Structure Revision of Asperjinone using Computer-Assisted Structure Elucidation (CASE)                                    ...
ABSTRACTThe elucidated structure of asperjinone (1), a natural product isolated from thermophilicAspergillus terreus, was ...
Computer Assisted Structure Elucidation (CASE)1, 2 methods are widely used to identifythe structures of newly isolated nat...
Figure 1. The previously proposed structure of asperjinone (1) and the revised structure, 2.     Even though an expert sys...
2,6        131.5       CH        7.63, d (8.1)        C-2, 1 ,2,4                          3,5        115.8       CH      ...
expert considerations common for a traditional approach regarding HMBC correlations wereintroduced. No structural inputs r...
experimental and calculated chemical shifts was selected as the “best” representative of a set ofidentical structures. The...
1                          Revised                2                                                    3                  ...
The program selected almost 180 structures, from which such ca. 150 structures werechosen that exhibit the closest similar...
structural component of structure 2. Both structures supplied with the assigned 13C chemicalshifts (for butyrolactone V on...
of a new compound at least by NMR chemical shift prediction using fast and fully automaticempirical methods.1EXPERIMENTAL ...
Upcoming SlideShare
Loading in …5
×

Structure revision of asperjinone using computer assisted structure elucidation methods

244 views
213 views

Published on

The elucidated structure of asperjinone, a natural product isolated from thermophilic Aspergillus terreus, was revised using the expert system Structure Elucidator. The reliability of the revised structure was confirmed using 180 structures containing the (3,3-dimethyloxiran-2-yl)methyl fragment as a basis for comparison and whose chemical shifts contradict the suggested structure.

Published in: Technology
0 Comments
1 Like
Statistics
Notes
  • Be the first to comment

No Downloads
Views
Total views
244
On SlideShare
0
From Embeds
0
Number of Embeds
3
Actions
Shares
0
Downloads
3
Comments
0
Likes
1
Embeds 0
No embeds

No notes for slide

Structure revision of asperjinone using computer assisted structure elucidation methods

  1. 1. Structure Revision of Asperjinone using Computer-Assisted Structure Elucidation (CASE) Methods.Mikhail Elyashberg, Kirill Blinov, Sergey Molodtsov‡ and Antony J. Williams.§* Advanced Chemistry Development, Moscow Department, 6 Akademik Bakulev Street, Moscow117513, Russian Federation,‡ Novosibirsk Institute of Organic Chemistry, Siberian Division, Russian Academy of Sciences, 9Akademik Lavrentev Av., Novosibirsk, 630090 Russian Federation§ Royal Society of Chemistry, 904 Tamaras Circle, Wake Forest, NC-27587, USACorresponding author:Antony J. Williams904 Tamaras Circle, Wake Forest, NC-27587, USAPhone: +1 (919) 201-1516Fax:Email: tony27587@gmail.com 1
  2. 2. ABSTRACTThe elucidated structure of asperjinone (1), a natural product isolated from thermophilicAspergillus terreus, was revised using the expert system Structure Elucidator. The reliability ofthe revised structure (2) was confirmed using 180 structures containing the (3,3-dimethyloxiran-2-yl)methyl fragment (3) as a basis for comparison and whose chemical shifts contradict thesuggested structure (1). 2
  3. 3. Computer Assisted Structure Elucidation (CASE)1, 2 methods are widely used to identifythe structures of newly isolated natural products as well as new products of organic synthesis. Inthe past decade it has been shown based on multiple comparisons2, 3 that the most advancedCASE expert system is ACD/Structure Elucidator.3, 4 The system was developed with theintention of elucidating the chemical structures of organic molecules from their MS, 1D and 2DNMR spectra, generally employed in combination. In the literature there are many examplesdocumenting the successful application of Structure Elucidator, not only for the elucidation ofcomplex natural products but also for the purpose of structure revision.5, 6 Recently thesuccessful computer-assisted structure elucidation of an organic synthesis product whosestructure seemed undecipherable by traditional 2D NMR methods was described,7 while Codinaet al8 utilized the system for the analysis of a complex organic mixture. Further development of the system is driven primarily by continuously challenging theprogram with new structural problems described in the literature and, because of the generalcomplexity of the compounds described, especially new compounds reported in the Journal ofNatural Products. During the course of this work we utilized spectroscopic data reported by Liaoet al9 for deducing the structure of a new natural product named as asperjinone 1 and presentedin Figure 1. This compound was isolated, along with other 12 known compounds, fromAspergillus terreus. As a result of our analysis using Structure Elucidator the structure of 1 wasrevised and we suggest that structure 2 is the correct structure (see Figure 1). 3
  4. 4. Figure 1. The previously proposed structure of asperjinone (1) and the revised structure, 2. Even though an expert system in general mimics human thinking during the molecularstructure elucidation process from spectroscopic data, the associated mathematical algorithms actin other ways. The program automatically forms a set of “axioms” and hypotheses on the basis ofthe available spectroscopic data and then deduces all (without any exception) structures whichare logical corollaries of the initial set of “axioms”. The molecular formula C22H20O6 and theNMR data presented in Table 1 obtained from the reported work9 were used as input into theStructure Elucidator software.Table 1. 1D and 2D Spectroscopic data used for the structure elucidation of asperjinone9 (600MHz, Acetone-d6). Position C Type H (J in Hz) HMBCa 1 165.7 C 2 140.7 C 3 137.5 C 4 166.8 C 5 29.2 CH2 3.97, d (11.2) C-2, 3, 4, 1 ",2" 3.98, d (11.2) 1 119.0 C 4
  5. 5. 2,6 131.5 CH 7.63, d (8.1) C-2, 1 ,2,4 3,5 115.8 CH 7.01, d (8.1) C-1 ,4 4 160.3 C 1" 127.5 C 2" 129.6 CH 6.99, m C-4",6",7" 3" 120.9 C 4" 152.2 C 5" 117.0 CH 6.66, d (8.6) C-3",4" 6" 127.3 CH 6.99, m C-5 7" 31.2 CH2 2.67, dd (16.9, C-2",3",4",8",9" 8.0) 2.94, dd (16.9, 5.0) 8" 68.8 CH 3.76, m 9" 77.0 C 10" 19.7 CH3 1.22, s C-8",9",11" 11" 25.3 CH3 1.33, s C-8",9",10"a HMBC correlations, optimized for 6 Hz, are from the proton(s) stated to the indicated carbon .The Molecular Connectivity Diagram (MCD) automatically created by the program is presentedin Figure 2. The MCD shows atoms with their chemical shifts and their associated properties.These include the hybridization states and the possibility of neighboring with heteroatoms aswell as HMBC connectivities between atoms. sp3-hybridized carbons are colored in blue, sp2 inviolet and atoms with ambiguous hybridization (sp3 or sp2) are colored in light blue. The symbol“ob” indicates that a given atom has a heteroatom as a neighbor. The symbol “fb” shows thatsuch a heteroatom neighbor is forbidden. Two atoms (colored in pale blue) in the MCD –C(119.0) and C(120.9)  were classified as having ambiguous hybridization because thementioned chemical shifts are characteristic both for the C=C double bonds (sp2) and for C(sp3)atom if it is included into an O-C-O fragment. Carbons with chemical shifts falling into theinterval 152-167 ppm are likely connected with at least one oxygen atom. The informationpresented in MCD was used by the program for the purpose of structure generation.1 As a resultall structures in agreement with the HMBC correlations and atom properties were produced. No 5
  6. 6. expert considerations common for a traditional approach regarding HMBC correlations wereintroduced. No structural inputs regarding the presence of aromatic rings or other conceivablerings in the structure were made.Figure 2. The Molecular Connectivity Diagram (MCD) extracted from the spectroscopic data.Atoms are artificially arranged in such a manner which approximately corresponds to atompositions in revised structure 2. The following results from the structure generation process were obtained:k=365826411939, tg = 1 m 50 s. This indicates that 3658 isomeric structures were generatedin 1 m 50 s, and 2641 structures were stored on disc after spectral and structural filtering.413 C NMR chemical shifts were then calculated for the stored structures using an incrementalapproach10 (this procedure took 8 sec) and duplicate structures were removed to give 1939structures. During the latter procedure an isomer with the minimal deviation between the 6
  7. 7. experimental and calculated chemical shifts was selected as the “best” representative of a set ofidentical structures. The output structural file was ranked in ascending order of the chemical shiftdeviation. 13C chemical shifts were predicted for all 1939 structures using a neural network basedprogram (14 seconds calculation time) and then for the first 15 structures of the ranked file usinga HOSE code based program1 (1 minute calculation time). The first 9 structures of the ranked fileare displayed in Figure 3. Atoms for which  = |Ccalc-Cexp| value, the difference betweenexperimental and calculated chemical shifts, is less than 3 ppm marked by green circles, yellowcircles corresponds for =3-15 ppm and red  for >15 ppm. The figure shows that the firstranked structure (fully green) is characterized by the smallest deviations calculated by HOSEcode and neural network based methods, while the structure proposed by Liao and co-workers9was placed in third position by the ranking procedure. The deviation is almost twice the size ofthat given for the structure ranked in first position. To confirm the revised structure, 2, we performed a search for the (3,3-dimethyloxiran-2-yl)methyl fragment existing in structure 1 in the ACD/NMR Database containing 425,000structures with assigned 13C and 1H chemical shifts. H3C11" CH3 10" 7" 9" 8" O R 7
  8. 8. 1 Revised 2 3 Proposed HO HO HO O O CH3 O O CH3 O O HO O O O O O HO H3C OH H3C CH3 H3C OdN(13C): 1.372 dN(13C): 2.273 dN(13C): 2.434dA(13C): 1.384 dA(13C): 2.814 dA(13C): 2.8594 5 6 H3C CH3 HO OH O O O CH3 O OH CH3 HO O HO O O O O H3C CH3HO O O OdN(13C): 2.574 dN(13C): 2.696 dN(13C): 2.752dA(13C): 2.494 dA(13C): 2.438 dA(13C): 2.5587 8 9 H3C HO OH CH3 OH H3C CH3 O O O O HO O HO O O O O O H3C CH3 O O OHdN(13C): 2.833 dN(13C): 2.890 dN(13C): 2.915dA(13C): 2.630 dA(13C): 2.507 dA(13C): 2.541Figure 3. The first 9 structures of the output file ranked by deviations calculated using a neuralnetwork and HOSE code based 13C NMR prediction programs. Colored circles on the atomsdisplay chemical shift differences. Green color denotes the difference less than 3 ppm, yellow -between 3 and 15 ppm, and read - more than 15 ppm. Designation of deviations: dA – HOSEcode based algorithm, dN – neural network based algorithm. 8
  9. 9. The program selected almost 180 structures, from which such ca. 150 structures werechosen that exhibit the closest similarity with the environment of the oxirane fragment. For thesestructures, a scatter plot was created (see Figure 4). Here 13C chemical shifts related to the C-8”and C-9” atoms of structure 1 are presented for all selected structures. The chemical shift values(69 and 77 ppm) assigned to the corresponding atoms C-8” and C-9” in the original structure 1are also shown by their labels on the right side of the graph.Figure 4. A scatter plot of the 13C chemical shift values related to atoms 8” and 9” of the originalstructure 1. Series 1 (blue circles) corresponds to atom 9” (C 77 ppm in structure 1), series 2(violet triangles) – to atom 8” (C 69 ppm in structure 1). Inspection of the scatter plot convincingly confirms the incorrectness of the originalstructure: the chemical shifts of C-8’’ (68.8 ppm in structure 1) are observed in the range of 60-65 ppm while for C-9’’(77.0 ppm in structure 1) the corresponding range is 57-59 ppm. On the other hand, corroboration of the revised structure 2 was found in the SupportingInformation of the original work9. One of the compounds separated by the authors9 along withasperjinone (designated as butyrolactone V) was characterized and its 13C and 1H NMR chemicalshifts were assigned to the structure of butyrolactone V. This compound contains the revised 9
  10. 10. structural component of structure 2. Both structures supplied with the assigned 13C chemicalshifts (for butyrolactone V only partial assignment is shown) are presented in Figure 5.Figure 5. Comparison of chemical shift in revised part of structure 2 with those in butyrolactoneV.The structure comparison leaves no doubts regarding the correctness of structure 2. Moreover,oxirane 1JCH couplings are typically ~180 Hz, far larger than other oxygen-bearing aliphaticcarbon and the existence of an oxirane ring in the asperjinone structure proved to be erroneous.We believe that the true structure of asperjinone is as shown in 2, that is: 3-[(3-hydroxy-2,2-dimethyl-3,4-dihydro-2H-chromen-6-yl)methyl]-4-(4-hydroxyphenyl)furan-2,5-dione. Theapplication of a CASE system to the structure elucidation of this natural product would haveallowed the authors to avoid this incorrect structure as an output from their analysis. It should benoted that as far as we know this is the first example when reliable structure revision wasperformed only with the aid of CASE system without additional experiments and quantumchemical NMR shift calculations. Our research shows how it is important to verify the structure 10
  11. 11. of a new compound at least by NMR chemical shift prediction using fast and fully automaticempirical methods.1EXPERIMENTAL SECTION. All calculations were performed using the expert systemACD/Structure Elucidator v.12 installed on PC 2.8 GHz, RAM 3 Gb.REFERENCES AND NOTES.1. Elyashberg, M. E.; Williams, A. J.; Blinov, K. A. Contemporary Computer-AssistedApproaches to Molecular Structure Elucidation. RSC Publishing: Cambridge, 2012.2. Elyashberg, M. E.; Williams, A. J.; Martin, G. E. Prog. NMR Spectr. 2008, 53, 1-104.3. Steinbeck, C. Nat. Prod. Rep. 2004, 21, 512-518.4. Elyashberg, M. E.; Blinov, K. A.; Molodtsov, S. G.; Williams, A. J.; Martin, G. E. J.Chem. Inf. Comput. Sci. 2004, 44, 771-792.5. Williams, A. J.; Elyashberg, M. E.; Blinov, K. A.; Lankin, D. C.; Martin, G. E.;Reynolds, W. F.; Porco, J. A., Jr.; Singleton, C. A.; S, Su. J. Nat. Prod. 2008, 71, 581-588.6. Elyashberg, M.; Williams, A.; Blinov, K. Nat. Prod. Rep. 2010, 27, 1296–1328.7. Elyashberg, M. E.; Blinov, K. A.; Molodtsov, S. G.; Williams, A. J. Magn. Reson. Chem.2012, 50, 22-27.8. Codina, A.; Ryan, R. W.; Joyce, R.; Richards, D. S. Anal. Chem. 2010, 82, 9127-9133.9. Liao, W.-Y.; Shen, C.-N.; Lin, L.-H.; Yang, Y.-L.; Han, H.-Y.; Chen, J.-W.; Kuo, S.-C.;Wu, S.-H.; Liaw, C.-C. J. Nat. Prod. 2012, 75, 630-635.10. Smurnyy, Y. D.; Blinov, K. A.; Churanova, T. S.; Elyashberg, M. E.; Williams, A. J. J.Chem. Inf. Model. 2008, 48, 128-134. 11

×