| Literature DB >> 18728732 |
Lorentz Jäntschi1, Sorana D Bolboaca.
Abstract
Quantitative structure-activity relationship models were obtained by applying the Molecular Descriptor Family approach to eight ordnance compounds with different toxicity on five marine species (arbacia punctulata, dinophilus gyrociliatus, sciaenops ocellatus, opossum shrimp, and ulva fasciata). The selection of the best among molecular descriptors generated and calculated from the ordnance compounds structures lead to accurate monovariate models. The resulting models obtained for six endpoints proved to be accurate in estimation (the squared correlation coefficient varied from 0.8186 to 0.9997) and prediction (the correlation coefficient obtained in leave-one-out analysis varied from 0.7263 to 0.9984).Entities:
Keywords: Molecular Descriptors Family (MDF); Ordnance compounds; Regression analysis; Structure-Activity Relationship (SAR); Toxicity
Mesh:
Substances:
Year: 2008 PMID: 18728732 PMCID: PMC2525494 DOI: 10.3390/md20080017
Source DB: PubMed Journal: Mar Drugs ISSN: 1660-3397 Impact factor: 5.118
Figure 12D structure of ordnance compounds.
Ordnance compounds toxicity: experimental EC50.
| Specie | Endpoint | 2,4-DNT | 2,6-DNT | 1,3-DNB | 2,4,6-TNT | 1,3,5-TNB | PAc | Tetryl | RDX |
|---|---|---|---|---|---|---|---|---|---|
| sea urchin | fertilization | 1.8325 | n.a. | 2.4116 | n.a. | 1.9243 | 2.5428 | 0.4771 | n.a. |
| embryological development | 1.7110 | 0.8261 | 1.9638 | 1.0792 | 0.1139 | 2.4487 | −1.0969 | n.a. | |
| germination | 0.3979 | 0.8261 | −0.0706 | 0.3979 | −1.0969 | 2.6180 | −0.1739 | 1.0792 | |
| polychaete | survival and reproductive success | 0.7559 | 0.3222 | 0.5682 | 0.2553 | −0.2218 | 2.1903 | −1.6990 | 1.4150 |
| redfish | larvae survival | 1.6812 | 1.5315 | 1.6628 | 0.9138 | 0.1461 | 2.1038 | 0.2553 | n.a. |
| mysid | juveniles survival | 0.7324 | 0.7482 | 0.8513 | −0.0088 | 0.1139 | 1.1139 | 0.1139 | 1.6628 |
| macro-alga | germling length | 0.2304 | 0.4624 | −0.3872 | −0.1192 | −1.3010 | 1.9731 | −0.4685 | 0.9085 |
| germling cell number | 0.3222 | 0.6232 | −0.3468 | 0.1461 | −1.2218 | 2.0719 | −0.3979 | 0.9912 | |
| survival | 1.3222 | 1.1139 | 1.1761 | 0.8865 | 0.3222 | 2.4232 | −1.2218 | n.a. | |
EC50 = Effective Concentration to 50% of the organism expressed as logarithmic scale;
2,4-DNT = 2,4-dinitrotoluene; 2,6-DNT = 2,6-dinitrotoluene;
1,3-DNB = 1,3-dinitrobenzene; 2,4,6-TNT = 2,4,6-trinitrotoluene;
1,3,5-TNB = 1,3,5-trinitrobenzene; PAc = 2,4,6-trinitrophenol (picric acid);
Tetryl = 2,4,6-trinitrophenylmethylnitramine;
RDX = hexahydro-1,3,5-trinitro-1,3,5-triazine (Royal Demolition Explosive); n.a. = not available (experimental data expressed as greater than – mg/L)
Ordnance compounds toxicity: experimental NOEC values.
| Specie | Endpoint | 2,4-DNT | 2,6-DNT | 1,3-DNB | 2,4,6-TNT | 1,3,5-TNB | PAc | Tetryl | RDX |
|---|---|---|---|---|---|---|---|---|---|
| sea urchin | fertilization | 1.5911 | 1.3617 | 1.9243 | 2.0128 | 1.5441 | 2.2504 | n.a. | 1.8751 |
| embryological development | 1.2553 | n.a. | n.a. | 0.3222 | −0.6198 | 2.2504 | −1.4437 | 1.8751 | |
| germination | −0.0269 | 0.3424 | −0.5229 | 0.2304 | −1.3372 | 2.2279 | −0.3010 | 0.9638 | |
| polychaete | laid eggs/female | n.a. | n.a. | 0.3802 | 0.1461 | −0.4559 | 2.0334 | −1.8239 | 1.0755 |
| redfish | larvae survival | 1.5391 | 1.1367 | 1.4014 | 0.7993 | −0.0044 | 1.9868 | 0.0792 | 1.8325 |
| mysid | survival | 0.5563 | 0.6990 | 0.7160 | −0.1871 | −0.0177 | 0.9638 | 0.0414 | 1.6721 |
| macro-alga | germling length and cell number | n.a. | n.a. | n.a. | n.a. | −1.5376 | n.a. | −1.0088 | n.a. |
| survival | 0.9777 | 1.1644 | 0.9868 | 0.7853 | 0.0792 | 2.2989 | −1.5850 | 1.6902 | |
NOEC = No Observed Effect Concentration;
2,4-DNT = 2,4-dinitrotoluene; 2,6-DNT = 2,6-dinitrotoluene;
1,3-DNB = 1,3-dinitrobenzene; 2,4,6-TNT = 2,4,6-trinitrotoluene;
1,3,5-TNB = 1,3,5-trinitrobenzene; PAc = 2,4,6-trinitrophenol (picric acid);
Tetryl = 2,4,6-trinitrophenylmethylnitramine; RDX = hexahydro-1,3,5-trinitro-1,3,5-triazine (Royal Demolition Explosive);
n.a. = not available (experimental data expressed as greater than a value – mg/L)
Ordnance compounds toxicity: experimental LOEC values.
| Specie | Endpoint | 2,4-DNT | 2,6-DNT | 1,3-DNB | 2,4,6-TNT | 1,3,5-TNB | PAc | Tetryl | RDX |
|---|---|---|---|---|---|---|---|---|---|
| sea urchin | fertilization | 1.8751 | 1.6532 | 2.0414 | n.a. | 1.6812 | 2.5465 | −0.2218 | n.a. |
| embryological development | 1.5911 | 0.6990 | 1.9243 | 0.9590 | −0.3188 | 2.5465 | −1.0809 | n.a. | |
| germination | 0.2553 | 0.6721 | −0.1871 | 0.5315 | −1.0315 | 2.5263 | 0.0000 | 1.1959 | |
| polychaete | laid eggs/female | 0.3802 | 0.2553 | 0.6435 | 0.4472 | −0.2147 | 2.2967 | −1.5850 | 1.3747 |
| redfish | larvae survival | 1.8248 | 1.5051 | 1.6955 | 1.0334 | 0.3010 | 2.2718 | 0.4150 | n.a. |
| mysid | survival | 0.8325 | 0.9912 | 0.9868 | 0.1271 | 0.2742 | 1.3139 | 0.3010 | n.a. |
| macro-alga | germling length and number | cell −0.3188 | 0.0792 | −0.6778 | −0.6778 | −1.3372 | 1.9638 | −0.6021 | 0.6990 |
| survival | 1.2788 | 1.4713 | 1.2923 | 1.0645 | 0.3802 | 2.5786 | −1.2518 | n.a. | |
LOEC = Lowest Observed Effect Concentration;
2,4-DNT = 2,4-dinitrotoluene; 2,6-DNT = 2,6-dinitrotoluene;
1,3-DNB = 1,3-dinitrobenzene; 2,4,6-TNT = 2,4,6-trinitrotoluene;
1,3,5-TNB = 1,3,5-trinitrobenzene; PAc = 2,4,6-trinitrophenol (picric acid);
Tetryl = 2,4,6-trinitrophenylmethylnitramine; RDX = hexahydro-1,3,5-trinitro-1,3,5-triazine (Royal Demolition Explosive)
n.a. = not available (experimental data expressed as greater than a value – mg/L)
MDF SAR monovariate models: EC50.
| sea urchin
| |||
|---|---|---|---|
| Endpoint | fertilization | embryological development | germination |
| MDF SAR Equation | Ŷ = − 0.16 – 0.37·X | Ŷ = −7.09 – 1.09·X | Ŷ = −1.50 + 6.28·10−2·X |
| (Eq_no) | Eq_01 | Eq_02 | Eq_03 |
| Correlation coefficient (r) | 0.9997 | 0.9650 | 0.9435 |
| 95% confidence interval for r | [0.9885–0.9999] | [0.6193–0.9973] | [0.5477–0.9942] |
| Standard error of estimated (s) | 0.02 | 0.35 | 0.39 |
| Fisher parameter (p-value) | 5674 (p = 5.16·10−6) | 68 (p = 4.32·10−4) | 49 (p = 4.32·10−4) |
| Cross-validation leave-one-out score (rcv-loo2) | 0.9984 | 0.8460 | 0.8333 |
| Sample size | 5 | 7 | 8 |
| Descriptor (X) | LIMmwQt | lNPmfQt | aIDmjQg |
| Dominant Atomic Property | Partial charge ( | Partial charge ( | Partial charge ( |
| • Interaction via | Bonds ( | Bonds ( | Space ( |
| • Interaction Model | Q2/d | Q2/d2 | (Q·d)−1 |
| • Structure on Activity Scale | Logarithmic | Logarithmic | Inversed |
| MDF SAR Equation | Ŷ = −1.73 + 16.91·X | Ŷ = 0.28 − 1.31·X | Ŷ = 3.93 − 0.80·X |
| Eq | Eq_04 | Eq_05 | Eq_06 |
| Correlation coefficient (r) | 0.9655 | 0.9531 | 0.9787 |
| 95% confidence interval | [0.7000–0.9965] | [0.5186–0.9963] | [0.7511–0.9983] |
| Standard error of estimated (s) | 0.32 | 0.25 | 0.10 |
| Fisher parameter (p-value) | 82 (p = 1.00·10−4) | 50 (p = 8.92·10−4) | 114 (p = 1.25·10−4) |
| Cross-validation leave-one-out score (rcv-loo2) | 0.8852 | 0.8412 | 0.9267 |
| Sample size | 8 | 7 | 7 |
| MDF Descriptor | anDRJQt | LHDmjQg | imMrtCg |
| Dominant Atomic Property | Partial charge ( | Partial charge ( | Cardinality ( |
| • Interaction via | Bonds ( | Space ( | Space ( |
| • Interaction Model | Q·d | (Q·d)−1 | C2/d4 |
| • Structure on Activity Scale | Inversed | Logarithmic | Inversed |
| MDF SAR Equation | Ŷ = −6.13 − 1.88·X | Ŷ = −6.02 − 1.87·X | Ŷ = −0.79 − 102.72·X |
| Eq | Eq_07 | Eq_08 | Eq_09 |
| Correlation coefficient (r) | 0.9445 | 0.9359 | 0.9835 |
| 95% confidence interval | [0.7170–0.9901] | [0.6790–0.9885] | [0.8884–0.9976] |
| Standard error of estimated (s) | 0.35 | 0.38 | 0.22 |
| Fisher parameter (p-value) | 50 (p = 4.09·10−4) | 42 (p = 6.28·10−4) | 148 (p = 6.65·10−5) |
| Cross-validation leave-one-out score (rcv-loo2) | 0.8045 | 0.7933 | 0.9503 |
| Sample size | 8 | 8 | 7 |
| Descriptor (X) | LIDmjQg | LIDmjQg | IAPmtQt |
| Dominant Atomic Property | Partial charge ( | Partial charge ( | Partial charge ( |
| • Interaction via | Space ( | Space ( | Bonds ( |
| • Interaction Model | (Q·d) −1 | (Q·d) −1 | Q2·d−4 |
| • Structure on Activity Scale | Logarithm | Logarithm | Identity |
d = distance
MDF SAR monovariate models: NOEC.
| sea urchin
| |||
|---|---|---|---|
| Endpoint | fertilization | embryological development | germination |
| MDF SAR Equation | Ŷ = 1.42 + 0.17·X | Ŷ = −1.27 + 1.27·10−3·X | Ŷ = −1.74 + 6.08·10−2·X |
| (Eq_no) | Eq_10 | Eq_11 | Eq_12 |
| Correlation coefficient (r) | 0.9739 | 0.9859 | 0.9355 |
| 95% confidence interval for r | [0.8283–0.9962] | [0.8721–0.9985] | [0.6772–0.9885] |
| Standard error of estimated (s) | 0.08 | 0.27 | 0.41 |
| Fisher parameter (p-value) | 92 (p = 2.09·10−4) | 139 (p = 2.97·10−4) | 42 (p = 6.38·10−4) |
| Cross-validation leave-one-out score (rcv-loo2) | 0.9101 | 0.9417 | 0.8105 |
| Sample size | 7 | 6 | 8 |
| Descriptor (X) | ASPmwQg | asmrfQt | aIDmjQg |
| Dominant Atomic Property | Partial charge ( | Partial charge ( | Partial charge ( |
| • Interaction via | Space ( | Bonds ( | Space ( |
| • Interaction Model | Q2·d−1 | Q2·d−2 | (Q·d) −1 |
| • Structure on Activity Scale | Absolute | Inversed | Inversed |
| MDF SAR Equation | Ŷ = −10.25 − 1.42·X | Ŷ = 9.35·10−2 − 1.37·X | Ŷ = 19.24 + 668.36·X |
| Eq | Eq_13 | Eq_14 | Eq_15 |
| Correlation coefficient (r) | 0.9754 | 0.9542 | 0.9048 |
| 95% confidence interval | [0.7861–0.9974] | [0.7616–0.9919] | [0.5521–0.9828] |
| Standard error of estimated (s) | 0.32 | 0.24 | 0.28 |
| Fisher parameter (p-value) | 78 (p = 8.98·10−4) | 61 (p = 2.33·10−4) | 27 (p = 2.01·10−3) |
| Cross-validation leave-one-out score (rcv-loo2) | 0.9060 | 0.8394 | 0.7263 |
| Sample size | 6 | 8 | 8 |
| MDF Descriptor | LsmrfQg | LHDmjQg | iBPMwEt |
| Dominant Atomic Property | Partial charge ( | Partial charge ( | Electronegativity ( |
| • Interaction via | Space ( | Space ( | Bonds ( |
| • Interaction Model | Q2·d−2 | Q2·d−2 | E2·d−1 |
| • Structure on Activity Scale | Logarithm | Logarithm | Inversed |
| MDF SAR Equation | Ŷ = 3.71 − 1.28·X | ||
| Eq | Eq_16 | ||
| Correlation coefficient (r) | 0.9578 | ||
| 95% confidence interval | [0.7786–0.9925] | ||
| Standard error of estimated (s) | 0.36 | ||
| Fisher parameter (p-value) | 67 (p = 1.83·10−4) | ||
| Cross-validation leave-one-out score (rcv-loo2) | 0.8532 | ||
| Sample size | 8 | ||
| Descriptor (X) | LnDRJQt | ||
| Dominant Atomic Property | Partial charge ( | ||
| • Interaction via | Bonds ( | ||
| • Interaction Model | Q·d | ||
| • Structure on Activity Scale | Logarithm | ||
d = distance
MDF SAR monovariate models: LOEC.
| sea urchin
| |||
|---|---|---|---|
| Endpoint | fertilization | embryological development | germination |
| MDF SAR Equation | Ŷ = 0.57 − 47.56·X | Ŷ = −7.62 −1.14·X | Ŷ = −1.43 + 6.02·10−2·X |
| (Eq_no) | Eq_17 | Eq_18 | Eq_19 |
| Correlation coefficient (r) | 0.9993 | 0.9653 | 0.9357 |
| 95% confidence interval for r | [0.9932–0.9999] | [0.7771–0.9950] | [0.6781–0.9885] |
| Standard error of estimated (s) | 0.04 | 0.36 | 0.40 |
| Fisher parameter (p-value) | 2781 (p = 7.74·10−7) | 68 (p = 4.22·10−4) | 42 (p = 6.33·10−4) |
| Cross-validation leave-one-out score (rcv-loo2) | 0.9962 | 0.8753 | 0.8140 |
| Sample size | 6 | 7 | 8 |
| Descriptor (X) | IAPmfQt | lNPmfQt | aIDmjQg |
| Dominant Atomic Property | Partial charge ( | Partial charge ( | Partial charge ( |
| • Interaction via | Bonds ( | Bonds ( | Space ( |
| • Interaction Model | Q2·d−2 | Q2·d−2 | Q2·d−2 |
| • Structure on Activity Scale | Identity | Logarithm | Inversed |
| MDF SAR Equation | Ŷ = −1.69 + 16.60·X | Ŷ = 0.39 − 1.30·X | Ŷ = 4.22 − 0.83·X |
| Eq | Eq_20 | Eq_21 | Eq_22 |
| Correlation coefficient (r) | 0.9612 | 0.9694 | 0.9897 |
| 95% confidence interval | [0.7949–0.9931] | [0.8012–0.9956] | [0.9290–0.9985] |
| Standard error of estimated (s) | 0.34 | 0.20 | 0.07 |
| Fisher parameter (p-value) | 73 (p = 1.42·10−4) | 78 (p = 3.09·10−4) | 239 (p = 2.06·10−5) |
| Cross-validation leave-one-out score (rcv-loo2) | 0.8763 | 0.8844 | 0.9585 |
| Sample size | 8 | 7 | 7 |
| MDF Descriptor | anDRJQt | LHDmjQg | imMrtCg |
| Dominant Atomic Property | Partial charge ( | Partial charge ( | Cardinality ( |
| • Interaction via | Bonds ( | Space ( | Space ( |
| • Interaction Model | Q·d | Q2·d−2 | Q2·d−4 |
| • Structure on Activity Scale | Inversed | Logarithm | Inversed |
| MDF SAR Equation | Ŷ = −2.02 + 5.99·10−2·X | Ŷ = 3.69 + 0.11·X | |
| Eq | Eq_23 | Eq_24 | |
| Correlation coefficient (r) | 0.9504 | 0.9764 | |
| 95% confidence interval | [0.7439–0.9912] | [0.8436–0.9966] | |
| Standard error of estimated (s) | 0.35 | 0.28 | |
| Fisher parameter (p-value) | 56 (p = 2.94·10−4) | 102 (p = 1.62·10−4) | |
| Cross-validation leave-one-out score (rcv-loo2) | 0.8686 | 0.9091 | |
| Sample size | 8 | 7 | |
| Descriptor (X) | aIDmjQg | iIDdPQg | |
| Dominant Atomic Property | Partial charge (Q) | Partial charge (Q) | |
| • Interaction via | Space (geometry) | Space (geometry) | |
| • Interaction Model | Q2·d−2 | Q2 | |
| • Structure on Activity Scale | Inversed | Inversed | |
d = distance
Figure 2Relationship between experimental and estimated EC50: fertilization (Eq_01, left hand graphic), and embryological development of sea urchin (Eq_02, right hand graphic).
Figure 13Relationship between experimental and estimated LOEC: germling length and cell number (Eq_22, left hand graphic), and survival of macro-alga (Eq_24, right hand graphic).
Predicted activities of ordnance compounds by using the MDF SAR mono-variate models.
| Activity - Specie | Toxicity | Compound | Eq_ | X | |
|---|---|---|---|---|---|
| Fertilization - | EC50 | 2,6-DNT | 01 | −4.9295 | 1.6618 |
| EC50 | 2,4,6-TNT | 01 | −6.6904 | 2.3116 | |
| EC50 | RDX | 01 | −5.8418 | 1.9984 | |
| LOEC | RDX | 17 | −0.0398 | 2.4593 | |
| Embryological development - | EC50 | RDX | 02 | −7.9917 | 1.6018 |
| NOEC | 2,6-DNT | 11 | 6355.74 | 6.8112 | |
| 1,3-DNB | 11 | 2900.88 | 2.4159 | ||
| LOEC | RDX | 18 | −5.8418 | 1.9984 | |
| Fertilization - | NOEC | Tetryl | 10 | 333.40 | 56.8491 |
| Larvae survival - | EC50 | RDX | 05 | −1.0141 | 1.6124 |
| LOEC | RDX | 21 | −1.0141 | 1.7153 | |
| Juveniles survival - | EC50 | RDX | 06 | 4.6574 | 0.1832 |
| Survival - | LOEC | RDX | 22 | 4.6574 | 0.3365 |
| Laid eggs/female - | NOEC | 2,4-DNT | 13 | −7.2544 | 0.0519 |
| 2,6-DNT | 13 | −8.5506 | 1.8932 | ||
| Survival - | EC50 | RDX | 09 | −0.0562 | 4.9762 |
| LOEC | RDX | 24 | 32.7066 | −0.1848 | |
X = value of the molecular descriptors used by MDF SAR equation – see Tables 4 – 6;
2,6-DNT = 2,6-dinitrotoluene; 2,4,6-TNT = 2,4,6-trinitrotoluene; RDX = hexahydro-1,3,5-trinitro-1,3,5-triazine;
ŶPred = predicted activity