Linker Design Research Articles

Abstract B170: Discovery of tubulysin payloads for antibody drug conjugates with potent in vitro activity and in vivo efficacy in solid tumor models

Abstract Antibody drug conjugates (ADCs) combine the specificity of antibodies with the potency of small molecule cytotoxic drugs and have the potential to provide significant efficacy as a treatment for cancer. The objective of this work was to identify potent new cytotoxic ADC payloads that can be used to target diverse tumor types. Here we report for the first time the discovery of fully synthetic tubulysin payloads which belong to a class of highly cytotoxic natural products that disrupt the cellular microtubule network leading to apoptosis of tumor cells. Our fully synthetic tubulysin payloads are comprised of: (i) a tubulysin warhead that displays pM potency, (ii) a protease cleavable amino-acid sequence and (iii) a tether bearing a reactive maleimide group. Tubulysin-based ADCs were generated via site-specific conjugation of these payloads to cysteines engineered into antibodies against cancer antigen target oncofetal protein 5T4. The resulting ADCs showed potent in vitro cell killing and in vivo efficacy in multiple solid tumor xenograft models including prostate cancer, non-small cell lung adenocarcinoma, breast cancer and gastric carcinoma. Furthermore, specific structural features of the tubulysin warhead, linker design and antibody engineering were shown to impact the overall in vitro and in vivo properties of the ADCs. Thus, these synthetic tubulysin payloads represent novel microtubule network disrupting compounds that display potent preclinical anti-tumor activity as an ADC that could be advanced to the clinic. Citation Format: Dorin Toader, Jay Harper, Chris Lloyd, Rose Marwood, David Bannister, Shenlan Mao, Cui (Tracy) Chen, Haihon (Helen) Zhong, Vahe Bedian, Fengjiang Wang, Lakshmaiah Gingipalli, Melisa Vasbinder, Pamela Thompson, Ryan Fleming, Byniam Bezabeh, Nazzareno Dimasi, Changshou Gao, Adeela Kamal. Discovery of tubulysin payloads for antibody drug conjugates with potent in vitro activity and in vivo efficacy in solid tumor models. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2015 Nov 5-9; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2015;14(12 Suppl 2):Abstract nr B170.

Investigation of Specific Binding Proteins to Photoaffinity Linkers for Efficient Deconvolution of Target Protein.

Photoaffinity-based target identification has received recent attention as an efficient research tool for chemical biology and drug discovery. The major obstacle of photoaffinity-based target identification is the nonspecific interaction between target identification probes and nontarget proteins. Consequently, the rational design of photoaffinity linkers has been spotlighted for successful target identification. These nonspecific interactions have been considered as random events, and therefore no systematic investigation has been conducted regarding nonspecific interactions between proteins and photoaffinity linkers. Herein, we report the protein-labeling analysis of photoaffinity linkers containing three photoactivatable moieties: benzophenone, diazirine, and arylazide. Each photoaffinity linker binds to a different set of proteins in a structure-dependent manner, in contrast to the previous conception. The list of proteins labeled by each photoaffinity linker was successfully used to eliminate the nonspecific binding proteins from target candidates, thereby increasing the success rate of target identification.

Failure of single phenolic chains and cross-links: Energetics, mechanisms, and alternative linker design

The stretching of a single chain of phenolic polymer is studied using density functional theory (DFT) and the reactive force field (ReaxFF) potential. The most detailed studies are performed at 0 K, which shows the breaking of the C(ring)-CH2 bridge bond can be delayed to longer polymer length by a ring opening mechanism that relieves the strain. Molecular dynamics (MD) simulations, using the DFT approach, show that C–CH2 bridge bond breaking occurs much more frequently than the ring opening. The stretching potentials determined using ReaxFF compare favorably with the DFT results. Using ReaxFF, stretching of cross-linked systems were considered and compared to single chains. The effect of changing the linking group on the bond stretching portion of the potential is found to be relatively small, but the effect on the bond energies can be significant.

Thiol versus hydroxamate as zinc binding group in HDAC inhibition: An ab initio QM/MM molecular dynamics study.

Zinc-dependent histone deacetylases (HDACs) play a critical role in transcriptional repression and gene silencing, and are among the most attractive targets for the development of new therapeutics against cancer and various other diseases. Two HDAC inhibitors have been approved by FDA as anti-cancer drugs: one is SAHA whose hydroxamate is directly bound to zinc, the other is FK228 whose active form may use thiol as the zinc binding group. In spite of extensive studies, it remains to be ambiguous regarding how thiol and hydroxamate are bound to the zinc active site of HDACs. In this work, our computational approaches center on Born-Oppenheimer ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics with umbrella sampling, which allow for modeling of the zinc active site with reasonable accuracy while properly including dynamics and effects of protein environment. Meanwhile, an improved short-long effective function (SLEF2) to describe non-bonded interactions between zinc and other atoms has been employed in initial MM equilibrations. Our ab initio QM/MM MD simulations have confirmed that hydroxamate is neutral when it is bound to HDAC8, and found that thiol is deprotonated when directly bound to zinc in the HDAC active site. By comparing thiol and hydroxamate, our results elucidated the differences in their binding environment in the HDAC active sites, and emphasized the importance of the linker design to achieve more specific binding toward class IIa HDACs.

Abstract 639: Site specific conjugation of ARX-788, an antibody drug conjugate (ADC) targeting HER2, generates a potent and stable targeted therapeutic for multiple cancers

Abstract Creation of ADCs by conjugating drug linkers and toxin payloads to available native lysines or cysteines generates ADCs with highly variable drug to antibody loading and linker stability profiles. Variable drug loading, amino acid position, conjugation chemistry and linker design affect the pharmacokinetic characteristics, potency and toxicity of the ADC. We describe here the synthesis and pharmacology of an ADC comprising a site-specifically conjugated dolastatin analog to an antibody targeting the EGF family receptor, HER2. To specify the site of conjugation and drug loading, a non-natural amino acid, para acetyl phenylalanine (pAcF), was incorporated at defined sites within the antibody primary sequence. This non-natural amino acid provides a linkable platform for covalent conjugation of a diverse array of payloads through a stable oxime bond. The dolastatin analog, MMAF, was coupled via a non-cleavable linker to the HER2 antibody at two specific sites to generate the ADC; ARX-788. In vitro cytotoxicity assays of ARX-788 generated picomolar IC50's across a spectrum of HER2 + cell lines from breast, ovarian, lung and gastric cancer. Multiple in vivo murine xenograft studies demonstrated a potent increase in anti-tumor activity when compared to T-DM1. A single injection of ARX-788 in established xenograft models of HER2 positive ovarian, gastric and breast cancer cell lines (SKOV3, BT474, N-87, and HCC1954) induced rapid regression in all models. ARX-788 induced regression in a Herceptin-resistant derived breast xenograft (JIMT-1) and was significantly more effective than T-DM1 at equivalent doses. Pharmacokinetic evaluation of ARX-788 in rodent and non-human primates (NHP) revealed long term stability of 12 and 8 days respectively. Importantly, the conjugated form of ARX-788 remained intact over the course of the 3 week study in NHP. Precise payload stability and effective half-life of ARX-788 due to site-specific conjugation provides an improved therapeutic window for this HER2-targeting ADC. ARX-788 is currently completing non-human safety and PK studies in anticipation of clinical trial evaluation in 2015. Citation Format: Robin C. Humphreys, Jessica Kirtely, Amha Hewit, Sandra Biroc, Nick Knudsen, Lillian Skidmore, Alan Wahl. Site specific conjugation of ARX-788, an antibody drug conjugate (ADC) targeting HER2, generates a potent and stable targeted therapeutic for multiple cancers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 639. doi:10.1158/1538-7445.AM2015-639

Antibody-Drug Conjugates for Tumor Targeting-Novel Conjugation Chemistries and the Promise of non-IgG Binding Proteins.

Antibody-drug conjugates (ADCs) have emerged as a promising class of anticancer agents, combining the specificity of antibodies for tumor targeting and the destructive potential of highly potent drugs as payload. An essential component of these immunoconjugates is a bifunctional linker capable of reacting with the antibody and the payload to assemble a functional entity. Linker design is fundamental, as it must provide high stability in the circulation to prevent premature drug release, but be capable of releasing the active drug inside the target cell upon receptor-mediated endocytosis. Although ADCs have demonstrated an increased therapeutic window, compared to conventional chemotherapy in recent clinical trials, therapeutic success rates are still far from optimal. To explore other regimes of half-life variation and drug conjugation stoichiometries, it is necessary to investigate additional binding proteins which offer access to a wide range of formats, all with molecularly defined drug conjugation. Here, we delineate recent progress with site-specific and biorthogonal conjugation chemistries, and discuss alternative, biophysically more stable protein scaffolds like Designed Ankyrin Repeat Proteins (DARPins), which may provide such additional engineering opportunities for drug conjugates with improved pharmacological performance.

Designing the furin-cleavable linker in recombinant immunotoxins based on Pseudomonas exotoxin A.

Recombinant immunotoxins (RITs) are fusion proteins that join antibodies to protein toxins for targeted cell killing. RITs armed with Pseudomonas exotoxin A (PE) are undergoing clinical trials for the treatment of cancer. The current design of PE-based RITs joins an antibody fragment to the catalytic domain of PE using a polypeptide linker that is cleaved by the protease furin. Intracellular cleavage of native PE by furin is required for cytotoxicity, yet the PE cleavage site has been shown to be a poor furin substrate. Here we describe the rational design of more efficiently cleaved furin linkers in PE-based RITs, and experiments evaluating their effects on cleavage and cytotoxicity. We found that changes to the furin site could greatly influence both cleavage and cytotoxicity, but the two parameters were not directly correlated. Furthermore, the effects of alterations to the furin linker were not universal. Identical mutations in the anti-CD22 RIT HA22-LR often displayed different cytotoxicity from mutations in the anti-mesothelin RIT SS1-LR/GGS, underscoring the prominent role of the target site in their intoxication pathways. Combining several beneficial mutations in HA22-LR resulted in a variant (HA22-LR/FUR) with a remarkably enhanced cleavage rate and improved cytotoxicity against five B cell lines and similar or enhanced cytotoxicity in five out of six hairy cell leukemia patient samples. This result informs the design of protease-sensitive linkers and suggests that HA22-LR/FUR may be a candidate for further preclinical development.

Current ADC Linker Chemistry.

The list of ADCs in the clinic continues to grow, bolstered by the success of first two marketed ADCs: ADCETRIS® and Kadcyla®. Currently, there are 40 ADCs in various phases of clinical development. However, only 34 of these have published their structures. Of the 34 disclosed structures, 24 of them use a linkage to the thiol of cysteines on the monoclonal antibody. The remaining 10 candidates utilize chemistry to surface lysines of the antibody. Due to the inherent heterogeneity of conjugation to the multiple lysines or cysteines found in mAbs, significant research efforts are now being directed toward the production of discrete, homogeneous ADC products, via site-specific conjugation. These site-specific conjugations may involve genetic engineering of the mAb to introduce discrete, available cysteines or non-natural amino acids with an orthogonally-reactive functional group handle such as an aldehyde, ketone, azido, or alkynyl tag. These site-specific approaches not only increase the homogeneity of ADCs but also enable novel bio-orthogonal chemistries that utilize reactive moieties other than thiol or amine. This broadens the diversity of linkers that can be utilized which will lead to better linker design in future generations of ADCs.Electronic supplementary materialThe online version of this article (doi:10.1007/s11095-015-1657-7) contains supplementary material, which is available to authorized users.

Effect of linker flexibility and length on the functionality of a cytotoxic engineered antibody fragment

Engineered antibody fragments often contain natural or synthetic linkers joining the antigen-binding domain and multimerization regions, and the roles of these linkers have largely been overlooked. To investigate linker effects on structural properties and functionality, six bivalent cytotoxic antibody fragments with of linkers of varying flexibility and length were constructed: (1) 10-AA mouse IgG3 upper hinge region, (2) 20-AA mouse IgG3 upper hinge region repeat, (3) 10-AA glycine and serine linker, (4) 20-AA glycine and serine linker repeat, (5) 21-AA artificial linker, and (6) no-linker control. Interestingly, a higher cytotoxicity was observed for fragments bearing the rigid short linkers compared to the flexible longer linkers. More importantly, amino acid composition related to the rigidity/flexibility was found to be of greater importance upon cytotoxicity than linker length alone. To further study the structure–function relationship, molecular modelling and dynamics simulation were exploited. Resultantly, the rigid mouse IgG3 upper hinge region was predicted to enhance structural stability of the protein during the equilibrium state, indicating the improved cytotoxicity over other combinations of fragments. This prediction was validated by measuring the thermal stability of the mouse IgG3 upper hinge as compared to the artificial linker, and shown to have a higher melting temperature which coincides with a higher structural stability. Our findings clearly suggest that appropriate linker design is required for enhancing the structural stability and functionality of engineered antibody fragments.

Antibody drug conjugates: design and selection of linker, payload and conjugation chemistry.

Antibody drug conjugates (ADCs) have emerged as an important pharmaceutical class of drugs designed to harness the specificity of antibodies with the potency of small molecule therapeutics. The three main components of ADCs are the antibody, the linker, and the payload; the majority of early work focused intensely on improving the functionality of these pieces. Recently, considerable attention has been focused on developing methods to control the site and number of linker/drug conjugated to the antibody, with the aim of producing more homogenous ADCs. In this article, we review popular conjugation methods and highlight recent approaches including "click" conjugation and enzymatic ligation. We discuss current linker technology, contrasting the characteristics of cleavable and non-cleavable linkers, and summarize the essential properties of ADC payload, centering on chemotherapeutics. In addition, we report on the progress in characterizing to determine physicochemical properties and on advances in purifying to obtain homogenous products. Establishing a set of selection and analytical criteria will facilitate the translation of novel ADCs and ensure the production of effective biosimilars.

A Hetero-Bifunctional Spacer for the Smart Engineering of Carbon-Based Nanostructures.

Efforts have been made in recent years to develop novel functionalisation protocols aimed at imparting multimodality and improved properties to complex carbon-based nanostructures. The incorporation of cleavable bonds to the nanomaterial surface for the controlled release (or exchange) of specific molecules under appropriate chemical and biological settings is relatively unexplored. The design and synthesis of a hetero-bifunctional linker joining a "cleavable" disulfide moiety for the covalent anchoring of a wide range of thiol end-capped (bio)molecules and a "clickable" terminal acetylene group is described. The strategy is based on the well-established copper-mediated acetylene-azide coupling reaction between the acetylene linker and single-walled carbon nanotubes decorated with phenylazido pendant arms. As a result, easily "post-derivatisable" and traceable nanostructured platforms containing a linking group potentially available for a wide range of biological probes are prepared and completely characterised.

Antibody–drug conjugates: targeted weapons against cancer

Antibody–drug conjugates: targeted weapons against cancer Luisa Iamele, Luca Vecchia, Claudia ScottiDepartment of Molecular Medicine, Unit of Immunology and General Pathology, University of Pavia, Pavia, PV, Italy  All authors contributed equally to this work Abstract: Antibody–drug conjugates (ADCs) are formed by a targeting antibody conjugated to a chemotherapeutic molecule through a linker. Recent data demonstrate that ADCs represent a valuable advancement for the clinics and, despite their recent appearance in medicine, they are already undergoing an innovation wave aimed at targeting all three ADC building blocks. Thus, new antibody formats are being engineered, site-specific linkers are being designed, and highly toxic molecules, like RNA polymerase inhibitors, are starting to be used for conjugation. These molecules were previously considered extremely toxic and could not be used as chemotherapeutic drugs. In this review, we will present an overview of current cancer treatments and their limitations, and the logic that has led to the generation of ADCs. Their mechanism of action will be outlined, and the most recent novelties in linker design and optimization will be discussed, along with present and near future discoveries in the current ADC research pipeline. Keywords: immunoconjugates, antibody–drug conjugates, antibody fragments, cancer, monoclonal antibodies

Design rules for metal binding biomolecules: understanding of amino acid adsorption on platinum crystallographic facets from density functional calculations.

Understanding the mechanism of biomolecules' interaction with inorganic surfaces might pave the way for the design of material interfaces with controlled and highly predictable properties. Here we have focused on the adsorption mechanism of facet-specific amino acids in the sequence of peptides selected for programmed synthesis of Pt(111) and Pt(100) nanocrystals. Using the first principles calculations we have demonstrated that the specific surface recognition of amino acid side chains occurs due to the combination of multiple processes: electron exchange, partial charge transfer and/or dispersive effects providing a high binding affinity to both polar and non-polar residues against both Pt facets. Our approach points towards promising novel routes for controlled design of material-specific linkers for future materials engineering.

Computer Aided Design of Aptamer for Prothrombin Detection in Blood

Computational Biology is a widely study tool in the field of molecular biology. There is also much information from structural biology of biomolecules. We propose to exploit both resources in the aptamers based structure design. As case study, we report the use of computer tools for the development of a modified Dot Blot for prothrombin quantitation in blood. This Dot Blot uses two aptamers as the recognition prothrombin complex; one for target binding and another for NMM IX binding, a fluorophore whose emission will be converted into concentration.We executed the design of these complexes using VMD software by an algorithm for aptamers selection. This software allows the visualization of molecular crystallography and NMR structures obtained in the Protein Data Bank of each aptamer. Thus, it is possible to analyze the structural details of the aptamers such as; size and orientation of the molecule, distances between nucleotides, interactions involved in folding, residues that form part of the prothrombin binding sites, and another analysis provided by the software. Therefore, is possible select the aptamers with an appropriate sequence, high affinity to targets, simple folding conditions and without interference problems when are assembled together. If necessary, the software will help in the design of linkers to combat interference generated in the assembly.MALDI mass spectrometry was performed to test the proper assembly of the complex and the efficiency of algorithm design. The results obtained from this work will be used in future projects in which this algorithm will be applied in computational selection of new aptamers to use this technique with other proteins of clinical interest.

Polymer-doxycycline conjugates as fibril disrupters: An approach towards the treatment of a rare amyloidotic disease

The term amyloidosis describes neurological diseases where an abnormal protein is misfolded and accumulated as deposits in organs and tissues, known as amyloid, disrupting their normal function. In the most common familial amyloid polyneuropathy (FAP), transthyretin (TTR) displays this role primarily affecting the peripheral nervous system (PNS). Advanced stages of this inherited rare amyloidosis, present as fibril deposits that are responsible for disease progression. In order to stop disease progression, herein we designed an efficient family of nanoconjugates as fibril disrupters. These polymer conjugates are based on doxycycline (doxy), already in phase II trials for Alzheimer's disease, covalently linked to poly-l-glutamic acid (PGA). The conjugates were rationally designed, looking at drug loading and drug release rate by adequate linker design, always considering the physiological conditions at the molecular target site. Conjugation of doxycycline exhibited greater potential towards TTR fibril disaggregation in vitro compared to the parent drug. Exhaustive physico-chemical evaluation of these polymer-drug conjugates concluded that drug release was unnecessary for activity, highlighting the importance of an appropriate linker. Furthermore, biodistribution studies through optical imaging (OI) and the use of radiolabelled polymer-drug conjugates demonstrated conjugate safety profile and renal clearance route of the selected PGA-doxy candidate, settling the adequacy of our conjugate for future in vivo evaluation. Furthermore, preliminary studies in an FAP in vivo model at early stages of disease development showed non-organ toxicity evidences. This nanosized-system raises a promising treatment for advanced stages of this rare amyloidotic disease, and also presents a starting point for possible application within other amyloidosis-related diseases, such as Alzheimer's disease.

Design and Synthesis of New Acid Cleavable Linkers for DNA Sequencing by Synthesis

A new kind of acid sensitive tetrahydrofuranyl (THF) linker was synthesized and then reacted with 5-(6)-carboxytetramethylrhodaminesuccinimidyl ester (5(6)-TAMRA, SE), followed by di(N-succinimidyl) carbonate (DSC) and modified 2′-deoxyuridine triphosphate (dUTP); the final product, as a reversible terminator for DNA sequencing by synthesis (DNA SBS), was given obtained and confirmed by 1H-NMR, 31P-NMR, and HRMS with purity of up to 99%. The synthesized dye-labeled terminator incorporated into DNA strand successfully, and the fluorophore was cleaved completely under acidic conditions. The preliminary results encourage us to explore more acid-sensitive linkers for DNA SBS to increase the cleavage efficiency under weakly acidic conditions.

Chemoproteomics demonstrates target engagement and exquisite selectivity of the clinical phosphodiesterase 10A inhibitor MP-10 in its native environment.

Phosphodiesterases (PDEs) regulate the levels of the second messengers cAMP and cGMP and are important drug targets. PDE10A is highly enriched in medium spiny neurons of the striatum and is an attractive drug target for the treatment of basal ganglia diseases like schizophrenia, Parkinson's disease, or Huntington's disease. Here we describe the design, synthesis, and application of a variety of chemical biology probes, based on the first clinically tested PDE10A inhibitor MP-10, which were used to characterize the chemoproteomic profile of the clinical candidate in its native environment. A clickable photoaffinity probe was used to measure target engagement of MP-10 and revealed differences between whole cell and membrane preparations. Moreover, our results illustrate the importance of the linker design in the creation of functional probes. Biotinylated affinity probes allowed identification of drug-interaction partners in rodent and human tissue and quantitative mass spectrometry analysis revealed highly specific binding of MP-10 to PDE10A with virtually no off-target binding. The profiling of PDE10A chemical biology probes described herein illustrates a strategy by which high affinity inhibitors can be converted into probes for determining selectivity and target engagement of drug candidates in complex biological matrices from native sources.

ChemInform Abstract: Tuning the Structure and Function of Metal—Organic Frameworks via Linker Design

AbstractReview: 291 refs.

ChemInform Abstract: Multifunctional Metal—Organic Frameworks Constructed from meta‐Benzenedicarboxylate Units

AbstractReview: 197 refs.

Design and characterization of structured protein linkers with differing flexibilities.

Engineered fusion proteins containing two or more functional polypeptides joined by a peptide or protein linker are important for many fields of biological research. The separation distance between functional units can impact epitope access and the ability to bind with avidity; thus the availability of a variety of linkers with different lengths and degrees of rigidity would be valuable for protein design efforts. Here, we report a series of designed structured protein linkers incorporating naturally occurring protein domains and compare their properties to commonly used Gly4Ser repeat linkers. When incorporated into the hinge region of an immunoglobulin G (IgG) molecule, flexible Gly4Ser repeats did not result in detectable extensions of the IgG antigen-binding domains, in contrast to linkers including more rigid domains such as β2-microglobulin, Zn-α2-glycoprotein and tetratricopeptide repeats. This study adds an additional set of linkers with varying lengths and rigidities to the available linker repertoire, which may be useful for the construction of antibodies with enhanced binding properties or other fusion proteins.