Modeling Natural Anti-Inflammatory Compounds by Molecular Topology
Abstract
:1. Introduction
2. Materials and Methods
2.1. Analyzed Compounds
2.2. Molecular Descriptors
2.3. Modeling Techniques
- TP (True positive): Active compounds correctly classified or predicted.
- FP (False positive): Inactive compounds classified as anti-inflammatory.
- TN (True negative): Inactive compounds correctly classified.
- FN (False negative): Anti-inflammatory compounds classified as inactive.
2.4. Pharmacological-Activity Distribution Diagrams
2.5. Topological Virtual Screening
3. Results and Discussion
3.1. Similarity Study
3.2. Mathematical Modeling
3.3. Topological Virtual Screening
4. Conclusions
Supplementary Material
ijms-12-09481-s001.pdfAcknowledgments
References
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Symbol | Name | Ref. |
---|---|---|
TI1 | first Mohar index | [21] |
ATS7m | 2D Broto-Moreau autocorrelation of a topological structure-lag7/weighted by atomic masses | [22] |
ATS4v | 2D Broto-Moreau autocorrelation of a topological structure-lag4/weighted by Van der Waal volumes | [23] |
ATS7v | 2D Broto-Moreau autocorrelation of a topological structure-lag7/weighted by Van der Waal volumes | [23] |
ATS1p | 2D Broto-Moreau autocorrelation of a topological structure-lag4/weighted by Atomic polarizabilities | [23] |
Percent-Correct | Compounds Classified as Active | Compounds Classified as Inactive | |
---|---|---|---|
Training Set | |||
Active Group | 50 | 61 | 62 |
Inactive Group | 98 | 5 | 284 |
Test Set | |||
Active Group | 59 | 24 | 17 |
Inactive Group | 86 | 6 | 37 |
Compound | TI1 | ATS7m | ATS4v | ATS7v | ATS1p | DF | Class. | Ref. |
---|---|---|---|---|---|---|---|---|
Value | Pred. | |||||||
Active Group | ||||||||
2′,β-DIHYDROXYCHALCONE | 25.6 | 2.79 | 2.81 | 2.57 | 2.91 | 0.82 | A | [24] |
3,7-DIMETHOXYFLAVONE | 49 | 3 | 3.27 | 2.73 | 3.01 | −2.19 | I | [25] |
4-METHYLESCULETIN | 11.21 | 1.02 | 2.51 | 0.23 | 2.59 | 6.44 | A | [26] |
ANISODAMINE | 66.85 | 3.2 | 3.02 | 2.93 | 3.05 | 1.22 | A | [27] |
BERGENIN | 51.11 | 3.32 | 3.37 | 2.52 | 2.97 | −0.82 | I | [28,29] |
β-CARYOPHYLLENE ALCOHOL | 23.75 | 0 | 3.12 | 0 | 2.92 | 5.13 | A | [30] |
BICUCULLINE (+) | 158.89 | 3.69 | 3.66 | 3.24 | 3.25 | −0.95 | I | [31,32] |
BOLDINE | 73.83 | 3.38 | 3.7 | 2.83 | 3.16 | −1.75 | I | [33,34] |
BRAZILEIN | 58.35 | 2.98 | 3.35 | 2.24 | 3.08 | 3.31 | A | [35,36] |
CAMPTOTHECIN | 113.6 | 3.45 | 3.64 | 3.14 | 3.27 | −0.33 | I | [37,38] |
CAPSAICIN | 0 | 3.01 | 2.95 | 2.71 | 3 | 1.8 | A | [39,40] |
CARNOSIC ACID | 54.11 | 2.93 | 3.81 | 2.68 | 3.21 | −2.66 | I | [41] |
CARVACROL | 0 | 0 | 2.08 | 0 | 2.44 | 3.68 | A | [14] |
DIHYDROTANSHINONE I | 57.02 | 2.66 | 3.51 | 2.4 | 3.13 | −0.49 | I | [42,43] |
ELLAGIC ACID | 56.29 | 2.61 | 3.43 | 1.72 | 3.02 | 3.35 | A | [44,45] |
EPIAFZELECHIN (2R,3R)(−) | 44.79 | 3.02 | 3.06 | 2.53 | 2.98 | 1.45 | A | [46] |
EUPHOL | 146.22 | 3.66 | 4.11 | 3.61 | 3.54 | −1.62 | I | [47] |
GALLIC ACID | 0 | 0 | 1.93 | 0 | 2.33 | 2.36 | A | [48] |
GENISTEIN | 44.57 | 2.88 | 3.09 | 2.45 | 2.98 | 1.15 | A | [14] |
HARMALINE | 26.93 | 1.98 | 2.93 | 1.48 | 2.8 | 1.62 | A | [49] |
HEMATEIN | 63.65 | 3.11 | 3.4 | 2.34 | 3.1 | 3.01 | A | [50,51] |
HIERACIN | 53.56 | 3.3 | 3.17 | 2.72 | 3.03 | 1.38 | A | [52] |
IRIGENIN TRIMETHYL ETHER | 90.88 | 3.73 | 3.75 | 3.27 | 3.17 | −4.15 | I | [53] |
ISOLIQUIRITIGENIN | 29.12 | 2.87 | 2.78 | 2.61 | 2.94 | 2 | A | [54] |
KOPARIN 2′-METHYL ETHER | 59.21 | 3.2 | 3.37 | 2.81 | 3.05 | −1.78 | I | [55] |
KYNURENINE | 0 | 2.45 | 2.51 | 1.7 | 2.61 | 1.89 | A | [56] |
LAWSONE | 9.48 | 0 | 2.43 | 0 | 2.59 | 4 | A | [57] |
LUTEOLIN GLUCOSIDE | 171.97 | 4.01 | 3.57 | 3.45 | 3.35 | 2.44 | A | [14] |
MADECASSIC ACID | 189.69 | 4.04 | 4.43 | 3.75 | 3.63 | −2.1 | I | [58] |
METHYL ORSELLINATE | 0 | 0.85 | 2.39 | 0.41 | 2.42 | 0.59 | I | [59,60] |
N-METHYLANTHRANILIC ACID | 0 | 0 | 2.14 | 0 | 2.32 | −0.42 | I | [61] |
OLEANOLIC ACID | 163.48 | 3.85 | 4.28 | 3.68 | 3.59 | −1.63 | I | [14] |
OUABAIN | 358.36 | 4.4 | 4.26 | 3.88 | 3.66 | 0.84 | A | [62] |
p-HYDROXYCINNAMALDEHYDE | 0 | 1.3 | 1.95 | 0.71 | 2.39 | 4.75 | A | [63,64] |
QUERCETIN | 52.38 | 3.27 | 3.2 | 2.67 | 3.03 | 1.29 | A | [65] |
QUERCETIN TETRAMETHYL (5,7,3′,4′) ETHER | 74.79 | 3.59 | 3.54 | 3.09 | 3.11 | −2.49 | I | [14] |
SANTONIN | 31.04 | 1.86 | 3.2 | 1.19 | 2.94 | 4.27 | A | [66] |
SILIBININ | 243.99 | 4.1 | 3.85 | 3.61 | 3.48 | 1.68 | A | [67–69] |
TECTORIGENIN | 53.39 | 3.12 | 3.26 | 2.68 | 3.03 | −0.42 | I | [70,71] |
UMBELLIFERONE | 8.36 | 0 | 2.12 | 0 | 2.47 | 4.15 | A | [14] |
UVAOL | 153.27 | 3.74 | 4.29 | 3.61 | 3.58 | −2.13 | I | [72] |
Inactive Group | ||||||||
2-METHYL GRAMINE | 13.23 | 1.1 | 2.73 | 1.1 | 2.65 | −1.78 | I | - |
3-DEACETYLKHIVORIN | 285.72 | 4.57 | 4.44 | 4.14 | 3.62 | −3.59 | I | - |
3-PINANONE OXIME | 9.02 | 0 | 2.19 | 0 | 2.56 | 5.84 | A | - |
ASARYLALDEHYDE | 0 | 1.2 | 2.61 | 0.92 | 2.41 | −4.9 | I | - |
BAEOMYCESIC ACID | 47.58 | 3.65 | 3.52 | 3.25 | 3.16 | −1.82 | I | - |
BOVINOCIDIN (3-NITROPROPIONIC ACID) | −8.58 | 0 | 1.01 | 0 | 1.63 | −6.92 | I | - |
CHOLEST-5-EN-3-ONE | 128.51 | 3.42 | 3.89 | 3.37 | 3.45 | −0.65 | I | - |
CONESSINE | 112.88 | 3.25 | 3.84 | 3.16 | 3.36 | −1.57 | I | - |
CRASSIN ACETATE | 37.49 | 3.91 | 3.71 | 3.52 | 3.23 | −3.06 | I | - |
CRINAMINE | 78.42 | 2.9 | 3.48 | 2.38 | 3.09 | 0.22 | I | - |
DEACETOXY-7-OXISOGEDUNIN | 188.23 | 3.82 | 4.25 | 3.46 | 3.5 | −2.23 | I | - |
DEOXYANDIROBIN | 161.25 | 3.95 | 4.14 | 3.62 | 3.47 | −2.48 | I | - |
DIPHENYLUREA | 21.73 | 2.4 | 2.5 | 2.4 | 2.77 | −0.23 | I | - |
DUARTIN. DIMETHYL ETHER | 76.8 | 3.39 | 3.6 | 3.04 | 3.11 | −3.9 | I | - |
EPI(13)TORULOSOL | 30.87 | 3.08 | 3.56 | 2.87 | 3.13 | −2.72 | I | - |
EUDESMIC ACID | 0 | 1.3 | 2.7 | 0.71 | 2.45 | −2.3 | I | - |
EVOXINE | 76.98 | 3.47 | 3.43 | 2.99 | 3.08 | −1.8 | I | - |
GLUCITOL-4-GUCOPYANOSIDE | 0 | 3.66 | 3.06 | 2.82 | 2.83 | −1.71 | I | - |
HEXAMETHYLQUERCETAGETIN | 88.94 | 3.82 | 3.75 | 3.33 | 3.17 | −4.27 | I | - |
ISOOSAJIN | 153.22 | 3.79 | 3.85 | 3.61 | 3.42 | −1.22 | I | - |
JUAREZIC ACID | 0 | 2.23 | 2.2 | 1.8 | 2.56 | 1.88 | A | - |
KHAYASIN | 274.26 | 4.48 | 4.38 | 4.11 | 3.65 | −2.18 | I | - |
LEOIDIN | 68.47 | 3.83 | 3.74 | 3.25 | 3.22 | −1.74 | I | - |
LOMATIN | 31.81 | 2.35 | 3.04 | 1.99 | 2.88 | −0.07 | I | - |
MEDICARPIN | 56.7 | 2.78 | 3.17 | 2.43 | 3.01 | 0.37 | I | - |
MEROGEDUNIN | 72.24 | 3.21 | 3.94 | 2.75 | 3.27 | −1.63 | I | - |
METAMECONINE | 12.34 | 0.85 | 2.5 | 0.41 | 2.5 | 1.53 | A | - |
METHYL EVERNINATE | 0 | 1.61 | 2.56 | 0.93 | 2.46 | −0.68 | I | - |
METHYL ROBUSTONE | 146.49 | 3.65 | 3.68 | 3.34 | 3.3 | −1.03 | I | - |
N-METHYLISOLEUCINE | −11.17 | 0 | 2.05 | 0 | 2.1 | −5.69 | I | - |
PLECTOCOMINE METHYL ETHER | 23.69 | 1.52 | 2.76 | 1.21 | 2.74 | 1.61 | A | - |
PODOTOTARIN | 346.77 | 4.54 | 4.56 | 4.38 | 3.85 | −1.06 | I | - |
PRENYLETIN | 24.04 | 2.78 | 2.76 | 2.43 | 2.82 | −0.07 | I | - |
PTAEROXYLIN | 35.11 | 2.49 | 3.15 | 2.26 | 2.93 | −1.55 | I | - |
RETUSOQUINONE | 0 | 1.3 | 2.35 | 0.71 | 2.52 | 3.8 | A | - |
RHETSININE | 94.88 | 3.23 | 3.46 | 2.98 | 3.19 | −0.36 | I | - |
RHODINYL ACETATE | −25.56 | 2.04 | 2.36 | 1.8 | 2.52 | −2.14 | I | - |
ROBUSTIC ACID | 114.56 | 3.69 | 3.71 | 3.36 | 3.28 | −1.77 | I | - |
SARMENTOSIDE B | 484.87 | 4.66 | 4.42 | 4.15 | 3.75 | −0.04 | I | - |
SENECRASSIDIOL 6-ACETATE | 41.44 | 2.6 | 3.42 | 2.06 | 3.04 | 0.77 | I | - |
THEANINE | −17.76 | 1.76 | 2.01 | 1.31 | 2.22 | −3.61 | I | - |
TROPINE | 5.68 | 0 | 1.22 | 0 | 2.34 | 10.88 | N.C. | - |
XANTHOXYLIN | 0 | 1.2 | 2.63 | 0.92 | 2.46 | −3.75 | I | - |
Compound | TI1 | ATS7m | ATS4v | ATS7v | ATS1p | DF Value | Ref. |
---|---|---|---|---|---|---|---|
1,5-NORCARYOPHYLLEN-3-ONE | 12.95 | 0 | 3.07 | 0 | 2.8 | 2.43 | [73] |
2′,4′-DIHYDROXYCHALCONE 4′-GLUCOSIDE | 119.2 | 3.71 | 3.36 | 3.29 | 3.28 | 3.08 | nr |
2-HYDROXYXANTHONE | 24.98 | 1.73 | 2.85 | 1.39 | 2.82 | 2.58 | [74] |
3-HYDROXYCOUMARIN | 8.25 | 0 | 2.15 | 0 | 2.47 | 3.79 | [75] |
3-NOR-3-OXOPANASINSAN-6-OL | 24.04 | 0 | 3.03 | 0 | 2.89 | 5.32 | nr |
alpha-TOCHOPHEROL | 83.77 | 3.37 | 3.68 | 3.28 | 3.45 | 2.53 | nr |
APIIN | 345.29 | 4.46 | 3.8 | 3.88 | 3.55 | 3.35 | [76] |
AVOCADANE ACETATE | −70.27 | 3.07 | 2.96 | 2.76 | 3.01 | 2.16 | nr |
BATYL ALCOHOL | −83.55 | 2.94 | 2.96 | 2.81 | 3.08 | 3.3 | [77] |
BERGAPTOL | 22.16 | 1.3 | 2.67 | 0.71 | 2.69 | 4.85 | [78] |
BIXIN | −103.7 | 3.31 | 3.33 | 3.18 | 3.27 | 2.98 | [79] |
BRAZILIN | 58.35 | 2.98 | 3.35 | 2.24 | 3.08 | 3.31 | [80] |
CANTHARIDIN | 18.37 | 0 | 2.32 | 0 | 2.62 | 6.04 | nr |
CAPSANTHIN | 187.67 | 3.83 | 3.96 | 3.77 | 3.77 | 6.06 | [81] |
CARYOPHYLLENE [t(−)] | 11.37 | 0 | 2.89 | 0 | 2.77 | 3.75 | [82] |
CEDROL | 23.5 | 0 | 3.14 | 0 | 2.92 | 4.87 | [83] |
CHAULMOOGRIC ACID | 0 | 2.69 | 2.77 | 2.57 | 2.99 | 3.14 | [84] |
CHLOROGENIC ACID | 48.22 | 3.36 | 3.09 | 2.78 | 3.07 | 3.29 | [85] |
CINEOLE | 6.55 | 0 | 2.08 | 0 | 2.48 | 4.81 | [86] |
COSMOSIIN | 162.44 | 3.92 | 3.54 | 3.41 | 3.33 | 2.27 | [87] |
COTININE | 11.53 | 0.85 | 2.43 | 0.41 | 2.53 | 3.21 | [88] |
CULMORIN | 25.72 | 0 | 3.2 | 0 | 2.94 | 4.8 | nr |
DESOXYPEGANINE HYDROCHLORIDE | 16.37 | 0 | 2.49 | 0 | 2.65 | 4.82 | nr |
DIALLYL SULFIDE | −7.5 | 0 | 1.39 | 0 | 2.12 | 2.63 | [89] |
DICTAMNINE | 22.62 | 0 | 2.88 | 0 | 2.71 | 2.05 | nr |
DIGITOXIN | 1046.2 | 4.61 | 4.4 | 4.15 | 3.93 | 2.34 | [62] |
DIGOXIN | 1069.1 | 4.64 | 4.43 | 4.16 | 3.94 | 2.11 | [62] |
DJENKOLIC ACID | −28.53 | 2.37 | 2.28 | 1.86 | 2.69 | 4.92 | [90] |
EPOXY (1,11)HUMULENE | 15.16 | 0 | 3.05 | 0 | 2.83 | 3.48 | [91] |
GARLICIN | −9.74 | 0.69 | 1.64 | 0.69 | 2.4 | 5.34 | [92] |
GIBBERELLIC ACID | 92.61 | 2.83 | 3.8 | 2.26 | 3.27 | 2.08 | [93] |
GUAIAZULENE | 13.61 | 0 | 3 | 0 | 2.83 | 4.22 | [94] |
GUVACINE HYDROCHLORIDE | 0 | 0 | 1.32 | 0 | 2.1 | 2.91 | nr |
HAEMATOXYLIN | 63.65 | 3.11 | 3.4 | 2.34 | 3.1 | 3.01 | nr |
HARMALOL HYDROCHLORIDE | 22.47 | 1.65 | 2.81 | 0.87 | 2.77 | 5.94 | nr |
HARMANE | 19.16 | 0 | 2.76 | 0 | 2.74 | 4.34 | [95] |
HARMOL HYDROCHLORIDE | 22.47 | 1.65 | 2.81 | 0.87 | 2.77 | 5.94 | [96] |
HARPAGOSIDE | 218.6 | 4.16 | 3.56 | 3.65 | 3.4 | 2.86 | [97] |
HELENINE | 28.19 | 1.79 | 3.07 | 1.26 | 2.91 | 4.05 | [98] |
HESPERIDIN | 421.88 | 4.48 | 3.87 | 3.88 | 3.6 | 3.8 | [99] |
HINOKITIOL | 0 | 0 | 2.26 | 0 | 2.48 | 2.74 | [100] |
HUMULENE (alpha) | 0 | 0 | 3 | 0 | 2.77 | 2.56 | [82] |
INDOLE-3-CARBINOL | 7.49 | 0 | 2.09 | 0 | 2.46 | 4.19 | [101] |
INOSITOL | 0 | 0 | 1.73 | 0 | 2.28 | 3.12 | [102] |
ISOBERGAPTENE | 25.9 | 0.85 | 2.91 | 0.41 | 2.72 | 2.91 | nr |
ISOKOBUSONE | 14.57 | 1.3 | 3.12 | 0.71 | 2.83 | 3.55 | nr |
JUGLONE | 9.48 | 0 | 2.47 | 0 | 2.59 | 3.48 | [103] |
KOBUSONE | 26.62 | 0 | 3.12 | 0 | 2.85 | 3.35 | nr |
L(+/−)-ALLIIN | −14.57 | 1.3 | 1.97 | 0.71 | 2.36 | 3.65 | [104] |
LYCOPODINE PERCHLORATE | 36.79 | 0 | 3.48 | 0 | 3.01 | 3.55 | [105] |
MENADIONE | 9.48 | 0 | 2.53 | 0 | 2.63 | 3.95 | [106] |
MENTHOL(−) | 0 | 0 | 2.2 | 0 | 2.44 | 2.26 | [107] |
MENTHONE | 0 | 0 | 2.2 | 0 | 2.44 | 2.26 | [108] |
MIMOSINE | 0 | 2.31 | 2.25 | 1.23 | 2.43 | 3.19 | [109] |
MUUROLLADIE-3-ONE | 15 | 1.3 | 3.09 | 0.71 | 2.86 | 4.75 | nr |
OCTOPAMINE HYDROCHLORIDE | 0 | 0.94 | 1.94 | 0.3 | 2.36 | 5.54 | nr |
PATULIN | 7.06 | 0 | 1.81 | 0 | 2.28 | 2.2 | [110] |
PECTOLINARIN | 427.48 | 4.54 | 3.93 | 3.96 | 3.61 | 3.01 | [111] |
PHLORIDZIN | 127.51 | 4.08 | 3.47 | 3.57 | 3.31 | 2.28 | [112] |
PICROTOXININ | 68.36 | 2.09 | 3.46 | 1.2 | 3.05 | 5.58 | nr |
PIPERINE | 74.81 | 2.87 | 2.93 | 2.6 | 3 | 2.01 | [113] |
PLUMBAGIN | 10.92 | 0 | 2.67 | 0 | 2.67 | 3.28 | [114] |
PUNCTAPORONIN B | 17.9 | 1.41 | 3.3 | 0.57 | 2.91 | 5.6 | nr |
PURPURIN | 33.76 | 2.12 | 3.22 | 1.62 | 2.96 | 2.28 | [115] |
RHAPONTIN | 125.6 | 3.82 | 3.42 | 3.38 | 3.28 | 2.06 | [116] |
RHOIFOLIN | 357.18 | 4.51 | 3.85 | 3.93 | 3.57 | 3.3 | [117] |
RUTOSIDE (rutin) | 392.19 | 4.68 | 3.88 | 4.07 | 3.6 | 3.12 | [118] |
SAFROLGLYCOL | 14.58 | 2.26 | 2.4 | 1.4 | 2.54 | 2.79 | [119] |
SCOPOLETIN | 11.82 | 1.33 | 2.47 | 0.82 | 2.54 | 2.11 | [120] |
SECURININE | 31.65 | 0.85 | 3.02 | 0.41 | 2.85 | 5.28 | nr |
SHIKIMIC ACID | 0 | 0 | 1.93 | 0 | 2.33 | 2.36 | [121,122] |
THYMOQUINONE | 0 | 0 | 2.31 | 0 | 2.48 | 2.11 | [123] |
TRYPTAMINE | 9.75 | 0.77 | 2.38 | 0.53 | 2.56 | 3.05 | [124] |
XANTHURENIC ACID | 13.51 | 1.3 | 2.65 | 0.71 | 2.64 | 3.73 | [56] |
© 2011 by the authors; licensee MDPI, Basel, Switzerland. This article is an open-access article distributed under the terms and conditions of the Creative Commons Attribution license (http://creativecommons.org/licenses/by/3.0/).
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Galvez-Llompart, M.; Zanni, R.; García-Domenech, R. Modeling Natural Anti-Inflammatory Compounds by Molecular Topology. Int. J. Mol. Sci. 2011, 12, 9481-9503. https://doi.org/10.3390/ijms12129481
Galvez-Llompart M, Zanni R, García-Domenech R. Modeling Natural Anti-Inflammatory Compounds by Molecular Topology. International Journal of Molecular Sciences. 2011; 12(12):9481-9503. https://doi.org/10.3390/ijms12129481
Chicago/Turabian StyleGalvez-Llompart, María, Riccardo Zanni, and Ramón García-Domenech. 2011. "Modeling Natural Anti-Inflammatory Compounds by Molecular Topology" International Journal of Molecular Sciences 12, no. 12: 9481-9503. https://doi.org/10.3390/ijms12129481