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Research Article | Open Access

Therapeutic molecules for multiple human diseases identified from pigeon pea (Cajanus cajan L. Millsp.) through GC–MS and molecular docking

Deepu Mathew (), P. Lidiya John, T.M. Manila, P. Divyasree, V.T.K. Sandhya Rajan
Finishing School in Biotechnology, Centre for Plant Biotechnology and Molecular Biology, Kerala Agricultural University, Thrissur, Kerala 680 656, India

Peer review under responsibility of Beijing Academy of Food Sciences.

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Abstract

Molecular mechanism behind the therapeutic potential of pigeon pea over the human diseases such as rheumatoid arthritis, breast cancer, type II diabetes, malaria, measles and sickle cell disease were revealed through docking of GC–MS identified phyto-compound ligands with candidate disease proteins. Of the 242 ligands, three dimensional structures of 47 compounds had to be drawn using ChemSketch and the remaining structures were retrieved from PubChem and docked with the active sites of candidate proteins. The molecules identified through docking were further subjected to ADMET analysis and promising drug candidates were identified for each disease. This paper presents a precise account of the chemoprofile of pigeon pea leaves, stems and seeds, interaction of these molecules with target proteins and suggests 26 highly potential molecules which are drug candidates for multiple human diseases. Pigeon pea seeds are especially proven as invaluable source for therapeutic molecules.

Keywords

Breast cancerDrug discoveryHerbal medicineIn silicoMalariaMeaslesPhyto-compoundsRheumatoid arthritisSickle cell diseaseType II diabetes

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Food Science and Human Wellness
Volume 6 Issue 4,
December 2017
Pages 202-216
DOI: 10.1016/j.fshw.2017.09.003
Cite this article:
Mathew D, Lidiya John P, Manila T, et al. Therapeutic molecules for multiple human diseases identified from pigeon pea (Cajanus cajan L. Millsp.) through GC–MS and molecular docking. Food Science and Human Wellness, 2017, 6(4): 202-216. https://doi.org/10.1016/j.fshw.2017.09.003
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Number of phytocompounds identified from leaves, stems and seeds through GC–MS.

Plant part used for extractionExtractionTotal number of phytocompounds identifiedNumber of phytocompounds unique to the extraction
LeavesEthyl acetate3027
Hexane5245
Methanol3426
SeedsEthyl acetate119
Hexane3429
Methanol2318
StemsEthyl acetate3723
Hexane6838
Methanol3127
Total320242

Active sites of target disease specific proteins selected for in silico docking studies.

DiseaseTarget proteinPDB IDActive sites
ArthritisiNOSox3E7GGln263, Arg266, Asn283, Phe286, Val305, Tyr347 and Arg388
Breast cancerPolo-like kinase 13KB7Cys67, Asp194, Asp194
DiabetesDipeptidyl peptidase IV3F8STyr631, Val656, Trp662, Tyr666, Val711, Asn710, Phe357, Tyr662, Arg125, Ser630, Glu205, Glu206
MalariaPlasmepsin II1SMESer218, Asp34, Asp214, Ser79, Gly36, Asn76, Val78.
MeaslesICAM-11IC1Gln181
Sickle cell diseaseOxyHb2DN1Leu83, Phe43, Phe98, Phe46, Leu101, His58

Molecular docking scores of pigeon pea phytocompounds with arthritis target protein iNOSox (CCLE – Leaves Ethyl acetate extracted, CCLH – Leaves Hexane extracted, CCLM – Leaves Methanol extracted, CCPE – Seeds Ethyl acetate extracted, CCPH – Seeds Hexane extracted, CCPM – Seeds Methanol extracted, CCSE – Stems Ethyl acetate extracted, CCSH – Stems Hexane extracted, CCSM – Stems Methanol extracted).

Sl. No.SourcePhytocompoundPlant partPubChem IDCDOCKER energy (−kcal/mol)CDOCKER interaction energy (−kcal/mol)H bond distance (A°)H bond residuesBinding energy (kcal/mol)Protein energy (kcal/mol)Complex energy (kcal/mol)
1CCLE2′,6′-Dihydroxy-4′-methoxychalconeLeaf531679319.9135.312.26A:TYR347:HH – 5316793:O1−68.86−17318.53−17331.55
2CCLH4-(2-Methyl-3-oxocyclohexyl)butanalLeaf57388621.9429.512.42A:TYR347:HH – 573886:O1−63.28−17318.53−17371.56
1.95A:TYR373:HH – 573886:O1
3CCLM3,5-Dimethoxy-4-hydroxyphenylacetic acidLeaf7809326.2135.302.07A:TYR347:HH – 78093:O2−66.28−17318.53−17381.87
1.99A:TYR373:HH – 78093:O3
2.1878093:H26 – A:ASP382:OD2
4CCPEN-Methyl-N-[4-(1-pyrrolidinyl)-2-butynyl]-2-aminoacetamideStem57793822.1534.372.24A:TYR373:HH – 577938:O1−138.08−24281.92−24357.83
2.05A:ASP382:HN – A:GLU377:O
2.09577938:H33 – A:GLU377:OE1
2.01577938:H33 – A:GLU377:OE2
1.86577938:H34 – A:GLU377:O
2.01577938:H36 – A:ASP382:OD1
2.03577938:H36 – A:ASP382:OD2
5CCPHCyclo-propanebutanoic acidStem1975845620.8926.192.25A:GLN263:HE22 – 19758456:O1−89.04−24281.92−24373.32
6CCPHHeptanoic acidStem809427.4025.362.26A:GLN263:HE22 – 8094:O1−81.08−24281.92−24371.89
7CCSE4-Hydroxy-2-methoxycinnamaldehydeSeed537460419.0727.982.07A:TYR347:HH – 5374604:O1−56.19−24281.92−24334.27
8CCSE3,5-Dimethoxy-4-hydroxybenzaldehydeSeed865519.1728.232.17A:TYR347:HH – 8655:O1−50.52−24281.92−24325.17
2.33A:TYR373:HH – 8655:O1
2.318655:H23 – A:TYR347:OH
9CCSE4-Hydroxy-3,5-dimethoxybenzoic acidSeed1074222.4931.252.13A:TYR347:HH – 10742:O2−80.21−24281.92−24372.82
10CCSEQuinazolin-2-olSeed34438122.9628.192.10A:TYR347:HH – 344381:O1−77.82−24281.92−24368.13
1.91A:TYR373:HH – 344381:O1
2.05344381:H18 – A:ASP382:OD1
2.10344381:H18 – A:ASP382:OD2
11CCSEDesaspidinolSeed59763023.3032.662.20A:TYR347:HH – 597630:O3−66.39−24281.92−24303.14
2.30597630:H29 – A:GLU377:OE1
12CCSE1H-Pyrrolo[3,2-d]pyrimidine-2,4(3H,5H)-dioneSeed59209723.4822.412.45A:TYR347:HH – 592097:O1−58.37−24281.92−24396.73
2.05A:TYR373:HH – 592097:O1
2.34592097:H14 – A:ASP382:OD1
2.22592097:H15 – A:ASP382:OD1
2.05592097:H15 – A:ASP382:OD2
13CCSM3-Hydroxy-4-methoxymandelic acidSeed10715330.0331.691.86A:ARG388:HH11 – 107153:O1−101.39−24281.92−24398.42
2.22107153:H22 – A:ASP385:OD2

Molecular docking scores of pigeon pea phytocompounds with breast cancer target protein polo-like kinase 1.

Sl. No.SourcePhytocompoundPlant partPubChem IDCDOCKER energy (−kcal/mol)CDOCKER interaction energy (−kcal/mol)H bond distance (A°)H bond residuesBinding energy (kcal/mol)Protein energy (kcal/mol)Complex energy (kcal/mol)
1CCLEOxybenzoneLeaf463221.9533.751.93562A:CYS133:HN – 4632:O3−60.76−11047.20−11076.78
2.108134632:H29 – A:CYS133:O
2CCLE/CCSH2′,6′-Dihydroxy-4′-methoxychalconeLeaf, Seed531679321.7526.492.25321A:CYS133:HN – 5316793:O4−160.95−11047.20−11145.70
2.442195316793:H34 – A:GLU131:O
2.24911A:CYS67:HG – 5316793:O3
3CCLM3,5-Dimethoxy-4-hydroxyphenylacetic acidLeaf7809332.3640.002.49252A:CYS67:HG – 78093:O2−118.74−11047.20−11164.54
2.1229A:ASP194:HN – 78093:O4
4CCPHCyclopropanebutanoic acidStem1975845628.4333.702.07A:ASP194:HN – 19758456:O2−102.50−11047.20−11152.13
5CCPM2-(4-Nitrophenyl)-2-oxoethyl 3-phenyl propanoateStem56885134.4842.622.08A:LYS82:HZ2 – 568851:O4−57.41−11047.20−11101.20
2.15A:ASP194:HN – 568851:O5
6CCSE3,5-Dimethoxy-4-hydroxybenzaldehydeSeed865530.8936.731.98842A:CYS67:HG – 8655:O3−75.58−11047.20−11103.65
1.95629A:CYS133:HN – 8655:O4
7CCSEDesaspidinolSeed59763041.9245.902.45922A:CYS67:HG – 597630:O4−143.55−11047.20−11131.35
1.69835A:LYS82:HZ2 – 597630:O3
8CCSE4-Hydroxy-3,5-dimethoxybenzoic acidSeed1074237.2444.112.26608A:CYS67:HG – 10742:O1−123.95−11047.20−11185.21
2.07745A:LYS82:HZ2 – 10742:O4
2.08456A:ASP194:HN – 10742:O5
9CCSMMethyl 7-hydroxy-3,7- dimethyloctanoateSeed56813034.4942.652.32A:CYS67:HG – 568130:O1−59.93−11047.20−11123.10
2.25A:CYS133:HN – 568130:O3
2.28568130:H36 – A:CYS67:SG
10CCSM3-Hydroxy-4-methoxymandelic acidSeed10715337.6240.032.43A:CYS67:HG – 107153:O3−121.10−11047.20−11187.74
2.09A:ASP194:HN – 107153:O5

Molecular docking scores of pigeon pea phytocompounds with type II diabetes target protein dipeptidyl peptidase IV.

Sl. No.SourcePhytocompoundPlant partPubChem IDCDOCKER energy (−kcal/mol)CDOCKER interaction energy (−kcal/mol)H bond distance (A°)H bond residuesBinding energy (−kcal/mol)Protein energy (−kcal/mol)Complex energy (−kcal/mol)
1CCLE2′,6′-Dihydroxy-4′-methoxychalconeLeaf and Seed531679329.4336.082.49A:ARG125:HH21 – 5316793:O3138.6828982.5629053.84
1.82A:TYR547:HH – 5316793:O2
1.85A:TYR666:HH – 5316793:O2
2.315316793:H33 – A:GLU205:OE2
2CCLH4-(2-Methyl-3-oxocyclohexyl)butanalLeaf57388624.3731.482.04A:TYR547:HH – 573886:O157.3428982.5629031.43
2.15A:TYR666:HH – 573886:O1
3CCLH3,5,3′,5′-TetramethylbenzidineLeaf4120617.4524.532.2341206:H38 – A:GLU206:OE141.4828982.5629045.68
2.4741206:H38 – A:GLU206:OE2
4CCLM2-Propen-1-oneLeaf26170422.7735.202.24A:ARG125:HH22 – 261704:O356.0928982.5629018.82
1.94261704:H34 – A:ASN710:OD1
5CCPHBenzyl alcoholStem24415.9118.332.11A:ARG669:HH22 – 244:O145.4028982.5629025.12
1.98244:H16 – A:GLU206:OE1
6CCPH2-PhenethylethanolStem605418.2421.902.126054:H19 – A:GLU206:OE150.4528982.5629026.64
7CCPM3-Oxo-4-phenylbutyronitrileStem56266623.8725.162.08A:TYR547:HH – 562666:O167.9528982.5629050.71
2.34A:TYR666:HH – 562666:O1
8CCPM3-tert-Butyl-4-methoxyphenolStem693214.3122.561.886932:H29 – A:GLU205:O71.9128982.5629054.56
9CCPMVinylbitalStem7213516.6130.742.14A:ARG125:HH22 – 72135:O157.1428982.5629050.38
2.09A:TYR547:HH – 72135:O2
10CCSM3,5-Dimethoxy-4-hydroxybenzaldehydeSeed865521.6237.142.07A:ARG125:HH22 – 8655:O476.5928982.5629025.20
1.86A:TYR547:HH – 8655:O3
1.82A:TYR666:HH – 8655:O3
11CCSEDesaspidinolSeed59763026.1035.332.05A:TYR547:HH – 597630:O275.9628982.5629013.62
2.36597630:H28 – A:GLU206:OE1
2.05597630:H28 – A:GLU206:OE2
1.92597630:H29 – A:TYR547:OH
2.22597630:H29 – 597630:O2
12CCSEQuinazolin-2-olSeed34438130.5238.122.02344381:H17 – A:GLU206:OE1199.2028982.5629187.22
2.31344381:H18 – A:GLU205:OE2
2.38344381:H18 – A:GLU205:O
13CCSE1H-Pyrrolo[3,2-d]pyrimidine-2,4(3H,5H)-dioneSeed59209715.4225.482.48A:ARG125:HH21 – 592097:O261.1528982.5629020.38
2.25A:ARG125:HH22 – 592097:O2
2.43A:TYR547:HH – 592097:O1
2.31592097:H14 – A:TYR666:OH
1.90592097:H16 – A:ASN710:OD1
14CCSH4-Hydroxy-2-methoxybenaldehydeSeed51954130.9834.262.04A:ARG125:HH22 – 519541:O390.6628982.5629088.81
1.87A:TYR547:HH – 519541:O2
1.81A:TYR666:HH – 519541:O2
15CCSH3,5-Dimethoxy-4-hydroxybenzaldehydeSeed865517.5928.241.88A:TYR547:HH – 8655:O366.11−28982.56−29028.39
1.86A:TYR666:HH – 8655:O3
1.968655:H23 – A:ASN710:OD1
16CCSMMethyl 7-hydroxy-3,7- dimethyloctanoateSeed56813034.7237.702.02A:TYR547:HH – 568130:O343.4628982.5629043.95
2.36A:TYR666:HH – 568130:O3
1.95568130:H36 – A:GLU206:OE1
17CCSM3-Hydroxy-4-methoxymandelic acidSeed10715327.8727.972.09A:ARG125:HH12 – 107153:O4104.6828982.5629107.58
2.29A:ARG125:HH12 – 107153:O5
2.28A:ARG125:HH22 – 107153:O5
18CCSM2′,6′-DihydroxyacetophenoneSeed6968721.1126.372.41A:ARG125:HH21 – 69687:O1−73.1128982.5629026.99
1.99A:TYR547:HH – 69687:O2
2.12A:TYR666:HH – 69687:O2
2.4969687:H18 – A:TYR662:OH
2.4069687:H18 – A:ASN710:OD1

Molecular docking scores of pigeon pea phytocompounds with malaria target protein Plasmepsin II.

Sl. No.SourcePhytocompoundPlant partPubchem IDCDOCKER energy (−kcal/mol)CDOCKER interaction energy (−kcal/mol)H bond distance (A°)H bond residuesBinding energy (−kcal/mol)Protein energy (−kcal/mol)Complex energy (−kcal/mol)
1CCLE2-Methyl-4-hydroxybenzoxazolLeaf34576217.2120.361.98345762:H18 – A:ASP34:OD232.2812758.0112787.51
2CCLH1,4,5-TrimethylimidazoleLeaf57359829.7330.352.02573598:H19 – A:ASP34:OD2122.4312758.0112863.79
3CCLM1,3-Dimethyl pyrogallateLeaf704115.2823.052.127041:H21 – A:SER79:OG35.0212758.0112780.48
4CCPH2-PhenethylethanolStem605417.6120.902.29A:SER79:HN – 6054:O141.6012758.0112792.27
5CCPM3-Aminophenyl-.beta.-phenylpropionateStem57306328.7429.752.47A:SER79:HN – 573063:O251.0612758.0112817.96
2.20573063:H32 – A:SER218:OG
6CCSEQuinazolin-2-olSeed34438136.8934.221.96344381:H17 – A:ASP34:OD2142.3112758.0112908.14
2.27344381:H18 – A:ASP34:OD1
7CCSE1H-Pyrrolo[3,2-d]pyrimidine-2,4(3H,5H)-dioneSeed59209724.1228.832.22A:SER79:HG – 592097:O271.6412758.0112834.64
2.04592097:H14 – A:ASP34:OD2
2.09592097:H16 – A:ASP34:OD2
8CCSEIsocoumarinSeed6810819.7220.572.13A:SER79:HG – 68108:O240.5612758.0112781.98
9CCSM3,5-Dimethoxy-4-hydroxybenzaldehydeSeed865525.5026.092.15A:SER79:HG – 8655:O342.3912758.0112781.61
2.018655:H23 – A:GLY36:O
10CCSM2′,6′-DihydroxyacetophenoneSeed6968724.8028.612.3069687:H19 – A:ASP34:OD250.6312758.0112779.66

Molecular docking scores of pigeon pea phytocompounds with measles target protein ICAM-1.

Sl. No.SourcePhytocompoundPlant partPubChem IDCDOCKER energy (−kcal/mol)CDOCKER interaction energy (−kcal/mol)H bond distance (A°)H bond residuesBinding energy (-kcal/mol)Protein energy (-kcal/mol)Complex energy (-kcal/mol)
1CCSEQuinazolin-2-olSeed34438118.2522.712.48344381:H17 – B:GLN181:OE181.765450.845541.41

Molecular docking scores of pigeon pea phytocompounds with sickle cell disease target protein OxyHb.

Sl. No.SourcePhytocompoundPlant partPubChem IDCDOCKER energy (−kcal/mol)CDOCKER interaction energy (−kcal/mol)H bond distance (A°)H bond residuesBinding energy (−kcal/mol)Protein energy (−kcal/mol)Complex energy (−kcal/mol)
1CCPM2,6-dimethoxyphenolStem704114.2621.892.11A:HIS58:HE2 – 7041:O380.455333.965401.94
2CCPM2-(4-Nitrophenyl)-2-oxoethyl 3-phenyl propanoateStem56885128.5936.562.48A:HIS58:HE2 – 568851:O339.795333.965369.01

Docking summary showing the number of promising phytocompounds identified from each part and the most promising molecules for each disease.

Sl. No.DiseaseNumber of promising phytocompoundsMost promising phytocompoundsSource of most promising phytocompounds
LeavesStemsSeeds
1Rheumatoid arthritis337N-Methyl-N-[4-(1-pyrrolidinyl)-2-butynyl]-2-aminoacetamideStem
3-Hydroxy-4-methoxymandelic acidSeed
2Breast cancer3262′,6′-Dihydroxy-4′-methoxychalconeLeaf and Seed
DesaspidinolSeed
3Type II Diabetes459Quinazolin-2-olSeed
2′,-Dihydroxy-4′-methoxychalconeLeaf and Seed
4Malaria325Quinazolin-2-olSeed
1,4,5-TrimethylimidazoleLeaf
5Measles001Quinazolin-2-olSeed
6Sickle cell disease0202,6-dimethoxyphenolStem
2-(4-Nitrophenyl)-2-oxoethyl 3-phenyl propanoateStem

ADMET values for 26 phytocompounds which have passed the drug-likeliness screening (Desirable values are presented in brackets).

Sl. No.PubChem IDPhytocompoundPlant partIdentified forSolubility LevelBBB Level (2–4)Hepatotoxic prediction (False)AlogP98 (<4.0)Absorption Level (0–1)CYP2D6 Prediction (False)
15738864-(2-Methyl-3-oxocyclohexyl)butanalLeafArthritis, Diabetes32False2.1410False
25735981,4,5-TrimethylimidazoleLeafMalaria44True0.3511False
3780933,5-Dimethoxy-4-hydroxyphenylacetic acidLeafArthritis, Breast cancer43True1.2190False
453167932′,6′-Dihydroxy-4′-methoxychalconeLeaf, SeedBreast cancer, Diabetes, Arthritis32False3.2010False
570412,6-DimethoxyphenolLeaf, StemMalaria, Sickle cell disease42True1.5550False
6577938N-Methyl-N-[4-(1-pyrrolidinyl)-2-butynyl]-2-aminoacetamideStemArthritis43False−0.1920False
719758456Cyclopropanebutanoic acidStemArthritis, Breast cancer42False1.7110False
88094Heptanoic acidStemArthritis42False2.2870False
9244Benzyl alcoholStemDiabetes42False1.2250False
1060542-Phenethyl ethanolStemDiabetes, Malaria42False1.5460False
115626663-Oxo-4-phenylbutyronitrileStemDiabetes32False1.6540False
1269323-tert-Butyl-4-methoxyphenolStemDiabetes31True2.9710False
135730633-Aminophenyl-.beta.-phenylpropionateStemMalaria32False3.0060False
145688512-(4-Nitrophenyl)-2-oxoethyl 3-phenyl propanoateStemBreast cancer, Sickle cell disease32False3.3260False
1572135VinylbitalStemDiabetes32True1.6670False
1653746044-Hydroxy-2-methoxycinnamaldehydeSeedArthritis42False1.6910False
1786553,5-Dimethoxy-4-hydroxybenzaldehydeSeedArthritis, Breast cancer, Diabetes, Malaria43False1.3140False
18107424-Hydroxy-3,5-dimethoxybenzoic acidSeedArthritis, Breast cancer43True1.1850False
19344381Quinazolin-2-olSeedArthritis, Diabetes, Malaria, Measles32True1.3760False
20597630DesaspidinolSeedArthritis, Breast cancer, Diabetes33True2.1920False
215920971H-Pyrrolo[3,2-d]pyrimidine-2,4(3H,5H)-dioneSeedArthritis, Diabetes, Malaria43True0.1440False
221071533-Hydroxy-4-methoxymandelic acidSeedArthritis, Diabetes, Breast cancer43True0.5840False
2368108IsocoumarinSeedMalaria21True4.2830False
245195414-Hydroxy-2-methoxybenaldehydeSeedDiabetes42False1.330False
25568130Methyl 7-hydroxy-3,7- dimethyloctanoateSeedDiabetes, Breast cancer42False2.1210False
26696872\',6\'-DihydroxyacetophenoneSeedDiabetes, Malaria43True1.0850False