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Published in final edited form as: ACS Chem Biol. 2018 Feb 28;13(4):958–964. doi: 10.1021/acschembio.8b00107

A Switchable Site-Specific Antibody Conjugate

Zhigang Lyu †,#, Lei Kang ‡,§,#, Zakey Yusuf Buuh †, Dawei Jiang §,||, Jeffrey C McGuth †, Juanjuan Du ⊥, Haley L Wissler †, Weibo Cai §, Rongsheng E Wang †,*
PMCID: PMC5910183  NIHMSID: NIHMS947284  PMID: 29461804

Abstract

Genetic incorporation of unnatural amino acids (UAAs) provides a unique approach to the synthesis of site-specific antibody conjugates that are homogeneous and better defined constructs than random conjugates. Yet, the yield varies for every antibody, and the process is costly and time-consuming. We have developed a switchable αGCN4-Fab conjugate that incorporates UAA p-acetylphenylalanine. The GCN4 peptide is used as a switch, and antibodies fused by GCN4 can direct the αGCN4-Fab conjugate to target different cancer cells for diagnosis, imaging, or therapeutic treatment. More importantly, this switchable conjugate demonstrated an impressive potential for pretargeted imaging in vivo. This approach illustrates the utility of an orthogonal switch as a general strategy to endow versatility to a single antibody conjugate, which should facilitate the application of UAA-based site-specific conjugates for a host of biomedical uses in the future.

Graphical Abstract

graphic file with name nihms947284u1.jpg

Over the past decades, antibody conjugates with small molecules,1–3 oligomers,4 and proteins5 have been extensively pursued for immunoassay, imaging-based detection, and diagnosis, as well as therapeutic development. In particular, antibody-drug conjugates (ADCs) emerge as a promising class of immunotherapeutics, with trastuzumab-DM1, brentuximab-vedotin, and inotuzumab-ozogamicin being recently FDA-approved for the treatment of breast cancer, Hodgkin’s lymphoma, and acute lymphoblastic leukemia, respectively.2,3,6 The most common antibody conjugation method relies on a random reaction with surface-exposed cysteines or lysines, which results in a heterogeneous mixture of conjugates with distinct stabilities, efficacies, and pharmacokinetics/pharmacodynamics.7,8 Using site-specific conjugation, homogeneous antibody conjugates with precise control of site and stoichiometry can now be generated to possess improved efficacy, pharmacokinetics, and therapeutic indexes, as well as increased signal-to-noise ratios during in vivo molecular imaging, relative to conventionally made random conjugates.7,9,10 One method for synthesizing site-specific antibody conjugates involves the amber-suppression mediated genetic incorporation of unnatural amino acids (UAAs),11 in which a pair of orthogonal tRNA/aminoacyl-tRNA synthetase specific for the UAA were evolved in order to incorporate the UAA based on the amber codon TAG to the selected sites of a protein.11–13 To date, approximately 200 structurally distinct UAAs have been systematically added to proteins.14

A typical UAA with the desired chemical reactivity is p-acetylphenylalanine (pAcF), which has been successfully coupled to small molecules, oligonucleotides, polymers, or proteins of interest via a stable oxime linkage.13,15–18 Yet, the strategy based on UAA is deemed intrinsically complicated, costly, and consuming in terms of time and labor.8,12 More importantly, the yields of UAA mutants, conjugation efficiency, and conjugate stability vary and largely depend on each individual antibody.7,8,12,15,18 Thus, we asked whether we can focus on synthesizing one site-specific antibody conjugate using genetically encoded UAAs, optimizing the yield and conjugation site, and eventually applying this conjugate to target different protein targets.

RESULTS AND DISCUSSION

Rationale

Recently, a 14-mer peptide sequence from the yeast transcription factor GCN4 was fused to antibodies, thereby directing the targeting of GCN4-selective CAR-T cells to CD19- or CD20-positive tumor cells.19 The fact that this “GCN4 tag” has a low probability of immunogenicity and satisfactory in vivo stability and is orthogonal to human proteins19 suggests that it may be usable as a switch to mediate the targeting of GCN4-selective antibody conjugates (Scheme 1). Primary IgGs could be readily fused with the GCN4 peptide in order to direct αGCN4 antibody conjugates toward their cognate antigens on tumor surfaces. For proof of concept, we picked trastuzumab to target HER2-positive breast cancer2 and FMC63 to target αCD19-positive B-cell lymphoma,20 both of which are popular targets for immunotherapy. The 14-mer sequence from GCN4 was inserted into the loop of the antibody to replace Lys169 at the CL constant region of the light chain (LC) or Ser180–Gly181 at the CH1 constant region of the heavy chain (HC), following the reported procedures3,19,21 for direct peptide–antibody loop fusion. The peptide was flanked with a (Gly)4Ser linker to afford the desired flexibility. The resulting fusion constructs were expressed in HEK293F cells by transient transfection, with yields of more than 10 mg/L after column purification. SDS/ PAGE analysis revealed that all four fusion antibodies migrated as a single band, with >95% purity and a molecular mass of ~165 kDa (Supporting Information Figure S1). After DTT reduction, the light chains migrated close to ~25 kDa, whereas the heavy chains migrated at ~50 kDa, matching the expected molecular weights. Their identities were further confirmed by ESI-MS analysis (Figure S2).

Scheme 1.

Scheme 1

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Schematic Representation of the Switch-Mediated Antibody Conjugate (SAC)

Design and Synthesis of Anti-GCN4 Fab

Among all the available scaffolds that can be used to create an αGCN4 antibody, we are especially interested in Fab fragments, which have much shorter circulation half-lives than a full-length IgG and may incur less off-target-related systematic toxicity for therapeutic treatment or background signals for imaging diagnosis.22 Compared to other small sized antibody fragments, Fab still has constant regions that are distal to antigen-binding sites to allow for point mutation and conjugation. On the basis of the sequence of an αGCN4 single-chain variable fragment (ScFv) that has a binding affinity of about 5 pM,23 we constructed a plasmid (pBAD_αGCN4) harboring the heavy-and lambda light-chain genes of the Fab fragment following an stII signal peptide.24 The wild type αGCN4 Fab was expressed in E. coli in shake flask cultures, yielding 7.4 mg/L after purification.

Optimization of Labeling Sites

The genetic incorporation of UAAs such as pAcF not only allows us to site-specifically modify the protein surface but also facilitates our exploration of various Fab conjugates with different geometries and stabilities.24 For example, previous studies on a Fab fragment bearing a kappa light chain revealed solvent-exposed sites such as HC-K129 that has a high expression yield and coupling efficiency, as well as little interference with antigen-binding.15,24 Nonetheless, a mutation site on the lambda light chain has not been explored yet. In a search for an optimal conjugation site, we selected three additional sites (LC-S155X, LC-S193X, LC-G202X) on the lambda light chain of αGCN4, which are surface-exposed, in flexible loops, and distal to binding sites (Figure 1A). Briefly, the pBAD plasmid that encodes the αGCN4 Fab with double mutations to the TAG codon on HC-K129X, and one of the sites from LC-S155X, LC-S193X, or LC-G202X, was cotransformed into the DH10B strain with a plasmid (pUltra_pAcF)24 that encodes the Mj-tRNA/tyrosyl-tRNA synthetase pair evolved to incorporate the pAcF UAA. The shake-flask expression yield for αGCN4-Fab (LC-S155X, HC-K129X, X = pAcF) was 3.4 mg/L, while the yields for αGCN4-Fab (LC-S193X, HC-K129X, X = pAcF) and αGCN4-Fab (LC-G202X, HC-K129X, X = pAcF) were 0.68 mg/L and 0.34 mg/L, respectively. The varying yields for these Fab mutants confirmed that antibody stability depends on the site of mutation, which may also suggest that the closer the amber suppression is toward the N-terminus, the more stable the mutant is. Nevertheless, all the aforementioned αGCN4 Fab antibodies migrated as a single band on SDS/PAGE analysis, with >95% purity and a molecular mass of ~46 kDa (Figure S3). Follow-up ESI-MS analysis further confirmed their identities, with the results correlating well to the theoretical molecular weights (Figure S4). Through an ELISA assay, we also assessed the affinity of these mutants. As shown in Figure S5, the mutated αGCN4 Fab fragments have an affinity indistinguishable from the wild-type Fab, with a half-maximal binding constant (EC50) of ~1 nM.

Figure 1.

Figure 1

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(A) Sites of mutation in αGCN4 Fab based on the crystal structure of a Fab with a lambda light chain (PDB: 4FQH). (B) ELISA analysis of site-specific αGCN4-Fab-MMAF conjugates captured by GCN4 antigen and detected with anti-human λ-HRP. Error bar represents the standard deviation of three replicates.

Next, we conjugated all the purified αGCN4 Fab mutants with a noncleavable auristatin F linker compound (MMAF)15,18(Scheme 1, Figure S6). Each pAcF-containing αGCN4-Fab was reacted with a 10-fold excess of aminooxy-derived MMAF in the presence of acetic hydrazide at 37 °C for 24 h and purified following the reported procedures.3,18 SDS/ PAGE (Figure S7) and ESI-MS analysis (Figure S6) showed that the final αGCN4 ADCs are >95% pure, and all have the desired molecular weight with a drug-to-antibody ratio (DAR) of 2 (Figure S6). Their binding affinity with GCN4 was assessed by ELISA (Figure 1B). All the conjugates have a similar affinity (EC50 ~ 1 nM) to the wild-type Fab, and also the mutant Fab’s before conjugation, demonstrating that the binding of the αGCN4 Fab is not affected by payload conjugation at the three selected sites.

On the basis of the expression yield (3.4 mg/L) of the mutant (LC-S155X, HC-K129X, X = pAcF), which is significantly higher than the other two αGCN4 Fab mutants and also higher than most reported UAA mutant antibodies (1–2 mg/L by shake flask),15,18,24 we decided to choose αGCN4-Fab (LC-S155X, HC-K129X, X = pAcF) for follow-up experiments.

In Vitro Cytotoxicities of Switchable Antibody–Drug Conjugates

To utilize GCN4 as a switch for the treatment of different cancers, we evaluated the in vitro cytotoxicity of the αGCN4-Fab-MMAF conjugate (LC-S155X, HC-K129X, X = pAcF) and/or GCN4-tagged primary IgGs at the end of their 72 h incubation with a CD19-positive Burkitt’s lymphoma cell line Ramos or a HER2-positive breast cancer cell line SK-BR-3 (Figure 2). The MMAF compound was used as a positive control and displayed medium cytotoxicity (EC50’s ~ 50–89 nM, Supporting Information Table S1) due to its limited cell permeability.18 When mixed with αCD19-GCN4 fusions at a molar ratio of 2:1, αGCN4-Fab-MMAF showed significant toxicity toward the Ramos cell line (EC50 = 12 ± 7 nM with αCD19-LC-GCN4; EC50 = 7 ± 4 nM with αCD19-HC-GCN4; Figure 2A, Table S1). Similarly, the mixture of αGCN4-Fab-MMAF and αHER2-GCN4 fusions potently killed SK-BR-3 breast cancer cells (EC50 = 23 ± 11 nM with αHER2-LC-GCN4; EC50 = 1.2 ± 0.6 nM with αHER2-HC-GCN4; Figure 2B, Table S1). Notably, the most potent mixture (αHER2-HC-GCN4: αGCN4-Fab-MMAF) is similar in efficacy to that of the previously reported Herceptin-MMAF conjugate (EC50 = 0.9 ± 0.2 nM when tested in parallel; Figure 2B, Table S1).15 On the other hand, the αGCN4-Fab-MMAF conjugate or any of the GCN4-tagged primary antibodies, when administered alone, turned out ineffective toward either cancer cell line (EC50s > 100 nM), indicating that the cytotoxic effects require the activation of the αGCN4-based ADC by GCN4. To examine the selectivity of GCN4-mediated ADCs, we also tested the cytotoxicity of αHER2-HC-GCN4:αGCN4-Fab-MMAF on Ramos cells that are HER2-negative (Figure S8A), and the cytotoxicity of αCD19-HC-GCN4:αGCN4-Fab-MMAF on SK-BR-3 cells that are CD19-negative (Figure S8B). In both cases, the combination failed to show any activity (EC50 > 100 nM), while the MMAF small molecule control worked well.

Figure 2.

Figure 2

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In vitro cytotoxicity of αGCN4-Fab MMAF (LC-S155X, HC-K129X) toward (A) the Ramos cancer cell line when mixed with or without αCD19-GCN4 fusions and (B) the SK-BR-3 cancer cell line when mixed with or without αHER2-GCN4 fusions. MMAF or GCN4-fused primary antibodies were also administered alone as controls.

The fact that the GCN4 peptide fused at the heavy chain (CH1) of the primary IgG led to more significant cytotoxicity compared to fusion at the light chain (CL) could be a pattern to possibly guide future antibody tagging with the GCN4 peptide. There could be more space surrounding the CH1 region for binding by αGCN4-Fab. Protein binding to the CH1 region may also interfere less with the primary IgGs’ interaction with antigens and their follow-up internalization. For more direct evidence, we also performed ELISA analysis to investigate the protein complexes’ antigen binding affinity (Figure S9). The αHer2-GCN4 fusion:αGCN4-Fab-MMAF complexes bound significantly to HER2 antigen but not to CD19 antigen, similarly to the Herceptin–MMAF conjugate. On the other hand, the αCD19–GCN4 fusion:αGCN4-Fab-MMAF complexes bound well to CD19 antigen but not HER2. Although the bindings toward cognate antigens are similar, the αGCN4 conjugate complexed with the GCN4–antibody heavy chain fusion seems to bind slightly better than the conjugate complexed with the GCN4–antibody light chain fusion, in both αHER2 and αCD19 affinity tests. These affinity data are highly consistent with the observed cytotoxicity results and suggest that GCN4 fusion at the heavy chain may eventually bring in less interference to the primary IgGs antigen binding.

Taken together, these results demonstrate that with a GCN4 switch, the site-specific αGCN4-Fab-MMAF conjugate can be directed by primary antibodies to selectively and tightly bind cognate biomarkers, thereby potently inhibiting the corresponding tumor cells’ proliferation. Further evaluation of the conjugate’s in vivo efficacy on tumor growth inhibition is currently ongoing to determine its therapeutic potential.

Detection and Imaging Using Switchable Antibody-Dye Conjugates

Next, we wanted to test if GCN4 can mediate the detection of different cancer cell lines. Alexa Fluor 488 (AF488) has been commonly used for flow cytometry assays and was conjugated to αGCN4-Fab (LC-S155X, HC-K129X, X = pAcF) through oxime coupling. The identity and purity of the final αGCN4-Fab-AF488 conjugate was confirmed by ESI-MS (Figure S10) and SDS/PAGE analysis (Figure S7). As shown in Figure 3, the AF488 fluorescence channel can selectively detect SK-BR-3 cells in a dose-responsive manner, when tumor cells were prestained by αGCN4-Fab-AF488 and αHER2-HC-GCN4 fusion rather than αGCN4-Fab-AF488 and αCD19-HC-GCN4 fusion. Similarly, Ramos cells can be detected only when they were preincubated with αCD19-HC-GCN4 and αGCN4-Fab-AF488. Moreover, the shifts of Ramos cells were weaker than that of SK-BR-3 when both were treated with the same amount of antibody mixtures. This indicates that the CD19 receptor on the Ramos surface may be less intensive than the HER2 receptor on SK-BR-3, which is also consistent with the weaker potencies of antibody conjugates on Ramos cells as revealed by cytotoxicity studies.

Figure 3.

Figure 3

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In vitro detection of cancer cells by flow cytometry using αGCN4-Fab AF488 (LC-S155X, HC-K129X) switched with GCN4-fused αHER2 or αCD19 IgG (CH1 fusion).

Encouraged by these in vitro results, we next performed in vivo imaging experiments to further gauge if the GCN4-mediated αGCN4-Fab conjugate can be developed as a switchable imaging agent to efficiently guide cancer therapy. Noninvasive molecular imaging emerges as a powerful tool to accurately and selectively evaluate receptor expression levels, which is crucial for the prediction and timely assessment of the effectiveness of biomarker-targeted cancer therapy.25 In particular, near-infrared fluorescent (NIRF) imaging allows for deep-penetration and hazard-free imaging of tumor tissues and has been routinely used to delineate tumor margins during surgery.26,27 Given that the commonly used NIRF dye Cyanine 7 (Cy7) is not compatible with the aminooxyl functional group (Cy7 has an intrinsic imine functionality), we developed a two-step coupling procedure for the synthesis of αGCN4-Fab-Cy7 (Scheme 1, Figure S11). The first step involved the modification of pAcF on αGCN4-Fab (LC-S155X, HC-K129X, X = pAcF) with an aminooxy-derived BCN linker,28 followed by desalting chromatography to introduce the azide-reactive BCN moiety at a stoichiometry of two per Fab. The modified αGCN4-Fab (LC-S155X, HC-K129X, X = pAcF-BCN) was then reacted with a 10-fold excess of Cy7-azide (Lumiprobe) at 37 °C for 12 h. After size-exclusion chromatography purification, the αGCN4-Fab-Cy7 was confirmed by ESI-MS (Figure S11C) and SDS/PAGE (Figure S11D) to be >95% pure and has the desired molecular weight with a DAR ~ 2.

For in vivo NIRF imaging, we incubated αGCN4-Fab-Cy7 (1.75 mg/kg) with either an αHER2-HC-GCN4 fusion or an αCD19-HC-GCN4 fusion (3 mg/kg) at a molar ratio of 2:1 and then injected them intravenously into mouse xenografts of SK-BR-3, and Ramos, respectively. The fluorescence signals in tumors increased and became saturated 4 h post injection (p.i.; Figure 4). The whole-body background fluorescence gradually reduced, while the tumor signals remained high until the end of the NIRF scan (72 h p.i.). The total radiant efficiency of the targeted antibody complex versus that of the nontargeted antibody complex on SKBR3 and Ramos-bearing mice were plotted, respectively (Figure S12). For both xenografts, the best signal ratios (>3) were achieved at 72 h. As expected, αGCN4-Fab-Cy7 was directed by αHER2-HC-GCN4 to selectively accumulate in the SK-BR-3 tumor instead of Ramos. On the other hand, αCD19-HC-GCN4 effectively directed αGCN4-Fab-Cy7 to the Ramos tumor but not SK-BR-3. Following the last NIRF scan at 72 h p.i., mice were sacrificed, with tumors and major organs resected for ex vivo NIRF imaging (Figure S13). The biodistribution data are highly consistent with the in vivo NIRF observations, indicating that the antibody probe was selectively enriched in tumors compared to the rest of tissues. Importantly, the stronger fluorescence in breast tumor SK-BR-3 compared to that of Ramos was consistent with the trends observed in the cytotoxicity assay and flow cytometry analysis. Thus, our switchable antibody conjugates may ubiquitously probe and distinguish the expression levels of cell-surface biomarkers, thereby serving as a convenient imaging tool.

Figure 4.

Figure 4

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In vivo near-infrared fluorescence (NIRF) imaging of SK-BR-3 and Ramos tumor bearing mice after administration of αHER2-HC-GCN4:αGCN4-Cy7 (LC-S155X, HC-K129X) or αCD19-HC-GCN4:αGCN4-Cy7 (LC-S155X, HC-K129X). Tumor regions were highlighted by circles.

Pretargeted in vivo Imaging Using Switchable Antibody-Dye Conjugates

Molecular imaging is also used to directly visualize the targeting process, including biodistribution and pharmacokinetics.25,29,30 The common approach relies on the direct labeling of immunoconjugates (IgGs) which requires a large dosage to overcome issues with the probe including biostability, photobleaching, and radiodecay (for nuclear imaging).26,27,31 Pretargeted imaging was recently proposed to improve tumor signal-to-background ratios and to reduce the dosage requirement, so that there is limited systemic exposure to harmful effects of the agent. We reasoned that our Fab-based αGCN4 conjugates could serve as a secondary diagnostic agent while the GCN4-tagged primary IgG could be an ideal pretargeting agent. In a pilot experiment with NIRF imaging, 3 mg (18 nmol)/kg of αHER2-HC-GCN4 or αCD19-HC-GCN4 was injected as a pretargeting agent to SK-BR-3 breast cancer bearing mouse xenografts, which showed better imaging signals than Ramos mouse xenografts. After ~4 h, during which the tumor could be maximally bound by the primary IgG, we began the injection of αGCN4-Fab-Cy7 at 1.75 mg (36 nmol)/ kg and monitored the NIRF thereafter. For the control group that was injected with only αGCN4-Fab-Cy7, the background fluorescence quickly cleared out and became negligible at the end of 48 h (Figure 5), which could be due to the short half-life of Fab fragments. With the pretargeting of αCD19-HC-GCN4, the fluorescence signal was initially strong (1–8 h post injection of Fab), thereby reflecting the GCN4-mediated recognition of αCD19 IgG by αGCN4-Fab-Cy7 in the circulating blood. However, the signal eventually decreased to a negligible level at 48 h p.i., presumably because the αCD19 IgG failed to specifically recognize the breast cancer tumor. Only with pretargeted recognition of the HER2-positive SK-BR-3 by αHER2-HC-GCN4 can αGCN4-Fab-Cy7 be enriched in the tumor region, which displayed a strong fluorescence signal from 16 h to 48 h p.i. (Figure 5). Our results showed that the GCN4-mediated site-specific antibody conjugates can also be used for pretargeted tumor imaging. For future work, we are preparing a radiolabeled αGCN4 Fab-NOTA conjugate which could be an ideal fit for pretargeted positron emission tomography (PET) imaging.31

Figure 5.

Figure 5

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In vivo pretargeted NIRF imaging of SK-BR-3 tumor bearing mice after injection with only αGCN4-Cy7 (LC-S155X, HC-K129X) or after preinjection with αHER2-HC-GCN4 or αCD19-HC-GCN4 followed by (after 4 h) injection with αGCN4-Cy7 (LC-S155X, HC-K129X). Tumor regions were highlighted by circles.

Conclusion

In summary, we have developed a switchable site-specific antibody conjugate based on the genetically encoded unnatural amino acid p-acetylphenylalanine (pAcF). This antibody conjugate was optimized at fixed sites and stoichiometry and specifically recognizes a GCN4 peptide tag that is orthogonal to human proteins. Using GCN4 as a switch, the antibody conjugate can be directed by different primary IgGs to target the cognate biomarkers unique to different tumors. With various payloads such as a toxin drug or imaging probes, this switchable approach demonstrated promising effects and flexibility in therapeutic treatment and imaging-guided diagnosis of breast cancer and B-cell lymphoma. The technology described here represents a significant step toward the field of protein conjugation. For future applications to different targeting proteins, one will only need to generate the GCN4-fusion protein accordingly, thereby facilitating a wide range of diagnosis and/or therapeutic treatment, especially when large scale production is needed. Finally, this work suggests that with an orthogonal switch, a fixed antibody conjugate can be used to rapidly deliver small molecule drugs, oligonucleotides, peptides, or proteins in the future to a diverse set of tumors or other disease-related target tissues.

MATERIALS AND METHODS

Please see the Supporting Information for experimental details.

Supplementary Material

SI

Acknowledgments

This work was supported by grant #15-175-22 from the American Cancer Society. R.E.W. and W.C. are also thankful for the support from Temple University Start-up Fund, the University of Wisconsin—Madison, the National Institutes of Health (P30CA014520), the American Cancer Society (125246-RSG-13-099-01-CCE), the National Natural Science Foundation of China (81441051), the Beijing Nova Program (Z171100001117024), and the Beijing Capital Special Development Application Program (Z141107002514159). R.E.W. thanks P. G. Schultz and F. Wang for helpful discussions. The aminooxy-derived BCN linker is a gift from C. H. Kim and P. G. Schultz.

Footnotes

Notes

The authors declare no competing financial interest.

Supporting Information

The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acschem-bio.8b00107.

Supporting Figures S1–S13, Table S1, and detailed descriptions of the experimental materials and methods applied in this study (PDF)

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