- Email: [email protected]
Pharmacoproteomics and toxicoproteomics: The field of dreams
J O U RN A L OF P ROT EO M I CS 7 4 ( 2 0 11 ) 25 4 9 –2 55 3
Available online at www.sciencedirect.com
www.elsevier.com/locate/jprot
Editorial
Pharmacoproteomics and toxicoproteomics: The field of dreams
Keywords: Pharmacoproteomics Toxicoproteomics Drug development Mechanism of action Biomarker Nanotechnology
Disease development is a complex process involving many factors including intrinsic physiological changes and harmful environmental exposure. Although disease causes are known in general to be related to genetic abnormalities, pathogen infections, aging, exposure to toxicants, etc., the exact initial causes remain unknown for a majority of the diseases including cancer, cardiovascular disease, diabetes, etc. Each type of disease, even for individual patients and subpopulations, has its own development paths and mechanisms, requiring personalized medicine for disease prevention and treatment [1,2]. The advancements of molecular technologies in the past decades have shed lights on the mechanisms of disease development and some key genes, proteins, pathways have been identified. These molecules have been or are being served as the targets or biomarkers for modern drug development [3,4]. According to the Federal Food, Drug, and Cosmetic Act (FD&C Act) of the United States of America, drugs are defined, in part, by their intended use, as “articles intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease” and “articles (other than food) intended to affect the structure or any function of the body of man or other animals” (www.fda. gov). Drug development is a complex, lengthy, and expensive process that takes several years to over a decade and costs several hundred millions to billions of dollars for a single regulatory approved drug. The attrition rate is very high in drug development. Expanded application of systems biology technologies in drug development [5–9] is expected to accelerate the drug development process and reduce associated cost. Inevitably, proteomics will play critical roles in this mission since proteins are the functional executors in disease development and response to toxicants. Proteomic
concepts and technologies have increasingly been applied in the past decades to the two closely associated disciplines in drug development and administration, pharmacology and toxicology [10–18]. Pharmacoproteomics, as implied its term, is the application of proteomic technologies in drug development and assessment of drug administration [19,20]. In contrast to empirical drug discovery where the initial drug lead is identified through functional screens without an understanding of its mechanism of action and target, modern drug development tends to rationally design or screen compounds that act against a particular biochemical target and its function. A typical path of rational drug development includes multiple consecutive knowledge-building steps, i.e., definition of drug targets, designing or screening compounds for lead compound identification, preclinical evaluation, clinical trials (I, II and III), regulatory approval, and sometimes followed by post-marketing phase IV clinical trials. Proteomic approaches can be applied to many stages or aspects in this path. While providing new tools to address the issues raised during drug development, the ultimate goal of pharmacoproteomics is to accelerate the drug development process, reduce costs, and provide tools for better management of diseases. Specifically, major aims of pharmacoproteomics research include a) verification and identification of drug targets, b) elucidation of molecular mechanisms of drug action including efficacy and toxicity, and c) development of protein biomarkers and assays for assessment of drug efficacy and toxicity for both preclinical and clinical applications. While closely associated with drug development, toxicoproteomics on the other hand focuses on the proteomic study of toxicity caused not only by drugs but also by other toxic substances, including toxins, environmental stressors, chemicals, and any other materials that may cause significant pathological responses (e.g., engineered nanomaterials) [21]. It combines with principles and methods of toxicology, pathology and other expertise to address toxicological questions. To achieve these aims, both pharmacoproteomics and toxicoproteomics are deemed to have common tasks in the analysis of protein expression, modifications, protein–protein/ drug/toxicant interactions, protein structures, protein activities, subcellular localization, etc. When new challenges come, novel proteomic technologies should be developed. A number of pharmacoproteomic and toxicoproteomic studies have been
2550
J O U RN A L OF P ROT EO M IC S 7 4 ( 2 0 11 ) 25 4 9 –25 5 3
performed and the field is being expanded dramatically. The major tools and applications or aims in the field of dreams of pharmacoproteomics and toxicoproteomics are illustrated in Fig. 1. Verification of the molecular target(s) for a particular drug is critical during drug development. Drug target analysis not only provides insights into the primary mechanism-ofaction of a drug but also can lead to an understanding of the side effects or toxicity as a result of “off-target” interactions, which will further provide the rationale for optimizing the drug lead to minimize toxicity [21]. Proteomic analysis of drug targets has been an active research area for many years. The analysis can often lead to the identification of novel therapeutic targets [22]. The predominant approach was to isolate drug associated proteins using affinity-based precipitation or chromatography and then identify and quantify them using mass spectrometry in conjunction with gel- or liquid chromatography-based separation techniques. Such analyses not only verified the target for which the drug was developed but also identified other direct targets, which provided insights into the mechanism of drug effectiveness and potential toxicity as well [23]. Proteomic approaches such as activity-based probing and protein/small molecule microarrays
have also been actively employed to identify drug targets [24]. For a long time, computational methods have been adopted to assist drug design and predict protein targets of small molecule drugs [25]. The in silico methods could have a substantial contribution to the design of multi-target drugs that will be one of the major developments in the pharmaceutical industry in the near future [26]. All these areas will continue to grow significantly. Proteomics has a great potential for understanding the mechanism of action of a drug in both preclinical and clinical development stages. Studies in this field represent the most developed areas of pharmacoprotemics over the past decade and it is expected such efforts will continue to grow rapidly. Besides the previously mentioned target identification and drug–protein interaction analysis, a variety of quantitative proteomic approaches have been applied to measure protein abundance changes upon drug treatment in in vitro cell systems, in vivo animal models and clinical samples to verify expected mechanisms of effectiveness and identify other novel mechanisms of action by analyzing large proteomic data at the pathway level [27,28]. Understanding the mechanisms of drug resistance at the proteome level was achieved substantially in the past several years, especially in the field of oncology [29]. Moreover, the power of proteomic technologies has been
Fig. 1 – The field of dreams of pharmacoproteomics and toxicoproteomics. A variety of proteomics technologies have been or are being applied to drug development and environmental health studies. Current areas of pharmacoproteomic and toxicoproteomics studies are broad, including but not limited to the identification of molecular targets of drugs and other toxicants, elucidation of mechanisms of action, biomarker development, addressing issues in pharmacokinetics and pharmacodynamics, evaluation of drug formulation and delivery, etc. Some of these research areas may cross-talk each other with the general goal of accelerating drug development, effective and safe use of drugs, and early detection of adverse effects. 2DE, two-dimensional gel electrophoresis; ESI-MS, electrospray ionization mass spectrometry; LC, liquid chromatography; MALDI-MS, matrix-assisted laser desorption/ionization mass spectrometry; MRM, multiple reaction monitoring; MS/MS, tandem mass spectrometry; MS imaging, mass spectrometry imaging; and PK/PD, pharmacokinetics/pharmacodynamics.
J O U RN A L OF P ROT EO M I CS 7 4 ( 2 0 11 ) 25 4 9 –2 55 3
demonstrated in analyzing protein modifications (e.g., adducts formed from drug metabolites), protein–protein interactions, activities, subcellular distributions, etc. Sustained application of proteomic approaches to the analysis of drug action in terms of effectiveness and toxicity will largely fulfill their roles in drug development. Safety evaluation is the highest priority throughout the drug development process. Application of proteomics concepts and technologies to drug toxicity issues is well fitted in the elucidation of toxicity mechanisms and in development of toxicity biomarkers. A biomarker is defined as “a characteristic that is objectively measured and evaluated as an indicator of normal biologic processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention” [30]. Generation of a large amount of toxicoproteomic data that might lead to biomarkers and a better mechanistic understanding would potentially reduce the attrition rate and costs in drug development by detecting or predicting toxicity at the earliest stage. This research area is steadily growing. As pointed out earlier, toxicoproteomic studies are not limited to drug development. In fact, a number of toxicoproteomic analyses have been performed for environmental toxicants including air pollutants, pesticides, chemicals in water systems, and so on [16,31]. Early detection of toxicity induced by drug administration and other toxicants using qualified biomarkers would have a great potential to prevent disease development. In the past decade, a major effort of proteomics has been biomarker development. However, a majority of proteomic studies have been focused on the discovery of biomarkers for early detection and diagnosis of diseases such as cancer. In the context of co-development of drugs and diagnostic tests [32,33], biomarkers are pivotal to stratify the patients that are likely to benefit from or have adverse reactions to a particular drug. Efforts have also been made in developing pharmacodynamic biomarkers for detection of therapeutic responses and drug actions (e.g., efficacy and toxicity) using proteomic approaches [34,35]. In line with biomarker discovery, endeavors have been started to develop mass spectrometry- and microarray-based proteomic biomarker assays such as multiple reaction monitoring (MRM) [36]. These tools are being expected to be used to measure clinical biomarkers. Currently, a bottleneck in biomarker development is biomarker biological qualification. The rate of successful qualification of biomarker candidates identified from the discovery stage has been extremely low [37]. Another challenge is to translate non-clinical biomarkers to clinical biomarkers. In addition to low statistical power and small sample size in many previous proteomic biomarker studies, insufficient consideration of “context of use” of biomarkers in clinical settings was also a major reason for the failure of biomarker qualification. Researchers have just begun to realize the importance of “context of use,” which should be kept in mind at the beginning of biomarker discovery. The situation is also true for biomarker assay development where “intended use” is a key element to be considered and is being discussed [38]. Although application of proteomic technologies to pharmacokinetics wasn't growing as fast as other areas of pharmacoproteomics, the research potential is still promising in several aspects of pharmacokinetics. Quantification of drug–
2551
protein interaction in body fluids and tissues is an interesting topic of pharmacokinetic studies. Measurement of protein adducts as a result of modification by a drug and/or its metabolites upon dosing is also drawing increasing interest. A fast developing area in spatial mapping of proteins, peptides, lipids, drugs and their metabolites is mass spectrometry imaging [39]. Along with rapid technical development in MS imaging, application of such a technique to the analysis of drug/metabolite tissue spatial distribution has been expanding dramatically [40]. Recent interesting MS imaging of drug formulations was reported in the analysis of ingredients and pharmaceutical elution of stents, tablets, and powders [40]. It should be noted that modeling pharmacokinetics (PK)/pharmacodynamics (PD) can be facilitated by pharmacodynamic biomarkers identified using proteomic approaches. Significant future advance in all these areas is expected. One of the emerging areas in medicine is the biomedical application of nanomaterials. The applications are broad, including diagnosis, drug delivery, imaging, etc. Although many studies have been performed, the area is still in its infancy. The pace of bringing nanomedicine to clinical application is slow. A great potential of nanotechnology in disease diagnosis and drug action monitoring is ultrasensitive detection of biomarkers. The sensitivity of nanomaterial-based biomarker assays can reach to femto- to atto-molar levels (i.e., 10− 15–10− 18 mol/L), which is several orders of magnitude higher (in terms of sensitivity) than that obtained from conventional immunoassays or existing proteomics techniques including ELISA methods, immunochromatography, MCE enzyme immunoassays, MS-based approaches and microarrays [41]. Nanotechnology-based proteomic biomarker development is just at the beginning, thus tremendous development is anticipated. It should be noted that safety concerns have been raised from not only biomedical application of nanomaterials but also increased human exposure to nanomaterials in the environment as a result of nano-industry activities [42]. Proteomic analysis of nanoparticles could lead to novel discoveries in the action of nanomaterials in human bodies. Therapeutic agents given to humans include biologics as well as small molecules. Vaccine and antibody development is very active in the prevention and treatment of infectious diseases, cancer, etc. Proteomic studies have expedited identification and characterization of antigens which are useful for vaccine development. The area was dramatically advanced recently by using proteomic strategies to identify new protein antigens and epitopes, assess host immune system response to infection and vaccination, identify new biomarkers for evaluation of vaccine efficacy or vaccination-induced adverse effects [43]. Although not fully discussing all the areas of pharmacoproteomics and toxicoproteomics, this special edition has a collection of manuscripts in many aspects of these two disciplines. The hope is not only to summarize some recent progresses of proteomic applications to the analysis of drugs and other toxicants in drug development and use but also to encourage further development in this field of dreams. I believe the dream will become true for pharmacoproteomics and toxicoproteomics to accelerate drug development and bring more drugs and tools to public health for the safe prevention and treatment of diseases.
2552
J O U RN A L OF P ROT EO M IC S 7 4 ( 2 0 11 ) 25 4 9 –25 5 3
Acknowledgments I would like to thank all the authors and reviewers who contributed to this special edition of Journal of Proteomics. Special thanks give to Editor-in-Chief, Professor Juan Calvete, for supporting the initiation of this special edition. I am also grateful to Andy Deelen and Gerard Duggan from Elsevier for their correspondence and editorial assistance throughout the whole process. The views presented in this article do not necessarily reflect those of the U. S. Food and Drug Administration.
REFERENCES
[1] Hamburg MA, Collins FS. The path to personalized medicine. N Engl J Med 2010;363:301–4. [2] Woodcock J. The prospects for “personalized medicine” in drug development and drug therapy. Clin Pharmacol Ther 2007;81:164–9. [3] Shawver LK, Slamon D, Ullrich A. Smart drugs: tyrosine kinase inhibitors in cancer therapy. Cancer Cell 2002;1:117–23. [4] Yu LR, Issaq HJ, Veenstra TD. Phosphoproteomics for the discovery of kinases as cancer biomarkers and drug targets. Proteomics Clin Appl 2007;1:1042–57. [5] Luesch H. Towards high-throughput characterization of small molecule mechanisms of action. Mol Biosyst 2006;2: 609–20. [6] Zhang QY, Mao JH, Liu P, Huang QH, Lu J, Xie YY, et al. A systems biology understanding of the synergistic effects of arsenic sulfide and Imatinib in BCR/ABL-associated leukemia. Proc Natl Acad Sci U S A 2009;106:3378–83. [7] Schrattenholz A, Groebe K, Soskic V. Systems biology approaches and tools for analysis of interactomes and multitarget drugs. Methods Mol Biol 2010;662:29–58. [8] Gonzalez-Angulo AM, Hennessy BT, Mills GB. Future of personalized medicine in oncology: a systems biology approach. J Clin Oncol 2010;28:2777–83. [9] Mendrick DL. Transcriptional profiling to identify biomarkers of disease and drug response. Pharmacogenomics 2011;12:235–49. [10] Moller A, Soldan M, Volker U, Maser E. Two-dimensional gel electrophoresis: a powerful method to elucidate cellular responses to toxic compounds. Toxicology 2001;160:129–38. [11] Bandara LR, Kennedy S. Toxicoproteomics — a new preclinical tool. Drug Discov Today 2002;7:411–8. [12] Kennedy S. The role of proteomics in toxicology: identification of biomarkers of toxicity by protein expression analysis. Biomarkers 2002;7:269–90. [13] Witzmann FA, Grant RA. Pharmacoproteomics in drug development. Pharmacogenomics J 2003;3:69–76. [14] Wetmore BA, Merrick BA. Toxicoproteomics: proteomics applied to toxicology and pathology. Toxicol Pathol 2004;32:619–42. [15] Dowling VA, Sheehan D. Proteomics as a route to identification of toxicity targets in environmental toxicology. Proteomics 2006;6:5597–604. [16] Monsinjon T, Knigge T. Proteomic applications in ecotoxicology. Proteomics 2007;7:2997–3009. [17] Arrell DK, Niederlander NJ, Perez-Terzic C, Chung S, Behfar A, Terzic A. Pharmacoproteomics: advancing the efficacy and safety of regenerative therapeutics. Clin Pharmacol Ther 2007;82:316–9. [18] Butler GS, Overall CM. Proteomic validation of protease drug targets: pharmacoproteomics of matrix metalloproteinase inhibitor drugs using isotope-coded affinity tag labeling and tandem mass spectrometry. Curr Pharm Des 2007;13:263–70.
[19] Jain KK. Role of pharmacoproteomics in the development of personalized medicine. Pharmacogenomics 2004;5:331–6. [20] D'Alessandro A, Zolla L. Pharmacoproteomics: a chess game on a protein field. Drug Discov Today 2010;15:1015–23. [21] Gao Y, Holland RD, Yu LR. Quantitative proteomics for drug toxicity. Brief Funct Genomic Proteomic 2009;8:158–66. [22] Han MH, Hwang SI, Roy DB, Lundgren DH, Price JV, Ousman SS, et al. Proteomic analysis of active multiple sclerosis lesions reveals therapeutic targets. Nature 2008;451:1076–81. [23] Bantscheff M, Eberhard D, Abraham Y, Bastuck S, Boesche M, Hobson S, et al. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat Biotechnol 2007;25:1035–44. [24] Sleno L, Emili A. Proteomic methods for drug target discovery. Curr Opin Chem Biol 2008;12:46–54. [25] Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, Hufeisen SJ, et al. Predicting new molecular targets for known drugs. Nature 2009;462:175–81. [26] Koutsoukas A, Simms B, Kirchmair J, Bond PJ, Whitmore AV, Zimmer S, et al. From in silico target prediction to multi-target drug design: current databases, methods and applications. J Proteomics 2011;74:2554–74. [27] Cohen AA, Geva-Zatorsky N, Eden E, Frenkel-Morgenstern M, Issaeva I, Sigal A, et al. Dynamic proteomics of individual cancer cells in response to a drug. Science 2008;322:1511–6. [28] Millard M, Pathania D, Shabaik Y, Taheri L, Deng J, Neamati N. Preclinical evaluation of novel triphenylphosphonium salts with broad-spectrum activity. PLoS One 2010;5:e13131doi: 10.1371/journal.pone.0013131. [29] Li X-H, Li C, Xiao Z-Q. Proteomics for identifying mechanisms and biomarkers of drug resistance in cancer. J Proteomics 2011;74:2642–9. [30] Atkinson AJ, Colburn WA, DeGruttola VG, DeMets DL, Downing GJ, Hoth DF, et al. Biomarkers and surrogate endpoints: preferred definitions and conceptual framework. Clinical Pharmacology & Therapeutics 2001;69:89–95. [31] Benninghoff AD. Toxicoproteomics—the next step in the evolution of environmental biomarkers. Toxicol Sci 2007;95:1–4. [32] Hinman LM, Carl KM, Spear BB, Salerno RA, Becker RL, Abbott BM, et al. Development and regulatory strategies for drug and diagnostic co-development. Pharmacogenomics 2010;11: 1669–75. [33] Goodsaid FM, Mendrick DL. Translational medicine and the value of biomarker qualification. Sci Transl Med 2010;2:47ps44. [34] Hennessy BT, Lu Y, Poradosu E, Yu Q, Yu S, Hall H, et al. Pharmacodynamic markers of perifosine efficacy. Clin Cancer Res 2007;13:7421–31. [35] Andersen JN, Sathyanarayanan S, Di Bacco A, Chi A, Zhang T, Chen AH, et al. Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors. Sci Transl Med 2010;2:43ra55. [36] Meng Z, Veenstra TD. Targeted mass spectrometry approaches for protein biomarker verification. J Proteomics 2011;74:2650–9. [37] Anderson NL. The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum. Clin Chem 2010;56:177–85. [38] Li J, Kelm KB, Tezak Z. Regulatory perspective on translating proteomic biomarkers to clinical diagnostics. J Proteomics 2011;74:2682–90. [39] Reyzer ML, Caprioli RM. MALDI-MS-based imaging of small molecules and proteins in tissues. Curr Opin Chem Biol 2007;11:29–35. [40] Greer T, Sturm R, Li L. Mass spectrometry imaging for drugs and metabolites. J Proteomics 2011;74:2617–31. [41] Ray S, Reddy PJ, Choudhary S, Raghu D, Srivastava S. Emerging nanoproteomics approaches for disease biomarker detection: a current perspective. J Proteomics 2011;74: 2660–81.
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[42] Thomas CR, George S, Horst AM, Ji Z, Miller RJ, Peralta-Videa JR, et al. Nanomaterials in the environment: from materials to high-throughput screening to organisms. ACS Nano 2011;5: 13–20. [43] Adamczyk-Poplawska M, Markowicz S, Jagusztyn-Krynicka EK. Proteomics for development of vaccine. J Proteomics 2011;74:2596–616.
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Corresponding author at: Center of Excellence for Proteomics, Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd., HFT-233, Jefferson, AR 72079, USA. Tel.: +1 870 543 7052; fax: +1 870 543 7686. E-mail address: [email protected]. 2 October 2011
Li-Rong Yu Center of Excellence for Proteomics, Division of Systems Biology, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA
Available online at www.sciencedirect.com
www.elsevier.com/locate/jprot
Editorial
Pharmacoproteomics and toxicoproteomics: The field of dreams
Keywords: Pharmacoproteomics Toxicoproteomics Drug development Mechanism of action Biomarker Nanotechnology
Disease development is a complex process involving many factors including intrinsic physiological changes and harmful environmental exposure. Although disease causes are known in general to be related to genetic abnormalities, pathogen infections, aging, exposure to toxicants, etc., the exact initial causes remain unknown for a majority of the diseases including cancer, cardiovascular disease, diabetes, etc. Each type of disease, even for individual patients and subpopulations, has its own development paths and mechanisms, requiring personalized medicine for disease prevention and treatment [1,2]. The advancements of molecular technologies in the past decades have shed lights on the mechanisms of disease development and some key genes, proteins, pathways have been identified. These molecules have been or are being served as the targets or biomarkers for modern drug development [3,4]. According to the Federal Food, Drug, and Cosmetic Act (FD&C Act) of the United States of America, drugs are defined, in part, by their intended use, as “articles intended for use in the diagnosis, cure, mitigation, treatment, or prevention of disease” and “articles (other than food) intended to affect the structure or any function of the body of man or other animals” (www.fda. gov). Drug development is a complex, lengthy, and expensive process that takes several years to over a decade and costs several hundred millions to billions of dollars for a single regulatory approved drug. The attrition rate is very high in drug development. Expanded application of systems biology technologies in drug development [5–9] is expected to accelerate the drug development process and reduce associated cost. Inevitably, proteomics will play critical roles in this mission since proteins are the functional executors in disease development and response to toxicants. Proteomic
concepts and technologies have increasingly been applied in the past decades to the two closely associated disciplines in drug development and administration, pharmacology and toxicology [10–18]. Pharmacoproteomics, as implied its term, is the application of proteomic technologies in drug development and assessment of drug administration [19,20]. In contrast to empirical drug discovery where the initial drug lead is identified through functional screens without an understanding of its mechanism of action and target, modern drug development tends to rationally design or screen compounds that act against a particular biochemical target and its function. A typical path of rational drug development includes multiple consecutive knowledge-building steps, i.e., definition of drug targets, designing or screening compounds for lead compound identification, preclinical evaluation, clinical trials (I, II and III), regulatory approval, and sometimes followed by post-marketing phase IV clinical trials. Proteomic approaches can be applied to many stages or aspects in this path. While providing new tools to address the issues raised during drug development, the ultimate goal of pharmacoproteomics is to accelerate the drug development process, reduce costs, and provide tools for better management of diseases. Specifically, major aims of pharmacoproteomics research include a) verification and identification of drug targets, b) elucidation of molecular mechanisms of drug action including efficacy and toxicity, and c) development of protein biomarkers and assays for assessment of drug efficacy and toxicity for both preclinical and clinical applications. While closely associated with drug development, toxicoproteomics on the other hand focuses on the proteomic study of toxicity caused not only by drugs but also by other toxic substances, including toxins, environmental stressors, chemicals, and any other materials that may cause significant pathological responses (e.g., engineered nanomaterials) [21]. It combines with principles and methods of toxicology, pathology and other expertise to address toxicological questions. To achieve these aims, both pharmacoproteomics and toxicoproteomics are deemed to have common tasks in the analysis of protein expression, modifications, protein–protein/ drug/toxicant interactions, protein structures, protein activities, subcellular localization, etc. When new challenges come, novel proteomic technologies should be developed. A number of pharmacoproteomic and toxicoproteomic studies have been
2550
J O U RN A L OF P ROT EO M IC S 7 4 ( 2 0 11 ) 25 4 9 –25 5 3
performed and the field is being expanded dramatically. The major tools and applications or aims in the field of dreams of pharmacoproteomics and toxicoproteomics are illustrated in Fig. 1. Verification of the molecular target(s) for a particular drug is critical during drug development. Drug target analysis not only provides insights into the primary mechanism-ofaction of a drug but also can lead to an understanding of the side effects or toxicity as a result of “off-target” interactions, which will further provide the rationale for optimizing the drug lead to minimize toxicity [21]. Proteomic analysis of drug targets has been an active research area for many years. The analysis can often lead to the identification of novel therapeutic targets [22]. The predominant approach was to isolate drug associated proteins using affinity-based precipitation or chromatography and then identify and quantify them using mass spectrometry in conjunction with gel- or liquid chromatography-based separation techniques. Such analyses not only verified the target for which the drug was developed but also identified other direct targets, which provided insights into the mechanism of drug effectiveness and potential toxicity as well [23]. Proteomic approaches such as activity-based probing and protein/small molecule microarrays
have also been actively employed to identify drug targets [24]. For a long time, computational methods have been adopted to assist drug design and predict protein targets of small molecule drugs [25]. The in silico methods could have a substantial contribution to the design of multi-target drugs that will be one of the major developments in the pharmaceutical industry in the near future [26]. All these areas will continue to grow significantly. Proteomics has a great potential for understanding the mechanism of action of a drug in both preclinical and clinical development stages. Studies in this field represent the most developed areas of pharmacoprotemics over the past decade and it is expected such efforts will continue to grow rapidly. Besides the previously mentioned target identification and drug–protein interaction analysis, a variety of quantitative proteomic approaches have been applied to measure protein abundance changes upon drug treatment in in vitro cell systems, in vivo animal models and clinical samples to verify expected mechanisms of effectiveness and identify other novel mechanisms of action by analyzing large proteomic data at the pathway level [27,28]. Understanding the mechanisms of drug resistance at the proteome level was achieved substantially in the past several years, especially in the field of oncology [29]. Moreover, the power of proteomic technologies has been
Fig. 1 – The field of dreams of pharmacoproteomics and toxicoproteomics. A variety of proteomics technologies have been or are being applied to drug development and environmental health studies. Current areas of pharmacoproteomic and toxicoproteomics studies are broad, including but not limited to the identification of molecular targets of drugs and other toxicants, elucidation of mechanisms of action, biomarker development, addressing issues in pharmacokinetics and pharmacodynamics, evaluation of drug formulation and delivery, etc. Some of these research areas may cross-talk each other with the general goal of accelerating drug development, effective and safe use of drugs, and early detection of adverse effects. 2DE, two-dimensional gel electrophoresis; ESI-MS, electrospray ionization mass spectrometry; LC, liquid chromatography; MALDI-MS, matrix-assisted laser desorption/ionization mass spectrometry; MRM, multiple reaction monitoring; MS/MS, tandem mass spectrometry; MS imaging, mass spectrometry imaging; and PK/PD, pharmacokinetics/pharmacodynamics.
J O U RN A L OF P ROT EO M I CS 7 4 ( 2 0 11 ) 25 4 9 –2 55 3
demonstrated in analyzing protein modifications (e.g., adducts formed from drug metabolites), protein–protein interactions, activities, subcellular distributions, etc. Sustained application of proteomic approaches to the analysis of drug action in terms of effectiveness and toxicity will largely fulfill their roles in drug development. Safety evaluation is the highest priority throughout the drug development process. Application of proteomics concepts and technologies to drug toxicity issues is well fitted in the elucidation of toxicity mechanisms and in development of toxicity biomarkers. A biomarker is defined as “a characteristic that is objectively measured and evaluated as an indicator of normal biologic processes, pathogenic processes, or pharmacologic responses to a therapeutic intervention” [30]. Generation of a large amount of toxicoproteomic data that might lead to biomarkers and a better mechanistic understanding would potentially reduce the attrition rate and costs in drug development by detecting or predicting toxicity at the earliest stage. This research area is steadily growing. As pointed out earlier, toxicoproteomic studies are not limited to drug development. In fact, a number of toxicoproteomic analyses have been performed for environmental toxicants including air pollutants, pesticides, chemicals in water systems, and so on [16,31]. Early detection of toxicity induced by drug administration and other toxicants using qualified biomarkers would have a great potential to prevent disease development. In the past decade, a major effort of proteomics has been biomarker development. However, a majority of proteomic studies have been focused on the discovery of biomarkers for early detection and diagnosis of diseases such as cancer. In the context of co-development of drugs and diagnostic tests [32,33], biomarkers are pivotal to stratify the patients that are likely to benefit from or have adverse reactions to a particular drug. Efforts have also been made in developing pharmacodynamic biomarkers for detection of therapeutic responses and drug actions (e.g., efficacy and toxicity) using proteomic approaches [34,35]. In line with biomarker discovery, endeavors have been started to develop mass spectrometry- and microarray-based proteomic biomarker assays such as multiple reaction monitoring (MRM) [36]. These tools are being expected to be used to measure clinical biomarkers. Currently, a bottleneck in biomarker development is biomarker biological qualification. The rate of successful qualification of biomarker candidates identified from the discovery stage has been extremely low [37]. Another challenge is to translate non-clinical biomarkers to clinical biomarkers. In addition to low statistical power and small sample size in many previous proteomic biomarker studies, insufficient consideration of “context of use” of biomarkers in clinical settings was also a major reason for the failure of biomarker qualification. Researchers have just begun to realize the importance of “context of use,” which should be kept in mind at the beginning of biomarker discovery. The situation is also true for biomarker assay development where “intended use” is a key element to be considered and is being discussed [38]. Although application of proteomic technologies to pharmacokinetics wasn't growing as fast as other areas of pharmacoproteomics, the research potential is still promising in several aspects of pharmacokinetics. Quantification of drug–
2551
protein interaction in body fluids and tissues is an interesting topic of pharmacokinetic studies. Measurement of protein adducts as a result of modification by a drug and/or its metabolites upon dosing is also drawing increasing interest. A fast developing area in spatial mapping of proteins, peptides, lipids, drugs and their metabolites is mass spectrometry imaging [39]. Along with rapid technical development in MS imaging, application of such a technique to the analysis of drug/metabolite tissue spatial distribution has been expanding dramatically [40]. Recent interesting MS imaging of drug formulations was reported in the analysis of ingredients and pharmaceutical elution of stents, tablets, and powders [40]. It should be noted that modeling pharmacokinetics (PK)/pharmacodynamics (PD) can be facilitated by pharmacodynamic biomarkers identified using proteomic approaches. Significant future advance in all these areas is expected. One of the emerging areas in medicine is the biomedical application of nanomaterials. The applications are broad, including diagnosis, drug delivery, imaging, etc. Although many studies have been performed, the area is still in its infancy. The pace of bringing nanomedicine to clinical application is slow. A great potential of nanotechnology in disease diagnosis and drug action monitoring is ultrasensitive detection of biomarkers. The sensitivity of nanomaterial-based biomarker assays can reach to femto- to atto-molar levels (i.e., 10− 15–10− 18 mol/L), which is several orders of magnitude higher (in terms of sensitivity) than that obtained from conventional immunoassays or existing proteomics techniques including ELISA methods, immunochromatography, MCE enzyme immunoassays, MS-based approaches and microarrays [41]. Nanotechnology-based proteomic biomarker development is just at the beginning, thus tremendous development is anticipated. It should be noted that safety concerns have been raised from not only biomedical application of nanomaterials but also increased human exposure to nanomaterials in the environment as a result of nano-industry activities [42]. Proteomic analysis of nanoparticles could lead to novel discoveries in the action of nanomaterials in human bodies. Therapeutic agents given to humans include biologics as well as small molecules. Vaccine and antibody development is very active in the prevention and treatment of infectious diseases, cancer, etc. Proteomic studies have expedited identification and characterization of antigens which are useful for vaccine development. The area was dramatically advanced recently by using proteomic strategies to identify new protein antigens and epitopes, assess host immune system response to infection and vaccination, identify new biomarkers for evaluation of vaccine efficacy or vaccination-induced adverse effects [43]. Although not fully discussing all the areas of pharmacoproteomics and toxicoproteomics, this special edition has a collection of manuscripts in many aspects of these two disciplines. The hope is not only to summarize some recent progresses of proteomic applications to the analysis of drugs and other toxicants in drug development and use but also to encourage further development in this field of dreams. I believe the dream will become true for pharmacoproteomics and toxicoproteomics to accelerate drug development and bring more drugs and tools to public health for the safe prevention and treatment of diseases.
2552
J O U RN A L OF P ROT EO M IC S 7 4 ( 2 0 11 ) 25 4 9 –25 5 3
Acknowledgments I would like to thank all the authors and reviewers who contributed to this special edition of Journal of Proteomics. Special thanks give to Editor-in-Chief, Professor Juan Calvete, for supporting the initiation of this special edition. I am also grateful to Andy Deelen and Gerard Duggan from Elsevier for their correspondence and editorial assistance throughout the whole process. The views presented in this article do not necessarily reflect those of the U. S. Food and Drug Administration.
REFERENCES
[1] Hamburg MA, Collins FS. The path to personalized medicine. N Engl J Med 2010;363:301–4. [2] Woodcock J. The prospects for “personalized medicine” in drug development and drug therapy. Clin Pharmacol Ther 2007;81:164–9. [3] Shawver LK, Slamon D, Ullrich A. Smart drugs: tyrosine kinase inhibitors in cancer therapy. Cancer Cell 2002;1:117–23. [4] Yu LR, Issaq HJ, Veenstra TD. Phosphoproteomics for the discovery of kinases as cancer biomarkers and drug targets. Proteomics Clin Appl 2007;1:1042–57. [5] Luesch H. Towards high-throughput characterization of small molecule mechanisms of action. Mol Biosyst 2006;2: 609–20. [6] Zhang QY, Mao JH, Liu P, Huang QH, Lu J, Xie YY, et al. A systems biology understanding of the synergistic effects of arsenic sulfide and Imatinib in BCR/ABL-associated leukemia. Proc Natl Acad Sci U S A 2009;106:3378–83. [7] Schrattenholz A, Groebe K, Soskic V. Systems biology approaches and tools for analysis of interactomes and multitarget drugs. Methods Mol Biol 2010;662:29–58. [8] Gonzalez-Angulo AM, Hennessy BT, Mills GB. Future of personalized medicine in oncology: a systems biology approach. J Clin Oncol 2010;28:2777–83. [9] Mendrick DL. Transcriptional profiling to identify biomarkers of disease and drug response. Pharmacogenomics 2011;12:235–49. [10] Moller A, Soldan M, Volker U, Maser E. Two-dimensional gel electrophoresis: a powerful method to elucidate cellular responses to toxic compounds. Toxicology 2001;160:129–38. [11] Bandara LR, Kennedy S. Toxicoproteomics — a new preclinical tool. Drug Discov Today 2002;7:411–8. [12] Kennedy S. The role of proteomics in toxicology: identification of biomarkers of toxicity by protein expression analysis. Biomarkers 2002;7:269–90. [13] Witzmann FA, Grant RA. Pharmacoproteomics in drug development. Pharmacogenomics J 2003;3:69–76. [14] Wetmore BA, Merrick BA. Toxicoproteomics: proteomics applied to toxicology and pathology. Toxicol Pathol 2004;32:619–42. [15] Dowling VA, Sheehan D. Proteomics as a route to identification of toxicity targets in environmental toxicology. Proteomics 2006;6:5597–604. [16] Monsinjon T, Knigge T. Proteomic applications in ecotoxicology. Proteomics 2007;7:2997–3009. [17] Arrell DK, Niederlander NJ, Perez-Terzic C, Chung S, Behfar A, Terzic A. Pharmacoproteomics: advancing the efficacy and safety of regenerative therapeutics. Clin Pharmacol Ther 2007;82:316–9. [18] Butler GS, Overall CM. Proteomic validation of protease drug targets: pharmacoproteomics of matrix metalloproteinase inhibitor drugs using isotope-coded affinity tag labeling and tandem mass spectrometry. Curr Pharm Des 2007;13:263–70.
[19] Jain KK. Role of pharmacoproteomics in the development of personalized medicine. Pharmacogenomics 2004;5:331–6. [20] D'Alessandro A, Zolla L. Pharmacoproteomics: a chess game on a protein field. Drug Discov Today 2010;15:1015–23. [21] Gao Y, Holland RD, Yu LR. Quantitative proteomics for drug toxicity. Brief Funct Genomic Proteomic 2009;8:158–66. [22] Han MH, Hwang SI, Roy DB, Lundgren DH, Price JV, Ousman SS, et al. Proteomic analysis of active multiple sclerosis lesions reveals therapeutic targets. Nature 2008;451:1076–81. [23] Bantscheff M, Eberhard D, Abraham Y, Bastuck S, Boesche M, Hobson S, et al. Quantitative chemical proteomics reveals mechanisms of action of clinical ABL kinase inhibitors. Nat Biotechnol 2007;25:1035–44. [24] Sleno L, Emili A. Proteomic methods for drug target discovery. Curr Opin Chem Biol 2008;12:46–54. [25] Keiser MJ, Setola V, Irwin JJ, Laggner C, Abbas AI, Hufeisen SJ, et al. Predicting new molecular targets for known drugs. Nature 2009;462:175–81. [26] Koutsoukas A, Simms B, Kirchmair J, Bond PJ, Whitmore AV, Zimmer S, et al. From in silico target prediction to multi-target drug design: current databases, methods and applications. J Proteomics 2011;74:2554–74. [27] Cohen AA, Geva-Zatorsky N, Eden E, Frenkel-Morgenstern M, Issaeva I, Sigal A, et al. Dynamic proteomics of individual cancer cells in response to a drug. Science 2008;322:1511–6. [28] Millard M, Pathania D, Shabaik Y, Taheri L, Deng J, Neamati N. Preclinical evaluation of novel triphenylphosphonium salts with broad-spectrum activity. PLoS One 2010;5:e13131doi: 10.1371/journal.pone.0013131. [29] Li X-H, Li C, Xiao Z-Q. Proteomics for identifying mechanisms and biomarkers of drug resistance in cancer. J Proteomics 2011;74:2642–9. [30] Atkinson AJ, Colburn WA, DeGruttola VG, DeMets DL, Downing GJ, Hoth DF, et al. Biomarkers and surrogate endpoints: preferred definitions and conceptual framework. Clinical Pharmacology & Therapeutics 2001;69:89–95. [31] Benninghoff AD. Toxicoproteomics—the next step in the evolution of environmental biomarkers. Toxicol Sci 2007;95:1–4. [32] Hinman LM, Carl KM, Spear BB, Salerno RA, Becker RL, Abbott BM, et al. Development and regulatory strategies for drug and diagnostic co-development. Pharmacogenomics 2010;11: 1669–75. [33] Goodsaid FM, Mendrick DL. Translational medicine and the value of biomarker qualification. Sci Transl Med 2010;2:47ps44. [34] Hennessy BT, Lu Y, Poradosu E, Yu Q, Yu S, Hall H, et al. Pharmacodynamic markers of perifosine efficacy. Clin Cancer Res 2007;13:7421–31. [35] Andersen JN, Sathyanarayanan S, Di Bacco A, Chi A, Zhang T, Chen AH, et al. Pathway-based identification of biomarkers for targeted therapeutics: personalized oncology with PI3K pathway inhibitors. Sci Transl Med 2010;2:43ra55. [36] Meng Z, Veenstra TD. Targeted mass spectrometry approaches for protein biomarker verification. J Proteomics 2011;74:2650–9. [37] Anderson NL. The clinical plasma proteome: a survey of clinical assays for proteins in plasma and serum. Clin Chem 2010;56:177–85. [38] Li J, Kelm KB, Tezak Z. Regulatory perspective on translating proteomic biomarkers to clinical diagnostics. J Proteomics 2011;74:2682–90. [39] Reyzer ML, Caprioli RM. MALDI-MS-based imaging of small molecules and proteins in tissues. Curr Opin Chem Biol 2007;11:29–35. [40] Greer T, Sturm R, Li L. Mass spectrometry imaging for drugs and metabolites. J Proteomics 2011;74:2617–31. [41] Ray S, Reddy PJ, Choudhary S, Raghu D, Srivastava S. Emerging nanoproteomics approaches for disease biomarker detection: a current perspective. J Proteomics 2011;74: 2660–81.
J O U RN A L OF P ROT EO M I CS 7 4 ( 2 0 11 ) 25 4 9 –2 55 3
[42] Thomas CR, George S, Horst AM, Ji Z, Miller RJ, Peralta-Videa JR, et al. Nanomaterials in the environment: from materials to high-throughput screening to organisms. ACS Nano 2011;5: 13–20. [43] Adamczyk-Poplawska M, Markowicz S, Jagusztyn-Krynicka EK. Proteomics for development of vaccine. J Proteomics 2011;74:2596–616.
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Corresponding author at: Center of Excellence for Proteomics, Division of Systems Biology, National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd., HFT-233, Jefferson, AR 72079, USA. Tel.: +1 870 543 7052; fax: +1 870 543 7686. E-mail address: [email protected]. 2 October 2011
Li-Rong Yu Center of Excellence for Proteomics, Division of Systems Biology, National Center for Toxicological Research, FDA, Jefferson, AR 72079, USA