Linker Design Research Articles

CirPred, the first structure modeling and linker design system for circularly permuted proteins

BackgroundThis work aims to help develop new protein engineering techniques based on a structural rearrangement phenomenon called circular permutation (CP), equivalent to connecting the native termini of a protein followed by creating new termini at another site. Although CP has been applied in many fields, its implementation is still costly because of inevitable trials and errors.ResultsHere we present CirPred, a structure modeling and termini linker design method for circularly permuted proteins. Compared with state-of-the-art protein structure modeling methods, CirPred is the only one fully capable of both circularly-permuted modeling and traditional co-linear modeling. CirPred performs well when the permutant shares low sequence identity with the native protein and even when the permutant adopts a different conformation from the native protein because of three-dimensional (3D) domain swapping. Linker redesign experiments demonstrated that the linker design algorithm of CirPred achieved subangstrom accuracy.ConclusionsThe CirPred system is capable of (1) predicting the structure of circular permutants, (2) designing termini linkers, (3) performing traditional co-linear protein structure modeling, and (4) identifying the CP-induced occurrence of 3D domain swapping. This method is supposed helpful for broadening the application of CP, and its web server is available at http://10.life.nctu.edu.tw/CirPred/ and http://lo.life.nctu.edu.tw/CirPred/.

Investigating How Proline Linkers Enhance Hybrid Antimicrobial Peptide Activity

To combat increasing antibiotic resistance in bacteria, antimicrobial peptides (AMPs) have been proposed as alternatives to conventional antibiotic treatments. AMPs are naturally found in many organisms, including humans, as part of the innate immune response. One approach to designing novel AMPs is to form a hybrid AMP by connecting two individual AMPs, often with a linker consisting of one or more amino acids. Previous studies have shown that some hybrid AMPs have increased antibacterial activity and reduced cytotoxicity to eukaryotic cells. The amino acid linker and hybrid design used may impact antibacterial activity; however, these effects have not yet been systematically evaluated. This study examines hybrid AMPs formed from two translocating histone-derived antimicrobial peptides (HDAPs): the naturally occurring buforin II (BF2) and the synthesized peptide DesHDAP1. Previous work in our laboratory has shown that proline linkers enhance the activity of these BF2/DesHDAP1 hybrids. To investigate which structural feature of proline contributes to this observed increase in activity, additional BF2/DesHDAP1 hybrids were designed using glycine and N-methyl alanine linkers. Antibacterial activity and circular dichroism spectroscopy results suggest that proline's inability to hydrogen bond contributes more to antibacterial activity than physical rigidity. Molecular dynamics simulations were also performed to compare the hybrids’ structure and interactions with membranes on a molecular level. Ongoing work is investigating the activity of these BF2/DesHDAP1 hybrid AMPs against eukaryotic cells.

Engineering the acyltransferase domain of epothilone polyketide synthase to alter the substrate specificity

BackgroundPolyketide synthases (PKSs) include ketone synthase (KS), acyltransferase (AT) and acyl carrier protein (ACP) domains to catalyse the elongation of polyketide chains. Some PKSs also contain ketoreductase (KR), dehydratase (DH) and enoylreductase (ER) domains as modification domains. Insertion, deletion or substitution of the catalytic domains may lead to the production of novel polyketide derivatives or to the accumulation of desired products. Epothilones are 16-membered macrolides that have been used as anticancer drugs. The substrate promiscuity of the module 4 AT domain of the epothilone PKS (EPOAT4) results in production of epothilone mixtures; substitution of this domain may change the ratios of epothilones. In addition, there are two dormant domains in module 9 of the epothilone PKS. Removing these redundant domains to generate a simpler and more efficient assembly line is a desirable goal.ResultsThe substitution of module 4 drastically diminished the activity of epothilone PKS. However, with careful design of the KS-AT linker and the post-AT linker, replacing EPOAT4 with EPOAT2, EPOAT6, EPOAT7 or EPOAT8 (specifically incorporating methylmalonyl-CoA (MMCoA)) significantly increased the ratio of epothilone D (4) to epothilone C (3) (the highest ratio of 4:3 = 4.6:1), whereas the ratio of 4:3 in the parental strain Schlegelella brevitalea 104-1 was 1.4:1. We also obtained three strains by swapping EPOAT4 with EPOAT3, EPOAT5, or EPOAT9, which specifically incorporate malonyl-CoA (MCoA). These strains produced only epothilone C, and the yield was increased by a factor of 1.8 compared to that of parental strain 104-1. Furthermore, mutations of five residues in the AT domain identified Ser310 as the critical factor for MMCoA recognition in EPOAT4. Then, the mutation of His308 to valine or tyrosine combined with the mutation of Phe310 to serine further altered the product ratios. At the same time, we successfully deleted the inactive module 9 DH and ER domains and fused the ΨKR domain with the KR domain through an ~ 25-residue linker to generate a productive and simplified epothilone PKS.ConclusionsThese results suggested that the substitution and deletion of catalytic domains effectively produces desirable compounds and that selection of the linkers between domains is crucial for maintaining intact PKS catalytic activity.

Building Block Symmetry Relegation Induces Mesopore and Abundant Open-Metal Sites in Metal–Organic Frameworks for Cancer Therapy

Building Block Symmetry Relegation Induces Mesopore and Abundant Open-Metal Sites in Metal–Organic Frameworks for Cancer Therapy

Ultrahigh Hydrogen Uptake in an Interpenetrated Zn 4 O-Based Metal–Organic Framework

As a highly promising candidate for hydrogen storage, crucial to vehicles powered by fuel cells, metal–organic frameworks (MOFs) have attracted the attention of chemists in recent decades. H2 uptak...

Characterizing the function of domain linkers in regulating the dynamics of multi-domain fusion proteins by microsecond molecular dynamics simulations and artificial intelligence.

Multi-domain proteins are not only formed through natural evolution but can also be generated by recombinant DNA technology. Because many fusion proteins can enhance the selectivity of cell targeting, these artificially produced molecules, called multi-specific biologics, are promising drug candidates, especially for immunotherapy. Moreover, the rational design of domain linkers in fusion proteins is becoming an essential step toward a quantitative understanding of the dynamics in these biopharmaceutics. We developed a computational framework to characterize the impacts of peptide linkers on the dynamics of multi-specific biologics. Specifically, we first constructed a benchmark containing six types of linkers that represent various lengths and degrees of flexibility and used them to connect two natural proteins as a test system. We then projected the microsecond dynamics of these proteins generated from Anton onto a coarse-grained conformational space. We further analyzed the similarity of dynamics among different proteins in this low-dimensional space by a neural-network-based classification model. Finally, we applied hierarchical clustering to place linkers into different subgroups based on the classification results. The clustering results suggest that the length of linkers, which is used to spatially separate different functional modules, plays the most important role in regulating the dynamics of this fusion protein. Given the same number of amino acids, linker flexibility functions as a regulator of protein dynamics. In summary, we illustrated that a new computational strategy can be used to study the dynamics of multi-domain fusion proteins by a combination of long timescale molecular dynamics simulation, coarse-grained feature extraction, and artificial intelligence.

Rational Linker Design to Accelerate Excretion and Reduce Background Uptake of Peptidomimetic PSMA-Targeting Hybrid Molecules.

The evolution of peptidomimetic hybrid molecules for preoperative imaging and guided surgery targeting the prostate-specific membrane antigen (PSMA) significantly progressed over the past few years, and some approaches are currently being evaluated for further clinical translation. However, accumulation in nonmalignant tissue such as kidney, bladder, spleen, or liver might limit tumor-to-background contrast for precise lesion delineation, particularly in a surgical setting. To overcome these limitations, a rational linker design aims at the development of a second generation of PSMA-11-based hybrid molecules with an enhanced pharmacokinetic profile and improved imaging contrast. Methods: A selection of rationally designed linkers was introduced to the PSMA-targeting hybrid molecule Glu-urea-Lys-HBED-CC-IRDye800CW, resulting in a second-generation peptidomimetic hybrid molecule library. The biologic properties were investigated in cell-based assays. In a preclinical proof-of-concept study with the radionuclide 68Ga, the impact of the modifications was evaluated by determination of specific tumor uptake, pharmacokinetics, and fluorescence imaging in tumor-bearing mice. Results: The modified hybrid molecules carrying various selected linkers revealed high PSMA-specific binding affinity and effective internalization. The highest tumor-to-background contrast of all modifications investigated was identified for the introduction of a histidine- (H) and glutamic acid (E)-containing linker ((HE)3-linker) between the PSMA-binding motif and the chelator. In comparison to the parental core structure, uptake in nonmalignant tissue was significantly reduced to a minimum, as exemplified by an 11-fold reduced spleen uptake from 38.12 ± 14.62 percentage injected dose (%ID)/g to 3.47 ± 1.39 %ID/g (1 h after injection). The specific tumor uptake of this compound (7.59 ± 0.95 %ID/g, 1 h after injection) was detected to be significantly higher than that of the parental tracer PSMA-11. These findings confirmed by PET and fluorescence imaging are accompanied by an enhanced pharmacokinetic profile with accelerated background clearance at early time points after injection. Conclusion: The novel generation of PSMA-targeting hybrid molecules reveals fast elimination, reduced background organ enrichment, and high PSMA-specific tumor uptake meeting the key demands for potent tracers in nuclear medicine and fluorescence-guided surgery. The approach's efficacy in improving the pharmacokinetic profile highlights the strengths of rational linker design as a powerful tool in strategic hybrid-molecule development.

Peptide nucleic acid Hoogsteen strand linker design for major groove recognition of DNA thymine bases

Sequence-specific targeting of double-stranded DNA and non-coding RNA via triple-helix-forming peptide nucleic acids (PNAs) has attracted considerable attention in therapeutic, diagnostic and nanotechnological fields. An E-base (3-oxo-2,3-dihydropyridazine), attached to the polyamide backbone of a PNA Hoogsteen strand by a side-chain linker molecule, is typically used in the hydrogen bond recognition of the 4-oxo group of thymine and uracil nucleic acid bases in the major groove. We report on the application of quantum chemical computational methods, in conjunction with spatial constraints derived from the experimental structure of a homopyrimidine PNA·DNA-PNA hetero-triplex, to investigate the influence of linker flexibility on binding interactions of the E-base with thymine and uracil bases in geometry-optimised model systems. Hydrogen bond formation between the N2 E-base atom and target pyrimidine base 4-oxo groups in model systems containing a β-alanine linker (J Am Chem Soc 119:11116, 1997) was found to incur significant internal strain energy and the potential disruption of intra-stand aromatic base stacking interactions in an oligomeric context. In geometry-optimised model systems containing a 3-trans olefin linker (Bioorg Med Chem Lett 14:1551, 2004) the E-base swung out away from the target pyrimidine bases into the solvent. These findings are in qualitative agreement with calorimetric measurements in hybridisation experiments at T-A and U-A inversion sites. In contrast, calculations on a novel 2-cis olefin linker design indicate that it could permit simultaneous E-base hydrogen bonding with the thymine 4-oxo group, circumvention and solvent screening of the thymine 5-methyl group, and maintenance of triplex intra-stand base stacking interactions.

Structural basis for the design of bisubstrate inhibitors of protein kinase CK2 provided by complex structures with the substrate-competitive inhibitor heparin.

The Ser/Thr kinase CK2, a member of the superfamily of eukaryotic protein kinases, has an acidophilic substrate profile with the substrate recognition sequence S/T-D/E-X-D/E, and it is inhibited by polyanionic substances like heparin. The latter, a highly sulphated glucosamino glycan composed mainly of repeating 2-O-sulpho-α-l-idopyranuronic acid/N,O6-disulpho-α-d-glucosamine disaccharide units, is the longest known substrate-competitive CK2 inhibitor. The structural basis of CK2's preference for anionic substrates and substrate-competitive inhibitors is only vaguely known which limits the value of the substrate-binding region for the structure-based development of CK2 bisubstrate inhibitors. Here, a tetragonal and a monoclinic co-crystal structure of CK2α, the catalytic subunit of CK2, with a decameric heparin fragment are described. In the tetragonal structure, the heparin molecule binds to the polybasic stretch at the beginning of CK2α's helix αC, whereas in the monoclinic structure it occupies the central substrate-recognition region around the P+1 loop. Together, the structures rationalize the inhibitory efficacy of heparin fragments as a function of chain length. The monoclinic CK2α/heparin structure, in which the heparin fragment is particularly well defined, is the first CK2 structure with an anionic inhibitor of considerable size at the central part of the substrate-recognition site. The bound heparin fragment is so close to the binding site of ATP-competitive inhibitors that it can guide the design of linkers and pave the way to efficient CK2 bisubstrate inhibitors in the future.

Linker Desymmetrization: Access to a Series of Rare-Earth Tetracarboxylate Frameworks with Eight-Connected Hexanuclear Nodes.

The exploration of metal-organic frameworks (MOFs) through the rational design of building units with specific sizes, geometries, and symmetries is essential for enriching the structural diversity of porous solids for applications including storage, separation, and conversion. However, it is still a challenge to directly synthesize rare-earth (RE) MOFs with less connected clusters as a thermodynamically favored product. Herein, we report a systematic investigation on the influence of size, rigidity, and symmetry of linkers over the formation of RE-tetracarboxylate MOFs and uncover the critical role of linker desymmetrization in constructing RE-MOFs with eight-connected hexanuclear clusters. Our results on nine new RE-MOFs, PCN-50X (X = 1-9), indicate that utilization of trapezoidal or tetrahedral linkers provides accesses to traditionally unattainable RE-tetracarboxylate MOFs with 8-c hexanuclear nodes, while the introduction of square or rectangular linkers during the assembly of RE-MOFs based on polynuclear clusters typically leads to the MOFs constructed from 12-c nodes with underlying shp topology. By rational linker design, MOFs with two unprecedented (4, 8)-c nets, lxl and jun, can also be obtained. This work highlights linker desymmetrization as a powerful strategy to enhance MOFs' structural complexity and access MOF materials with nondefault topologies that can be potentially used for separation and catalysis.

Strategic design and synthesis of star-shaped organic linkers for mesoporous MOFs.

In the process of designing new MOFs with the aim of having a specific morphology, the shape of the linkers and the choice of coordinating metals have major importance. In this study, the aim to create novel hnb non-interpenetrating MOFs led us to choose tritopic linkers. Novel star-shaped molecules, presenting trigonal geometry and based on aromatic rings, were synthesized. For more convenient synthesis of the library, C-C coupling reactions via a direct arylation methodology were performed. This new synthetic tool, together with the idea of a molecule as a modular combination of smaller building blocks, made possible the fast, cheap and reproducible production of this class of compounds and also its scale-up. With one of the compounds, a MOF was synthesized and characterised via its specific surface area, which varies between 1681 and 3770 m2 g-1.

Design and construction of chimeric linker library with controllable flexibilities for precision protein engineering.

Linkers play essential roles in the engineering of fusion proteins, and have been extensively demonstrated to affect protein properties such as expression level, solubility, and biological functions. For linker design and optimization, one of the key factors is the flexibility or rigidity of linkers, which describes the tendency of a linker to maintain a stable conformation when expressed, and can directly contribute to the physical distance between domains of a fusion protein. In this chapter, we discuss the design and engineering of linkers in fusion proteins, and describe a library-based method for optimization of linker flexibility. This approach is based on chimeric linkers, which are composed of both flexible and rigid (helix-forming) linker motifs. We demonstrate that the chimeric linker library capable of controlling the flexibility in a wide range can fill the gap between flexible and rigid linkers by molecular dynamics simulation and fluorescence resonance energy transfer experiments, as well as its applications in fusion protein optimization.

Deep generative design with 3D pharmacophoric constraints.

Generative models have increasingly been proposed as a solution to the molecular design problem. However, it has proved challenging to control the design process or incorporate prior knowledge, limiting their practical use in drug discovery. In particular, generative methods have made limited use of three-dimensional (3D) structural information even though this is critical to binding. This work describes a method to incorporate such information and demonstrates the benefit of doing so. We combine an existing graph-based deep generative model, DeLinker, with a convolutional neural network to utilise physically-meaningful 3D representations of molecules and target pharmacophores. We apply our model, DEVELOP, to both linker and R-group design, demonstrating its suitability for both hit-to-lead and lead optimisation. The 3D pharmacophoric information results in improved generation and allows greater control of the design process. In multiple large-scale evaluations, we show that including 3D pharmacophoric constraints results in substantial improvements in the quality of generated molecules. On a challenging test set derived from PDBbind, our model improves the proportion of generated molecules with high 3D similarity to the original molecule by over 300%. In addition, DEVELOP recovers 10× more of the original molecules compared to the baseline DeLinker method. Our approach is general-purpose, readily modifiable to alternate 3D representations, and can be incorporated into other generative frameworks. Code is available at https://github.com/oxpig/DEVELOP.

Optimizing the linker length for fusing an alcohol dehydrogenase with a cyclohexanone monooxygenase.

The use of enzymes in organic synthesis is highly appealing due their remarkably high chemo-, regio- and enantioselectivity. Nevertheless, for biosynthetic routes to be industrially useful, the enzymes must fulfill several requirements. Particularly, in case of cofactor-dependent enzymes self-sufficient systems are highly valuable. This can be achieved by fusing enzymes with complementary cofactor dependency. Such bifunctional enzymes are also relatively easy to handle, may enhance stability, and promote product intermediate channeling. However, usually the characteristics of the linker, fusing the target enzymes, are not thoroughly evaluated. A poor linker design can lead to detrimental effects on expression levels, enzyme stability and/or enzyme performance. In this chapter, the effect of the length of a glycine-rich linker was explored for the case study of ɛ-caprolactone synthesis through an alcohol dehydrogenase-cyclohexanone monooxygenase fusion system. The procedure includes cloning of linker variants, expression analysis, determination of thermostability and effect on activity and conversion levels of 15 variants of different linker sizes. The protocols can also be used for the creation of other protein-protein fusions.

Discovery of Novel and Highly Selective Cyclopropane ALK Inhibitors through a Fragment-Assisted, Structure-Based Drug Design.

Fragment screening is frequently used for hit identification. However, there was no report starting from a small fragment for the development of an anaplastic lymphoma kinase (ALK) inhibitor, despite the number of ALK inhibitors reported. We began our research with the fragment hit F-1 and our subsequent linker design, and its docking analysis yielded novel cis-1,2,2-trisubstituted cyclopropane 1. The fragment information was integrated with a structure-based approach to improve upon the selectivity over tropomyosin receptor kinase A, leading to the potent and highly selective ALK inhibitor, 4-trifluoromethylphenoxy-cis-1,2,2-trisubstituted cyclopropane 12. This work shows that fragments become a powerful tool for both lead generation and optimization, such as the improvement of selectivity, by combining them with a structure-based drug design approach, resulting in the fast and efficient development of a novel, potent, and highly selective compound.

Fully synthetic injectable depots with high drug content and tunable pharmacokinetics for long-acting drug delivery

Clinical studies have validated that antiretroviral (ARV) drugs can serve as an HIV pre-exposure prophylactic (PrEP) strategy. Dosing adherence remains a crucial factor determining the final efficacy outcomes, and both long-acting implants and injectable depot systems are being developed to improve patient adherence. Here, we describe an injectable depot platform that exploits a new mechanism for both formation and controlled release. The depot is a polymeric prodrug synthesized from monomers that incorporate an ARV drug tenofovir alafenamide (TAF) with degradable linkers that can be designed to control release rates. The prodrug monomers are synthetically incorporated into homopolymer or block designs that exhibit high drug weight percent (wt%) and also are hydrophobized in these prodrug segments to drive depot formation upon injection. Drug release converts those monomers to more hydrophilic pendant groups via linker cleavage, and as this drug release proceeds, the polymer chains losing hydrophobicity are then disassociated from the depot and released over time to provide a depot dissolution mechanism. We show that long-acting TAF depots can be designed as block copolymers or as homopolymers. They can also be designed with different linkers, for example with faster or slower degrading p-hydroxybenzyloxycarbonyl (Benzyl) and ethyloxycarbonyl (Alkyl) linkers, respectively. Diblock designs of p(glycerol monomethacrylate)-b-p(Alkyl-TAF-methacrylate) and p(glycerol monomethacrylate)-b-p(Benzyl-TAF-methacrylate) were first characterized in a mouse subcutaneous injection model. The alkylcarbamate linker design (TAF 51 wt%) showed excellent sustained release profiles of the key metabolite tenofovir (TFV) in skin and plasma over a 50-day period. Next, the homopolymer design with a high TAF drug wt% of 73% was characterized in the same model. The homopolymer depots with p(Alkyl-TAFMA) exhibited sustained TFV and TAF release profiles in skin and blood over 60 days, and TFV-DP concentrations in peripheral blood mononuclear cells (PBMC) were found to be at least 10-fold higher than the clinically suggested minimally EC90 protective concentration of 24 fmol/106 cells. These are the first reports of sustained parent TAF dosing observed in mouse and TFV-DP in mouse PBMC. IVIS imaging of rhodamine labeled homopolymer depots showed that degradation and release of the depot coincided with the sustained TAF release. Finally, these polymers showed excellent stability in accelerated stability studies over a six-month time period, and exceptional solubility of over 700 mg/mL in the DMSO formulation solvent. The homopolymer designs have a drug reservoir potential of well over a year at mg/day dosing and may not require cold chain storage for global health and developed world long-acting drug delivery applications.

Iridium Oxide-Based Potassium Sensitive Microprobe With Anti-Fouling Properties

Here, we present a new type of potassium sensor which possesses a combination of potassium sensing and anti-biofouling properties. Two major advancements were required to be developed with respect to the current technology; Firstly, design of surface linkers for this type of coating that would allow deposition of the potassium-selective coating on Iridium (Ir) wire or micro-spike surface for chronic monitoring for the first time. As this has never been done before, even for flat Ir surfaces, the material's small dimensions and surface area render this challenging. Secondly, the task of transformation of the coated wire into a sensor. Here we develop and bench-test the electrode sensitivity to potassium and determine its specificity to potassium versus sodium interference. For this purpose we also present a novel characterisation platform which enables dynamic characterization of the sensor including step and sinusoidal response to analyte changes. The developed sensor shows good sensitivity (<; 1 K <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> ions) and selectivity (up to approximately 10 times more sensitive to K <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> than Na <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">+</sup> concentration changes, depending on concentrations and ionic environment). In addition, the sensor displays very good mechanical properties for the small diameter involved (sub 150μm), which in combination with anti-biofouling properties, renders it an excellent potential tool for the chemical monitoring of neural and other physiological activities using implantable devices.

Design and Validation of Linkers for Site-Specific Preparation of Antibody-Drug Conjugates Carrying Multiple Drug Copies Per Cysteine Conjugation Site.

First-generation cysteine-based site-specific antibody–drug conjugates (ADCs) are limited to one drug per cysteine. However, certain applications require a high drug to antibody ratio (DAR), such as when low-potency payloads are used. Higher drug load can be achieved using classical cysteine conjugation methods, but these result in heterogeneity, suboptimal efficacy and pharmacokinetics. Here, we describe the design, synthesis and validation of heterobifunctional linkers that can be used for the preparation of ADCs with a DAR of two, three and four in a site-specific manner per single cysteine conjugation site, resulting in site-specific ADCs with a DAR of four, six and eight. The designed linkers carry a sulfhydryl-specific iodoacetyl reactive group, and multiple cyclic diene moieties which can efficiently react with maleimide-carrying payloads through the Diels–Alder reaction. As a proof of concept, we synthesized site-specific DAR four, six and eight ADCs carrying tubulysin (AZ13601508) using engineered antibodies with a cysteine inserted after position 239 in the antibody CH2 domain. We evaluated and compared the in vitro cytotoxicity of ADCs obtained via the site-specific platform described herein, with ADCs prepared using classical cysteine conjugation. Our data validated a novel cysteine-based conjugation platform for the preparation of site-specific ADCs with high drug load for therapeutic applications.

Remarkable Structural Diversity between Zr/Hf and Rare-Earth MOFs via Ligand Functionalization and the Discovery of Unique (4, 8)-c and (4, 12)-connected Frameworks.

Ligand modification in MOFs provides great opportunities not only for the development of functional materials with new or enhanced properties but also for the discovery of novel structures. We report here that a sulfone-functionalized tetrahedral carboxylate-based ligand is capable of directing the formation of new and fascinating MOFs when combined with Zr4+/Hf4+ and rare-earth metal cations (RE) with improved gas-sorption properties. In particular, the resulting M-flu-SO2 (M: Zr, Hf) materials display a new type of the augmented flu-a net, which is different as compared to the flu-a framework formed by the nonfunctionalized tetrahedral ligand. In terms of properties, a remarkable increase in the CO2 uptake is observed that reaches 76.6% and 61.6% at 273 and 298 K and 1 bar, respectively. When combined with REs, the sulfone-modified linker affords novel MOFs, RE-hpt-MOF-1 (RE: Y3+, Ho3+, Er3+), which displays a fascinating (4, 12)-coordinated hpt net, based on nonanuclear [RE9(μ3-Ο)2(μ3-ΟΗ)12(-COO)12] clusters that serve as hexagonal prismatic building blocks. In the absence of the sulfone groups, we discovered that the tetrahedral linker directs the formation of new RE-MOFs, RE-ken-MOF-1 (RE: Y3+, Ho3+, Er3+, Yb3+), that display an unprecedented (4, 8)-coordinated ken net based on nonanuclear RE9-clusters, to serve as bicapped trigonal prismatic building units. Successful activation of the representative member Y-ken-MOF-1 reveals a high BET surface area and total pore volume reaching 2621 m2 g-1 and 0.95 cm3 g-1, respectively. These values are the highest among all RE MOFs based on nonanuclear clusters and some of the highest in the entire RE family of MOFs. The present work uncovers a unique structural diversity existing between Zr/Hf and RE-based MOFs that demonstrates the crucial role of linker design. In addition, the discovery of the new RE-hpt-MOF-1 and RE-ken-MOF-1 families of MOFs highlights the great opportunities existing in RE-MOFs in terms of structural diversity that could lead to novel materials with new properties.

Abstract 1718: Design and optimization of a dendrimer-conjugated dual Bcl-2/Bcl-xL inhibitor, AZD0466, with improved therapeutic index

Abstract Dual Bcl-2/Bcl-xL inhibitors are expected to deliver therapeutic benefit in many hematological and solid tumors, but their clinical application has been limited by tolerability issues, including thrombocytopenia. AZD4320, a potent dual Bcl-2/Bcl-xL inhibitor, showed good efficacy but encountered dose limiting cardiovascular toxicity in preclinical species, and had challenging physicochemical properties which prevented its clinical development. Nanocarriers can provide prolonged circulation time, controlled release, tumor accumulation and retention. Consequently, they have been explored to improve the therapeutic index of small molecules in oncology. This work describes the design and development of AZD0466, a novel drug-dendrimer conjugate, where AZD4320 is chemically conjugated to Starpharma's DEP® dendrimer platform, a 5-generation PEGylated poly-lysine dendrimer via a hydrolytically labile linker. Release of AZD4320 is through hydrolytic cleavage of the linker, which is characterized by a “release half-life”, defined as the time to release 50% of the active moiety. This release half-life can be modified through linker design. Initially, three drug-dendrimer conjugates with a range of AZD4320 release half-lives (from 1.7 h to 217 h) were synthesized and efficacy was investigated in C.B-17 SCID mice bearing RS4;11 tumors while cardiovascular parameters and tolerance were assessed in a telemetered rat model. A mathematical model was developed and used to optimize the desired release rate of the active moiety, AZD4320, from the dendrimer conjugate for maximal therapeutic index in terms of preclinical anti-tumor efficacy and cardiovascular profile. Based on this modeling, AZD0466, with a release half-life of 25.5 h, was synthesized and selected for further in vivo efficacy and tolerability assessment. Efficacy studies in the RS4;11 xenograft model showed similar efficacy to AZD4320, while cardiovascular studies in rat and dog demonstrated that AZD0466 was tolerated at doses of active-moiety that are more than ten-fold higher. In addition, it can be easily formulated for intravenous administration due to significantly enhanced solubility. The AZD4320-dendrimer conjugate, AZD0466, identified in this study has resulted in an improved therapeutic index and enabled progression of this promising Bcl-2/Bcl-xL inhibitor into clinical development. Citation Format: Marianne B. Ashford, Srividya B. Balachander, Lorraine Graham, Iain Grant, Francis D. Gibbons, Kathryn J. Hill, Alexander R. Harmer, Sonya Gales, Sean Redmond, Brian Kelly, William McCoull, Shenghua Wen, Martin Wild, Eric Gangl, David J. Owen, Barry R. Davies. Design and optimization of a dendrimer-conjugated dual Bcl-2/Bcl-xL inhibitor, AZD0466, with improved therapeutic index [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1718.