124
Chapter III
M OLECULAR M ECHANISM OF I SOFORM -S ELECTIVE
125
220-328) lipid binding domains at the amino-terminus promiscuously bind polyphosphatidylinositols and negatively-charged phospholipids. These domains are also predicted to elicit regulatory functions that may dictate differences in isoform subcellular localization, activity, and protein-protein interactions. There are also reports of a conserved PI(4,5)P2 binding motif that lies between the conserved catalytic H(x)K(φ)4D motifs and facilitates translocation to PI(4,5)P2- containing membranes and catalytic activity.
Until recently it has not been possible to acutely and pharmacologically inhibit PLD catalytic activity in order to study its enzymology and specific function in cell signaling pathways. Historically, RNAi and primary alcohols have been the only tools available. RNAi knocks down PLD protein production over a short period of time allowing for compensation within signaling pathways, while treatment with primary alcohol merely diverts product formation to phosphatidylalcohol. Primary alcohols exploit the transphosphatidylation reaction characteristic of PLD-family members, in which the primary alcohol is the preferred nucleophile to water during substrate hydrolysis. Recently, in response to the void in the field, we reported identification and characterization of a class of small molecules that potently and isoform-selectively inhibit PLD activity, called VU-series compounds (chapter II) [290]. Structure-activity relationship characterization of this class lead to the development of compounds that are
>1700-fold PLD1-selective[292], and >75-fold PLD2-selective [291] to use as tools in delineating the distinct signaling roles of each isoform. Subsequent studies, in our own lab and in others, using these small molecule inhibitors have
126
yielded different results from those published using primary alcohols [79], [237].
This suggests that either the roles of PLD as discerned using primary alcohols have been widely overstated, or the mechanism of action of these small molecule PLD inhibitors extends beyond inhibiting PA formation. To address this discrepancy, we used backscattering interferometry (BSI), a highly sensitive and novel method for measuring protein-small molecule and protein-lipid binding affinities, to characterize the mechanism of action of these small molecule PLD inhibitors. For these studies we focus our characterization on the mammalian PLD1 isoform, and propose that a similar molecular mechanism also applies to VU-series-compound mediated PLD2 inhibition.
Here we demonstrate that these compounds directly target PLD1 and allosterically block lipid binding and catalytic activity. These in vitro findings are confirmed with cellular studies demonstrating that these compounds do not perturb basal PLD1 localization, but block stimulated enzyme translocation. This is a unique and underappreciated mechanism for inhibiting a lipid signaling enzyme, and is akin to the mechanism recently reported for an allosteric pharmacological inhibitor of Akt, Inhibitor VIII [293], [294].
Backscattering interferometry measures protein-ligand interactions PLD is an interfacial enzyme that must bind at the lipid surface (S, figure 2) prior to binding and hydrolyzing substrate. As such, the nature of the lipid interface has a great impact on the binding affinity for the lipid surface (1/Ks), accessibility and affinity for substrate (Km), and catalytic activity of the enzyme
127
Mirror HeNe Laser
CCD Array
Fringe Pattern
Microfluidic Chip with Channel
Pixel
Intensity
Protein or Ligand
Binding Occurs
Protein-ligand Complex
Intensity
Pixel Fringe Shift
Fringe Shift
10 20 30 40
-0.01 0.00 0.01 0.02 0.03 0.04 0.05
ligand concentration, [M]
change in phase Sample Control Protein and ligand Protein-ligand complex
Figure 19. Backscattering interferometry (BSI) technique optimized for measuring protein-small molecule and protein-lipid binding affinities (figure modified from[295]).
128
(kcat). Therefore, it was important to determine whether these small molecules were eliciting inhibition through direct interaction with soluble/non-lipid bound enzyme, or indirectly influencing the lipid interface, as is the case for neomycin [296] and tamoxifen [297] (unpublished data Selvy and Brown), or potentially selectively binding to interfacially-bound enzyme (Es), as is the case for some PLA2 inhibitors [298]. BSI has been validated as a method for measuring picomolar receptor-ligand binding affinities using nanomolar concentrations of protein [295], [299], [300], and was used here to measure protein-small molecule binding affinities for PLD1. In contrast to isothermal titration calorimetry (ITC) and surface plasmon resonance (SPR), binding affinities can be measured using BSI in a microliter-scale format for untagged protein free in solution. In this technique, a laser is reflected and refracted through a sample contained within the channel of a microfluidic chip and an interference pattern is created. The interference pattern consists of a specific set of well defined fringe spots, and a shift in the fringe spots correlates to a change in refractive index due to a change in salvation of a protein upon ligand binding (i.e. change in protein conformation).
A shift in fringe spots is quantified as a change in phase of a wave function using Fourier transform. The phase is measured for any set of samples and then graphed as the absolute change in phase relative to a control sample upon increasing ligand concentration.
129
Development of novel human PLD1 construct facilitates in vitro studies To ensure phase changes, as recorded by BSI, are due to bimolecular interactions between PLD1 and small molecule, highly purified recombinant protein was necessary. Recombinant expression of full length PLD1 is poor and because of the myriad of protein binding partners, full length protein remains a heterogeneous population following multiple chromatographic purification steps.
Therefore several robustly expressed and homogenously-purified truncation constructs of PLD1 were used to demonstrate direct bimolecular interactions. In our earlier report [290] we demonstrated that the VU-series compounds could inhibit an amino-terminally-truncated rat PLD1 construct lacking the first 311 amino acids. This construct comprises a truncation of the PX and PH domains, leaving 16aa of an alpha-helix at the C-terminus of the PH domain that is necessary for lipid binding (Henage, Selvy, and Brown, unpublished data).
For more rigorous mechanistic characterization of these VU-series compounds, however, we chose to study human PLD1. Characterization of human PLD1 splice variants using cDNA libraries detected a poorly studied PLD1c form. This PLD1 splice variant was initially reported by Steed et al. [173]
as a shortened protein whose transcript contains a single nucleotide deletion that results in a frame shift in protein translation. In nature, the PLD1c frame shift results in an early stop codon and a protein that is truncated following the first HKD motif (figure 20). Insertion of a single nucleotide corrects the frameshift and results in a catalytically active 2 HKD PLD enzyme with an 18 amino acid stretch of residues in the catalytic loop region. The shorter catalytic loop region,
130
PX PH HKD HKD
PX PH HKD HKD
PX PH HKD HKD
PX PH HKD HKD
hPLD1a
hPLD1b
hPLD1c (natural) hPLD1c (corected)
Figure 20. Illustration of the domains of the human PLD1 splice variants.
131
as compared to the loop regions found in PLD1a and PLD1b splice variants, facilitates robust recombinant expression, enhanced protein stability, and straightforward chromatographic purification. Corrected PLD1c maintains all the same biochemical and cellular characteristics of the natural PLD1a and PLD1b, including protein-activator response and robust receptor-stimulation.
VU-series PLD inhibitors directly interact with enzyme
Using BSI and silver-stain pure preparations of the amino-terminally truncated PLD1c splice variant, referred to here simply as PLD1.d311, we demonstrate this construct directly binds the compounds in a one-site binding model in the absence of lipid (figure 21). The Ki for benzimidalozone-containing small molecules (VU0155056 and VU0359595) was similar to IC50s measured for respective compounds in the biochemical liposome reconstitution assay.
Because the affinities and potencies for the benzimidalozone-containing compounds are similar for their respective compounds, we conclude that these compounds are acting directly on the enzyme and not indirectly inhibiting activity by disrupting access to PI(4,5)P2 or substrate at the lipid interface.
Small molecule PLD inhibitors block lipid binding
PLD‟s phospholipid substrate is located at a lipid interface and is not freely soluble, therefore classic Michaelis-Menten assumptions do not apply. In order to study PLD kinetics and the mechanism of action for these small molecule
132
10 20 30 40
-0.01 0.00 0.01 0.02 0.03 0.04 0.05
VU0359595 concentration, [M]
change in phase
0.00 0.25 0.50 0.75 1.00 1.25 -0.01
0.01 0.03 0.05 0.07 0.09 0.11
Tungstate concentration, [M]
change in phase
HFMT.hPLD1c.d311 + 1154 binding
0 10 20 30 40 50 60
-0.005 0.005 0.015 0.025 0.035 0.045 0.055
VU40355-1 concentration, [M]
change in phase
Tungstate
VU040355-1 VU0359595
-9 -8 -7 -6 -5 -4 -3 -2 -1 0 0
25 50 75
100 VU0359595
Tungstate VU040355-1 VU0155056
Compound Concentration, Log [M]
%Total Activity
VU0155056 VU0359595 VU040355-1 Tungstate IC50 4.7μM 0.605μM 33.8μM 1.8mM
0 10 20 30 40 50 60
0.00 0.01 0.02 0.03 0.04 0.05 0.06
VU0155056 concententration, [M]
Change in phase
VU0155056
10 20 30 40
-0.01 0.00 0.01 0.02 0.03 0.04 0.05
VU0359595 concentration, [M]
change in phase
0.00 0.25 0.50 0.75 1.00 1.25 -0.01
0.01 0.03 0.05 0.07 0.09 0.11
Tungstate concentration, [M]
change in phase
HFMT.hPLD1c.d311 + 1154 binding
0 10 20 30 40 50 60
-0.005 0.005 0.015 0.025 0.035 0.045 0.055
VU40355-1 concentration, [M]
change in phase
Tungstate
VU040355-1 VU0359595
Kd=3.1mM
Kd=15.5μM Kd=0.36μM
-9 -8 -7 -6 -5 -4 -3 -2
0 25 50 75 100
VU0359595 VU0155056
Compound Concentration, Log [M]
%Total Activity
4.1μM VU0155056
27μM VU0364739-1 0.605μM
IC50
VU0359595
0 10 20 30 40 50 60
0.00 0.01 0.02 0.03 0.04 0.05 0.06
VU0155056 concententration, [M]
Change in phase
VU0155056
Kd=4.7μM
Raloxifene VU0359595 (EVJ) VU040355-1 (1154)
W
O O
O O
Tungstate VU0155056 (5WO) VU0155069 (809) VU0155069 (JWJ)
O N
Tamoxifen
Figure modified from Deems 2000