• Comparative Molecular Docking of Antitrypanosomal Natural ...


  •   
  • FileName: pdf [read-online]
    • Abstract: shown to have growth inhibitory activity against Trypanosoma brucei were docked into ... Human African Trypanosomiasis (HAT) caused by Trypanosoma brucei gambiense/rhodesiense. remains of one the world\'s most neglected parasitic diseases, endangering millions of people and ...

Download the ebook

Molecules 2009, 14, 1513-1536; doi:10.3390/molecules14041513
OPEN ACCESS
molecules
ISSN 1420-3049
www.mdpi.com/journal/molecules
Article
Comparative Molecular Docking of Antitrypanosomal Natural
Products into Multiple Trypanosoma brucei Drug Targets
Ifedayo V. Ogungbe and William N. Setzer *
Department of Chemistry, University of Alabama in Huntsville, Huntsville, AL 35899, USA
E-mail: dayo[email protected] (I-V.O.)
* Author to whom correspondence should be addressed; E-mail: [email protected]
Received: 22 February 2009; in revised form: 7 April 2009 / Accepted: 8 April 2009 /
Published: 14 April 2009
Abstract: Antitrypanosomal natural products with different structural motifs previously
shown to have growth inhibitory activity against Trypanosoma brucei were docked into
validated drug targets of the parasite, which include trypanothione reductase, rhodesain,
farnesyl diphosphate synthase, and triosephosphate isomerase. The in-silico calculations
predicted that lowest energy docked poses of a number of the compounds can interact with
catalysis-dependent residues, thus making them possible catalytic inhibitors and of course
physiologically active. Compounds that possess a number of hydrogen-bond-accepting
and/or -donating groups like phenolics and quinones show extensive interactions with the
targets. Compounds like cissampeloflavone, 3-geranylemodin and ningpogenin thus offer
profound promise.
Keywords: Docking; Antitrypanosomal agents; Natural products; Trypanosoma brucei;
Protease; Sleeping sickness.
1. Introduction
Human African Trypanosomiasis (HAT) caused by Trypanosoma brucei gambiense/rhodesiense
remains of one the world’s most neglected parasitic diseases, endangering millions of people and
livestock in sub-Saharan Africa [1]. Although promising lead compounds to combat the disease have
been discovered in the last decade, current treatments are still ineffective and have serious adverse
effects. Thus, prospecting for antitrypanosomal agents is pertinent and requires continued effort.
Molecules 2009, 14 1514
Compounds from nature or their synthetic homologues have, however, continued to provide a vast
majority of drug leads in almost all disease conditions [2].
In-silico screening of small molecules has been in the forefront of drug discovery in recent years.
Despite its array of applications in synthetic medicinal chemistry, its application to natural products
drug discovery (NPDD) remains very sparse. There has, however, been much interest lately on the
application of virtual screening to the highly laborious drug discovery efforts from nature and how it
can stimulate the much needed renewed enthusiasm in NPDD [3].
A number of drug targets have been identified in T. brucei. These include trypanothione reductase
(TR), rhodesain, triosephosphate isomerase (TIM) and farnesyl diphosphate synthase (FDS), in line
with the fact that target-based drug discovery efforts remain a front runner in lead identification [4].
Coupled with this, several antitrypanosomal agents from plants have been characterized while
considerable efforts are still being put into the search for more antiparasitic compounds that have been
evolutionarily derived from nature, resulting from the co-existence of parasitic pathogens with other
life forms. This work presents the molecular docking of antitrypanosomal natural products into T.
brucei drug targets with a view of obtaining structural motifs that preferentially interact with these
targets. Comparative docking of those compounds with the best binding properties to parasitic targets
was also carried out with human homologues. This will not only help in designing synthetic analogues
but also in planning extract purification and compound isolation schemes for target-based bioassays,
which could lead to the isolation of potent antitrypanosomal agents that can become leads for drug
development.
2. Results and Discussion
All the docked compounds have been previously reported to exhibit antitrypanosomal activity. The
rerank score of the top poses calculated for all the compounds docked and their corresponding in-vitro
IC50 against T. brucei cells in culture is presented in Table 1 below. The docking results revealed
compounds with more favorable interactions with the targets and also indicated that some classes of
compounds present certain structural motifs that could make them form extensive Van der Waals
interactions and hydrogen bonding with targets.
2.1. Farnesyl Diphosphate Synthase
FDS catalyzes the formation of farnesyl diphosphate via consecutive condensation of two
molecules of isopentenyl diphosphate with dimethylallyl diphosphate in the isoprenoid biosynthetic
pathway, thus providing a precursor for the synthesis of ubiquinones, dolichols, sterols, heme a, and of
course the prenylation of certain proteins [5]. Numerous reports have indicated that FDS is a
therapeutic target in T. brucei [6,7]. Biphosphates, used in treating bone resorption, have been noted to
have antiparasitic activity by way of FDS inhibition and are being investigated as potential
antitrypanosomal drugs [8,9]. Table 2 below shows the top five compounds with favorable interactions
with FDS. Angoroside C and cissampeloflavone led the top hit compounds for FDS based on the
rerank score. Angoroside C has been previously shown to have moderate growth inhibitory activity
against T. brucei rhodesiense [10]. Molecular docking calculations indicate that angoroside C and
Molecules 2009, 14 1515
eleven other docked compounds (Tables 1 and 2) have more favorable interactions with T. brucei FDS
than the co-crystallized ligand, phenylalkyl bisphosphate-BPH-210, a potent inhibitor of FDS.
Table 1. Molecular docking pose scores of antitrypanosomal agents and the reported IC50
for T. brucei.
Rerank Pose Scorea
Triosephosphate Farnesyl IC50 for T.
Compounds Trypanothione
Rhodesain Isomerase diphosphate brucei (µM)
reductase (TR)
(TIM) synthase (FDS)
Iridiods
6-O-methylcatalpol -83.03 -86.80 -110.00 -104.04 86 [10]
6-O-β-D-xylopyranosylaucubin -83.91 -77.47 -121.65 -83.30 79 [10]
Ajugol -21.62 -87.10 -109.50 -102.89 91 [10]
Ajugoside -78.81 -99.60 -113.83 -113.83 144 [10]
Aucubin -80.26 -98.53 -101.28 -119.70 148 [10]
Catalpol -66.34 -75.50 -75.14 -81.19 151 [10]
Ningpogenin -101.68 -79.62 -124.27 -122.97 172 [10]
Scrolepidoside -68.48 -68.83 -101.37 -89.86 49 [10]
Isoquinone Alkaloids
Ancistroealaine A -70.34 -68.84 -57.11 -74.17 8.25 [11]
Ancistrogriffine A -67.72 -79.84 -77.90 -88.33 5.53 [12]
Ancistrogriffine C -64.00 -86.71 -88.96 -78.06 7.85 [12]
Ancistrogriffithine A -85.35 -95.68 137.47 -53.62 1.15 [12]
Ancistrolikokine D -79.61 -81.58 -94.94 -68.74 6.93 [13]
Ancistrotanzanine A -76.87 -90.86 -43.39 -53.78 1.7 [14]
Ancistrotanzanine B -71.15 -89.98 -83.70 -73.43 1.7 [16]
Ancistrotanzanine C -76.33 -84.97 -35.30 -6.62 3.2 [15]
Ancistrotectonine -68.12 -84.82 -93.37 14.88 10.2 [15]
Aromoline -29.94 -76.77 160.86 -51.33 1.48 [16]
Berbamine 20.95 -36.57 478.31 -24.28 2.6 [17]
Berberine -82.07 -86.90 -92.33 -107.69 0.53 [17]
Dioncophylline E -74.74 -93.87 -71.17 -88.05 2.1 [18]
Emetine -69.79 -98.46 -111.37 -103.12 0.039 [17]
Korupensamine A -69.39 -89.57 -76.20 -4.14 4.93 [19]
Nangustine -29.03 -83.45 -88.71 -91.92 33 [20]
Pancracine -64.51 -87.31 -86.07 -89.97 2.4 [20]
Miscellaneous Alkaloid
3-O-Acetylsanguinine -66.14 -77.68 -84.68 -85.43 3.5 [21]
Miscellaneous Compounds
8-Hydroxyheptadeca-1-ene-4,6-
-93.68 -109.03 -118.13 -132.24 0.46 [22]
diyn-3-yl acetate
8-Hydroxylheptadeca-4,6-diyn-
-105.81 -100.58 -103.24 -127.20 18 [22]
3-yl acetate
16-Acetoxy-11-
hydroxyoctadeca-17-ene-12,14- -88.38 -88.12 -94.64 -117.40 1.1 [22]
diynyl acetate
Aculeatin D -58.63 -92.09 -122.28 -129.51 0.48 [23]
Molecules 2009, 14 1516
Table 1. Cont.
Rerank Pose Scorea
Triosephosphate Farnesyl IC50 for T.
Compounds Trypanothione
Rhodesain Isomerase diphosphate brucei (µM)
reductase (TR)
(TIM) synthase (FDS)
Phenolics
1,7-bis(4-hydrophenyl)-heptane-
-42.99 -49.29 -76.29 -91.90 7.4-8.3 [24]
3,5-dione
1,7-bis(4-hydrophenyl)-heptene-
-49.35 -53.42 -72.18 -97.44 8.4 [24]
3,5-dione
Ambigol A -83.14 -90.16 -96.41 -106.15 33 [25]b
Ambigol C -85.42 -95.93 -101.70 -111.03 11 [25]b
Angoroside C -63.53 -93.95 -152.16 -98.74 75 [10]
Chaetoxanthone A -51.70 -52.59 -52.79 -43.16 12.69 [26]
Chaetoxanthone B -47.56 -57.78 -48.26 -29.30 26.26 [26]
Cissampeloflavone -105.24 -114.60 -141.43 -135.28 1.99 [27]
Letestuianin C -73.82 -69.42 -89.89 -112.69 7.36 [24]
Piscatorin -89.25 -110.52 -118.69 -123.04 6.10 [28]
Punicalagin -31.50 10.55 389.14 189.60 1.75 [29]
Vismione D -97.84 -102.02 -121.43 -127.88 22 [30]
Quinoline Alkaloids
Cinchonidine -40.27 -77.57 -93.47 -92.77 7.1 [17]
Cinchonine -47.11 -80.25 -93.21 -114.67 1.2 [17]
Cryptolepine -73.02 -82.82 -72.71 -90.88 0.6 [31]
Neocryptolepine -73.12 -87.48 -78.55 -89.50 2.23 [31]
Quinidine -61.61 -84.40 -84.17 -98.87 0.77 [17]
Quinine -60.77 -84.20 -85.38 -114.96 4.9 [17]
Quinones
2-(1-hydroxylethyl)naphtho[2,3-
-75.43 -90.81 -74.83 -99.66 0.05 [32]
b]furan-4,9-quinone
3-Geranylemodin -93.20 -97.03 -129.13 -138.76 35.4 [30]
4′-O-demethylknipholone-4′-O-
-78.06 -92.32 -129.29 -115.47 1.2 [33]
β-D-glucopyranoside
Emodin -79.37 -93.13 -82.46 -83.17 67 [30]
Gabroquinone A -90.99 -96.68 -113.22 -70.45 11.3 [33]
Gabroquinone B -91.59 -95.34 -114.86 -86.95 101 [33]
Isokigelinol -64.21 -59.06 -68.31 -66.08 11.11 [32]
Isopinnatal -55.03 -55.51 -77.04 -93.08 0.73 [32]
Kigelinol -59.03 -74.05 -64.27 -70.88 21.28 [32]
Knipholone -77.99 -100.24 -83.91 -63.32 21.4 [33]
Terpenoids
Arnicolide A -73.97 -73.66 -82.65 -56.31 1.42 [34]
Helenalin -77.08 -71.00 -84.45 -63.25 0.051 [34]
Isoalantolactone -61.91 -69.31 -62.40 -78.73 23.4 [34]
Ivalin -56.83 -72.21 -66.62 -78.14 7.8 [34]
Mexicanin 1 -56.40 -62.47 -74.63 -76.12 0.318 [34]
Vernoguinoside -86.81 -69.78 -108.12 -95.31 6 [35]
Vernoguinosterol -60.89 -78.61 -107.89 -50.99 8 [35]
a
The rerank score is a linear combination of the E-inter (steric, Van der Waals, hydrogen bonding,
electrostatic) between the ligand and the protein, and E-intra (torsion, sp2-sp2, hydrogen bonding,
steric, Van der Waals, electrostatic) of the ligand weighted by pre-defined coefficients [49].
b
Reported as MIC.
Molecules 2009, 14 1517
Table 2. Top hit compounds for docking to farnesyl diphosphate synthase (FDS).
Class of Rerank Pose H-bonding ETotal
Compounds
Compound Score (kJ/mol) (kJ/mol)
T. brucei Human T. brucei Human T. brucei Human
Angoroside C phenolic -152.16 80.14 -43.56 -33.83 -207.79 -56.03
Cissampeloflavone phenolic -141.43 54.45 -8.01 -15.44 -192.64 -88.88
4′-O-demethylknipholone-
quinone -129.29 148.82 -41.50 -8.81 -159.31 -44.02
4′-O-β-D-glucopyranoside
3-Geranylemodin quinone -129.13 -69.92 -13.43 -14.75 -147.73 -121.73
Ningpogenin iridoid -124.27 -79.16 -7.14 -10.41 -164.20 -94.61
BPH-210 a --- 114.55 --- -8.65 --- -138.81 ---
a
N-[methyl(4-phenylbutyl)]-3-aminopropyl-1-hydroxy-1,1-bisphosphonate; the co-crystallized
ligand.
Figure 1. Some predicted interactions (green dashed lines) between angoroside C (white
and red) and active site residues Arg 112, Ser 109, Lys 269, Gly 45, and Asp 255 of T
brucei FDS.
Extensive interactions are observed between angoroside C and the Asp residues 103, 104, 107, 255,
259 of the protein’s repeating DDXXD motifs, Lys 212, 269, and Arg 112 (Figure 1); residues that
have been noted as important for the binding and inhibitory action of BPH-210 (Figure 2) [36]. In
comparison with the human FDS homologue, angoroside C and all the other compounds with top
poses as shown in Table 2 have more favorable interaction energy based on both the rerank scores and
total energies with the parasitic FDS than the human enzyme. Shown in Figure 3 is the orientation of
angoroside in the isopentenyl pyrophosphate binding site of Human FDS.
Protein-ligand hydrogen bonding interactions are more extensive in the FDS-angoroside C complex
compared to that of BPH-10, each having values -43.56 and -8.65 respectively (Table 2). Thus,
Molecules 2009, 14 1518
phenolic and quinone compounds like angoroside C, cissampeloflavone and 3-geranylemodin could
provide structural leads for more potent and selective FDS inhibitors.
Figure 2. BPH-210 (green) in the active site of T.brucei FDS. Predicted hydrogen bonding
interactions (green dashed lines) can be seen between BPH-210 and active residues Lys
212, Lys 269, Asp 103 and Arg 112.
Figure 3. Top pose of angoroside C (white and red) and the co-crystallized ligand;
alendronate (yellow) in the binding site of Human FDS, illustrating the orientation of
important binding site residues Lys 257, Arg 112, Asp 107, Asp 103, Lys 200 around the
phenolic compound.
Hydrogen bonding interactions between the ligand and protein are more extensive in the FDS-
angoroside C complex compared to that of BPH-10 with a value of -43.56 to -8.6 respectively (Table
2). Thus, phenolic and quinone compounds like angoroside C, cissampeloflavone and 3-geranylemodin
could provide structural leads for more potent and selective FDS inhibitors.
Molecules 2009, 14 1519
2.2 . Rhodesain
Parasitic proteases have been a subject of extensive investigations to identify novel
antitrypanosomal agents due to the enormous roles they play in the parasites [37]. Rhodesain, the
major cathepsin L-like protease in African trypanosomes, is a target for new HAT chemotherapy [38,
39]. Interaction of compounds to the residues at the S4, S3, S2, S1 and the S1′, S2′, S3′ of the
enzyme’s substrate binding cleft has been linked to their inhibitory activities [40]. Also, specific
interactions with Cys 25, His 162, and Asn 182 that form the catalytic triad as well as Trp 184 and Gln
19 in rhodesain are essential. 8-Hydroxylheptadeca-4,6-diyn-3-yl acetate and 8-hydroxyheptadeca-1-
ene-4,6-diyn-3-yl acetate, polyacetylenes from Cussiona zimmermanni, recently reported [22] to have
antiparasitic activity, are among the five top compounds obtained from this docking study (Table 3).
8-Hydroxylheptadeca-4,6-diyn-3-yl acetate shows extensive interactions with residues along the
substrate binding sites of rhodesain (Figure 4). Of particular importance is the predicted hydrogen
bonding between the compound and the all important cysteine residue (Supplementary Figure 1)
required for the protease’s activity. Target residues for K777 in the solved crystal structure and the
docked complex of rhodesain and 8-hydroxylheptadeca-4,6-diyn-3-yl acetate indicate similar
interactions with Ala 138, Asp 161, Cys 25, Gln 19, Gly 66, His 162, Leu 67, Trp 26, and 184 (Figures
4 and 5, and Supplementary Figures 2 and 3). Cathepsin inhibitor selectivity remains an important
issue when being considered for chemotherapy; this is not unconnected with the very similar
specificity of cathepsins. However, structural differences are now being exploited in drug design.
Poorer pose scores and weaker pose energies (Table 3) were obtained for the top compounds docked to
the catalytic site of cathepsin L compare to the parasitic protease, indicating possible selectivity, with
the interaction of 8-hydroxylheptadeca-4,6-diyn-3-yl acetate and the proteins revealing significant
energy differences. Testing of this compound for inhibitory activity could provide valuable clue on its
possible potency against the protease.
Table 3. Top hit compounds for docking to rhodesain and corresponding energy values for
human cathepsin L.
Rerank Pose H-bonding ETotal
Class of
Compounds Score (kJ/mol) (kJ/mol)
compound
T. brucei Human T. brucei Human T. brucei Human
8-Hydroxylheptadeca-
diacetylene -105.81 -92.08 -2.77 -2.70 -134.90 -109.49
4,6-diyn-3-yl acetate
Cissampeloflavone phenolic -105.24 -103.15 -4.81 -8.14 -159.29 -151.00
Ningpogenin iridoid -101.68 -66.52 -12.27 -8.05 -138.13 -81.82
Vismione D phenolic -97.84 -82.51 -2.50 -6.23 -110.79 -95.88
8-Hydroxyheptadeca-1-
diacetylene -93.68 -92.38 -3.63 -2.78 -129.03 -113.74
ene-4,6-diyn-3-yl acetate
K777a --- -87.75 --- -6.61 --- -135.61 ---
a
N-methylpiperazine-Phe-homoPhe-vinylsulfone-phenyl
Molecules 2009, 14 1520
Figure 4. 8-Hydroxylheptadeca-4,6-diyn-3-yl acetate interacting with rhodesain’s active
site residues. Hydrogen bonding interactions are shown as green dashed lines.
Figure 5. K777, rhodesain’s co-crystallized ligand, is shown interacting with the active site
residues. Hydrogen bonding interactions are shown as green dashed lines.
2.3. Trypanothione reductase
TR is an attractive drug target in trypanosomatids due to its uniqueness in maintaining redox
balance in these organisms, comparable to the ubiquitous glutathione/glutathione reductase system in
mammalian hosts. Its vitality to the survival of the parasites has been reported [41]. The X-ray crystal
structure of T. brucei recently solved by Jones et al. [42] provides a significant leap in pursuing T.
brucei TR-selective inhibitors. Docking of these compounds into the predicted binding site of TR
reveals that FAD has a comparatively higher rerank pose score and hydrogen bonding affinity than all
the compounds (Table 4); however significant interactions are observed between the top pose of 3-
Molecules 2009, 14 1521
geranylemodin and Ser 15, Gly 16 and Asp 329 residues of the protein. These residues have been
previously noted to provide structural motifs for the binding of FAD (Figures 6 and 7). In addition,
predicted interaction of the ligand with Cys 53 at the disulfide substrate binding site, thus providing a
long range interaction with the target residues, could be a major factor in its inhibitory potency. Of
particular note is the fact that tricyclic compounds have been previously characterized as one of the
known classes of TR inhibitors [4]. 3-Geranylemodin, a tricyclic anthraquinone previously shown to
have moderate anti T. brucei activity is predicted from this calculation as the most likely TR inhibitor
of the compounds considered. It also has a better ligand pose score for TR than for the human
glutathione reductase, and this also occurs for the compound cissampeloflavone. In contrast, aculeatin
D, vismione D and 8-hydroxyheptadeca-1-ene-4,6-diyn-3-yl acetate have poorer pose scores for TR
but the total interaction energy between 8-hydroxyheptadeca-1-ene-4,6-diyn-3-yl acetate and TR is
still more favorable than that of GR.
Table 4. Top hit compounds for docking to trypanothione reductase (TR) and
corresponding values for human glutathione reductase.
Rerank Pose H-bonding ETotal
Class of
Compounds Score (kJ/mol) (kJ/mol)
compound
T. brucei Human T. brucei Human T. brucei Human
3-Geranylemodin quinone -138.76 -103.23 -15.08 -2.91 -207.63 -178.49
Cissampeloflavone phenolic -135.28 20.09 -5.62 -2.06 -159.57 -166.18
8-Hydroxyheptadeca-1-ene-
diacetylene -132.24 -155.71 -11.30 -2.72 -197.78 -181.85
4,6-diyn-3-yl acetate
Aculeatin D miscellaneous -129.51 -142.87 -1.14 3.38 -178.63 -182.96
Vismione D phenolic -127.88 -155.17 -6.95 -4.75 -155.87 -187.92
FADa --- -162.98 -295.81 -17.69 -33.86 -207.63 -351.32
a
Flavin adenine dinucleotide; co-crystallized ligand.
Figure 6. 3-Geranylemodin (brown) and FAD (white, red and blue) interacting with
residues at the FAD binding site of TR. Hydrogen bonding interactions are shown as green
dashed lines.
Molecules 2009, 14 1522
Figure 7. A close up on the orientation of 3-geranylemodin (brown) and FAD (white, red
and blue) on a solid surface of TR.
2.4. Triosephosphate Isomerase
TIM catalyzes the interconversion between glyceraldehyde 3-phosphate and dihydroxyacetone
phosphate in the glycolytic pathway. The glycolytic pathway is particularly important in the
bloodstream form of T. brucei due to their dependence on it for energy metabolism [43]. Although the
ubiquitous nature of TIM and metabolic flux analysis have suggested that inhibiting glucose transport
could prove more effective in killing trypanosomes by chemical agents [44], the structural differences
in mammalian and trypanosomal TIM as reported by Olivares-Illana et al. [45] indicate, however, that
T. brucei TIM remains a drug target and its specific inhibitors can be obtained from nature or
designed. Table 5 below shows compounds predicted to have more favorable interaction with TIM,
this enzyme possesses catalysis-dependent Glu-165 and His-95 and/or Lys-13 residues [46]. Each of
these compounds is found to interact with these residues like the HPO42- group, a competitive inhibitor
of TIM. One of the phenyl groups of cissampeloflavone is found to dock exactly at the HPO42- site
with its methoxy and hydroxy substituents predicted to form extensive hydrogen bonding to nearby
glycine and serine residues (Figures 8 and 9). Considerably lower interaction energies are, however,
obtained for the top poses docked to similar HPO42- binding site of the mammalian TIM (Table 5).
These values give strong suggestions of significantly higher positive interaction between the ligands
and the parasitic TIM in comparison to the mammalian TIM and of course this predicted selectivity
can be exploited for drug design, synthesis and experimental validation.
Molecules 2009, 14 1523
Table 5. Top hit compounds for docking to triosephosphate isomerase (TIM).
Rerank Pose H-bonding ETotal
Class of Score (kJ/mol) (kJ/mol)
Compounds
compound T.
T. brucei Human T. brucei Human Human
brucei
Cissampeloflavone phenolic -114.60 -9.91 -7.97 -2.50 -168.78 -21.80
Piscatorin phenolic -110.52 8.07 -6.70 -2.42 -144.90 -41.04
8-Hydroxyheptadeca-1-
diacetylene -109.03 -34.68 -8.24 -1.10 -140.88 -52.57
ene-4,6-diyn-3-yl acetate
Vismione D phenolic -102.02 -3.94 -9.78 0.00 -116.24 -10.10
8-Hydroxylheptadeca-4,6-
diacetylene -100.58 -38.15 -10.54 0.00 -132.00 -44.82
diyn-3-yl acetate
HPO42- --- -38.82 --- -8.23 --- -47.00 ---
Figure 8. Cissampeloflavone (red and white) and HPO42- (green) at the phosphate binding
site of TIM. Hydrogen bonding interactions are shown as green dashed lines.
Figure 9. Electrostatic surface of TIM showing the insertion of a substituted phenyl ring of
cissampeloflavone (red and white) into the HPO42- (green) binding groove.
Molecules 2009, 14 1524
2.5. Summary
The docking calculations in this study revealed that most of the compounds with top poses are
phenolic and quinone compounds rather than the isoquinoline alkaloids out of the compound dataset
used. Although these compounds have been shown to have growth inhibitory action against T. brucei,
target-based screening of the compounds will provide information about selectivity and mechanism of
action. It is important to note that since enzyme inhibition experimental data are not available for these
compounds, structure-activity analysis thus becomes impossible, but target-based isolation schemes
and/or synthesis of hit compounds predicted by in-silico investigations in conjunction with
ethnomedicinal approaches is highly recommended and could eventually lead to new chemotherapy
that can save humans and livestock from sleeping sickness in localities where the disease is endemic.
3. Experimental
3.1. Compound Dataset
Antitrypanosomal agents from plants (Figure 10) were obtained from the natural products
literature. These compounds include iridoids, phenolics, terpenoids, alkaloids, quinones and a few
miscellaneous compounds. Their exact structures were obtained from the Dictionary of Natural
Products [47] and/or primary articles, drawn with correct stereochemistry using ChemSketch [48],
energy minimized and saved as mol files.
3.2. Computation
Molecular docking was carried out using Molegro Virtual Docker (MVD) [49]. MVD is based on
a differential evolution algorithm; the solution of the algorithm takes into account the sum of the
intermolecular interaction energy between the ligand and the protein, and the intramolecular
interaction energy of the ligand. The docking energy scoring function is based on a modified
piecewise linear potential (PLP) with new hydrogen bonding and electrostatic terms included. Full
description of the algorithm and its reliability compared to other common docking algorithm can be
found in reference [49]. The small molecules and the PDB crystal structure atomic coordinates
determined by x-ray crystallography of TIM, rhodesain, FDS and TR [PDB Id: 1AG1, 2P7U, 2P1C
and TVE2 respectively] were imported, potential binding sites were predicted. The binding cavity was
set at X: 46.05, Y: 16.79, Z: -10.89 for TIM, X: 67.89, Y: 37.05, Z: -2.46 for FDS, X: 8.81, Y: 24.62,
Z: 22.66 for TR and X: -8.23, Y: 2.30, Z: 10.28 for rhodesain. RMSD threshold for multiple cluster
poses was set at < 1.00Å. The docking algorithm was set at maximum iterations of 1500 with a
simplex evolution population size of 50 and a minimum of 10 runs. Representative superposition of
poses of docked compounds is shown for FDS and rhodesain in Supplementary Figures 5 and 6 to
show that docked poses have similar binding modes.
Molecules 2009, 14 1525
Figure 10. Structures of docked antitrypanosomal natural products discussed in this work.
HO H
XylO H CH3O
H H
HO O O
O O O
O
HO H
H HO H OGlc H
HO OGlc HO OGlc
6-O-β-D-Xylo Catalpol
Ningpogenin 6-O-Methylcatalpol
-pyranosylaucubin
CH3
HO H HO H CH3O CH3
N
O O H
CH3O
AcO H HO H OH CH3
OGlc OGlc
HO
Ajugoside Ajugol
Ancistrogriffine C
O OH
HO CH3 CH3O HO
O HO
O H
N H 3C
CH3 CH3O
O H
CH3O CH3 O
CH3O
HO H
O OGlc
HO CH3
HO H Aucubin
Ancistrogriffine A OGlc
Scrolepidoside
CH3O OCH 3 CH3O OCH 3
CH3
H
N
CH3 CH3
CH3 CH3O CH3 CH3O CH3
HO OCH 3 N N
CH3
OH OCH 3 CH3O CH3 CH3O CH3
Ancistroealaine A Ancistrotanzanine B
CH3O OH
CH3
CH3O OH
CH3O OH
HO CH3
CH3
CH3O OH
CH3 N
N CH3
H HO CH3
CH3O CH3
CH3


Use: 0.3832