androgens are a class of natural or synthetic steroid hormone compounds such as testosterone , dihydrotestosterone and androstenedione ( 1 ) . physiological androgens play vital roles in the regulation of anabolic metabolism and expression of male phenotype . they are actually eminent for regulation of male development particularly the male reproductive system ( 2 ) . the diverse effects of androgens are mediated by complex cell type - specific signaling pathways that always involve the androgen receptor ( ar ) ( 3 ) . the androgen receptor ( ar ) is a type of nuclear receptor that acts as a dna - binding transcription factor to regulate gene expression ( 4 ) . dysregulation of androgen / ar signaling perturbs normal reproductive development and accounts for a wide range of pathological conditions such as prostate cancer ( 2 ) . recent experimental findings conform the expression of ar in androgen - dependent , androgen - independent or hormone refractory prostate cancers , where ar expression is maintained throughout prostate cancer progression ( 5 ) . interestingly , a number of clinical studies suggest that prostate cancer initiation and progression is also uniquely dependent on ar expression ( 6 ) . this pathogenic role of ar has made it a major therapeutic target in aggressive prostate cancer ( 7 ) . phuti - kadam  and has an abundant distribution in bangladesh and india . in traditional medicinal practice the bark of h. excelsumis used as an astringent and febrifuge and for treatment of fever and tumors , while the leaves are used to treat ulcers , sialitis , sore throat , tonsillitis and inflammatory conditions ( 8) . the stem bark of h. excelsum contains tannin , toxic alkaloid , hymenodictine , esculin , an apioglucoside of scopoletin andhymexelsin ( 9 ) . anthraquinones , rubiadin and its methyl ether , lucidin , nordamnacanthal , damnacanthal , 2-benzylzanthopurpurin , anthragallol , soranjidiol and morindone have also been isolated from roots ( 10 ) . the plant has been reported to have antioxidant and anti - inflammatory properties ( 11 ) . the present study aimed to investigate h. excelsum s phytochemicals with anti - prostate cancer activity and to predict their mechanisms of action using a computational molecular simulation study . the therapeutic effects of a medicinal plant are attributed to the phytochemical constituents of that plant . therefore , it is feasible to study individual phytochemicals present in plants when investigating the therapeutic effects of medicinal plants . from the literature search , eight phytochemicals were taken into consideration for the molecular simulation study including anthragallol , damnacanthal , esculin , lucidin , morindone , nordamnacanthal , rubiadin and soranjidiol . canonical smiles file of these selected ligand molecules were retrieved from the pubchem compound server ( https://pubchem.ncbi.nlm.nih.gov/ ) . canonical smiles files were entered in to the corina online demo to generate 3d protein data bank ( pdb ) files . protein data bank ( pdb ) file of human ar ligand binding domain ( pdb i d : 1e3 g ) was downloaded from rcsb pdb database ( http://www.rcsb.org/pdb/home/home.do ) . prior to molecular simulation study the drug likeness and safety of the chosen ligands were evolved by empirical computational tools . the molinspiration cheminformatics server was exploited to calculate the molecular properties associated with drug - likeness and to predict bioactivity of components including the nuclear receptor ligand and enzyme inhibitor ( 12 ) . the osiris property explorer was used to evolve the toxicity of the selected ligands in term of mutagenic , tumorigenic and irritant properties ( 13 ) . the site of the receptor that interacted with the ligands was predicted by the molegro virtual docker ( mdv ) inbuilt cavity detection algorithm and the pocket - finder server ( 14 ) . the outputs from both of the computational tools were synchronized to predict the ultimate ligand binding site and exploited in the subsequent docking study . molegro virtual docker ( mvd ) was used for the computer simulated docking study ( 15 ) . molegro virtual docker includes moldock and plants score for evaluating docking solutions followed by a rank for the best conformations . the solution to the function is the sum of intermolecular interaction energy between protein and ligand with the intra - molecular interaction energy of the ligand . the docking energy scoring function is based on a modified piecewise linear potential ( plp ) with new hydrogen bonding and electrostatics terms included . a lower score always indicates a higher affinity .   before initiation of the docking operation , both protein and ligands were prepared by mvd through assigning bonds , bond orders , explicit hydrogens , charges and flexible torsions at the missing region only . potential binding sites ( cavities or active sites ) were identified using the built - in cavity detection algorithm of mvd with a grid resolution (  ) of 0.30 . internal electrostatic interactions , internal hydrogen bonds , and sp2-sp2 torsions were selected as ligand evaluation terms . the  moldock se  was set as the searching algorithm for ten runs using a maximum of 1500 iterations with a total population size of 50 . energy minimization and optimized h - bonds were enabled as post - docking steps for more accurate refinement of the docking results . multiple poses were clustered based on the rmsd threshold of 1.0 , ignoring similar poses with rmsd threshold of 1.0 . the therapeutic effects of a medicinal plant are attributed to the phytochemical constituents of that plant . therefore , it is feasible to study individual phytochemicals present in plants when investigating the therapeutic effects of medicinal plants . from the literature search , eight phytochemicals were taken into consideration for the molecular simulation study including anthragallol , damnacanthal , esculin , lucidin , morindone , nordamnacanthal , rubiadin and soranjidiol . canonical smiles file of these selected ligand molecules were retrieved from the pubchem compound server ( https://pubchem.ncbi.nlm.nih.gov/ ) . canonical smiles files were entered in to the corina online demo to generate 3d protein data bank ( pdb ) files . protein data bank ( pdb ) file of human ar ligand binding domain ( pdb i d : 1e3 g ) was downloaded from rcsb pdb database ( http://www.rcsb.org/pdb/home/home.do ) . prior to molecular simulation study the drug likeness and safety of the chosen ligands were evolved by empirical computational tools . the molinspiration cheminformatics server was exploited to calculate the molecular properties associated with drug - likeness and to predict bioactivity of components including the nuclear receptor ligand and enzyme inhibitor ( 12 ) . the osiris property explorer was used to evolve the toxicity of the selected ligands in term of mutagenic , tumorigenic and irritant properties ( 13 ) . the site of the receptor that interacted with the ligands was predicted by the molegro virtual docker ( mdv ) inbuilt cavity detection algorithm and the pocket - finder server ( 14 ) . the outputs from both of the computational tools were synchronized to predict the ultimate ligand binding site and exploited in the subsequent docking study . molegro virtual docker ( mvd ) was used for the computer simulated docking study ( 15 ) . molegro virtual docker includes moldock and plants score for evaluating docking solutions followed by a rank for the best conformations . the solution to the function is the sum of intermolecular interaction energy between protein and ligand with the intra - molecular interaction energy of the ligand . the docking energy scoring function is based on a modified piecewise linear potential ( plp ) with new hydrogen bonding and electrostatics terms included . a lower score always indicates a higher affinity .   before initiation of the docking operation , both protein and ligands were prepared by mvd through assigning bonds , bond orders , explicit hydrogens , charges and flexible torsions at the missing region only . potential binding sites ( cavities or active sites ) were identified using the built - in cavity detection algorithm of mvd with a grid resolution (  ) of 0.30 . internal electrostatic interactions , internal hydrogen bonds , and sp2-sp2 torsions were selected as ligand evaluation terms . the  moldock se  was set as the searching algorithm for ten runs using a maximum of 1500 iterations with a total population size of 50 . energy minimization and optimized h - bonds were enabled as post - docking steps for more accurate refinement of the docking results . multiple poses were clustered based on the rmsd threshold of 1.0 , ignoring similar poses with rmsd threshold of 1.0 . the site of the receptor that interacted with the ligands was predicted by the molegro virtual docker ( mdv ) inbuilt cavity detection algorithm and the pocket - finder server ( 14 ) . the outputs from both of the computational tools were synchronized to predict the ultimate ligand binding site and exploited in the subsequent docking study . molegro virtual docker ( mvd ) was used for the computer simulated docking study ( 15 ) . molegro virtual docker includes moldock and plants score for evaluating docking solutions followed by a rank for the best conformations . the solution to the function is the sum of intermolecular interaction energy between protein and ligand with the intra - molecular interaction energy of the ligand . the docking energy scoring function is based on a modified piecewise linear potential ( plp ) with new hydrogen bonding and electrostatics terms included . before initiation of the docking operation , both protein and ligands were prepared by mvd through assigning bonds , bond orders , explicit hydrogens , charges and flexible torsions at the missing region only . potential binding sites ( cavities or active sites ) were identified using the built - in cavity detection algorithm of mvd with a grid resolution (  ) of 0.30 . internal electrostatic interactions , internal hydrogen bonds , and sp2-sp2 torsions were selected as ligand evaluation terms . the  moldock se  was set as the searching algorithm for ten runs using a maximum of 1500 iterations with a total population size of 50 . energy minimization and optimized h - bonds were enabled as post - docking steps for more accurate refinement of the docking results . multiple poses were clustered based on the rmsd threshold of 1.0 , ignoring similar poses with rmsd threshold of 1.0 . result of the drug likeness and toxicity evaluation of the ligand have been summarized in table 1 . the results from the molinspiration cheminformatics server showed that all the selected ligands met the lipinski 's rule of drug likeness without violation of any condition . additionally , all the ligands fitted more or less with nuclear receptor ligands and enzyme inhibitors . the output from the osiris property explorer suggested the esculin , lucidin , morindone and soranjidiol were safe ligands with no mutagenic or tumorigenic effects . thus , the probable phytochemicals were filtered , as they were more potent physiologically active molecules without any harmless effects . abbreviations : ei , enzyme inhibitor ; milogp , octanol - water partition coefficient developed at molinspiration ; n , no ; nv , number of violation of lipinski 's rule of drug likeness ; tpsa , total molecular polar surface area ; nrl , nuclear receptor ligand ; y , yes . initial prediction of the probable ligand - binding site was performed by the pocket - finder and mdv cavity search . the prediction showed an active site of 409 cubic angstroms with a maximum coordination of 8  42  12 from the pocket - finder output ( figure 1 ) . the cavity searching algorithm built in the mvd tool fetched a cavity of 86.02 cubic angstroms with a maximum coordination of 0.41  31.67  4.44 and surface of 204.8 square angstroms . output of the pocket - finder was synchronized with the mdv cavity search output for screening the prediction with higher degree of accuracy . as , these two outputs overlapped and the selected molecule had a surface of ~95 square angstroms at best , the cavity coordination of 0.41  31.67  4.44 was set as the desired ligand interaction site or binding site . the pocket - finder works by scanning the probe radius 1.6 angstroms along all gridlines of the grid resolution , 0.9 angstroms surrounding the protein . the output of the pocket - finder shows the highest precision ( 52.7 ) for site two , which was also energetically most favorable . the computational docking study of the ligand with the receptor ( coordinate : 0.41  31.67  4.44 ) by mvd was evolved in terms of moldock score for best pose . this observation is concordant with previous study with r 18 - 100 that has inhibitory effect on the ar . among the studied ligands , esculin exhibited the most favorable binding to the receptor followed by morindone , anthragallol , soranjidiol , lucidin and damnacanthal . the moldock score also revealed that esculin s interaction with the receptor is likely to be more energetically economic than that of the dihydrotestosterone ( table 2 ) .   during dihydrotestosterone interaction with the receptor , the amino acid residues , including gln 711 , arg 752 and thr 877 , were involved in hydrogen bonding while gln 711 , met 745 and phn 764 were involved in steric interaction ( figure 2 a ) . the amino acid residues leu 704 , asn 705 , arg 752 and thr 877 were involved in hydrogen bonding in case of esculin s interaction receptor . esculin exploited leu 704 , gln 711 , leu 873 , phe 876 , met 787 and met 895 residues at the binding site to maintain a steric interaction with the receptor ( figure 2 b ) . thus , the amino acid residues arg 752 and thr 877 were the common residues involved in the hydrogen bonding of the receptor with esculin and dihydrotestosterone . , the residues of the receptor participating in hydrogen bonding with the corresponding ligand are shown in azure color . the interaction includes hydrogen bonding with gln 711 , arg 752 and thr 877 , steric interaction with gln 711 , met 745 and phn 764 . , the residues of the receptor participating in hydrogen bonding with corresponding ligands are shown in azure color . the interaction includes hydrogen bonding with leu 704 , asn 705 , arg 752 andthr 877steric interaction with leu 704 , gln 711 , leu 873 , phe 876 , met 787 and met 895 . result of the drug likeness and toxicity evaluation of the ligand have been summarized in table 1 . the results from the molinspiration cheminformatics server showed that all the selected ligands met the lipinski 's rule of drug likeness without violation of any condition . additionally , all the ligands fitted more or less with nuclear receptor ligands and enzyme inhibitors . the output from the osiris property explorer suggested the esculin , lucidin , morindone and soranjidiol were safe ligands with no mutagenic or tumorigenic effects . thus , the probable phytochemicals were filtered , as they were more potent physiologically active molecules without any harmless effects . abbreviations : ei , enzyme inhibitor ; milogp , octanol - water partition coefficient developed at molinspiration ; n , no ; nv , number of violation of lipinski 's rule of drug likeness ; tpsa , total molecular polar surface area ; nrl , nuclear receptor ligand ; y , yes . initial prediction of the probable ligand - binding site was performed by the pocket - finder and mdv cavity search . the prediction showed an active site of 409 cubic angstroms with a maximum coordination of 8  42  12 from the pocket - finder output ( figure 1 ) . the cavity searching algorithm built in the mvd tool fetched a cavity of 86.02 cubic angstroms with a maximum coordination of 0.41  31.67  4.44 and surface of 204.8 square angstroms . output of the pocket - finder was synchronized with the mdv cavity search output for screening the prediction with higher degree of accuracy . as , these two outputs overlapped and the selected molecule had a surface of ~95 square angstroms at best , the cavity coordination of 0.41  31.67  4.44 was set as the desired ligand interaction site or binding site . the pocket - finder works by scanning the probe radius 1.6 angstroms along all gridlines of the grid resolution , 0.9 angstroms surrounding the protein . the output of the pocket - finder shows the highest precision ( 52.7 ) for site two , which was also energetically most favorable . the computational docking study of the ligand with the receptor ( coordinate : 0.41  31.67  4.44 ) by mvd was evolved in terms of moldock score for best pose . this observation is concordant with previous study with r 18 - 100 that has inhibitory effect on the ar . among the studied ligands , esculin exhibited the most favorable binding to the receptor followed by morindone , anthragallol , soranjidiol , lucidin and damnacanthal . the moldock score also revealed that esculin s interaction with the receptor is likely to be more energetically economic than that of the dihydrotestosterone ( table 2 ) .   during dihydrotestosterone interaction with the receptor , the amino acid residues , including gln 711 , arg 752 and thr 877 , were involved in hydrogen bonding while gln 711 , met 745 and phn 764 were involved in steric interaction ( figure 2 a ) . the amino acid residues leu 704 , asn 705 , arg 752 and thr 877 were involved in hydrogen bonding in case of esculin s interaction receptor . esculin exploited leu 704 , gln 711 , leu 873 , phe 876 , met 787 and met 895 residues at the binding site to maintain a steric interaction with the receptor ( figure 2 b ) . thus , the amino acid residues arg 752 and thr 877 were the common residues involved in the hydrogen bonding of the receptor with esculin and dihydrotestosterone . , the residues of the receptor participating in hydrogen bonding with the corresponding ligand are shown in azure color . the interaction includes hydrogen bonding with gln 711 , arg 752 and thr 877 , steric interaction with gln 711 , met 745 and phn 764 . , the residues of the receptor participating in hydrogen bonding with corresponding ligands are shown in azure color . the interaction includes hydrogen bonding with leu 704 , asn 705 , arg 752 andthr 877steric interaction with leu 704 , gln 711 , leu 873 , phe 876 , met 787 and met 895 . initial prediction of the probable ligand - binding site was performed by the pocket - finder and mdv cavity search . the prediction showed an active site of 409 cubic angstroms with a maximum coordination of 8  42  12 from the pocket - finder output ( figure 1 ) . the cavity searching algorithm built in the mvd tool fetched a cavity of 86.02 cubic angstroms with a maximum coordination of 0.41  31.67  4.44 and surface of 204.8 square angstroms . output of the pocket - finder was synchronized with the mdv cavity search output for screening the prediction with higher degree of accuracy . as , these two outputs overlapped and the selected molecule had a surface of ~95 square angstroms at best , the cavity coordination of 0.41  31.67  4.44 was set as the desired ligand interaction site or binding site . the pocket - finder works by scanning the probe radius 1.6 angstroms along all gridlines of the grid resolution , 0.9 angstroms surrounding the protein . the output of the pocket - finder shows the highest precision ( 52.7 ) for site two , which was also energetically most favorable . the computational docking study of the ligand with the receptor ( coordinate : 0.41  31.67  4.44 ) by mvd was evolved in terms of moldock score for best pose . this observation is concordant with previous study with r 18 - 100 that has inhibitory effect on the ar . among the studied ligands , esculin exhibited the most favorable binding to the receptor followed by morindone , anthragallol , soranjidiol , lucidin and damnacanthal . the moldock score also revealed that esculin s interaction with the receptor is likely to be more energetically economic than that of the dihydrotestosterone ( table 2 ) .   during dihydrotestosterone interaction with the receptor , the amino acid residues , including gln 711 , arg 752 and thr 877 , were involved in hydrogen bonding while gln 711 , met 745 and phn 764 were involved in steric interaction ( figure 2 a ) . the amino acid residues leu 704 , asn 705 , arg 752 and thr 877 were involved in hydrogen bonding in case of esculin s interaction receptor . esculin exploited leu 704 , gln 711 , leu 873 , phe 876 , met 787 and met 895 residues at the binding site to maintain a steric interaction with the receptor ( figure 2 b ) . thus , the amino acid residues arg 752 and thr 877 were the common residues involved in the hydrogen bonding of the receptor with esculin and dihydrotestosterone . a ) dihydrotestosterone and androgen receptor interaction . here , the residues of the receptor participating in hydrogen bonding with the corresponding ligand are shown in azure color . the interaction includes hydrogen bonding with gln 711 , arg 752 and thr 877 , steric interaction with gln 711 , met 745 and phn 764 . , the residues of the receptor participating in hydrogen bonding with corresponding ligands are shown in azure color . the interaction includes hydrogen bonding with leu 704 , asn 705 , arg 752 andthr 877steric interaction with leu 704 , gln 711 , leu 873 , phe 876 , met 787 and met 895 . the purpose of the present study was to evaluate potential phytochemicals with anti - prostate cancer activity from h. excelsum with prediction of mechanism of action using a computational molecular simulation study . this study firstly investigated the anti - prostate cancer effect of h. excelsum phytochemicals with a mechanistic insight .   from the literature search , eight phytochemicals were selected as the subject ligands including anthragallol , damnacanthal , esculin , lucidin , morindone , nordamnacanthal , rubiadin , and soranjidiol while dihydrotestosterone was considered as the control . besides , human androgen receptor ( ar ) ligand binding domain was selected as the receptor for the subsequent computational docking study . all the ligands were screened for drug - likeness rules , biological activity and probable toxicity . esculin , lucidin , morindone and soranjidiol were found as more potent physiologically active molecules without any harmless effects ( table 1 ) .   upon the generation of the 3d pdb structure , the ligands were docked to the ar ligand binding residues by molegro virtual docker ( mvd ) tools . results of the docking study suggest a favorable binding of esculin to the receptor with respect to dihydrotestosterone ( table 2 ) . the coumarin glycoside esculin also scavenges superoxide radicals and decreases lipid peroxidation that is considered as a common strategy of a broad range on anti - cancer agents ( 16 ) . cichorium intybus , an esculin containing plant , has been reported to have a modest inhibitory effects on the proliferation of prostate , breast and colorectal cells ( 17 ) . analysis of amino acid residues involved in docking , hydrogen bonding energy contribution to docking score and steric interaction revealed a nearly similar ligand - receptor interaction for both of dihydrotestosterone and esculin . still , from the present molecular simulation study it was profound that the contribution of hydrogen bonding to moldock score was higher for esculin with respect to dihydrotestosterone ( table 2 ) . thus , hydrogen bonding and steric interaction patterns of esculin and dihydrotestosterone suggested a nearly similar ligand - receptor interaction pattern . therefore , esculin has the potency to act like an antagonist of dihydrotestosterone , while it also has a potential ar inhibitory effect .
background : hymenodictyon excelsum is a medicinal plant traditionally used for tumor treatment as it contains phytochemicals of anthraquinone and coumarin class.objectives:the aim of the present study was to unfold the therapeutic value of selected phytocompounds of hymenodictyon excelsum in prostate cancer.materials and methods : eight phytochemicals were selected based on the literature search including anthragallol , damnacanthal , esculin , lucidin , morindone , nordamnacanthal , rubiadin , and soranjidiol while dihydrotestosterone was considered as the control . 
 human androgen receptor ( ar ) ligand binding domain ( pdb i d : 1e3 g ) was selected as the receptor for subsequent computational docking study . 
 first , the selected phytocompounds were screened for their drug likeness and safety profile . 
 molegro virtual docker ( mvd ) was subjected only to drug - like and safe phytocompounds for the computational docking study.results:except for anthragallol , nordamnacanthal and rubiadin , all the ligands were drug - like and safe . 
 results of the docking study suggest a favorable binding of esculin to the receptor with respect to dihydrotestosterone . 
 analysis of docking pattern revealed a nearly similar ligand - receptor interaction for both dihydrotestosterone and esculin.conclusions:the anthraquinone and coumarin principles of h. excelsum have an anti - prostate cancer effect that has been proposed to be exerted by antagonistic effects on ar .