Applications of ESI-MS in drug discovery: interrogation of noncovalent complexes

For many years, analytical mass spectrometry has had numerous supporting roles in the drug development process, including the assessment of compound purity; quantitation of absorption, distribution, metabolism and excretion; and compound-specific pharmacokinetic analyses. More recently, mass spectrometry has emerged as an effective technique for identifying lead compounds on the basis of the characterization of noncovalent ligand–macromolecular target interactions. This approach offers several attractive properties for screening applications in drug discovery compared with other strategies, including the small quantities of target and ligands required, and the capacity to study ligands or targets without having to label them. Here, we review the application of electrospray ionization mass spectrometry to the interrogation of noncovalent complexes, highlighting examples from drug discovery efforts aimed at a range of target classes.

[1]  R. Griffey,et al.  Multiplexed screening of neutral mass-tagged RNA targets against ligand libraries with electrospray ionization FTICR MS: a paradigm for high-throughput affinity screening. , 1999, Analytical chemistry.

[2]  A. Heck,et al.  Interactions of α- and β-avoparcin with bacterial cell-wall receptor-mimicking peptides studied by electrospray ionization mass spectrometry , 1999 .

[3]  Richard D. Smith,et al.  Using Electrospray Ionization FTICR Mass Spectrometry To Study Competitive Binding of Inhibitors to Carbonic Anhydrase , 1995 .

[4]  Richard H. Griffey,et al.  Fourier transform ion cyclotron resonance mass spectrometry as a high throughput affinity screen to identify RNA binding ligands , 2000 .

[5]  G. Whitesides,et al.  Screening derivatized peptide libraries for tight binding inhibitors to carbonic anhydrase II by electrospray ionization-mass spectrometry. , 1996, Journal of medicinal chemistry.

[6]  J. Brodbelt,et al.  Evaluation of complexes of DNA duplexes and novel benzoxazoles or benzimidazoles by electrospray ionization mass spectrometry , 2004, Journal of the American Society for Mass Spectrometry.

[7]  J. Roeraade,et al.  Influence of droplet size, capillary-cone distance and selected instrumental parameters for the analysis of noncovalent protein-ligand complexes by nano-electrospray ionization mass spectrometry. , 2004, Journal of mass spectrometry : JMS.

[8]  F W McLafferty,et al.  Infrared multiphoton dissociation of large multiply charged ions for biomolecule sequencing. , 1994, Analytical chemistry.

[9]  C. Robinson,et al.  Probing the nature of interactions in SH2 binding interfaces–evidence from electrospray ionization mass spectrometry , 1999, Protein science : a publication of the Protein Society.

[10]  A. Heck,et al.  Subtle differences in molecular recognition between modified glycopeptide antibiotics and bacterial receptor peptides identified by electrospray ionization mass spectrometry , 1999 .

[11]  R. Bakhtiar Integrated strategies for drug discovery using mass spectrometry , 2006, Journal of the American Society for Mass Spectrometry.

[12]  C. Hendrickson,et al.  High-resolution electrospray ionization fourier transform mass spectrometry with infrared multiphoton dissociation of glucokinase from Bacillus stearothermophilus , 1998, Journal of the American Society for Mass Spectrometry.

[13]  D. Clemmer,et al.  Evidence for many resolvable structures within conformation types of electrosprayed ubiquitin ions. , 2006, The journal of physical chemistry. B.

[14]  V. Nesatyy Gas-phase binding of non-covalent protein complexes between bovine pancreatic trypsin inhibitor and its target enzymes studied by electrospray ionization tandem mass spectrometry. , 2001, Journal of mass spectrometry : JMS.

[15]  J. Aldrich-Wright,et al.  Comparison of the binding stoichiometries of positively charged DNA-binding drugs using positive and negative ion electrospray ionization mass spectrometry , 2004, Journal of the American Society for Mass Spectrometry.

[16]  H. M. Petrassi,et al.  Screening transthyretin amyloid fibril inhibitors: characterization of novel multiprotein, multiligand complexes by mass spectrometry. , 2002, Structure.

[17]  R. Griffey,et al.  Measuring dissociation constants of RNA and aminoglycoside antibiotics by electrospray ionization mass spectrometry. , 2000, Analytical biochemistry.

[18]  Jay J. Cheng,et al.  HYDROLYSIS OF LIGNOCELLULOSIC MATERIALS FOR ETHANOL PRODUCTION , 2002 .

[19]  C. Wong,et al.  Specificity of aminoglycoside antibiotics for the A-site of the decoding region of ribosomal RNA. , 1998, Chemistry & biology.

[20]  Zhongqi Zhang,et al.  Probing noncovalent structural features of proteins by mass spectrometry , 1994 .

[21]  J H Lakey,et al.  Measuring protein-protein interactions. , 1998, Current opinion in structural biology.

[22]  S. Courtneidge Role of Src in Signal Transduction Pathways , 2001 .

[23]  A. Kapur,et al.  Positive ion electrospray ionization mass spectrometry of double-stranded DNA/drug complexes. , 2001, Rapid communications in mass spectrometry : RCM.

[24]  Richard D. Smith,et al.  Preservation of non-covalent associations in electrospray ionization mass spectrometry: Multiply charged polypeptide and protein dimers , 1992 .

[25]  M. Gross,et al.  Non-Covalent Complexes between DNA-Binding Drugs and Double-Stranded Oligodeoxynucleotides: A Study by ESI Ion-Trap Mass Spectrometry , 2000 .

[26]  Juan Zhang,et al.  FT-ICR mass spectrometry in the drug discovery process. , 2005, Drug discovery today.

[27]  Hofstadler Sa,et al.  Mass spectrometry as a drug discovery platform against RNA targets. , 2000 .

[28]  H. M. Petrassi,et al.  Structure-Based Design of N-Phenyl Phenoxazine Transthyretin Amyloid Fibril Inhibitors , 2000 .

[29]  B. Ganem,et al.  Recognition of cell‐wall peptide ligands by vancomycin group antibiotics: Studies using ion spray mass spectrometry , 1995 .

[30]  R. Griffey,et al.  SAR by MS: a ligand based technique for drug lead discovery against structured RNA targets. , 2002, Journal of medicinal chemistry.

[31]  J. M. Bradshaw,et al.  SH2 Domains: From Structure to Energetics, a Dual Approach to the Study of Structure—Function Relationships , 1999 .

[32]  C. Robinson,et al.  Use of a microchip device coupled with mass spectrometry for ligand screening of a multi-protein target. , 2003, Analytical chemistry.

[33]  A. Heck,et al.  Direct determination of solution binding constants for noncovalent complexes between bacterial cell wall peptide analogues and vancomycin group antibiotics by electrospray ionization mass spectrometry , 1998 .

[34]  Yun He,et al.  Synthesis and evaluation of novel bacterial rRNA-binding benzimidazoles by mass spectrometry. , 2004, Bioorganic & medicinal chemistry letters.

[35]  Richard D. Smith,et al.  Carbonic Anhydrase-Inhibitor Binding: From Solution to the Gas Phase , 1997 .

[36]  Renato Zenobi,et al.  Quantitative determination of noncovalent binding interactions using soft ionization mass spectrometry , 2002 .

[37]  S. Courtneidge Role of Src in signal transduction pathways. The Jubilee Lecture. , 2002, Biochemical Society transactions.

[38]  S. Benner,et al.  Fourier transform-ion cyclotron resonance mass spectrometric resolution, identification, and screening of non-covalent complexes of Hck Src homology 2 domain receptor and ligands from a 324-member peptide combinatorial library , 2002, Journal of the American Society for Mass Spectrometry.

[39]  H. Noller,et al.  Mutations in 16S ribosomal RNA disrupt antibiotic–RNA interactions. , 1989, The EMBO journal.

[40]  Christopher A. Lipinski,et al.  Medicinal chemistry of aldose reductase inhibitors , 1988, Medicinal research reviews.

[41]  V. Nesatyy Mass spectrometry evaluation of the solution and gas-phase binding properties of noncovalent protein complexes , 2002 .

[42]  A. Heck,et al.  Covalent and non-covalent dissociations of gas-phase complexes of avoparcin and bacterial receptor mimicking precursor peptides studied by collisionally activated decomposition mass spectrometry. , 1999, Journal of mass spectrometry : JMS.

[43]  M. Gross,et al.  Gas-phase stability of double-stranded oligodeoxynucleotides and their noncovalent complexes with DNA-binding drugs as revealed by collisional activation in an ion trap , 2000, Journal of the American Society for Mass Spectrometry.

[44]  K. Breuker The study of protein–ligand interactions by mass spectrometry—a personal view , 2004 .

[45]  G. Anderson,et al.  Bio-affinity characterization mass spectrometry. , 1995, Rapid communications in mass spectrometry : RCM.

[46]  G. Whitesides,et al.  Probing the energetics of dissociation of carbonic anhydrase-ligand complexes in the gas phase. , 1999, Biophysical journal.

[47]  D. Moras,et al.  Binding of aldose reductase inhibitors: correlation of crystallographic and mass spectrometric studies , 1999, Journal of the American Society for Mass Spectrometry.

[48]  M. Siegel,et al.  Early discovery drug screening using mass spectrometry. , 2002, Current topics in medicinal chemistry.

[49]  Steven V. Ley,et al.  Targeting C-reactive protein for the treatment of cardiovascular disease , 2006, Nature.

[50]  M. Colgrave,et al.  Electrospray ionization mass spectrometry of oligonucleotide complexes with drugs, metals, and proteins. , 2001, Mass spectrometry reviews.

[51]  E. Pauw,et al.  Advantages and drawbacks of nanospray for studying noncovalent protein-DNA complexes by mass spectrometry. , 2002, Rapid communications in mass spectrometry : RCM.

[52]  D. Patel,et al.  Adaptive recognition by nucleic acid aptamers. , 2000, Science.

[53]  S. W. Bligh,et al.  Measurement of dissociation constants of inhibitors binding to Src SH2 domain protein by non‐covalent electrospray ionization mass spectrometry , 2003, Journal of molecular recognition : JMR.

[54]  P. Lansbury,et al.  Amyloid diseases: abnormal protein aggregation in neurodegeneration. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[55]  C. Robinson,et al.  Tandem mass spectrometry defines the stoichiometry and quaternary structural arrangement of tryptophan molecules in the multiprotein complex TRAP. , 2004, Journal of the American Chemical Society.

[56]  A. Kapur,et al.  Observation of daunomycin and nogalamycin complexes with duplex DNA using electrospray ionisation mass spectrometry. , 1999, Rapid communications in mass spectrometry : RCM.

[57]  J. Loo,et al.  Studying noncovalent protein complexes by electrospray ionization mass spectrometry. , 1997, Mass spectrometry reviews.

[58]  P. Roepstorff,et al.  Tandem mass spectrometry of specific vs. nonspecific noncovalent complexes of vancomycin antibiotics and peptide ligands , 2002 .

[59]  B. Ganem,et al.  Detection of noncovalent receptor-ligand complexes by mass spectrometry , 1991 .

[60]  R. Griffey,et al.  Characterization of Low-Affinity Complexes between RNA and Small Molecules Using Electrospray Ionization Mass Spectrometry† , 2000 .

[61]  J. M. Bradshaw,et al.  SH2 domains: From structure to energetics, a dual approach to the study of structure–function relationships , 1999, Medicinal research reviews.

[62]  R. Griffey,et al.  Multitarget affinity/specificity screening of natural products: finding and characterizing high-affinity ligands from complex mixtures by using high-performance mass spectrometry. , 2003, Journal of natural products.

[63]  R. Griffey,et al.  Analysis of noncovalent complexes of DNA and RNA by mass spectrometry. , 2001, Chemical reviews.

[64]  C. Robinson,et al.  Disassembly of intact multiprotein complexes in the gas phase. , 1999, Current opinion in structural biology.

[65]  E. Swayze,et al.  The synthesis and 16S A-site rRNA recognition of carbohydrate-free aminoglycosides. , 2005, Bioorganic & medicinal chemistry letters.

[66]  P. Salvadori,et al.  Non-covalent complexes between DNA-binding drugs and double-stranded deoxyoligonucleotides: a study by ionspray mass spectrometry. , 1997, Journal of mass spectrometry : JMS.

[67]  Alan G. Marshall,et al.  Stored waveform inverse Fourier transform (SWIFT) ion excitation in trapped-ion mass spectometry: Theory and applications , 1996 .

[68]  P. Roepstorff,et al.  Collision-induced dissociation of noncovalent complexes between vancomycin antibiotics and peptide ligand stereoisomers: evidence for molecular recognition in the gas phase , 1999 .

[69]  J. Brodbelt,et al.  A method for the determination of binding constants by electrospray ionization mass spectrometry , 2000, Analytical chemistry.

[70]  G. Varani,et al.  Recent solution structures of RNA and its complexes with drugs, peptides and proteins. , 1997, Current opinion in structural biology.

[71]  J. Puglisi,et al.  RNA sequence determinants for aminoglycoside binding to an A-site rRNA model oligonucleotide. , 1996, Journal of molecular biology.

[72]  J. M. Bradshaw,et al.  Mass spectrometric and thermodynamic studies reveal the role of water molecules in complexes formed between SH2 domains and tyrosyl phosphopeptides. , 1998, Structure.

[73]  J. Kelly,et al.  Amyloid fibril formation and protein misassembly: a structural quest for insights into amyloid and prion diseases. , 1997, Structure.

[74]  T. Gadek,et al.  Structure-activity relationships by mass spectrometry: identification of novel MMP-3 inhibitors. , 2004, Bioorganic & medicinal chemistry.

[75]  D. Draper,et al.  RNA structure , 1977, Quarterly Reviews of Biophysics.

[76]  E. De Pauw,et al.  Interaction between antitumor drugs and a double-stranded oligonucleotide studied by electrospray ionization mass spectrometry. , 1999, Journal of mass spectrometry : JMS.

[77]  J. Roeraade,et al.  Electrospray ionization mass spectrometry as a tool for determination of drug binding sites to human serum albumin by noncovalent interaction. , 2005, Rapid communications in mass spectrometry : RCM.

[78]  A. Heck,et al.  Native protein mass spectrometry: from intact oligomers to functional machineries. , 2004, Current opinion in chemical biology.

[79]  J. Roeraade,et al.  Automated Nano-Electrospray Mass Spectrometry for Protein-Ligand Screening by Noncovalent Interaction Applied to Human H-FABP and A-FABP , 2003, Journal of biomolecular screening.

[80]  R. Griffey,et al.  Determinants of aminoglycoside-binding specificity for rRNA by using mass spectrometry. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[81]  E. De Pauw,et al.  Determination of affinity, stoichiometry and sequence selectivity of minor groove binder complexes with double-stranded oligodeoxynucleotides by electrospray ionization mass spectrometry. , 2002, Nucleic acids research.

[82]  S. Courtneidge,et al.  Protein tyrosine kinases, with emphasis on the Src family. , 1994, Seminars in cancer biology.

[83]  J. Loo Teaching Editorial - Bioanalytical Mass Spectrometry: Many Flavors to Choose , 1995 .

[84]  M. Greig,et al.  Detection of Oligonucleotide-Ligand Complexes by ESI-MS (DOLCE-MS) as a Component of High Throughput Screening , 2000, Journal of biomolecular screening.

[85]  T Pawson,et al.  SH2 and SH3 domains: elements that control interactions of cytoplasmic signaling proteins. , 1991, Science.

[86]  D. Wilson,et al.  Quantitative determination of noncovalent binding interactions using automated nanoelectrospray mass spectrometry. , 2003, Analytical chemistry.

[87]  J. Loo,et al.  A study of Src SH2 domain protein-phosphopeptide binding interactions by electrospray ionization mass spectrometry , 1997 .

[88]  M. Bowers,et al.  Application of ion mobility to the gas-phase conformational analysis of polyhedral oligomeric silsesquioxanes (POSS) , 2003 .

[89]  C. Dobson,et al.  Probing the Nature of Noncovalent Interactions by Mass Spectrometry. A Study of Protein−CoA Ligand Binding and Assembly , 1996 .

[90]  Rangarajan Sampath,et al.  SAR by MS: discovery of a new class of RNA-binding small molecules for the hepatitis C virus: internal ribosome entry site IIA subdomain. , 2005, Journal of medicinal chemistry.

[91]  P. Hensley Defining the structure and stability of macromolecular assemblies in solution: the re-emergence of analytical ultracentrifugation as a practical tool. , 1996, Structure.