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ACD/NMR Workbook: A Toolkit for Pharma’sNMR Spectroscopist
Janet Caceres-CortesBristol-Myers Squibb Company
NMR in the Pharmaceutical Industry
NMR spectroscopy has evolved into an important technique in support of
critical activities within the discovery and development workspace:
SAR and lead optimization, process chemistry,
metabolite ID and quantification, mechanistic studies,
biophysical characterization, stability/degradation,
process optimization, safety assessments …
different structural modalities:
small molecules, millamolecules, proteins
synthetic intermediates and final products, drug
metabolites from in vivo and in vitro sources,
endogenous metabolites in biofluids, excipients,
residual solvent and impurities …
We support
We work with
We analyze
Discovery NMR Experts
DevelopmentNMR Experts
Medicinal Chemists
ProcessChemists
ACD/Labs: Spectrus Processor; 1H, 13C, 15N Predictors;
NMR Workbook, Spectrus DB
ACD/Labs NMR Landscape
ACD/Labs
Desktop Processing/Prediction
Batch Characterization Reports
Metabolite ID Reports
From OA to Email & Electronic Notebook:
PDF w/ Embedded JDX
Journals & Patents
Database 1H, 13C, 15N
1H NMR (DMSO-d6, 600MHz):d = 8.70 (d, J=4.4 Hz, 1H), 7.95(d, J=9.1 Hz, 1H), 7.53 (d, J=4.3Hz, 1H), 7.48 (br. s., 1H), 7.40(dd, J=9.0, 2.1 Hz, 1H)
Samples 1H 13C 15N
1 √ √
2 √ √ √
3 √ √
4 √ √ √
5 √ √
Integrated Work Practices
ACD/NMR Workbook…
Initially adopted for incorporation into metabolite ID workflow and reporting activities
DRUG
M1
M7
M8M10
M9
M3
M4
M5
M6
M2
Metabolite Identification
Drug Discovery: enables early identification of potential metabolic liabilities to help avoid failure at later stages : Soft spot analysis for SAR and lead optimization Assess contributions to pharmacokinetic parameters Toxicity evaluations in preclinical species
Drug Development: a strong emphasis is placed on truly understanding the efficacy and safety profile of drugsand the contributions of their metabolites to these profiles. Metabolite profiling Determination of metabolite exposures Assessment of metabolic clearance pathways in humans and toxicological species MIST - metabolite characterization plan.
8 7 6 5 4 3 2 1 0Chemical Shift (ppm)
9 8 7 6 5 4 3 2 1 0Chemical Shift (ppm)
NMR Metabolite ID Activities
Full Assignment of Parent compound from 1D and 2D spectra
Usually provided from a synthetic batch Available in milligram quantities Impurities left from the reaction mixture, solvents and other sources are small compared to parent NMR peaks
Comparison of metabolite spectra with parent (1D, and 2D when needed)
Generally isolated from in vitro and in vivo sources Available in low microgram quantities Impurities are at scale with or larger than metabolite NMR peaks
13C spectra usually not obtained
Metabolite spectra
Why ACD/NMR Workbook…Efficiency and Ease of useParent datasets:
Eliminates the need to print spectra and assign on paper Full assignments quickly obtained; assignments appear across all spectra
1H and 13C chemical shifts and coupling constants table generated Used for reporting, but also used for elucidating metabolite structures
Flexibility and Fit for PurposeMetabolite datasets:
Tile or overlay of parent and metabolite spectra (e.g. 1H/1H) Tile or overlay of metabolite spectra (e.g. HSQC/HMBC) Assignments by iterative inspection of 1D and 2D data accommodated Can utilize dark regions in 2D to tag impurity peaksPartial or targeted assignments for “fit for purpose” work practices (e.g. 1H spectrum yields an unambiguous structure or key correlations are established in a dataset where impurities preclude a full elucidation)
ACD/NMR Workbook
Easy access to data and structures; also can see experiment type
Easy access ‘one click’ buttons for routine tasks
Drag parent data into a project for assigning (can have multiple projects open)
Undo/redo buttons
1d spectra height adjusted with mouse scroll
Assignment numbers shown on vertical and horizontal axes
Create horizontal and vertical lines in 2D data to facilitate peak picking
ACD/NMR WorkbookACD v12
ACD v2012
ACD 12 peak picking sometime results in small chemical shift differences for the same carbon- program treats them as different carbons which can cause issues with table generation
ACD v2012 – can click to add horizontal lines, vertical lines or both
ACD/NMR Workbook
Peak picking can be performed in an automated fashion or manuallyAssignments are easily generated by selecting a peak of interest and scrolling to the corresponding atom on the structure
ACD/NMR Workbook Molecule can be renumbered or changed within the Workbook, without the need to go into ChemSketch.
ACD/NMR Workbook Structure and data windows can be detached from the Workbook providing increased flexibility to the users.
Metabolism and Disposition of BMS-690514
M1, M3, M6, M7, and M9 were the major circulating metabolites in human plasma after oral administration of BMS-690514.
Hong et al . Chem. Res. Toxicol. (2011)24, 125–134
M6 [NMR] M8 [NMR, mixture]
M7 [NMR]
M1 [NMR]
M2
M3
M9
M37
NMRSync allows synchronized peak peaking and assignment across a dataset
Toolbar –quick way to label peaks, define and edit multiplets and assignments Multiplet or peak picking in one spectrum transfers information to the others Chemical shifts are displayed on screen, making assigning easier
1
2
3
4
5
NMRSync generates tables summarizing the assignment information
Assignments, chemical shift, coupling constants and correlations are captured in tables eliminating the need to manually capture this information Eliminates errors associated with typing this information manually Can be copied to report editor or clipboard, exported , and inserted into a Microsoft Word or Excel table
Atom# XHn H Shift H Multiplicity C Shift COSY H HMBC C HMBC
2 CH2 3.069 d (7.23) 58.740 1.95 1.82, 2.92, 3.29, 3.73 73.52, 52.31, 55.30
2 CH2 1.954 br.s 58.740 3.07, 3.29, 2.11 1.82, 2.92, 3.29, 3.73 73.52, 55.30, 52.31
3 CH 3.292 d (3.73) 73.519 1.95, 2.46 1.32, 1.82, 1.95, 2.46, 3.07 58.74
4 CH 2.456 br.s 55.302 1.32, 3.29 1.32, 1.82, 1.95, 2.92, 3.07 32.09, 73.52
5 CH2 1.324 d (9.65) 32.094 1.82, 2.11, 2.46 2.11, 2.46, 2.92 55.30, 52.31, 73.52, 55.88
5 CH2 1.824 d (10.74) 32.094 1.32 2.11, 2.46, 2.92 55.88, 55.30, 58.74, 73.52
6 CH2 2.107 br.s 52.309 1.32, 1.95, 2.92 1.32, 1.95, 3.07, 3.73 32.09
6 CH2 2.923 d (10.74) 52.309 2.11 1.32, 1.95, 3.07, 3.73 58.74, 32.09, 55.30
7 CH2 3.731 br.s 55.883 1.32, 1.82, 6.58 113.58, 115.33, 52.31, 58.74, 114.14
8 C 114.145 3.73, 6.58, 7.47
9 C 115.331 3.73, 7.47
12 CH 7.777 s 148.203 154.47
14 C 154.474 7.78
15 CH 6.576 br.s 113.575 7.47 3.73, 7.47 118.66, 114.14, 55.88
16 CH 7.473 br.s 118.661 6.58 6.58 113.58, 115.33, 114.14
20 C 140.360 7.12, 7.28, 7.31
21 CH 7.282 br.s 109.246 7.12 6.75, 7.12, 7.31 110.88, 160.74, 115.70, 140.36
22 C 160.744 3.79, 6.75, 7.12, 7.28, 7.31
23 CH 6.751 d (7.45) 110.877 7.31 7.12, 7.28, 7.31 115.70, 109.25, 160.74
24 CH 7.308 t (8.79, 8.79) 131.060 6.75, 7.12 7.12 160.74, 109.25, 110.88, 140.36, 115.70
25 CH 7.118 d (7.23) 115.700 7.31, 7.28 6.75, 7.28, 7.31 140.36, 131.06, 110.88, 109.25, 160.74
27 CH3 3.793 s 56.233 160.74
Comparisons of parent and metabolite 1H spectra are usually performed first Tile by selecting the appropriate icon and setting the number of spectra to display. Parent spectra is displayed with assignments facilitating comparisons
Tile or overlay spectra for easy comparisons and to assist metabolite assignments
Overlay spectra by clicking on Series – Collect Spectra The spectra can be offset (shown here) or superimposed using the Manual Offset tool Parent spectra is displayed with assignments facilitating comparisons
Tile or overlay spectra for easy comparisons and to assist metabolite assignments
Tile or overlay spectra for easy comparisons and to assist metabolite assignments
Overlay spectra by clicking on Series – Collect Spectra The spectra can be offset (shown here) or superimposed using the Manual Offset tool Parent spectra is displayed with assignments facilitating comparisons
Comparisons of parent and metabolite COSY and HSQC are performed if the metabolite structure is not determined from its 1H spectrum. In overlay mode, spectra are distinguished by color and different font size Peak picking and assignments can be performed in overlay mode
Tile or overlay spectra of 2D data from Parent and Metabolite
ParentMetabolite
In Tile mode the cursor spans both tiles facilitating comparisons Peak picking and assignments can be performed in tile mode
Parent M1
Tile or overlay spectra of 2D data from Parent and Metabolite
Dark Regions are regions in the spectrum that are not taken into account by the program when performing peak picking, integration, and verification. Solvent and impurity peaks can be tagged in both the 1D and 2D spectra Very useful when assigning around regions with a lot of extraneous peaks
Dark Regions used to tag impurity peaks
After assignments are complete, dark regions can be removed or hidden. To hide a dark region without removing it, uncheck the Active box in the Dark Region Organizer.
Dark Regions can be hidden
Comparing COSY, HSQC and HMBC spectra from the metabolite facilitates iterative peak peaking to complete assignments
Tiling HSQC and HMBC spectra from the metabolite to complete assignments
8Hz 4Hz
Changing Structures Mid-Stream
Can use parent molecule or a proposed structure when beginning metabolite ID work. Structures can be changed in ChemSketch and re-incorporated into the NMR Workbook project
21
25
16
8.5 8.0 7.5 7.0 6.5 6.0Chemical Shift (ppm)
211523 16
1224
16
25
21
Easily incorporate assigned spectra and all associated data into reports
Ideal for comprehensive metabolite ID reports: ACD numbered structure,1D spectra of parent and metabolite with assignments, 2D spectra and structures with key correlations highlighted, Table of chemical shifts
4
3
5
6
N1
2
7
15
8
16
N10
9
N11
12
N13
14
N19
25
24
20
21
22
23
O26
CH3
27
OH17
NH218
OH28
4
3
56
N1
2
7
15
8
16
N10
9
N11
12
N13
14
NH19
25
24
20
2122
23
O26
CH3
27
OH17
NH218
1D ROE
ACD/NMR Workbook NMR Workbook is more efficient than assigning on spectral printouts
Syncing spectra in tile or overlay mode is central to metabolite ID work, where comparisons to parent data is routinely performed.
Dark regions can be used for ‘tagging’ impurities and are easily hidden for reporting.
Proposed structures can be changed once a definitive structure is elucidated
The Workbook has numerous advantages for reporting and publishing.
The v2012 edition of NMR Workbook has significant improvements over version 12 that better address the diverse spectral features of NMR datasets and it has an even more simplified user interface
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