powerful computing architectures and the accelerating growth of rich datasets are driving advances in multiscale modeling methods capable of bridging chemical and biological complexity from the atom to the cell. Particularly exciting is the development of highly detailed, structure-based, physical simulations of biochemical systems, which are now able to access experimentally relevant timescales for large systems and, at the same time, achieve unprecedented accuracy. In this Perspective, we discuss how emerging data-rich, physics-based multiscale approaches are of the cusp of realizing long-promised impact in the discovery, design and development of novel therapeutics. We highlight emerging methods and applications in this growing field, and outline how different scales can be combined in practical modelling and simulation strategies.

Entities:  

Year:  2018        PMID: 30949587      PMCID: PMC6445369          DOI: 10.1038/s41570-018-0148

Source DB:  PubMed          Journal:  Nat Rev Chem        ISSN: 2397-3358            Impact factor:   34.035


  121 in total

1.  Using path sampling to build better Markovian state models: predicting the folding rate and mechanism of a tryptophan zipper beta hairpin.

Authors:  Nina Singhal; Christopher D Snow; Vijay S Pande
Journal:  J Chem Phys       Date:  2004-07-01       Impact factor: 3.488

2.  Computing time scales from reaction coordinates by milestoning.

Authors:  Anton K Faradjian; Ron Elber
Journal:  J Chem Phys       Date:  2004-06-15       Impact factor: 3.488

Review 3.  The many roles of computation in drug discovery.

Authors:  William L Jorgensen
Journal:  Science       Date:  2004-03-19       Impact factor: 47.728

4.  Scalable molecular dynamics with NAMD.

Authors:  James C Phillips; Rosemary Braun; Wei Wang; James Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D Skeel; Laxmikant Kalé; Klaus Schulten
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376

Review 5.  Coarse-grained models for proteins.

Authors:  Valentina Tozzini
Journal:  Curr Opin Struct Biol       Date:  2005-04       Impact factor: 6.809

6.  OPM: orientations of proteins in membranes database.

Authors:  Mikhail A Lomize; Andrei L Lomize; Irina D Pogozheva; Henry I Mosberg
Journal:  Bioinformatics       Date:  2006-01-05       Impact factor: 6.937

7.  Identification of productive inhibitor binding orientation in fatty acid amide hydrolase (FAAH) by QM/MM mechanistic modelling.

Authors:  Alessio Lodola; Marco Mor; Silvia Rivara; Christo Christov; Giorgio Tarzia; Daniele Piomelli; Adrian J Mulholland
Journal:  Chem Commun (Camb)       Date:  2007-10-19       Impact factor: 6.222

8.  Molecular dynamics simulations of the complete satellite tobacco mosaic virus.

Authors:  Peter L Freddolino; Anton S Arkhipov; Steven B Larson; Alexander McPherson; Klaus Schulten
Journal:  Structure       Date:  2006-03       Impact factor: 5.006

9.  Selective protein degradation by ligand-targeted enzymes: towards the creation of catalytic antagonists.

Authors:  Benjamin G Davis; Rafael F Sala; David R W Hodgson; Astrid Ullman; Kanjai Khumtaveeporn; David A Estell; Karl Sanford; Richard R Bott; J Bryan Jones
Journal:  Chembiochem       Date:  2003-06-06       Impact factor: 3.164

10.  Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure.

Authors:  Winfried Denk; Heinz Horstmann
Journal:  PLoS Biol       Date:  2004-10-19       Impact factor: 8.029

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  22 in total

1.  Structural basis for ligand modulation of the CCR2 conformational landscape.

Authors:  Bryn C Taylor; Christopher T Lee; Rommie E Amaro
Journal:  Proc Natl Acad Sci U S A       Date:  2019-04-11       Impact factor: 11.205

2.  Visualizing protein-ligand binding with chemical energy-wise decomposition (CHEWD): application to ligand binding in the kallikrein-8 S1 Site.

Authors:  Saad Raza; Kara E Ranaghan; Marc W van der Kamp; Christopher J Woods; Adrian J Mulholland; Syed Sikander Azam
Journal:  J Comput Aided Mol Des       Date:  2019-04-15       Impact factor: 3.686

3.  Building Structural Models of a Whole Mycoplasma Cell.

Authors:  Martina Maritan; Ludovic Autin; Jonathan Karr; Markus W Covert; Arthur J Olson; David S Goodsell
Journal:  J Mol Biol       Date:  2021-11-10       Impact factor: 5.469

4.  SEEKR2: Versatile Multiscale Milestoning Utilizing the OpenMM Molecular Dynamics Engine.

Authors:  Lane W Votapka; Andrew M Stokely; Anupam A Ojha; Rommie E Amaro
Journal:  J Chem Inf Model       Date:  2022-06-27       Impact factor: 6.162

Review 5.  Thermodynamics and Kinetics of Drug-Target Binding by Molecular Simulation.

Authors:  Sergio Decherchi; Andrea Cavalli
Journal:  Chem Rev       Date:  2020-10-02       Impact factor: 60.622

Review 6.  Art and Science of the Cellular Mesoscale.

Authors:  David S Goodsell; Arthur J Olson; Stefano Forli
Journal:  Trends Biochem Sci       Date:  2020-03-21       Impact factor: 13.807

Review 7.  An integrated view of p53 dynamics, function, and reactivation.

Authors:  Özlem Demir; Emilia P Barros; Tavina L Offutt; Mia Rosenfeld; Rommie E Amaro
Journal:  Curr Opin Struct Biol       Date:  2021-01-02       Impact factor: 6.809

8.  Biomolecular QM/MM Simulations: What Are Some of the "Burning Issues"?

Authors:  Qiang Cui; Tanmoy Pal; Luke Xie
Journal:  J Phys Chem B       Date:  2021-01-06       Impact factor: 2.991

9.  Combining Evolutionary Conservation and Quantum Topological Analyses To Determine Quantum Mechanics Subsystems for Biomolecular Quantum Mechanics/Molecular Mechanics Simulations.

Authors:  Mark A Hix; Emmett M Leddin; G Andrés Cisneros
Journal:  J Chem Theory Comput       Date:  2021-06-04       Impact factor: 6.578

10.  Mechanism of inhibition of SARS-CoV-2 Mpro by N3 peptidyl Michael acceptor explained by QM/MM simulations and design of new derivatives with tunable chemical reactivity.

Authors:  Kemel Arafet; Natalia Serrano-Aparicio; Alessio Lodola; Adrian J Mulholland; Florenci V González; Katarzyna Świderek; Vicent Moliner
Journal:  Chem Sci       Date:  2020-11-27       Impact factor: 9.825

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