Literature DB >> 22458502

Thermodynamic studies for drug design and screening.

Nichola C Garbett1, Jonathan B Chaires.   

Abstract

INTRODUCTION: A key part of drug design and development is the optimization of molecular interactions between an engineered drug candidate and its binding target. Thermodynamic characterization provides information about the balance of energetic forces driving binding interactions and is essential for understanding and optimizing molecular interactions. AREAS COVERED: This review discusses the information that can be obtained from thermodynamic measurements and how this can be applied to the drug development process. Current approaches for the measurement and optimization of thermodynamic parameters are presented, specifically higher throughput and calorimetric methods. Relevant literature for this review was identified in part by bibliographic searches for the period 2004 - 2011 using the Science Citation Index and PUBMED and the keywords listed below. EXPERT OPINION: The most effective drug design and development platform comes from an integrated process utilizing all available information from structural, thermodynamic and biological studies. Continuing evolution in our understanding of the energetic basis of molecular interactions and advances in thermodynamic methods for widespread application are essential to realize the goal of thermodynamically driven drug design. Comprehensive thermodynamic evaluation is vital early in the drug development process to speed drug development toward an optimal energetic interaction profile while retaining good pharmacological properties. Practical thermodynamic approaches, such as enthalpic optimization, thermodynamic optimization plots and the enthalpic efficiency index, have now matured to provide proven utility in the design process. Improved throughput in calorimetric methods remains essential for even greater integration of thermodynamics into drug design.
© 2012 Informa UK, Ltd.

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Year:  2012        PMID: 22458502      PMCID: PMC3496183          DOI: 10.1517/17460441.2012.666235

Source DB:  PubMed          Journal:  Expert Opin Drug Discov        ISSN: 1746-0441            Impact factor:   6.098


  41 in total

1.  Enthalpy arrays.

Authors:  Francisco E Torres; Peter Kuhn; Dirk De Bruyker; Alan G Bell; Michal V Wolkin; Eric Peeters; James R Williamson; Gregory B Anderson; Gregory P Schmitz; Michael I Recht; Sandra Schweizer; Lincoln G Scott; Jackson H Ho; Scott A Elrod; Peter G Schultz; Richard A Lerner; Richard H Bruce
Journal:  Proc Natl Acad Sci U S A       Date:  2004-06-21       Impact factor: 11.205

2.  Thermodynamics: the world is flat.

Authors:  Harald Schwalbe; Jörg Rinnenthal
Journal:  Nat Chem Biol       Date:  2010-05       Impact factor: 15.040

3.  Energetic basis of molecular recognition in a DNA aptamer.

Authors:  G Reid Bishop; Jinsong Ren; Brandon C Polander; Benjamin D Jeanfreau; John O Trent; Jonathan B Chaires
Journal:  Biophys Chem       Date:  2006-08-17       Impact factor: 2.352

4.  Overcoming roadblocks in lead optimization: a thermodynamic perspective.

Authors:  Adam J Ruben; Yoshiaki Kiso; Ernesto Freire
Journal:  Chem Biol Drug Des       Date:  2006-01       Impact factor: 2.817

Review 5.  Adding calorimetric data to decision making in lead discovery: a hot tip.

Authors:  John E Ladbury; Gerhard Klebe; Ernesto Freire
Journal:  Nat Rev Drug Discov       Date:  2009-12-04       Impact factor: 84.694

Review 6.  Improving drug candidates by design: a focus on physicochemical properties as a means of improving compound disposition and safety.

Authors:  Nicholas A Meanwell
Journal:  Chem Res Toxicol       Date:  2011-07-26       Impact factor: 3.739

7.  Thermodynamic optimisation in drug discovery: a case study using carbonic anhydrase inhibitors.

Authors:  Andrew D Scott; Chris Phillips; Alexander Alex; Maria Flocco; Andrew Bent; Amy Randall; Ronan O'Brien; Luminita Damian; Lyn H Jones
Journal:  ChemMedChem       Date:  2009-12       Impact factor: 3.466

8.  Theoretical calculations of the helix-coil transition of DNA in the presence of large, cooperatively binding ligands.

Authors:  J D McGhee
Journal:  Biopolymers       Date:  1976-07       Impact factor: 2.505

9.  Possible origin of differences between van't Hoff and calorimetric enthalpy estimates.

Authors:  J B Chaires
Journal:  Biophys Chem       Date:  1997-02-28       Impact factor: 2.352

10.  Thermodynamics of ligand binding and efficiency.

Authors:  Charles H Reynolds; M Katharine Holloway
Journal:  ACS Med Chem Lett       Date:  2011-03-23       Impact factor: 4.345

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  28 in total

1.  Protein-ligand binding enthalpies from near-millisecond simulations: Analysis of a preorganization paradox.

Authors:  Amanda Li; Michael K Gilson
Journal:  J Chem Phys       Date:  2018-08-21       Impact factor: 3.488

2.  Discovery of a Cyclic Choline Analog That Inhibits Anaerobic Choline Metabolism by Human Gut Bacteria.

Authors:  Maud Bollenbach; Manuel Ortega; Marina Orman; Catherine L Drennan; Emily P Balskus
Journal:  ACS Med Chem Lett       Date:  2020-03-25       Impact factor: 4.345

3.  Measuring Biomolecular DSC Profiles with Thermolabile Ligands to Rapidly Characterize Folding and Binding Interactions.

Authors:  Robert W Harkness V; Philip E Johnson; Anthony K Mittermaier
Journal:  J Vis Exp       Date:  2017-11-21       Impact factor: 1.355

4.  Structural modification of aspirin to design a new potential cyclooxygenase (COX-2) inhibitors.

Authors:  Monir Uzzaman; Tareq Mahmud
Journal:  In Silico Pharmacol       Date:  2020-03-04

Review 5.  Recent developments in the use of differential scanning fluorometry in protein and small molecule discovery and characterization.

Authors:  Anton Simeonov
Journal:  Expert Opin Drug Discov       Date:  2013-06-06       Impact factor: 6.098

6.  Modeling complex equilibria in isothermal titration calorimetry experiments: thermodynamic parameters estimation for a three-binding-site model.

Authors:  Vu H Le; Robert Buscaglia; Jonathan B Chaires; Edwin A Lewis
Journal:  Anal Biochem       Date:  2012-12-19       Impact factor: 3.365

7.  Self-Consistent Framework Connecting Experimental Proxies of Protein Dynamics with Configurational Entropy.

Authors:  Markus Fleck; Anton A Polyansky; Bojan Zagrovic
Journal:  J Chem Theory Comput       Date:  2018-06-08       Impact factor: 6.578

8.  Comparative structural and functional studies of 4-(thiazol-5-yl)-2-(phenylamino)pyrimidine-5-carbonitrile CDK9 inhibitors suggest the basis for isotype selectivity.

Authors:  Alison J Hole; Sonja Baumli; Hao Shao; Shenhua Shi; Shiliang Huang; Chris Pepper; Peter M Fischer; Shudong Wang; Jane A Endicott; Martin E Noble
Journal:  J Med Chem       Date:  2013-01-29       Impact factor: 7.446

9.  Effect of G-quadruplex polymorphism on the recognition of telomeric DNA by a metal complex.

Authors:  Caterina Musetti; A Paul Krapcho; Manlio Palumbo; Claudia Sissi
Journal:  PLoS One       Date:  2013-03-13       Impact factor: 3.240

10.  Thermodynamic studies of a series of homologous HIV-1 TAR RNA ligands reveal that loose binders are stronger Tat competitors than tight ones.

Authors:  Lise Pascale; Stéphane Azoulay; Audrey Di Giorgio; Laura Zenacker; Marc Gaysinski; Pascal Clayette; Nadia Patino
Journal:  Nucleic Acids Res       Date:  2013-04-19       Impact factor: 16.971

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