Modern methods of drug design and development /

Detalles Bibliográficos
Clasificación:Libro Electrónico
Otros Autores: Lloyd, Matthew (Editor )
Formato: Electrónico eBook
Idioma:Inglés
Publicado: San Diego : Elsevier Science & Technology, 2023.
Edición:1st ed.
Colección:Methods in enzymology ; v. 690.
Temas:
Drug development > Methodology.
Drugs > Design > Methodology.
M�edicaments > D�eveloppement > M�ethodologie.
M�edicaments > Conception > M�ethodologie.
Electronic books.
Acceso en línea:Texto completo
Tabla de Contenidos:
  • Chapter Two: Steady-state kinetic analysis of reversible enzyme inhibitors: A case study on calf intestine alkaline phosphatase
  • 1 Introduction
  • 2 Measurements of 4-nitrophenol pKa
  • 2.1 Key resources table
  • 2.2 Materials and equipment
  • 2.2.1 Alternatives
  • 2.3 Step-by-step method details
  • 2.3.1 Making the series of buffers
  • 2.3.1.1 Timing: Day 1
  • 2.3.2 Measuring the 4-nitrophenol pKa value
  • 2.3.2.1 Timing: Day 1 or 2
  • 2.3.3 Data analysis
  • 2.3.3.1 Timing: Day 1 or 2
  • 2.4 Expected outcomes, advantages and limitations
  • 2.5 Statistical analysis
  • 2.6 Optimization and troubleshooting
  • 2.7 Safety considerations and standards
  • 3 Alkaline phosphatase assays
  • 3.1 Key resources table
  • 3.2 Materials and equipment
  • 3.2.1 Alternatives
  • 3.3 Step-by-step method details
  • 3.3.1 Determining the amount of enzyme required in the assay
  • 3.3.2 Calculation of adjusted 4-nitrophenol extinction coefficient
  • 3.3.3 Calculation of reaction rates
  • 3.3.4 Determining the effect of additives on the enzyme activity
  • 3.3.5 Determining kinetic parameters for alkaline phosphatase
  • 3.3.6 Determination of Km and Vmax values using the direct linear plot
  • 3.3.7 Determination of Km and Vmax values using the enzyme kinetics macro
  • 3.3.8 Calculation of numerical values for kinetic parameters
  • 3.3.9 Measurement of Z2
  • 3.3.10 Dose-response curves and determination of pIC50 values
  • 3.3.10.1 Data collection
  • 3.3.11 Data processing and determination of pIC50 values
  • 3.3.12 Rapid dilution experiment to determine inhibitor reversibility
  • 3.3.12.1 Collection of data
  • 3.3.13 Data processing
  • 3.3.14 Determination of Ki values
  • 3.3.15 Collection of data
  • 3.3.16 Data processing
  • 3.3.17 Determining the type of inhibition
  • 3.3.18 Statistical analysis of the results and determination of significance.
  • 3.4 Expected outcomes, advantages and limitations
  • 3.5 Statistical analysis
  • 3.6 Optimization and troubleshooting
  • 3.7 Safety considerations and standards
  • Acknowledgments
  • References
  • Chapter Three: Non-equilibrium modalities of inhibition: Characterizing irreversible inhibition for the ErbB receptor family membersHigh-throughput experimentation and analysis of irreversible inhibition
  • 1 Introduction
  • 1.1 Life as a kinetic state of matter
  • 1.2 Brief theory of slow binding and irreversible inhibition
  • 2 Protocol
  • 2.1 Key resource table
  • 2.2 Materials and equipment employed in this study
  • 2.3 Step-by-step method details
  • 2.3.1 Making the buffers, substrate and enzyme
  • 2.3.2 Step by step guide on how to run the assay
  • 2.3.3 Data analysis
  • 2.3.4 Considerations when interpreting assay results
  • 2.4 Optimization and troubleshooting
  • 2.5 Statistical analysis
  • 2.6 Safety considerations and standards
  • Acknowledgements
  • Declaration of conflicting interests
  • Data and software availability
  • Funding
  • References
  • Chapter Four: Analysis of continuous enzyme kinetic data using ICEKAT
  • 1 Introduction
  • 2 Program implementation
  • 3 User's guide to ICEKAT
  • 3.1 Required materials
  • 3.2 Continuous enzyme kinetic assay data analysis in ICEKAT
  • 3.2.1 Preparing and uploading data to ICEKAT
  • 3.2.2 Semi-automated ICEKAT data analysis
  • 3.3 Special considerations for specific ICEKAT analysis models
  • 3.3.1 pEC50/pIC50 model
  • 3.3.2 HTS model
  • 3.4 Special considerations for specific ICEKAT analysis modes
  • 3.4.1 Schnell-Mendoza mode
  • 3.4.2 Logarithmic Fit mode
  • 4 Data processing
  • 5 Expected outcomes, advantages, and limitations
  • 6 Conclusions
  • Acknowledgments
  • References.
  • 3.3.1.3 General Method C: Evan's auxiliary cleavage
  • 3.3.1.4 General Method D: Synthesis of acyl-CoA esters
  • 3.3.2 Synthesis of S-2-[13C]-2-[2H]-2-methyldecanoyl-CoA 10
  • 3.3.2.1 Synthesis of ethyl [2-13C]-2-ethoxycarbonyldecanoate 12
  • 3.3.2.2 Synthesis of 2-[13C]-2-[2H2]-decanoic acid 13
  • 3.3.3 Synthesis of Anti-(2R,3R)-3-fluoro-2-methyldecanoyl-CoA (17)
  • 3.3.3.1 Synthesis of (R)-4-benzyl-3-propanoyloxazolidin-2-one 19
  • 3.3.3.2 Synthesis of (R)-4-benzyl-3-[(2R,3S)-3-hydroxy-2-methyldecanoyl]oxazolidin-2-one 20
  • 3.3.3.3 Synthesis of (R)-4-benzyl-3-[(2S,3R)-3-fluoro-2-methyldecanoyl]oxazolidin-2-one 21
  • 3.3.3.4 Synthesis of (2S,3R)-3-fluoro-2-methyldecanoic acid 22
  • 3.3.3.5 Synthesis of (2R,3R)-3-fluoro-2-methyldecanoyl-CoA 17
  • 3.3.4 Synthesis of colorimetric substrate 23
  • 3.3.4.1 Synthesis of 2R,S-3-(2,4-dinitrophenoxy)-2-methylpropan-1-ol 26
  • 3.3.4.2 Synthesis of 2R,S-3-(2,4-dinitrophenoxy)-2-methylpropanoic acid 27
  • 3.3.4.3 Synthesis of 2R,S-3-(2,4-dinitrophenoxy)-2-methylpropanoyl-CoA 23
  • 3.4 Expected outcomes, advantages and limitations
  • 3.4.1 Synthesis of precursor acids
  • 3.4.2 Synthesis of acyl-CoA esters (General Method D)
  • 3.5 Optimization and troubleshooting
  • 3.6 Safety considerations and standards
  • 4 NMR assays of recombinant human AMACR 1A
  • 4.1 Key resources table
  • 4.2 Materials and equipment
  • 4.3 Step-by-step method details
  • 4.3.1 2H-exchange assay for acyl-CoA ester substrates
  • 4.3.2 Analysis of the stereochemical outcome of the reaction of 2-methylacyl-CoA esters with AMACR
  • 4.4 Expected outcomes, advantages and limitations
  • 4.5 Quantification and data analysis methods
  • 4.5.1 Data collection and referencing
  • 4.5.2 Data processing
  • 4.5.3 NMR assays with double labeled substrates
  • 4.5.4 NMR assays with eliminating substrates
  • 4.6 Optimization and troubleshooting
  • 4.7 Safety considerations and standards.

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