Research advance on the interaction of pharmaceutical molecules with target proteins

LI An; ZHOU Xiaoqing; SUN Kuo; YANG Jinru; ZHU Yongfei; LU Yiming

doi:10.3969/j.issn.1006-0111.2019.01.001

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Article Navigation > Journal of Pharmaceutical Practice and Service > 2019 > 37(1): 1-4,31

LI An, ZHOU Xiaoqing, SUN Kuo, YANG Jinru, ZHU Yongfei, LU Yiming. Research advance on the interaction of pharmaceutical molecules with target proteins[J]. Journal of Pharmaceutical Practice and Service, 2019, 37(1): 1-4,31. doi: 10.3969/j.issn.1006-0111.2019.01.001

Citation:

LI An, ZHOU Xiaoqing, SUN Kuo, YANG Jinru, ZHU Yongfei, LU Yiming. Research advance on the interaction of pharmaceutical molecules with target proteins[J]. Journal of Pharmaceutical Practice and Service, 2019, 37(1): 1-4,31. doi: 10.3969/j.issn.1006-0111.2019.01.001

Research advance on the interaction of pharmaceutical molecules with target proteins

doi: 10.3969/j.issn.1006-0111.2019.01.001

1.
School of Pharmacy, Naval Medical University, Shanghai 200433, China
2.
School of Medicine, Hunan Normal University, Changsha 410013, China

Received Date: 2018-09-19
Rev Recd Date: 2018-11-16

Abstract

The function of drugs is based on the interaction between drug molecules and their targets.Qualitative analysis and quantitative detection of drug-target interactions run through the whole process from drug discovery to clinical practice.After decades of development, the study methods on the interaction between drug molecules and target proteins have been transformed from traditional biochemical experiments to a diversity of efficient and accurate technology systems supported by advanced molecular biology and biophysics theory.In this review, representative methods and techniques were introduced from aspects of target discovery and validation, affinity determination, interaction sites and structural analysis, which might provide some references for drug discovery and mechanism exploration.
- interaction,
- target protein,
- drug screening,
- affinity,
- binding sites

References

[1]	MARTINEZ MOLINA D,JAFARI R,IGNATUSHCHENKO M,et al.Monitoring drug target engagement in cells and tissues using the cellular thermal shift assay[J].Science,2013,341(6141):84-87.
[2]	SHAW J,LEVERIDGE M,NORLING C,et al.Determining direct binders of the androgen receptor using a high-throughput cellular thermal shift assay[J].Sci Rep,2018,8(1):163.
[3]	ROUX K J,KIM D I,BURKE B,et al.BioID:a screen for protein-protein interactions[J].Curr Protoc in Protein Sci,2018,91:1-15.
[4]	ZHUANG M,GUAN S,WANG H,et al.Substrates of IAP ubiquitin ligases identified with a designed orthogonal E3 ligase,the NEDDylator[J].Mol Cell,2013,49(2):273-282.
[5]	HILL Z B,POLLOCK S B,ZHUANG M,et al.Direct proximity tagging of small molecule protein targets using an engineered NEDD8 ligase[J].J Am Chem Soc,2016,138(40):13123-13126.
[6]	LINKUVIENÉ V,TALIBOV V O,DANIELSON U H,et al.Introduction of intrinsic kinetics of protein-ligand interactions and their implications for drug design[J].J Med Chem,2018,61(6):2292-2302.
[7]	POLONSCHⅡ C,DAVID S,GáSPáR S,et al.Complementarity of EIS and SPR to reveal specific and nonspecific binding when interrogating a model bioaffinity sensor; perspective offered by plasmonic based EIS[J].Anal Chem,2014,86(17):8553-8562.
[8]	HALPERN A R,WOOD J B,WANG Y,et al.Single-nanoparticle near-infrared surface plasmon resonance microscopy for real-time measurements of DNA hybridization adsorption[J].ACS Nano,2013,8(1):1022-1030.
[9]	WANG S,SHAN X,PATEL U,et al.Label-free imaging,detection,and mass measurement of single viruses by surface plasmon resonance[J].Proc Natl Acad Sci USA,2010,107(37):16028-16032.
[10]	SYAL K,WANG W,SHAN X,et al.Plasmonic imaging of protein interactions with single bacterial cells[J].Biosens Bioelectron,2015,63:131-137.
[11]	WELSCH M E,KAPLAN A,CHAMBERS J M,et al.Multivalent small-molecule pan-RAS inhibitors[J].Cell,2017,168(5):878-889.e29.
[12]	DI TRANI J M,DE CESCO S,O'LEARY R,et al.Rapid measurement of inhibitor binding kinetics by isothermal titration calorimetry[J].Nat Commun,2018,9(1):893.
[13]	WIENKEN C J,BAASKE P,ROTHBAUER U,et al.Protein-binding assays in biological liquids using microscale thermophoresis[J].Nat Commun,2010,1(7):100.
[14]	PARKER J L,NEWSTEAD S.Molecular basis of nitrate uptake by the plant nitrate transporter NRT1.1[J].Nature,2014,507(7490):68-72.
[15]	SEIDEL S A,DIJKMAN P M,LEA W A,et al.Microscale thermophoresis quantifies biomolecular interactions under previously challenging conditions[J].Methods,2013,59(3):301-315.
[16]	JERABEK-WILLEMSEN M,WIENKEN C J,BRAUN D,et al.Molecular interaction studies using microscale thermophoresis[J].Assay Drug Dev Technol,2011,9(4):342-353.
[17]	WANG J,LI H,HAN Z,et al.Allosteric receptor activation by the plant peptide hormone phytosulfokine[J].Nature,2015,525(7568):265-268.
[18]	SCHIEBEL J, RADEVA N, KÖSTER H,et al.One question,multiple answers:Biochemical and biophysical screening methods retrieve deviating fragment hit lists[J].ChemMedChem,2015,10(9):1511-1521.
[19]	BLUNDELL T L,PATEL S.High-throughput X-ray crystallography for drug discovery[J].Curr Opin Pharmacol,2004,4(5):490-496.
[20]	HUBBARD R E,MURRAY J B.Experiences in fragment-based lead discovery[J].Meth Enzymol,2011,493:509-531.
[21]	CALA O,GUILLIERE F,KRIMM I.NMR-based analysis of protein-ligand interactions[J].Anal Bioanal Chem,2014,406:943-956.
[22]	PELLECCHIA M,BERTINI I,COWBURN D,et al.Perspectives on NMR in drug discovery:a technique comes of age[J].Nat Rev Drug Discov,2008,7:738-745.
[23]	HARNER M J,FRANK A O,FESIK S W.Fragment-based drug discovery using NMR spectroscopy[J].J Biomol NMR,2013,56:65-75.
[24]	WU B,BARILE E,DE S K,et al.High-throughput screening by nuclear magnetic resonance (HTS by NMR) for the identification of PPIs antagonists[J].Curr Top Med Chem,2015,15:2032-2042.
[25]	VESTERGAARD B,SAYERS Z.Investigating increasingly complex macromolecular systems with small-angle X-ray scattering[J].IUCrJ,2014,1(Pt 6):523-529.
[26]	TUUKKANEN A T,SVERGUN D I.Weak protein-ligand interactions studied by small-angle X-ray scattering[J].FEBS J,2014,281(8):1974-1987.
[27]	NAGATOISHI S,YAMAGUCHI S,KATOH E,et al.A combination of 19F NMR and surface plasmon resonance for site-specific hit selection and validation of fragment molecules that bind to the ATP-binding site of a kinase[J].Bioorg Med Chem,2018,26(8):1929-1938.
[28]	YAN C,LIU D,LI L,et al.Discovery and characterization of small molecules that target the GTPase Ral[J].Nature,2014,515(7527):443-447.
[29]	RENAUD J P,CHUNG C W,DANIELSON U H,et al.Biophysics in drug discovery:impact,challenges and opportunities[J].Nat Rev Drug Discov,2016,15(10):679-698.

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通讯作者: 陈斌, [email protected]

1.
沈阳化工大学材料科学与工程学院沈阳 110142

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Research advance on the interaction of pharmaceutical molecules with target proteins

1. School of Pharmacy, Naval Medical University, Shanghai 200433, China

2. School of Medicine, Hunan Normal University, Changsha 410013, China

Received Date: 2018-09-19

Rev Recd Date: 2018-11-16

Key words:

Abstract: The function of drugs is based on the interaction between drug molecules and their targets.Qualitative analysis and quantitative detection of drug-target interactions run through the whole process from drug discovery to clinical practice.After decades of development, the study methods on the interaction between drug molecules and target proteins have been transformed from traditional biochemical experiments to a diversity of efficient and accurate technology systems supported by advanced molecular biology and biophysics theory.In this review, representative methods and techniques were introduced from aspects of target discovery and validation, affinity determination, interaction sites and structural analysis, which might provide some references for drug discovery and mechanism exploration.

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Reference (29)

[1]	MARTINEZ MOLINA D,JAFARI R,IGNATUSHCHENKO M,et al.Monitoring drug target engagement in cells and tissues using the cellular thermal shift assay[J].Science,2013,341(6141):84-87.
[2]	SHAW J,LEVERIDGE M,NORLING C,et al.Determining direct binders of the androgen receptor using a high-throughput cellular thermal shift assay[J].Sci Rep,2018,8(1):163.
[3]	ROUX K J,KIM D I,BURKE B,et al.BioID:a screen for protein-protein interactions[J].Curr Protoc in Protein Sci,2018,91:1-15.
[4]	ZHUANG M,GUAN S,WANG H,et al.Substrates of IAP ubiquitin ligases identified with a designed orthogonal E3 ligase,the NEDDylator[J].Mol Cell,2013,49(2):273-282.
[5]	HILL Z B,POLLOCK S B,ZHUANG M,et al.Direct proximity tagging of small molecule protein targets using an engineered NEDD8 ligase[J].J Am Chem Soc,2016,138(40):13123-13126.
[6]	LINKUVIENÉ V,TALIBOV V O,DANIELSON U H,et al.Introduction of intrinsic kinetics of protein-ligand interactions and their implications for drug design[J].J Med Chem,2018,61(6):2292-2302.
[7]	POLONSCHⅡ C,DAVID S,GáSPáR S,et al.Complementarity of EIS and SPR to reveal specific and nonspecific binding when interrogating a model bioaffinity sensor; perspective offered by plasmonic based EIS[J].Anal Chem,2014,86(17):8553-8562.
[8]	HALPERN A R,WOOD J B,WANG Y,et al.Single-nanoparticle near-infrared surface plasmon resonance microscopy for real-time measurements of DNA hybridization adsorption[J].ACS Nano,2013,8(1):1022-1030.
[9]	WANG S,SHAN X,PATEL U,et al.Label-free imaging,detection,and mass measurement of single viruses by surface plasmon resonance[J].Proc Natl Acad Sci USA,2010,107(37):16028-16032.
[10]	SYAL K,WANG W,SHAN X,et al.Plasmonic imaging of protein interactions with single bacterial cells[J].Biosens Bioelectron,2015,63:131-137.
[11]	WELSCH M E,KAPLAN A,CHAMBERS J M,et al.Multivalent small-molecule pan-RAS inhibitors[J].Cell,2017,168(5):878-889.e29.
[12]	DI TRANI J M,DE CESCO S,O'LEARY R,et al.Rapid measurement of inhibitor binding kinetics by isothermal titration calorimetry[J].Nat Commun,2018,9(1):893.
[13]	WIENKEN C J,BAASKE P,ROTHBAUER U,et al.Protein-binding assays in biological liquids using microscale thermophoresis[J].Nat Commun,2010,1(7):100.
[14]	PARKER J L,NEWSTEAD S.Molecular basis of nitrate uptake by the plant nitrate transporter NRT1.1[J].Nature,2014,507(7490):68-72.
[15]	SEIDEL S A,DIJKMAN P M,LEA W A,et al.Microscale thermophoresis quantifies biomolecular interactions under previously challenging conditions[J].Methods,2013,59(3):301-315.
[16]	JERABEK-WILLEMSEN M,WIENKEN C J,BRAUN D,et al.Molecular interaction studies using microscale thermophoresis[J].Assay Drug Dev Technol,2011,9(4):342-353.
[17]	WANG J,LI H,HAN Z,et al.Allosteric receptor activation by the plant peptide hormone phytosulfokine[J].Nature,2015,525(7568):265-268.
[18]	SCHIEBEL J, RADEVA N, KÖSTER H,et al.One question,multiple answers:Biochemical and biophysical screening methods retrieve deviating fragment hit lists[J].ChemMedChem,2015,10(9):1511-1521.
[19]	BLUNDELL T L,PATEL S.High-throughput X-ray crystallography for drug discovery[J].Curr Opin Pharmacol,2004,4(5):490-496.
[20]	HUBBARD R E,MURRAY J B.Experiences in fragment-based lead discovery[J].Meth Enzymol,2011,493:509-531.
[21]	CALA O,GUILLIERE F,KRIMM I.NMR-based analysis of protein-ligand interactions[J].Anal Bioanal Chem,2014,406:943-956.
[22]	PELLECCHIA M,BERTINI I,COWBURN D,et al.Perspectives on NMR in drug discovery:a technique comes of age[J].Nat Rev Drug Discov,2008,7:738-745.
[23]	HARNER M J,FRANK A O,FESIK S W.Fragment-based drug discovery using NMR spectroscopy[J].J Biomol NMR,2013,56:65-75.
[24]	WU B,BARILE E,DE S K,et al.High-throughput screening by nuclear magnetic resonance (HTS by NMR) for the identification of PPIs antagonists[J].Curr Top Med Chem,2015,15:2032-2042.
[25]	VESTERGAARD B,SAYERS Z.Investigating increasingly complex macromolecular systems with small-angle X-ray scattering[J].IUCrJ,2014,1(Pt 6):523-529.
[26]	TUUKKANEN A T,SVERGUN D I.Weak protein-ligand interactions studied by small-angle X-ray scattering[J].FEBS J,2014,281(8):1974-1987.
[27]	NAGATOISHI S,YAMAGUCHI S,KATOH E,et al.A combination of 19F NMR and surface plasmon resonance for site-specific hit selection and validation of fragment molecules that bind to the ATP-binding site of a kinase[J].Bioorg Med Chem,2018,26(8):1929-1938.
[28]	YAN C,LIU D,LI L,et al.Discovery and characterization of small molecules that target the GTPase Ral[J].Nature,2014,515(7527):443-447.
[29]	RENAUD J P,CHUNG C W,DANIELSON U H,et al.Biophysics in drug discovery:impact,challenges and opportunities[J].Nat Rev Drug Discov,2016,15(10):679-698.

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Research advance on the interaction of pharmaceutical molecules with target proteins

doi: 10.3969/j.issn.1006-0111.2019.01.001

Abstract

References

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通讯作者: 陈斌, [email protected]

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