1. Introduction

2. PATs and thioesterases

3. PATs, substrate specificity and

human disease

4. Palmitoyl-cysteine prediction

5. Methods for palmitoyl-cysteine

enrichment and quantitation

6. Pharmacological modulation

and inhibitors of

palmitoylation

7. Conclusion

8. Expert opinion

Review

Targeting protein palmitoylation:selective inhibitors andimplications in diseaseBurzin Chavda, John A Arnott & Sonia Lobo Planey†

The Commonwealth Medical College, Department of Basic Sciences, Scranton, PA, USA

Introduction: Palmitoylation describes the enzymatic attachment of the

16-carbon fatty acid, palmitate, to specific cysteines of proteins via a labile

thioester bond. This post-translational modification increases the lipophilicity

of the modified protein, thus regulating its subcellular distribution and func-

tion. The transfer of palmitate to a substrate is mediated by palmitoyl

acyltransferases (PATs), while depalmitoylation is catalyzed by acyl protein

thioesterases (APTs). Nearly one-third of the 23 genes that encode PATs

are linked to human diseases, representing important targets for drug

development.

Areas covered: In this review, the authors summarize the recent technical

advances in the field of palmitoylation and how they will affect our ability

to understand palmitoylation and its relevance to human disease. They also

review the current literature describing existing palmitoylation inhibitors.

The aim of this article is to increase the awareness of the importance of palmi-

toylation in disease by reviewing the recent progress made in identifying

pharmacological modulators of PATs/APTs. It also aims to provide suggestions

for general considerations in the development of selective and potent PAT

inhibitors.

Expert opinion: Developing therapeutically useful pharmacological modula-

tors of palmitoylation will require that they be developed within the context

of well-characterized PAT/APT-related signaling systems. The successful

development of potent, specific drugs in similarly complex systems suggests

that development of useful drugs targeting PATs is feasible.

Keywords: acyl protein thioesterases, Asp-His-His-Cys, Asp-His-His-Cys 2, cancer, cysteine,

palmitoyl acyltransferases, palmitoylation

Expert Opin. Drug Discov. [Early Online]

1. Introduction

Protein palmitoylation describes the enzymatic, covalent attachment of the16-carbon fatty acid palmitate to specific cysteine residues of a protein via a labilethioester bond. This essential post-translational modification increases thelipophilicity of the modified protein, thereby dynamically regulating its subcellulardistribution, trafficking and function in dramatic and subtle ways. Recent proteo-mic studies have revealed that the number of palmitoylated proteins in mammalsis both abundant (hundreds) and diverse; some being initially synthesized oncytosolic ribosomes, whereas others are integral membrane proteins synthesizedon endoplasmic reticulum (ER)-bound ribosomes [1,2]. In the former case, palmi-toylation serves as a hydrophobic membrane anchor that permits controlled associ-ation of the cytosolic protein with a membrane, often resulting in its redistributionto a specific membrane compartment as is seen for Ras proteins [3,4]. Similarly, thepalmitoylation of integral membrane proteins at cysteines adjacent to or within thetransmembrane domain (TMD) can regulate their intracellular trafficking from one

10.1517/17460441.2014.933802 © 2014 Informa UK, Ltd. ISSN 1746-0441, e-ISSN 1746-045X 1All rights reserved: reproduction in whole or in part not permitted

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membrane system to another, such as from the ER to theplasma membrane (PM) [5]. More subtle changes (in termsof distance) can also occur at the nanoscale level within amembrane as a result of palmitoylation. For instance, theincrease in lipophilicity upon palmitoylation often results inan altered affinity of a protein for a particular lipid microen-vironment within that membrane [6]. For example, lipid raftsare small yet dynamic islands in membranes with distinct lipidcompositions that selectively attract or exclude both periph-eral (often exclusively by virtue of palmitoylation) and inte-gral membrane proteins [7]. Palmitoylated proteins haveaffinity for lipid rafts that are rich in cholesterol, whereas pre-nylated proteins have little or no affinity for these rafts [6].Such lipophilicity-driven changes in protein distributionmay alter the access of a palmitoylated protein to extracellularligands, protein--protein interactions or the engagement of thepalmitoyl-protein in multimolecular signaling complexes.Although palmitate may be the most common lipid species

to occupy cysteine residues, it is not the only one. MarilynResh and colleagues identified the lipid moieties resident onthe cysteine residue of the N-terminal tail of Src familykinases [8-10]. For these proteins, although the cysteine residuenear the N-terminus is most frequently palmitoylated, it isalso modified by palmitoleate, stearate or oleate with afrequency that is apparently related to the abundance ofpalmitate in cells [11]. The physiological differences that resultfrom proteins being modified by these other lipids have not

been explored extensively; however, given their differentphysical properties, it seems reasonable that their impact ona protein should be subtly different than palmitate.

2. PATs and thioesterases

The cellular concentrations of palmitoyl-CoA are generallyinsufficient for spontaneous palmitoylation to occur as wasonce believed, as the concentration of free unbound acyl-CoA esters is in the low nanomolar range under normalphysiological conditions and buffered by specific acyl-CoAbinding proteins [12]. Furthermore, it is now well establishedthat palmitoylation is mostly enzymatic and mediated by afamily of Asp-His-His-Cys (DHHC) motif containing palmi-toyl acyltransferases (PATs), although exception to thiscommon view exists [4]. The highly conserved DHHCcysteine-rich domain (DHHC-CRD) not only defines PATsbut is also directly involved in the transfer of palmitate to asubstrate [13,14]. Most PATs also have a conserved aspartate-proline-glycine motif and Thr-Thr-Xxx-Glu motif, but theirrole in PAT function is not yet known. The DHHC proteinsencoded by these genes all contain four or more TMDs andhave the greatest diversity at the amino acid level in the N-and C-terminal, cytoplasmic tails.

Mammalian genomes contain at least 23 members ofthe ZDHHC PAT gene family. The genomic structure ofZDHHC genes varies widely, including the number anddifferential use of exons that are knit together to generatethe mRNA. ECgene analyses (http://genome.ewha.ac.kr/ECgene/) of the mRNAs that encode PATs suggest that allof the genes are alternatively spliced at various sites through-out the protein coding sequence as well as within untranslatedregions. Many of the putative, alternatively spliced exons arepredicted to encode small peptides that change the structureof the protein in a way that may alter substrate specificity.Likewise, splicing may alter sites for other post-translationalmodifications, such as phosphorylation or glycosylation allof which may regulate activity, substrate specificity, subcellu-lar distribution or interactions with nonsubstrate proteins. Forexample, ZDHHC7 alters the use of a 111 bp exon that isdifferentially and specifically expressed in tissues such as pla-centa, lung, liver, thymus and small intestine [15]. This exonencodes a 37-residue peptide within the cytoplasmic loopbetween TM2 and TM3 that contains a protein kinase Cphosphorylation site. As it is known that multiple PATs canpalmitoylate a single substrate, one might speculate that alter-native splicing of a PAT like ZDHHC7 (or its substrate forthat matter) might shift the balance of responsibility forpalmitoylation of a substrate between multiple PATs.

As predicted by hydropathy analyses, the DHHC proteinsencoded by these genes all contain four or more TMDs. Pre-dictions using TopPred II 1.1 [16] as presented by Ohno andcolleagues show that most PATs have an even number of TMdomains with the DHHC-CRD motif in the cytoplasm andusually located between the second and third TM domain [15].

Article highlights.

. Protein palmitoylation describes the enzymaticattachment of the 16-carbon fatty acid, palmitate, tospecific cysteine residues of a protein via a labilethioester bond.

. In humans, there are at least 23 members of the ZDHHCpalmitoyl acyltransferases (PAT) gene family withpossible overlapping or at least partially overlappingmechanisms/motifs for substrate recognition, specificityand activity.

. Approximately one-third of the genes encoding PATs areassociated with human diseases, including neurological/neuropsychiatric disorders, cancer, dermatologicalpathologies and, most recently, osteoporosis.

. Recent methodological advances in higher throughputproteomic quantification and site-specific labeling haveimproved our ability to annotate palmitoylated proteinson a larger scale and to identify PAT/substrate pairs.

. The field of protein palmitoylation has suffered from alack of specific, potent inhibitors, previously relying ongeneric lipid-based compounds such as2-bromopalmitate, tunicamycin and cerulenin withmultiple, undesired off-target effects.

. The development of specific PAT/APT (acyl proteinthioesterase) inhibitors would provide vital reagents withwhich to study the pathophysiological importance ofmany palmitoylated proteins and may offer potential fortherapeutic development.

This box summarizes key points contained in the article.

B. Chavda et al.

2 Expert Opin. Drug Discov. (2014) 9 (9)

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In addition to the importance of PAT membrane topology,their membrane system of residence is likely to be an importantaspect of their function. Most mammalian DHHC proteinshave been shown to localize to the ER and Golgi [15]; however,some have also been localized to the PM or to endocyticvesicles [15,17,18]. Yet, little is known about how these proteinsachieve their respective localizations. Some interesting excep-tions include DHHC4/6 and DHHC2. Lysine-based sortingsignals were mapped in DHHC4 (KXX) and DHHC6(KKXX) that determine their restricted localization to ERmembranes [19]. DHHC2 has recently been shown to trafficbetween the PM and intracellular membranes via recyclingendosomes [20]. PM targeting of DHHC2 has also been shownto recruit postsynaptic density-95 to the PM and is essential forpostsynaptic nanodomain formation [21]. Importantly, the C-terminal 68 amino acids of DHHC2 were shown to play animportant role in defining its intracellular localization;however, a defined targeting signal present within this regionof DHHC2 and in other DHHC proteins has yet to bedefined.

Palmitoylation is reversed by a small and not well-characterized family of enzymes called acyl protein thioesterases(APTs), which includes APT1, APT2, APTL1 and PPT1(palmitoyl-protein thioesterase-1). APT1 and APT2, whichare encoded by genes LYPLA1 and LYPLA2, respectively, wereoriginally isolated as lysophospholipases and later demonstratedto be effective as cytosolic protein thioesterases [22-25]. Com-pared with the molecular diversity of PATs, only one APT(i.e., APT1) has been shown to deacylate intracellular proteinsunder conditions where it could play a role in physiologicalregulation of reversible palmitoylation. APT1 appears to beengaged in regulation of the acylation-deacylation cycle ofseveral cytoplasmic proteins including Ga subunits, H-Ras,endothelial nitric oxide synthase and synaptosomal-associatedprotein (SNAP)-23 [2,23,25,26]. APT2 is 68% homologous toAPT1 [24] but catalyzes the depalmitoylation of semisyntheticNRas more efficiently than APT1 [27], and specifically depami-toylates the axonal, peripheral membrane-associated GAP-43[23]. APTL1 (LYPLAL1) is a distant homolog of APT1 thatwas shown to have limited function as a palmitoyl thioesterasedue to its narrow substrate-binding pocket and preference forshort-chain lipid substrates in vitro [28]; however, genetic studiesshow that it is upregulated in obesity [29]. PPT1 is a lysosomalenzyme involved in the degradation of palmitoylated pro-teins [30] and inactivating mutations in the PPT1 gene are acause of infantile neuronal ceroid lipofuscinosis [25]. The dispro-portionately small number of APTs relative to PATs is reminis-cent of the disparity between phosphatases (< 100) and proteinkinases (> 500) in human cells, suggesting that APTs may func-tion as broad specificity enzymes that depalmitoylate a widerange of substrates, whereas PATs harbor the specificity fordynamic palmitoylation. Alternatively, this disparitymay reflectthe fact that only a limited subset of proteins undergo palmitoy-lation turnover. Yet, it is also possible that manymore thioester-ases exist but have yet to be identified.

3. PATs, substrate specificity and humandisease

Discovering the molecular identity of PATs was a pivotal eventthat dramatically accelerated the pace of discovery in the field.Likewise, there has been increased interest in palmitoylationpartly because many of the genes encoding PATs have beenlinked to human diseases. Over the last several years, an increas-ing body of evidence from genetic studies and animal modelsystems has demonstrated the involvement of palmitoylationin numerous and diverse pathological conditions including neu-rological/neuropsychiatric disorders, cancer, dermatologicalpathologies and, most recently, osteoporosis. To date, sevenPAT genes have been shown to be associated with humandisease [31-38], and others have been suggested to be associatedwith disease based on phenotypes seen in animal models [39-41].

The majority of these diseases or phenotypes occur as a resultof the disruption of the homeostatic balance of protein palmi-toylation in the nervous system, highlighting the importanceof palmitoylation for normal neuronal function. To date, eightPATs including ZDHHC7, ZDHHC21, ZDHHC17/huntington interacting protein (HIP)14, HIP14L, ZDHHC8,ZDHHC9, ZD HHC12 and ZDHHC15 and the thioesterasePPT1 have been implicated in neurological/neuropsychiatricdisorders, including Huntington’s disease (HD) [32,42],Alzheimer’s disease [43-45], schizophrenia [31], bipolar disorder[31,46], X-linked mental retardation [33,34,47] and forms of neuro-nal ceroid lipofuscinosis [48,49]. In general, PATs appear tomanifest their effects in neuronal tissue through regulation ofclustering and activity of postsynaptic scaffolds, receptors, ionchannels and other vesicle-associated proteins whose palmitoy-lation status is critical for proper localization and function.

The best studied of these associations is involvement of

DHHC17/HIP14 in HD. HD is a fatal, autosomal-dominant

neuropsychiatric disorder characterized by motor control defi-

cits, depression, anxiety, irritability and cognitive decline [50].

HD is caused bymutation of the huntingtin gene (HTT) result-

ing in abnormal expansion of polyglutamine-encoding CAG

trinucleotide greater than 35 repeats [51]. Genetic and molecular

studies have suggested that mutated HTT with abnormal

expansion of glutamine leads to neuronal damage by gain of

toxic function; however, strong evidence also suggests that

loss of function of HTT also plays a role in pathological

mechanisms of HD [50]. More recently, aberrant HTT palmi-

toylation has been implicated in HD pathogenesis. HTT

palmitoylation is reduced in the brain of the yeast artificial chro-

mosome (YAC)128 mouse model for HD, and this can be

reversed with DHHC17/HIP14 overexpression in YAC128

cortical neurons [32]. Additionally, mutation of HTT, rendering

it palmitoylation resistant, resulted in toxicity and other neuro-

nal cell changes associated with HTT-mutant mouse models of

HD [32,52].HTT has also been shown to interact with PATs.

DHHC17/HIP14 is highly expressed in the brain and has

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several other known synaptic substrates [53-55]. DHHC17/HIP14 was recently discovered to be a PAT for HTT [32],and its interaction/binding with HTT is inversely correlatedwith GAC length, suggesting importance in HD pathogene-sis [56]. These observations have recently been explored inmore detail in animal models. In Drosophila, DHHC17/HIP14 loss of function impairs neurotransmitter release [57]

and DHHC17/HIP14 knockout mice share similarities toother late-stage HD mouse models in behavioral, biochemicaland neuropathological features [53]. For example, DHHC17/HIP14 knockout mice generated from gene-trapped ES celllines revealed that loss of DHHC17/HIP14 resulted in striatalnerve count and volume reduction, together with reductionin neurochemical signaling and behavioral deficits seen inHD patients [53]. Recently, a secondary analysis on theseDHHC17/HIP14 knockout mice also revealed marked alter-ations in synaptic function in varied brain regions and signif-icantly impaired hippocampal memory and synaptic plasticity[58]. Interestingly, HTT palmitoylation was not altered inthese mice; however, other DHHC17/HIP14 substrateswere found to be hypo-palmitoylated [53]. This suggests thatother PATs may compensate for DHHC17/HIP14 loss, butthat this compensation is incomplete as not all DHHC17/HIP14 substrates are palmitoylated [48]. Significantly though,these results demonstrated that even though the substrate pooloverlaps for the 23 known PATs, loss of function of a singlePAT could have dramatic pathological effects.DHHC13/HIP14L is a DHHC17/HIP14 homolog [56].

DHHC13/HIP14L-deficient mice develop adult-onset, wide-spread and progressive neuropathology accompanied by earlymotor deficits in climbing, impaired motor learning andreduced palmitoylation of the novel HIP14L substrate,SNAP25 [59]. Although the phenotype in these mice is similarto DHHC17/HIP14 mutant mice, a more progressive pheno-type, similar to that of the YAC128 transgenic mouse modelof HD, was observed. Interestingly, in a different DHHC13/HIP14L mutant mouse model (Hip14LR425X), a severe pheno-type with profound and diverse pathology involving multior-gan/systems was found. These mice developed cachexia,alopecia, osteoporosis, systemic amyloidosis, failure to thriveand early death [41]. This was the first study that implicatedPATs in regulation of skeletal physiology. More detailed exam-ination of the skeletal phenotype in these mice revealedZDHHC13 appears to be a novel regulator of postnatal skeletaldevelopment and bone mass acquisition as mutants displayeddelayed ossification, disorganized growth and early osteoporo-sis [60]. The bone developmental regulator membrane type 1-metalloprotease (MT1-MMP) was identified as a target ofZDHHC13/HIP14L palmitoylation [60], suggesting thatZDHHC13-mediated MT1-MMP palmitoylation is a keymodulator of bone homeostasis. However, this report did notexamine any brain or neurological phenotypes and thus wasunable to corroborate the neuropathology seen in the otherDHHC13/HIP14L-deficient mouse model. Thus, althoughboth DHHC17/HIP14 and DHHC13/HIP14L may be

dysfunctional inHD [59], DHHC13/HIP14Lmutation appearsto be more severe and may also be involved in skeletal and skindiseases/pathologies.

Studies have implicated the loss of ZDHHC8 function toschizophrenia [61]; however, there is still some debate concern-ing the consistency of this finding among various populationsof patients tested [62-66]. The ZDHHC8 gene is located onchromosome 22 and is part of large subset of genes on this chro-mosome responsible for 22q11.2 deletion syndrome [31,67-69]. Inchildren, microdeletions in chromosome 22q11 can result in arange of symptoms including birth defects and various neurode-velopmental and neuropsychiatric symptoms. It is estimatedthat ~ 30%of these patients will develop schizophrenia or schiz-oaffective disorder in adolescence or early adulthood [70,71].Recent work in DHHC8 null mice confirmed that these micemanifest a sexually dimorphic phenotype where only femalemice displayed a decrease in exploratory activity and a defi-ciency in prepulse inhibition, deficits consistent in individualswith schizophrenia [31]. These DHHC8 null mice abnormalitiesare also similar to affects seen in the mouse model for22q11.2 deletion syndrome [72]. Additional genetic associationevidence in the form a single-nucleotide polymorphism inDHHC8 that links it to schizophrenia has also beenfound [31,46], but a link between this small nucleotide polymor-phism and schizophrenia is not a consistent finding [63,65,73].

Other PATs have also been implicated in other neurologi-cal conditions. For example, genetic studies have linkedimpaired ZDHHC15 and ZDHHC9 expression/function tobe a potential cause in X-linked mental retardation [33,34].Additionally, although no direct genetic link has yet to beestablished between palmitoylation and Alzheimer’s disease,ZDHHC12 is thought to contribute to the trafficking andmetabolism of amyloid precursor protein (APP), the precur-sor protein for the generation of neurotoxic b-amyloid seenin Alzheimer’s disease [74]. Palmitoylation may also be impor-tant for localization of the enzymes involved in the APPcleavage process [75,76].

To date, ZDHHC2, ZDHHC7, ZDHHC8, ZDHHC9,ZDHHC11, ZDHHC14, ZDHHC17 and ZDHHC20 haveall been associated with cancer [35-38,77-80]. These PATs canfunction in an antimetastasis or in an oncogenic manner. Forexample, deletion or epigenomic silencing of ZDHHC2, previ-ously known as REAM, for reduced expression associated withmetastasis [35], has been detected in various types of metastaticcancers including breast [81,82], lung [83,84], urinary bladder [85],prostate [86], colorectal [87], hepatocellular [83] and gastriccancers [88], suggesting that palmitoylation of DHHC2 sub-strates impairs metastatic potential. Conversely, ZDHHC17(HIP14) is oncogenic and ZDHHC9 and ZDHHC11 displaycharacteristics that strongly suggest they are oncogenic whenoverexpressed [36-38]. Overexpression of ZDHHC17 has theability to induce colony formation and anchorage-independentgrowth in cell culture and tumors in mice and it palmitoylatesoncogenic RAS proteins [38]. ZDHHC9 is strongly upregulatedin some adenocarcinomas of the gastrointestinal tract at the

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transcript and protein levels [37] and it too palmitoylates onco-genic RAS proteins in vitro. Additionally, ZDHHC11 is pres-ent on chromosome 5 that has a high incidence of additionalgenomic copies in cases of bladder cancers with high malignantpotential and in nonsmall cell lung cancer [36].

A single amino acid deletion in DHHC21, resulting in lossof PAT activity, has recently been mapped to the depilatedmutant mouse model [40]. The depilated mutant mouse wasdescribed over three decades ago and results in a recessive phe-notype characterized by variable hair loss, with thinner andshorter hairs remaining in a greasy coat [89]. A more detailedstudy of the phenotype demonstrates that lack of ZDHHC21palmitoylation results in hyperplasia of the interfollicular epi-dermis and sebaceous glands and delayed differentiation ofthe hair shaft [40]. Although the exact DHHC21 substrate(s)responsible for the phenotype have not been identified, Fyn,a member of the Src family of protein tyrosine kinases, wasidentified as a target and was mislocalized in the mutantmice hair follicles [40].

From these examples, it is clear that disrupting the homeo-static balance of protein palmitoylation causes significant anddeleterious effects on normal physiology and further identifi-cation of the substrates of each of these and other DHHCproteins will provide important information concerning themolecular mechanisms underlying human disease as well asreveal novel targets for pharmacological intervention. Thedevelopment of specific DHHC protein inhibitors wouldprovide vital reagents with which to study the pathophysio-logical importance of many palmitoylated proteins and mayoffer potential for therapeutic development.

4. Palmitoyl-cysteine prediction

Due to the recent widespread interest in the effects of proteinpalmitoylation and in the possible outcomes of pharmacolog-ical modulation of palmitoylation dynamics, more and morestudies have focused on identifying and annotating palmitoy-lated proteins [1,2,90-93]. This increasing dataset has fosteredthe development of improved and more accurate algorithmsfor predicting palmitoyl-cysteines.

Although PAT specificity for palmitoylating a particularcysteine residue is highly selective, no unique consensus sitesfor palmitoylation have been definitively established. However,sequence and structural alignment studies have highlightedsome common patterns. For example, palmitoylation iscommonly observed close to the cytosolic side of TMDs.Cysteine-rich motifs as well as cysteines proximal to the N-and C-termini are also commonly palmitoylated [94]. The firstmodel for predicting palmitoylation sites was developed byZhou et al. by employing a clustering and scoring strategy(CSS) (known as CSS-Palm 1.0) using a training set of210 experimentally determined palmitoylation sites from83 distinct proteins [95]. Since 2006, updated versions of CSS-Palm have been released with considerable improvements inprediction capacity and efficiency [96,97]. The current version,

CSS-Palm 4.0, utilizes the latest training set containing 583palmitoylation sites from 277 distinct proteins.

Other popular in silico platforms for palmitoyl-cysteineprediction include incremental feature selection (IFS)-Palm [98], weight, amino acid composition and position spe-cific scoring (WAP)-Palm [99] and PalmPred [100]. PalmPred’sapproach for identification of palmitoylation sites relies on fea-tures extracted only from the primary amino acid sequence,viz., sequence conservation, secondary structure and disor-dered regions, and is claimed to be more efficient than IFS-Palm and WAP-Palm. However, experimental determinationof palmitoyl-cysteines should be emphasized, which, with theapplication of emerging chemo-proteomic approaches, isbecoming more routine and straightforward. Nevertheless,such prediction algorithms offer a much needed support toolfor rapid preliminary characterization and/or validation ofpalmitoylation sites.

5. Methods for palmitoyl-cysteine enrichmentand quantitation

Initial attempts to identify palmitoylated proteins and assign-ing PAT/substrate specificity relied on metabolic labelingwith 3H-palmitate and subsequent candidate detection bySDS-PAGE and fluorography and/or immunoblotting [101,102].Due to recent advances in higher throughput proteomic quan-tification technologies, newer site-specific labeling methodolo-gies have emerged that permit nonradioactive and lesstime-consuming enrichment and annotation of palmitoylatedproteins on a much larger scale.

The first systematic approach for palmitoyl-cysteine enrich-ment, called acyl-biotin exchange (ABE), is based on a muchearlier technique called thiol-disulfide interchange, which wasfirst introduced as a method for isolating cysteine-containingenzymes like cysteine endopeptidases [103]. ABE utilizes selec-tive thioester cleavage by hydroxylamine, which follows ablocking step to cap free (nonpalmitoylated) cysteines. Thefreshly exposed (formerly palmitoylated) cysteines are thenlabeled with a thiol-reactive biotinylated probe via stable(but reversible) disulfide interaction for subsequent biotinylenrichment and detection by mass spectrometry. The firstdemonstration of ABE for large-scale analysis of palmitoy-lated proteins was accomplished by Roth et al. in yeast [92]

and has since been widely used to identify hundreds of palmi-toylated proteins in a variety of proteomes [2,90,104-106].

In a variation of ABE, Forrester et al. demonstrated the useof a thiol affinity resin for direct palmitoyl-cysteine enrich-ment that bypasses biotin-streptavidin capture, thus eliminat-ing nonspecific enrichment of endogenous biotinylatedproteins [107]. Similar in concept to ABE, we developedanother method for identifying substrates of specific PATsin mammalian cells, called palmitoyl-cysteine isolation cap-ture and analysis (PICA), by incorporating isotope-codedaffinity tags (ICAT) [108]. In PICA, heavy (H) and light (L)thiol-reactive, biotinylated ICAT reagents are used to

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differentially label newly exposed cysteines (after selectivethioester cleavage, as in ABE) in control cells versus cells inwhich levels of a single PAT are reduced by si-RNA-mediatedknockdown (Figure 1). This allows rapid identification ofpotential PAT substrates following tandem mass spectrometry(MS/MS) and analyzing H/L ratios to quantify the robustnessof palmitoylation. Using this method, we identified and con-firmed by incorporation of radiolabeled palmitate thatcytoskeleton-associated protein 4 (CKAP4) is a key physiolog-ical substrate of DHHC2 in HeLa cells and demonstratedthat loss of DHHC2 expression impairs trafficking ofCKAP4 to the cell surface where it acts as a receptor for anti-proliferative factor (APF) [108]. Without surface expression ofCKAP4, APF is unable to initiate a wide range of downstreameffects, including halting cellular proliferation and altering theexpression of genes related to cancer progression [18]. The dis-covery that CKAP4 is a substrate of DHHC2 provides animportant link between the proliferative properties of manytypes of cancer cells and the reduced expression or mutationof ZDHHC2 that has been associated with metastatic cellularbehavior [35,88,109]. Thus, PICA provides the advantage ofspecifically identifying the palmitoyl-cysteine(s) within apalmitoyl protein, allowing a rapid transition to follow-upexperiments to evaluate the specific role of the palmitoyl-cysteine(s) (versus the many non-palmitoyl-cysteines existingin the protein) to the function of the protein and downstreamsignaling pathways.Hemsley and coworkers described yet another ABE enhance-

ment by employing a biotin switch isobaric tagging for relativeand absolute quantification-based approach to identifyS-acylated proteins from Arabidopsis [93,110]. They identified~ 600 putative S-acylated proteins involved in diverse cellularprocesses and also reported experimental validation on a subsetof those proteins via various in vitro S-acylation assays.Although ABE has proved to be a largely successful methodfor identifying palmitoylated proteins, there are some inherentdrawbacks. For example, there is the requirement of highfidelity protocols for blocking free cysteines as well as for selec-tive thioester hydrolysis, disulfide--interchange reactions andbiotin--streptavidin-based enrichment. Challenges associatedwith such techniques can result in substantial false-positives [92].Another method that has recently gained prominence in

palmitoylation-related studies is target protein labeling withw-azido-fatty acids [111-113]. Building on these initial reports,Martin and Cravatt first demonstrated the use of such azido-fatty acid probes as a method for large-scale identification ofpalmitoylated proteins using the commercially available alkynylfatty acid analogue 17-octadecynoic acid (17-ODYA) [1].17-ODYA is readily incorporated into endogenous palmitoyla-tion sites by the cellular palmitoylation machinery and is thenconjugated to rhodamine-azide or biotin-azide reporter tagsby Cu(I)-catalyzed click chemistry for subsequent gel-baseddetection or biotinyl enrichment. Approximately 125 putativepalmitoylated proteins were identified in human Jurkat T-cellsusing this approach. To improve sensitivity and quantification

of dynamic palmitoylation events, Martin et al. reported anenhancement of their 17-ODYA labeling technique by combin-ing it with stable isotope labeling of cells (SILAC) [91]. Usingthis modified approach, they identified over 400 palmitoylatedproteins in mouse T-cell hybridoma cells. Furthermore, theydemonstrated the applicability of this technique in measuringdynamic palmitoylation turnover by pulse chase experimentswith a serine lipase-specific inhibitor. The subset of these palmi-toylated proteins susceptible to presumably APT-mediatedturnover was identified to contain oncogenes and other proteinslinked to aberrant cell growth, migration and cancer [91], thusalso implying the importance of APTs as targets forpharmacological modulation.

In contrast to ABE, target labeling with bioorthogonalprobes such as 17-ODYA offers some distinct advantages.Chiefly, this approach minimizes nonspecific labeling andthus circumvents generation of false-positives associated withABE protocols, as discussed earlier. It offers flexibility withdetection methods for rapid validation, and temporal controlof probe incorporation to accommodate pulse chaseanalysis [114]. Additionally, in comparison to the traditionallyused spectral counting method for quantitation of palmitoy-lated proteins, SILAC significantly improves on reproducibil-ity, accuracy and sensitivity toward quantifying subtle changesassociated with palmitoylation turnover. However, it shouldalso be noted that chemical probes require metabolic labelingof cells or organisms, unlike in vitro methods such as ABEthat can be performed directly with tissue or cell lysates.

6. Pharmacological modulation and inhibitorsof palmitoylation

As discussed earlier, palmitoylation is catalyzed by PATs,whereas deacylation by APTs. In recent years, the develop-ment of pharmacological modulators of these enzymes hasgarnered increasing interest due to the prospect of alteringthe localization and activity of palmitoylated proteins, severalof which are involved in pathological processes.

6.1 PAT inhibitorsThe use of lipid-based PAT inhibitors such as cerulenin,tunicamycin and the palmitate analog, 2-bromopalmitate(2-BP), has been featured extensively in the literature, with2-BP being most common (Figure 2). Over the years 2-BPhas been widely utilized as an inhibitor of PAT-mediatedpalmitoylation [105,115-118], and sometimes even referred to asa ‘specific’ inhibitor of palmitoylation. Ironically, however,2-BP has long since been known to nonselectively inactivateseveral other types of membrane-bound enzymes [119], includ-ing several enzymes involved in lipid metabolism [120], andeven the deacylating enzymes, APT1 and APT2 [121]. Somerecent studies have explicitly highlighted the promiscuity of2-BP, thus further discrediting its use, at least as an exclusiveinhibitor of enzymatic palmitoylation [122].

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P P P

P1

P2

P3

P1

P2

P3

P1

P2

P3

P10

5

10

15

P2 P3

Protein extraction

MMTS

Hydroxylamine

• Protects free thiols (X)

• Palmitates are removed

Differential labelingwith biotinylated

thiol-reactive heavyand light ICAT

reagents

ICAT labeled proteinscombined 1:1,

digested with trypsin,purified with avidin affinity

column

MS/MS peptideidentification; focus on

proteins with reduced H/Lratio

Peptides

Rel

ativ

e ab

unda

nce

• No effect on palmitoylatedcysteines (P)

• Creates reactive thiols (SH)

Heavy

Light

HeavyLight

Ste

p 1

Ste

p 2

Ste

p 3

Ste

p 4

Ste

p 5

Ste

p 6

PATknockdown

Controlcells

Promitoyl-cysteine identification capture and analysis

X

X X XX

PP X

X

PP P P

PP

XX

SHSHSHSHSHSH

SH SH SHSH

SHSH SH

SH

X

X

XX

XXX

1:1

XXXX

X

X

XX

X

X

X

X

X

P P PX

Figure 1. Palmitoyl-cysteine identification capture and analysis: determining palmitoyl acyltransferase-substrate specificity

by differential labeling of palmitoylated proteins with isotope-coded affinity tags.H: Heavy; ICAT: Isotope-coded affinity tags; L: Light; MS: Mass spectrometry; PAT: Palmitoyl acyltransferase.

Targeting protein palmitoylation

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Due to the nonspecificity of 2-BP and other lipid-baseinhibitors, it is essential to screen for newer selective inhibitorsto accurately establish the role of individual PATs in regulat-ing protein palmitoylation and the resulting downstreameffects. Such efforts have been partly hindered due to a lackof suitable assays for high-throughput screening, as well asinsufficient knowledge of the precise mechanisms of PAT-mediated palmitoylation. Although recent studies haveoffered some mechanistic and kinetic evaluation of PATfunction [14,123,124], without a detailed atomic structure themechanism of palmitoylation remains largely unsubstanti-ated. Another complication arises due to the molecular diver-sity of PATs. There are at least 23 members of the ZDHHCPAT gene family in the mammalian genome with possibleoverlapping or at least partially overlapping mechanisms/motifs for substrate recognition, specificity and activity. Onthe assay front, novel methodologies for palmitoylation assaysthat are amenable to higher-throughput compound screeninghave been emerging (see review by Draper and Smith [125]).Smith and coworkers used a cell-based assay approach to

screen a compound library to identify more selective inhibi-tors of palmitoylation [126]. The screen utilized, among otherassays, cell-permeable green fluorescent protein-linked sub-strate peptides to observe the effects of each compound ininhibiting the localization of such substrates to the PM.They identified five lead compounds, designated compoundsI -- V (Figure 2), that inhibited cellular processes associatedwith palmitoylation. However, follow-up studies revealedthat just one of the compounds, compound V (or2-(2-hydroxy-5-nitro-benzylidene)-benzo[b]thiophen-3-one),inhibited the activity of all four DHHC proteins that weretested [127]. It was also determined that compound V inhibits

PAT autoacylation, a common property of all knownPATs [13], in the same way that 2-BP does; thus, it wouldnot be selective for different PATs. However, unlike 2-BP,inhibition by compound V was largely reversible. Conse-quently, given that 2-BP is also known to inhibit otherenzyme families, compound V is a good candidate for futurestructure-activity tuning studies to increase selectivityand potency.

6.2 APT inhibitorsCertain palmitoylated proteins are dynamically regulated bythe palmitoylation machinery and undergo enzymatic deacy-lation catalyzed by APTs. The cyclic regulation of acylationand deacylation constitutes an important trigger for governingthe intracellular trafficking of such proteins and distinct sig-naling pathways, as was demonstrated with Ras isoforms [128].As mentioned previously, APTs have not been characterizedas extensively as PATs, and only two cytosolic APTs (APT1and APT2) have been reported to have depalmitoylatingactivity against diverse palmitoylated substrate proteinsin vitro [23,129-131], making them attractive targets for pharma-cological intervention. The availability of the APT1 crystalstructure [132] has further enhanced the discovery of APTinhibitors.

One of the first efforts to identify novel APT inhibitors wasbased on the commercially marketed weight loss drug tetrahy-drolipstatin (THL or Orlistat), a prototypical serine hydrolaseinhibitor, following its observed structural homology withgastric lipase [26]. THL possesses an electrophilic b-lactonemoiety that covalently inactivates certain serine hydro-lases [133]. Derivatization of the b-lactone scaffold and screen-ing for inhibition against APT1 led to the discovery of

2-bromopalmitate

Compound V [100][2-(2-hydroxy-5-nitro-benzylidene)-benzo[b]thiophen-3-one]

Cerulenin

Tunicamycin

Figure 2. Palmitoyl acyltransferase inhibitors.

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palmostatin B (APT1 IC50 = 5.4 nM) (Table 1), the first com-pound shown to inhibit Ras depalmitoylation in cells [26].Further optimization yielded a more potent and more solubleanalog, palmostatin M (APT1 IC50 = 2.5 nM) (Table 1) [134].Both palmostatin B and palmostatin M are mechanism-basedinhibitors of APTs that covalently modify and inactivate theactive site serine residue. Although both compounds displayhigh selectivity for APTs among other cellular lipid esterases,neither is selective between the two APT isoforms, APT1 andAPT2 [26,134].

In search of a newer APT inhibitor chemotype, Zimmer-man et al. screened a compound library of natural productsand inhibitors for APT binding, and identified boronic acidderivatives as a new class of potent APT inhibitors [135]. Theboron-based inhibitors were observed to have similar inhibi-tion characteristics as palmostatins. Although less potentthen palmostatins, boron-based inhibitors displayed somefavorable attributes, like robust APT binding (slower off-rates), low toxicity, as well as some selectivity between APTisoforms, thus establishing them as a new APT inhibitor che-motype and suitable candidates for future optimization [135].

Recently, Bachovchin et al. introduced an enhancedsubstrate-free methodology, called fluopol-activity-based pro-tein profiling (ABPP), to accommodate high-throughputscreening programs aimed at identifying inhibitor compoundsfor largely uncharacterized enzymes [136]. Fluopol-ABPP capi-talizes on existing ABPP technology by incorporating the useof broad spectrum fluorescent probes. The assay relies oncompetitive active site occupancy between putative inhibitorsand the fluorescent probe, enabling real-time measurementof deviations in enzymatic activity by monitoring the

fluorescence polarization signal [136]. With the aim of develop-ing APT isoform specific inhibitors, fluopol-ABPP was usedto screen a large compound library (315,004 compounds)against APT1 and APT2 in parallel, and the resulting leadcompounds were then selected for downstream gel-basedABPP assays [137]. The authors reported that a majority ofthe lead compounds contained a piperazine amide motif,establishing yet another APT inhibitor chemotype. Eventuallytwo compounds, designated inhibitor 21 and inhibitor 1,were identified as potent and selective inhibitors of APT1and APT2, respectively (Table 1); moreover, the compoundswere reported to maintain in vivo potency and selectivity inmice, thus representing valuable tools for future studiestoward profiling dynamic protein palmitoylation as well asindividually establishing the roles of APTs.

7. Conclusion

Protein palmitoylation increases the lipophilicity of proteins,thereby dynamically regulating their subcellular distribution,trafficking and function in dramatic and subtle ways. Suchlipophilicity-driven changes in protein distribution can alteraccess of a palmitoylated protein to extracellular ligands, canaffect protein--protein interactions or alter the engagementof the palmitoyl-protein in multimolecular signaling com-plexes that can have dramatic resultant physiological andpathological effects. Indeed, over the last several years, anincreasing body of evidence from genetic studies and animalmodel systems has demonstrated that disrupting the homeo-static balance of protein palmitoylation causes significantand deleterious effects on normal physiology. Identification

Table 1. Acyl protein thioesterase inhibitors.

Inhibitor Structure Inhibition-APT1 Inhibition-APT2

Palmostatin B OO

OCH3

OCH3

IC50 = 5.4 nM[16]

IC50 = 37.7 nM[16]

Palmostatin M OO

S

O ONMe2

IC50 = 2.5 nM[107]

IC50 = 19.6 nM[107]

Inhibitor 21

F

CI

NN

O

O

O

FF

NH

Ki = 300 nM[110]

Ki > 10 µM[110]

Inhibitor 1

N

H3CO

N

O

S SO

O

Ki > 10 µM[110]

Ki = 230 nM[110]

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of the full complement of substrates of each of these PATsand other DHHC proteins will provide important informa-tion concerning the molecular mechanisms and targets under-lying human diseases. In recent years, the development ofpharmacological modulators of PATs, and more recently,APTs, has garnered increasing interest due to the prospectof altering the localization and activity of palmitoylated pro-teins, several of which are involved in pathological processes.Developing therapeutically useful, pharmacological modula-tors of palmitoylation will require that they be developedwithin the context of well-characterized PAT/APT-relatedsignaling systems. Thus, the further development/refinementof screening approaches for palmitoylated proteins and sub-strates is necessary to identify targets and provide vitalreagents with which to study the pathophysiological impor-tance of many palmitoylated proteins. The successful develop-ment of potent, specific drugs in similarly complex systemssuggests that development of useful drugs targeting PATsis feasible.

8. Expert opinion

Our ability to understand palmitoylation and its importanceto human health and disease is only as good as the technolog-ical methods we use to make accurate and valid measure-ments. Recent methodological advances have improved ourability to annotate palmitoylated proteins and to identifyPAT/substrate pairs, yet a framework for predicting PAT/substrate selectivity is lacking and our understanding of howpalmitoylation affects disease-related signaling processes stillunclear. Selective and potent pharmacological inhibitors ofPATs, like those recently developed for APT, would signifi-cantly advance progress in this field.One major consideration regarding the design of PAT

inhibitors is the specificity of PAT/substrate recognition. TheDHHC motif in a PAT defines the active site and is highlyconserved in all known mammalian PATs [13]. Studies havedemonstrated that for all DHHC proteins studied so farmutation of just the cysteine in the DHHC motif preventsPAT autoacylation and subsequent substrate palmitoylation.This high degree of homology within the active site is not aunique feature to PATs and is seen in many kinases [138,139],where development of selective and potent active-site, ATP-competitive inhibitors has been successful [140]. Evidencederived from knockout animal models clearly demonstratesthat even though the substrate pool overlaps for all the knownPATs, loss of function of a single PAT can have dramaticpathological effects. Presumably, this is the direct result ofhypo-palmitoylation of a combination of multiple substratesconsisting of PAT-specific substrates and more common (i.e.,substrates palmitoylated by multiple PATs) target substrates.However, given the homology of the DHHC protein activesites, specificity of palmitoylation must be derived in partfrom other unique physical interactions of individual PATswith their substrates. It is known that the sequence of amino

acids surrounding a substrate cysteine partially defines thepotential for that cysteine to be palmitoylated. However, thephysical determinants for substrate recognition will likelyextend throughout the accessible portions of the PAT and sub-strate, as is the case for DHHC17 [55]. An important futurestep will be to identify and characterize substrates for sequencepatterns and other potential predictors of activation via specificPATs. Additionally, other factors that are likely to regulatepalmitoylation are the temporal and spatial aspects of PATand substrate expression.

Another complication of PAT-substrate recognition lies inthat each PAT can traverse the membrane multiple times.Thus, it is logical to assume that beyond sequence alone, thelocal membrane environment (i.e., exposed/accessible regionsof each PAT) is important for determining in vivo PAT struc-ture and substrate recognition. However, several PATs havebeen purified from membrane that can remain enzymaticallyactive [127], so it may be possible to use enzyme activity-basedand drug-binding screens for selective PAT inhibitors.

Until such selective PAT inhibitors are available, we shouldbe mindful that using compounds like 2BP, cerulenin andtunicamycin may continue to lead to erroneous conclusionsabout every aspect of palmitoylation. Further, we should notlimit our view of PAT function (or many other proteinsfor that matter) only to palmitoylation as both HIP14(DHHC17) and HIP14L (DHHC13) have been shown tomediate the transport of Mg2+ and fall into a category ofenzymes called ‘chanzymes’ or ion channels that also haveenzymatic activity [141]. Developing nonlipid, selective inhib-itors that target the PAT active site is feasible, and thechallenges that exist are similar to those faced during thedevelopment of selective, small-molecule inhibitors of kinasesthat do not resemble ATP. Targeting those PATs forwhich overexpression is oncogenic----DHHC9, DHHC17 orDHHC11----may be the most logical ones to target first.More conclusive data from in vivo experiments that linkPATs to oncogenesis are warranted to motivate drug discoveryprograms on a large scale toward this goal.

Acknowledgements

The opinions, interpretations, conclusions and recommenda-tions are those of the authors and are not necessarily endorsedby the US Army.

Declaration of interest

The authors declare support from the CommonwealthMedical College. B Chavda is also supported by the USArmy Medical Research and Material Command underAward No W81XWH-13-1-0454. The authors have no otherrelevant affiliations or financial involvement with any organi-zation or entity with a financial interest in or financial conflictwith the subject matter or materials discussed in themanuscript apart from those disclosed.

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AffiliationBurzin Chavda, John A Arnott &

Sonia Lobo Planey†

†Author for correspondence

The Commonwealth Medical College,

Department of Basic Sciences, Scranton,

PA 18509, USA

E-mail: splaney@tcmedc.org

Targeting protein palmitoylation

Expert Opin. Drug Discov. (2014) 9(9) 15

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