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S ER I ES
Computer-Aided Molecular Design
Applications in Agrochemicals, Materials, and Pharmaceuticals
Charles H. Reynolds, Editor
Rohm and Haas Company
M. Katharine Holloway, Editor
Merck Research Laboratories
Harold K. Cox, Editor
Zeneca Ag Products
Developed from a symposium sponsored by the Division of Computers in Chemistry and the Division of Agrochemicals at the 207th National Meeting of the American Chemical Society, San Diego, California, March 13-17, 1994
American Chemical Society, Washington, DC 1995
Structures of the synthesized compounds are shown in Figure 1. Cmpophilus hemipterus (L.4). Significant differences in aggregation pheromone CoMFA-coefficient contour maps were observed in the presence and absence of the "host-type" volatile coattractant.) (Coleoptera: Nitidulidae) Richard J. National Center for Agricultural Utilization Research. The pheromone components were tentatively identified by spectroscopic methods then the assigned structures were proven by synthesis (3-5). OR 45242 The driedfruit beetle. Agricultural Research Service. both before and after harvest.S. The driedfruit beetle. Peoria. hemipterus pheromone blend (3. Cmpophilus hemipterus (L. all compounds (A to Z) were tested for activity both with and 0097-6156/95/0589-0197$12. during storage after harvest or in transport (1). of Agriculture National Center for Agricultural Utilization Research. attacks a large number of agricultural commodities in the field. Attractiveness of the male-produced aggregation pheromone is enhanced by the presence of a "host-type" volatile coattractant. U. A wind tunnel bioassay guided the isolation of eleven all-E tetraene hydrocarbons.Supplied by U.00/0 © 1995 American Chemical Society . Cincinnati. Illinois Chapter 14 '7327 Insect Aggregation Pheromone Response Synergized by "Host-Type" Volatiles Molecular Modeling Evidence for Close Proximity Binding of Pheromone and Coattractant in Carpophilushemipterns (L.4). In order to investigate relationships between the structure of the pheromone molecule and biological activity. Department of Agriculture. termed host-type volatiles or host-type coattractants (6-9). S. Peoria. Both sexes of C. IL 61604 2Marion Merrell Dow. Petroski l and Roy Vaz 2 lBioactive Constituents Research. the additional compounds were prepared to explore structure activity relationships (4). A set of 26 compounds was used to explore relationships between pheromone structure and activity by 3DQSAR/CoMFA methods. hemipterus respond to a male-produced aggregation pheromone (3). two Z-isomer tetraene hydrocarbons and one all-E triene hydrocarbon (3. Compounds A to N have been identified in the C.) is a worldwide pest of avariety of fruits and grains. Previous studies have shown that aggregation pheromone activity may be enhanced when the pheromone is used in combination with attractive chemicals produced by the host plant or associated microorganisms. It js also able to vector microorganisms responsible for the souring of figs (1) and mycotoxin production in corn (2). as well as explore possible additional relationships between the coattractant and pheromone structureactivity relationships. Dept.) (Coleoptera: Nitidulidae).
198 COMPUTER·AlDED MOLECULAR DESIGN p ~ Q~ Figure 1. . Hydrocarbon structures used in the Carpophilus hemipterus data set.
If there were any extensions made. Structure A was subjected to conformational searching about the rotatable bonds using the Tripos 5. Chemical structures (Figure 1) and the corresponding bioassay data with and without coattractant (Table 1) were taken from Bartelt et al. two treatment preparations to be compared (pheromone versus control or pheromone plus coattractant versus control) were applied to pieces of filter paper. With CoMFA. The 3D structures represented in Figure 1 were constructed using structure A from the figure as a template. This observation is consistent with a hypothesis that all the structures interact with a single recognition site or a family of component recognition sites having conservation of the required bioactive conformation of the ligands at the recognition sites. The doubly substituted structure is twisted more than the singly substituted structure. (4). Some conformational searching is required to find the low energy conformations. The coattractant (propyl acetate) alone vs a blank filter paper control was only minimally attractive to C.14. Hence. Materials and Methods Data. Recent advances in computational chemistry enabled us to probe quantitative structure-activity relationships (QSAR) in three-dimensional space. as opposed to an obligate requirement for a blend of compounds (4). a suitable sampling of the steric and electrostatic fields surrounding a set of ligand molecules might provide all the information necessary for understanding their observed biological properties (13). An obligate requirement for a blend of compounds would indicate the action of distinctly different recognition sites. The minima encountered in the conformational search of compound A were optimized with the AMI Hamiltonian and the minimum conformation was used as the template. relative bioassay activity was less than 5 percent (4). PETROSKI & VAZ Insect Aggregation Pheromone Response 199 without adding a host-type coattractant (propyl acetate) to the bioassay treatments (4). a molecular mechanics force field conforma- . The results of this previous work are summarized in Table 1. Individual compounds are capable of eliciting the pheromonal response. The amount of delocalization decreases as substituent methyl groups are introduced in the progression. The data corresponded to a counting of the number of beetles alighting on pieces of filter paper in a wind tunnel bioassay. We report 3D QSAR studies with the aid of Comparative Molecular Field Analysis (CoMFA) methodology (10-13). Establishing the Conformation of Each Molecule. the single bonds in structure A were assumed to be rotatable with a reasonable energy barrier in terms of all states being populated at room temperature. A computation using the MOPAC (14) program and the AMI Hamiltonian was done on the sequence of model structures shown in Figure 2 which shows the optimal geometries as well as the bond orders. in terms of adding rotatable bonds to structure A such as in structure B. and those were hung side by side in the upwind end of the wind tunnel. one for the data without a coattractant (propyl acetate) and one for the data with the coattractant.2 Molecular Mechanics Force Field (10). each with its own structural and conformational requirements. hemipterus. Two CoMFA analyses were done.
.6E.~ Figure 2. 8E.1. A sequence of model structures (2E.. r" JJO f< ORlHOGONAL VlPN "'~ ~..-tetradecenes having 0. or 2 methyl substituents on carbons 5 and 7) showing lower delocalization and thus lowering the rotational barrier for the single bond between carbons 5 and 6 with lesser substitution.4E.200 COMPUTER·AlDED MOLECULAR DESIGN -r-.
sometimes termed the PRESS (Predictive Residual Sum of Squares). 6.5532) respectively. The overlapped structures are depicted in Figure 4.2 force field (10).6170. Superimposing the Molecules Within a Region. Points in the region where the energy of the carbon probe exceeded 30 kcal/mol were dropped from the analysis.2766. The biological activities used were those listed in Table 1.0 kcal/mol were ignored in the calculation. reduces the probability of accepting a chance correlation (13). Substituting PLS. 7. In PLS. the iterations are continued until the PRESS no longer decreases significantly. . optimized using the AMI Hamiltonian and the energies compared. This region containing the superimposed structures was utilized in a Comparative Molecular Field Analysis (CoMFA) experiment (Figure 5). Since all the compounds examined in this study are only unsaturated hydrocarbons. The result of the cross-validation is the sum of squared prediction errors. One probe is a carbon atom with no charge and the other probe is a positive charge (with no mass or van der Waals radius). -5. The points were separated at intervals of 2 AO along each axis. Comparative Molecular Field Analysis.14. choosing the minimum energy conformation again. The region only had carbon atoms used as probes and the lowest and highest points had the coordinates of 9. and the coulombic terms representing coulombic forces arising from point charges. A region. The cross-validation cycle is repeated. Normally in a CoMFA. Once an optimal conformation was obtained for all the structures. The resulting equation is used to predict the experimental measurement for the omitted compound. which operates on one independent variable at a time.4. changing the dropped columns to those having a standard deviation of less than 1. as shown in Figure 4. Cross-validation involves pretending that one of the rows does not have experimental data. The resulting individual squared errors of prediction are accumulated. The energy of the probe at each point of the region is calculated using the Tripos 5. which operates on all independent variables simultaneously. PETROSKI & VAZ Insect Aggregation Pheromone Response 201 tional search was again done on the additional rotatable bond and the minima obtained. Also. two probes are used.0 kcal/mol did not have any significant impact on the statistics. CoMFA columns whose standard deviation was less than 2. leaving out one different compound until each compound has been excluded and predicted exactly once. The predictive ability of both models (3D QSAR with and without coattractant) were evaluated using cross-validation in which the cross-validation was done using as many groups as there were rows except as noted. The two terms of interest in the force field are the 6-12 van der Waals terms which account for the London dispersion forces.2695.4965. "solvent" effect on conformations at the putative pheromone recognition site located on an insect antenna should be minimal. was then constructed such that all structures fell at least 2 N away from the region extents. for regression. The positive charge probe was not used in this study because the 1t electron clouds of the unsaturated hydrocarbons in the analysis are not reflected by the charge on the carbon atoms.0496) and (10. This reduced the number of columns involved in the Partial Least Squares (PLS) statistical analysis (15) substantially. Conformations described here are vapor phase. the structures were then overlapped via an RMS fit using the atoms labeled with an asterisk in Figure 3.
All optimized structures aligned using the atoms marked in Figure 3.202 COMPUTER·AlDED MOLECULAR DESIGN * Figure 3. The carbons marked by an asterisk are used to match the other structures after they are optimized. Figure 4. .
.. + + + + + + + + + . +..... Activity... Schematic of the CoMFA sterlc field for structure A. .+ .14. . ... + + . . .... C1·VDW1 . . .. ......... . . .....+ + .. ...+ .. + f of + ..."i- + + + ..... .. +... . . .... + .. .+ .. ... . + + .. PETROSKI&VAZ Insect Aggregation Pheromone Response 203 ... + . + .. .. . . + + + + + + + anargy fait by probe at point i Activity point i point j A B c + Partial Least Squares (PLS) . ++ .. .. . + ... . ..+ .. ........ .... f- + . + .. .. + .. f- + + + + + + .. + ... . structura A .. + . .+ ...... .. + ...... + + + ... + + + +1 . . + . . .. .... C2·VDW2 + Figure 5... + •.... const .... ... + + + . + ........ . . . + + . ...-.. .. + . .... + . + + . + ~ + + + + + ..+ ....
J. H. (7) The presence of cis double bonds at any position reduces activity (compounds M. A more refmed examination is gained by using modem 3D QSAR methods. Beyond this observation.g. substitution of ethyl for methyl renders the compound inactive or nearly so. the 5-ethyl group in compound D) also renders the compound inactive. (4) The right-hand alkyl branch (e. the CoMPA results also support the hypothesis of either a single pheromone recognition site or (less likely) a family of . P. compounds 0. which were never detected from the beetles (compounds 0 to Z in Table 1). showed activity in the bioassay (e. Although insights can be acquired by looking at two-dimensional representations of structures as are shown in Figure 1. compounds A. P and Q). the crossvalidated R-squared values (PLS) range from negative infInity to 1.g. however. 0. however. but the ethyl group seems most consistent with high activity. that insect pheromone communication systems are not as rigid as once thought. N. ethyl (compound B) or propyl (compound W) and still have activity.g. (3) An ethyl group as the middle alkyl branch (e. K.. Results and Discussion Some synthetic analogs.. Compounds A. or propyl (as in compound V) and still have activity. (6) Alkyl groups in the 9-position (compound Y) or in the 2-position (compound Z) greatly reduce activity. Thus. maximal activity in the presence of the coattractant was observed when the right-hand terminal alkyl group was ethyl. and 0 all have methyl as the terminal alkyl group. activity decreased in the presence of the coattractant.g. N. it is hard to imagine a more precise role for the coattractant without use of modem computational tools. These observations revealed a relationship between the structure of the hydrocarbon tested and the role of the coattractant. but the one example with an ethyl group at that position (compound R) did have slight activity. Some generalizations can be made about structure-activity relationships (4): (1) The left-hand terminal alkyl group (as drawn in structure A) should be methyl. ethyl (as in compound F). and 0). and X have low or no activity. V and W). In some cases (e.204 COMPUTER·AlDED MOLECULAR DESIGN Conventional R-squared values (regression range from 0 to 1. (5) The right-hand terminal alkyl group can be methyl (compound A). The R-squared values and other relevant statistics for both analyses are reasonable (Table 2). Compounds E. Relative activity was often enhanced when each unsaturated hydrocarbon was separately tested in the presence of the coattractant but the proportion of enhancement varied from hydrocarbon to hydrocarbon tested. the 7-position of compound B) can be methyl. N.0. The predicted versus actual plots for the 3D-QSAR analyses with and without the coattractant show that both CoMPA models are workable predictors of biological activity (Figure 6). shared by others (16). (2) The left-hand alkyl branch should be methyl. the compounds are actually threedimensional. only a hydrogen in that position (compounds S and T) renders the compound inactive. This observation led us to the conclusion. Another important general feature was evident from the results shown in Table 1.
14.5 + * + ++ + ~ $ '5 Predicted vs actual for structures with coattractant Ace Figure 6. Plots of predicted versus actual biological activity values for structures with and without coattractant. . 28 - + +++ + ++ + + + + ·2 + + + +++ *.+ -2 28 Ace Predicted vs actual for structures without coattractant Prado . PEfROSKI & VAZ Insect Aggregation Pheromone Response 205 Prod.
K. 10% In minerai oil).J.X.I 'The A-squared is related to the "PRESS" via the equation: (S. is the sum over all moleeiles of squared deviations of each biol09ical parameter from the mean and PAESS (Predictive Sum of Squares) is the sum over all molecules of the squared differences between the actual and predicted biological parameters (range is neg infinity to 1).811 6.851 0.964 0.490 6. Table 2 Partial Least Squares (PLS) Analysis of CoMFA Data (only steric field included) Without Coallractant With Coallractant Statistics Number of components Standard error of estimate A-squared A-squared (crossvalidated') Standard error of prediction Compounds dropped from analysis 4 3. J. where S.957 0.D.• PRESS)/S.D.727 0. Eeol. 18(3) 379-402 (1992).W U. Chern.D. .730 V.206 COMPUTER-AIDED MOLECUlAR DESIGN Table 1 Bioassay Activity for Individual Hydrocarbons a Relative Activity Hydrocarbon A B C E Without Coallractant (%) With Coallractant o 24 29 21 o 2 18 60 41 2 3 F G H I J K L M 16 49 8 17 1 o o o 4 5 5 2 o o P Q N 11 11 13 7 6 5 5 3 3 8 17 4 6 A S T U V W X y Z o o o 3 o 8 35 14 o 1 1 41 12 11 8 4 'Data from Bartelt et al.. The coattractant was propyl acetate (20 pi.891 3 2.
the new most negative area would still reside at the 10-position. These plots are actually contours of the standard deviation times PLS coefficient [(std dev)*(coefficient)] at each point in the region that fall in a particular range. These contours have the same meaning as the plots in reference 3 viz.14. hemipterus. in that case. The significant change in the CoMFA contour plot with coattractant versus the corresponding CoMFA contour plot without coattractant suggests a close proximity in binding sites for the pheromone and the coattractant near the la-position of the pheromone (e. Also. The region corresponding to the most negative coefficient region for the analysis without the coattractant is still present in the analysis with the coattractant. This can be derived from the equation in Figure 5. puts this latter methylene in a negative coefficient region. even though both regions have positive coefficients. The main analysis tools. PETROSKI & VAZ Insect Aggregation Pheromone Response 207 pheromone component recognition sites having bioactive conformation conservation in C.g.14 (black. The field times coefficient field where the field value represents the product of the molecule's field energy and the PLS coefficient from the appropriate analysis from which they were dropped between the two analyses did not lead to any activity in the new negative region for the appropriate dropped molecules.7 (light gray.19 (black. which would be over the methylene portion of the right-hand terminal ethyl group. The contour plot from the analysis of the structures with a coattractant is quite interesting. A new. Figure 8) with structure A embedded in the contour plots. Figure 7) or 0. their relative values are different and thus the structural extensions have different consequences on the activity. and very well-defined most-negative region seems to have been created which could possibly be attributed to the coattractant occupying this region on the putative receptor. in terms of computer aided molecular design. no change would be made in that region for increased activity. that region in space would need lower van der Waals interaction energies if a carbon probe atom were placed in that region or at the very most. The contours are centered at -0. An . are the coefficient plots as shown in figures 7 and 8. The field is created as the point by point product of the PLS coefficient and the standard deviation of energies at the point among all compounds in the study.. thereby eliminating this new region as arising from the outliers not used in the analysis. both Figures) and 0. Similarly. if the contour is for a region corresponding to a negative value. The view of this field is preferred to the view of only the PLS coefficients field because it reduces the visual cluster of moderately large coefficients that arise by chance association with larger scale trends. The positive and negative coefficient regions show that extending the structure A by a methylene in the direction as in structure B puts the methylene in a positive coefficient region and similarly extending structure A by a methylene in the other direction. The (field)*(coefficient) plot represents the contribution of this field for this molecule to its predicted activity. a positive region would prefer increased van dar Waals interaction energies for a carbon probe for increased activity. extending molecule A by a methylene such as in structure B or differently such as in structure C. as in structure E. sharp. compound A in Figure 8) If compound B were pictured in the figure.
Most Negative Coefficient \ \ \ .208 COMPUTER·AlDED MOLECUlAR DESIGN .... * coefficient CoMFA contour plot for the structures with coattractant showing only structure A. .. * coefficient Co MFA contour plot for the structures without coattractant showing only structure A. .. The std... Figure 8. .. .. dey.. The std...' • Figure 7. dey. w.. .... Most Negative Coefficient .
A. E. 1988.. Van Opdenbosh. J. Jarrold and Sons: Norwich. Patterson. E. it might be possible that an oxygen atom from the coattractant (propyl acetate) resides at this new most negative site. hemipterus pheromone recognition sites have enough fluidity then it is theoretically possible to develop pheromone analogs that serve as species-specific insect control agents.. Walgenbach. 1989.. R. J. Khan. 7. R. It is also theoretically possible that pherolnone perception inhibitors (antagonists) could be developed against C. H. Carefully designed pheromone analogs. R. D. Pierce H. Bunce.... Chou. The Netherlands. J. 1.. Carde. 1. R. J. D. 1988. Weisleder.. 1993. Clark. D. D. Cramer III. 1945. It would be interesting to place an oxygen atom in a pheromone analog at this position in 3D space. 18. W. W. C. Birch. . Kabinyi. A. p263. F. A. D.. 1. Eds. R. R. Plattner.14. N. E. Institute of Botany. Waller.9: Taipei. Entomo!.K. 1. 1992. Bprden. 1984. 2192. M. 6. Mycotoxins and Insect Pheromones and Allomones. S.. M. 16. 18.11. 1015. H.. 1. Dowd. p 443. might surpass the natural pheromone in biological activity. This placement of the coattractant would not have been possible without a 3D analysis. PETROSKI & VAZ Insect Aggregation Pheromone Response 209 alternative.. or stability under field conditions. Weisleder. 2.. Bell. interpretation of our CoMFA data would be binding of the coattractant at a separate binding site but affecting the binding of the pheromone (allosterism). J. ROC. D. R. Bartelt. 443 pp. A Monograph of the Beetles Associated with Stored Products. 5959. or blends thereof.. Food Chem. but this has yet to be tested experimentally. Eco!.. Agric.. T. Chem. ease of preparation. E. Hinton. Chem. Chem. 2071..10. R. In Phytochemical Ecology: Allelochemicals. J. R. Chem. 1. Jackson. in "3D QSAR in Drug Design: Theory and Applications". Schaner. Am. G. U. but less likely. M. Cramer III. 1990.. Pierce. C.. M. hemipterus. OeWscWager. Weisleder. Jr. A. A. J.. R. Based on our CoMFA results. Hecht. D. C. D. 1. H.... Z.. Burkholder. D.. D. 10. R. Compo Chem. 5. 1987.. R. Wicklow. Sinauer Assoc. Cramer III. 379. J Econ. D. Physiol. 1990. Plattner. 9. 763. In Chemical Ecology ofInsects. Entomo!.. Ed. Such analogs would iinprove our ability to monitor pest populations. Eeo!. 8. Plattner. or lower pest populations by use of combinations of pheromone and either insecticides or biological control agents. ESCOM. M. C. 1986. Eco!. . 110. Dowd. Bartelt. Literature Cited 1. 11. P. Chapter 12. Curtis. 80. P. Bartelt. D. Bartelt.. Eds. J.: Sunderland.. Soc. D. A. 12. J. H. 1989.. lower pest populations by mass trapping. F. If C.367. T. Academia Sinica Monograph Series No. 14.. 4. 3. Massachusetts. P. D. Patterson. Pheromone perception inhibitors could be used for the protection of commodities during storage or transport. 982.. DePriest.
Frank. 16. 309. Struct. D. 1988. IN. Bloomington. Indiana University. P.. McLaughlin. and Harold K.Act. Patterson. V. Quant. and Pharmaceuticals Charles H. A.. Cramer III. Bioi. 18.210 COMPUTER·AIDED MOLECUlAR DESIGN 13. Chern. 7.. in "QSAR: Rat ion a I Approaches to the Design ofBioactive Compounds". Materials.. 589 Computer-Aided Molecular Design: Applications in Agrochemicals. E. D.. Amsterdam 14. D. Eds. and Vittoria. Experientia 1982.... 1995 Reprinted from ACS Symposium Series No. Bunce. Carlson.0 is available from QCPE. Pharmacol. 15. E. SHipo. J. Elsevier Science Publishers B. RECEIVED January 31. J. Patterson. C. M. Cox. 38. R. MOPAC 5. D. A. Editors Copyright © 1995 by the American Chemical Society Reprinted by permission of the copyright owner . 1. D. Simeroth. Reynolds. Relat. E. D. R. Cramer III. Katherine Holloway. R..
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