Enhanced Binding Affinity Research Articles

Design, synthesis, biological evaluation and docking study of some new aryl and heteroaryl thiomannosides as FimH antagonists

FimH is a mannose-recognizing lectin that is expressed by Escherichia coli guiding its ability to adhere and infect cells. It is involved in pathogenesis of urinary tract infections and Chron’s disease. Several X-ray structure-guided ligand design studies were extensively utilized in the discovery and optimization of small molecule aryl mannoside FimH antagonists. These antagonists retain key specific interactions of the mannose scaffolds with the FimH carbohydrate recognition domains. Thiomannosides are attractive and stable scaffolds, and this work reports the synthesis of some of their new aryl and heteroaryl derivatives as FimH antagonists. FimH-competitive binding assays as well as biofilm inhibition of the new compounds (24–32) were determined in comparison with the reference n-heptyl α-d-mannopyranoside (HM). The affinity among these compounds was found to be governed by the structure of the aryl and heteroarylf aglycones. Two compounds 31 and 32 revealed higher activity than HM. Molecular docking and total hydrophobic to topological polar surface area ratio calculations attributed to explain the obtained biological results. Finally, the SAR study suggested that introducing an aryl or heteroaryl aglycone of sufficient hydrophobicity and of proper orientation within the tyrosine binding site considerably enhance binding affinity. The potent and synthetically feasible FimH antagonists described herein hold potential as leads for the development of sensors for detection of E. coli and treatment of its diseases.

Sialic Acid Conjugate-Modified Cationic Liposomal Paclitaxel for Targeted Therapy of Lung Metastasis in Breast Cancer: What a Difference the Cation Content Makes.

Cationic lipids play a pivotal role in developing novel drug delivery systems for diverse biomedical applications, owing to the success of mRNA vaccines against COVID-19 and the Phase III antitumor agent EndoTAG-1. However, the therapeutic potential of these positively charged liposomes is limited by dose-dependent toxicity. While an increased content of cationic lipids in the formulation can enhance the uptake and cytotoxicity toward tumor-associated cells, it is crucial to balance these advantages with the associated toxic side effects. In this work, we synthesized the cationic lipid HC-Y-2 and incorporated it into sialic acid (SA)-modified cationic liposomes loaded with paclitaxel to target tumor-associated immune cells efficiently. The SA-modified cationic liposomes exhibited enhanced binding affinity toward both RAW264.7 cells and 4T1 tumor cells in vitro due to the increased ratios of cationic HC-Y-2 content while effectively inhibiting 4T1 cell lung metastasis in vivo. By leveraging electrostatic forces and ligand-receptor interactions, the SA-modified cationic liposomes specifically target malignant tumor-associated immune cells such as tumor-associated macrophages (TAMs), reduce the proportion of cationic lipids in the formulation, and achieve dual objectives: high cellular uptake and potent antitumor efficacy. These findings highlight the potential advantages of this innovative approach utilizing cationic liposomes.

Robust Synthesis of Targeting Glyco-nanoparticles for Surface Enhanced Resonance Raman Based Image-Guided Tumor Surgery.

Surface Enhanced Resonance Raman (SERS) is a powerful optical technique, which can help enhance the sensitivity of Raman spectroscopy aided by noble metal nanoparticles (NPs). However, current SERS-NPs are often suboptimal, which can aggregate under physiological conditions with much reduced SERS enhancement. Herein, a robust one-pot method has been developed to synthesize SERS-NPs with more uniform core diameters of 50 nm, which is applicable to both non-resonant and resonant Raman dyes. The resulting SERS-NPs are colloidally stable and bright, enabling NP detection with low-femtomolar sensitivity. An algorithm has been established, which can accurately unmix multiple types of SERS-NPs enabling potential multiplex detection. Furthermore, a new liposome-based approach has been developed to install a targeting carbohydrate ligand, i.e., hyaluronan, onto the SERS-NPs bestowing significantly enhanced binding affinity to its biological receptor CD44 overexpressed on tumor cell surface. The liposomal HA-SERS-NPs enabled visualization of spontaneously developed breast cancer in mice in real time guiding complete surgical removal of the tumor, highlighting the translational potential of these new glyco-SERS-NPs.

Inhibition of SARS-CoV-2 replication by a ssDNA aptamer targeting the nucleocapsid protein.

The nucleocapsid protein of SARS-CoV-2 plays significant roles in viral assembly, immune evasion, and viral stability. Due to its immunogenicity, high expression levels during COVID-19, and conservation across viral strains, it represents an attractive target for antiviral treatment. In this study, we identified and characterized a single-stranded DNA aptamer, N-Apt17, which effectively disrupts the liquid-liquid phase separation (LLPS) mediated by the N protein. To enhance the aptamer's stability, a circular bivalent form, cb-N-Apt17, was designed and evaluated. Our findings demonstrated that cb-N-Apt17 exhibited improved stability, enhanced binding affinity, and superior inhibition of N protein LLPS; thus, it has the potential inhibition ability on viral replication. These results provide valuable evidence supporting the potential of cb-N-Apt17 as a promising candidate for the development of antiviral therapies against COVID-19.IMPORTANCEVariants of SARS-CoV-2 pose a significant challenge to currently available COVID-19 vaccines and therapies due to the rapid epitope changes observed in the viral spike protein. However, the nucleocapsid (N) protein of SARS-CoV-2, a highly conserved structural protein, offers promising potential as a target for inhibiting viral replication. The N protein forms complexes with genomic RNA, interacts with other viral structural proteins during virion assembly, and plays a critical role in evading host innate immunity by impairing interferon production during viral infection. In this investigation, we discovered a single-stranded DNA aptamer, designated as N-Apt17, exhibiting remarkable affinity and specificity for the N protein. Notably, N-Apt17 disrupts the liquid-liquid phase separation (LLPS) of the N protein. To enhance the stability and molecular recognition capabilities of N-Apt17, we designed a circular bivalent DNA aptamer termed cb-N-Apt17. In both in vivo and in vitro experiments, cb-N-Apt17 exhibited increased stability, enhanced binding affinity, and superior LLPS disrupting ability. Thus, our study provides essential proof-of-principle evidence supporting the further development of cb-N-Apt17 as a therapeutic candidate for COVID-19.

Oligomeric Zinc Thiolates Tethering Multidentate Carboxylates for Nondestructive Aqueous Phase Transfer of Quantum Dots.

Functionalization of quantum dots (QDs) via ligand exchange is prone to debase their photoluminescence quantum yield (PL QY) owing to the unavoidable surface damage by excess reactants, and even worse in aqueous medium. Herein, the oligomeric zinc thiolate as the multidentate hydrophilic ligand featuring facile synthetic protocol is proposed. A simple reaction between ZnCl2 and 3-mercaptopropionic acid produces oligomeric ligands containing 3-6 zinc thiolate units, where the terminal moieties provide multidentate anchoring to the surface as well as hydrophilicity. 2D proton nuclear Overhauser effect spectroscopy (2D 1H NOESY) and X-ray photoelectron spectroscopy (XPS) reveal that the oligomeric zinc thiolate ligands adsorb on the surface via multidentate metal carboxylate bindings without destruction of molecular structure, regardless of partial dissociation of thiolate branches in aqueous phase. Enhanced binding affinity granted by the multidentate nature allows for the effective exchange of original surface ligands without considerable surface deterioration. The zinc thiolate-capped Cd-free aqueous QDs exhibit a high photoluminescence quantum yield of ≈90% and extended stability against long-term storage and photochemical stress.

Unique quinoline orientations shape the modified aptamer to sclerostin for enhanced binding affinity and bone anabolic potential

Osteogenesis imperfecta is a rare genetic disease characterized by bone fragility and bone formation. Sclerostin could negatively regulate bone formation by antagonizing Wnt signal pathway, whereas impose severe cardiac ischemic events in clinic. Our team has screened an aptamer, which could promote bone anabolic potential without cardiovascular risk. However, the affinity of the aptamer is lower and needs to be improved. In the study, hydrophobic quinoline molecule with unique orientations (7 subtypes) were incorporated into key sites of a bone anabolic aptamer against sclerostin to form a modified aptamer library. Among all the quinoline modifications, 5-quinoline modification could shape the molecular recognition of modified aptamers to sclerostin to facilitate enhancing its binding to sclerostin towards the highest affinity by interacting with newly participated binding sites in sclerostin. Further, 5-quinoline modification could facilitate the modified aptamer attenuating the suppressed effect of the transfected sclerostin on both Wnt signaling and bone formation marker expression levels in vitro, promoting bone anabolism in osteogenesis imperfecta mice (Col1a2+/G610C). The proposed quinoline-oriented modification strategy could shape the molecular recognition of modified aptamers to proteins to facilitate enhancing its binding affinity and therapeutic potency.

Mechanistic study of the transmission pattern of the SARS-CoV-2 omicron variant.

The omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) characterized by 30 mutations in its spike protein, has rapidly spread worldwide since November 2021, significantly exacerbating the ongoing COVID-19 pandemic. In order to investigate the relationship between these mutations and the variant's high transmissibility, we conducted a systematic analysis of the mutational effect on spike-angiotensin-converting enzyme-2 (ACE2) interactions and explored the structural/energy correlation of key mutations, utilizing a reliable coarse-grained model. Our study extended beyond the receptor-binding domain (RBD) of spike trimer through comprehensive modeling of the full-length spike trimer rather than just the RBD. Our free-energy calculation revealed that the enhanced binding affinity between the spike protein and the ACE2 receptor is correlated with the increased structural stability of the isolated spike protein, thus explaining the omicron variant's heightened transmissibility. The conclusion was supported by our experimental analyses involving the expression and purification of the full-length spike trimer. Furthermore, the energy decomposition analysis established those electrostatic interactions make major contributions to this effect. We categorized the mutations into four groups and established an analytical framework that can be employed in studying future mutations. Additionally, our calculations rationalized the reduced affinity of the omicron variant towards most available therapeutic neutralizing antibodies, when compared with the wild type. By providing concrete experimental data and offering a solid explanation, this study contributes to a better understanding of the relationship between theories and observations and lays the foundation for future investigations.

Molecular Insights into the Specific Targeting of c-MYC G-Quadruplex by Thiazole Peptides.

Stabilization of a G-quadruplex (G4) in the promotor of the c-MYC proto-oncogene leads to inhibition of gene expression, and it thus represents a potentially attractive new strategy for cancer treatment. However, most G4 stabilizers show little selectivity among the many G4s present in the cellular complement of DNA and RNA. Intriguingly, a crescent-shaped cell-penetrating thiazole peptide, TH3, preferentially stabilizes the c-MYC G4 over other promotor G4s, but the mechanisms leading to this selective binding remain obscure. To investigate these mechanisms at the atomic level, we performed an in silico comparative investigation of the binding of TH3 and its analogue TH1 to the G4s from the promotors of c-MYC, c-KIT1, c-KIT2, and BCL2. Molecular docking and molecular dynamics simulations, combined with in-depth analyses of non-covalent interactions and bulk and per-nucleotide binding free energies, revealed that both TH3 and TH1 can induce the formation of a sandwich-like framework through stacking with both the top and bottom G-tetrads of the c-MYC G4 and the adjacent terminal capping nucleotides. This framework produces enhanced binding affinities for c-MYC G4 relative to other promotor G4s, with TH3 exhibiting an outstanding binding priority. Van der Waals interactions were identified to be the key factor in complex formation in all cases. Collectively, our findings fully agree with available experimental data. Therefore, the identified mechanisms leading to specific binding of TH3 towards c-MYC G4 provide valuable information to guide the development of new selective G4 stabilizers.

Potent inhibitors targeting cyclin-dependent kinase 9 discovered via virtual high-throughput screening and absolute binding free energy calculations.

Due to the crucial regulatory mechanism of cyclin-dependent kinase 9 (CDK9) in mRNA transcription, the development of kinase inhibitors targeting CDK9 holds promise as a potential treatment strategy for cancer. A structure-based virtual screening approach has been employed for the discovery of potential novel CDK9 inhibitors. First, compounds with kinase inhibitor characteristics were identified from the ZINC15 database via virtual high-throughput screening. Next, the predicted binding modes were optimized by molecular dynamics simulations, followed by precise estimation of binding affinities using absolute binding free energy calculations based on the free energy perturbation scheme. The binding mode of molecule 006 underwent an inward-to-outward flipping, and the new binding mode exhibited binding affinity comparable to the small molecule T6Q in the crystal structure (PDB ID: 4BCF), highlighting the essential role of molecular dynamics simulation in capturing a plausible binding pose bridging docking and absolute binding free energy calculations. Finally, structural modifications based on these findings further enhanced the binding affinity with CDK9. The results revealed that enhancing the molecule's rigidity through ring formation, while maintaining the major interactions, reduced the entropy loss during the binding process and, thus, enhanced binding affinities.

Effect of base methylation on binding and mobility of bacterial protein Hfq on double-stranded DNA.

Regulation of protein mobility is a fundamental aspect of cellular processes. In this study, we examined the impact of DNA methylation on the diffusion of nucleoid associated protein Hfq. This protein is one of the most abundant proteins that shapes the bacterial chromosome and is involved in several aspects of nucleic acid metabolism. Fluorescence microscopy was employed to monitor the movement of Hfq along double-stranded DNA, which was stretched due to confinement within a nanofluidic channel. The mobility of Hfq is significantly influenced by DNA methylation. Our results underscore the importance of bacterial epigenetic modifications in governing the movement of nucleoid associated proteins such as Hfq. Increased levels of methylation result in enhanced binding affinity, which in turn slows down the diffusion of Hfq on DNA. The reported control of protein mobility by DNA methylation has potential implications for the mechanisms involved in target DNA search processes and dynamic modelling of the bacterial chromosome.

Computational Mutagenesis and Inhibition of Staphylococcus aureus AgrA LytTR Domain Using Phenazine Scaffolds: Insight From a Biophysical Study.

Biofilm formation by Staphylococcus aureus is a major challenge in clinical settings due to its role in persistent infections. The AgrA protein, a key regulator in biofilm development, is a promising target for therapeutic intervention. This study investigates the antibiofilm potential of halogenated phenazine compounds by targeting AgrA and explores their molecular interactions to provide insights for drug development. We employed molecular docking, molecular dynamics simulations, and computational mutagenesis to evaluate the binding of halogenated phenazine compounds (C1 to C7, HP, and HP-14) to AgrA. Binding free energy analysis was performed to assess the affinity of these compounds for the AgrA-DNA complex. Additionally, the impact of these compounds on AgrA's structural conformation and salt bridge interactions was examined. The binding-free energy analysis revealed that all compounds enhance binding affinity compared to the Apo form of AgrA, which has a ΔGbind of -80.75 kcal/mol. The strongest binding affinities were observed with compounds C7 (-113.84 kcal/mol), HP-14 (-115.23 kcal/mol), and HP (-112.28 kcal/mol), highlighting their effectiveness. Molecular dynamics simulations demonstrated that these compounds bind at the hydrophobic cleft of AgrA, disrupting essential salt bridge interactions between His174-Glu163 and His174-Glu226. This disruption led to structural conformational changes and reduced DNA binding affinity, aligning with experimental findings on biofilm inhibition. The halogenated phenazine compounds effectively inhibit biofilm formation by targeting AgrA, disrupting its DNA-binding function. The study supports the potential of these compounds as antibiofilm agents and provides a foundation for rational drug design targeting the AgrA-DNA interaction. Future research should focus on further optimizing these lead compounds and exploring additional active sites on AgrA to develop novel treatments for biofilm-associated infections.

TRL-PROTAC: A pre-trained generator of PROTACs targeting specific proteins optimized by reinforcement learning

Proteolysis-targeting chimeras (PROTACs) introduce a novel paradigm in drug development, incorporating three essential components: the warhead, the E3 ligand, and the linker. The complexity of the ternary structure, particularly the intricate design of the linker, presents a significant challenge in PROTACs drug design. Here an integrated protocol for design and evaluation of PROTACs targeting specific proteins, called TRL-PROTAC is proposed. TRL-PROTAC is focused on the de novo design of complete PROTACs by effectively joining the designed ligands targeting the proteins of interest (POI) with linkers. The ligands for POIs and E3 ligases are generated by a molecular generation model for targeting proteins, and the linker design is generated by a sequence-to-sequence model consisting of a transformer variant and the policy-based reinforcement learning method which is employed to optimize the reward values for generating PROTACs. The three components are then integrated and optimized based on their pharmacokinetic (PK) and degradation (DEG) properties. The experimental results have strongly confirmed that TRL-PROTAC is superior in optimizing properties. For existing PROTACs, TRL-PROTAC improves DEG scores by 0.45 and lowers PK scores by 1.20. Moreover, TRL-PROTAC enhances binding affinity by 2.15 in PROTACs generated from scratch.

Enhancing the antibacterial efficacy of vancomycin analogues: targeting metallo-β-lactamases and cell wall biosynthesis.

Vancomycin is a crucial last-resort antibiotic for tackling Gram-positive bacterial infections. However, its potency fails against the more difficult-to-treat Gram-negative bacteria (GNB). Vancomycin derivatives have shown promise as broad-spectrum antibacterials, but are still underexplored. Toward this, we present a novel strategy wherein we substitute the sugar moiety of vancomycin with a dipicolyl amine group, yielding VanNHdipi. This novel glycopeptide enhances its efficacy against vancomycin-resistant bacteria by up to 100-fold. A comprehensive approach involving microbiological assays, biochemical analyses, proteomics, and computational studies unraveled the impact of this design on biological activity. Our investigations reveal that VanNHdipi, like vancomycin, disrupts membrane-bound steps of cell wall synthesis inducing envelope stress, while also interfering with the structural integrity of the cytoplasmic membrane, setting it apart from vancomycin. Most noteworthy is its potency against critical GNB producing metallo-β-lactamases (MBLs). VanNHdipi effectively inactivates various MBLs with IC50 in the range of 0.2-10 μM resulting in resensitization of MBL-producing bacteria to carbapenems. Molecular docking and molecular dynamics (MD) studies indicate that H-bonding interactions between the sugar moiety of the vancomycin derivative with the amino acids on the surface of NDM-1 facilitate enhanced binding affinity for the enzyme. This work expands the scope of vancomycin derivatives and offers a promising new avenue for combating antibiotic resistance.

Synthesis and elucidation of strained galactopyronose esters as selective cyclooxygenase-2 inhibitor: a comprehensive computational approach.

Cyclooxygenase-2 (COX-2) is critically implicated in various pathologies, including inflammation, cancer, disorders involving the nervous system, and multidrug resistance. In both academic and pharmaceutical research, the development of COX-2 selective drugs as anti-inflammatory and anti-tumor therapeutics is a key focus. Traditional nonsteroidal anti-inflammatory drugs (NSAIDs) have ulcerogenic, gastrointestinal adverse effects, and myocardial infarction risk, which resulted in their limited applications. In response to this challenge, we synthesized a series of glycoconjugates featuring six-membered sugar rings and acyl chains of varying lengths attached at the C-6 position. Using molecular docking techniques, we identified galactose esters with optimal acyl chain lengths that selectively and effectively bind to the active site of COX-2 over COX-1. These compounds exhibited enhanced binding affinity and superior inhibition constants (pK i) for COX-2, thereby offering selective inhibition with potentially reduced ulcerogenic risks, as COX-1 inhibition is thought to contribute to these side effects. The molecular docking study identified two potential compounds, G6 and G8, which were validated via MD simulation for the assessment of their stability and were compared to the complex of the standard drugs, aspirin and rofecoxib. In addition, compound structures were optimized using the DFT method under the B3LYP/6-31+g(d,p) basis set to study their physio-spectral properties, frontier molecular orbitals (HOMO-LUMO), and their energy gap that correlates to their reactivity and stability. ADMET, drug-likeness, and PASS analyses were also carried out to assess their drug-ability and toxicity profiling.

A bivalent inhibitor against TDRD3 to suppress phase separation of methylated G3BP1.

The formation of membrane-less organelles is driven by multivalent weak interactions while mediation of such interactions by small molecules remains an unparalleled challenge. Here, we uncovered a bivalent inhibitor that blocked the recruitment of TDRD3 by the two methylated arginines of G3BP1. Relative to the monovalent inhibitor, this bivalent inhibitor demonstrated an enhanced binding affinity to TDRD3 and capability to suppress the phase separation of methylated G3BP1, TDRD3, and RNAs, and in turn inhibit the stress granule growth in cells. Our result paves a new path to mediate multivalent interactions involved in SG assembly for potential combinational chemotherapy by bivalent inhibitors.

Antimicrobial and FAD synthetases modulating activities of leporins A-C isolated from the sponge-associated fungus Trichoderma sp.

Abstract. Losung F, Ginting EL, Abdjul B, Kapojos MM, Maarisit W, Mentang F, Sumilat DA, Balansa W, Mangindaan REP. 2023. Antimicrobial and FAD synthetases modulating activities of leporins A-C isolated from the sponge-associated fungus Trichoderma sp. Biodiversitas 24: 6502-6515. The emergence of microbial resistance poses a formidable threat to human health, requiring the discovery of new antibiotics. In this study, we investigated the antimicrobial potential and molecular structures of the metabolites produced by a sponge's symbiont fungal species, Trichoderma sp., in vitro against S. aureus IAM 12544T and Candida albicans IFM 4954 and in-silico against the emerging antibacterial target, prokaryotic bifunctional synthetases (FADS). The molecular structures were determined using spectroscopic techniques (1D, 2D NMR, HRESIMS), while the assessment of biological activities, physicochemical properties, and molecular modifications was performed through a slightly modified disk agar diffusion method, molecular docking, SwissAdme and pkCMS tools, and bioisosterism, respectively. The analysis of spectroscopic data supported the identification of leporins A-C (1-3) as the metabolites, which exhibited strong binding affinities against the 2X0K protein target (-8.9 to -9.4 kcal/mol). Despite their being slightly weaker than known FADS modulators such as compounds 4 (-10.5 kcal/mol) and 5 (-10.5 kcal/mol), leporins A-C demonstrated a stronger binding affinity than compound 6 (-9.6 to -10.5 kcal/mol). Notably, substituting a methyl group with a fluorine atom in 1-3 resulted in lepofluorins A-C (1a-3a), which exhibited enhanced binding affinities and improved physicochemical properties compared to the existing FADS modulators. These findings suggest that leporins A-C (1-3), particularly lepofluorins A-C (1a-3a), have potential as putative novel modulators of FADS. This study provides valuable insights into the design and development of new antibiotics to combat microbial resistance.

Design And Evaluating The Efficacy Of Novel Antibodies Enhancing Binding On CTLA-4 And PD-1 Immune Checkpoints

Immune checkpoint proteins, including CTLA-4 and PD-1, have emerged as promising targets for cancer immunotherapy due to their vital role in immune regulation. In this comprehensive study, we conducted a thorough analysis of antibody-protein interactions by employing structural analysis, mutational studies, and antibody-antigen docking simulations. Our findings revealed that antibodies 1 and 2 exhibited strong binding affinities towards CTLA-4 and PD-1 proteins, respectively. Further analysis through alanine scanning identified specific residues, namely Tyr91 on antibody 1, along with Asn31 and Asp96 on antibody 2, as potential mutation sites. Introducing these mutations resulted in the generation of two novel antibodies, 1a, 2a and 2b, which displayed enhanced binding affinity towards their respective target proteins. With their improved binding capabilities, these novel antibodies hold tremendous promise for enhancing the effectiveness of antibody-based therapies designed to target immune checkpoints in cancer treatment. The ultimate objective is to significantly improve the health outcomes of patients by leveraging the potential of these novel antibodies.

Impact of mutations on Omicron's spike protein: Insights from variants found in Vietnam

The SARS-CoV-2 virus is the primary agent responsible for the ongoing COVID-19 pandemic, leading to the loss of millions of lives worldwide. In 2023, the COVID-19 pandemic's impact is primarily driven by the Omicron variant, which features many unique mutations compared to previously identified SARS-CoV-2 variants. Through analysis of the network of Omicron variants collected in Vietnam, we determined variants expected to have high transmission efficiency and positive influence before studying the impact of mutations on the structural behavior of spike proteins and their affinity with hACE2. Our computational analysis indicates that these Omicron variants not only exhibit a significantly higher binding affinity than the Wildtype but also demonstrate increased binding free energy among variants. This enhanced binding affinity of Omicron variant is reflected in the enhanced stability of the hACE2 binding structure compared to the Wildtype. This study further elucidates the specific contributions of point mutations to the binding free energy. Notably, such mutations as W152R, F157L, G257S, S371F, S373P, S375F, T376A, D405N, N440K, S477N, T478K, E484A, Q493R, Q498R, N501Y, D614G, N679K, P681H, N764K, D796Y, and N969K were found increasing the binding free energy of Omicron's spike protein in complex with hACE2.

A Transformable Supramolecular Bispecific Cell Engager for Augmenting Natural Killer and T Cell-Based Cancer Immunotherapy.

Immune cells are pivotal in cancer immunotherapy, yet their therapeutic effectiveness is often hampered by limited tumor infiltration and inhibitory tumor microenvironments. An alkaline phosphatase (ALP)-responsive and transformable supramolecular bis-specific cell engager (Supra-BiCE) to harness natural killer (NK)/T cells for effective cancer immunotherapy is introduced here. The Supra-BiCE, consisting of both SA-P (a phosphorylated peptide targeting and blocking programmed cell death ligand 1 (PD-L1)) and SA-T (a phosphorylated peptide targeting and blocking T cell immunoglobulin and ITIM domain (TIGIT)) is constructed by a simple co-assembling strategy. Upon intravenous administration, Supra-BiCE self-assembles into nanoribbons and interacts with NK/T cells via TIGIT. Notably, these nanoribbons undergo transformation into long nanofibrils within ALP-overexpressing tumor regions, resulting in enhanced binding affinities of Supra-BiCE to both PD-L1 and TIGIT. Consequently, this leads to the accumulation and retention of NK/T cells within tumor regions. Furthermore, the combinatorial blockade of checkpoints by Supra-BiCE activates infiltrating NK/T cells. Moreover, the adjustable peptide ratio in Supra-BiCE enables customization for optimal therapeutic effects against distinct tumor types. Particularly, Supra-BiCE (T:P = 1:3) achieved 98.27% tumor suppression rate against colon carcinoma model. Overall, this study offers a promising tool for engaging NK and T cells for cancer immunotherapy.

Abstract B123: Mechanism of action of ivonescimab (AK112/SMT112): a first-in-class tetravalent Fc-silent bispecific antibody with dual blockade of PD-1 and VEGF that promotes cooperative biological effects

Abstract Background: Combination treatments using anti-PD-1/PD-L1 antibodies with other VEGF antagonists have shown enhanced clinical antitumor activities1. The expression of PD-1 and VEGF are found to be frequently upregulated and co-expressed in solid tumors. Importantly, VEGF promotes tumor angiogenesis and suppresses antitumor immune response2,3. Consequently, we characterized the mechanism-of-action of a novel first-in-class anti-PD-1/VEGF bispecific antibody, ivonescimab, designed to simultaneously inhibit PD-1-mediated immunosuppression and block tumor angiogenesis in the tumor microenvironment. Methods: Binding activity of ivonescimab to PD-1/VEGF were assessed by ELISA. Blockade of PD-1/VEGF signaling pathways was determined in luciferase reporter cell assays. Ivonescimab-VEGF complex formation was detected by SEC-HPLC. Cooperative binding of ivonescimab-VEGF complex to PD-1 or ivonescimab-PD-1 complex to VEGF was measured by Octet BLI. The enhanced PD-1 blockade bioactivity of ivonescimab with VEGF was evaluated in hPBMC and engineered cell-line co-culture/luciferase-reporter cell assays. Antitumor activity of ivonescimab was investigated in hPBMC-humanized SCID/Beige mice implanted with HCC827 (mEGFR lung adenocarcinoma) or U87MG (glioblastoma). Immuno-safety was assessed by FcγR binding, ADCC, ADCP assays, and reported clinical irAEs. Results: Ivonescimab displayed strong binding activity to human PD-1 and VEGF alone or simultaneously, effectively blocking interactions with ligands and the downstream signaling effects. In presence of VEGF, ivonescimab forms soluble complexes with VEGF dimers, leading to over 10-fold enhanced binding affinity (KD) of ivonescimab to PD-1. The avidity increase was consistent with reduced cell surface PD-1 expression on human T-cell lines, increased potency on blockade of PD-1/PD-L1 signaling and subsequent enhanced T cell activation in-vitro. Likewise, PD-1 binding enhanced ivonescimab binding to VEGF which was associated with enhanced VEGF-signaling blockade. Also, ivonescimab treatment demonstrated statistically significant dose-dependent antitumor response in hPBMC-humanized murine HCC827 and U87MG tumor models. Additionally, ivonescimab enhanced antitumor response in combination with anti-CD47 (AK117) or anti-CD73 (AK119) in mouse models. Finally, ivonescimab contains Fc-silencing mutations abrogating FcγRI/IIIa binding and showed significantly reduced ADCC, ADCP activities and cytokine release in-vitro. Clinically, this is consistent with the safety profile in Phase 1/2 studies of ivonescimab in advanced solid tumors4,5. Conclusions: Ivonescimab is a novel tetravalent anti-PD-1/VEGF bispecific antibody displaying unique cooperative binding to each of its intended targets consistent with increased in-vitro functional bioactivities compared with bevacizumab or PD-1 inhibitors alone. Importantly, the Fc-null IgG1 design resulted in reduced FcgR interactions and minimal ADCC, ADCP activities consistent with its clinical immunosafety profile. Ivonescimab is currently in Ph3 NSCLC trials in the US and EU. Citation Format: Tingting Zhong, Zhaoliang Huang, Xinghua Pang, Chunshan Jin, Xinrong He, Jose G Montoya, Betty Y Chang, Michelle Xia, Baiyong Li, Jing Min. Mechanism of action of ivonescimab (AK112/SMT112): a first-in-class tetravalent Fc-silent bispecific antibody with dual blockade of PD-1 and VEGF that promotes cooperative biological effects [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr B123.