Hot spots in protein-protein interfaces: towards drug discovery.

Identification of drug-like small molecules that alter protein-protein interactions might be a key step in drug discovery. However, it is very challenging to find such molecules that target interface regions in protein complexes. Recent findings indicate that such molecules usually target specifically energetically favored residues (hot spots) in protein-protein interfaces. These residues contribute to the stability of protein-protein complexes. Computational prediction of hot spots on bound and unbound structures might be useful to find druggable sites on target interfaces. We review the recent advances in computational hot spot prediction methods in the first part of the review and then provide examples on how hot spots might be crucial in drug design.

[1]  R E Hubbard,et al.  Locating interaction sites on proteins: The crystal structure of thermolysin soaked in 2% to 100% isopropanol , 1999, Proteins.

[2]  David C Fry,et al.  Small-molecule inhibitors of protein-protein interactions: how to mimic a protein partner. , 2012, Current pharmaceutical design.

[3]  Ozlem Keskin,et al.  Analysis and network representation of hotspots in protein interfaces using minimum cut trees , 2010, Proteins.

[4]  Haruki Nakamura,et al.  The worldwide Protein Data Bank (wwPDB): ensuring a single, uniform archive of PDB data , 2006, Nucleic Acids Res..

[5]  Peter A. Kollman,et al.  Computational alanine scanning of the 1:1 human growth hormone–receptor complex , 2002, J. Comput. Chem..

[6]  Massimiliano Pontil,et al.  Prediction of hot spot residues at protein-protein interfaces by combining machine learning and energy-based methods , 2009, BMC Bioinformatics.

[7]  Michelle R Arkin,et al.  Discovery of a potent small molecule IL-2 inhibitor through fragment assembly. , 2003, Journal of the American Chemical Society.

[8]  B. Villoutreix,et al.  A leap into the chemical space of protein-protein interaction inhibitors. , 2012, Current pharmaceutical design.

[9]  Luhua Lai,et al.  Nonnatural protein–protein interaction-pair design by key residues grafting , 2007, Proceedings of the National Academy of Sciences.

[10]  Mieczyslaw Torchala,et al.  Characterizing Changes in the Rate of Protein-Protein Dissociation upon Interface Mutation Using Hotspot Energy and Organization , 2013, PLoS Comput. Biol..

[11]  Ozlem Keskin,et al.  HotSprint: database of computational hot spots in protein interfaces , 2007, Nucleic Acids Res..

[12]  P. Bamborough,et al.  Discovery and characterization of small molecule inhibitors of the BET family bromodomains. , 2011, Journal of medicinal chemistry.

[13]  O. Dym,et al.  The modular architecture of protein-protein binding interfaces. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[14]  Pedro A Fernandes,et al.  Hot spots—A review of the protein–protein interface determinant amino‐acid residues , 2007, Proteins.

[15]  Jinyan Li,et al.  ‘Double water exclusion’: a hypothesis refining the O-ring theory for the hot spots at protein interfaces , 2009, Bioinform..

[16]  A. Bogan,et al.  Anatomy of hot spots in protein interfaces. , 1998, Journal of molecular biology.

[17]  David Ryan Koes,et al.  Small-molecule inhibitor starting points learned from protein–protein interaction inhibitor structure , 2011, Bioinform..

[18]  Ozlem Keskin,et al.  Identification of computational hot spots in protein interfaces: combining solvent accessibility and inter-residue potentials improves the accuracy , 2009, Bioinform..

[19]  Ozlem Keskin,et al.  Protein-protein interfaces integrated into interaction networks: implications on drug design. , 2012, Current pharmaceutical design.

[20]  Christopher L. McClendon,et al.  Reaching for high-hanging fruit in drug discovery at protein–protein interfaces , 2007, Nature.

[21]  L. Lai,et al.  Towards structure-based protein drug design. , 2011, Biochemical Society transactions.

[22]  Gilles Marcou,et al.  Hot-Spots-Guided Receptor-Based Pharmacophores (HS-Pharm): A Knowledge-Based Approach to Identify Ligand-Anchoring Atoms in Protein Cavities and Prioritize Structure-Based Pharmacophores , 2008, J. Chem. Inf. Model..

[23]  Ozlem Keskin,et al.  Restricted mobility of conserved residues in protein-protein interfaces in molecular simulations. , 2008, Biophysical journal.

[24]  Ozlem Keskin,et al.  Integrating Structure to Protein-Protein Interaction Networks That Drive Metastasis to Brain and Lung in Breast Cancer , 2013, PloS one.

[25]  Pedro Alexandrino Fernandes,et al.  Computational alanine scanning mutagenesis—An improved methodological approach , 2007, J. Comput. Chem..

[26]  Harry Jubb,et al.  Structural biology and drug discovery for protein-protein interactions. , 2012, Trends in pharmacological sciences.

[27]  Philip M. Kim,et al.  Relating Three-Dimensional Structures to Protein Networks Provides Evolutionary Insights , 2006, Science.

[28]  S. Vajda,et al.  Anchor residues in protein-protein interactions. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[29]  D. Ringe,et al.  Locating and characterizing binding sites on proteins , 1996, Nature Biotechnology.

[30]  David E. Kim,et al.  Computational Alanine Scanning of Protein-Protein Interfaces , 2004, Science's STKE.

[31]  Ozlem Keskin,et al.  HotPoint: hot spot prediction server for protein interfaces , 2010, Nucleic Acids Res..

[32]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[33]  P. Chakrabarti,et al.  Conservation and relative importance of residues across protein-protein interfaces , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[34]  Ozlem Keskin,et al.  Analysis of Hot Region Organization in Hub Proteins , 2010, Annals of Biomedical Engineering.

[35]  Nir London,et al.  Druggable protein-protein interactions--from hot spots to hot segments. , 2013, Current opinion in chemical biology.

[36]  Michael A. Newton,et al.  Mutations in Protein-Binding Hot-Spots on the Hub Protein Smad3 Differentially Affect Its Protein Interactions and Smad3-Regulated Gene Expression , 2011, PloS one.

[37]  Julie C. Mitchell,et al.  KFC2: A knowledge‐based hot spot prediction method based on interface solvation, atomic density, and plasticity features , 2011, Proteins.

[38]  A. Panchenko,et al.  Phosphorylation in protein-protein binding: effect on stability and function. , 2011, Structure.

[39]  Dima Kozakov,et al.  Relationship between Hot Spot Residues and Ligand Binding Hot Spots in Protein-Protein Interfaces , 2012, J. Chem. Inf. Model..

[40]  Holger Gohlke,et al.  DrugScorePPI webserver: fast and accurate in silico alanine scanning for scoring protein–protein interactions , 2010, Nucleic Acids Res..

[41]  D. Baker,et al.  The structural and energetic basis for high selectivity in a high-affinity protein-protein interaction , 2010, Proceedings of the National Academy of Sciences.

[42]  Hong Ma,et al.  A small molecule inhibitor of beta-catenin/CREB-binding protein transcription [corrected]. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[43]  M. Sternberg,et al.  Protein–protein interaction sites are hot spots for disease‐associated nonsynonymous SNPs , 2012, Human mutation.

[44]  R. Nussinov,et al.  Allosteric post-translational modification codes. , 2012, Trends in biochemical sciences.

[45]  R. Nussinov,et al.  Non-Redundant Unique Interface Structures as Templates for Modeling Protein Interactions , 2014, PloS one.

[46]  Antonín Pavelka,et al.  HotSpot Wizard: a web server for protein engineering , 2009 .

[47]  David Jou,et al.  Fragment-based drug design and drug repositioning using multiple ligand simultaneous docking (MLSD): identifying celecoxib and template compounds as novel inhibitors of signal transducer and activator of transcription 3 (STAT3). , 2011, Journal of medicinal chemistry.

[48]  M. Vidal,et al.  Edgetic perturbation models of human inherited disorders , 2009, Molecular systems biology.

[49]  Burak Erman,et al.  Analysis of correlations between energy and residue fluctuations in native proteins and determination of specific sites for binding. , 2009, Physical review letters.

[50]  R. Nussinov,et al.  Hot regions in protein--protein interactions: the organization and contribution of structurally conserved hot spot residues. , 2005, Journal of molecular biology.

[51]  Ozlem Keskin,et al.  HotRegion: a database of predicted hot spot clusters , 2011, Nucleic Acids Res..

[52]  Z Liu,et al.  Construction of protein binding sites in scaffold structures. , 2000, Biopolymers.

[53]  Dima Kozakov,et al.  Hot Spot Analysis for Driving the Development of Hits into Leads in Fragment-Based Drug Discovery , 2012, J. Chem. Inf. Model..

[54]  A. Bateman,et al.  Protein interactions in human genetic diseases , 2008, Genome Biology.

[55]  C. Straub Targeting IAPs as an approach to anti-cancer therapy. , 2011, Current topics in medicinal chemistry.

[56]  Michelle R. Arkin,et al.  Binding of small molecules to an adaptive protein–protein interface , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[57]  H. Wolfson,et al.  Spatial chemical conservation of hot spot interactions in protein-protein complexes , 2007, BMC Biology.

[58]  L. Vassilev,et al.  Small-molecule inhibitors of the p53-MDM2 interaction. , 2011, Current topics in microbiology and immunology.

[59]  Luhua Lai,et al.  Structure-based method for analyzing protein–protein interfaces , 2004, Journal of molecular modeling.

[60]  Jie Liang,et al.  Protein-protein interactions: hot spots and structurally conserved residues often locate in complemented pockets that pre-organized in the unbound states: implications for docking. , 2004, Journal of molecular biology.

[61]  Xing-Ming Zhao,et al.  APIS: accurate prediction of hot spots in protein interfaces by combining protrusion index with solvent accessibility , 2010, BMC Bioinformatics.

[62]  W. Delano Unraveling hot spots in binding interfaces: progress and challenges. , 2002, Current opinion in structural biology.

[63]  T. Clackson,et al.  A hot spot of binding energy in a hormone-receptor interface , 1995, Science.

[64]  J. Parsons,et al.  pp125FAK-dependent tyrosine phosphorylation of paxillin creates a high-affinity binding site for Crk , 1995, Molecular and cellular biology.

[65]  Juan Fernández-Recio,et al.  Prediction of protein binding sites and hot spots , 2011 .

[66]  Haiyuan Yu,et al.  Three-dimensional reconstruction of protein networks provides insight into human genetic disease , 2012, Nature Biotechnology.

[67]  Holger Gohlke,et al.  Targeting protein-protein interactions with small molecules: challenges and perspectives for computational binding epitope detection and ligand finding. , 2006, Current medicinal chemistry.

[68]  Baw-Jhiune Liu,et al.  Identification of hot regions in protein-protein interactions by sequential pattern mining , 2007, BMC Bioinformatics.

[69]  F. J. Luque,et al.  Binding site detection and druggability index from first principles. , 2009, Journal of medicinal chemistry.

[70]  Kurt S. Thorn,et al.  ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions , 2001, Bioinform..

[71]  L. Serrano,et al.  Predicting changes in the stability of proteins and protein complexes: a study of more than 1000 mutations. , 2002, Journal of molecular biology.

[72]  William B. Smith,et al.  Selective inhibition of BET bromodomains , 2010, Nature.

[73]  David C Fry,et al.  Protein-protein interactions as targets for small molecule drug discovery. , 2006, Biopolymers.

[74]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[75]  R. Nussinov,et al.  Network-based strategies can help mono- and poly-pharmacology drug discovery: a systems biology view. , 2014, Current pharmaceutical design.

[76]  Ruth Nussinov,et al.  Druggable orthosteric and allosteric hot spots to target protein-protein interactions. , 2014, Current pharmaceutical design.

[77]  Alexander Dömling,et al.  Small molecular weight protein-protein interaction antagonists: an insurmountable challenge? , 2008, Current opinion in chemical biology.

[78]  L. Lai,et al.  Automatch: Target‐binding protein design and enzyme design by automatic pinpointing potential active sites in available protein scaffolds , 2012, Proteins.

[79]  Antonín Pavelka,et al.  HotSpot Wizard: a web server for identification of hot spots in protein engineering , 2009, Nucleic Acids Res..

[80]  Doheon Lee,et al.  A feature-based approach to modeling protein–protein interaction hot spots , 2009, Nucleic acids research.

[81]  Salam A. Assi,et al.  PCRPi: Presaging Critical Residues in Protein interfaces, a new computational tool to chart hot spots in protein interfaces , 2009, Nucleic acids research.

[82]  Solène Grosdidier,et al.  Identification of hot-spot residues in protein-protein interactions by computational docking , 2008, BMC Bioinformatics.

[83]  Burkhard Rost,et al.  Protein–Protein Interaction Hotspots Carved into Sequences , 2007, PLoS Comput. Biol..

[84]  D. Baker,et al.  A simple physical model for binding energy hot spots in protein–protein complexes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[85]  Sharon R Grossman,et al.  Integrating common and rare genetic variation in diverse human populations , 2010, Nature.

[86]  P. Hajduk,et al.  Druggability indices for protein targets derived from NMR-based screening data. , 2005, Journal of medicinal chemistry.

[87]  Ozlem Keskin,et al.  The Structural Pathway of Interleukin 1 (IL-1) Initiated Signaling Reveals Mechanisms of Oncogenic Mutations and SNPs in Inflammation and Cancer , 2014, PLoS Comput. Biol..

[88]  G. Otting,et al.  Organic solvents identify specific ligand binding sites on protein surfaces , 1997, Nature Biotechnology.

[89]  Sandor Vajda,et al.  Identification of hot spots within druggable binding regions by computational solvent mapping of proteins. , 2007, Journal of medicinal chemistry.

[90]  Kenny Q. Ye,et al.  An integrated map of genetic variation from 1,092 human genomes , 2012, Nature.

[91]  D. Bailey,et al.  The Binding Interface Database (BID): A Compilation of Amino Acid Hot Spots in Protein Interfaces , 2003, Bioinform..

[92]  A. del Sol,et al.  Small‐world network approach to identify key residues in protein–protein interaction , 2004, Proteins.

[93]  Ozlem Keskin,et al.  Similar binding sites and different partners: implications to shared proteins in cellular pathways. , 2007, Structure.

[94]  Michelle R. Arkin,et al.  Small-molecule inhibitors of protein–protein interactions: progressing towards the dream , 2004, Nature Reviews Drug Discovery.

[95]  N. Ben-Tal,et al.  ConSurf: an algorithmic tool for the identification of functional regions in proteins by surface mapping of phylogenetic information. , 2001, Journal of molecular biology.

[96]  Seren Soner,et al.  Hot Spots in a Network of Functional Sites , 2013, PloS one.

[97]  Laurie E. Grove,et al.  Structural conservation of druggable hot spots in protein–protein interfaces , 2011, Proceedings of the National Academy of Sciences.

[98]  Julie C. Mitchell,et al.  An automated decision‐tree approach to predicting protein interaction hot spots , 2007, Proteins.

[99]  G. Schneider,et al.  Context-based identification of protein-protein interfaces and "hot-spot" residues. , 2011, Chemistry & biology.

[100]  Yongli Bao,et al.  A compound‐based computational approach for the accurate determination of hot spots , 2013, Protein science : a publication of the Protein Society.

[101]  Dajun Yang,et al.  MI-63: A novel small-molecule inhibitor targets MDM2 and induces apoptosis in embryonal and alveolar rhabdomyosarcoma cells with wild-type p53 , 2009, British Journal of Cancer.

[102]  C. Rice,et al.  Suppression of inflammation by a synthetic histone mimic , 2010, Nature.

[103]  Philippe Roche,et al.  2P2Idb: a structural database dedicated to orthosteric modulation of protein–protein interactions , 2012, Nucleic Acids Res..

[104]  Timothy A. Whitehead,et al.  Computational Design of Proteins Targeting the Conserved Stem Region of Influenza Hemagglutinin , 2011, Science.

[105]  Thomas Madej,et al.  Modulating protein-protein interactions with small molecules: the importance of binding hotspots. , 2012, Journal of molecular biology.

[106]  T. Komiyama,et al.  Inhibitors of difficult protein-protein interactions identified by high-throughput screening of multiprotein complexes. , 2013, ACS Chemical Biology.

[107]  A. Hopkins,et al.  The druggable genome , 2002, Nature Reviews Drug Discovery.

[108]  Joshua M. Stuart,et al.  The Cancer Genome Atlas Pan-Cancer analysis project , 2013, Nature Genetics.

[109]  T. Berg Modulation of protein-protein interactions with small organic molecules. , 2003, Angewandte Chemie.

[110]  C. Tse,et al.  ABT-263: a potent and orally bioavailable Bcl-2 family inhibitor. , 2008, Cancer research.

[111]  Xiang-Sun Zhang,et al.  Prediction of hot spots in protein interfaces using a random forest model with hybrid features. , 2012, Protein engineering, design & selection : PEDS.