Literature DB >> 22160626

Molecular simulation methods in drug discovery: a prospective outlook.

Xavier Barril1, F Javier Luque.   

Abstract

Over the last decades, molecular simulations have spread through the drug discovery arena. This trend is expected to continue in the foreseeable future thanks to increased performance and the positive impact they can exert on productivity. In this article we highlight three aspects of molecular modelling for which we expect significant improvements over the next 25 years. Increased computational resources, faster algorithms and novel methods to sample rare events will provide a better handle on target flexibility and its relation with ligand binding. More accurate target druggability predictions will improve the success, but also broaden the scope of target-based drug discovery strategies. Finally, the use of higher levels of theory will increase the accuracy of protein-ligand binding affinity predictions, resulting in better hit identification success rates as well as more efficient lead optimization processes.

Mesh:

Year:  2011        PMID: 22160626     DOI: 10.1007/s10822-011-9506-1

Source DB:  PubMed          Journal:  J Comput Aided Mol Des        ISSN: 0920-654X            Impact factor:   3.686


  71 in total

1.  Understanding and predicting druggability. A high-throughput method for detection of drug binding sites.

Authors:  Peter Schmidtke; Xavier Barril
Journal:  J Med Chem       Date:  2010-08-12       Impact factor: 7.446

2.  Single-molecule pulling simulations can discern active from inactive enzyme inhibitors.

Authors:  Francesco Colizzi; Remo Perozzo; Leonardo Scapozza; Maurizio Recanatini; Andrea Cavalli
Journal:  J Am Chem Soc       Date:  2010-06-02       Impact factor: 15.419

3.  Drug-like density: a method of quantifying the "bindability" of a protein target based on a very large set of pockets and drug-like ligands from the Protein Data Bank.

Authors:  Robert P Sheridan; Vladimir N Maiorov; M Katharine Holloway; Wendy D Cornell; Ying-Duo Gao
Journal:  J Chem Inf Model       Date:  2010-10-26       Impact factor: 4.956

4.  Toward a Separate Reproduction of the Contributions to the Hartree-Fock and DFT Intermolecular Interaction Energies by Polarizable Molecular Mechanics with the SIBFA Potential.

Authors:  Jean-Philip Piquemal; Hilaire Chevreau; Nohad Gresh
Journal:  J Chem Theory Comput       Date:  2007-05       Impact factor: 6.006

Review 5.  Critical review of the role of HTS in drug discovery.

Authors:  Ricardo Macarron
Journal:  Drug Discov Today       Date:  2006-04       Impact factor: 7.851

6.  Acceleration of a QM/MM-QMC simulation using GPU.

Authors:  Yutaka Uejima; Tomoharu Terashima; Ryo Maezono
Journal:  J Comput Chem       Date:  2011-05-03       Impact factor: 3.376

7.  Solvated interaction energy (SIE) for scoring protein-ligand binding affinities. 2. Benchmark in the CSAR-2010 scoring exercise.

Authors:  Traian Sulea; Qizhi Cui; Enrico O Purisima
Journal:  J Chem Inf Model       Date:  2011-07-13       Impact factor: 4.956

8.  Pyrano[3,2-c]quinoline-6-chlorotacrine hybrids as a novel family of acetylcholinesterase- and beta-amyloid-directed anti-Alzheimer compounds.

Authors:  Pelayo Camps; Xavier Formosa; Carles Galdeano; Diego Muñoz-Torrero; Lorena Ramírez; Elena Gómez; Nicolás Isambert; Rodolfo Lavilla; Albert Badia; M Victòria Clos; Manuela Bartolini; Francesca Mancini; Vincenza Andrisano; Mariana P Arce; M Isabel Rodríguez-Franco; Oscar Huertas; Thomai Dafni; F Javier Luque
Journal:  J Med Chem       Date:  2009-09-10       Impact factor: 7.446

9.  Studying enzyme binding specificity in acetylcholinesterase using a combined molecular dynamics and multiple docking approach.

Authors:  Jeremy Kua; Yingkai Zhang; J Andrew McCammon
Journal:  J Am Chem Soc       Date:  2002-07-17       Impact factor: 15.419

10.  Localized thermodynamic coupling between hydrogen bonding and microenvironment polarity substantially stabilizes proteins.

Authors:  Jianmin Gao; Daryl A Bosco; Evan T Powers; Jeffery W Kelly
Journal:  Nat Struct Mol Biol       Date:  2009-06-14       Impact factor: 15.369

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  5 in total

1.  Docking-undocking combination applied to the D3R Grand Challenge 2015.

Authors:  Sergio Ruiz-Carmona; Xavier Barril
Journal:  J Comput Aided Mol Des       Date:  2016-10-05       Impact factor: 3.686

2.  Multiscale approach to investigate self-assembly of telodendrimer based nanocarriers for anticancer drug delivery.

Authors:  Wenjuan Jiang; Juntao Luo; Shikha Nangia
Journal:  Langmuir       Date:  2015-01-12       Impact factor: 3.882

3.  Molecular Simulation Elaborating the Mechanism of 1β-Hydroxy Alantolactone Inhibiting Ubiquitin-Conjugating Enzyme UbcH5s.

Authors:  Youdong Xu; Xianli Meng
Journal:  Sci Rep       Date:  2020-01-10       Impact factor: 4.379

4.  Identification of 1, 2, 4-Triazine and Its Derivatives Against Lanosterol 14-Demethylase (CYP51) Property of Candida albicans: Influence on the Development of New Antifungal Therapeutic Strategies.

Authors:  Abhishek Kumar Verma; Aarfah Majid; Md Shahadat Hossain; Sk Faisal Ahmed; Mohammad Ashid; Ali Asger Bhojiya; Sudhir K Upadhyay; Naveen Kumar Vishvakarma; Mudassir Alam
Journal:  Front Med Technol       Date:  2022-03-28

5.  Enhanced Monte Carlo Sampling through Replica Exchange with Solute Tempering.

Authors:  Daniel J Cole; Julian Tirado-Rives; William L Jorgensen
Journal:  J Chem Theory Comput       Date:  2014-01-17       Impact factor: 6.006

  5 in total

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