The reaction between C-terminal α-thioester and N-terminal cysteinyl peptides is known as native chemical ligation (NCL). Alkyl α-thioesters are traditionally prepared in NCL due to their higher thermodynamic stability, which endows resistance to hydrolysis and easier peptide handling. However, the ligation kinetics of these species are slow, and the reaction times exceed the practical limits for chemical protein synthesis. Therefore, conversion to a more reactive phenyl α-thioesters through thiol-thioester exchange is usually employed to enhance the NCL reaction rate. In addition, phenyl thiols can reverse the formation of the less reactive branched thioesters, i.e., thioesters formed with internal Cys residues, and thiolactones. Interestingly, the fastest NCL rates are achieved with phenyl α-selenoesters, though phenylselenol is a poor catalyst for the selenol-(α-alkyl thioester) exchange, particularly with β-branched residues. Hence, it is usually necessary to preform the phenyl α-selenoester and protect internal cysteine residues to preserve the kinetic advantage. Moreover, an ∼2-5-fold excess of the N-terminal cysteine acceptor peptide is typically required to prevent the competition from the cysteine of the ligation product for the phenyl α-selenoester donor that leads to the branched thioester formation. Based on these precedents, we have designed sodium 2-selenoethanesulfonate (SeESNa) as a new selenol catalyst that can overcome these limitations. SeESNa reacts with alkyl α-thioester, N-acyl benzotriazole, and N-acylurea peptides, giving α-SeESNa species. We have determined the rate constants for the ligation with preformed α-SeESNa peptides and show that it is a superior catalyst compared to the known 4-mercaptophenylacetic and 4-mercaptobenzoic acids. The utility of SeESNA was proved through the synthesis of the cardiotoxin A5, a snake venom peptide that contains eight cysteines, without orthogonal cysteine protection. Importantly, it has enabled expressed protein ligation under folding conditions with extraordinary speed, as shown with the Sonic Hedgehog and SUMO2 proteins. Thus, SeESNa is envisaged to have broad applicability in synthetic and semisynthetic protein chemistry.

Native chemical ligation (NCL) ligates two unprotected peptides in an aqueous buffer. One of the fragments features a C-terminal alpha-thioester functional group, and the second bears an N-terminal cysteine. The reaction mechanism depicts two steps: an intermolecular thiol-thioester exchange resulting in a transient thioester, followed by an intramolecular S-to-N acyl shift to yield the final native peptide bond. Although this mechanism is well established, the direct observation of the transient thioester has been elusive because the fast intramolecular rearrangement prevents its accumulation. Here, the use of alpha-selenoester peptides allows a faster first reaction and an early buildup of the intermediate, enabling its quantification and the kinetic monitoring of the first and second steps. The results show a correlation between the steric hindrance in the alpha-thioester residue and the rearrangement rate. In bulky residues, the S-to-N acyl shift has a significant contribution to the overall reaction rate. This is particularly notable for valine and likely for other similar beta-branched amino acids.

Protein palmitoylation or S-acylation has emerged as a key regulator of cellular processes. Increasing evidence shows that this modification is not restricted to palmitate but it can include additional fatty acids, raising the possibility that differential S-acylation contributes to the fine-tuning of protein activity. However, methods to profile the acyl moieties attached to proteins are scarce. Herein, we report a method for the identification and quantification of lipids bound to proteins that relies on hydroxylamine treatment and mass spectrometry analysis of fatty acid hydroxamates. This method has enabled unprecedented and extensive profiling of the S-acylome in different cell lines and tissues and has shed light on the substrate specificity of some S-acylating enzymes. Moreover, we could extend it to quantify also the acyl-CoAs, which are thioesters formed between a fatty acid and a coenzyme A, overcoming many of the previously described challenges for the detection of such species. Importantly, the simultaneous analysis of the lipid fraction and the proteome allowed us to establish, for the first time, a direct correlation between the endogenous levels of acyl-CoAs and the S-acylation profile of its proteome.

Peptide–( o -aminoanilides) prepared on a solid phase yield peptide–Nbz and peptide–Bt. Both undergo thioesterification in the presence of thiols, as well as selenoesterification in peptide–Bt. They are readily used in NCL for protein synthesis.

Inherent susceptibility of peptides to enzymatic degradation in the gastrointestinal tract is a key bottleneck in oral peptide drug development. Here, we present a systematic analysis of (i) the gut stability of disulfide-rich peptide scaffolds, orally administered peptide therapeutics, and well-known neuropeptides and (ii) medicinal chemistry strategies to improve peptide gut stability. Among a broad range of studied peptides, cyclotides were the only scaffold class to resist gastrointestinal degradation, even when grafted with non-native sequences. Backbone cyclization, a frequently applied strategy, failed to improve stability in intestinal fluid, but several site-specific alterations proved efficient. This work furthermore highlights the importance of standardized gut stability test conditions and suggests defined protocols to facilitate cross-study comparison. Together, our results provide a comparative overview and framework for the chemical engineering of gut-stable peptides, which should be valuable for the development of orally administered peptide therapeutics and molecular probes targeting receptors within the gastrointestinal tract.

Native chemical ligation (NCL) enables the direct chemical synthesis and semisynthesis of proteins of different sizes and compositions, streamlining the access to proteins containing posttranslational modifications (PTMs). NCL assembles peptide fragments through the chemoselective reaction of a C-terminal alpha-thioester peptide, prepared either by chemical synthesis or via intein-splicing technology, and a recombinant or synthetic peptide containing an N-terminal Cys. Whereas the generation of C-terminal alpha-thioester proteins can be achieved via the recombinant fusion of the sequence of interest to an intein domain, chemical methods can also be used for synthetically accessible proteins. The use of Fmoc solid-phase peptide synthesis (Fmoc-SPPS) to obtain alpha-thioester peptides requires the development of novel strategies to overcome the lability of the thioester bond toward piperidine Fmoc-removal conditions. These new synthetic methods enable the easy introduction of PTMs in the thioester fragment. In this chapter, we describe an approach for the synthesis and use of C-terminal alpha-N-acylbenzimidazolinone (Nbz) and alpha-Nacyl-N' -methylbenzimidazolinone (MeNbz) peptides in NCL. Following stepwise peptide elongation, acylation with p-nitrophenylchloroformate and cyclization affords the Nbz/MeNbz peptides. The optimization of the coupling conditions allows the chemoselective incorporation of the C-terminal amino acid (aa) on the 3,4-diaminobenzoyl (Dbz) and prevents undesired diacylations of the resulting o-aminoanilide. Following synthesis, these Nbz/MeNbz peptides undergo NCL straightforwardly at neutral pH catalyzed by the presence of arylthiols. Herein, we apply the Nbz technology solid phase synthesis, NCL-mediated cyclization and folding of the heterodimeric RTD-1 defensin, an antimicrobial peptide isolated from the rhesus macaque leukocytes.

Besides being regulated by G-protein-coupled receptors, the activity of heterotrimeric G proteins is modulated by many cytoplasmic proteins. GIV/Girdin and DAPLE (Dvl-associating protein with a high frequency of leucine) are the best-characterized members of a group of cytoplasmic regulators that contain a Gα-binding and -activating (GBA) motif and whose dysregulation underlies human diseases, including cancer and birth defects. GBA motif-containing proteins were originally reported to modulate G proteins by binding Gα subunits of the Gi/o family (Gαi) over other families (such as Gs, Gq/11, or G12/13), and promoting nucleotide exchange in vitro However, some evidence suggests that this is not always the case, as phosphorylation of the GBA motif of GIV promotes its binding to Gαs and inhibits nucleotide exchange. The G-protein specificity of DAPLE and how it might affect nucleotide exchange on G proteins besides Gαi remain to be investigated. Here, we show that DAPLE's GBA motif, in addition to Gαi, binds efficiently to members of the Gs and Gq/11 families (Gαs and Gαq, respectively), but not of the G12/13 family (Gα12) in the absence of post-translational phosphorylation. We pinpointed Met-1669 as the residue in the GBA motif of DAPLE that diverges from that in GIV and enables better binding to Gαs and Gαq Unlike the nucleotide-exchange acceleration observed for Gαi, DAPLE inhibited nucleotide exchange on Gαs and Gαq These findings indicate that GBA motifs have versatility in their G-protein-modulating effect, i.e. they can bind to Gα subunits of different classes and either stimulate or inhibit nucleotide exchange depending on the G-protein subtype.

Besides being regulated by G-protein?coupled receptors, the activity of heterotrimeric G proteins is modulated by many cytoplasmic proteins. GIV/Girdin and DAPLE (Dvl-associating protein with a high frequency of leucine) are the best-characterized members of a group of cytoplasmic regulators that contain a G?-binding and -activating (GBA) motif and whose dysregulation underlies human diseases, including cancer and birth defects. GBA motif?containing proteins were originally reported to modulate G proteins by binding G? subunits of the G(i/o) family (G?(i)) over other families (such as G(s), G(q/11), or G(12/13)), and promoting nucleotide exchange in vitro. However, some evidence suggests that this is not always the case, as phosphorylation of the GBA motif of GIV promotes its binding to G?(s) and inhibits nucleotide exchange. The G-protein specificity of DAPLE and how it might affect nucleotide exchange on G proteins besides G?(i) remain to be investigated. Here, we show that DAPLE's GBA motif, in addition to G?(i), binds efficiently to members of the G(s) and G(q/11) families (G?(s) and G?(q), respectively), but not of the G(12/13) family (G?(12)) in the absence of post-translational phosphorylation. We pinpointed Met-1669 as the residue in the GBA motif of DAPLE that diverges from that in GIV and enables better binding to G?(s) and G?(q). Unlike the nucleotide-exchange acceleration observed for G?(i), DAPLE inhibited nucleotide exchange on G?(s) and G?(q). These findings indicate that GBA motifs have versatility in their G-protein?modulating effect, i.e. they can bind to G? subunits of different classes and either stimulate or inhibit nucleotide exchange depending on the G-protein subtype.

Recent evidence has revealed that heterotrimeric G-proteins can be activated by cytoplasmic proteins that share an evolutionarily conserved sequence called the Gα-binding-and-activating (GBA) motif. This mechanism provides an alternative to canonical activation by G-protein-coupled receptors (GPCRs) and plays important roles in cell function, and its dysregulation is linked to diseases such as cancer. Here, we describe a discovery pipeline that uses biochemical and genetic approaches to validate GBA candidates identified by sequence similarity. First, putative GBA motifs discovered in bioinformatics searches were synthesized on peptide arrays and probed in batch for Gαi3 binding. Then, cDNAs encoding proteins with Gαi3-binding sequences were expressed in a genetically-modified yeast strain that reports mammalian G-protein activity in the absence of GPCRs. The resulting GBA motif candidates were characterized by comparison of their biochemical, structural, and signaling properties with those of all previously described GBA motifs in mammals (GIV/Girdin, DAPLE, Calnuc, and NUCB2). We found that the phospholipase Cδ4 (PLCδ4) GBA motif binds G-proteins with high affinity, has guanine nucleotide exchange factor activity in vitro, and activates G-protein signaling in cells, as indicated by bioluminescence resonance energy transfer (BRET)-based biosensors of G-protein activity. Interestingly, the PLCδ4 isoform b (PLCδ4b), which lacks the domains required for PLC activity, bound and activated G-proteins more efficiently than the full-length isoform a, suggesting that PLCδ4b functions as a G-protein regulator rather than as a PLC. In summary, we have identified PLCδ4 as a nonreceptor activator of G-proteins and established an experimental pipeline to discover and characterize GBA motif-containing proteins.

Despite the tremendous potential of Toll-like receptor 4 (TLR4) agonists in vaccines, their efficacy as monotherapy to treat cancer has been limited. Only some lipopolysaccharides (LPS) isolated from particular bacterial strains or structures like monophosphoryl lipid A (MPLA) derived from lipooligosaccharide (LOS), avoid toxic overactivation of innate immune responses while retaining adequate immunogenicity to act as adjuvants. Here, different LOS structures are incorporated into nanoparticle-filled phospholipid micelles for efficient vaccine delivery and more potent cancer immunotherapy. The structurally unique LOS of the plant pathogen Xcc is incorporated into phospholipid micelles encapsulating iron oxide nanoparticles, producing stable pathogen-mimicking nanostructures suitable for targeting antigen presenting cells in the lymph nodes. The antigen is conjugated via a hydrazone bond, enabling rapid, easy-to-monitor and high-yield antigen ligation at low concentrations. The protective effect of these constructs is investigated against a highly aggressive model for tumor immunotherapy. The results show that the nanovaccines lead to a higher-level antigen-specific cytotoxic T lymphocyte (CTL) effector and memory responses, which when combined with abrogation of the immunosuppressive programmed death-ligand 1 (PD-L1), provide 100% long-term protection against repeated tumor challenge. This nanovaccine platform in combination with checkpoint inhibition of PD-L1 represents a promising approach to improve the cancer immunotherapy of TLR4 agonists.

A simple procedure for C-terminal activation of peptides in solution and its application in native chemical ligation and protein synthesis is described. This method involves a mild thioesterification based on the conversion of an aryloxy-o-methylaminoanilide to thioester under aqueous conditions and in situ ligation with an N-terminal cysteine peptide. The versatility is shown in pH-controlled sequential ligations. To illustrate the usefulness of this methodology, we synthesized the palmitoylated N-terminal domain of human Sonic Hedgehog, a morphogen protein that binds the transmembrane receptor Patched and activates the Hedgehog signaling pathway, involved in embryonic development and in the proliferation of multiple tumors. This approach extends the chemical toolset of chemical protein synthesis based on o-aminoanilide and o-methylaminoanilide peptides.

Native chemical ligation (NCL) employing the N-methylbenzimidazolinone (MeNbz) linker readily provided the linear precursor of a 16-mer peptide that is difficult to obtain by stepwise solid-phase peptide synthesis. NCL and the workup conditions were improved toward a protocol that allows for quantitative removal of the 4-hydroxymercaptophenol additive and subsequent formation of the disulfide bridge in the NCL cocktail by oxidation in air, tolerated by the presence of tris(hydroxypropyl)phosphine.

Heterotrimeric G proteins are quintessential signalling switches activated by nucleotide exchange on Gα. Although activation is predominantly carried out by G-protein-coupled receptors (GPCRs), non-receptor guanine-nucleotide exchange factors (GEFs) have emerged as critical signalling molecules and therapeutic targets. Here we characterize the molecular mechanism of G-protein activation by a family of non-receptor GEFs containing a Gα-binding and -activating (GBA) motif. We combine NMR spectroscopy, computational modelling and biochemistry to map changes in Gα caused by binding of GBA proteins with residue-level resolution. We find that the GBA motif binds to the SwitchII/α3 cleft of Gα and induces changes in the G-1/P-loop and G-2 boxes (involved in phosphate binding), but not in the G-4/G-5 boxes (guanine binding). Our findings reveal that G-protein-binding and activation mechanisms are fundamentally different between GBA proteins and GPCRs, and that GEF-mediated perturbation of nucleotide phosphate binding is sufficient for Gα activation.

Heterotrimeric G proteins are usually activated by the guanine-nucleotide exchange factor (GEF) activity of GPCRs. However, some non-receptor proteins are also GEFs. GIV (a.k.a Girdin) was the first non-receptor protein for which the GEF activity was ascribed to a well-defined protein sequence that directly binds Gαi. GIV expression promotes metastasis and disruption of its binding to Gαi blunts the pro-metastatic behavior of cancer cells. Although this suggests that inhibition of the Gαi-GIV interaction is a promising therapeutic strategy, protein-protein interactions (PPIs) are considered poorly "druggable" targets requiring case-by-case validation. Here, we set out to investigate whether Gαi-GIV is a druggable PPI. We tested a collection of >1,000 compounds on the Gαi-GIV PPI by in silico ligand screening and separately by a chemical high-throughput screening (HTS) assay. Two hits, ATA and NF023, obtained in both screens were confirmed in secondary HTS and low-throughput assays. The binding site of NF023, identified by NMR spectroscopy and biochemical assays, overlaps with the Gαi-GIV interface. Importantly, NF023 did not disrupt Gαi-Gβγ binding, indicating its specificity toward Gαi-GIV. This work establishes the Gαi-GIV PPI as a druggable target and sets the conceptual and technical framework for the discovery of novel inhibitors of this PPI.

GIV (a.k.a Girdin) is a non‐receptor Guanine‐nucleotide Exchange Factor (GEF) for heterotrimeric G proteins. Dysregulation of signaling networks dependent on such G proteins is a contributing factor in many human pathologies from cancer to psychiatric disorders. Therapeutic development in this area has been very successful by targeting G protein‐coupled receptors (GPCRs) – the targets of greater than 30% of marketed drugs – but structural and mechanistic insights into regulators such as GIV have opened novel routes to pharmacological intervention. GIV itself is overexpressed in a variety of human cancers and promotes metastatic properties in tumor cells. Moreover, disrupting GIV binding to Gαi blunts this metastatic behavior. These findings situate the GIV‐Gαi interaction as a promising therapeutic target. Despite protein‐protein interactions (PPIs) generally being considered poorly “druggable,” here we provide structural details about the Gαi‐GIV interface and demonstrate its chemical tractability. In testing a collection of >1,000 bioactive compounds with two high‐throughput screening approaches (structure‐guided virtual screening and a fluorescence polarization assay), we discovered two common micromolar potency hits, which were confirmed as true inhibitors by orthogonal assays. We mapped the binding site of the top hit by NMR spectroscopy and biochemical assays, showing that it overlaps with the GIV engagement site on Gαi, thereby validating its mode of action. Moreover, this inhibitor did not block Gβγ binding to Gαi, indicating that GIV binding can be specifically inhibited. This work empirically confirms the Gαi‐GIV PPI as a druggable target and outlines a discovery approach for anti‐metastatic small molecules. We will present our progress to date in screening a larger library of 200,000 compounds. Support or Funding Information Funded by NIH R01GM112631 and the Hartwell Foundation

Significance Dysregulation of signaling via heterotrimeric G proteins leads to pathogenesis. Thus, developing an efficient armamentarium to study G protein regulation is crucial for understanding the molecular basis of disease. The classical view of G protein activation as an exclusive function of G protein-coupled receptors has been challenged by the discovery of nonreceptor G protein activators. Dysregulation of a family of such nonreceptor activators has been linked to human disorders like cancer or birth defects, but the underlying mechanisms remain poorly understood due to the lack of experimental tools. Here, we use protein engineering to rationally design a genetically encoded inhibitor of these G protein activators and demonstrate its usefulness to block aberrant signaling in cancer cells and abrogate developmental malformations in animal embryos.

We previously showed that guanine nucleotide-binding (G) protein a subunit (G alpha)-interacting vesicle-associated protein (GIV), a guanine-nucleotide exchange factor (GEF), transactivates G alpha activity-inhibiting polypeptide 1 (G alpha i) proteins in response to growth factors, such as EGF, using a short C-terminal motif. Subsequentwork demonstrated that GIV also binds G alpha s and that inactive G alpha s promotes maturation of endosomes and shuts down mitogenic MAPK-ERK1/2 signals from endosomes. However, the mechanism and consequences of dual coupling of GIV to two G proteins, G alpha i and G alpha s, remained unknown. Here we report that GIV is a bifunctional modulator of G proteins; it serves as a guanine nucleotide dissociation inhibitor (GDI) for G alpha s using the same motif that allows it to serve as a GEF for G alpha i. Upon EGF stimulation, GIV modulates G alpha i and G alpha s sequentially: first, a key phosphomodification favors the assembly of GIV-G alpha i complexes and activates GIV's GEF function; then a second phosphomodification terminates GIV's GEF function, triggers the assembly of GIV-G alpha s complexes, and activates GIV's GDI function. By comparing WT and GIV mutants, we demonstrate that GIV inhibits G alpha s activity in cells responding to EGF. Consequently, the cAMP -> PKA -> cAMP response element-binding protein signaling axis is inhibited, the transit time of EGF receptor through early endosomes are accelerated, mitogenic MAPK-ERK1/2 signals are rapidly terminated, and proliferation is suppressed. These insights define a paradigm in G-protein signaling in which a pleiotropically actingmodulator uses the same motif both to activate and to inhibit G proteins. Our findings also illuminate how such modulation of two opposing G alpha proteins integrates downstream signals and cellular responses.