FREE ENERGY CALCULATIONS IN RATIONAL DRUG DESIGN Edited by M Rami Reddy and Mark D Erion Metabasis Therapeutic, Inc San Diego, California Kluwer Academic / Plenum Publishers New York, Boston, Dordrecht, London, Moscow Library of Congress Cataloging-in-Publication Data ISBN: 0-306-46676-7 ©2001 Kluwer Academic/Plenum Publishers, New York 233 Spring Street, New York, N.Y 10013 http://www.wkap.nl/ 10 A C.I.P record for this book is available from the Library of Congress All rights reserved No part of this book may be reproduced, stored in a retrieval system, or transmitted in any form or by any means, electronic, mechanical, photocopying, microfilming, recording, or otherwise, without written permission from the Publisher Printed in the United States of America In Memory of Peter Andrew Kollman, Ph.D (7/26/44 - 5/25/01) Few scientists have had an impact on their chosen research field as much as Peter Kollman on computer-aided molecular modeling and its application to problems in both chemistry and biology Sadly, Peter died in May leaving behind many friends and scientific collaborators from around the world Peter was born in Iowa City, Iowa in 1944 He received his BS in Chemistry from Grinnell College in 1966 and his doctorate from Princeton University in 1970 He spent a year at Cambridge University as a postdoctoral fellow before joining the faculty of the University of California at San Francisco in 1971 At UCSF, Peter rapidly became a well-recognized leader in computational chemistry through his publications and lectures about his numerous insightful discoveries In 1980 he was awarded a full professorship and later he became the Associate Dean for Academic Affairs in the School of Pharmacy During his tenure at the University, Peter trained 17 Ph.D candidates and over 60 post-doctoral fellows as well as a multitude of visiting scholars Peter was instrumental in the design and development of AMBER, a suite of molecular mechanics programs currently used in over 300 laboratories around the world conducting research in the fields of biophysics and pharmaceutical chemistry Using AMBER, Peter and his team showed that free energy calculations provide accurate predictions and valuable insight into reaction mechanisms, protein structure-function and drug design Peter was a unique, vibrant and friendly individual who exhibited enormous enthusiasm for both science and life He will be missed CONTRIBUTORS Atul Agarwal Wyeth-Ayerst Research/AHP 401 N Middletown Rd Pearl River, NY 10965 Krzysztof Appelt Agouron Pharmaceuticals, Inc 3565 General Atomics Ct San Diego, CA 92121 Johan Aqvist Dept of Cell & Molecular Biology Uppsala University Biomedical Center Box 596 SE-751 24 Uppsala, Sweden Shinichi Banba Mitsui Chemical, Inc 580-32 Nagura Sodegaura-City Chiba, Japan 299-0265 J Phillip Bowen Department of Chemistry Computational Center for Molecular Structure and Design University of Georgia Athens, GA 30602 Charles L Brooks, III The Scripps Research Institute Department of MoI Biology 10550 North Torrey Pines Road La Jolla, CA 92037 Frank K Brown R.W Johnson, PRI 1000 Route 202 P.O BOX 300 Raritan, NJ 08869 Christopher J Cramer Department of Chemistry & Supercomputer Institute University of Minnesota Kolthoff and Smith Halls 207 Pleasant Street SE Minneapolis, MN 55455 Peter L Cummins Department of Biochemistry and Molecular Biology John Curtin School of Med Research Australian National University P.O Box 334 Canberra, ACT 2601 Australia Oreola Donini Kinetek Pharmaceuticals, Inc 1779 75th Ave W Vancouver, BC V6P 6P2 Canada Mark D Erion Metabasis Therapeutics, Inc 9390 Towne Centre Drive San Diego, CA 92121 Jill E Gready Department of Biochemistry and Molecular Biology John Curtin School of Med Research Australian National University P.O Box 334 Canberra, ACT 2601 Australia Zhuyan Guo Schering-Plough Research Institute 2000 Galloping Hill Road Kenilworth, NJ 07033 Frederick H Hausheer BioNumerik Pharmaceuticals, Inc 8122Datapoint#1250 San Antonio, TX 78229 Shuanghong Huo Dept of Pharmaceutical Chemistry Univ of California at San Francisco Box 0446, S-924 San Francisco, CA 94143 William L Jorgensen Department of Chemistry Yale University P.O Box 208107 New Haven, CT 06520-8107 J Andrew McCammon Howard Hughes Med Institute Dept of Chemistry & Biochemistry Department of Pharmacology University of California at San Diego 9500 Oilman Drive 0365 La Jolla, CA 92093-0365 David Pearlman Vertex Pharmaceuticals, Inc 130WaverlySt Cambridge, MA 02139 Paul M King School of Biological and Chemical Sciences Birkbeck College 29 Gordon Square London WClH OPP U.K Albert C Pierce Department of Chemistry Yale University P.O Box 208107 New Haven, CT 06520-8107 Peter A Kollman Dept of Pharmaceutical Chemistry Univ of California at San Francisco Box 0446, S-924 San Francisco, CA 94143 Daniel J Price Department of Chemistry Yale University P.O Box 208107 New Haven, CT 06520-8107 Bernd Kuhn Dept of Pharmaceutical Chemistry Univ of California at San Francisco Box 0446, S-924 San Francisco, CA 94143 Melissa L P Price Department of Chemistry Yale University P.O Box 208107 New Haven, CT 06520-8107 Tai-Sung Lee Molecular Simulations, Inc 9685 Scranton Road San Diego, CA 92121 K Ramnarayan ImmunoPharmaceutics, Inc 11011 Via Frontera San Diego, CA 92127 John Marelius Dept of Cell & Molecular Biology Uppsala University Biomedical Center Box 596 SE-751 24 Uppsala, Sweden B Govinda Rao Vertex Pharmaceuticals, Inc 130 Waverly Street Cambridge, MA 02139 M Rami Reddy Metabasis Therapeutics, Inc 9390 Towne Center Drive San Diego, CA 92121 Robert C Rizzo Department of Chemistry Yale University P.O Box 208107 New Haven, CT 06520-8107 Junmei Wang Dept of Pharmaceutical Chemistry Univ of California at San Francisco Box 0446, S-924 San Francisco, CA 94143 Suresh B Singh Merck Research Laboratories P.O Box 2000 Rahway, NJ 07065 Graham A Worth Theoretical Chemistry Dept Chemistry King's College London Strand WC2R 2LS U.K U Chandra Singh AM Technologies, Inc Thornhurst Road San Antonio, TX 78218 Julian Tirado-Rives Department of Chemistry Yale University P.O Box 208107 New Haven, CT 06520-8107 Pat Metthe Todebush Department of Chemistry Computational Center for Molecular Structure and Design University of Georgia Athens, GA 30602 Donald G Truhlar Department of Chemistry & Supercomputer Institute University of Minnesota Kolthoff and Smith Halls 207 Pleasant Street SE Minneapolis, MN 55455 Deping Wang Department of Chemistry Yale University P.O Box 208107 New Haven, CT 06520-8107 Preface The holy grail of structure-based drug design is the design and rapid identification of highly potent and specific enzyme inhibitors using only computational methods and protein structural information to determine ligand binding affinities Success depends upon the accuracy of the calculated binding affinities, which until recently was severely compromised by limitations in computer power and the approximations associated with the force field potential energy equations used to describe the ligand binding energetics Advances in computer speed in the 1990s led to the inclusion of additional terms in the energy equations and ultimately to an increase in calculation accuracy The aim of this book is to provide computational chemists and medicinal chemists with a comprehensive review of the methods used to calculate free energies and of the studies applying these methods to drug design The potential of free energy calculations for predicting inhibitor binding affinities was first realized in 1986 following calculations conducted by Wong and McCammon on two benzamidine inhibitors of trypsin Since then, numerous studies have appeared in the literature demonstrating the value of FEP calculations in predicting ligand binding affinities and identifying molecular factors that influence substrate binding and catalysis J Andrew McCammon's overview of the free energy perturbation (FEP) approach in Chapter one provides a historical perspective for these studies as well as the challenges that lie ahead While the FEP approach remains the method that consistently generates the most accurate free energies, its high CPU requirements and inability to evaluate compounds that differ significantly in structure, clearly limit the impact and value of FEP calculations on drug design Accordingly, efforts are on-going to develop faster methods that have the potential to evaluate large compound libraries semi-quantitatively These methods include the ligand interaction energy approach, ^-dynamics or Chemical Monte Carlo/molecular dynamics (CMC/MD), Molecular Mechanics-Poisson Boltzmann Surface Area (MMPBSA) and ligand interaction scanning With these advances, free energy calculations are becoming more common in the design and analysis of potential drug candidates as evidenced by the exponential increase in the number of studies appearing in the literature over the past 10 years The background theory that underlies the FEP method as well as the molecular mechanics force fields that relate molecular structure to energy are reviewed in section one of the book Section two describes the use of free energy calculations for determining molecular properties of ligands, including solvation, as calculated using both implicit and explicit water models, ionization and tautomerization Section three reviews some of the original calculations that showed that the FEP method produced accurate relative binding free energies for small molecules interacting with macromolecules such as enzymes, as represented by the proteases Thermolysin and Rhizopus pepsin, as well as DNA Section four reviews several alternative methods for estimating ligand binding affinities and how these methods are used in ligand design and analysis The scope and limitations of each method are discussed as well as the advantage of the method relative to FEP Promising results are reported for the linear interaction energy method as well as the MM-PBSA method These methods, as well as methods designed to screen multiple ligands simultaneously or to scan binding site interactions, are expected to enable rapid analysis of the ligand and binding site SAR and therefore to be useful in drug design The final chapter of this section describes the combining of quantum mechanical calculations with molecular mechanics for predicting reaction free energy profiles, which are often useful in drug design since they can provide valuable insight into the enzyme catalytic mechanism, the transition state structure stabilized by the enzyme and possible compounds that could act as high affinity transition state mimetics Studies using free energy calculations for the design and analysis of potential drug candidates are reviewed in section five The chapters in this section cover drug discovery programs targeting fructose 1,6-bisphosphatase (diabetes), COX-2 (inflammation), SRC SH2 domain (osteoporosis and cancer), HTV reverse transcriptase (AIDS), HIV-I protease (AIDS), thymidylate synthase (cancer), dihydrofolate reductase (cancer) and adenosine deaminase (iiximunosuppression, myocardial ischemia) Overall, this book provides for the first time an extensive overview of the scope and limitations of free energy calculations and their application to rational drug design The authors contributing to the book are wellrecognized leaders of this field of research representing academic institutions and pharmaceutical companies located in the U.S., Europe, Australia, and Asia The editors would like to thank the authors for their chapters and their input The editors would also like to thank Ms Lisa Weston and Ms Juliette Jomini for their efforts formatting the chapters and assembling the book Last, we are grateful to Mr Kenneth Howell and Kluwer Academic/Plenum Publishers for their enthusiasm and support for this project Mark D Erion M Kami Reddy June 2001 Contents Contributors vii Preface xi Historical Overview and Future Challenges Introduction Theory and Methods Outstanding Problems Prospects References Section One: Theory Free Energy Calculations: Methods for Estimating Ligand Binding Affinities Introduction Exact Free Energy Calculations 10 Free Energy Calculations in Practice 14 Convergence and Errors 19 Issues and Tricks 22 Choosing Simulation Control 26 Approximate Free Energy Calculations 28 Conclusions 31 References 31 This page has been reformatted by Knovel to provide easier navigation xiii 381 Index terms Links CHELPG 230 Chemical coordinate 197 Chemical Monte Carlo/Molecular Dynamics (CMC/MD) 195 Chemical potential 156 Cimetidine 126 CMIP procedure 303 Collagenase 97 Collective-solvent-coordinate model 80 Conductor-like screening model (COSMO) 325 244 64 α-Chymotrypsin Combinatorial libraries 288 319 81 Conformational sampling 189 Conformational variables 17 Continuum solvent models 64 80 solvation free energies 86 244 generalized Born/surface area (GB/SA) 98 86 217 Convergence profile simulation length 100 101 RMS deviation 290 326 328 Coordinate coupling dihydrofolate reductase 253 solvation free energies 113 theory 261 Coulomb's law 48 Coupling parameter 197 Covalent hydration adenosine deaminase 365 carbonyl compounds 368 free energy calculations 368 inhibitor design 366 heteroaromatic bases 369 pteridine analogues 370 369 371 This page has been reformatted by Knovel to provide easier navigation 373 382 Index terms Links Covalent hydration(Continued) purine riboside 366 369 373 COX, see Cyclooxygenase Cyclooxygenase (COX) binding free energies MC-FEP 304 mutant COX 305 Celecoxib 304 Cytochrome c peroxidase 217 Cytochrome P450-camphor 183 Cytosine 111 D Daunomycin 155 Deaza AMP analogues 232 Dehydroxystatine 150 DELPHI 245 Density functional theory 38 2'-Deoxycoformycin 365 2'-Deoxycytidine 5'-monophosphate 337 2'-Deoxyuridine 5'-monophosphate 337 Desolvation penalty 330 Diabetes 229 Dielectric constant 47 Dielectric descreening 81 7,8-Dihydrofolate tautomeric equilibrium 254 285 255 255 Dihydrofolate reductase (DHFR) binding free energy calculations 149 197 337 367 catalytic mechanism 254 276 dipole moment effects 265 290 359 This page has been reformatted by Knovel to provide easier navigation 301 329 383 Index terms Links Dihydrofolate reductase (DHFR) (Continued) hydride transfer free energy profile 270 protein interactions 272 hydrophobic hydration 355 inhibitors 343 linear interaction energy calculations 180 linear response approximation 354 mechanism-based substrates 344 346 proton transfer free energy profile 264 substrate interactions 268 QM/MM 259 solvent role 356 8-substituted deazapterins 344 346 355 8-substituted-pterin substrates 344 346 355 transition state 254 258 266 Dipole moment 48 51 265 Dipole-dipole interactions 47 Dispersion 83 163 164 Dissociation constants 231 Distamycin 155 DOCKing 248 Double topology 98 Double-wide sampling 20 321 DNA-ligand complex acridine 155 anthracycline antibiotics 155 DAPI 155 daunomycin 155 distamycin 155 ethidium 155 free energy calculations 158 163 This page has been reformatted by Knovel to provide easier navigation 271 165 384 Index terms Links DNA-ligand complex (Continued) Hoechst 33258 155 netropsin 159 DNA minor groove 155 162 Drug resistance 161 162 310 Dynamically Modified Windows (DMW) 22 E Electrostatics coefficients 175 179 180 decoupling 24 106 261 free energy 262 Poisson-Boltzmann equation 30 Empirical scoring methods 172 Endothiapepsin 143 inhibitors 28 Energy distribution method 175 14 Enthalpy calculation of 16 74 30 200 202 246 248 307 Entropy calculation of conformational 249 translational 248 rotational 248 vibrational 248 Equilibrium modeling 79 Error estimation 328 ESP fitted atomic partial charges 107 Ewald summation 124 Exchange repulsion 83 This page has been reformatted by Knovel to provide easier navigation 213 244 385 Index terms Explicit Solvent Models Links 97 TIP3P 98 SPC/E 98 F Fatty acid binding protein 181 FKBP 303 Floating independent reference frame (FIRF) 201 Fluorine scanning 202 5-Fluoro-2'deoxyuridylate monophosphate (FdUMP) 336 Force fields, Molecular Mechanics AMBER 41 CFF 41 CHARMM 41 GALAXY 259 GROMOS 175 MM3 41 MMFF 41 OPLS 41 Formycin A monophosphate 295 10-Formyl-5,8-dideazafolic acid (FDDF) 336 245 259 109 300 Free energy calculations, see also covalent hydration; linear interaction energy; lambda dynamics; ligand scanning; MM/PBSA; adenosine deaminase 373 cyclooxygenase 304 dihydrofolate reductase 258 DNA complexes 159 fructose 1,6-bisphosphatase 291 high throughput methods 172 HIV-1 protease 324 HIV reverse transcriptase 308 overview 345 200 226 10 This page has been reformatted by Knovel to provide easier navigation 243 386 Index terms Links Free energy calculations (Continued) pepsin 150 solvation 86 SRC SH2 domain 306 tautomerisation 122 thermolysin 144 thrombin 312 thymidylate synthase 338 Free energy decoupling 261 Free energy grid 100 29 Free energy perturbation (FEP), convergence 14 19 error estimation 19 329 historical overview method 13 outstanding problems theory 10 validation 197 319 322 Free energy profile 259 Fructose 1,6-bisphosphatase 285 289 AMP mimetic design 229 291 binding free energies 231 236 ligand scanning 228 287 G GALAXY program 259 Generalized Born/Surface Area (GB/SA) 98 Generalized Born model 81 Debye-Hückel modification 214 82 Ghost forces 210 Gluconeogenesis 285 GROMOS program 175 Guanine 111 128 This page has been reformatted by Knovel to provide easier navigation 290 292 387 Index terms Links H H2 receptor 126 Hellmann-Feynman theorem 83 Henry's law 69 Heteroaromatic hydration 369 Histamine 126 HIV-1 protease 146 175 317 drug design 317 324 330 free energy calculations 319 324 327 330 inhibitors 321 322 324 328 244 299 308 HIV reverse transcriptase drug resistance 310 HEPT 308 mutants 310 non-nucleoside inhibitors 308 TIBO analogues 218 Holonomic constraints Homology models Hook's law 329 309 308 310 311 227 229 232 229 234 238 18 143 42 Hydration free energy 123 see also covalent hydration Hydrogen bond 226 234 Acceptor 233 donor 232 strength 226 Hydrophobic free energy 175 Hydrophobic hydration 355 2-(4'-Hydroxyazobenzene) benzoic acid (HABA) 246 Hydroxyethylamine (Hea)-based inhibitor 144 Hypertension 146 323 This page has been reformatted by Knovel to provide easier navigation 233 388 Index terms Links I Ideal mixtures 66 Ideal solution 72 2-Imidazole distamycin 157 IMPACT program 108 Ionisation 123 weak acids and bases 304 131 J Jacobian factor Jean's equation 47 JG365 323 K K+-18-crown-6 complex 176 Knowledge-based scoring approaches 172 L Lambda dynamics continuum solvent 214 cytochrome c peroxidase 217 HIV reverse transcriptase 218 multiple ligand screening 195 multiple topology model 209 non-linear lambda scaling 26 pathway 216 sampling 205 theory 203 trypsin 217 Ligand interaction map 227 200 203 237 Ligand scanning AMP analogues 232 This page has been reformatted by Knovel to provide easier navigation 205 389 Index terms Links Ligand scanning (Continued) computational details 230 drug design 238 fructose 1,6-bisphosphatase 229 relative binding affinity 231 Ligand screening lambda dynamics 203 ligand interaction energies 238 ligand interaction scanning 225 239 (LIA) 182 200 continuum solvent 202 Linear Interaction Approximation Linear Interaction Energy (LIE) 28 accessible surface area 201 COX inhibitors 304 18-crown-6 176 DHFR inhibitors 180 endothiapepsin 175 FKBP12 183 free energies of hydration 302 HIV protease 182 HIV reverse transcriptase 308 mutants 173 243 310 LIE/SA 175 302 303 linear response approximation 173 182 354 Monte Carlo simulations 303 retinol binding protein 181 scoring 171 177 189 SRC SH2 domain 306 theory 173 thrombin 184 trypsin 175 312 This page has been reformatted by Knovel to provide easier navigation 302 390 Index terms Links Local density function (LDF) approach 254 Lysine binding protein 181 Lysozyme 182 M Matador 304 Matrix metalloproteinase (MMP) 244 MCPRO program 301 Methotrexate (MTX) 130 181 9-Methylpurine 372 375 MM3 program 41 51 Model validation 289 Molecular electrostatic potential (MEP) 347 253 Molecular mechanics, see also Force fields, angle bending 43 bond polarization 48 bond stretching 42 cross term function 48 dipole terms 47 electrostatic 47 hydrogen-bonding interactions 46 Lennard-Jones 6-12 potential 45 London dispersion forces 45 non-bonded interactions 44 overview 39 parameterization 50 torsion 46 288 Molecular-mechanics with Possion-Boltzmann/surface area approach (MM/PBSA) 202 avidin-biotin complexes 249 cathepsin D inhibitors 246 244 This page has been reformatted by Knovel to provide easier navigation 335 343 391 Index terms Links Molecular-mechanics with Possion-Boltzmann/surface area approach (MM/PBSA) (Continued) HIV RT inhibitors 248 MMP inhibitors 246 theory 244 Monte Carlo ensemble average sampling Multiple ligand screening methods 105 299 112 300 301 205 see also Chemical Monte Carlo/molecular dynamics; Lambda dynamics Multiple topology method Multipole expansion 209 82 N Netropsin, see DNA-ligand complex Neuraminidase 190 Nevirapine 309 Nicotinic acid 135 Non-additivity 338 Nonequilibrium solvation effects 87 Nonequilibrium properties 87 Nonideal solution 68 Non-linear Poisson-Boltzmann model Non-linear λ scaling 156 26 Non-steroidal anti-inflammatory drugs (NSAIDs) 304 Nucleic acid bases 111 P Parallelization PARSE radii 245 Particle insertion method Pepsin, Rhizopus free energy calculations 14 143 146 150 This page has been reformatted by Knovel to provide easier navigation 392 Index terms Links Pepsin, Rhizopus (Continued) inhibitors 149 mutation 147 Pepstatin 149 Phosphoramidate 144 Pictorial Representation of Free Energy Components (PROFEC) 201 339 30 Polarizable continuum model (PCM) 82 136 Potential energy surfaces 40 Potential of Mean Forces (PMF) 17 Poisson-Boltzmann equation 10-Propargyl-5,8-dideazafolic acid (PDDF) 336 Pteridine 370 Purine nucleoside phosphorylase 227 Purine riboside hydration 369 82 371 Q Quantum Mechanics ab initio 38 55 Hartree-Fock theory 52 245 Moller-Plesset corrections 52 368 255 259 Quantum Mechanics/Molecular Mechanics (QM/MM) dihydrofolate reductase 254 coordinate coupling 261 Quasi-harmonic analysis 248 QUEST program 147 368 R Rapamycin 184 Reaction field methods 80 Regression methods 319 Relative inhibitory potency 373 Renin 143 88 This page has been reformatted by Knovel to provide easier navigation 393 Index terms Links Residue-based cutoff radii 347 Resonance energy 376 Restrained electrostatic potential (RESP) 245 Retinol binding protein 181 335 Rhizopus Pepsin, see Pepsin S Sampling Schrodinger equation Screening virtual libraries Self-consistent reaction field 38 172 81 Semi-empirical quantum mechanics AM1 38 MNDO 38 PM3 38 Single topology 349 320 Slow growth method 13 Solubility 77 159 Solvation, absolute free energy convergence 98 108 112 99 369 100 explicit solvent models nucleic acid 98 111 relative free energy simulation length theory 97 100 74 Solvent accessible surface area 244 Solvent descriptors 84 Solvent/solute partitioning models 85 SRC SH2 domain 306 This page has been reformatted by Knovel to provide easier navigation 394 Index terms Statistical mechanics Links 64 free energy 79 models 64 theory Streptavidin-biotin 156 Structure-function studies 225 Subtilisin 225 Surface curvature Sustiva 84 308 T Tautomerism DNA bases 128 formycin A 129 free energy calculations 121 long range forces 134 sampling 135 solvent 138 guanine 119 heterocycles 126 histamine 126 134 imidazole 126 132 nicotinic acid 128 135 2-oxopyrimidine 129 triazole 127 Tethered water (TW) model 357 Tetraazanaphthalene 370 Thermodynamic integration method Thermolysin 128 133 134 12 143 binding free energy 145 Thread methodology 98 290 321 This page has been reformatted by Knovel to provide easier navigation 372 395 Index terms Thrombin Links 184 299 binding pocket 312 LIE analysis 183 312 130 335 binding free energy calculations 336 337 inhibitor design 340 non-additivity 338 TIBO analogues 247 308 Transition state 257 366 Trapezoidal rule 13 Thymidylate synthase Trimethoprim 350 Trypsin 175 217 Umbrella sampling 18 198 United-atom Hartree-Fock model (UHF) 83 312 339 U V Virtual bonds 374 W Weighted histogram analysis methods (WHAM) Window statistics 14 199 328 X XchemEdit program 303 Z Zinc ion constraints 374 ZMP 289 This page has been reformatted by Knovel to provide easier navigation 340 ... free energies and of the studies applying these methods to drug design The potential of free energy calculations for predicting inhibitor binding affinities was first realized in 1986 following... Interaction Scanning Using Free Energy Calculations 225 Introduction 225 Interaction Scanning Using Free Energy Calculations 228 Scanning the AMP Binding Site of FBPase ... Calculations: Methods for Estimating Ligand Binding Affinities Introduction Exact Free Energy Calculations 10 Free Energy Calculations in Practice 14 Convergence