Role of Ligand Reorganization and Conformational Restraints on the Binding Free Energies of DAPY Non-Nucleoside Inhibitors to HIV Reverse Transcriptase.

The results of computer simulations of the binding of etravirine (TMC125) and rilpivirine (TMC278) to HIV reverse transcriptase are reported. It is confirmed that consistent binding free energy estimates are obtained with or without the application of torsional restraints when the free energies of imposing the restraints are taken into account. The restraints have a smaller influence on the thermodynamics and apparent kinetics of binding of TMC125 compared to the more flexible TMC278 inhibitor. The concept of the reorganization free energy of binding is useful to understand and categorize these effects. Contrary to expectations, the use of conformational restraints did not consistently enhance convergence of binding free energy estimates due to suppression of binding/unbinding pathways and due to the influence of rotational degrees of freedom not directly controlled by the restraints. Physical insights concerning the thermodynamic driving forces for binding and the role of "jiggling" and "wiggling" motion of the ligands are discussed. Based on these insights we conclude that an ideal inhibitor, if chemically realizable, would possess the electrostatic charge distribution of TMC125, so as to form strong interactions with the receptor, and the larger and more flexible substituents of TMC278, so as to minimize reorganization free energy penalties and the effects of resistance mutations, suitably modified, as in TMC125, so as to disfavor the formation of non-binding competent extended conformations when free in solution.

[1]  W. L. Jorgensen,et al.  Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids , 1996 .

[2]  M. Gilson,et al.  Ligand configurational entropy and protein binding , 2007, Proceedings of the National Academy of Sciences.

[3]  K. Dill,et al.  On the use of orientational restraints and symmetry corrections in alchemical free energy calculations. , 2006, The Journal of chemical physics.

[4]  Alexander D. MacKerell,et al.  Computational evaluation of protein-small molecule binding. , 2009, Current opinion in structural biology.

[5]  Emilio Gallicchio,et al.  Advances in all atom sampling methods for modeling protein-ligand binding affinities. , 2011, Current opinion in structural biology.

[6]  Alexander McPherson,et al.  Advances in Protein Chemistry and Structural Biology , 2010, Advances in Protein Chemistry and Structural Biology.

[7]  Heidi Joshi,et al.  What You See Is Not Always What You Get , 2008 .

[8]  Koen Andries,et al.  TMC125, a Novel Next-Generation Nonnucleoside Reverse Transcriptase Inhibitor Active against Nonnucleoside Reverse Transcriptase Inhibitor-Resistant Human Immunodeficiency Virus Type 1 , 2004, Antimicrobial Agents and Chemotherapy.

[9]  Emilio Gallicchio,et al.  The AGBNP2 Implicit Solvation Model. , 2009, Journal of chemical theory and computation.

[10]  B. Roux,et al.  Computations of standard binding free energies with molecular dynamics simulations. , 2009, The journal of physical chemistry. B.

[11]  Michael R. Shirts,et al.  Statistically optimal analysis of samples from multiple equilibrium states. , 2008, The Journal of chemical physics.

[12]  Stephen F Martin,et al.  Thermodynamic and structural effects of conformational constraints in protein-ligand interactions. Entropic paradoxy associated with ligand preorganization. , 2009, Journal of the American Chemical Society.

[13]  Stephen H Hughes,et al.  In search of a novel anti-HIV drug: multidisciplinary coordination in the discovery of 4-[[4-[[4-[(1E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2- pyrimidinyl]amino]benzonitrile (R278474, rilpivirine). , 2005, Journal of medicinal chemistry.

[14]  M. Gilson,et al.  Calculation of protein-ligand binding affinities. , 2007, Annual review of biophysics and biomolecular structure.

[15]  P. Procacci,et al.  Intraligand hydrophobic interactions rationalize drug affinities for peptidyl-prolyl cis-trans isomerase protein. , 2011, The journal of physical chemistry. B.

[16]  Helmut Grubmüller,et al.  Linear‐scaling soft‐core scheme for alchemical free energy calculations , 2011, J. Comput. Chem..

[17]  Tjelvar S. G. Olsson,et al.  The good, the bad and the twisted: a survey of ligand geometry in protein crystal structures , 2012, Journal of Computer-Aided Molecular Design.

[18]  Emilio Gallicchio,et al.  The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities. , 2010, Journal of chemical theory and computation.

[19]  Richard A. Friesner,et al.  Integrated Modeling Program, Applied Chemical Theory (IMPACT) , 2005, J. Comput. Chem..

[20]  Emilio Gallicchio,et al.  Recent theoretical and computational advances for modeling protein-ligand binding affinities. , 2011, Advances in protein chemistry and structural biology.

[21]  Ronald M. Levy,et al.  Conformational populations of ligand‐sized molecules by replica exchange molecular dynamics and temperature reweighting , 2009, J. Comput. Chem..

[22]  Paul J Lewi,et al.  Concentration and pH dependent aggregation of hydrophobic drug molecules and relevance to oral bioavailability. , 2005, Journal of medicinal chemistry.

[23]  J Desmyter,et al.  Rapid and automated tetrazolium-based colorimetric assay for the detection of anti-HIV compounds. , 1988, Journal of virological methods.

[24]  R. Friesner,et al.  Evaluation and Reparametrization of the OPLS-AA Force Field for Proteins via Comparison with Accurate Quantum Chemical Calculations on Peptides† , 2001 .

[25]  David L. Mobley,et al.  Let’s get honest about sampling , 2011, Journal of Computer-Aided Molecular Design.

[26]  M. Gilson,et al.  The statistical-thermodynamic basis for computation of binding affinities: a critical review. , 1997, Biophysical journal.

[27]  Y. Frenkel.  The roles of structural variability and amphiphilicity of TMC278/rilpivirine in mechanisms of HIV drug resistance avoidance and enhanced oral bioavailability , 2009 .

[28]  Xiaohong Liu,et al.  Crystal structures of HIV-1 reverse transcriptase with etravirine (TMC125) and rilpivirine (TMC278): implications for drug design. , 2010, Journal of medicinal chemistry.

[29]  P. Charifson,et al.  Conformational analysis of drug-like molecules bound to proteins: an extensive study of ligand reorganization upon binding. , 2004, Journal of medicinal chemistry.

[30]  W. L. Jorgensen.  The Many Roles of Computation in Drug Discovery , 2004, Science.

[31]  J. Straub,et al.  Generalized simulated tempering for exploring strong phase transitions. , 2010, The Journal of chemical physics.

[32]  David L. Mobley,et al.  Chapter 4 Alchemical Free Energy Calculations: Ready for Prime Time? , 2007 .

[33]  S. Menichetti,et al.  New Perspective on How and Why Immunophilin FK506-Related Ligands Work , 2011 .

[34]  Stephen H Hughes,et al.  High-resolution structures of HIV-1 reverse transcriptase/TMC278 complexes: Strategic flexibility explains potency against resistance mutations , 2008, Proceedings of the National Academy of Sciences.

[35]  R. Levy,et al.  Antigenic characteristics of rhinovirus chimeras designed in silico for enhanced presentation of HIV-1 gp41 epitopes [corrected]. , 2010, Journal of molecular biology.

[36]  Ronald M. Levy,et al.  Prediction of SAMPL3 host-guest affinities with the binding energy distribution analysis method (BEDAM) , 2012, Journal of Computer-Aided Molecular Design.

[37]  Ronald M. Levy,et al.  AGBNP: An analytic implicit solvent model suitable for molecular dynamics simulations and high‐resolution modeling , 2004, J. Comput. Chem..

[38]  Chao-Yie Yang,et al.  Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction. , 2009, Journal of the American Chemical Society.

[39]  Stephen H Hughes,et al.  Crystallography and the design of anti-AIDS drugs: conformational flexibility and positional adaptability are important in the design of non-nucleoside HIV-1 reverse transcriptase inhibitors. , 2005, Progress in biophysics and molecular biology.

[40]  Enhancing QM/MM molecular dynamics sampling in explicit environments via an orthogonal-space-random-walk-based strategy. , 2011, The journal of physical chemistry. B.

[41]  David L Mobley,et al.  The Confine-and-Release Method: Obtaining Correct Binding Free Energies in the Presence of Protein Conformational Change. , 2007, Journal of chemical theory and computation.

[42]  K. Dill,et al.  Binding of small-molecule ligands to proteins: "what you see" is not always "what you get". , 2009, Structure.

[43]  Emilio Gallicchio,et al.  Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations. , 2012, Journal of chemical theory and computation.

[44]  Cen Gao,et al.  Accounting for ligand conformational restriction in calculations of protein-ligand binding affinities. , 2010, Biophysical journal.

[45]  Michael K Gilson,et al.  On the theory of noncovalent binding. , 2004, Biophysical journal.

[46]  Emilio Gallicchio,et al.  In silico vaccine design based on molecular simulations of rhinovirus chimeras presenting HIV-1 gp41 epitopes. , 2009, Journal of molecular biology.

[47]  David L Mobley,et al.  Alchemical free energy methods for drug discovery: progress and challenges. , 2011, Current opinion in structural biology.

[48]  H. M. Vinkers,et al.  Roles of conformational and positional adaptability in structure-based design of TMC125-R165335 (etravirine) and related non-nucleoside reverse transcriptase inhibitors that are highly potent and effective against wild-type and drug-resistant HIV-1 variants. , 2004, Journal of medicinal chemistry.

[49]  Emilio Gallicchio,et al.  Molecular dynamics study of non-nucleoside reverse transcriptase inhibitor 4-[[4-[[4-[(E)-2-cyanoethenyl]-2,6-dimethylphenyl]amino]-2-pyrimidinyl]amino]benzonitrile (TMC278/rilpivirine) aggregates: correlation between amphiphilic properties of the drug and oral bioavailability. , 2009, Journal of medicinal chemistry.