Rosa Maria Vitale1, Cristina Avonto2, Danilo Del Prete3, Aniello Schiano Moriello4,5, Pietro Amodeo1, Giovanni Appendino3, Luciano De Petrocellis4. 1. Institute of Biomolecular Chemistry, National Research Council (ICB-CNR), Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy. 2. National Center for Natural Products Research, Research Institute of Pharmaceutical Science, School of Pharmacy, The University of Mississippi, University, Mississippi 38677, United States. 3. Dipartimento di Scienze del Farmaco, Università del Piemonte Orientale, Largo Donegani 2, 28100 Novara, Italy. 4. Endocannabinoid Research Group (ERG), Institute of Biomolecular Chemistry, National Research Council (ICB-CNR), Via Campi Flegrei 34, 80078 Pozzuoli (NA), Italy. 5. Epitech Group SpA, Saccolongo, Padova, Italy.
Abstract
As part of a study on triterpenoid conjugates, the dietary pentacyclic triterpenoids oleanolic (2a) and ursolic acids (3a) were coupled with vanillamine, and the resulting amides (2b and 3b, respectively) were assayed for activity on the vanilloid receptor TRPV1. Despite a structural difference limited to the location of a methyl group in their conformationally rigid pentacyclic core, oleanoloyl vanillamide dramatically outperformed ursoloyl vanillamide in terms of potency (EC50 = 35 ± 2 nM for 2b and 5.4 ± 2.3 μM for 3b). Using molecular docking and dynamics, this difference was translated into distinct accommodation modes at the TRPV1 vanillyl ligand pocket, suggesting a critical role of a C-H πphenyl interaction between the triterpenoid C-29 methyl and Phe591 of TRPV1. Because the molecular mechanisms underlying the activation process of transient receptor channels (TRPs) remain to be fully elucidated, the observation of spatially restricted structure-activity information is of significant relevance to identify the molecular detail of TRPV1 ligand gating.
As part of a study on triterpenoid conjugates, the dietary pentacyclictriterpenoidsoleanolic (2a) and ursolic acids (3a) were coupled with vanillamine, and the resulting amides (2b and 3b, respectively) were assayed for activity on the vanilloid receptor TRPV1. Despite a structural difference limited to the location of a methyl group in their conformationally rigid pentacyclic core, oleanoloyl vanillamide dramatically outperformed ursoloyl vanillamide in terms of potency (EC50 = 35 ± 2 nM for 2b and 5.4 ± 2.3 μM for 3b). Using molecular docking and dynamics, this difference was translated into distinct accommodation modes at the TRPV1 vanillyl ligand pocket, suggesting a critical role of a C-H πphenyl interaction between the triterpenoidC-29 methyl and Phe591 of TRPV1. Because the molecular mechanisms underlying the activation process of transient receptor channels (TRPs) remain to be fully elucidated, the observation of spatially restricted structure-activity information is of significant relevance to identify the molecular detail of TRPV1 ligand gating.
TRPV1, a member of the vanilloid
subfamily of transient potential receptor channels (TRPs), is critically
involved in the transduction of nociceptive stimuli and is responsible
for the irritant and burning sensation of capsaicin (1), the active ingredient of hot chili pepper.[1] Structure–activity studies have identified the critical structural
determinants for TRPV1 activation by capsaicinoids,[2] and cryo-EM studies of this ion channel bound to a set
of ligands (the plant diterpenoid resiniferatoxin, the tarantula toxin
DkTx, the synthetic antagonist capsazepine) have provided insights
into protein–ligand interactions in the TRPV1 vanillyl pocket.[3−5] However, given the complexity and multimodal action of this class
of receptors, the molecular details of the ligand–channel interactions
have largely remained elusive, in particular, and paradoxically, for
the archetypal ligand capsaicin (1).[6] To this aim, data that translate into unambiguous and spatially
restricted structure–activity information are of considerable
relevance. In this context, we report the discovery of a “magic”
methyl shift effect[7,8] in the activity of the vanillamides
of oleanolic (2a) and ursolic acid (3a)
and its rationalization in terms of docking and molecular dynamics
(MD) experiments in the TRPV1 ligand pocket.Oleanolic and ursolic acids (2a and 3a, respectively) are pentacyclic triterpenoids with a broad distribution
in Nature and with a significant human dietary exposure due to their
occurrence in edible plants (olives), herbs (sage), fruits (apple),[9] and caffeinated spices (mate).[10] Their profile of bioactivity is of considerable interest
in the realm of inflammation, pain, and metabolic syndrome, but their
insolubility and dismally low oral absorption have so far prevented
pharmaceutical advancement.[9] Derivatization
of the carboxylate function, as in bardoxolone methyl,[11] is known to improve the pharmacokinetic profile
of oleanolic and ursolic acids,[11] and provided
a rationale for the synthesis of conjugates of the natural compounds.
Biogenic amines seemed an attractive class of conjugation candidates,
as lipophilic acids like fatty acids can be converted in vivo in amide
conjugates.[12] Since oleanolic and ursolic
acid show an intrinsic modest antagonist activity on TRPV1,[13,14] conjugation with vanillamines seemed, in the context of control
of pain and inflammation, a rational strategy to improve both the
pharmacodynamic and the pharmacokinetic properties of the natural
products.The neopentylic C-28 carboxylic group of triterpenoid acids is
poorly reactive and requires forced conditions for its esterification
and amidation, with additional complications observed for phenolic
amines due to competition with the formation of phenolic esters.[15] We previously developed a protocol for the amidation
of triterpenoid acids with phenolic amines based on the activation
of the carboxylic group by in situ formation of a mixed phosphoric
anhydride.[15] However, modest yields were
obtained with ursolic acid, and yield further dropped with oleanolic
acid, presumably because the gem-dimethyl substitution
further encumbers the C-28 carboxylic group. Much better yields could,
however, be obtained by ex situ activation with hydroxysuccinimide
and reaction with an excess of free amine. In this way, improved yields
(20–30%) were obtained for various amino alcohols and aminophenols,
including vanillamine.Vanilloid activity was evaluated in HEK-293 cells overexpressing
hTRPV1. Despite the consistent tendency for compounds of the ursolic
acid series to outperform those from the corresponding oleanolic series,[9] about 2 orders of magnitude greater potency for
the vanillamide of oleanolic acid was observed compared to that of
ursolic acid (EC50 = 35 ± 2 nM for 2b vs 5.4 ± 2.3 μM for 3b, Table ).
Table 1
TRPV1 Activity Data for the Vanillamides 2b and 3b Compared to the Activity of Capsaicin (1)
compound
efficacy (relative to ionomycin 4 μM)
potency EC50
IC50 (capsaicin 0.1 μM)
2b (oleanoyl vanillamide)
72 ± 1
35 ± 2 nM
50 ± 2 nM
3b (ursoloyl vanillamide)
16 ± 1
5.4 ± 2.3 μM
7.5 ± 0.7 μM
1 (capsaicin)
79 ± 1
5.3 ± 0.4 nM
8.0 ± 0.3 nM
Data were obtained in HEK-293 cells,
stably transfected with recombinant human TRPV1 (hTRPV1).
Data were obtained in HEK-293 cells,
stably transfected with recombinant humanTRPV1 (hTRPV1).The pentacyclic triterpenoid scaffold of oleanolic and ursolic
acid is devoid of conformational mobility, and the two compounds only
differ in the location of a methyl group, making it possible that
the presence of a substitution at C-19 interferes, by steric hindrance,
with the fitting of 3b into the ligand binding site of
TRPV1. However, a docking study by using the available structure of
TRPV1 in its activated state (PDB id: 5IRX) suggested a more complex and different
scenario. In fact, both compounds docked into the vanilloid-binding
pocket, as defined by the S3–S4 helices, S4–S5 linker
of one subunit, and the S5–S6 helices of the adjacent subunit.[10] The two best not-redundant poses in terms of
binding energy value for each compound (Figures and 2, panel B) only
differed in the orientation of the vanillyl moiety (hereinafter referred
to as OMe-in when the methoxy group points toward the cleft between
helices S3 and S4 and OMe-out when it is rotated by 180°).
Figure 1
Representative energy-minimized OMe-in docking poses of 2b and 3b (tan and olive drab, respectively, panel A)
and capsaicin (salmon, panel B) after best fit of the protein backbone.
Ligands are shown in ball-and-stick representation, whereas protein
residues within 4.5 Å from the ligand are shown in stick representation.
Ribbons and selected side chain stick bonds of TRPV1 monomers A and
B are colored in dark gray and sky blue, respectively. Oxygen, nitrogen,
and sulfur atoms are colored in red, blue, and yellow, respectively.
Only polar hydrogens are shown and colored white.
Figure 2
Representative energy-minimized OMe-out docking poses of 2b and 3b (tan and olive drab, respectively,
panel A) and capsaicin (salmon, panel B) after best fit of the protein
backbone. Ligands are shown in ball-and-stick representation, whereas
protein residues within 4.5 Å from the ligand are shown in stick
representation. Ribbons and selected side chain stick bonds of TRPV1
monomers A and B are colored in dark gray and sky blue, respectively.
Oxygen, nitrogen, and sulfur atoms are colored in red, blue, and yellow,
respectively. Only polar hydrogen are shown and colored white.
Representative energy-minimized OMe-in docking poses of 2b and 3b (tan and olive drab, respectively, panel A)
and capsaicin (salmon, panel B) after best fit of the protein backbone.
Ligands are shown in ball-and-stick representation, whereas protein
residues within 4.5 Å from the ligand are shown in stick representation.
Ribbons and selected side chain stick bonds of TRPV1 monomers A and
B are colored in dark gray and sky blue, respectively. Oxygen, nitrogen,
and sulfur atoms are colored in red, blue, and yellow, respectively.
Only polar hydrogens are shown and colored white.Representative energy-minimized OMe-out docking poses of 2b and 3b (tan and olive drab, respectively,
panel A) and capsaicin (salmon, panel B) after best fit of the protein
backbone. Ligands are shown in ball-and-stick representation, whereas
protein residues within 4.5 Å from the ligand are shown in stick
representation. Ribbons and selected side chain stick bonds of TRPV1
monomers A and B are colored in dark gray and sky blue, respectively.
Oxygen, nitrogen, and sulfur atoms are colored in red, blue, and yellow,
respectively. Only polar hydrogen are shown and colored white.At odds with the starting hypothesis, in the emerging scenario
the β-oriented methyl on C-19 does not prevent accommodation
of 3b in the binding site, but its translocation on C-20
rather induces a better fit of 2b in the binding site.
In fact, in both poses, the vanillyl group of 2b is deeper
inside the pocket than in 3b, and this arrangement is
promoted by a C–H πphenyl interaction[16,17] between the C-29 methyl group and Phe591 (S5 helix-B monomer) side
chain, which pushes down the terpenoid scaffold. Conversely, the lack
of this methyl in 3b induces a shift of the terpenoid
scaffold toward Phe591, resulting in a looser binding of the vanillyl
group in the ligand pocket. In the OMe-in orientation, both vanillamides
are engaged in H-bonds between the hydroxyl group and both the Ser512
(S3) and Arg557 (S4) side chains, whereas in the OMe-out orientation
only the phenolic hydroxy of 2b can form a H-bond with
the Ser512 side chain, whereas the methoxy groups of both isomers
are H-bonded to the Arg557 side chain. The C-3 hydroxy of the cyclic
scaffold of both isomers is close to the sulfur atom of the Met581
(S4–S5 linker) side chain in both the OMe-in and OMe-out orientation.
Because in rigid systems the effect of substitution can be directly
translated into the occupancy of a specific area of the ligand-binding
space, it was interesting to investigate if the site of the C–H
πphenyl interaction of the C-29 oleanoyl methyl was
also occupied by capsaicin. When this archetypal vanilloid ligand
was docked into the vanilloid-binding pocket, one of the ω-methyls
was indeed spatially close to Phe591 (S5-B), with two orientations
of the vanillyl group of the same OMe-in and OMe-out type being observed,
in accordance to the binding mode of 2b and 3b (Figures and 2, panel B). On account of a major conformational
mobility and a slender carbon–carbon connectivity, the branched
acyl tail of capsaicin allows two H-bonds of its amide group with
either both the Thr550 (S4) and the Tyr511 (S3) side chains (OMe-out
orientation) or, alternatively, Tyr511 (S3) (OMe-in orientation),
rationalizing the higher potency of capsaicin compared to 2b (EC50 = 5.3 and 35 nM, respectively). For comparison
purposes, we also evaluated the activity of the corresponding acidic
parent triterpenoids (oleanolic and ursolic acids, 2a and 3a, respectively), previously reported to act as
weak antagonists at TRPV1.[13,14] We confirmed that both
compounds behave as weak antagonists, inhibiting the capsaicin response
by 20 ± 3% and 30 ± 1% at 25 μM, respectively. The
corresponding docking complexes are reported in Figure S1. Ursolic acid (2a) engages a H-bond
between its carboxylate and the Thr550 side chain, while the arrangement
of the polycyclic moiety is substantially preserved in comparison
to its vanillamide-conjugated derivative. Conversely, oleanolic acid
adopts a completely different orientation, engaging Ser512 with a
H-bond with its hydroxy group. A hypothetical corresponding pose of
ursolic acid, with the carboxylate group forming a H-bond with Thr550,
is prevented by a steric clash between the C-29 methyl group and Phe591.
Thus, since both acidic precursors are endowed with a weak and comparable
inhibitory activity, the dramatic difference in the activity profile
between 2b and 3b can be ascribed to the
introduction of a vanillamide group. To confirm and further explore
the better accommodation of 2b vs 3b within
the site emerging from the docking, we carried out 100 ns of molecular
dynamics in the membrane environment for both OMe-in complexes. The
root mean square deviation (rmsd) of both protein and ligands, shown
in Figure , shows
smaller fluctuations in both protein and ligands for the 2b complex in comparison with those of 3b. In fact, the
latter is characterized by both a drift in protein backbone and a
higher mobility of the ligand in the four binding sites of the tetramer.
Thus, MD calculations show a relative structural destabilization on
going from 2b to 3b of the active form of
TRPV1 used to derive the theoretical complexes, corresponding to the
cryo-EM structure in complex with resiniferatoxin. The greater structural
stability of 2b is also confirmed by the network of H-bonds
engaged within each binding site in comparison to that of 3b, as shown in Table , reporting H-bond occurrences greater than 10% over the simulated
100 ns of production run. In fact, while 3b forms only
one H-bond with Ser152 with an occurrence of ∼40% in three
sites out of four, 2b forms additional H-bonds with Arg557
and/or Glu570, with an overall occurrence of H-bonds well above 50%,
up to ∼74%. Moreover, methyl C29 forms stable hydrophobic interactions
with both Phe591 and Ala549 during the whole simulated period, as
shown in Figure S2. The representative
frames from molecular dynamics are shown in Figure . The greater capability of 2b to stabilize the active form of TRPV1 is fully consistent with the
higher agonist efficacy observed for this compound in comparison with 3b.
Figure 3
Root mean square deviation (rmsd) of protein backbone atoms (panels
A, C) and the respective ligands (B, D) after protein best fit. Plot
lines were smoothed with a five-point window running average.
Table 2
Occurrence of Ligand–Protein H-Bonds for TRPV1
in Complex with Compounds 3b and 2b during
100 ns of MD
Representative frames from MD of 2b (A) and 3b (B) complexes with TRPV1. The color code is the same used
for Figure . Red dotted
lines represent the distance between C29 and both Ala549 and Phe591
in complex 2b.
Root mean square deviation (rmsd) of protein backbone atoms (panels
A, C) and the respective ligands (B, D) after protein best fit. Plot
lines were smoothed with a five-point window running average.Representative frames from MD of 2b (A) and 3b (B) complexes with TRPV1. The color code is the same used
for Figure . Red dotted
lines represent the distance between C29 and both Ala549 and Phe591
in complex 2b.In conclusion, a comparative analysis of bioactivity data, docking
experiments, and MD simulations has highlighted the critical role
of the C-29 methyl of triterpenoids for significant and effective
binding to TRPV1, with only the oleanane skeleton having this methyl
in the correct location for the interaction. As the rigid ring system
of both triterpenoid vanillamides encompasses conformationally constrained
versions of the side chain of capsaicin, it is not unrealistic that
a similar interaction may occur between Phe591 and one of the ω-methyls
of capsaicin, thus disclosing a role for this residue in agonist binding
and receptor activation.
Experimental Section
General
Experimental Procedures
IR spectra were obtained on an Avatar
370 FT-IR Thermo Nicolet. 1H (300 MHz) and 13C (75 MHz) NMR spectra were measured on a Bruker spectrometer. 1H (500 MHz) and 13C (126 MHz) NMR spectra were
measured on an Agilent spectrometer. Chemical shifts were referenced
to the residual solvent signal (CDCl3, δH = 7.26, δC = 77.16, or DMSO-d6, δH = 2.50, δC = 39.52,
hept). Low- and high-resolution ESIMS spectra were obtained on an
LTQ OrbitrapXL (Thermo Scientific) mass spectrometer. Silica gel 60
(63–200 mesh) used for gravity column chromatography was purchased
from Merck. Reactions were monitored by TLC on silica gel Merck 60
F254 (0,25 μm) plates and neutral alumina Macherey-Nagel ALUGRAM
(0,20 μm) plates that were visualized by UV inspection (254
and 365 nm) and/or staining with 5% H2SO4 in
EtOH and heating. Organic phases were dried with anhydrous Na2SO4 before evaporation. Chemical reagents and solvents
were from Sigma-Aldrich.
Synthesis
of Triterpenoid Vanillamides. Synthesis of Oleanoyl Vanillamide (2b) as Representative
(a) Carboxylate activation:
To a stirred solution of N-hydroxysuccinimide (1.51
g; 13.1 mmol) in EtOAc (50 mL) were added oleanolic acid (2.05 g;
4.5 mmol) and dicyclohexylcarbodiimde (DCC, 4.58 g; 22.2 mmol). The
suspension was stirred at room temperature (rt) for 16 h and then
worked up by filtration and evaporation. The residue was purified
by gravity column chromatography using petroleum ether/EtOAc (8:2)
as mobile phase, to give the hydroxysuccinimide ester as a white powder
(1.32 g, 52% yield): 1H NMR (300 MHz, CDCl3)
δ 5.31 (1H, brt), 3.46 (1H, m), 3.20 (1H, m), 2.79 (4H, m),
1.15 (3H, s), 0.98 (3H, s), 0.92 (3H, s), 0.91 (3H, s), 0.90 (3H,
s), 0.80 (3H, s), 0.76 (3H, s). (b) Amidation: To a stirred solution
of oleanoyl hydroxysuccinimide (300 mg, 0.54 mmol) in CH2Cl2 (4 mL) was added vanillamine (150 mg, 1.1 mmol). The
mixture was stirred at rt for 24 h and then worked up by dilution
with brine and extraction with CH2Cl2. The organic
phase was treated with Na2SO4 and filtered,
and the solvent evaporated. The residue was purified by gravity column
chromatography using petroleum ether/EtOAc (3:7) to give 2b as a white powder (66 mg, 20% yield).
The starting ligand
geometry of the ligands was built with Ghemical 2.99[18] and energy minimized at molecular mechanics level first,
using Tripos 5.2 force field parametrization[19] and then optimized using the GAMESS program[20] at the Hartree–Fock level with the STO-3G basis set, followed
by a single-point HF energy evaluation at the 6-31G* level to derive
the partial atomic charges for the ligand by the RESP procedure.[21] Docking studies were performed with AutoDock
4.2.[22] hTRPV1 (PDB id: 5IRX) and the ligands
were processed with AutoDock Tools (ADT) package version 1.5.6rc1
to merge nonpolar hydrogens, calculate Gasteiger charges, and select
rotatable side chain bonds. Grid dimensions of 60 × 50 ×
60, respectively, centered in the binding pocket, were generated with
the program AutoGrid 4.2 included in the Autodock 4.2 distribution,
with a spacing of 0.375 Å. A total of 100 molecular docking runs
for each docking calculation were performed adopting a Lamarckian
Genetic Algorithm (LGA) and the protocol already published.[23] Flexibility was used for all rotatable bonds
of the docked ligands. For each docking run, the best not-redundant
poses in terms of binding energy values were selected as representatives
and underwent energy minimization with the Amber16 package[24] using the ff14SB version of AMBER ff14SB force
field for the protein and gaff parameters for the ligand. UCSF Chimera
1.14[25] was used for figures of the molecular
complexes. The energy-minimized complexes were embedded in a POPC
bilayer using the charmmgui web-interface, and then MD simulations
in the membrane environment were carried out with the pmemd.cuda module
of the Amber16 package, using lipid 14 (lipids), ff14SB force (protein),
and gaff (ligand) force field parametrization. MD production runs
were carried out for 100 ns. The Cpptraj module of AmberTools16 was
used for trajectory analysis. The full MD protocol has been published
elsewhere.[27]
TRPV1
Channel Assay
Compound effects on intracellular Ca2+ concentration ([Ca2+]i) were determined using
the selective intracellular fluorescent probe for Ca2+Fluo-4,
and assays were performed as described.[26] Briefly, HEK-293 cells, stably transfected with recombinant humanTRPV1 (selected by Geneticin 600 μg mL–1)
or not transfected were cultured in EMEM + 2 mM glutamine +1% nonessential
amino acids + 10% FBS and maintained at 37 °C with 5% CO2. The day of the experiment the cells were loaded in the dark
at rt for 1 h with Fluo-4 AM (4 μM in DMSO containing 0.02%
Pluronic F-127). After that, the cells were rinsed and resuspended
in Tyrode’s solution (145 mM NaCl, 2.5 mM KCl, 1.5 mM CaCl2, 1.2 mM MgCl2, 10 mM d-glucose, and 10
mM HEPES, pH 7.4), then transferred to a quartz cuvette of a spectrofluorimeter
(PerkinElmer LS50B; λEX = 488 nm, λEM = 516 nm) under continuous stirring. Cell fluorescence before and
after the addition of various concentrations of test compounds was
measured normalizing the effects against the response to ionomycin
(4 μM). The potency of the compounds (EC50 values)
is determined as the concentration required to produce half-maximal
increases in [Ca2+]i. Antagonist behavior is
evaluated against the agonist of the TRPV1capsaicin (100 nM) and
analyzed by adding the compounds directly in the quartz cuvette 5
min before stimulation of cells with the agonist. IC50 is
expressed as the concentration exerting a half-maximal inhibition
of agonist effect, taking as 100% the effect on [Ca2+]i exerted by capsaicin (100 nM) alone. Dose–response
curve fitting (sigmoidal dose–response variable slope) and
parameter estimation were performed with Graph-Pad Prism8 (GraphPad
Software Inc.). All determinations were performed at least in triplicate.
Authors: Eric F Pettersen; Thomas D Goddard; Conrad C Huang; Gregory S Couch; Daniel M Greenblatt; Elaine C Meng; Thomas E Ferrin Journal: J Comput Chem Date: 2004-10 Impact factor: 3.376
Authors: Giovanni Appendino; Alberto Minassi; Aniello Schiano Morello; Luciano De Petrocellis; Vincenzo Di Marzo Journal: J Med Chem Date: 2002-08-15 Impact factor: 7.446
Authors: Fabio Arturo Iannotti; Fabrizia De Maio; Elisabetta Panza; Giovanni Appendino; Orazio Taglialatela-Scafati; Luciano De Petrocellis; Pietro Amodeo; Rosa Maria Vitale Journal: Molecules Date: 2020-03-03 Impact factor: 4.411